Starting phenix.real_space_refine on Thu Jul 31 09:55:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yg0_33803/07_2025/7yg0_33803_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yg0_33803/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7yg0_33803/07_2025/7yg0_33803.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yg0_33803/07_2025/7yg0_33803.map" model { file = "/net/cci-nas-00/data/ceres_data/7yg0_33803/07_2025/7yg0_33803_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yg0_33803/07_2025/7yg0_33803_neut.cif" } resolution = 3.75 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 19 Time building chain proxies: 7.37, per 1000 atoms: 0.55 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: 3.45 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.30 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: 4.20 Time building geometry restraints manager: 4.00 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: 1.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 31.030 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.190 ------------------------------------------------------------------------------- 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 : 25.32 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (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 TRP 0.037 0.002 TRP B 939 HIS 0.003 0.001 HIS B 907 PHE 0.016 0.001 PHE B 665 TYR 0.023 0.001 TYR B 627 ARG 0.005 0.000 ARG A 719 Details of bonding type rmsd hydrogen bonds : bond 0.17260 ( 744) hydrogen bonds : angle 6.72434 ( 2151) SS BOND : bond 0.00537 ( 4) SS BOND : angle 0.77153 ( 8) covalent geometry : bond 0.00510 (13653) covalent geometry : angle 0.93353 (18539) *********************** 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 : 1.600 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: A 229 VAL cc_start: 0.7773 (t) cc_final: 0.7407 (t) REVERT: A 441 ILE cc_start: 0.6761 (tt) cc_final: 0.6041 (tt) REVERT: A 581 MET cc_start: 0.6009 (ttm) cc_final: 0.5533 (ttm) REVERT: A 599 LEU cc_start: 0.7811 (mt) cc_final: 0.7549 (mt) REVERT: A 671 LEU cc_start: 0.6431 (tp) cc_final: 0.6002 (tp) REVERT: A 776 MET cc_start: 0.3869 (pmm) cc_final: 0.3054 (pmm) REVERT: B 269 THR cc_start: 0.6876 (m) cc_final: 0.6360 (p) REVERT: B 505 PRO cc_start: 0.4614 (Cg_endo) cc_final: 0.3654 (Cg_exo) REVERT: B 642 ARG cc_start: 0.7413 (OUTLIER) cc_final: 0.6921 (mmm-85) outliers start: 17 outliers final: 5 residues processed: 486 average time/residue: 0.2492 time to fit residues: 177.4251 Evaluate side-chains 287 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 281 time to evaluate : 1.447 ------------------------------------------------------------------------------- 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 143 optimal weight: 7.9990 chunk 128 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 68 optimal weight: 0.0040 chunk 133 optimal weight: 10.0000 chunk 51 optimal weight: 6.9990 chunk 81 optimal weight: 9.9990 chunk 99 optimal weight: 9.9990 chunk 154 optimal weight: 4.9990 overall best weight: 2.9998 ------------------------------------------------------------------------------- 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 327 GLN B 534 ASN B 566 ASN B 762 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.081603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.064449 restraints weight = 71381.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.065954 restraints weight = 54050.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.067089 restraints weight = 43425.306| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.3705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 13657 Z= 0.206 Angle : 0.836 11.799 18547 Z= 0.425 Chirality : 0.050 0.285 2118 Planarity : 0.006 0.112 2320 Dihedral : 5.405 48.778 1854 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 27.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 5.03 % Allowed : 22.73 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.20), residues: 1696 helix: 0.58 (0.17), residues: 946 sheet: -1.64 (0.54), residues: 86 loop : -2.34 (0.22), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 699 HIS 0.010 0.001 HIS A 234 PHE 0.035 0.003 PHE A 341 TYR 0.045 0.003 TYR A 627 ARG 0.015 0.001 ARG A 642 Details of bonding type rmsd hydrogen bonds : bond 0.05294 ( 744) hydrogen bonds : angle 5.65138 ( 2151) SS BOND : bond 0.00304 ( 4) SS BOND : angle 0.80908 ( 8) covalent geometry : bond 0.00448 (13653) covalent geometry : angle 0.83619 (18539) *********************** 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 375 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 303 time to evaluate : 1.562 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: 0.6823 (ttp) cc_final: 0.5866 (mmm) REVERT: A 144 ILE cc_start: 0.8618 (mt) cc_final: 0.8283 (tp) REVERT: A 147 MET cc_start: 0.7872 (mmt) cc_final: 0.7571 (mmt) REVERT: A 156 TYR cc_start: 0.7695 (m-80) cc_final: 0.7462 (m-10) REVERT: A 172 TRP cc_start: 0.7947 (m100) cc_final: 0.7554 (m100) REVERT: A 177 LEU cc_start: 0.9396 (tp) cc_final: 0.9168 (tp) REVERT: A 328 ASN cc_start: 0.9015 (m-40) cc_final: 0.8679 (m110) REVERT: A 348 PHE cc_start: 0.8625 (t80) cc_final: 0.8268 (t80) REVERT: A 509 TYR cc_start: 0.8539 (m-80) cc_final: 0.7888 (m-80) REVERT: A 581 MET cc_start: 0.8462 (ttm) cc_final: 0.8092 (ttm) REVERT: A 1018 PHE cc_start: 0.5717 (OUTLIER) cc_final: 0.4593 (t80) REVERT: B 157 LEU cc_start: 0.8806 (mt) cc_final: 0.8554 (tp) REVERT: B 187 LEU cc_start: 0.9345 (mt) cc_final: 0.9092 (mt) REVERT: B 276 LEU cc_start: 0.8670 (mt) cc_final: 0.8043 (pp) REVERT: B 328 ASN cc_start: 0.8636 (m110) cc_final: 0.8365 (m110) REVERT: B 505 PRO cc_start: 0.7431 (Cg_endo) cc_final: 0.6938 (Cg_exo) REVERT: B 540 TYR cc_start: 0.8456 (m-10) cc_final: 0.8222 (m-10) REVERT: B 548 PHE cc_start: 0.8624 (t80) cc_final: 0.8397 (t80) REVERT: B 549 HIS cc_start: 0.8868 (OUTLIER) cc_final: 0.8498 (t70) REVERT: B 642 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.7433 (mmm-85) REVERT: B 658 LEU cc_start: 0.9022 (mp) cc_final: 0.8815 (mp) REVERT: B 674 CYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8196 (p) REVERT: B 691 LEU cc_start: 0.9589 (mt) cc_final: 0.9347 (mt) REVERT: B 774 MET cc_start: 0.6725 (mtp) cc_final: 0.6418 (mtp) outliers start: 72 outliers final: 34 residues processed: 354 average time/residue: 0.2374 time to fit residues: 126.7678 Evaluate side-chains 304 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 266 time to evaluate : 1.452 ------------------------------------------------------------------------------- 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 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 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 673 ILE 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 959 LEU Chi-restraints excluded: chain B residue 962 ILE Chi-restraints excluded: chain B residue 965 ASP Chi-restraints excluded: chain B residue 1001 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 71 optimal weight: 20.0000 chunk 53 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 chunk 143 optimal weight: 8.9990 chunk 25 optimal weight: 0.8980 chunk 154 optimal weight: 1.9990 chunk 138 optimal weight: 0.2980 chunk 63 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 83 optimal weight: 5.9990 chunk 142 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 900 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 ASN B 534 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.081315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.064339 restraints weight = 72362.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.065868 restraints weight = 54236.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.067031 restraints weight = 43244.957| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 13657 Z= 0.164 Angle : 0.789 10.309 18547 Z= 0.392 Chirality : 0.048 0.259 2118 Planarity : 0.005 0.087 2320 Dihedral : 5.100 34.339 1846 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 24.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 4.06 % Allowed : 23.50 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.20), residues: 1696 helix: 0.62 (0.17), residues: 943 sheet: -1.78 (0.49), residues: 94 loop : -2.11 (0.23), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 699 HIS 0.007 0.001 HIS A 234 PHE 0.042 0.003 PHE A 462 TYR 0.031 0.002 TYR B 513 ARG 0.007 0.001 ARG B 145 Details of bonding type rmsd hydrogen bonds : bond 0.04781 ( 744) hydrogen bonds : angle 5.38301 ( 2151) SS BOND : bond 0.00259 ( 4) SS BOND : angle 0.80549 ( 8) covalent geometry : bond 0.00370 (13653) covalent geometry : angle 0.78873 (18539) *********************** 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 347 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 289 time to evaluate : 2.320 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 143 MET cc_start: 0.7074 (ttp) cc_final: 0.6071 (mmm) REVERT: A 144 ILE cc_start: 0.8612 (mt) cc_final: 0.8209 (tp) REVERT: A 147 MET cc_start: 0.7929 (mmt) cc_final: 0.7674 (mmt) REVERT: A 161 TRP cc_start: 0.8752 (t60) cc_final: 0.8536 (t60) REVERT: A 177 LEU cc_start: 0.9415 (tp) cc_final: 0.9202 (tp) REVERT: A 219 ILE cc_start: 0.9237 (mt) cc_final: 0.9034 (tp) REVERT: A 328 ASN cc_start: 0.8966 (m-40) cc_final: 0.8624 (m110) REVERT: A 386 TYR cc_start: 0.8711 (m-80) cc_final: 0.8099 (m-80) REVERT: A 457 ILE cc_start: 0.9099 (OUTLIER) cc_final: 0.8444 (tp) REVERT: A 509 TYR cc_start: 0.8528 (m-80) cc_final: 0.8003 (m-80) REVERT: A 686 MET cc_start: 0.5779 (ttt) cc_final: 0.5157 (ttp) REVERT: A 872 MET cc_start: 0.3989 (tpt) cc_final: 0.3295 (mmm) REVERT: A 1018 PHE cc_start: 0.5941 (OUTLIER) cc_final: 0.4841 (t80) REVERT: B 156 TYR cc_start: 0.8318 (m-80) cc_final: 0.8067 (m-10) REVERT: B 187 LEU cc_start: 0.9314 (mt) cc_final: 0.9057 (mt) REVERT: B 240 GLU cc_start: 0.8909 (tm-30) cc_final: 0.8636 (tp30) REVERT: B 276 LEU cc_start: 0.8527 (mt) cc_final: 0.8154 (pp) REVERT: B 509 TYR cc_start: 0.7968 (m-80) cc_final: 0.7670 (m-80) REVERT: B 540 TYR cc_start: 0.8367 (m-10) cc_final: 0.8107 (m-10) REVERT: B 548 PHE cc_start: 0.8613 (t80) cc_final: 0.8299 (t80) REVERT: B 549 HIS cc_start: 0.8854 (OUTLIER) cc_final: 0.8513 (t70) REVERT: B 642 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.7342 (mmm-85) REVERT: B 658 LEU cc_start: 0.8975 (mp) cc_final: 0.8709 (mp) REVERT: B 774 MET cc_start: 0.6574 (mtp) cc_final: 0.6291 (mtp) outliers start: 58 outliers final: 29 residues processed: 325 average time/residue: 0.2253 time to fit residues: 112.5170 Evaluate side-chains 289 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 256 time to evaluate : 1.624 ------------------------------------------------------------------------------- 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 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 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 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 337 ASP Chi-restraints excluded: chain B residue 350 SER 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 109 optimal weight: 6.9990 chunk 137 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 138 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 106 optimal weight: 0.1980 chunk 143 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 21 optimal weight: 0.0870 overall best weight: 0.8360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 900 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.084586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.065419 restraints weight = 69945.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.067392 restraints weight = 48438.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.068939 restraints weight = 36756.527| |-----------------------------------------------------------------------------| r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.4903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13657 Z= 0.153 Angle : 0.781 10.609 18547 Z= 0.381 Chirality : 0.049 0.291 2118 Planarity : 0.005 0.063 2320 Dihedral : 5.040 34.067 1845 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 21.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 4.13 % Allowed : 23.99 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.20), residues: 1696 helix: 0.60 (0.17), residues: 945 sheet: -1.57 (0.50), residues: 94 loop : -2.02 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 699 HIS 0.006 0.001 HIS A 234 PHE 0.032 0.002 PHE B 325 TYR 0.032 0.002 TYR B 513 ARG 0.004 0.000 ARG A 145 Details of bonding type rmsd hydrogen bonds : bond 0.04443 ( 744) hydrogen bonds : angle 5.24688 ( 2151) SS BOND : bond 0.00265 ( 4) SS BOND : angle 0.72252 ( 8) covalent geometry : bond 0.00334 (13653) covalent geometry : angle 0.78132 (18539) *********************** 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 338 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 279 time to evaluate : 1.351 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 143 MET cc_start: 0.7254 (ttp) cc_final: 0.6919 (mmm) REVERT: A 144 ILE cc_start: 0.8689 (OUTLIER) cc_final: 0.8327 (tp) REVERT: A 147 MET cc_start: 0.8513 (mmt) cc_final: 0.8141 (mmp) REVERT: A 165 GLN cc_start: 0.9354 (mm-40) cc_final: 0.8978 (mm-40) REVERT: A 328 ASN cc_start: 0.9341 (m-40) cc_final: 0.9097 (m110) REVERT: A 348 PHE cc_start: 0.8738 (t80) cc_final: 0.8357 (t80) REVERT: A 386 TYR cc_start: 0.9270 (m-80) cc_final: 0.8555 (m-80) REVERT: A 480 PHE cc_start: 0.9330 (t80) cc_final: 0.9087 (t80) REVERT: A 509 TYR cc_start: 0.8788 (m-80) cc_final: 0.8376 (m-80) REVERT: A 536 PHE cc_start: 0.9402 (m-80) cc_final: 0.9060 (t80) REVERT: A 582 PHE cc_start: 0.9475 (m-10) cc_final: 0.9250 (m-10) REVERT: A 686 MET cc_start: 0.6247 (ttt) cc_final: 0.5631 (ttp) REVERT: A 872 MET cc_start: 0.4132 (tpt) cc_final: 0.2502 (mmm) REVERT: B 158 ARG cc_start: 0.8756 (mmt-90) cc_final: 0.8523 (mmt-90) REVERT: B 165 GLN cc_start: 0.8542 (tp40) cc_final: 0.7853 (tp-100) REVERT: B 240 GLU cc_start: 0.9117 (tm-30) cc_final: 0.8764 (tp30) REVERT: B 244 ASP cc_start: 0.8645 (m-30) cc_final: 0.7957 (m-30) REVERT: B 276 LEU cc_start: 0.8752 (mt) cc_final: 0.8479 (pp) REVERT: B 348 PHE cc_start: 0.9387 (t80) cc_final: 0.8931 (t80) REVERT: B 377 MET cc_start: 0.8802 (mmt) cc_final: 0.8563 (ttt) REVERT: B 509 TYR cc_start: 0.8180 (m-80) cc_final: 0.7790 (m-80) REVERT: B 513 TYR cc_start: 0.8729 (t80) cc_final: 0.8421 (t80) REVERT: B 525 LEU cc_start: 0.9091 (mt) cc_final: 0.8863 (mm) REVERT: B 540 TYR cc_start: 0.8382 (m-10) cc_final: 0.8167 (m-10) REVERT: B 548 PHE cc_start: 0.8968 (t80) cc_final: 0.8606 (t80) REVERT: B 549 HIS cc_start: 0.8850 (OUTLIER) cc_final: 0.8598 (t70) REVERT: B 581 MET cc_start: 0.9225 (ptm) cc_final: 0.8446 (ppp) REVERT: B 642 ARG cc_start: 0.7711 (OUTLIER) cc_final: 0.7116 (mmm-85) REVERT: B 774 MET cc_start: 0.7310 (mtp) cc_final: 0.6881 (mtp) REVERT: B 914 MET cc_start: 0.8485 (ttp) cc_final: 0.8268 (mtt) outliers start: 59 outliers final: 30 residues processed: 315 average time/residue: 0.2749 time to fit residues: 135.6689 Evaluate side-chains 281 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 248 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ILE 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 288 LEU Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 547 CYS 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 761 LEU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 849 LEU 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 242 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 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 583 LEU Chi-restraints excluded: chain B residue 642 ARG Chi-restraints excluded: chain B residue 670 SER Chi-restraints excluded: chain B residue 677 VAL Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 975 ILE Chi-restraints excluded: chain B residue 994 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 21 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 168 optimal weight: 8.9990 chunk 2 optimal weight: 4.9990 chunk 146 optimal weight: 4.9990 chunk 106 optimal weight: 0.6980 chunk 8 optimal weight: 5.9990 chunk 151 optimal weight: 9.9990 chunk 101 optimal weight: 5.9990 chunk 13 optimal weight: 8.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 ASN ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 HIS ** A 900 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 GLN ** 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 = 0.4048 r_free = 0.4048 target = 0.080440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.062381 restraints weight = 71983.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.064176 restraints weight = 50426.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.065561 restraints weight = 38575.524| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.5372 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= 0.181 Angle : 0.775 11.683 18547 Z= 0.383 Chirality : 0.049 0.337 2118 Planarity : 0.005 0.045 2320 Dihedral : 5.048 33.250 1845 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 25.32 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.36 % Favored : 95.52 % Rotamer: Outliers : 4.41 % Allowed : 26.22 % Favored : 69.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.20), residues: 1696 helix: 0.69 (0.17), residues: 953 sheet: -1.52 (0.49), residues: 94 loop : -1.98 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 161 HIS 0.004 0.001 HIS B 234 PHE 0.041 0.002 PHE A 297 TYR 0.025 0.002 TYR B 513 ARG 0.006 0.001 ARG B 145 Details of bonding type rmsd hydrogen bonds : bond 0.04326 ( 744) hydrogen bonds : angle 5.32073 ( 2151) SS BOND : bond 0.00751 ( 4) SS BOND : angle 0.76897 ( 8) covalent geometry : bond 0.00399 (13653) covalent geometry : angle 0.77482 (18539) *********************** 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 316 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 253 time to evaluate : 1.483 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: A 143 MET cc_start: 0.7431 (ttp) cc_final: 0.6390 (mmm) REVERT: A 144 ILE cc_start: 0.8779 (OUTLIER) cc_final: 0.8498 (tp) REVERT: A 147 MET cc_start: 0.8162 (mmt) cc_final: 0.7957 (mmt) REVERT: A 328 ASN cc_start: 0.9048 (m-40) cc_final: 0.8827 (m110) REVERT: A 329 LEU cc_start: 0.9615 (mt) cc_final: 0.9295 (mt) REVERT: A 348 PHE cc_start: 0.8768 (t80) cc_final: 0.8562 (t80) REVERT: A 386 TYR cc_start: 0.8906 (m-80) cc_final: 0.8278 (m-80) REVERT: A 509 TYR cc_start: 0.8694 (m-80) cc_final: 0.8310 (m-80) REVERT: A 686 MET cc_start: 0.6570 (ttt) cc_final: 0.5883 (ttp) REVERT: A 835 TRP cc_start: 0.6672 (m100) cc_final: 0.6319 (m100) REVERT: A 872 MET cc_start: 0.3779 (tpt) cc_final: 0.2088 (mmm) REVERT: B 151 TRP cc_start: 0.7613 (m-10) cc_final: 0.6805 (m-10) REVERT: B 165 GLN cc_start: 0.8107 (tp40) cc_final: 0.7679 (tp-100) REVERT: B 221 LEU cc_start: 0.9388 (OUTLIER) cc_final: 0.9004 (mp) REVERT: B 240 GLU cc_start: 0.8850 (tm-30) cc_final: 0.8433 (tm-30) REVERT: B 276 LEU cc_start: 0.8524 (mt) cc_final: 0.8206 (pp) REVERT: B 509 TYR cc_start: 0.8210 (m-80) cc_final: 0.7873 (m-80) REVERT: B 513 TYR cc_start: 0.8843 (t80) cc_final: 0.8532 (t80) REVERT: B 548 PHE cc_start: 0.8833 (t80) cc_final: 0.8523 (t80) REVERT: B 642 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.7301 (mmm-85) REVERT: B 725 MET cc_start: 0.9082 (ppp) cc_final: 0.8692 (ppp) REVERT: B 774 MET cc_start: 0.6570 (mtp) cc_final: 0.6301 (mtm) REVERT: B 914 MET cc_start: 0.8574 (OUTLIER) cc_final: 0.8364 (mtp) outliers start: 63 outliers final: 41 residues processed: 294 average time/residue: 0.2078 time to fit residues: 94.6201 Evaluate side-chains 271 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 226 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ILE 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 288 LEU Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 350 SER 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 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 990 TYR Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain B residue 153 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 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 534 ASN 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 671 LEU Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 677 VAL 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 914 MET 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 20 optimal weight: 0.9990 chunk 85 optimal weight: 10.0000 chunk 118 optimal weight: 8.9990 chunk 94 optimal weight: 0.9990 chunk 127 optimal weight: 9.9990 chunk 159 optimal weight: 1.9990 chunk 106 optimal weight: 0.0270 chunk 13 optimal weight: 3.9990 chunk 50 optimal weight: 0.0050 chunk 65 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 overall best weight: 0.8058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 GLN ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 ASN ** A 900 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.081997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.063868 restraints weight = 72031.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.065751 restraints weight = 50013.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.067205 restraints weight = 38058.632| |-----------------------------------------------------------------------------| r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.5751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 13657 Z= 0.143 Angle : 0.794 13.950 18547 Z= 0.381 Chirality : 0.049 0.357 2118 Planarity : 0.005 0.045 2320 Dihedral : 5.023 33.931 1845 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 21.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.30 % Favored : 95.64 % Rotamer: Outliers : 3.36 % Allowed : 28.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.20), residues: 1696 helix: 0.63 (0.17), residues: 965 sheet: -1.32 (0.51), residues: 94 loop : -1.94 (0.24), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP B 151 HIS 0.007 0.001 HIS B 234 PHE 0.031 0.002 PHE A 297 TYR 0.023 0.002 TYR B 513 ARG 0.014 0.001 ARG A 685 Details of bonding type rmsd hydrogen bonds : bond 0.04212 ( 744) hydrogen bonds : angle 5.21954 ( 2151) SS BOND : bond 0.00284 ( 4) SS BOND : angle 0.95637 ( 8) covalent geometry : bond 0.00321 (13653) covalent geometry : angle 0.79403 (18539) *********************** 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 317 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 269 time to evaluate : 1.595 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: A 143 MET cc_start: 0.7445 (ttp) cc_final: 0.6385 (mmm) REVERT: A 348 PHE cc_start: 0.8679 (t80) cc_final: 0.8389 (t80) REVERT: A 386 TYR cc_start: 0.8644 (m-80) cc_final: 0.8311 (m-80) REVERT: A 400 ASP cc_start: 0.7969 (p0) cc_final: 0.7043 (p0) REVERT: A 509 TYR cc_start: 0.8626 (m-80) cc_final: 0.8366 (m-80) REVERT: A 536 PHE cc_start: 0.9244 (OUTLIER) cc_final: 0.8763 (t80) REVERT: A 686 MET cc_start: 0.6190 (ttt) cc_final: 0.5585 (ttp) REVERT: A 835 TRP cc_start: 0.6655 (m100) cc_final: 0.6434 (m100) REVERT: A 872 MET cc_start: 0.3630 (tpt) cc_final: 0.2055 (mmm) REVERT: B 165 GLN cc_start: 0.8145 (tp40) cc_final: 0.7761 (tp-100) REVERT: B 177 LEU cc_start: 0.8727 (mm) cc_final: 0.8521 (mp) REVERT: B 240 GLU cc_start: 0.8843 (tm-30) cc_final: 0.8292 (tm-30) REVERT: B 509 TYR cc_start: 0.8303 (m-80) cc_final: 0.8067 (m-80) REVERT: B 513 TYR cc_start: 0.8822 (t80) cc_final: 0.8451 (t80) REVERT: B 642 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.7479 (mmm-85) REVERT: B 725 MET cc_start: 0.8964 (ppp) cc_final: 0.8373 (ppp) REVERT: B 914 MET cc_start: 0.8495 (ttp) cc_final: 0.8284 (mtp) REVERT: B 933 MET cc_start: 0.8709 (mpp) cc_final: 0.8313 (ppp) outliers start: 48 outliers final: 28 residues processed: 303 average time/residue: 0.2201 time to fit residues: 104.1770 Evaluate side-chains 270 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 240 time to evaluate : 1.465 ------------------------------------------------------------------------------- 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 345 SER Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 536 PHE Chi-restraints excluded: chain A residue 547 CYS Chi-restraints excluded: chain A residue 597 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 1008 ILE Chi-restraints excluded: chain B residue 211 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 359 ASN 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 583 LEU Chi-restraints excluded: chain B residue 642 ARG Chi-restraints excluded: chain B residue 677 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 137 optimal weight: 9.9990 chunk 1 optimal weight: 0.9990 chunk 11 optimal weight: 0.3980 chunk 158 optimal weight: 3.9990 chunk 111 optimal weight: 0.8980 chunk 72 optimal weight: 20.0000 chunk 59 optimal weight: 1.9990 chunk 141 optimal weight: 0.7980 chunk 119 optimal weight: 5.9990 chunk 69 optimal weight: 7.9990 chunk 28 optimal weight: 20.0000 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 900 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.081690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.063542 restraints weight = 71858.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.065382 restraints weight = 50233.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.066790 restraints weight = 38356.924| |-----------------------------------------------------------------------------| r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.6030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 13657 Z= 0.145 Angle : 0.803 15.190 18547 Z= 0.384 Chirality : 0.049 0.368 2118 Planarity : 0.004 0.046 2320 Dihedral : 4.972 32.721 1845 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 21.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.48 % Favored : 95.46 % Rotamer: Outliers : 3.57 % Allowed : 28.67 % Favored : 67.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.20), residues: 1696 helix: 0.64 (0.17), residues: 955 sheet: -1.21 (0.51), residues: 94 loop : -1.87 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 151 HIS 0.005 0.001 HIS B 234 PHE 0.035 0.002 PHE A 347 TYR 0.029 0.002 TYR B 627 ARG 0.007 0.000 ARG A 685 Details of bonding type rmsd hydrogen bonds : bond 0.04172 ( 744) hydrogen bonds : angle 5.21588 ( 2151) SS BOND : bond 0.00270 ( 4) SS BOND : angle 0.81242 ( 8) covalent geometry : bond 0.00329 (13653) covalent geometry : angle 0.80296 (18539) *********************** 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 306 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 255 time to evaluate : 1.464 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 172 TRP cc_start: 0.9168 (m100) cc_final: 0.8332 (m100) REVERT: A 348 PHE cc_start: 0.8869 (t80) cc_final: 0.8453 (t80) REVERT: A 400 ASP cc_start: 0.8203 (p0) cc_final: 0.7304 (p0) REVERT: A 457 ILE cc_start: 0.9204 (pt) cc_final: 0.8787 (mp) REVERT: A 509 TYR cc_start: 0.8800 (m-80) cc_final: 0.8446 (m-80) REVERT: A 536 PHE cc_start: 0.9510 (OUTLIER) cc_final: 0.8881 (t80) REVERT: A 686 MET cc_start: 0.6449 (ttt) cc_final: 0.5868 (ttp) REVERT: A 835 TRP cc_start: 0.7098 (m100) cc_final: 0.6801 (m100) REVERT: A 872 MET cc_start: 0.3748 (tpt) cc_final: 0.2228 (mmm) REVERT: B 143 MET cc_start: 0.7002 (ttt) cc_final: 0.6679 (ttt) REVERT: B 147 MET cc_start: 0.9159 (tpp) cc_final: 0.8925 (tmm) REVERT: B 165 GLN cc_start: 0.8677 (tp40) cc_final: 0.8116 (tp-100) REVERT: B 240 GLU cc_start: 0.8958 (tm-30) cc_final: 0.8525 (tm-30) REVERT: B 509 TYR cc_start: 0.8277 (m-80) cc_final: 0.8043 (m-80) REVERT: B 513 TYR cc_start: 0.8925 (t80) cc_final: 0.8487 (t80) REVERT: B 581 MET cc_start: 0.9235 (ppp) cc_final: 0.8857 (ppp) REVERT: B 642 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.7378 (mmm-85) REVERT: B 725 MET cc_start: 0.9178 (ppp) cc_final: 0.8873 (ppp) REVERT: B 914 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.8332 (mtp) REVERT: B 933 MET cc_start: 0.8920 (mpp) cc_final: 0.8715 (ppp) outliers start: 51 outliers final: 40 residues processed: 289 average time/residue: 0.2067 time to fit residues: 92.8168 Evaluate side-chains 279 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 236 time to evaluate : 1.458 ------------------------------------------------------------------------------- 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 262 ILE Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 536 PHE Chi-restraints excluded: chain A residue 547 CYS Chi-restraints excluded: chain A residue 597 LEU 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 990 TYR 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 162 ILE Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 227 ASN 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 359 ASN 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 583 LEU 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 772 CYS Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 914 MET Chi-restraints excluded: chain B residue 975 ILE Chi-restraints excluded: chain B residue 977 LEU 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 42 optimal weight: 8.9990 chunk 69 optimal weight: 0.4980 chunk 156 optimal weight: 10.0000 chunk 90 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 150 optimal weight: 6.9990 chunk 128 optimal weight: 10.0000 chunk 71 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 GLN A 566 ASN ** A 900 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 GLN ** 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 = 0.3985 r_free = 0.3985 target = 0.078495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.062533 restraints weight = 76014.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.063809 restraints weight = 58740.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.064771 restraints weight = 48047.638| |-----------------------------------------------------------------------------| r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.6273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 13657 Z= 0.165 Angle : 0.805 13.463 18547 Z= 0.388 Chirality : 0.050 0.372 2118 Planarity : 0.005 0.045 2320 Dihedral : 5.003 32.609 1845 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 23.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.66 % Favored : 95.28 % Rotamer: Outliers : 3.99 % Allowed : 29.16 % Favored : 66.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.20), residues: 1696 helix: 0.67 (0.17), residues: 954 sheet: -1.16 (0.51), residues: 94 loop : -1.85 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP A 172 HIS 0.005 0.001 HIS B 637 PHE 0.038 0.002 PHE A 348 TYR 0.021 0.002 TYR B 513 ARG 0.015 0.001 ARG A 685 Details of bonding type rmsd hydrogen bonds : bond 0.04188 ( 744) hydrogen bonds : angle 5.29399 ( 2151) SS BOND : bond 0.00212 ( 4) SS BOND : angle 0.82970 ( 8) covalent geometry : bond 0.00369 (13653) covalent geometry : angle 0.80510 (18539) *********************** 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 292 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 235 time to evaluate : 1.607 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: A 143 MET cc_start: 0.7113 (mmm) cc_final: 0.6437 (mmt) REVERT: A 147 MET cc_start: 0.7712 (mmt) cc_final: 0.7444 (mmt) REVERT: A 229 VAL cc_start: 0.9472 (t) cc_final: 0.9245 (p) REVERT: A 400 ASP cc_start: 0.7771 (p0) cc_final: 0.7507 (p0) REVERT: A 509 TYR cc_start: 0.8678 (m-80) cc_final: 0.8465 (m-80) REVERT: A 536 PHE cc_start: 0.9073 (OUTLIER) cc_final: 0.8713 (t80) REVERT: A 686 MET cc_start: 0.6466 (ttt) cc_final: 0.5842 (ttp) REVERT: A 835 TRP cc_start: 0.6788 (m100) cc_final: 0.6467 (m100) REVERT: A 872 MET cc_start: 0.3872 (tpt) cc_final: 0.2698 (mmm) REVERT: B 143 MET cc_start: 0.6792 (ttt) cc_final: 0.6489 (ttt) REVERT: B 157 LEU cc_start: 0.8818 (mt) cc_final: 0.8361 (tp) REVERT: B 240 GLU cc_start: 0.8757 (tm-30) cc_final: 0.8422 (tm-30) REVERT: B 377 MET cc_start: 0.6979 (ttt) cc_final: 0.6281 (ttt) REVERT: B 513 TYR cc_start: 0.8822 (t80) cc_final: 0.8535 (t80) REVERT: B 548 PHE cc_start: 0.8552 (t80) cc_final: 0.8348 (t80) REVERT: B 581 MET cc_start: 0.9141 (ppp) cc_final: 0.8826 (ppp) REVERT: B 642 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7577 (mmm-85) REVERT: B 725 MET cc_start: 0.8846 (ppp) cc_final: 0.8583 (ppp) REVERT: B 933 MET cc_start: 0.8873 (mpp) cc_final: 0.8566 (ppp) outliers start: 57 outliers final: 42 residues processed: 273 average time/residue: 0.2182 time to fit residues: 92.2972 Evaluate side-chains 272 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 228 time to evaluate : 1.639 ------------------------------------------------------------------------------- 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 345 SER Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 536 PHE Chi-restraints excluded: chain A residue 547 CYS Chi-restraints excluded: chain A residue 597 LEU 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 985 CYS Chi-restraints excluded: chain A residue 990 TYR 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 162 ILE Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 246 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 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 571 LEU 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 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 782 VAL Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 975 ILE Chi-restraints excluded: chain B residue 977 LEU 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 109 optimal weight: 4.9990 chunk 81 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 165 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 164 optimal weight: 7.9990 chunk 134 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 135 optimal weight: 0.1980 chunk 127 optimal weight: 7.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 544 ASN A 668 ASN ** A 900 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.080646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.062332 restraints weight = 71933.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.064087 restraints weight = 50819.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.065465 restraints weight = 39192.837| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.6477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 13657 Z= 0.145 Angle : 0.831 15.040 18547 Z= 0.390 Chirality : 0.051 0.356 2118 Planarity : 0.004 0.044 2320 Dihedral : 5.006 35.645 1845 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 21.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.78 % Favored : 95.17 % Rotamer: Outliers : 3.85 % Allowed : 29.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.21), residues: 1696 helix: 0.66 (0.17), residues: 960 sheet: -1.05 (0.51), residues: 93 loop : -1.82 (0.24), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 151 HIS 0.005 0.001 HIS B 637 PHE 0.048 0.002 PHE A 348 TYR 0.022 0.002 TYR B 627 ARG 0.010 0.001 ARG A 685 Details of bonding type rmsd hydrogen bonds : bond 0.04152 ( 744) hydrogen bonds : angle 5.22960 ( 2151) SS BOND : bond 0.00246 ( 4) SS BOND : angle 0.85427 ( 8) covalent geometry : bond 0.00335 (13653) covalent geometry : angle 0.83086 (18539) *********************** 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 302 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 247 time to evaluate : 1.608 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 143 MET cc_start: 0.7166 (mmm) cc_final: 0.6368 (mmt) REVERT: A 147 MET cc_start: 0.8299 (mmt) cc_final: 0.7988 (mmt) REVERT: A 229 VAL cc_start: 0.9575 (t) cc_final: 0.9358 (p) REVERT: A 352 THR cc_start: 0.9189 (p) cc_final: 0.8747 (p) REVERT: A 400 ASP cc_start: 0.8300 (p0) cc_final: 0.8071 (p0) REVERT: A 457 ILE cc_start: 0.9245 (pt) cc_final: 0.8854 (mp) REVERT: A 509 TYR cc_start: 0.8900 (m-80) cc_final: 0.8546 (m-80) REVERT: A 536 PHE cc_start: 0.9477 (OUTLIER) cc_final: 0.8798 (t80) REVERT: A 686 MET cc_start: 0.6601 (ttt) cc_final: 0.5980 (ttp) REVERT: A 835 TRP cc_start: 0.7089 (m100) cc_final: 0.6695 (m100) REVERT: A 872 MET cc_start: 0.4196 (tpt) cc_final: 0.3042 (mmm) REVERT: B 143 MET cc_start: 0.7008 (ttt) cc_final: 0.6643 (ttm) REVERT: B 157 LEU cc_start: 0.9099 (mt) cc_final: 0.8580 (tp) REVERT: B 165 GLN cc_start: 0.8215 (tp40) cc_final: 0.7657 (tp-100) REVERT: B 240 GLU cc_start: 0.9003 (tm-30) cc_final: 0.8695 (tm-30) REVERT: B 290 PHE cc_start: 0.8842 (t80) cc_final: 0.8599 (t80) REVERT: B 513 TYR cc_start: 0.8962 (t80) cc_final: 0.8583 (t80) REVERT: B 581 MET cc_start: 0.9324 (ppp) cc_final: 0.9001 (ppp) REVERT: B 642 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.7397 (mmm-85) REVERT: B 725 MET cc_start: 0.9158 (ppp) cc_final: 0.8937 (ppp) REVERT: B 933 MET cc_start: 0.8907 (mpp) cc_final: 0.8628 (ppp) outliers start: 55 outliers final: 45 residues processed: 286 average time/residue: 0.2160 time to fit residues: 96.5305 Evaluate side-chains 285 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 238 time to evaluate : 1.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ILE 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 267 SER Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 536 PHE Chi-restraints excluded: chain A residue 547 CYS Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 668 ASN 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 985 CYS Chi-restraints excluded: chain A residue 990 TYR 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 162 ILE Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 246 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 528 ILE Chi-restraints excluded: chain B residue 534 ASN Chi-restraints excluded: chain B residue 549 HIS 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 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 782 VAL Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 858 LYS Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 975 ILE Chi-restraints excluded: chain B residue 977 LEU 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 87 optimal weight: 0.9990 chunk 107 optimal weight: 20.0000 chunk 62 optimal weight: 10.0000 chunk 69 optimal weight: 8.9990 chunk 61 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 112 optimal weight: 0.2980 chunk 27 optimal weight: 8.9990 chunk 130 optimal weight: 0.0050 chunk 51 optimal weight: 0.6980 chunk 20 optimal weight: 6.9990 overall best weight: 1.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 668 ASN ** A 900 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.078993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.062605 restraints weight = 74615.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.063860 restraints weight = 58420.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.064791 restraints weight = 48318.375| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.6644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 13657 Z= 0.151 Angle : 0.844 14.099 18547 Z= 0.397 Chirality : 0.052 0.367 2118 Planarity : 0.004 0.044 2320 Dihedral : 4.970 34.663 1845 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 22.34 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.36 % Favored : 95.58 % Rotamer: Outliers : 3.57 % Allowed : 30.00 % Favored : 66.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.21), residues: 1696 helix: 0.64 (0.17), residues: 961 sheet: -0.95 (0.51), residues: 93 loop : -1.77 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP B 151 HIS 0.005 0.001 HIS B 637 PHE 0.046 0.002 PHE A 348 TYR 0.021 0.001 TYR B 627 ARG 0.014 0.001 ARG A 667 Details of bonding type rmsd hydrogen bonds : bond 0.04112 ( 744) hydrogen bonds : angle 5.27037 ( 2151) SS BOND : bond 0.00236 ( 4) SS BOND : angle 0.86407 ( 8) covalent geometry : bond 0.00351 (13653) covalent geometry : angle 0.84428 (18539) ********************** 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 294 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 243 time to evaluate : 1.488 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 143 MET cc_start: 0.7389 (mmm) cc_final: 0.6507 (mmt) REVERT: A 147 MET cc_start: 0.7810 (mmt) cc_final: 0.7572 (mmt) REVERT: A 172 TRP cc_start: 0.8605 (m100) cc_final: 0.8192 (m100) REVERT: A 229 VAL cc_start: 0.9508 (t) cc_final: 0.9289 (p) REVERT: A 352 THR cc_start: 0.8718 (p) cc_final: 0.8500 (p) REVERT: A 509 TYR cc_start: 0.8690 (m-80) cc_final: 0.8449 (m-80) REVERT: A 536 PHE cc_start: 0.9062 (OUTLIER) cc_final: 0.8558 (t80) REVERT: A 686 MET cc_start: 0.6814 (ttt) cc_final: 0.6287 (ttp) REVERT: A 872 MET cc_start: 0.3819 (tpt) cc_final: 0.2618 (mmm) REVERT: A 926 ASP cc_start: 0.9348 (m-30) cc_final: 0.8855 (t0) REVERT: A 933 MET cc_start: 0.8707 (ptp) cc_final: 0.8194 (ppp) REVERT: B 143 MET cc_start: 0.6763 (ttt) cc_final: 0.6275 (ttm) REVERT: B 165 GLN cc_start: 0.7433 (tp40) cc_final: 0.7066 (tp-100) REVERT: B 240 GLU cc_start: 0.8759 (tm-30) cc_final: 0.8483 (tp30) REVERT: B 290 PHE cc_start: 0.8472 (t80) cc_final: 0.8268 (t80) REVERT: B 359 ASN cc_start: 0.8425 (OUTLIER) cc_final: 0.8201 (p0) REVERT: B 513 TYR cc_start: 0.8810 (t80) cc_final: 0.8500 (t80) REVERT: B 581 MET cc_start: 0.9203 (ppp) cc_final: 0.8875 (ppp) REVERT: B 642 ARG cc_start: 0.7978 (OUTLIER) cc_final: 0.7575 (mmm-85) REVERT: B 725 MET cc_start: 0.8834 (ppp) cc_final: 0.8550 (ppp) REVERT: B 933 MET cc_start: 0.8862 (mpp) cc_final: 0.8459 (ppp) outliers start: 51 outliers final: 43 residues processed: 278 average time/residue: 0.2101 time to fit residues: 90.2337 Evaluate side-chains 280 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 234 time to evaluate : 1.587 ------------------------------------------------------------------------------- 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 267 SER Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 536 PHE Chi-restraints excluded: chain A residue 547 CYS Chi-restraints excluded: chain A residue 597 LEU 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 985 CYS Chi-restraints excluded: chain A residue 990 TYR 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 162 ILE Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain B residue 246 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 359 ASN Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 534 ASN Chi-restraints excluded: chain B residue 549 HIS 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 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 782 VAL Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 858 LYS Chi-restraints excluded: chain B residue 975 ILE Chi-restraints excluded: chain B residue 977 LEU 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 22 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 168 optimal weight: 5.9990 chunk 116 optimal weight: 5.9990 chunk 12 optimal weight: 8.9990 chunk 94 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 78 optimal weight: 0.0970 chunk 77 optimal weight: 30.0000 chunk 66 optimal weight: 0.0060 chunk 16 optimal weight: 5.9990 overall best weight: 2.4200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 900 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.077797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.061534 restraints weight = 75714.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.062757 restraints weight = 59563.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.063659 restraints weight = 49388.794| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.6831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 13657 Z= 0.160 Angle : 0.842 13.686 18547 Z= 0.398 Chirality : 0.050 0.349 2118 Planarity : 0.004 0.043 2320 Dihedral : 4.988 34.682 1845 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 23.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.54 % Favored : 95.40 % Rotamer: Outliers : 3.43 % Allowed : 30.63 % Favored : 65.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.20), residues: 1696 helix: 0.61 (0.17), residues: 960 sheet: -0.80 (0.53), residues: 91 loop : -1.76 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP A 172 HIS 0.005 0.001 HIS B 637 PHE 0.047 0.002 PHE A 348 TYR 0.021 0.002 TYR B 513 ARG 0.009 0.000 ARG A 685 Details of bonding type rmsd hydrogen bonds : bond 0.04139 ( 744) hydrogen bonds : angle 5.33014 ( 2151) SS BOND : bond 0.00233 ( 4) SS BOND : angle 0.91337 ( 8) covalent geometry : bond 0.00367 (13653) covalent geometry : angle 0.84223 (18539) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5213.20 seconds wall clock time: 93 minutes 9.50 seconds (5589.50 seconds total)