Starting phenix.real_space_refine on Sat Nov 16 06:01:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8omo_16973/11_2024/8omo_16973.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8omo_16973/11_2024/8omo_16973.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8omo_16973/11_2024/8omo_16973.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8omo_16973/11_2024/8omo_16973.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8omo_16973/11_2024/8omo_16973.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8omo_16973/11_2024/8omo_16973.cif" } resolution = 3.43 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= 0.001 sd= 0.022 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 48 5.16 5 C 6520 2.51 5 N 1761 2.21 5 O 1953 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 10290 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 715, 5626 Classifications: {'peptide': 715} Link IDs: {'PTRANS': 20, 'TRANS': 694} Chain breaks: 5 Chain: "B" Number of atoms: 4600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4600 Classifications: {'peptide': 573} Link IDs: {'PTRANS': 17, 'TRANS': 555} Chain breaks: 2 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.85, per 1000 atoms: 0.57 Number of scatterers: 10290 At special positions: 0 Unit cell: (92.3342, 106.961, 161.813, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 48 16.00 P 6 15.00 Mg 2 11.99 O 1953 8.00 N 1761 7.00 C 6520 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.99 Conformation dependent library (CDL) restraints added in 1.4 seconds 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2430 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 7 sheets defined 57.6% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 184 through 195 Processing helix chain 'A' and resid 207 through 220 removed outlier: 4.073A pdb=" N LYS A 212 " --> pdb=" O GLY A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 245 Processing helix chain 'A' and resid 265 through 277 removed outlier: 3.905A pdb=" N LEU A 277 " --> pdb=" O VAL A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 310 Processing helix chain 'A' and resid 325 through 331 Processing helix chain 'A' and resid 335 through 348 removed outlier: 3.637A pdb=" N GLN A 348 " --> pdb=" O GLN A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 369 removed outlier: 3.637A pdb=" N GLU A 358 " --> pdb=" O ASN A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 379 removed outlier: 3.532A pdb=" N ARG A 373 " --> pdb=" O ASP A 369 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASP A 379 " --> pdb=" O THR A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 396 Processing helix chain 'A' and resid 400 through 423 removed outlier: 3.538A pdb=" N CYS A 404 " --> pdb=" O ASN A 400 " (cutoff:3.500A) Proline residue: A 415 - end of helix Processing helix chain 'A' and resid 429 through 457 Proline residue: A 439 - end of helix removed outlier: 4.566A pdb=" N LYS A 449 " --> pdb=" O SER A 445 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N PHE A 450 " --> pdb=" O ASP A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 466 Processing helix chain 'A' and resid 475 through 503 Processing helix chain 'A' and resid 553 through 587 removed outlier: 4.848A pdb=" N GLU A 580 " --> pdb=" O ALA A 576 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASN A 583 " --> pdb=" O LYS A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 615 removed outlier: 3.629A pdb=" N ALA A 615 " --> pdb=" O VAL A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 692 Processing helix chain 'A' and resid 723 through 739 removed outlier: 3.633A pdb=" N THR A 732 " --> pdb=" O GLU A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 772 Processing helix chain 'A' and resid 786 through 788 No H-bonds generated for 'chain 'A' and resid 786 through 788' Processing helix chain 'A' and resid 789 through 794 removed outlier: 3.829A pdb=" N GLN A 793 " --> pdb=" O ALA A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 834 removed outlier: 4.037A pdb=" N VAL A 830 " --> pdb=" O PHE A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 851 Processing helix chain 'A' and resid 874 through 890 removed outlier: 3.798A pdb=" N GLN A 885 " --> pdb=" O GLU A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 930 Processing helix chain 'B' and resid 538 through 545 Processing helix chain 'B' and resid 560 through 565 Processing helix chain 'B' and resid 569 through 582 removed outlier: 3.703A pdb=" N GLN B 582 " --> pdb=" O LYS B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 602 Processing helix chain 'B' and resid 606 through 616 Processing helix chain 'B' and resid 620 through 630 removed outlier: 3.685A pdb=" N HIS B 630 " --> pdb=" O CYS B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 663 Proline residue: B 657 - end of helix Processing helix chain 'B' and resid 666 through 679 removed outlier: 4.031A pdb=" N ILE B 672 " --> pdb=" O LEU B 668 " (cutoff:3.500A) Proline residue: B 676 - end of helix Processing helix chain 'B' and resid 683 through 688 removed outlier: 3.553A pdb=" N LYS B 687 " --> pdb=" O GLU B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 697 Processing helix chain 'B' and resid 705 through 708 removed outlier: 3.952A pdb=" N ASP B 708 " --> pdb=" O ASP B 705 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 705 through 708' Processing helix chain 'B' and resid 709 through 737 removed outlier: 3.835A pdb=" N ARG B 715 " --> pdb=" O LEU B 711 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLN B 731 " --> pdb=" O ARG B 727 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N GLU B 732 " --> pdb=" O MET B 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 764 removed outlier: 3.787A pdb=" N CYS B 763 " --> pdb=" O SER B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 772 through 775 Processing helix chain 'B' and resid 782 through 817 removed outlier: 4.088A pdb=" N HIS B 817 " --> pdb=" O LYS B 813 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 844 removed outlier: 3.687A pdb=" N GLY B 844 " --> pdb=" O VAL B 840 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 871 Processing helix chain 'B' and resid 901 through 919 Processing helix chain 'B' and resid 944 through 948 removed outlier: 3.951A pdb=" N GLY B 948 " --> pdb=" O ILE B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 950 through 966 Processing helix chain 'B' and resid 982 through 1000 Processing helix chain 'B' and resid 1011 through 1016 removed outlier: 3.802A pdb=" N CYS B1015 " --> pdb=" O TYR B1011 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU B1016 " --> pdb=" O PRO B1012 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1011 through 1016' Processing helix chain 'B' and resid 1017 through 1021 Processing helix chain 'B' and resid 1068 through 1076 removed outlier: 3.584A pdb=" N VAL B1072 " --> pdb=" O TYR B1068 " (cutoff:3.500A) Processing helix chain 'B' and resid 1079 through 1111 Processing helix chain 'B' and resid 1118 through 1123 Processing sheet with id=AA1, first strand: chain 'A' and resid 172 through 178 removed outlier: 4.162A pdb=" N VAL A 166 " --> pdb=" O VAL A 147 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N VAL A 147 " --> pdb=" O VAL A 166 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N VAL A 148 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 8.868A pdb=" N VAL A 150 " --> pdb=" O PRO A 202 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N CYS A 199 " --> pdb=" O THR A 225 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ARG A 227 " --> pdb=" O CYS A 199 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU A 201 " --> pdb=" O ARG A 227 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 512 through 516 removed outlier: 6.226A pdb=" N THR A 552 " --> pdb=" O THR A 541 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N THR A 541 " --> pdb=" O THR A 552 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 653 through 655 removed outlier: 6.575A pdb=" N VAL A 655 " --> pdb=" O LYS A 635 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N LYS A 635 " --> pdb=" O VAL A 655 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER A 699 " --> pdb=" O LYS A 635 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 710 through 711 removed outlier: 6.704A pdb=" N HIS A 665 " --> pdb=" O PHE A 780 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N PHE A 664 " --> pdb=" O ASN A 798 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N LEU A 800 " --> pdb=" O PHE A 664 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ILE A 666 " --> pdb=" O LEU A 800 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N VAL A 802 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N THR A 668 " --> pdb=" O VAL A 802 " (cutoff:3.500A) removed outlier: 8.799A pdb=" N ALA A 804 " --> pdb=" O THR A 668 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ASN A 799 " --> pdb=" O LYS A 818 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N LYS A 818 " --> pdb=" O ASN A 799 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N HIS A 801 " --> pdb=" O GLN A 816 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N GLN A 816 " --> pdb=" O HIS A 801 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N THR A 803 " --> pdb=" O LEU A 814 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU A 814 " --> pdb=" O THR A 803 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 754 through 756 Processing sheet with id=AA6, first strand: chain 'B' and resid 880 through 882 removed outlier: 7.167A pdb=" N THR B 882 " --> pdb=" O LYS B 860 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N LYS B 860 " --> pdb=" O THR B 882 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU B 926 " --> pdb=" O LYS B 860 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 935 through 937 removed outlier: 6.251A pdb=" N PHE B 936 " --> pdb=" O ILE B 973 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ASP B 975 " --> pdb=" O PHE B 936 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N VAL B 972 " --> pdb=" O LEU B1006 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N VAL B1008 " --> pdb=" O VAL B 972 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LEU B 974 " --> pdb=" O VAL B1008 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N VAL B 891 " --> pdb=" O GLY B1026 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N TYR B1028 " --> pdb=" O VAL B 891 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N ILE B 893 " --> pdb=" O TYR B1028 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N MET B1030 " --> pdb=" O ILE B 893 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N THR B 895 " --> pdb=" O MET B1030 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N PHE B1032 " --> pdb=" O THR B 895 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N GLN B1058 " --> pdb=" O GLY B1031 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N LEU B1033 " --> pdb=" O LEU B1056 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N LEU B1056 " --> pdb=" O LEU B1033 " (cutoff:3.500A) 554 hydrogen bonds defined for protein. 1617 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.42 Time building geometry restraints manager: 3.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2755 1.34 - 1.46: 2845 1.46 - 1.58: 4775 1.58 - 1.71: 10 1.71 - 1.83: 75 Bond restraints: 10460 Sorted by residual: bond pdb=" CA SER B 904 " pdb=" CB SER B 904 " ideal model delta sigma weight residual 1.529 1.479 0.050 1.55e-02 4.16e+03 1.03e+01 bond pdb=" C LEU A 414 " pdb=" O LEU A 414 " ideal model delta sigma weight residual 1.244 1.214 0.029 9.80e-03 1.04e+04 9.00e+00 bond pdb=" C LEU B 618 " pdb=" O LEU B 618 " ideal model delta sigma weight residual 1.249 1.224 0.025 8.50e-03 1.38e+04 8.84e+00 bond pdb=" O5' ATP A2000 " pdb=" PA ATP A2000 " ideal model delta sigma weight residual 1.579 1.611 -0.032 1.10e-02 8.26e+03 8.60e+00 bond pdb=" CA SER B 836 " pdb=" CB SER B 836 " ideal model delta sigma weight residual 1.529 1.485 0.044 1.55e-02 4.16e+03 7.89e+00 ... (remaining 10455 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.22: 14015 4.22 - 8.44: 103 8.44 - 12.65: 1 12.65 - 16.87: 1 16.87 - 21.09: 2 Bond angle restraints: 14122 Sorted by residual: angle pdb=" PA ATP B2000 " pdb=" O3A ATP B2000 " pdb=" PB ATP B2000 " ideal model delta sigma weight residual 136.83 115.74 21.09 1.00e+00 1.00e+00 4.45e+02 angle pdb=" PB ATP B2000 " pdb=" O3B ATP B2000 " pdb=" PG ATP B2000 " ideal model delta sigma weight residual 139.87 118.82 21.05 1.00e+00 1.00e+00 4.43e+02 angle pdb=" PB ATP A2000 " pdb=" O3B ATP A2000 " pdb=" PG ATP A2000 " ideal model delta sigma weight residual 139.87 124.96 14.91 1.00e+00 1.00e+00 2.22e+02 angle pdb=" C5' ATP B2000 " pdb=" O5' ATP B2000 " pdb=" PA ATP B2000 " ideal model delta sigma weight residual 121.27 112.00 9.27 1.00e+00 1.00e+00 8.60e+01 angle pdb=" PA ATP A2000 " pdb=" O3A ATP A2000 " pdb=" PB ATP A2000 " ideal model delta sigma weight residual 136.83 128.43 8.40 1.00e+00 1.00e+00 7.06e+01 ... (remaining 14117 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 5480 17.91 - 35.82: 716 35.82 - 53.74: 156 53.74 - 71.65: 33 71.65 - 89.56: 27 Dihedral angle restraints: 6412 sinusoidal: 2666 harmonic: 3746 Sorted by residual: dihedral pdb=" CA ASP B1077 " pdb=" C ASP B1077 " pdb=" N VAL B1078 " pdb=" CA VAL B1078 " ideal model delta harmonic sigma weight residual 180.00 153.72 26.28 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA GLY A 504 " pdb=" C GLY A 504 " pdb=" N LEU A 505 " pdb=" CA LEU A 505 " ideal model delta harmonic sigma weight residual -180.00 -155.45 -24.55 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" CA PRO B 619 " pdb=" C PRO B 619 " pdb=" N ASP B 620 " pdb=" CA ASP B 620 " ideal model delta harmonic sigma weight residual 180.00 155.81 24.19 0 5.00e+00 4.00e-02 2.34e+01 ... (remaining 6409 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 907 0.071 - 0.141: 521 0.141 - 0.212: 159 0.212 - 0.282: 27 0.282 - 0.353: 3 Chirality restraints: 1617 Sorted by residual: chirality pdb=" CA ARG A 171 " pdb=" N ARG A 171 " pdb=" C ARG A 171 " pdb=" CB ARG A 171 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.11e+00 chirality pdb=" CA GLU A 808 " pdb=" N GLU A 808 " pdb=" C GLU A 808 " pdb=" CB GLU A 808 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" CA GLU A 278 " pdb=" N GLU A 278 " pdb=" C GLU A 278 " pdb=" CB GLU A 278 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.63e+00 ... (remaining 1614 not shown) Planarity restraints: 1796 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' ATP A2000 " -0.053 2.00e-02 2.50e+03 2.45e-02 1.65e+01 pdb=" C2 ATP A2000 " -0.010 2.00e-02 2.50e+03 pdb=" C4 ATP A2000 " 0.020 2.00e-02 2.50e+03 pdb=" C5 ATP A2000 " 0.012 2.00e-02 2.50e+03 pdb=" C6 ATP A2000 " 0.010 2.00e-02 2.50e+03 pdb=" C8 ATP A2000 " -0.010 2.00e-02 2.50e+03 pdb=" N1 ATP A2000 " -0.017 2.00e-02 2.50e+03 pdb=" N3 ATP A2000 " 0.028 2.00e-02 2.50e+03 pdb=" N6 ATP A2000 " -0.025 2.00e-02 2.50e+03 pdb=" N7 ATP A2000 " 0.011 2.00e-02 2.50e+03 pdb=" N9 ATP A2000 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 953 " 0.010 2.00e-02 2.50e+03 2.08e-02 4.32e+00 pdb=" C MET B 953 " -0.036 2.00e-02 2.50e+03 pdb=" O MET B 953 " 0.014 2.00e-02 2.50e+03 pdb=" N GLU B 954 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 807 " -0.022 2.00e-02 2.50e+03 1.01e-02 2.56e+00 pdb=" CG TRP B 807 " 0.012 2.00e-02 2.50e+03 pdb=" CD1 TRP B 807 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP B 807 " 0.011 2.00e-02 2.50e+03 pdb=" NE1 TRP B 807 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 807 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 807 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 807 " -0.009 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 807 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP B 807 " -0.009 2.00e-02 2.50e+03 ... (remaining 1793 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.17: 6 2.17 - 2.85: 3680 2.85 - 3.54: 16542 3.54 - 4.22: 25566 4.22 - 4.90: 41807 Nonbonded interactions: 87601 Sorted by model distance: nonbonded pdb=" OE2 GLU B 889 " pdb=" OH TYR B1028 " model vdw 1.488 3.040 nonbonded pdb=" O2G ATP A2000 " pdb="MG MG A2001 " model vdw 1.783 2.170 nonbonded pdb=" O2B ATP B2000 " pdb="MG MG B2001 " model vdw 1.973 2.170 nonbonded pdb=" OG SER A 676 " pdb="MG MG A2001 " model vdw 1.983 2.170 nonbonded pdb=" O2B ATP A2000 " pdb="MG MG A2001 " model vdw 1.992 2.170 ... (remaining 87596 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.980 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: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 26.050 Find NCS groups from input model: 0.140 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: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 10460 Z= 0.478 Angle : 1.363 21.092 14122 Z= 0.941 Chirality : 0.090 0.353 1617 Planarity : 0.004 0.030 1796 Dihedral : 17.683 89.561 3982 Min Nonbonded Distance : 1.488 Molprobity Statistics. All-atom Clashscore : 21.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 4.68 % Allowed : 14.92 % Favored : 80.41 % Cbeta Deviations : 0.16 % 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: -3.82 (0.19), residues: 1270 helix: -1.72 (0.16), residues: 695 sheet: -2.97 (0.38), residues: 143 loop : -3.53 (0.24), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.005 TRP B 807 HIS 0.010 0.003 HIS A 428 PHE 0.019 0.004 PHE B 810 TYR 0.021 0.004 TYR A 815 ARG 0.012 0.001 ARG A 680 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 307 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.7145 (ttt) cc_final: 0.6879 (ttt) REVERT: A 299 TYR cc_start: 0.8732 (m-80) cc_final: 0.8346 (m-80) REVERT: A 313 PHE cc_start: 0.8165 (m-80) cc_final: 0.7941 (m-10) REVERT: A 331 ASN cc_start: 0.8317 (t0) cc_final: 0.7939 (t0) REVERT: A 340 ARG cc_start: 0.8542 (mtm110) cc_final: 0.7909 (mtp180) REVERT: A 344 GLN cc_start: 0.8902 (tm-30) cc_final: 0.8668 (tm-30) REVERT: A 347 LYS cc_start: 0.9009 (tptp) cc_final: 0.8689 (tptp) REVERT: A 369 ASP cc_start: 0.8116 (t0) cc_final: 0.7674 (t0) REVERT: A 382 ARG cc_start: 0.8279 (ttt180) cc_final: 0.7795 (ttp-110) REVERT: A 397 GLN cc_start: 0.8988 (mt0) cc_final: 0.8751 (mm-40) REVERT: A 409 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.8380 (mm-40) REVERT: A 418 ILE cc_start: 0.8788 (tp) cc_final: 0.8389 (tt) REVERT: A 422 GLU cc_start: 0.9015 (mt-10) cc_final: 0.8737 (mt-10) REVERT: A 423 LYS cc_start: 0.8880 (tttt) cc_final: 0.8651 (ttmt) REVERT: A 459 ASP cc_start: 0.7659 (p0) cc_final: 0.7177 (m-30) REVERT: A 460 MET cc_start: 0.8461 (mtp) cc_final: 0.8201 (mtp) REVERT: A 464 GLU cc_start: 0.9368 (mp0) cc_final: 0.9162 (mp0) REVERT: A 466 HIS cc_start: 0.8791 (m90) cc_final: 0.8444 (m90) REVERT: A 485 MET cc_start: 0.8431 (mtm) cc_final: 0.8091 (mtm) REVERT: A 646 ASP cc_start: 0.8717 (p0) cc_final: 0.8506 (p0) REVERT: A 672 MET cc_start: 0.8368 (tpt) cc_final: 0.7877 (tpt) REVERT: A 682 THR cc_start: 0.8412 (m) cc_final: 0.8159 (t) REVERT: A 685 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.7600 (tt) REVERT: A 691 ILE cc_start: 0.8114 (mt) cc_final: 0.7823 (mm) REVERT: A 695 VAL cc_start: 0.8603 (t) cc_final: 0.8391 (t) REVERT: A 704 ILE cc_start: 0.8432 (mt) cc_final: 0.8196 (mt) REVERT: A 719 LEU cc_start: 0.8893 (mm) cc_final: 0.8457 (mt) REVERT: A 726 MET cc_start: 0.8314 (ttm) cc_final: 0.7305 (ttm) REVERT: A 741 LYS cc_start: 0.8478 (tptp) cc_final: 0.8144 (tptp) REVERT: A 742 ASP cc_start: 0.8140 (p0) cc_final: 0.7842 (p0) REVERT: A 757 TYR cc_start: 0.8959 (m-80) cc_final: 0.8688 (m-10) REVERT: A 762 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8224 (tt) REVERT: A 802 VAL cc_start: 0.8648 (t) cc_final: 0.8347 (m) REVERT: A 813 MET cc_start: 0.7972 (mmt) cc_final: 0.7388 (mmt) REVERT: A 847 LYS cc_start: 0.8921 (tptt) cc_final: 0.8636 (tptp) REVERT: B 546 GLU cc_start: 0.8361 (mp0) cc_final: 0.8017 (pm20) REVERT: B 553 ASP cc_start: 0.8496 (t0) cc_final: 0.7996 (t0) REVERT: B 554 MET cc_start: 0.8539 (mmm) cc_final: 0.8211 (mmm) REVERT: B 586 LYS cc_start: 0.8784 (mmtt) cc_final: 0.8383 (mmmm) REVERT: B 591 ASN cc_start: 0.8356 (m-40) cc_final: 0.8079 (m-40) REVERT: B 593 ARG cc_start: 0.7953 (mtt180) cc_final: 0.7332 (mtt180) REVERT: B 617 LYS cc_start: 0.8739 (mmmt) cc_final: 0.8536 (mmmm) REVERT: B 637 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7562 (pt0) REVERT: B 653 GLN cc_start: 0.8570 (tp40) cc_final: 0.8224 (tp40) REVERT: B 660 ASN cc_start: 0.8946 (m-40) cc_final: 0.8738 (m-40) REVERT: B 672 ILE cc_start: 0.8472 (tt) cc_final: 0.8137 (mt) REVERT: B 674 GLU cc_start: 0.8493 (tt0) cc_final: 0.8140 (tt0) REVERT: B 683 GLU cc_start: 0.8155 (tt0) cc_final: 0.7954 (tt0) REVERT: B 684 HIS cc_start: 0.8791 (t70) cc_final: 0.8570 (t-170) REVERT: B 699 LYS cc_start: 0.9212 (mttt) cc_final: 0.8977 (mtmm) REVERT: B 712 ILE cc_start: 0.8532 (mm) cc_final: 0.8236 (tp) REVERT: B 714 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7847 (mmtm) REVERT: B 739 ASN cc_start: 0.8505 (OUTLIER) cc_final: 0.8134 (t0) REVERT: B 791 HIS cc_start: 0.9119 (t-90) cc_final: 0.8891 (t70) REVERT: B 794 GLN cc_start: 0.8653 (tm-30) cc_final: 0.8439 (tm-30) REVERT: B 796 ARG cc_start: 0.8777 (mtp-110) cc_final: 0.8515 (mtp180) REVERT: B 798 GLN cc_start: 0.8332 (tp-100) cc_final: 0.7933 (tp40) REVERT: B 860 LYS cc_start: 0.8695 (tttm) cc_final: 0.8383 (ttmt) REVERT: B 884 LEU cc_start: 0.8611 (mt) cc_final: 0.8339 (mm) REVERT: B 892 MET cc_start: 0.8250 (ttm) cc_final: 0.8036 (ttm) REVERT: B 899 MET cc_start: 0.7922 (tpt) cc_final: 0.7262 (tpt) REVERT: B 917 GLN cc_start: 0.8552 (mt0) cc_final: 0.7664 (mt0) REVERT: B 926 GLU cc_start: 0.8551 (tm-30) cc_final: 0.8348 (tp30) REVERT: B 956 LEU cc_start: 0.8213 (mt) cc_final: 0.7992 (mt) REVERT: B 995 GLU cc_start: 0.8507 (tt0) cc_final: 0.8219 (tt0) REVERT: B 1000 ASP cc_start: 0.8336 (t0) cc_final: 0.8049 (t0) REVERT: B 1027 ASN cc_start: 0.8595 (m-40) cc_final: 0.8159 (m-40) REVERT: B 1057 TYR cc_start: 0.8567 (m-80) cc_final: 0.8353 (m-80) REVERT: B 1088 HIS cc_start: 0.7203 (t70) cc_final: 0.6945 (t-90) outliers start: 53 outliers final: 25 residues processed: 353 average time/residue: 0.2854 time to fit residues: 133.6706 Evaluate side-chains 304 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 274 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 400 ASN Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 436 PHE Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 926 ILE Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 714 LYS Chi-restraints excluded: chain B residue 739 ASN Chi-restraints excluded: chain B residue 770 LYS Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 921 TYR Chi-restraints excluded: chain B residue 963 ILE Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 1060 THR Chi-restraints excluded: chain B residue 1072 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 0.1980 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 0.3980 chunk 33 optimal weight: 20.0000 chunk 65 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 0.9990 chunk 38 optimal weight: 8.9990 chunk 61 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 chunk 116 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN A 285 ASN A 413 GLN A 560 ASN A 613 ASN A 653 ASN ** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 824 GLN A 879 GLN A 885 GLN B 544 ASN B 582 GLN B 739 ASN B 750 GLN ** B 781 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 817 HIS B 852 GLN B 880 ASN ** B 898 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1058 GLN B1098 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10460 Z= 0.264 Angle : 0.680 8.181 14122 Z= 0.361 Chirality : 0.044 0.146 1617 Planarity : 0.004 0.045 1796 Dihedral : 9.986 87.334 1495 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 17.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 4.68 % Allowed : 19.68 % Favored : 75.64 % 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: -2.39 (0.22), residues: 1270 helix: -0.47 (0.18), residues: 700 sheet: -2.80 (0.39), residues: 143 loop : -2.92 (0.27), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 764 HIS 0.015 0.001 HIS B 614 PHE 0.022 0.002 PHE A 178 TYR 0.016 0.002 TYR A 656 ARG 0.010 0.001 ARG B1066 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 279 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.7055 (ttt) cc_final: 0.6759 (ttt) REVERT: A 299 TYR cc_start: 0.8669 (m-80) cc_final: 0.8273 (m-80) REVERT: A 308 ARG cc_start: 0.8727 (mtt180) cc_final: 0.8517 (mtt180) REVERT: A 326 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7812 (tt) REVERT: A 340 ARG cc_start: 0.8534 (mtm110) cc_final: 0.7678 (mtp180) REVERT: A 347 LYS cc_start: 0.8988 (tptp) cc_final: 0.8683 (tptp) REVERT: A 359 ARG cc_start: 0.8303 (mtt180) cc_final: 0.7973 (ttm170) REVERT: A 369 ASP cc_start: 0.8103 (t0) cc_final: 0.7688 (t0) REVERT: A 382 ARG cc_start: 0.8090 (ttt180) cc_final: 0.7809 (ttm110) REVERT: A 396 ARG cc_start: 0.8985 (mtm110) cc_final: 0.8612 (mtm110) REVERT: A 397 GLN cc_start: 0.9007 (mt0) cc_final: 0.8573 (mp10) REVERT: A 409 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.8213 (mm-40) REVERT: A 418 ILE cc_start: 0.8707 (tp) cc_final: 0.8303 (tt) REVERT: A 419 GLN cc_start: 0.8655 (tm-30) cc_final: 0.8369 (tm-30) REVERT: A 422 GLU cc_start: 0.8840 (mt-10) cc_final: 0.8515 (mt-10) REVERT: A 423 LYS cc_start: 0.8720 (tttt) cc_final: 0.8459 (ttmt) REVERT: A 458 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7674 (pp) REVERT: A 459 ASP cc_start: 0.7411 (p0) cc_final: 0.6903 (m-30) REVERT: A 460 MET cc_start: 0.8423 (mtp) cc_final: 0.8166 (mtp) REVERT: A 464 GLU cc_start: 0.9283 (OUTLIER) cc_final: 0.8932 (mp0) REVERT: A 466 HIS cc_start: 0.8760 (m90) cc_final: 0.8393 (m90) REVERT: A 485 MET cc_start: 0.8383 (mtm) cc_final: 0.8051 (mtm) REVERT: A 589 VAL cc_start: 0.8683 (p) cc_final: 0.8291 (t) REVERT: A 603 ASP cc_start: 0.8045 (t0) cc_final: 0.7598 (t0) REVERT: A 660 ASP cc_start: 0.8466 (t0) cc_final: 0.8225 (t0) REVERT: A 672 MET cc_start: 0.7980 (tpt) cc_final: 0.7506 (tpt) REVERT: A 685 ILE cc_start: 0.8286 (OUTLIER) cc_final: 0.8062 (mt) REVERT: A 699 SER cc_start: 0.8213 (m) cc_final: 0.7917 (p) REVERT: A 705 VAL cc_start: 0.7967 (t) cc_final: 0.7737 (m) REVERT: A 726 MET cc_start: 0.8107 (ttm) cc_final: 0.7396 (tpp) REVERT: A 737 ARG cc_start: 0.8606 (mtt-85) cc_final: 0.8352 (mtt180) REVERT: A 741 LYS cc_start: 0.8268 (tptp) cc_final: 0.7923 (tptp) REVERT: A 802 VAL cc_start: 0.8677 (t) cc_final: 0.8372 (m) REVERT: A 813 MET cc_start: 0.7862 (mmt) cc_final: 0.7373 (mmt) REVERT: A 847 LYS cc_start: 0.8812 (tptt) cc_final: 0.8473 (tptp) REVERT: B 532 MET cc_start: 0.8474 (mpp) cc_final: 0.7943 (mpp) REVERT: B 535 MET cc_start: 0.7430 (ttm) cc_final: 0.7034 (ttm) REVERT: B 546 GLU cc_start: 0.8417 (mp0) cc_final: 0.8053 (pm20) REVERT: B 553 ASP cc_start: 0.8423 (t0) cc_final: 0.7939 (t0) REVERT: B 554 MET cc_start: 0.8504 (mmm) cc_final: 0.8224 (mmm) REVERT: B 573 ARG cc_start: 0.7868 (ttt180) cc_final: 0.7651 (ttm110) REVERT: B 582 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7719 (pt0) REVERT: B 586 LYS cc_start: 0.8694 (mmtt) cc_final: 0.8325 (mmmm) REVERT: B 593 ARG cc_start: 0.7767 (mtt180) cc_final: 0.7501 (mtt90) REVERT: B 620 ASP cc_start: 0.8487 (t0) cc_final: 0.8019 (t0) REVERT: B 628 ILE cc_start: 0.8662 (OUTLIER) cc_final: 0.8394 (mm) REVERT: B 653 GLN cc_start: 0.8460 (tp40) cc_final: 0.8148 (tp40) REVERT: B 672 ILE cc_start: 0.8365 (tt) cc_final: 0.8119 (mt) REVERT: B 674 GLU cc_start: 0.8394 (tt0) cc_final: 0.7986 (tt0) REVERT: B 699 LYS cc_start: 0.9120 (mttt) cc_final: 0.8670 (mtmm) REVERT: B 718 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8127 (mm-30) REVERT: B 791 HIS cc_start: 0.9055 (t-90) cc_final: 0.8790 (t70) REVERT: B 794 GLN cc_start: 0.8459 (tm-30) cc_final: 0.8179 (tm-30) REVERT: B 796 ARG cc_start: 0.8691 (mtp-110) cc_final: 0.8224 (mtt180) REVERT: B 798 GLN cc_start: 0.8076 (tp-100) cc_final: 0.7667 (tp40) REVERT: B 884 LEU cc_start: 0.8587 (mt) cc_final: 0.8328 (mm) REVERT: B 899 MET cc_start: 0.7714 (tpt) cc_final: 0.7336 (tpt) REVERT: B 917 GLN cc_start: 0.8409 (mt0) cc_final: 0.7465 (mt0) REVERT: B 932 VAL cc_start: 0.8488 (OUTLIER) cc_final: 0.8181 (m) REVERT: B 939 MET cc_start: 0.8334 (ptp) cc_final: 0.8104 (ptp) REVERT: B 949 ARG cc_start: 0.8128 (mtm110) cc_final: 0.7858 (mtm110) REVERT: B 956 LEU cc_start: 0.8240 (mt) cc_final: 0.8017 (mt) REVERT: B 995 GLU cc_start: 0.8356 (tt0) cc_final: 0.7965 (tt0) REVERT: B 1000 ASP cc_start: 0.8240 (t0) cc_final: 0.7926 (t0) REVERT: B 1057 TYR cc_start: 0.8420 (m-80) cc_final: 0.8169 (m-80) REVERT: B 1077 ASP cc_start: 0.8454 (t0) cc_final: 0.7565 (t70) REVERT: B 1092 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8031 (mm-30) outliers start: 53 outliers final: 29 residues processed: 316 average time/residue: 0.2752 time to fit residues: 115.7493 Evaluate side-chains 305 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 268 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 464 GLU Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 752 ARG Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 777 PHE Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 885 GLN Chi-restraints excluded: chain A residue 926 ILE Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 628 ILE Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 692 GLN Chi-restraints excluded: chain B residue 713 LYS Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 819 HIS Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 932 VAL Chi-restraints excluded: chain B residue 1060 THR Chi-restraints excluded: chain B residue 1072 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 0.8980 chunk 36 optimal weight: 8.9990 chunk 96 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 32 optimal weight: 8.9990 chunk 116 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 115 optimal weight: 0.5980 chunk 39 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 GLN A 218 GLN A 409 GLN ** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 681 GLN ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 718 GLN B 582 GLN ** B 781 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 852 GLN ** B 898 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.123 10460 Z= 0.353 Angle : 0.670 7.943 14122 Z= 0.357 Chirality : 0.046 0.176 1617 Planarity : 0.005 0.056 1796 Dihedral : 9.466 89.453 1468 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 17.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 5.30 % Allowed : 22.42 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.22), residues: 1270 helix: -0.07 (0.19), residues: 702 sheet: -2.57 (0.42), residues: 133 loop : -2.58 (0.27), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 764 HIS 0.013 0.001 HIS B 614 PHE 0.032 0.002 PHE A 436 TYR 0.017 0.002 TYR A 656 ARG 0.008 0.001 ARG B 734 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 278 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.6992 (ttt) cc_final: 0.6685 (ttt) REVERT: A 299 TYR cc_start: 0.8656 (m-80) cc_final: 0.8255 (m-80) REVERT: A 326 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7935 (tt) REVERT: A 340 ARG cc_start: 0.8566 (mtm110) cc_final: 0.7700 (mtp180) REVERT: A 347 LYS cc_start: 0.8909 (tptp) cc_final: 0.8651 (tptp) REVERT: A 369 ASP cc_start: 0.8077 (t0) cc_final: 0.7631 (t0) REVERT: A 396 ARG cc_start: 0.8998 (mtm110) cc_final: 0.8624 (mtm110) REVERT: A 418 ILE cc_start: 0.8757 (tp) cc_final: 0.8331 (tt) REVERT: A 419 GLN cc_start: 0.8666 (tm-30) cc_final: 0.8397 (tm-30) REVERT: A 422 GLU cc_start: 0.8902 (mt-10) cc_final: 0.8567 (mt-10) REVERT: A 423 LYS cc_start: 0.8795 (tttt) cc_final: 0.8533 (ttmt) REVERT: A 458 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7715 (pp) REVERT: A 459 ASP cc_start: 0.7485 (p0) cc_final: 0.6801 (m-30) REVERT: A 460 MET cc_start: 0.8356 (mtp) cc_final: 0.8080 (mtp) REVERT: A 464 GLU cc_start: 0.9275 (OUTLIER) cc_final: 0.8907 (mp0) REVERT: A 466 HIS cc_start: 0.8782 (m90) cc_final: 0.8397 (m90) REVERT: A 485 MET cc_start: 0.8424 (mtm) cc_final: 0.8071 (mtm) REVERT: A 589 VAL cc_start: 0.8443 (p) cc_final: 0.8194 (t) REVERT: A 672 MET cc_start: 0.7953 (tpt) cc_final: 0.7476 (tpt) REVERT: A 705 VAL cc_start: 0.8004 (t) cc_final: 0.7752 (m) REVERT: A 726 MET cc_start: 0.8121 (ttm) cc_final: 0.7269 (tpp) REVERT: A 728 GLU cc_start: 0.8097 (tt0) cc_final: 0.7637 (mm-30) REVERT: A 737 ARG cc_start: 0.8585 (mtt-85) cc_final: 0.8357 (mtt180) REVERT: A 741 LYS cc_start: 0.8347 (tptp) cc_final: 0.7991 (tptp) REVERT: A 802 VAL cc_start: 0.8671 (t) cc_final: 0.8373 (m) REVERT: A 813 MET cc_start: 0.7834 (mmt) cc_final: 0.7354 (mmt) REVERT: A 847 LYS cc_start: 0.8760 (tptt) cc_final: 0.8482 (tptp) REVERT: B 532 MET cc_start: 0.8444 (mpp) cc_final: 0.7908 (mpp) REVERT: B 534 PHE cc_start: 0.8168 (m-80) cc_final: 0.7929 (m-80) REVERT: B 535 MET cc_start: 0.7457 (ttm) cc_final: 0.7053 (ttm) REVERT: B 546 GLU cc_start: 0.8378 (mp0) cc_final: 0.8025 (mp0) REVERT: B 554 MET cc_start: 0.8477 (mmm) cc_final: 0.8155 (mmm) REVERT: B 573 ARG cc_start: 0.7856 (ttt180) cc_final: 0.7651 (ttm-80) REVERT: B 586 LYS cc_start: 0.8694 (mmtt) cc_final: 0.8270 (mmmm) REVERT: B 591 ASN cc_start: 0.8299 (m-40) cc_final: 0.8010 (m-40) REVERT: B 599 GLU cc_start: 0.8684 (tp30) cc_final: 0.8105 (tt0) REVERT: B 620 ASP cc_start: 0.8535 (t0) cc_final: 0.8081 (t0) REVERT: B 628 ILE cc_start: 0.8698 (OUTLIER) cc_final: 0.8410 (mm) REVERT: B 649 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7403 (tmtt) REVERT: B 674 GLU cc_start: 0.8352 (tt0) cc_final: 0.7928 (tt0) REVERT: B 699 LYS cc_start: 0.9059 (mttt) cc_final: 0.8725 (mtmm) REVERT: B 725 GLU cc_start: 0.8883 (mt-10) cc_final: 0.8313 (mm-30) REVERT: B 791 HIS cc_start: 0.9069 (t-90) cc_final: 0.8790 (t70) REVERT: B 794 GLN cc_start: 0.8437 (tm-30) cc_final: 0.8205 (tm-30) REVERT: B 796 ARG cc_start: 0.8731 (mtp-110) cc_final: 0.8389 (mtt180) REVERT: B 798 GLN cc_start: 0.8140 (tp-100) cc_final: 0.7745 (tp40) REVERT: B 899 MET cc_start: 0.7618 (OUTLIER) cc_final: 0.7252 (tpt) REVERT: B 917 GLN cc_start: 0.8426 (mt0) cc_final: 0.7522 (mt0) REVERT: B 932 VAL cc_start: 0.8509 (OUTLIER) cc_final: 0.8205 (m) REVERT: B 949 ARG cc_start: 0.8168 (mtm110) cc_final: 0.7902 (mtm110) REVERT: B 991 TYR cc_start: 0.8513 (t80) cc_final: 0.8060 (t80) REVERT: B 1000 ASP cc_start: 0.8253 (t0) cc_final: 0.7923 (t0) REVERT: B 1057 TYR cc_start: 0.8465 (m-80) cc_final: 0.8118 (m-80) REVERT: B 1077 ASP cc_start: 0.8449 (t0) cc_final: 0.7380 (t0) REVERT: B 1092 GLU cc_start: 0.8607 (mm-30) cc_final: 0.7947 (mm-30) outliers start: 60 outliers final: 37 residues processed: 318 average time/residue: 0.2756 time to fit residues: 118.1243 Evaluate side-chains 312 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 268 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 464 GLU Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 752 ARG Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 777 PHE Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 628 ILE Chi-restraints excluded: chain B residue 634 SER Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 649 LYS Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 692 GLN Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 803 CYS Chi-restraints excluded: chain B residue 819 HIS Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 899 MET Chi-restraints excluded: chain B residue 932 VAL Chi-restraints excluded: chain B residue 1023 HIS Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain B residue 1060 THR Chi-restraints excluded: chain B residue 1070 LEU Chi-restraints excluded: chain B residue 1072 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 0.5980 chunk 87 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 12 optimal weight: 6.9990 chunk 55 optimal weight: 0.6980 chunk 78 optimal weight: 0.7980 chunk 116 optimal weight: 1.9990 chunk 123 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 ASN A 665 HIS A 718 GLN A 885 GLN ** B 781 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 852 GLN ** B 898 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 10460 Z= 0.262 Angle : 0.654 12.182 14122 Z= 0.339 Chirality : 0.044 0.185 1617 Planarity : 0.004 0.054 1796 Dihedral : 9.069 88.672 1461 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 5.30 % Allowed : 23.74 % Favored : 70.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.23), residues: 1270 helix: 0.24 (0.19), residues: 700 sheet: -2.47 (0.42), residues: 133 loop : -2.27 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 764 HIS 0.013 0.001 HIS B 614 PHE 0.021 0.002 PHE A 436 TYR 0.014 0.002 TYR A 656 ARG 0.007 0.000 ARG B 734 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 277 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.6937 (ttt) cc_final: 0.6664 (ttt) REVERT: A 299 TYR cc_start: 0.8675 (m-80) cc_final: 0.8246 (m-80) REVERT: A 326 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7860 (tt) REVERT: A 347 LYS cc_start: 0.8889 (tptp) cc_final: 0.8635 (tptp) REVERT: A 359 ARG cc_start: 0.8326 (mtt180) cc_final: 0.7999 (ttm170) REVERT: A 369 ASP cc_start: 0.8015 (t0) cc_final: 0.7577 (t0) REVERT: A 382 ARG cc_start: 0.8043 (ttt180) cc_final: 0.7653 (ttp-110) REVERT: A 396 ARG cc_start: 0.8990 (mtm110) cc_final: 0.8606 (mtm110) REVERT: A 418 ILE cc_start: 0.8746 (tp) cc_final: 0.8318 (tt) REVERT: A 419 GLN cc_start: 0.8669 (tm-30) cc_final: 0.8402 (tm-30) REVERT: A 422 GLU cc_start: 0.8856 (mt-10) cc_final: 0.8525 (mt-10) REVERT: A 423 LYS cc_start: 0.8760 (tttt) cc_final: 0.8497 (ttmt) REVERT: A 458 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7721 (pp) REVERT: A 459 ASP cc_start: 0.7507 (p0) cc_final: 0.6791 (m-30) REVERT: A 460 MET cc_start: 0.8343 (mtp) cc_final: 0.8038 (mtp) REVERT: A 464 GLU cc_start: 0.9267 (OUTLIER) cc_final: 0.8879 (mp0) REVERT: A 466 HIS cc_start: 0.8764 (m90) cc_final: 0.8369 (m90) REVERT: A 485 MET cc_start: 0.8444 (mtm) cc_final: 0.8078 (mtm) REVERT: A 603 ASP cc_start: 0.8047 (t0) cc_final: 0.7643 (t0) REVERT: A 626 GLU cc_start: 0.8399 (pm20) cc_final: 0.8121 (pm20) REVERT: A 672 MET cc_start: 0.7831 (tpt) cc_final: 0.7408 (tpt) REVERT: A 705 VAL cc_start: 0.7951 (t) cc_final: 0.7716 (m) REVERT: A 726 MET cc_start: 0.8067 (ttm) cc_final: 0.7213 (tpp) REVERT: A 737 ARG cc_start: 0.8565 (mtt-85) cc_final: 0.8364 (mtt180) REVERT: A 741 LYS cc_start: 0.8322 (tptp) cc_final: 0.7955 (tptp) REVERT: A 802 VAL cc_start: 0.8674 (t) cc_final: 0.8402 (m) REVERT: A 813 MET cc_start: 0.7806 (mmt) cc_final: 0.7309 (mmt) REVERT: A 847 LYS cc_start: 0.8748 (tptt) cc_final: 0.8448 (tptp) REVERT: B 532 MET cc_start: 0.8408 (mpp) cc_final: 0.7907 (mpp) REVERT: B 534 PHE cc_start: 0.8097 (m-80) cc_final: 0.7874 (m-10) REVERT: B 535 MET cc_start: 0.7417 (ttm) cc_final: 0.7046 (ttm) REVERT: B 554 MET cc_start: 0.8419 (mmm) cc_final: 0.8094 (mmm) REVERT: B 573 ARG cc_start: 0.7848 (ttt180) cc_final: 0.7643 (ttm-80) REVERT: B 586 LYS cc_start: 0.8547 (mmtt) cc_final: 0.8136 (mmmm) REVERT: B 591 ASN cc_start: 0.8352 (m-40) cc_final: 0.8018 (m-40) REVERT: B 620 ASP cc_start: 0.8447 (t0) cc_final: 0.8001 (t0) REVERT: B 628 ILE cc_start: 0.8665 (OUTLIER) cc_final: 0.8346 (mm) REVERT: B 649 LYS cc_start: 0.8076 (OUTLIER) cc_final: 0.7583 (tmtt) REVERT: B 674 GLU cc_start: 0.8303 (tt0) cc_final: 0.7909 (tt0) REVERT: B 699 LYS cc_start: 0.9084 (mttt) cc_final: 0.8761 (mtmm) REVERT: B 704 LYS cc_start: 0.8724 (mmmm) cc_final: 0.8519 (mmmm) REVERT: B 718 GLU cc_start: 0.8596 (mm-30) cc_final: 0.8150 (mm-30) REVERT: B 791 HIS cc_start: 0.9103 (t-90) cc_final: 0.8894 (t70) REVERT: B 796 ARG cc_start: 0.8703 (mtp-110) cc_final: 0.8367 (mtt180) REVERT: B 798 GLN cc_start: 0.8080 (tp-100) cc_final: 0.7391 (tp40) REVERT: B 855 ARG cc_start: 0.7973 (ptm160) cc_final: 0.7594 (ptm160) REVERT: B 863 ARG cc_start: 0.7976 (ptp-170) cc_final: 0.7607 (mtm180) REVERT: B 899 MET cc_start: 0.7555 (OUTLIER) cc_final: 0.7186 (tpt) REVERT: B 917 GLN cc_start: 0.8435 (mt0) cc_final: 0.7503 (mt0) REVERT: B 932 VAL cc_start: 0.8454 (OUTLIER) cc_final: 0.8136 (m) REVERT: B 975 ASP cc_start: 0.7626 (t0) cc_final: 0.7397 (t0) REVERT: B 991 TYR cc_start: 0.8478 (t80) cc_final: 0.7978 (t80) REVERT: B 1000 ASP cc_start: 0.8190 (t0) cc_final: 0.7832 (t0) REVERT: B 1057 TYR cc_start: 0.8408 (m-80) cc_final: 0.8064 (m-80) REVERT: B 1077 ASP cc_start: 0.8414 (t0) cc_final: 0.7738 (t0) REVERT: B 1081 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8183 (mm-30) REVERT: B 1092 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8034 (mm-30) outliers start: 60 outliers final: 38 residues processed: 321 average time/residue: 0.2760 time to fit residues: 120.0044 Evaluate side-chains 315 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 270 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 464 GLU Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 752 ARG Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 777 PHE Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 885 GLN Chi-restraints excluded: chain A residue 926 ILE Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 628 ILE Chi-restraints excluded: chain B residue 634 SER Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 649 LYS Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 692 GLN Chi-restraints excluded: chain B residue 770 LYS Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 803 CYS Chi-restraints excluded: chain B residue 819 HIS Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 899 MET Chi-restraints excluded: chain B residue 932 VAL Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1023 HIS Chi-restraints excluded: chain B residue 1060 THR Chi-restraints excluded: chain B residue 1070 LEU Chi-restraints excluded: chain B residue 1072 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 0.9990 chunk 70 optimal weight: 20.0000 chunk 1 optimal weight: 2.9990 chunk 92 optimal weight: 7.9990 chunk 51 optimal weight: 0.5980 chunk 105 optimal weight: 0.9990 chunk 85 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 63 optimal weight: 0.5980 chunk 111 optimal weight: 0.1980 chunk 31 optimal weight: 9.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 885 GLN B 582 GLN ** B 781 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 852 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 10460 Z= 0.242 Angle : 0.631 11.447 14122 Z= 0.329 Chirality : 0.044 0.184 1617 Planarity : 0.004 0.057 1796 Dihedral : 8.692 88.011 1460 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 5.47 % Allowed : 24.62 % Favored : 69.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.11 (0.23), residues: 1270 helix: 0.49 (0.19), residues: 700 sheet: -2.34 (0.41), residues: 138 loop : -2.15 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 764 HIS 0.011 0.001 HIS B 614 PHE 0.018 0.002 PHE A 436 TYR 0.015 0.001 TYR A 656 ARG 0.003 0.000 ARG B 734 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 279 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.6935 (ttt) cc_final: 0.6593 (ttt) REVERT: A 299 TYR cc_start: 0.8672 (m-80) cc_final: 0.8208 (m-80) REVERT: A 326 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7841 (tt) REVERT: A 347 LYS cc_start: 0.8870 (tptp) cc_final: 0.8634 (tptp) REVERT: A 359 ARG cc_start: 0.8346 (mtt180) cc_final: 0.8033 (ttm170) REVERT: A 369 ASP cc_start: 0.7987 (t0) cc_final: 0.7528 (t0) REVERT: A 382 ARG cc_start: 0.7993 (ttt180) cc_final: 0.7757 (ttp80) REVERT: A 396 ARG cc_start: 0.8991 (mtm110) cc_final: 0.8606 (mtm110) REVERT: A 418 ILE cc_start: 0.8729 (tp) cc_final: 0.8308 (tt) REVERT: A 419 GLN cc_start: 0.8668 (tm-30) cc_final: 0.8401 (tm-30) REVERT: A 422 GLU cc_start: 0.8832 (mt-10) cc_final: 0.8504 (mt-10) REVERT: A 423 LYS cc_start: 0.8742 (tttt) cc_final: 0.8484 (ttmt) REVERT: A 458 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7609 (pp) REVERT: A 459 ASP cc_start: 0.7550 (p0) cc_final: 0.6746 (m-30) REVERT: A 464 GLU cc_start: 0.9265 (OUTLIER) cc_final: 0.8966 (mt-10) REVERT: A 466 HIS cc_start: 0.8764 (m90) cc_final: 0.8369 (m90) REVERT: A 485 MET cc_start: 0.8444 (mtm) cc_final: 0.8055 (mtm) REVERT: A 569 GLU cc_start: 0.8201 (pt0) cc_final: 0.7913 (pp20) REVERT: A 603 ASP cc_start: 0.8033 (t0) cc_final: 0.7596 (t0) REVERT: A 626 GLU cc_start: 0.8393 (pm20) cc_final: 0.8126 (pm20) REVERT: A 672 MET cc_start: 0.7778 (tpt) cc_final: 0.7398 (tpt) REVERT: A 698 GLU cc_start: 0.8300 (tm-30) cc_final: 0.7789 (tm-30) REVERT: A 726 MET cc_start: 0.8047 (ttm) cc_final: 0.7783 (tpp) REVERT: A 737 ARG cc_start: 0.8542 (mtt-85) cc_final: 0.8248 (mtt180) REVERT: A 741 LYS cc_start: 0.8318 (tptp) cc_final: 0.7955 (tptp) REVERT: A 802 VAL cc_start: 0.8664 (t) cc_final: 0.8406 (m) REVERT: A 813 MET cc_start: 0.7777 (mmt) cc_final: 0.7289 (mmt) REVERT: A 847 LYS cc_start: 0.8757 (tptt) cc_final: 0.8439 (tptp) REVERT: B 532 MET cc_start: 0.8393 (mpp) cc_final: 0.7895 (mpp) REVERT: B 535 MET cc_start: 0.7386 (ttm) cc_final: 0.7059 (ttm) REVERT: B 586 LYS cc_start: 0.8459 (mmtt) cc_final: 0.8101 (mmmm) REVERT: B 620 ASP cc_start: 0.8396 (t0) cc_final: 0.7958 (t0) REVERT: B 628 ILE cc_start: 0.8680 (OUTLIER) cc_final: 0.8346 (mm) REVERT: B 649 LYS cc_start: 0.8040 (OUTLIER) cc_final: 0.7540 (tmtt) REVERT: B 674 GLU cc_start: 0.8221 (tt0) cc_final: 0.7836 (tt0) REVERT: B 699 LYS cc_start: 0.9077 (mttt) cc_final: 0.8751 (mtmm) REVERT: B 718 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8130 (mm-30) REVERT: B 728 MET cc_start: 0.8341 (ppp) cc_final: 0.8087 (ppp) REVERT: B 796 ARG cc_start: 0.8709 (mtp-110) cc_final: 0.8416 (mtp180) REVERT: B 798 GLN cc_start: 0.8010 (tp-100) cc_final: 0.7628 (tp40) REVERT: B 863 ARG cc_start: 0.7963 (ptp-170) cc_final: 0.7687 (mtm180) REVERT: B 917 GLN cc_start: 0.8432 (mt0) cc_final: 0.7628 (mt0) REVERT: B 932 VAL cc_start: 0.8420 (OUTLIER) cc_final: 0.8074 (m) REVERT: B 975 ASP cc_start: 0.7567 (t0) cc_final: 0.7288 (t70) REVERT: B 991 TYR cc_start: 0.8483 (t80) cc_final: 0.8130 (t80) REVERT: B 1000 ASP cc_start: 0.8149 (t0) cc_final: 0.7788 (t0) REVERT: B 1057 TYR cc_start: 0.8354 (m-80) cc_final: 0.8017 (m-80) REVERT: B 1077 ASP cc_start: 0.8344 (t0) cc_final: 0.7729 (t0) REVERT: B 1081 GLU cc_start: 0.8480 (mm-30) cc_final: 0.8274 (mm-30) REVERT: B 1092 GLU cc_start: 0.8629 (mm-30) cc_final: 0.8074 (mm-30) outliers start: 62 outliers final: 42 residues processed: 320 average time/residue: 0.2823 time to fit residues: 121.9280 Evaluate side-chains 313 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 265 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 464 GLU Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 885 GLN Chi-restraints excluded: chain A residue 926 ILE Chi-restraints excluded: chain B residue 551 GLN Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 628 ILE Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 649 LYS Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 775 LYS Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 803 CYS Chi-restraints excluded: chain B residue 819 HIS Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 899 MET Chi-restraints excluded: chain B residue 932 VAL Chi-restraints excluded: chain B residue 939 MET Chi-restraints excluded: chain B residue 965 LYS Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1023 HIS Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain B residue 1060 THR Chi-restraints excluded: chain B residue 1070 LEU Chi-restraints excluded: chain B residue 1100 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 0.8980 chunk 111 optimal weight: 0.5980 chunk 24 optimal weight: 0.0970 chunk 72 optimal weight: 0.6980 chunk 30 optimal weight: 0.1980 chunk 123 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 57 optimal weight: 0.4980 chunk 10 optimal weight: 6.9990 chunk 40 optimal weight: 0.7980 chunk 65 optimal weight: 0.4980 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 885 GLN B 852 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10460 Z= 0.208 Angle : 0.622 9.640 14122 Z= 0.323 Chirality : 0.044 0.191 1617 Planarity : 0.004 0.056 1796 Dihedral : 8.260 87.040 1457 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 5.30 % Allowed : 26.30 % Favored : 68.40 % 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: -0.85 (0.23), residues: 1270 helix: 0.70 (0.19), residues: 698 sheet: -2.41 (0.40), residues: 142 loop : -1.94 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 764 HIS 0.005 0.001 HIS B 984 PHE 0.027 0.002 PHE B 784 TYR 0.013 0.001 TYR A 656 ARG 0.005 0.000 ARG B1066 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 280 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.6879 (ttt) cc_final: 0.6567 (ttt) REVERT: A 299 TYR cc_start: 0.8646 (m-80) cc_final: 0.8148 (m-80) REVERT: A 326 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7776 (tt) REVERT: A 347 LYS cc_start: 0.8852 (tptp) cc_final: 0.8630 (tptp) REVERT: A 369 ASP cc_start: 0.7972 (t0) cc_final: 0.7495 (t0) REVERT: A 382 ARG cc_start: 0.7932 (ttt180) cc_final: 0.7561 (ttp-110) REVERT: A 383 ARG cc_start: 0.8093 (ttp-170) cc_final: 0.7813 (ttp-110) REVERT: A 396 ARG cc_start: 0.8958 (mtm110) cc_final: 0.8572 (mtm110) REVERT: A 418 ILE cc_start: 0.8710 (tp) cc_final: 0.8333 (tt) REVERT: A 419 GLN cc_start: 0.8603 (tm-30) cc_final: 0.8329 (tm-30) REVERT: A 422 GLU cc_start: 0.8807 (mt-10) cc_final: 0.8488 (mt-10) REVERT: A 423 LYS cc_start: 0.8712 (tttt) cc_final: 0.8446 (ttmt) REVERT: A 459 ASP cc_start: 0.7526 (p0) cc_final: 0.6876 (m-30) REVERT: A 464 GLU cc_start: 0.9253 (OUTLIER) cc_final: 0.8995 (mt-10) REVERT: A 466 HIS cc_start: 0.8714 (m90) cc_final: 0.8340 (m90) REVERT: A 485 MET cc_start: 0.8463 (mtm) cc_final: 0.8062 (mtm) REVERT: A 523 PHE cc_start: 0.5719 (OUTLIER) cc_final: 0.5287 (t80) REVERT: A 569 GLU cc_start: 0.8165 (pt0) cc_final: 0.7878 (pp20) REVERT: A 603 ASP cc_start: 0.7959 (t0) cc_final: 0.7523 (t0) REVERT: A 626 GLU cc_start: 0.8409 (pm20) cc_final: 0.8095 (pm20) REVERT: A 672 MET cc_start: 0.7695 (tpt) cc_final: 0.7345 (tpt) REVERT: A 702 VAL cc_start: 0.8467 (OUTLIER) cc_final: 0.7577 (t) REVERT: A 726 MET cc_start: 0.8012 (ttm) cc_final: 0.7743 (tpp) REVERT: A 741 LYS cc_start: 0.8272 (tptp) cc_final: 0.7911 (tptp) REVERT: A 786 GLU cc_start: 0.8454 (tp30) cc_final: 0.8035 (tp30) REVERT: A 802 VAL cc_start: 0.8673 (t) cc_final: 0.8430 (m) REVERT: A 813 MET cc_start: 0.7802 (mmt) cc_final: 0.7317 (mmt) REVERT: A 847 LYS cc_start: 0.8702 (tptt) cc_final: 0.8338 (tptp) REVERT: B 532 MET cc_start: 0.8240 (mpp) cc_final: 0.7763 (mpp) REVERT: B 534 PHE cc_start: 0.7678 (m-10) cc_final: 0.7187 (m-10) REVERT: B 582 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.7503 (pt0) REVERT: B 586 LYS cc_start: 0.8379 (mmtt) cc_final: 0.8062 (mmmm) REVERT: B 591 ASN cc_start: 0.8381 (m-40) cc_final: 0.8131 (m-40) REVERT: B 620 ASP cc_start: 0.8321 (t0) cc_final: 0.7868 (t0) REVERT: B 628 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.8388 (mm) REVERT: B 649 LYS cc_start: 0.7973 (OUTLIER) cc_final: 0.7441 (tmtt) REVERT: B 674 GLU cc_start: 0.8231 (tt0) cc_final: 0.7798 (tt0) REVERT: B 699 LYS cc_start: 0.9066 (mttt) cc_final: 0.8752 (mtmm) REVERT: B 718 GLU cc_start: 0.8593 (mm-30) cc_final: 0.8105 (mm-30) REVERT: B 728 MET cc_start: 0.8388 (ppp) cc_final: 0.8130 (ppp) REVERT: B 796 ARG cc_start: 0.8704 (mtp-110) cc_final: 0.8413 (mtp180) REVERT: B 798 GLN cc_start: 0.7917 (tp-100) cc_final: 0.7547 (tp40) REVERT: B 917 GLN cc_start: 0.8419 (mt0) cc_final: 0.7705 (mt0) REVERT: B 932 VAL cc_start: 0.8349 (OUTLIER) cc_final: 0.8049 (m) REVERT: B 949 ARG cc_start: 0.8185 (mtm110) cc_final: 0.7819 (ttm-80) REVERT: B 1000 ASP cc_start: 0.8118 (t0) cc_final: 0.7789 (t0) REVERT: B 1057 TYR cc_start: 0.8257 (m-80) cc_final: 0.7909 (m-80) REVERT: B 1077 ASP cc_start: 0.8253 (t0) cc_final: 0.7739 (t0) REVERT: B 1081 GLU cc_start: 0.8436 (mm-30) cc_final: 0.8234 (mm-30) REVERT: B 1092 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8059 (mm-30) outliers start: 60 outliers final: 41 residues processed: 324 average time/residue: 0.3530 time to fit residues: 153.1839 Evaluate side-chains 306 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 257 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 464 GLU Chi-restraints excluded: chain A residue 523 PHE Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 777 PHE Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 885 GLN Chi-restraints excluded: chain A residue 926 ILE Chi-restraints excluded: chain B residue 551 GLN Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 628 ILE Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 649 LYS Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 775 LYS Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 803 CYS Chi-restraints excluded: chain B residue 817 HIS Chi-restraints excluded: chain B residue 819 HIS Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 899 MET Chi-restraints excluded: chain B residue 932 VAL Chi-restraints excluded: chain B residue 939 MET Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1023 HIS Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain B residue 1070 LEU Chi-restraints excluded: chain B residue 1072 VAL Chi-restraints excluded: chain B residue 1100 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 0.0970 chunk 13 optimal weight: 1.9990 chunk 70 optimal weight: 7.9990 chunk 90 optimal weight: 2.9990 chunk 104 optimal weight: 0.5980 chunk 69 optimal weight: 7.9990 chunk 123 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 429 GLN A 690 GLN B 852 GLN B1010 HIS B1088 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 10460 Z= 0.364 Angle : 0.671 10.081 14122 Z= 0.352 Chirality : 0.047 0.175 1617 Planarity : 0.004 0.064 1796 Dihedral : 8.032 89.409 1452 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 16.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 5.56 % Allowed : 27.54 % Favored : 66.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.23), residues: 1270 helix: 0.57 (0.19), residues: 700 sheet: -2.50 (0.40), residues: 141 loop : -1.91 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 764 HIS 0.007 0.001 HIS B 614 PHE 0.031 0.002 PHE A 436 TYR 0.014 0.002 TYR A 815 ARG 0.008 0.001 ARG B 734 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 269 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASP cc_start: 0.2550 (OUTLIER) cc_final: 0.2238 (t0) REVERT: A 210 MET cc_start: 0.6850 (ttt) cc_final: 0.6538 (ttt) REVERT: A 299 TYR cc_start: 0.8686 (m-80) cc_final: 0.8206 (m-80) REVERT: A 347 LYS cc_start: 0.8871 (tptp) cc_final: 0.8623 (tptp) REVERT: A 369 ASP cc_start: 0.7937 (t0) cc_final: 0.7454 (t0) REVERT: A 382 ARG cc_start: 0.8035 (ttt180) cc_final: 0.7633 (ttp-110) REVERT: A 396 ARG cc_start: 0.8977 (mtm110) cc_final: 0.8607 (mtm110) REVERT: A 418 ILE cc_start: 0.8727 (tp) cc_final: 0.8338 (tt) REVERT: A 419 GLN cc_start: 0.8605 (tm-30) cc_final: 0.8318 (tm-30) REVERT: A 422 GLU cc_start: 0.8894 (mt-10) cc_final: 0.8575 (mt-10) REVERT: A 423 LYS cc_start: 0.8789 (tttt) cc_final: 0.8534 (ttmt) REVERT: A 459 ASP cc_start: 0.7620 (p0) cc_final: 0.6641 (m-30) REVERT: A 464 GLU cc_start: 0.9265 (OUTLIER) cc_final: 0.8976 (mt-10) REVERT: A 485 MET cc_start: 0.8475 (mtm) cc_final: 0.8085 (mtm) REVERT: A 523 PHE cc_start: 0.5744 (OUTLIER) cc_final: 0.5316 (t80) REVERT: A 569 GLU cc_start: 0.8237 (pt0) cc_final: 0.7954 (pp20) REVERT: A 603 ASP cc_start: 0.8021 (t0) cc_final: 0.7600 (t0) REVERT: A 626 GLU cc_start: 0.8426 (pm20) cc_final: 0.8140 (pm20) REVERT: A 672 MET cc_start: 0.7836 (tpt) cc_final: 0.7487 (tpt) REVERT: A 702 VAL cc_start: 0.8561 (OUTLIER) cc_final: 0.7751 (t) REVERT: A 726 MET cc_start: 0.8126 (ttm) cc_final: 0.7551 (ttm) REVERT: A 741 LYS cc_start: 0.8354 (tptp) cc_final: 0.7990 (tptp) REVERT: A 786 GLU cc_start: 0.8476 (tp30) cc_final: 0.8034 (tp30) REVERT: A 802 VAL cc_start: 0.8669 (t) cc_final: 0.8397 (m) REVERT: A 813 MET cc_start: 0.7823 (mmt) cc_final: 0.7351 (mmt) REVERT: A 847 LYS cc_start: 0.8677 (tptt) cc_final: 0.8374 (tptp) REVERT: B 532 MET cc_start: 0.8228 (mpp) cc_final: 0.7753 (mpp) REVERT: B 534 PHE cc_start: 0.7751 (m-10) cc_final: 0.7271 (m-10) REVERT: B 582 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7523 (pt0) REVERT: B 586 LYS cc_start: 0.8412 (mmtt) cc_final: 0.8058 (mmmm) REVERT: B 591 ASN cc_start: 0.8394 (m-40) cc_final: 0.8160 (m-40) REVERT: B 620 ASP cc_start: 0.8483 (t0) cc_final: 0.8043 (t0) REVERT: B 628 ILE cc_start: 0.8673 (OUTLIER) cc_final: 0.8409 (mm) REVERT: B 649 LYS cc_start: 0.8018 (OUTLIER) cc_final: 0.7403 (tmtt) REVERT: B 674 GLU cc_start: 0.8255 (tt0) cc_final: 0.7767 (tt0) REVERT: B 677 GLU cc_start: 0.8465 (tm-30) cc_final: 0.8048 (tm-30) REVERT: B 699 LYS cc_start: 0.9083 (mttt) cc_final: 0.8754 (mtmm) REVERT: B 718 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8147 (mm-30) REVERT: B 725 GLU cc_start: 0.8925 (mt-10) cc_final: 0.8309 (tp30) REVERT: B 728 MET cc_start: 0.8330 (ppp) cc_final: 0.7550 (ppp) REVERT: B 784 PHE cc_start: 0.8406 (t80) cc_final: 0.8193 (t80) REVERT: B 796 ARG cc_start: 0.8756 (mtp-110) cc_final: 0.8446 (mtt180) REVERT: B 798 GLN cc_start: 0.8009 (tp-100) cc_final: 0.7643 (tp40) REVERT: B 917 GLN cc_start: 0.8429 (mt0) cc_final: 0.7722 (mt0) REVERT: B 932 VAL cc_start: 0.8411 (OUTLIER) cc_final: 0.8107 (m) REVERT: B 946 TYR cc_start: 0.8225 (m-80) cc_final: 0.7664 (m-10) REVERT: B 1000 ASP cc_start: 0.8177 (t0) cc_final: 0.7831 (t0) REVERT: B 1057 TYR cc_start: 0.8417 (m-80) cc_final: 0.8172 (m-80) REVERT: B 1077 ASP cc_start: 0.8218 (t0) cc_final: 0.7751 (t0) REVERT: B 1081 GLU cc_start: 0.8505 (mm-30) cc_final: 0.8218 (mm-30) REVERT: B 1092 GLU cc_start: 0.8602 (mm-30) cc_final: 0.8052 (mm-30) outliers start: 63 outliers final: 42 residues processed: 315 average time/residue: 0.2622 time to fit residues: 111.5392 Evaluate side-chains 312 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 262 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 464 GLU Chi-restraints excluded: chain A residue 523 PHE Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 777 PHE Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 926 ILE Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 628 ILE Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 649 LYS Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 775 LYS Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 803 CYS Chi-restraints excluded: chain B residue 817 HIS Chi-restraints excluded: chain B residue 819 HIS Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 899 MET Chi-restraints excluded: chain B residue 932 VAL Chi-restraints excluded: chain B residue 939 MET Chi-restraints excluded: chain B residue 956 LEU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1023 HIS Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain B residue 1060 THR Chi-restraints excluded: chain B residue 1070 LEU Chi-restraints excluded: chain B residue 1100 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 0.7980 chunk 73 optimal weight: 0.5980 chunk 37 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 78 optimal weight: 0.3980 chunk 84 optimal weight: 0.8980 chunk 60 optimal weight: 0.5980 chunk 11 optimal weight: 8.9990 chunk 96 optimal weight: 3.9990 chunk 112 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 885 GLN B 852 GLN B1010 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 10460 Z= 0.247 Angle : 0.631 8.315 14122 Z= 0.330 Chirality : 0.045 0.180 1617 Planarity : 0.004 0.060 1796 Dihedral : 7.822 89.188 1452 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 5.30 % Allowed : 27.27 % Favored : 67.43 % 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: -0.77 (0.23), residues: 1270 helix: 0.71 (0.19), residues: 698 sheet: -2.36 (0.40), residues: 147 loop : -1.79 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 764 HIS 0.009 0.001 HIS B 614 PHE 0.028 0.002 PHE A 760 TYR 0.012 0.001 TYR B1011 ARG 0.005 0.000 ARG B1066 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 264 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASP cc_start: 0.2482 (OUTLIER) cc_final: 0.2228 (t0) REVERT: A 210 MET cc_start: 0.6823 (ttt) cc_final: 0.6542 (ttt) REVERT: A 299 TYR cc_start: 0.8654 (m-80) cc_final: 0.8151 (m-80) REVERT: A 347 LYS cc_start: 0.8909 (tptp) cc_final: 0.8640 (tptp) REVERT: A 369 ASP cc_start: 0.7899 (t0) cc_final: 0.7365 (t0) REVERT: A 382 ARG cc_start: 0.8075 (ttt180) cc_final: 0.7797 (ttp80) REVERT: A 396 ARG cc_start: 0.8940 (mtm110) cc_final: 0.8589 (mtm110) REVERT: A 418 ILE cc_start: 0.8734 (tp) cc_final: 0.8337 (tt) REVERT: A 419 GLN cc_start: 0.8602 (tm-30) cc_final: 0.8320 (pp30) REVERT: A 422 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8526 (mt-10) REVERT: A 423 LYS cc_start: 0.8753 (tttt) cc_final: 0.8491 (ttpt) REVERT: A 451 GLN cc_start: 0.8082 (tm-30) cc_final: 0.7696 (tm-30) REVERT: A 458 LEU cc_start: 0.7779 (pp) cc_final: 0.7465 (pp) REVERT: A 459 ASP cc_start: 0.7653 (p0) cc_final: 0.6730 (m-30) REVERT: A 464 GLU cc_start: 0.9252 (OUTLIER) cc_final: 0.8951 (mt-10) REVERT: A 485 MET cc_start: 0.8478 (mtm) cc_final: 0.8085 (mtm) REVERT: A 523 PHE cc_start: 0.5699 (OUTLIER) cc_final: 0.5272 (t80) REVERT: A 569 GLU cc_start: 0.8236 (pt0) cc_final: 0.7951 (pp20) REVERT: A 603 ASP cc_start: 0.7973 (t0) cc_final: 0.7509 (t0) REVERT: A 626 GLU cc_start: 0.8406 (pm20) cc_final: 0.8136 (pm20) REVERT: A 663 MET cc_start: 0.7529 (tpp) cc_final: 0.7110 (tpp) REVERT: A 672 MET cc_start: 0.7767 (tpt) cc_final: 0.7468 (tpt) REVERT: A 702 VAL cc_start: 0.8484 (OUTLIER) cc_final: 0.7631 (t) REVERT: A 706 ASP cc_start: 0.8458 (t0) cc_final: 0.7961 (t0) REVERT: A 726 MET cc_start: 0.8083 (ttm) cc_final: 0.7188 (tpp) REVERT: A 741 LYS cc_start: 0.8332 (tptp) cc_final: 0.7966 (tptp) REVERT: A 768 GLU cc_start: 0.8197 (tm-30) cc_final: 0.7871 (tm-30) REVERT: A 786 GLU cc_start: 0.8455 (tp30) cc_final: 0.8000 (tp30) REVERT: A 802 VAL cc_start: 0.8672 (t) cc_final: 0.8415 (m) REVERT: A 813 MET cc_start: 0.7813 (mmt) cc_final: 0.7320 (mmt) REVERT: A 847 LYS cc_start: 0.8675 (tptt) cc_final: 0.8352 (tptp) REVERT: B 532 MET cc_start: 0.8127 (mpp) cc_final: 0.7641 (mpp) REVERT: B 534 PHE cc_start: 0.7678 (m-10) cc_final: 0.7167 (m-10) REVERT: B 535 MET cc_start: 0.7374 (ttm) cc_final: 0.7166 (ttm) REVERT: B 582 GLN cc_start: 0.8008 (OUTLIER) cc_final: 0.7434 (pt0) REVERT: B 586 LYS cc_start: 0.8371 (mmtt) cc_final: 0.7992 (mmmm) REVERT: B 620 ASP cc_start: 0.8366 (t0) cc_final: 0.7933 (t0) REVERT: B 628 ILE cc_start: 0.8640 (OUTLIER) cc_final: 0.8354 (mm) REVERT: B 649 LYS cc_start: 0.8014 (OUTLIER) cc_final: 0.7466 (tmtt) REVERT: B 674 GLU cc_start: 0.8125 (tt0) cc_final: 0.7645 (tt0) REVERT: B 677 GLU cc_start: 0.8451 (tm-30) cc_final: 0.8030 (tm-30) REVERT: B 699 LYS cc_start: 0.9118 (mttt) cc_final: 0.8794 (mtmm) REVERT: B 718 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8138 (mm-30) REVERT: B 725 GLU cc_start: 0.8888 (mt-10) cc_final: 0.8287 (tp30) REVERT: B 728 MET cc_start: 0.8298 (ppp) cc_final: 0.7528 (ppp) REVERT: B 796 ARG cc_start: 0.8736 (mtp-110) cc_final: 0.8432 (mtt180) REVERT: B 798 GLN cc_start: 0.7917 (tp-100) cc_final: 0.7561 (tp40) REVERT: B 899 MET cc_start: 0.7498 (OUTLIER) cc_final: 0.7106 (tpt) REVERT: B 917 GLN cc_start: 0.8378 (mt0) cc_final: 0.7978 (mt0) REVERT: B 946 TYR cc_start: 0.8135 (m-80) cc_final: 0.7720 (m-10) REVERT: B 1004 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8062 (mp) REVERT: B 1057 TYR cc_start: 0.8297 (m-80) cc_final: 0.7969 (m-80) REVERT: B 1077 ASP cc_start: 0.8174 (t0) cc_final: 0.7634 (t70) REVERT: B 1081 GLU cc_start: 0.8462 (mm-30) cc_final: 0.8258 (mm-30) REVERT: B 1092 GLU cc_start: 0.8592 (mm-30) cc_final: 0.8069 (mm-30) outliers start: 60 outliers final: 43 residues processed: 306 average time/residue: 0.2659 time to fit residues: 109.6812 Evaluate side-chains 309 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 257 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 464 GLU Chi-restraints excluded: chain A residue 523 PHE Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 641 CYS Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 885 GLN Chi-restraints excluded: chain A residue 926 ILE Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 628 ILE Chi-restraints excluded: chain B residue 634 SER Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 649 LYS Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 775 LYS Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 803 CYS Chi-restraints excluded: chain B residue 817 HIS Chi-restraints excluded: chain B residue 819 HIS Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 899 MET Chi-restraints excluded: chain B residue 939 MET Chi-restraints excluded: chain B residue 956 LEU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1023 HIS Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain B residue 1070 LEU Chi-restraints excluded: chain B residue 1072 VAL Chi-restraints excluded: chain B residue 1100 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 114 optimal weight: 0.6980 chunk 69 optimal weight: 5.9990 chunk 50 optimal weight: 0.5980 chunk 90 optimal weight: 0.9990 chunk 35 optimal weight: 8.9990 chunk 103 optimal weight: 1.9990 chunk 108 optimal weight: 0.0980 chunk 75 optimal weight: 0.9980 chunk 121 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 653 ASN B 852 GLN B1010 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 10460 Z= 0.255 Angle : 0.652 14.729 14122 Z= 0.337 Chirality : 0.045 0.176 1617 Planarity : 0.004 0.059 1796 Dihedral : 7.737 89.453 1452 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 5.47 % Allowed : 26.83 % Favored : 67.70 % 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: -0.69 (0.24), residues: 1270 helix: 0.76 (0.19), residues: 698 sheet: -2.21 (0.39), residues: 160 loop : -1.76 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 764 HIS 0.009 0.001 HIS B 614 PHE 0.038 0.002 PHE B 784 TYR 0.011 0.001 TYR A 656 ARG 0.007 0.000 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 265 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.6819 (ttt) cc_final: 0.6486 (ttt) REVERT: A 299 TYR cc_start: 0.8636 (m-80) cc_final: 0.8152 (m-80) REVERT: A 347 LYS cc_start: 0.8884 (tptp) cc_final: 0.8635 (tptp) REVERT: A 369 ASP cc_start: 0.7861 (t0) cc_final: 0.7327 (t0) REVERT: A 382 ARG cc_start: 0.8093 (ttt180) cc_final: 0.7802 (ttp80) REVERT: A 396 ARG cc_start: 0.8920 (mtm110) cc_final: 0.8551 (mtm110) REVERT: A 418 ILE cc_start: 0.8722 (tp) cc_final: 0.8338 (tt) REVERT: A 419 GLN cc_start: 0.8601 (tm-30) cc_final: 0.8322 (pp30) REVERT: A 422 GLU cc_start: 0.8842 (mt-10) cc_final: 0.8527 (mt-10) REVERT: A 423 LYS cc_start: 0.8762 (tttt) cc_final: 0.8494 (ttpt) REVERT: A 451 GLN cc_start: 0.8061 (tm-30) cc_final: 0.7678 (tm-30) REVERT: A 458 LEU cc_start: 0.7805 (pp) cc_final: 0.7488 (pp) REVERT: A 459 ASP cc_start: 0.7652 (p0) cc_final: 0.6698 (m-30) REVERT: A 464 GLU cc_start: 0.9252 (OUTLIER) cc_final: 0.8951 (mt-10) REVERT: A 485 MET cc_start: 0.8471 (mtm) cc_final: 0.8086 (mtm) REVERT: A 523 PHE cc_start: 0.5680 (OUTLIER) cc_final: 0.5248 (t80) REVERT: A 569 GLU cc_start: 0.8236 (pt0) cc_final: 0.7954 (pp20) REVERT: A 603 ASP cc_start: 0.7958 (t0) cc_final: 0.7530 (t0) REVERT: A 626 GLU cc_start: 0.8404 (pm20) cc_final: 0.8116 (pm20) REVERT: A 663 MET cc_start: 0.7487 (tpp) cc_final: 0.7119 (tpp) REVERT: A 672 MET cc_start: 0.7778 (tpt) cc_final: 0.7477 (tpt) REVERT: A 702 VAL cc_start: 0.8471 (OUTLIER) cc_final: 0.7601 (t) REVERT: A 706 ASP cc_start: 0.8384 (t0) cc_final: 0.7868 (t0) REVERT: A 726 MET cc_start: 0.8096 (ttm) cc_final: 0.7209 (tpp) REVERT: A 741 LYS cc_start: 0.8312 (tptp) cc_final: 0.7952 (tptp) REVERT: A 768 GLU cc_start: 0.8178 (tm-30) cc_final: 0.7825 (tm-30) REVERT: A 786 GLU cc_start: 0.8457 (tp30) cc_final: 0.8004 (tp30) REVERT: A 802 VAL cc_start: 0.8664 (t) cc_final: 0.8405 (m) REVERT: A 813 MET cc_start: 0.7818 (mmt) cc_final: 0.7331 (mmt) REVERT: A 847 LYS cc_start: 0.8669 (tptt) cc_final: 0.8372 (tptp) REVERT: B 532 MET cc_start: 0.8107 (mpp) cc_final: 0.7614 (mpp) REVERT: B 534 PHE cc_start: 0.7671 (m-10) cc_final: 0.7234 (m-10) REVERT: B 535 MET cc_start: 0.7371 (ttm) cc_final: 0.7134 (ttm) REVERT: B 582 GLN cc_start: 0.8032 (OUTLIER) cc_final: 0.7463 (pt0) REVERT: B 586 LYS cc_start: 0.8368 (mmtt) cc_final: 0.7987 (mmmm) REVERT: B 620 ASP cc_start: 0.8377 (t0) cc_final: 0.7940 (t0) REVERT: B 628 ILE cc_start: 0.8646 (OUTLIER) cc_final: 0.8412 (mm) REVERT: B 649 LYS cc_start: 0.7992 (OUTLIER) cc_final: 0.7474 (tmtt) REVERT: B 674 GLU cc_start: 0.8139 (tt0) cc_final: 0.7634 (tt0) REVERT: B 677 GLU cc_start: 0.8467 (tm-30) cc_final: 0.8040 (tm-30) REVERT: B 699 LYS cc_start: 0.9097 (mttt) cc_final: 0.8770 (mtmm) REVERT: B 718 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8136 (mm-30) REVERT: B 725 GLU cc_start: 0.8867 (mt-10) cc_final: 0.8262 (tp30) REVERT: B 728 MET cc_start: 0.8237 (ppp) cc_final: 0.7441 (ppp) REVERT: B 796 ARG cc_start: 0.8738 (mtp-110) cc_final: 0.8360 (mtt180) REVERT: B 798 GLN cc_start: 0.7904 (tp-100) cc_final: 0.7548 (tp40) REVERT: B 823 LYS cc_start: 0.8229 (ttmm) cc_final: 0.8005 (ttmt) REVERT: B 899 MET cc_start: 0.7495 (OUTLIER) cc_final: 0.7101 (tpt) REVERT: B 917 GLN cc_start: 0.8355 (mt0) cc_final: 0.7952 (mt0) REVERT: B 932 VAL cc_start: 0.8299 (OUTLIER) cc_final: 0.8006 (m) REVERT: B 946 TYR cc_start: 0.8136 (m-80) cc_final: 0.7760 (m-10) REVERT: B 953 MET cc_start: 0.8629 (tpt) cc_final: 0.8329 (tpp) REVERT: B 1004 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8163 (mt) REVERT: B 1057 TYR cc_start: 0.8297 (m-80) cc_final: 0.7981 (m-80) REVERT: B 1077 ASP cc_start: 0.8144 (t0) cc_final: 0.7605 (t0) REVERT: B 1092 GLU cc_start: 0.8584 (mm-30) cc_final: 0.8029 (mm-30) outliers start: 62 outliers final: 43 residues processed: 308 average time/residue: 0.2652 time to fit residues: 110.4850 Evaluate side-chains 311 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 259 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 464 GLU Chi-restraints excluded: chain A residue 523 PHE Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 641 CYS Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 926 ILE Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 628 ILE Chi-restraints excluded: chain B residue 634 SER Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 649 LYS Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 775 LYS Chi-restraints excluded: chain B residue 803 CYS Chi-restraints excluded: chain B residue 817 HIS Chi-restraints excluded: chain B residue 819 HIS Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 899 MET Chi-restraints excluded: chain B residue 932 VAL Chi-restraints excluded: chain B residue 939 MET Chi-restraints excluded: chain B residue 956 LEU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1023 HIS Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain B residue 1070 LEU Chi-restraints excluded: chain B residue 1072 VAL Chi-restraints excluded: chain B residue 1100 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 0.3980 chunk 57 optimal weight: 0.9980 chunk 84 optimal weight: 0.1980 chunk 127 optimal weight: 10.0000 chunk 117 optimal weight: 0.6980 chunk 101 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 681 GLN A 885 GLN B1010 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10460 Z= 0.246 Angle : 0.669 13.160 14122 Z= 0.342 Chirality : 0.046 0.306 1617 Planarity : 0.004 0.057 1796 Dihedral : 7.639 88.596 1452 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 4.68 % Allowed : 27.98 % Favored : 67.34 % 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 (0.24), residues: 1270 helix: 0.82 (0.19), residues: 698 sheet: -2.32 (0.39), residues: 150 loop : -1.68 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 764 HIS 0.009 0.001 HIS B 614 PHE 0.040 0.002 PHE B 784 TYR 0.010 0.001 TYR B1011 ARG 0.006 0.000 ARG B1103 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 268 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.6793 (ttt) cc_final: 0.6470 (ttt) REVERT: A 299 TYR cc_start: 0.8628 (m-80) cc_final: 0.8147 (m-80) REVERT: A 312 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7625 (mt) REVERT: A 347 LYS cc_start: 0.8855 (tptp) cc_final: 0.8618 (tptp) REVERT: A 369 ASP cc_start: 0.7875 (t0) cc_final: 0.7368 (t0) REVERT: A 382 ARG cc_start: 0.8102 (ttt180) cc_final: 0.7817 (ttp80) REVERT: A 396 ARG cc_start: 0.8900 (mtm110) cc_final: 0.8547 (mtm110) REVERT: A 418 ILE cc_start: 0.8721 (tp) cc_final: 0.8346 (tt) REVERT: A 419 GLN cc_start: 0.8609 (tm-30) cc_final: 0.8319 (pp30) REVERT: A 422 GLU cc_start: 0.8854 (mt-10) cc_final: 0.8532 (mt-10) REVERT: A 423 LYS cc_start: 0.8733 (tttt) cc_final: 0.8475 (ttpt) REVERT: A 451 GLN cc_start: 0.8034 (tm-30) cc_final: 0.7644 (tm-30) REVERT: A 458 LEU cc_start: 0.7796 (pp) cc_final: 0.7482 (pp) REVERT: A 459 ASP cc_start: 0.7660 (p0) cc_final: 0.6683 (m-30) REVERT: A 464 GLU cc_start: 0.9246 (OUTLIER) cc_final: 0.8946 (mt-10) REVERT: A 485 MET cc_start: 0.8471 (mtm) cc_final: 0.8086 (mtm) REVERT: A 523 PHE cc_start: 0.5654 (OUTLIER) cc_final: 0.5233 (t80) REVERT: A 569 GLU cc_start: 0.8235 (pt0) cc_final: 0.7958 (pp20) REVERT: A 603 ASP cc_start: 0.7954 (t0) cc_final: 0.7524 (t0) REVERT: A 626 GLU cc_start: 0.8404 (pm20) cc_final: 0.8124 (pm20) REVERT: A 663 MET cc_start: 0.7504 (tpp) cc_final: 0.7140 (tpp) REVERT: A 672 MET cc_start: 0.7790 (tpt) cc_final: 0.7468 (tpt) REVERT: A 702 VAL cc_start: 0.8435 (OUTLIER) cc_final: 0.7561 (t) REVERT: A 706 ASP cc_start: 0.8381 (t0) cc_final: 0.8062 (t0) REVERT: A 726 MET cc_start: 0.8092 (ttm) cc_final: 0.7209 (tpp) REVERT: A 768 GLU cc_start: 0.8180 (tm-30) cc_final: 0.7806 (tm-30) REVERT: A 786 GLU cc_start: 0.8484 (tp30) cc_final: 0.8004 (tp30) REVERT: A 793 GLN cc_start: 0.8755 (tt0) cc_final: 0.8403 (tp40) REVERT: A 802 VAL cc_start: 0.8671 (t) cc_final: 0.8415 (m) REVERT: A 813 MET cc_start: 0.7825 (mmt) cc_final: 0.7354 (mmt) REVERT: A 847 LYS cc_start: 0.8670 (tptt) cc_final: 0.8348 (tptp) REVERT: B 532 MET cc_start: 0.8079 (mpp) cc_final: 0.7585 (mpp) REVERT: B 534 PHE cc_start: 0.7692 (m-10) cc_final: 0.7345 (m-10) REVERT: B 582 GLN cc_start: 0.8004 (OUTLIER) cc_final: 0.7432 (pt0) REVERT: B 586 LYS cc_start: 0.8346 (mmtt) cc_final: 0.7967 (mmmm) REVERT: B 620 ASP cc_start: 0.8344 (t0) cc_final: 0.7912 (t0) REVERT: B 628 ILE cc_start: 0.8644 (OUTLIER) cc_final: 0.8408 (mm) REVERT: B 629 TYR cc_start: 0.8113 (t80) cc_final: 0.7782 (t80) REVERT: B 649 LYS cc_start: 0.7980 (OUTLIER) cc_final: 0.7513 (tmtt) REVERT: B 674 GLU cc_start: 0.8143 (tt0) cc_final: 0.7637 (tt0) REVERT: B 677 GLU cc_start: 0.8464 (tm-30) cc_final: 0.8035 (tm-30) REVERT: B 699 LYS cc_start: 0.9125 (mttt) cc_final: 0.8803 (mtmm) REVERT: B 718 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8133 (mm-30) REVERT: B 725 GLU cc_start: 0.8854 (mt-10) cc_final: 0.8281 (tp30) REVERT: B 728 MET cc_start: 0.8191 (ppp) cc_final: 0.7475 (ppp) REVERT: B 796 ARG cc_start: 0.8721 (mtp-110) cc_final: 0.8429 (mtp180) REVERT: B 798 GLN cc_start: 0.7858 (tp-100) cc_final: 0.7500 (tp40) REVERT: B 823 LYS cc_start: 0.8214 (ttmm) cc_final: 0.7998 (ttmt) REVERT: B 899 MET cc_start: 0.7488 (OUTLIER) cc_final: 0.7089 (tpt) REVERT: B 917 GLN cc_start: 0.8330 (mt0) cc_final: 0.7876 (mt0) REVERT: B 932 VAL cc_start: 0.8278 (OUTLIER) cc_final: 0.7956 (m) REVERT: B 953 MET cc_start: 0.8605 (tpt) cc_final: 0.8281 (tpp) REVERT: B 1004 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8138 (mt) REVERT: B 1057 TYR cc_start: 0.8232 (m-80) cc_final: 0.7906 (m-80) REVERT: B 1077 ASP cc_start: 0.8130 (t0) cc_final: 0.7814 (t0) REVERT: B 1092 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8056 (mm-30) outliers start: 53 outliers final: 39 residues processed: 305 average time/residue: 0.3534 time to fit residues: 145.8782 Evaluate side-chains 311 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 262 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 464 GLU Chi-restraints excluded: chain A residue 523 PHE Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 641 CYS Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 885 GLN Chi-restraints excluded: chain A residue 926 ILE Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 628 ILE Chi-restraints excluded: chain B residue 634 SER Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 649 LYS Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 775 LYS Chi-restraints excluded: chain B residue 803 CYS Chi-restraints excluded: chain B residue 817 HIS Chi-restraints excluded: chain B residue 819 HIS Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 899 MET Chi-restraints excluded: chain B residue 932 VAL Chi-restraints excluded: chain B residue 939 MET Chi-restraints excluded: chain B residue 956 LEU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1023 HIS Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain B residue 1070 LEU Chi-restraints excluded: chain B residue 1072 VAL Chi-restraints excluded: chain B residue 1100 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 31 optimal weight: 9.9990 chunk 93 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 42 optimal weight: 0.1980 chunk 104 optimal weight: 0.6980 chunk 12 optimal weight: 0.0870 chunk 18 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 5 optimal weight: 0.0570 overall best weight: 0.3476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN B1010 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.179608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.149961 restraints weight = 16291.935| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 2.58 r_work: 0.3703 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3689 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3689 r_free = 0.3689 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3688 r_free = 0.3688 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3688 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.218 10460 Z= 0.349 Angle : 0.966 59.156 14122 Z= 0.542 Chirality : 0.048 0.617 1617 Planarity : 0.004 0.057 1796 Dihedral : 7.500 88.598 1449 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 21.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 4.50 % Allowed : 27.80 % Favored : 67.70 % Cbeta Deviations : 0.08 % 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 (0.24), residues: 1270 helix: 0.82 (0.19), residues: 698 sheet: -2.32 (0.39), residues: 150 loop : -1.67 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 764 HIS 0.008 0.001 HIS B 614 PHE 0.033 0.002 PHE B 784 TYR 0.041 0.002 TYR B 846 ARG 0.015 0.000 ARG B 734 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3054.41 seconds wall clock time: 56 minutes 23.45 seconds (3383.45 seconds total)