Starting phenix.real_space_refine on Sat Aug 23 16:38:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yg0_33803/08_2025/7yg0_33803_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yg0_33803/08_2025/7yg0_33803.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7yg0_33803/08_2025/7yg0_33803_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yg0_33803/08_2025/7yg0_33803_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yg0_33803/08_2025/7yg0_33803.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yg0_33803/08_2025/7yg0_33803.map" } resolution = 3.75 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= 0.021 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 80 5.16 5 C 8685 2.51 5 N 2231 2.21 5 O 2340 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 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: 13336 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 854, 6673 Classifications: {'peptide': 854} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 36, 'TRANS': 817} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 6663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 854, 6663 Classifications: {'peptide': 854} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 36, 'TRANS': 817} Chain breaks: 2 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'TRP:plan': 1, 'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 19 Time building chain proxies: 3.05, per 1000 atoms: 0.23 Number of scatterers: 13336 At special positions: 0 Unit cell: (158.992, 84.726, 111.922, 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 80 16.00 O 2340 8.00 N 2231 7.00 C 8685 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 416 " - pdb=" SG CYS A 421 " distance=2.03 Simple disulfide: pdb=" SG CYS A 430 " - pdb=" SG CYS A 436 " distance=2.04 Simple disulfide: pdb=" SG CYS B 416 " - pdb=" SG CYS B 421 " distance=2.03 Simple disulfide: pdb=" SG CYS B 430 " - pdb=" SG CYS B 436 " distance=2.04 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: 1.19 Conformation dependent library (CDL) restraints added in 526.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3140 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 2 sheets defined 63.6% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 142 through 151 Processing helix chain 'A' and resid 153 through 158 Processing helix chain 'A' and resid 158 through 194 removed outlier: 6.787A pdb=" N ILE A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 9.201A pdb=" N VAL A 169 " --> pdb=" O GLN A 165 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU A 170 " --> pdb=" O ALA A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 212 Processing helix chain 'A' and resid 212 through 249 removed outlier: 3.718A pdb=" N ALA A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 277 removed outlier: 3.600A pdb=" N ILE A 260 " --> pdb=" O PRO A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 306 removed outlier: 3.548A pdb=" N LEU A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 316 Processing helix chain 'A' and resid 321 through 329 Processing helix chain 'A' and resid 339 through 348 removed outlier: 3.644A pdb=" N ILE A 346 " --> pdb=" O GLY A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 351 No H-bonds generated for 'chain 'A' and resid 349 through 351' Processing helix chain 'A' and resid 353 through 361 removed outlier: 4.211A pdb=" N GLY A 357 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA A 358 " --> pdb=" O LEU A 355 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE A 360 " --> pdb=" O GLY A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 395 Proline residue: A 372 - end of helix Processing helix chain 'A' and resid 418 through 424 removed outlier: 3.559A pdb=" N CYS A 421 " --> pdb=" O GLY A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 434 Processing helix chain 'A' and resid 445 through 451 Processing helix chain 'A' and resid 453 through 486 removed outlier: 3.759A pdb=" N ILE A 457 " --> pdb=" O PHE A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 497 removed outlier: 3.646A pdb=" N PHE A 494 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY A 496 " --> pdb=" O GLY A 493 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LYS A 497 " --> pdb=" O PHE A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 521 Processing helix chain 'A' and resid 524 through 553 Proline residue: A 530 - end of helix Processing helix chain 'A' and resid 566 through 585 removed outlier: 3.629A pdb=" N THR A 585 " --> pdb=" O MET A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 605 removed outlier: 3.611A pdb=" N ALA A 589 " --> pdb=" O THR A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 631 removed outlier: 3.878A pdb=" N ALA A 624 " --> pdb=" O SER A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 634 No H-bonds generated for 'chain 'A' and resid 632 through 634' Processing helix chain 'A' and resid 655 through 665 removed outlier: 4.194A pdb=" N VAL A 659 " --> pdb=" O ARG A 655 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N PHE A 665 " --> pdb=" O PHE A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 703 removed outlier: 4.686A pdb=" N GLN A 690 " --> pdb=" O MET A 686 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N LEU A 691 " --> pdb=" O PRO A 687 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ILE A 692 " --> pdb=" O GLU A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 726 removed outlier: 3.518A pdb=" N LEU A 724 " --> pdb=" O GLY A 720 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN A 726 " --> pdb=" O GLN A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 767 removed outlier: 3.987A pdb=" N ASP A 756 " --> pdb=" O ALA A 752 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU A 761 " --> pdb=" O TYR A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 removed outlier: 5.315A pdb=" N PHE A 822 " --> pdb=" O ALA A 818 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLN A 823 " --> pdb=" O THR A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 840 through 844 removed outlier: 3.507A pdb=" N THR A 843 " --> pdb=" O GLY A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 852 Processing helix chain 'A' and resid 854 through 858 removed outlier: 3.792A pdb=" N LYS A 858 " --> pdb=" O ARG A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 884 removed outlier: 3.743A pdb=" N SER A 884 " --> pdb=" O ILE A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 901 removed outlier: 4.274A pdb=" N ASN A 900 " --> pdb=" O PRO A 897 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLN A 901 " --> pdb=" O ASP A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 914 removed outlier: 3.518A pdb=" N THR A 908 " --> pdb=" O ARG A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 923 No H-bonds generated for 'chain 'A' and resid 921 through 923' Processing helix chain 'A' and resid 924 through 934 Processing helix chain 'A' and resid 949 through 966 removed outlier: 3.677A pdb=" N SER A 953 " --> pdb=" O ASN A 949 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 998 removed outlier: 4.378A pdb=" N SER A 998 " --> pdb=" O LEU A 994 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 151 removed outlier: 4.504A pdb=" N ILE B 144 " --> pdb=" O LYS B 140 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ARG B 145 " --> pdb=" O GLY B 141 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN B 149 " --> pdb=" O ARG B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 158 Processing helix chain 'B' and resid 158 through 166 Processing helix chain 'B' and resid 167 through 194 removed outlier: 3.527A pdb=" N VAL B 181 " --> pdb=" O LEU B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 211 Processing helix chain 'B' and resid 212 through 249 removed outlier: 3.761A pdb=" N SER B 218 " --> pdb=" O GLU B 214 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 277 Processing helix chain 'B' and resid 281 through 306 removed outlier: 4.696A pdb=" N VAL B 287 " --> pdb=" O SER B 283 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU B 288 " --> pdb=" O LYS B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 316 Processing helix chain 'B' and resid 321 through 330 removed outlier: 4.211A pdb=" N VAL B 330 " --> pdb=" O VAL B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 348 removed outlier: 3.627A pdb=" N ILE B 346 " --> pdb=" O GLY B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 351 No H-bonds generated for 'chain 'B' and resid 349 through 351' Processing helix chain 'B' and resid 353 through 361 removed outlier: 3.826A pdb=" N ASN B 359 " --> pdb=" O ALA B 356 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE B 360 " --> pdb=" O GLY B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 394 Proline residue: B 372 - end of helix Processing helix chain 'B' and resid 418 through 424 Processing helix chain 'B' and resid 428 through 434 Processing helix chain 'B' and resid 445 through 451 removed outlier: 3.692A pdb=" N MET B 449 " --> pdb=" O GLN B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 486 removed outlier: 3.842A pdb=" N ILE B 457 " --> pdb=" O PHE B 453 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU B 470 " --> pdb=" O LEU B 466 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LYS B 478 " --> pdb=" O VAL B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 521 Processing helix chain 'B' and resid 524 through 553 Proline residue: B 530 - end of helix Processing helix chain 'B' and resid 566 through 585 removed outlier: 3.631A pdb=" N THR B 585 " --> pdb=" O MET B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 605 removed outlier: 3.618A pdb=" N ALA B 589 " --> pdb=" O THR B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 628 removed outlier: 3.785A pdb=" N SER B 626 " --> pdb=" O ASN B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 665 removed outlier: 3.749A pdb=" N VAL B 659 " --> pdb=" O ARG B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 703 Processing helix chain 'B' and resid 717 through 728 removed outlier: 4.089A pdb=" N LEU B 724 " --> pdb=" O GLY B 720 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN B 726 " --> pdb=" O GLN B 722 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA B 727 " --> pdb=" O ILE B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 730 through 734 Processing helix chain 'B' and resid 750 through 767 removed outlier: 4.266A pdb=" N VAL B 754 " --> pdb=" O HIS B 750 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU B 761 " --> pdb=" O TYR B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 812 through 820 Processing helix chain 'B' and resid 821 through 824 Processing helix chain 'B' and resid 841 through 852 Proline residue: B 847 - end of helix Processing helix chain 'B' and resid 853 through 859 removed outlier: 3.997A pdb=" N LYS B 858 " --> pdb=" O ARG B 855 " (cutoff:3.500A) Processing helix chain 'B' and resid 872 through 886 removed outlier: 4.325A pdb=" N ALA B 878 " --> pdb=" O GLN B 874 " (cutoff:3.500A) Processing helix chain 'B' and resid 896 through 900 removed outlier: 3.901A pdb=" N ILE B 899 " --> pdb=" O LEU B 896 " (cutoff:3.500A) Processing helix chain 'B' and resid 904 through 914 Processing helix chain 'B' and resid 924 through 935 Processing helix chain 'B' and resid 949 through 965 Processing helix chain 'B' and resid 986 through 998 Processing sheet with id=AA1, first strand: chain 'A' and resid 711 through 713 removed outlier: 4.337A pdb=" N GLY A 741 " --> pdb=" O LEU A 648 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ARG A 775 " --> pdb=" O VAL A1005 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 708 through 712 removed outlier: 3.760A pdb=" N PHE B 708 " --> pdb=" O MET B 672 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N CYS B 645 " --> pdb=" O ILE B 673 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N GLY B 675 " --> pdb=" O CYS B 645 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL B 647 " --> pdb=" O GLY B 675 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N VAL B 677 " --> pdb=" O VAL B 647 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU B 646 " --> pdb=" O VAL B 739 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N MET B 774 " --> pdb=" O VAL B 740 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N ILE B 973 " --> pdb=" O ILE B1006 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ILE B1008 " --> pdb=" O ILE B 973 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE B 975 " --> pdb=" O ILE B1008 " (cutoff:3.500A) 744 hydrogen bonds defined for protein. 2151 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: 2.24 Time building geometry restraints manager: 1.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2096 1.32 - 1.44: 3718 1.44 - 1.57: 7715 1.57 - 1.69: 0 1.69 - 1.81: 124 Bond restraints: 13653 Sorted by residual: bond pdb=" N SER B 422 " pdb=" CA SER B 422 " ideal model delta sigma weight residual 1.456 1.378 0.079 1.31e-02 5.83e+03 3.61e+01 bond pdb=" CD GLN B 165 " pdb=" OE1 GLN B 165 " ideal model delta sigma weight residual 1.231 1.329 -0.098 1.90e-02 2.77e+03 2.64e+01 bond pdb=" CD GLN A 563 " pdb=" OE1 GLN A 563 " ideal model delta sigma weight residual 1.231 1.328 -0.097 1.90e-02 2.77e+03 2.63e+01 bond pdb=" CG ASN B 359 " pdb=" OD1 ASN B 359 " ideal model delta sigma weight residual 1.231 1.327 -0.096 1.90e-02 2.77e+03 2.53e+01 bond pdb=" C ASN A 426 " pdb=" N PHE A 427 " ideal model delta sigma weight residual 1.334 1.272 0.062 1.24e-02 6.50e+03 2.51e+01 ... (remaining 13648 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 18059 2.53 - 5.05: 397 5.05 - 7.58: 66 7.58 - 10.11: 16 10.11 - 12.63: 1 Bond angle restraints: 18539 Sorted by residual: angle pdb=" N LEU A 836 " pdb=" CA LEU A 836 " pdb=" C LEU A 836 " ideal model delta sigma weight residual 113.97 101.34 12.63 1.28e+00 6.10e-01 9.74e+01 angle pdb=" N ALA A 878 " pdb=" CA ALA A 878 " pdb=" C ALA A 878 " ideal model delta sigma weight residual 111.28 102.13 9.15 1.09e+00 8.42e-01 7.04e+01 angle pdb=" N ASP B 943 " pdb=" CA ASP B 943 " pdb=" C ASP B 943 " ideal model delta sigma weight residual 112.87 103.14 9.73 1.20e+00 6.94e-01 6.57e+01 angle pdb=" N LEU B 780 " pdb=" CA LEU B 780 " pdb=" C LEU B 780 " ideal model delta sigma weight residual 111.07 103.10 7.97 1.07e+00 8.73e-01 5.55e+01 angle pdb=" C LEU A1016 " pdb=" CA LEU A1016 " pdb=" CB LEU A1016 " ideal model delta sigma weight residual 111.89 101.99 9.90 1.42e+00 4.96e-01 4.86e+01 ... (remaining 18534 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 7140 17.59 - 35.18: 729 35.18 - 52.76: 140 52.76 - 70.35: 24 70.35 - 87.94: 6 Dihedral angle restraints: 8039 sinusoidal: 3138 harmonic: 4901 Sorted by residual: dihedral pdb=" CB CYS B 416 " pdb=" SG CYS B 416 " pdb=" SG CYS B 421 " pdb=" CB CYS B 421 " ideal model delta sinusoidal sigma weight residual 93.00 151.41 -58.41 1 1.00e+01 1.00e-02 4.57e+01 dihedral pdb=" CA GLY A 152 " pdb=" C GLY A 152 " pdb=" N VAL A 153 " pdb=" CA VAL A 153 " ideal model delta harmonic sigma weight residual -180.00 -150.47 -29.53 0 5.00e+00 4.00e-02 3.49e+01 dihedral pdb=" CA GLY B 152 " pdb=" C GLY B 152 " pdb=" N VAL B 153 " pdb=" CA VAL B 153 " ideal model delta harmonic sigma weight residual -180.00 -153.12 -26.88 0 5.00e+00 4.00e-02 2.89e+01 ... (remaining 8036 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 1948 0.085 - 0.169: 147 0.169 - 0.254: 17 0.254 - 0.338: 3 0.338 - 0.423: 3 Chirality restraints: 2118 Sorted by residual: chirality pdb=" CA LYS A 784 " pdb=" N LYS A 784 " pdb=" C LYS A 784 " pdb=" CB LYS A 784 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.47e+00 chirality pdb=" CA HIS A 750 " pdb=" N HIS A 750 " pdb=" C HIS A 750 " pdb=" CB HIS A 750 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.57e+00 chirality pdb=" CA ARG B 334 " pdb=" N ARG B 334 " pdb=" C ARG B 334 " pdb=" CB ARG B 334 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.97e+00 ... (remaining 2115 not shown) Planarity restraints: 2320 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B1002 " 0.039 5.00e-02 4.00e+02 5.87e-02 5.51e+00 pdb=" N PRO B1003 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO B1003 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B1003 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 939 " -0.014 2.00e-02 2.50e+03 1.37e-02 4.66e+00 pdb=" CG TRP B 939 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP B 939 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP B 939 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 939 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 939 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 939 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 939 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 939 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP B 939 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS B 421 " -0.010 2.00e-02 2.50e+03 1.98e-02 3.90e+00 pdb=" C CYS B 421 " 0.034 2.00e-02 2.50e+03 pdb=" O CYS B 421 " -0.013 2.00e-02 2.50e+03 pdb=" N SER B 422 " -0.012 2.00e-02 2.50e+03 ... (remaining 2317 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2661 2.76 - 3.29: 14136 3.29 - 3.83: 23694 3.83 - 4.36: 28426 4.36 - 4.90: 45802 Nonbonded interactions: 114719 Sorted by model distance: nonbonded pdb=" O SER A 345 " pdb=" OG SER A 533 " model vdw 2.222 3.040 nonbonded pdb=" O SER B 345 " pdb=" OG SER B 533 " model vdw 2.227 3.040 nonbonded pdb=" OE2 GLU B 755 " pdb=" OG SER B 987 " model vdw 2.230 3.040 nonbonded pdb=" OH TYR A 156 " pdb=" OG SER A 296 " model vdw 2.234 3.040 nonbonded pdb=" OH TYR B 156 " pdb=" OG SER B 296 " model vdw 2.234 3.040 ... (remaining 114714 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 137 through 959 or (resid 960 and (name N or name CA or na \ me C or name O or name CB )) or resid 961 through 989 or (resid 990 and (name N \ or name CA or name C or name O or name CB )) or resid 991 through 1020)) selection = chain 'B' } 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: 1.080 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: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.020 Find NCS groups from input model: 0.190 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: 0.010 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5882 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 13657 Z= 0.310 Angle : 0.933 12.634 18547 Z= 0.609 Chirality : 0.051 0.423 2118 Planarity : 0.005 0.059 2320 Dihedral : 14.361 87.938 4887 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 25.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 1.19 % Allowed : 18.46 % Favored : 80.35 % Cbeta Deviations : 0.06 % 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: -1.07 (0.20), residues: 1696 helix: 0.74 (0.17), residues: 930 sheet: -1.64 (0.56), residues: 71 loop : -2.75 (0.21), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 719 TYR 0.023 0.001 TYR B 627 PHE 0.016 0.001 PHE B 665 TRP 0.037 0.002 TRP B 939 HIS 0.003 0.001 HIS B 907 Details of bonding type rmsd covalent geometry : bond 0.00510 (13653) covalent geometry : angle 0.93353 (18539) SS BOND : bond 0.00537 ( 4) SS BOND : angle 0.77153 ( 8) hydrogen bonds : bond 0.17260 ( 744) hydrogen bonds : angle 6.72434 ( 2151) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 472 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 VAL cc_start: 0.7773 (t) cc_final: 0.7477 (t) REVERT: A 441 ILE cc_start: 0.6761 (tt) cc_final: 0.5937 (tt) REVERT: A 581 MET cc_start: 0.6009 (ttm) cc_final: 0.5553 (ttm) REVERT: A 599 LEU cc_start: 0.7811 (mt) cc_final: 0.7545 (mt) REVERT: A 671 LEU cc_start: 0.6431 (tp) cc_final: 0.5998 (tp) REVERT: A 776 MET cc_start: 0.3869 (pmm) cc_final: 0.3051 (pmm) REVERT: B 269 THR cc_start: 0.6876 (m) cc_final: 0.6357 (p) REVERT: B 505 PRO cc_start: 0.4614 (Cg_endo) cc_final: 0.3651 (Cg_exo) REVERT: B 642 ARG cc_start: 0.7413 (OUTLIER) cc_final: 0.6919 (mmm-85) outliers start: 17 outliers final: 5 residues processed: 486 average time/residue: 0.1146 time to fit residues: 82.4974 Evaluate side-chains 289 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 283 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain B residue 642 ARG Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 821 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 0.0980 chunk 149 optimal weight: 40.0000 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN A 327 GLN A 544 ASN A 566 ASN A 632 ASN A 817 GLN A 891 HIS ** A 900 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 999 GLN A1014 ASN ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 534 ASN B 566 ASN B 762 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.082572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.065428 restraints weight = 71207.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.066887 restraints weight = 54447.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.067971 restraints weight = 44044.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.068855 restraints weight = 37360.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.069542 restraints weight = 32675.460| |-----------------------------------------------------------------------------| r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 13657 Z= 0.204 Angle : 0.842 12.438 18547 Z= 0.427 Chirality : 0.050 0.274 2118 Planarity : 0.006 0.116 2320 Dihedral : 5.383 48.438 1854 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 26.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 5.10 % Allowed : 22.38 % Favored : 72.52 % 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: -0.96 (0.20), residues: 1696 helix: 0.58 (0.17), residues: 950 sheet: -1.47 (0.56), residues: 80 loop : -2.37 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 642 TYR 0.045 0.003 TYR A 627 PHE 0.030 0.003 PHE A 462 TRP 0.018 0.002 TRP A 699 HIS 0.009 0.001 HIS A 234 Details of bonding type rmsd covalent geometry : bond 0.00453 (13653) covalent geometry : angle 0.84246 (18539) SS BOND : bond 0.00319 ( 4) SS BOND : angle 0.78932 ( 8) hydrogen bonds : bond 0.05298 ( 744) hydrogen bonds : angle 5.63540 ( 2151) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 314 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 MET cc_start: 0.6724 (ttp) cc_final: 0.5704 (mtp) REVERT: A 144 ILE cc_start: 0.8562 (mt) cc_final: 0.8273 (tp) REVERT: A 156 TYR cc_start: 0.7735 (m-80) cc_final: 0.7505 (m-10) REVERT: A 173 ILE cc_start: 0.9064 (mm) cc_final: 0.8837 (tt) REVERT: A 177 LEU cc_start: 0.9354 (tp) cc_final: 0.9122 (tp) REVERT: A 328 ASN cc_start: 0.8945 (m-40) cc_final: 0.8617 (m110) REVERT: A 348 PHE cc_start: 0.8565 (t80) cc_final: 0.8173 (t80) REVERT: A 509 TYR cc_start: 0.8432 (m-80) cc_final: 0.7821 (m-80) REVERT: A 538 CYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8444 (m) REVERT: A 581 MET cc_start: 0.8394 (ttm) cc_final: 0.7922 (ttm) REVERT: A 1018 PHE cc_start: 0.5582 (OUTLIER) cc_final: 0.4459 (t80) REVERT: B 157 LEU cc_start: 0.8805 (mt) cc_final: 0.8553 (tp) REVERT: B 187 LEU cc_start: 0.9320 (mt) cc_final: 0.9072 (mt) REVERT: B 276 LEU cc_start: 0.8679 (mt) cc_final: 0.8084 (pp) REVERT: B 328 ASN cc_start: 0.8527 (m110) cc_final: 0.8290 (m110) REVERT: B 377 MET cc_start: 0.8448 (tpp) cc_final: 0.8045 (tpp) REVERT: B 505 PRO cc_start: 0.7065 (Cg_endo) cc_final: 0.6680 (Cg_exo) REVERT: B 540 TYR cc_start: 0.8397 (m-10) cc_final: 0.8154 (m-10) REVERT: B 549 HIS cc_start: 0.8851 (OUTLIER) cc_final: 0.8470 (t70) REVERT: B 642 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.7437 (mmm-85) REVERT: B 674 CYS cc_start: 0.8593 (OUTLIER) cc_final: 0.8228 (p) REVERT: B 691 LEU cc_start: 0.9588 (mt) cc_final: 0.9345 (mt) REVERT: B 774 MET cc_start: 0.6739 (mtp) cc_final: 0.6473 (mtp) REVERT: B 849 LEU cc_start: 0.9170 (mp) cc_final: 0.8908 (tt) outliers start: 73 outliers final: 33 residues processed: 367 average time/residue: 0.1058 time to fit residues: 59.0659 Evaluate side-chains 308 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 270 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 547 CYS Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 642 ARG Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 808 ASP Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 877 LYS Chi-restraints excluded: chain A residue 1018 PHE Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 457 ILE Chi-restraints excluded: chain B residue 534 ASN Chi-restraints excluded: chain B residue 549 HIS Chi-restraints excluded: chain B residue 559 ARG Chi-restraints excluded: chain B residue 561 SER Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 642 ARG Chi-restraints excluded: chain B residue 645 CYS Chi-restraints excluded: chain B residue 661 PHE Chi-restraints excluded: chain B residue 670 SER Chi-restraints excluded: chain B residue 674 CYS Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 962 ILE Chi-restraints excluded: chain B residue 965 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 100 optimal weight: 2.9990 chunk 68 optimal weight: 0.3980 chunk 166 optimal weight: 20.0000 chunk 76 optimal weight: 8.9990 chunk 134 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 156 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 98 optimal weight: 5.9990 chunk 131 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 442 ASN ** A 900 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 ASN B 534 ASN B 762 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.080586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.063772 restraints weight = 74411.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.065220 restraints weight = 56099.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.066344 restraints weight = 45067.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.067210 restraints weight = 37970.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.067826 restraints weight = 33127.017| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.4479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 13657 Z= 0.177 Angle : 0.782 10.501 18547 Z= 0.393 Chirality : 0.048 0.179 2118 Planarity : 0.005 0.086 2320 Dihedral : 5.124 33.981 1846 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 25.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 4.55 % Allowed : 22.59 % Favored : 72.87 % 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: -0.84 (0.20), residues: 1696 helix: 0.60 (0.17), residues: 951 sheet: -1.77 (0.48), residues: 94 loop : -2.13 (0.23), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 145 TYR 0.034 0.002 TYR B 513 PHE 0.042 0.003 PHE A 462 TRP 0.020 0.002 TRP A 699 HIS 0.007 0.001 HIS A 234 Details of bonding type rmsd covalent geometry : bond 0.00392 (13653) covalent geometry : angle 0.78173 (18539) SS BOND : bond 0.00236 ( 4) SS BOND : angle 0.78147 ( 8) hydrogen bonds : bond 0.04878 ( 744) hydrogen bonds : angle 5.41647 ( 2151) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 286 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 LEU cc_start: 0.9406 (tp) cc_final: 0.9202 (tp) REVERT: A 219 ILE cc_start: 0.9211 (mt) cc_final: 0.8998 (tp) REVERT: A 328 ASN cc_start: 0.8902 (m-40) cc_final: 0.8682 (m110) REVERT: A 386 TYR cc_start: 0.8799 (m-80) cc_final: 0.8062 (m-80) REVERT: A 457 ILE cc_start: 0.9041 (OUTLIER) cc_final: 0.8434 (tp) REVERT: A 509 TYR cc_start: 0.8547 (m-80) cc_final: 0.8041 (m-80) REVERT: A 581 MET cc_start: 0.8289 (ttm) cc_final: 0.7934 (ttm) REVERT: A 686 MET cc_start: 0.5528 (ttt) cc_final: 0.5014 (ttp) REVERT: A 872 MET cc_start: 0.3813 (tpt) cc_final: 0.3145 (mmm) REVERT: A 1018 PHE cc_start: 0.5957 (OUTLIER) cc_final: 0.4803 (t80) REVERT: B 156 TYR cc_start: 0.8316 (m-80) cc_final: 0.8000 (m-10) REVERT: B 240 GLU cc_start: 0.8836 (tm-30) cc_final: 0.8458 (tp30) REVERT: B 267 SER cc_start: 0.8837 (m) cc_final: 0.8509 (p) REVERT: B 276 LEU cc_start: 0.8571 (mt) cc_final: 0.8136 (pp) REVERT: B 343 MET cc_start: 0.8281 (mmm) cc_final: 0.7988 (mmm) REVERT: B 540 TYR cc_start: 0.8428 (m-10) cc_final: 0.8209 (m-10) REVERT: B 549 HIS cc_start: 0.8799 (OUTLIER) cc_final: 0.8475 (t70) REVERT: B 642 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.7472 (mmm-85) REVERT: B 658 LEU cc_start: 0.9063 (mp) cc_final: 0.8851 (mp) outliers start: 65 outliers final: 34 residues processed: 327 average time/residue: 0.0971 time to fit residues: 49.0017 Evaluate side-chains 285 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 247 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 547 CYS Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 642 ARG Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1018 PHE Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 227 ASN Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 457 ILE Chi-restraints excluded: chain B residue 549 HIS Chi-restraints excluded: chain B residue 559 ARG Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 642 ARG Chi-restraints excluded: chain B residue 645 CYS Chi-restraints excluded: chain B residue 670 SER Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 785 MET Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 962 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 chunk 79 optimal weight: 20.0000 chunk 50 optimal weight: 0.5980 chunk 114 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 38 optimal weight: 8.9990 chunk 27 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 159 optimal weight: 6.9990 chunk 163 optimal weight: 9.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 566 ASN ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.079567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.061795 restraints weight = 73448.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.063610 restraints weight = 50830.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.065020 restraints weight = 38539.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.066060 restraints weight = 31136.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.066938 restraints weight = 26369.002| |-----------------------------------------------------------------------------| r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6410 moved from start: 0.5149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 13657 Z= 0.219 Angle : 0.793 12.465 18547 Z= 0.401 Chirality : 0.049 0.293 2118 Planarity : 0.005 0.067 2320 Dihedral : 5.158 34.760 1845 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 27.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.83 % Favored : 95.11 % Rotamer: Outliers : 5.38 % Allowed : 26.08 % Favored : 68.53 % 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: -0.88 (0.20), residues: 1696 helix: 0.50 (0.16), residues: 955 sheet: -1.77 (0.47), residues: 100 loop : -2.03 (0.23), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 158 TYR 0.030 0.002 TYR B 513 PHE 0.049 0.003 PHE A 462 TRP 0.026 0.002 TRP B 151 HIS 0.009 0.001 HIS B 762 Details of bonding type rmsd covalent geometry : bond 0.00474 (13653) covalent geometry : angle 0.79315 (18539) SS BOND : bond 0.00243 ( 4) SS BOND : angle 0.71203 ( 8) hydrogen bonds : bond 0.04678 ( 744) hydrogen bonds : angle 5.50892 ( 2151) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 259 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 LYS cc_start: 0.8291 (mttt) cc_final: 0.8049 (mmmt) REVERT: A 328 ASN cc_start: 0.9040 (m-40) cc_final: 0.8654 (m110) REVERT: A 386 TYR cc_start: 0.9532 (m-80) cc_final: 0.8884 (m-80) REVERT: A 509 TYR cc_start: 0.8822 (m-80) cc_final: 0.8478 (m-80) REVERT: A 682 HIS cc_start: 0.9299 (OUTLIER) cc_final: 0.9082 (p90) REVERT: A 686 MET cc_start: 0.5200 (ttt) cc_final: 0.4671 (ttp) REVERT: A 708 PHE cc_start: 0.8717 (m-80) cc_final: 0.8338 (m-80) REVERT: A 725 MET cc_start: 0.9540 (ptt) cc_final: 0.9328 (ptt) REVERT: A 835 TRP cc_start: 0.7012 (m100) cc_final: 0.6777 (m100) REVERT: A 872 MET cc_start: 0.5230 (tpt) cc_final: 0.4009 (mmm) REVERT: B 157 LEU cc_start: 0.8556 (tp) cc_final: 0.8163 (tp) REVERT: B 348 PHE cc_start: 0.9233 (t80) cc_final: 0.8990 (t80) REVERT: B 509 TYR cc_start: 0.8565 (m-80) cc_final: 0.8171 (m-80) REVERT: B 548 PHE cc_start: 0.8885 (t80) cc_final: 0.8523 (t80) REVERT: B 581 MET cc_start: 0.8923 (ptm) cc_final: 0.8522 (ppp) REVERT: B 642 ARG cc_start: 0.6613 (OUTLIER) cc_final: 0.6099 (mmm-85) REVERT: B 933 MET cc_start: 0.9179 (ptp) cc_final: 0.8859 (ptt) outliers start: 77 outliers final: 48 residues processed: 307 average time/residue: 0.0979 time to fit residues: 47.0324 Evaluate side-chains 279 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 229 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 547 CYS Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 642 ARG Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 682 HIS Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 990 TYR Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 227 ASN Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 457 ILE Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 534 ASN Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 559 ARG Chi-restraints excluded: chain B residue 642 ARG Chi-restraints excluded: chain B residue 645 CYS Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 674 CYS Chi-restraints excluded: chain B residue 677 VAL Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 772 CYS Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 785 MET Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 962 ILE Chi-restraints excluded: chain B residue 975 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 86 optimal weight: 9.9990 chunk 44 optimal weight: 0.6980 chunk 19 optimal weight: 0.3980 chunk 2 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 116 optimal weight: 5.9990 chunk 121 optimal weight: 9.9990 chunk 42 optimal weight: 7.9990 chunk 108 optimal weight: 7.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 HIS A 891 HIS ** A 900 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 ASN B 549 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.081739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.063659 restraints weight = 71464.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.065517 restraints weight = 49217.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.066950 restraints weight = 37316.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.068088 restraints weight = 30125.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.068922 restraints weight = 25333.812| |-----------------------------------------------------------------------------| r_work (final): 0.3913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6350 moved from start: 0.5519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 13657 Z= 0.151 Angle : 0.799 13.503 18547 Z= 0.383 Chirality : 0.048 0.350 2118 Planarity : 0.005 0.044 2320 Dihedral : 5.078 35.728 1845 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 23.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.89 % Favored : 95.05 % Rotamer: Outliers : 4.34 % Allowed : 27.13 % Favored : 68.53 % 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: -0.79 (0.20), residues: 1696 helix: 0.57 (0.17), residues: 957 sheet: -1.50 (0.49), residues: 94 loop : -2.04 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 145 TYR 0.041 0.002 TYR B 156 PHE 0.040 0.002 PHE A 462 TRP 0.046 0.002 TRP B 151 HIS 0.005 0.001 HIS B 762 Details of bonding type rmsd covalent geometry : bond 0.00335 (13653) covalent geometry : angle 0.79875 (18539) SS BOND : bond 0.00267 ( 4) SS BOND : angle 0.72369 ( 8) hydrogen bonds : bond 0.04381 ( 744) hydrogen bonds : angle 5.28792 ( 2151) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 256 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 LEU cc_start: 0.9455 (tp) cc_final: 0.9111 (mt) REVERT: A 328 ASN cc_start: 0.9051 (m-40) cc_final: 0.8568 (m110) REVERT: A 348 PHE cc_start: 0.8709 (t80) cc_final: 0.8407 (t80) REVERT: A 509 TYR cc_start: 0.8836 (m-80) cc_final: 0.8563 (m-80) REVERT: A 581 MET cc_start: 0.9178 (ttm) cc_final: 0.8965 (tmm) REVERT: A 672 MET cc_start: 0.8435 (pmm) cc_final: 0.8129 (pmm) REVERT: A 708 PHE cc_start: 0.8499 (m-80) cc_final: 0.8062 (m-80) REVERT: A 725 MET cc_start: 0.9562 (ptt) cc_final: 0.9269 (ptt) REVERT: A 835 TRP cc_start: 0.7027 (m100) cc_final: 0.6729 (m100) REVERT: A 872 MET cc_start: 0.4947 (tpt) cc_final: 0.3734 (mmm) REVERT: B 525 LEU cc_start: 0.9510 (mt) cc_final: 0.9290 (mm) REVERT: B 548 PHE cc_start: 0.8858 (t80) cc_final: 0.8456 (t80) REVERT: B 642 ARG cc_start: 0.6650 (OUTLIER) cc_final: 0.6182 (mmm-85) REVERT: B 677 VAL cc_start: 0.5761 (OUTLIER) cc_final: 0.5561 (p) outliers start: 62 outliers final: 37 residues processed: 293 average time/residue: 0.0957 time to fit residues: 44.6375 Evaluate side-chains 274 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 235 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 547 CYS Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 227 ASN Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain B residue 457 ILE Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 534 ASN Chi-restraints excluded: chain B residue 559 ARG Chi-restraints excluded: chain B residue 642 ARG Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 677 VAL Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 772 CYS Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 962 ILE Chi-restraints excluded: chain B residue 975 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 20.0000 chunk 62 optimal weight: 7.9990 chunk 73 optimal weight: 9.9990 chunk 9 optimal weight: 0.9980 chunk 18 optimal weight: 20.0000 chunk 52 optimal weight: 20.0000 chunk 15 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 chunk 56 optimal weight: 7.9990 chunk 61 optimal weight: 0.7980 chunk 101 optimal weight: 9.9990 overall best weight: 5.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 426 ASN A 640 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.075614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.059723 restraints weight = 77829.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.060884 restraints weight = 60194.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.061802 restraints weight = 49662.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.062467 restraints weight = 42761.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.062984 restraints weight = 38173.104| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.6103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 13657 Z= 0.260 Angle : 0.819 13.892 18547 Z= 0.419 Chirality : 0.050 0.315 2118 Planarity : 0.005 0.046 2320 Dihedral : 5.253 33.884 1845 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 30.11 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.01 % Favored : 93.93 % Rotamer: Outliers : 5.45 % Allowed : 27.27 % Favored : 67.27 % 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: -0.97 (0.20), residues: 1696 helix: 0.33 (0.16), residues: 966 sheet: -1.58 (0.49), residues: 100 loop : -1.97 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 158 TYR 0.027 0.002 TYR B 156 PHE 0.053 0.003 PHE A 462 TRP 0.055 0.002 TRP B 151 HIS 0.008 0.001 HIS B 762 Details of bonding type rmsd covalent geometry : bond 0.00551 (13653) covalent geometry : angle 0.81894 (18539) SS BOND : bond 0.02783 ( 4) SS BOND : angle 0.84112 ( 8) hydrogen bonds : bond 0.04676 ( 744) hydrogen bonds : angle 5.62662 ( 2151) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 238 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 328 ASN cc_start: 0.9115 (m-40) cc_final: 0.8808 (m110) REVERT: A 386 TYR cc_start: 0.8671 (m-80) cc_final: 0.8199 (m-80) REVERT: A 447 MET cc_start: 0.9343 (ppp) cc_final: 0.8724 (ppp) REVERT: A 509 TYR cc_start: 0.8618 (m-80) cc_final: 0.8358 (m-80) REVERT: A 642 ARG cc_start: 0.7456 (OUTLIER) cc_final: 0.6654 (mmm160) REVERT: A 725 MET cc_start: 0.9052 (ptt) cc_final: 0.8426 (ptt) REVERT: A 872 MET cc_start: 0.3872 (tpt) cc_final: 0.2235 (mmm) REVERT: B 143 MET cc_start: 0.7622 (mmm) cc_final: 0.6834 (tpt) REVERT: B 157 LEU cc_start: 0.8899 (tp) cc_final: 0.8464 (tp) REVERT: B 290 PHE cc_start: 0.8696 (t80) cc_final: 0.8454 (t80) REVERT: B 548 PHE cc_start: 0.8621 (t80) cc_final: 0.8325 (t80) REVERT: B 581 MET cc_start: 0.9038 (ppp) cc_final: 0.8737 (ppp) REVERT: B 642 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.7495 (mmm-85) outliers start: 78 outliers final: 53 residues processed: 290 average time/residue: 0.1013 time to fit residues: 45.5906 Evaluate side-chains 275 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 220 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 547 CYS Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 642 ARG Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 940 LYS Chi-restraints excluded: chain A residue 990 TYR Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 227 ASN Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 457 ILE Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 534 ASN Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 549 HIS Chi-restraints excluded: chain B residue 559 ARG Chi-restraints excluded: chain B residue 642 ARG Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 677 VAL Chi-restraints excluded: chain B residue 708 PHE Chi-restraints excluded: chain B residue 744 LYS Chi-restraints excluded: chain B residue 765 PHE Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 842 LEU Chi-restraints excluded: chain B residue 962 ILE Chi-restraints excluded: chain B residue 975 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 95 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 137 optimal weight: 10.0000 chunk 67 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 73 optimal weight: 10.0000 chunk 162 optimal weight: 6.9990 chunk 135 optimal weight: 8.9990 chunk 60 optimal weight: 3.9990 chunk 43 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 668 ASN A 891 HIS ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.075797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.059821 restraints weight = 77559.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.060977 restraints weight = 59764.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.061903 restraints weight = 49275.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.062609 restraints weight = 42532.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.063060 restraints weight = 37811.852| |-----------------------------------------------------------------------------| r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.6444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 13657 Z= 0.194 Angle : 0.806 12.419 18547 Z= 0.401 Chirality : 0.050 0.344 2118 Planarity : 0.005 0.044 2320 Dihedral : 5.282 35.041 1845 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 26.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.72 % Favored : 94.22 % Rotamer: Outliers : 4.69 % Allowed : 28.74 % Favored : 66.57 % 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: -0.98 (0.20), residues: 1696 helix: 0.34 (0.16), residues: 962 sheet: -1.60 (0.49), residues: 100 loop : -1.99 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 158 TYR 0.022 0.002 TYR B 156 PHE 0.040 0.002 PHE A 325 TRP 0.066 0.002 TRP B 151 HIS 0.006 0.001 HIS B 762 Details of bonding type rmsd covalent geometry : bond 0.00423 (13653) covalent geometry : angle 0.80608 (18539) SS BOND : bond 0.00217 ( 4) SS BOND : angle 0.85464 ( 8) hydrogen bonds : bond 0.04534 ( 744) hydrogen bonds : angle 5.52378 ( 2151) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 238 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 MET cc_start: 0.8019 (mmm) cc_final: 0.7702 (tpt) REVERT: A 509 TYR cc_start: 0.8612 (m-80) cc_final: 0.8348 (m-80) REVERT: A 540 TYR cc_start: 0.8919 (m-10) cc_final: 0.8619 (m-80) REVERT: A 725 MET cc_start: 0.9025 (ptt) cc_final: 0.8315 (ptt) REVERT: A 872 MET cc_start: 0.3811 (tpt) cc_final: 0.2209 (mmm) REVERT: B 221 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.9032 (mt) REVERT: B 290 PHE cc_start: 0.8597 (t80) cc_final: 0.8360 (t80) REVERT: B 548 PHE cc_start: 0.8571 (t80) cc_final: 0.8313 (t80) REVERT: B 642 ARG cc_start: 0.8010 (OUTLIER) cc_final: 0.7579 (mmm-85) REVERT: B 685 ARG cc_start: 0.7890 (mpt180) cc_final: 0.7470 (mpt180) REVERT: B 725 MET cc_start: 0.9003 (ppp) cc_final: 0.8674 (ppp) REVERT: B 730 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8461 (pp) outliers start: 67 outliers final: 43 residues processed: 288 average time/residue: 0.0978 time to fit residues: 44.2436 Evaluate side-chains 271 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 225 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 547 CYS Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 668 ASN Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 227 ASN Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain B residue 457 ILE Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 534 ASN Chi-restraints excluded: chain B residue 549 HIS Chi-restraints excluded: chain B residue 559 ARG Chi-restraints excluded: chain B residue 642 ARG Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 674 CYS Chi-restraints excluded: chain B residue 677 VAL Chi-restraints excluded: chain B residue 708 PHE Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 744 LYS Chi-restraints excluded: chain B residue 772 CYS Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 975 ILE Chi-restraints excluded: chain B residue 979 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 121 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 149 optimal weight: 5.9990 chunk 131 optimal weight: 4.9990 chunk 102 optimal weight: 10.0000 chunk 122 optimal weight: 0.8980 chunk 63 optimal weight: 9.9990 chunk 169 optimal weight: 6.9990 chunk 133 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 60 optimal weight: 8.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 891 HIS ** A 956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.074915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.058834 restraints weight = 76271.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.060017 restraints weight = 59445.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.060885 restraints weight = 49132.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.061533 restraints weight = 42585.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.062047 restraints weight = 38211.366| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.6794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 13657 Z= 0.196 Angle : 0.837 13.904 18547 Z= 0.414 Chirality : 0.051 0.399 2118 Planarity : 0.005 0.064 2320 Dihedral : 5.296 34.845 1845 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 28.07 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.96 % Favored : 93.99 % Rotamer: Outliers : 4.90 % Allowed : 29.02 % Favored : 66.08 % 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: -0.98 (0.20), residues: 1696 helix: 0.31 (0.16), residues: 961 sheet: -1.53 (0.51), residues: 93 loop : -1.96 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 852 TYR 0.013 0.002 TYR B 848 PHE 0.044 0.003 PHE A 348 TRP 0.083 0.002 TRP B 151 HIS 0.006 0.001 HIS B 637 Details of bonding type rmsd covalent geometry : bond 0.00436 (13653) covalent geometry : angle 0.83730 (18539) SS BOND : bond 0.00224 ( 4) SS BOND : angle 0.81517 ( 8) hydrogen bonds : bond 0.04611 ( 744) hydrogen bonds : angle 5.59046 ( 2151) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 240 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 MET cc_start: 0.8021 (mmm) cc_final: 0.7690 (mmm) REVERT: A 377 MET cc_start: 0.8566 (mtm) cc_final: 0.8023 (mpp) REVERT: A 509 TYR cc_start: 0.8504 (m-80) cc_final: 0.8286 (m-80) REVERT: A 540 TYR cc_start: 0.8757 (m-10) cc_final: 0.8467 (m-80) REVERT: A 725 MET cc_start: 0.8866 (ptt) cc_final: 0.8288 (ptt) REVERT: A 774 MET cc_start: 0.5960 (tpt) cc_final: 0.5706 (tpt) REVERT: A 872 MET cc_start: 0.3776 (tpt) cc_final: 0.2170 (mmm) REVERT: B 221 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.9030 (mt) REVERT: B 346 ILE cc_start: 0.9512 (mm) cc_final: 0.9271 (mm) REVERT: B 642 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7670 (mmm-85) REVERT: B 685 ARG cc_start: 0.7784 (mpt180) cc_final: 0.7269 (mpt180) REVERT: B 725 MET cc_start: 0.8827 (ppp) cc_final: 0.8614 (ppp) REVERT: B 933 MET cc_start: 0.8743 (ptp) cc_final: 0.8376 (ppp) REVERT: B 972 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8755 (mm) outliers start: 70 outliers final: 51 residues processed: 289 average time/residue: 0.1004 time to fit residues: 45.4701 Evaluate side-chains 283 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 229 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 547 CYS Chi-restraints excluded: chain A residue 582 PHE Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 877 LYS Chi-restraints excluded: chain A residue 940 LYS Chi-restraints excluded: chain A residue 990 TYR Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 227 ASN Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain B residue 457 ILE Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 534 ASN Chi-restraints excluded: chain B residue 549 HIS Chi-restraints excluded: chain B residue 642 ARG Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 674 CYS Chi-restraints excluded: chain B residue 677 VAL Chi-restraints excluded: chain B residue 708 PHE Chi-restraints excluded: chain B residue 744 LYS Chi-restraints excluded: chain B residue 765 PHE Chi-restraints excluded: chain B residue 772 CYS Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 972 LEU Chi-restraints excluded: chain B residue 975 ILE Chi-restraints excluded: chain B residue 979 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 146 optimal weight: 5.9990 chunk 118 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 26 optimal weight: 20.0000 chunk 12 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 75 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 544 ASN A 891 HIS ** A 956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.075169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.059087 restraints weight = 76942.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.060272 restraints weight = 59759.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.061165 restraints weight = 49378.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.061670 restraints weight = 42722.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.062282 restraints weight = 38736.704| |-----------------------------------------------------------------------------| r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.7023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 13657 Z= 0.179 Angle : 0.850 13.520 18547 Z= 0.413 Chirality : 0.050 0.377 2118 Planarity : 0.005 0.065 2320 Dihedral : 5.281 35.051 1845 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 25.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.96 % Favored : 93.99 % Rotamer: Outliers : 4.34 % Allowed : 30.28 % Favored : 65.38 % 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: -0.90 (0.20), residues: 1696 helix: 0.34 (0.16), residues: 971 sheet: -1.47 (0.52), residues: 91 loop : -1.90 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 934 TYR 0.013 0.002 TYR B 848 PHE 0.056 0.002 PHE A 348 TRP 0.080 0.002 TRP B 151 HIS 0.009 0.001 HIS B 234 Details of bonding type rmsd covalent geometry : bond 0.00396 (13653) covalent geometry : angle 0.84953 (18539) SS BOND : bond 0.00239 ( 4) SS BOND : angle 0.88351 ( 8) hydrogen bonds : bond 0.04518 ( 744) hydrogen bonds : angle 5.53048 ( 2151) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 238 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 MET cc_start: 0.8091 (mmm) cc_final: 0.7521 (mmm) REVERT: A 172 TRP cc_start: 0.8838 (m100) cc_final: 0.8180 (m100) REVERT: A 377 MET cc_start: 0.8635 (mtm) cc_final: 0.8115 (mpp) REVERT: A 386 TYR cc_start: 0.8565 (m-80) cc_final: 0.8085 (m-80) REVERT: A 509 TYR cc_start: 0.8551 (m-80) cc_final: 0.8308 (m-80) REVERT: A 540 TYR cc_start: 0.8853 (m-10) cc_final: 0.8564 (m-80) REVERT: A 725 MET cc_start: 0.8965 (ptt) cc_final: 0.8622 (ptt) REVERT: A 774 MET cc_start: 0.6067 (tpt) cc_final: 0.5778 (tpt) REVERT: A 854 ARG cc_start: 0.8694 (ttp80) cc_final: 0.8100 (ttp80) REVERT: A 872 MET cc_start: 0.3919 (tpt) cc_final: 0.2765 (mmm) REVERT: B 221 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.9057 (mt) REVERT: B 343 MET cc_start: 0.8751 (tpp) cc_final: 0.8496 (mmm) REVERT: B 346 ILE cc_start: 0.9554 (mm) cc_final: 0.9278 (mm) REVERT: B 447 MET cc_start: 0.8615 (mtt) cc_final: 0.8296 (mtp) REVERT: B 685 ARG cc_start: 0.7793 (mpt180) cc_final: 0.7227 (mpt180) REVERT: B 725 MET cc_start: 0.8914 (ppp) cc_final: 0.8606 (ppp) REVERT: B 776 MET cc_start: 0.7570 (tpp) cc_final: 0.7275 (ptm) REVERT: B 933 MET cc_start: 0.8777 (ptp) cc_final: 0.8319 (ppp) REVERT: B 972 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8816 (mm) outliers start: 62 outliers final: 45 residues processed: 282 average time/residue: 0.0845 time to fit residues: 37.6002 Evaluate side-chains 273 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 226 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 547 CYS Chi-restraints excluded: chain A residue 582 PHE Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 877 LYS Chi-restraints excluded: chain A residue 940 LYS Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain B residue 457 ILE Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 513 TYR Chi-restraints excluded: chain B residue 534 ASN Chi-restraints excluded: chain B residue 549 HIS Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 674 CYS Chi-restraints excluded: chain B residue 677 VAL Chi-restraints excluded: chain B residue 708 PHE Chi-restraints excluded: chain B residue 765 PHE Chi-restraints excluded: chain B residue 772 CYS Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 972 LEU Chi-restraints excluded: chain B residue 975 ILE Chi-restraints excluded: chain B residue 979 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 9.9990 chunk 165 optimal weight: 6.9990 chunk 155 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 113 optimal weight: 4.9990 chunk 46 optimal weight: 0.0870 chunk 57 optimal weight: 6.9990 chunk 22 optimal weight: 10.0000 chunk 110 optimal weight: 0.9990 chunk 142 optimal weight: 0.0000 overall best weight: 0.6168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 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 = 0.3966 r_free = 0.3966 target = 0.076962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.061101 restraints weight = 76761.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.062312 restraints weight = 59624.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.063235 restraints weight = 49122.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.063934 restraints weight = 42336.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.064468 restraints weight = 37755.062| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.7207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 13657 Z= 0.157 Angle : 0.879 14.012 18547 Z= 0.420 Chirality : 0.052 0.367 2118 Planarity : 0.005 0.044 2320 Dihedral : 5.164 38.532 1841 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 22.90 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.19 % Favored : 94.75 % Rotamer: Outliers : 2.66 % Allowed : 32.73 % Favored : 64.62 % 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: -0.84 (0.20), residues: 1696 helix: 0.39 (0.17), residues: 970 sheet: -0.97 (0.52), residues: 91 loop : -1.96 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG B 719 TYR 0.015 0.001 TYR A 513 PHE 0.048 0.002 PHE A 348 TRP 0.084 0.002 TRP B 151 HIS 0.010 0.001 HIS B 234 Details of bonding type rmsd covalent geometry : bond 0.00354 (13653) covalent geometry : angle 0.87945 (18539) SS BOND : bond 0.00272 ( 4) SS BOND : angle 0.90215 ( 8) hydrogen bonds : bond 0.04422 ( 744) hydrogen bonds : angle 5.43145 ( 2151) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 243 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 MET cc_start: 0.8129 (mmm) cc_final: 0.7613 (mmm) REVERT: A 172 TRP cc_start: 0.8721 (m100) cc_final: 0.8426 (m100) REVERT: A 240 GLU cc_start: 0.8149 (tt0) cc_final: 0.7400 (tm-30) REVERT: A 377 MET cc_start: 0.8524 (mtm) cc_final: 0.8147 (mpp) REVERT: A 386 TYR cc_start: 0.8428 (m-80) cc_final: 0.7934 (m-80) REVERT: A 540 TYR cc_start: 0.8707 (m-10) cc_final: 0.8340 (m-80) REVERT: A 725 MET cc_start: 0.8875 (ptt) cc_final: 0.8202 (ptt) REVERT: A 854 ARG cc_start: 0.8655 (ttp80) cc_final: 0.8138 (ttp80) REVERT: A 872 MET cc_start: 0.3651 (tpt) cc_final: 0.2500 (mmm) REVERT: B 147 MET cc_start: 0.7657 (OUTLIER) cc_final: 0.7346 (mmt) REVERT: B 279 MET cc_start: 0.8956 (ppp) cc_final: 0.8326 (ppp) REVERT: B 346 ILE cc_start: 0.9548 (mm) cc_final: 0.9317 (mm) REVERT: B 447 MET cc_start: 0.8552 (mtt) cc_final: 0.8247 (mtp) REVERT: B 535 PHE cc_start: 0.8573 (m-10) cc_final: 0.8296 (m-80) REVERT: B 548 PHE cc_start: 0.8355 (t80) cc_final: 0.8134 (t80) REVERT: B 725 MET cc_start: 0.8911 (ppp) cc_final: 0.8600 (ppp) REVERT: B 835 TRP cc_start: 0.8435 (p-90) cc_final: 0.8220 (p-90) REVERT: B 933 MET cc_start: 0.8841 (ptp) cc_final: 0.8406 (ppp) outliers start: 38 outliers final: 33 residues processed: 265 average time/residue: 0.0915 time to fit residues: 38.7164 Evaluate side-chains 261 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 227 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 547 CYS Chi-restraints excluded: chain A residue 582 PHE Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 940 LYS Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain B residue 457 ILE Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 534 ASN Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 677 VAL Chi-restraints excluded: chain B residue 708 PHE Chi-restraints excluded: chain B residue 772 CYS Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 975 ILE Chi-restraints excluded: chain B residue 979 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 0 optimal weight: 20.0000 chunk 154 optimal weight: 9.9990 chunk 147 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 6 optimal weight: 30.0000 chunk 27 optimal weight: 20.0000 chunk 11 optimal weight: 0.0670 chunk 114 optimal weight: 6.9990 chunk 61 optimal weight: 0.8980 overall best weight: 1.9924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 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 = 0.3945 r_free = 0.3945 target = 0.075830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.059786 restraints weight = 76819.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.060966 restraints weight = 60166.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.061856 restraints weight = 49924.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.062510 restraints weight = 43282.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.063050 restraints weight = 38823.702| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.7375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 13657 Z= 0.162 Angle : 0.869 15.426 18547 Z= 0.420 Chirality : 0.051 0.371 2118 Planarity : 0.005 0.068 2320 Dihedral : 5.151 40.318 1841 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 25.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.25 % Favored : 94.69 % Rotamer: Outliers : 3.36 % Allowed : 31.75 % Favored : 64.90 % 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: -0.80 (0.20), residues: 1696 helix: 0.42 (0.17), residues: 967 sheet: -0.96 (0.50), residues: 94 loop : -1.93 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 667 TYR 0.022 0.002 TYR B 627 PHE 0.051 0.002 PHE A 348 TRP 0.078 0.002 TRP B 151 HIS 0.010 0.001 HIS B 234 Details of bonding type rmsd covalent geometry : bond 0.00371 (13653) covalent geometry : angle 0.86899 (18539) SS BOND : bond 0.00237 ( 4) SS BOND : angle 0.92576 ( 8) hydrogen bonds : bond 0.04353 ( 744) hydrogen bonds : angle 5.50148 ( 2151) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2713.21 seconds wall clock time: 47 minutes 46.15 seconds (2866.15 seconds total)