Starting phenix.real_space_refine on Thu Mar 13 04:48:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rz9_19607/03_2025/8rz9_19607.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rz9_19607/03_2025/8rz9_19607.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rz9_19607/03_2025/8rz9_19607.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rz9_19607/03_2025/8rz9_19607.map" model { file = "/net/cci-nas-00/data/ceres_data/8rz9_19607/03_2025/8rz9_19607.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rz9_19607/03_2025/8rz9_19607.cif" } resolution = 3.02 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= 0.020 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 44 5.16 5 C 5433 2.51 5 N 1470 2.21 5 O 1616 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8571 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4232 Classifications: {'peptide': 534} Link IDs: {'PTRANS': 16, 'TRANS': 517} Chain breaks: 4 Chain: "B" Number of atoms: 4275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4275 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 15, 'TRANS': 517} Chain breaks: 3 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 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, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N THR A 320 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 THR A 320 " occ=0.00 residue: pdb=" N GLY A 322 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY A 322 " occ=0.00 residue: pdb=" N SER A 323 " occ=0.00 ... (4 atoms not shown) pdb=" OG SER A 323 " occ=0.00 Time building chain proxies: 5.92, per 1000 atoms: 0.69 Number of scatterers: 8571 At special positions: 0 Unit cell: (74.9644, 106.047, 146.272, 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 44 16.00 P 6 15.00 Mg 2 11.99 O 1616 8.00 N 1470 7.00 C 5433 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.71 Conformation dependent library (CDL) restraints added in 1.1 seconds 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2028 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 6 sheets defined 60.4% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 303 through 311 Processing helix chain 'A' and resid 325 through 331 Processing helix chain 'A' and resid 335 through 348 Processing helix chain 'A' and resid 352 through 369 removed outlier: 3.590A pdb=" N ILE A 356 " --> pdb=" O ASP A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 378 removed outlier: 3.611A pdb=" N ARG A 373 " --> pdb=" O ASP A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 396 Processing helix chain 'A' and resid 400 through 424 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: 4.808A pdb=" N LYS A 449 " --> pdb=" O SER A 445 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N PHE A 450 " --> pdb=" O ASP A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 503 Processing helix chain 'A' and resid 553 through 586 removed outlier: 3.772A pdb=" N GLU A 569 " --> pdb=" O LYS A 565 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N GLU A 580 " --> pdb=" O ALA A 576 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ASN A 583 " --> pdb=" O LYS A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 615 removed outlier: 3.654A pdb=" N ALA A 615 " --> pdb=" O VAL A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 692 removed outlier: 3.746A pdb=" N GLY A 692 " --> pdb=" O MET A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 739 removed outlier: 3.798A pdb=" N THR A 732 " --> pdb=" O GLU A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 773 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 Processing helix chain 'A' and resid 826 through 834 removed outlier: 3.512A 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 852 through 855 removed outlier: 3.774A pdb=" N GLN A 855 " --> pdb=" O GLU A 852 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 852 through 855' Processing helix chain 'B' and resid 538 through 545 Processing helix chain 'B' and resid 559 through 565 removed outlier: 3.565A pdb=" N VAL B 563 " --> pdb=" O SER B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 582 Processing helix chain 'B' and resid 586 through 602 removed outlier: 3.941A pdb=" N ILE B 590 " --> pdb=" O LYS B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 616 Processing helix chain 'B' and resid 620 through 630 removed outlier: 3.686A pdb=" N GLY B 624 " --> pdb=" O ASP B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 655 removed outlier: 3.651A pdb=" N VAL B 642 " --> pdb=" O PHE B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 660 Processing helix chain 'B' and resid 665 through 679 Proline residue: B 676 - end of helix Processing helix chain 'B' and resid 681 through 689 removed outlier: 4.058A pdb=" N TYR B 685 " --> pdb=" O PRO B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 697 removed outlier: 3.802A pdb=" N ALA B 694 " --> pdb=" O ASN B 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 708 Processing helix chain 'B' and resid 709 through 737 removed outlier: 4.067A pdb=" N ARG B 715 " --> pdb=" O LEU B 711 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLN B 731 " --> pdb=" O ARG B 727 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLU B 732 " --> pdb=" O MET B 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 782 through 816 Processing helix chain 'B' and resid 817 through 844 removed outlier: 3.857A pdb=" N VAL B 825 " --> pdb=" O LEU B 821 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLY B 844 " --> pdb=" O VAL B 840 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 872 Processing helix chain 'B' and resid 897 through 900 Processing helix chain 'B' and resid 901 through 919 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: 4.126A pdb=" N CYS B1015 " --> pdb=" O TYR B1011 " (cutoff:3.500A) removed outlier: 3.926A 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 1016 through 1021 removed outlier: 4.271A pdb=" N ASN B1020 " --> pdb=" O GLU B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1068 through 1076 Processing helix chain 'B' and resid 1079 through 1103 Processing sheet with id=AA1, first strand: chain 'A' and resid 512 through 513 Processing sheet with id=AA2, first strand: chain 'A' and resid 653 through 656 removed outlier: 7.013A pdb=" N VAL A 655 " --> pdb=" O LYS A 635 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N LYS A 635 " --> pdb=" O VAL A 655 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 708 through 711 removed outlier: 6.482A pdb=" N LEU A 709 " --> pdb=" O ILE A 746 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N HIS A 665 " --> pdb=" O PHE A 780 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N PHE A 664 " --> pdb=" O ASN A 798 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N LEU A 800 " --> pdb=" O PHE A 664 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ILE A 666 " --> pdb=" O LEU A 800 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N VAL A 802 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N THR A 668 " --> pdb=" O VAL A 802 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N ALA A 804 " --> pdb=" O THR A 668 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ASN A 799 " --> pdb=" O LYS A 818 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LYS A 818 " --> pdb=" O ASN A 799 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N HIS A 801 " --> pdb=" O GLN A 816 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N GLN A 816 " --> pdb=" O HIS A 801 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N THR A 803 " --> pdb=" O LEU A 814 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 769 through 772 removed outlier: 6.966A pdb=" N ARG B 779 " --> pdb=" O VAL B 771 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 880 through 885 removed outlier: 4.978A pdb=" N ASN B 880 " --> pdb=" O ASN B 861 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASN B 861 " --> pdb=" O ASN B 880 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 935 through 938 removed outlier: 6.050A pdb=" N PHE B 936 " --> pdb=" O ILE B 973 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N ASP B 975 " --> pdb=" O PHE B 936 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ARG B 938 " --> pdb=" O ASP B 975 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL B 972 " --> pdb=" O LEU B1006 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N VAL B1008 " --> pdb=" O VAL B 972 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU B 974 " --> pdb=" O VAL B1008 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N GLN B1058 " --> pdb=" O GLY B1031 " (cutoff:3.500A) removed outlier: 8.787A pdb=" N LEU B1033 " --> pdb=" O LEU B1056 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N LEU B1056 " --> pdb=" O LEU B1033 " (cutoff:3.500A) 477 hydrogen bonds defined for protein. 1404 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.50 Time building geometry restraints manager: 3.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.34: 2580 1.34 - 1.49: 2293 1.49 - 1.63: 3773 1.63 - 1.78: 2 1.78 - 1.93: 68 Bond restraints: 8716 Sorted by residual: bond pdb=" CD ARG A 382 " pdb=" NE ARG A 382 " ideal model delta sigma weight residual 1.458 1.602 -0.144 1.40e-02 5.10e+03 1.05e+02 bond pdb=" C ASP A 319 " pdb=" N THR A 320 " ideal model delta sigma weight residual 1.331 1.194 0.137 1.41e-02 5.03e+03 9.44e+01 bond pdb=" CA LYS B1102 " pdb=" CB LYS B1102 " ideal model delta sigma weight residual 1.528 1.387 0.142 1.56e-02 4.11e+03 8.25e+01 bond pdb=" CA SER B1090 " pdb=" CB SER B1090 " ideal model delta sigma weight residual 1.529 1.401 0.128 1.55e-02 4.16e+03 6.85e+01 bond pdb=" CA ASP B 705 " pdb=" CB ASP B 705 " ideal model delta sigma weight residual 1.523 1.425 0.099 1.27e-02 6.20e+03 6.03e+01 ... (remaining 8711 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 11077 2.32 - 4.64: 625 4.64 - 6.96: 58 6.96 - 9.27: 9 9.27 - 11.59: 4 Bond angle restraints: 11773 Sorted by residual: angle pdb=" N ILE B 675 " pdb=" CA ILE B 675 " pdb=" CB ILE B 675 " ideal model delta sigma weight residual 110.45 115.37 -4.92 7.80e-01 1.64e+00 3.97e+01 angle pdb=" CB GLU A 647 " pdb=" CG GLU A 647 " pdb=" CD GLU A 647 " ideal model delta sigma weight residual 112.60 122.37 -9.77 1.70e+00 3.46e-01 3.30e+01 angle pdb=" OD1 ASN B1071 " pdb=" CG ASN B1071 " pdb=" ND2 ASN B1071 " ideal model delta sigma weight residual 122.60 116.86 5.74 1.00e+00 1.00e+00 3.29e+01 angle pdb=" N LYS B 947 " pdb=" CA LYS B 947 " pdb=" CB LYS B 947 " ideal model delta sigma weight residual 110.73 119.58 -8.85 1.55e+00 4.16e-01 3.26e+01 angle pdb=" CA ASP A 646 " pdb=" CB ASP A 646 " pdb=" CG ASP A 646 " ideal model delta sigma weight residual 112.60 107.71 4.89 1.00e+00 1.00e+00 2.39e+01 ... (remaining 11768 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 4549 17.78 - 35.56: 556 35.56 - 53.34: 171 53.34 - 71.12: 36 71.12 - 88.90: 9 Dihedral angle restraints: 5321 sinusoidal: 2203 harmonic: 3118 Sorted by residual: dihedral pdb=" N ASN B 788 " pdb=" C ASN B 788 " pdb=" CA ASN B 788 " pdb=" CB ASN B 788 " ideal model delta harmonic sigma weight residual 122.80 135.09 -12.29 0 2.50e+00 1.60e-01 2.42e+01 dihedral pdb=" C ASN B 788 " pdb=" N ASN B 788 " pdb=" CA ASN B 788 " pdb=" CB ASN B 788 " ideal model delta harmonic sigma weight residual -122.60 -134.11 11.51 0 2.50e+00 1.60e-01 2.12e+01 dihedral pdb=" C ASP B1000 " pdb=" N ASP B1000 " pdb=" CA ASP B1000 " pdb=" CB ASP B1000 " ideal model delta harmonic sigma weight residual -122.60 -133.87 11.27 0 2.50e+00 1.60e-01 2.03e+01 ... (remaining 5318 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 1043 0.105 - 0.209: 276 0.209 - 0.314: 27 0.314 - 0.418: 4 0.418 - 0.523: 7 Chirality restraints: 1357 Sorted by residual: chirality pdb=" CA ASN B 788 " pdb=" N ASN B 788 " pdb=" C ASN B 788 " pdb=" CB ASN B 788 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.83e+00 chirality pdb=" CA LYS B1102 " pdb=" N LYS B1102 " pdb=" C LYS B1102 " pdb=" CB LYS B1102 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.91e+00 chirality pdb=" CA SER B1090 " pdb=" N SER B1090 " pdb=" C SER B1090 " pdb=" CB SER B1090 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.47e+00 ... (remaining 1354 not shown) Planarity restraints: 1489 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 382 " 0.321 9.50e-02 1.11e+02 1.44e-01 1.28e+01 pdb=" NE ARG A 382 " -0.020 2.00e-02 2.50e+03 pdb=" CZ ARG A 382 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 382 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 382 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 308 " 0.202 9.50e-02 1.11e+02 9.36e-02 1.25e+01 pdb=" NE ARG A 308 " -0.028 2.00e-02 2.50e+03 pdb=" CZ ARG A 308 " 0.045 2.00e-02 2.50e+03 pdb=" NH1 ARG A 308 " -0.017 2.00e-02 2.50e+03 pdb=" NH2 ARG A 308 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 323 " 0.017 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" C SER A 323 " -0.060 2.00e-02 2.50e+03 pdb=" O SER A 323 " 0.021 2.00e-02 2.50e+03 pdb=" N GLN A 324 " 0.022 2.00e-02 2.50e+03 ... (remaining 1486 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.33: 25 2.33 - 2.97: 4282 2.97 - 3.61: 13759 3.61 - 4.26: 20315 4.26 - 4.90: 33904 Nonbonded interactions: 72285 Sorted by model distance: nonbonded pdb=" O ASN B 898 " pdb=" O3B AGS B2001 " model vdw 1.685 3.040 nonbonded pdb=" OG SER A 676 " pdb="MG MG A2000 " model vdw 1.752 2.170 nonbonded pdb=" ND2 ASN A 311 " pdb=" OH TYR B 946 " model vdw 1.930 3.120 nonbonded pdb=" OD2 ASP A 369 " pdb=" ND1 HIS A 424 " model vdw 2.059 3.120 nonbonded pdb=" O MET B 728 " pdb=" OE1 GLU B 732 " model vdw 2.082 3.040 ... (remaining 72280 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=0.00 max=1.00 mean=0.90 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: 2.020 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: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.080 Process input model: 24.030 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 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 : 0.010 0.144 8716 Z= 0.671 Angle : 1.261 11.594 11773 Z= 0.830 Chirality : 0.095 0.523 1357 Planarity : 0.007 0.144 1489 Dihedral : 17.546 88.897 3293 Min Nonbonded Distance : 1.685 Molprobity Statistics. All-atom Clashscore : 25.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 3.61 % Allowed : 23.25 % Favored : 73.14 % Cbeta Deviations : 0.39 % 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: -1.70 (0.24), residues: 1049 helix: -0.15 (0.20), residues: 597 sheet: -2.23 (0.47), residues: 99 loop : -2.39 (0.30), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.004 TRP B 562 HIS 0.016 0.002 HIS B 729 PHE 0.019 0.004 PHE B 936 TYR 0.029 0.004 TYR A 570 ARG 0.050 0.002 ARG B 573 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 218 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 MET cc_start: 0.7929 (ttm) cc_final: 0.7458 (ttm) REVERT: A 301 LYS cc_start: 0.7879 (OUTLIER) cc_final: 0.7567 (mppt) REVERT: A 384 PHE cc_start: 0.8395 (OUTLIER) cc_final: 0.7947 (m-80) REVERT: A 691 ILE cc_start: 0.8075 (mm) cc_final: 0.7740 (mm) REVERT: B 553 ASP cc_start: 0.7911 (t0) cc_final: 0.7262 (t0) REVERT: B 555 LYS cc_start: 0.7855 (ptpp) cc_final: 0.7361 (mtmm) REVERT: B 589 GLU cc_start: 0.8798 (mp0) cc_final: 0.8428 (pm20) REVERT: B 688 ILE cc_start: 0.8071 (OUTLIER) cc_final: 0.7704 (mp) REVERT: B 702 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7365 (tt) outliers start: 34 outliers final: 14 residues processed: 239 average time/residue: 0.2508 time to fit residues: 78.6084 Evaluate side-chains 225 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 207 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 LYS Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 384 PHE Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain B residue 675 ILE Chi-restraints excluded: chain B residue 686 LEU Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 779 ARG Chi-restraints excluded: chain B residue 822 CYS Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 925 GLU Chi-restraints excluded: chain B residue 999 ARG Chi-restraints excluded: chain B residue 1033 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 27 optimal weight: 0.0670 chunk 54 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 83 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 chunk 96 optimal weight: 0.7980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 596 ASN ** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 684 HIS B 827 HIS B 944 ASN B1088 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.159644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.140976 restraints weight = 12481.385| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 2.04 r_work: 0.3883 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3739 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8716 Z= 0.250 Angle : 0.671 13.009 11773 Z= 0.349 Chirality : 0.045 0.213 1357 Planarity : 0.004 0.042 1489 Dihedral : 8.781 93.647 1219 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 5.52 % Allowed : 23.78 % Favored : 70.70 % 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: -0.75 (0.26), residues: 1049 helix: 0.66 (0.21), residues: 602 sheet: -2.28 (0.46), residues: 99 loop : -1.94 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP B 807 HIS 0.014 0.001 HIS B 729 PHE 0.011 0.001 PHE B 952 TYR 0.020 0.002 TYR A 769 ARG 0.006 0.001 ARG A 638 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 210 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 344 GLN cc_start: 0.7903 (tm-30) cc_final: 0.7664 (tm-30) REVERT: A 592 MET cc_start: 0.8329 (tmm) cc_final: 0.7999 (ptp) REVERT: A 629 GLN cc_start: 0.7536 (OUTLIER) cc_final: 0.6966 (mp10) REVERT: B 553 ASP cc_start: 0.7595 (t0) cc_final: 0.7165 (t0) REVERT: B 688 ILE cc_start: 0.7722 (OUTLIER) cc_final: 0.7329 (mp) REVERT: B 729 HIS cc_start: 0.7269 (t-170) cc_final: 0.6956 (t-170) outliers start: 52 outliers final: 29 residues processed: 241 average time/residue: 0.2377 time to fit residues: 75.8627 Evaluate side-chains 231 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 200 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 339 GLN Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 629 GLN Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 698 GLU Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 799 ASN Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain B residue 675 ILE Chi-restraints excluded: chain B residue 686 LEU Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 822 CYS Chi-restraints excluded: chain B residue 840 VAL Chi-restraints excluded: chain B residue 885 SER Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 1033 LEU Chi-restraints excluded: chain B residue 1066 ARG Chi-restraints excluded: chain B residue 1072 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 102 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 54 optimal weight: 0.8980 chunk 85 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 94 optimal weight: 0.7980 chunk 87 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 566 ASN A 613 ASN B 684 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.158397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.140159 restraints weight = 12620.906| |-----------------------------------------------------------------------------| r_work (start): 0.3961 rms_B_bonded: 2.04 r_work: 0.3863 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3719 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 8716 Z= 0.281 Angle : 0.650 12.569 11773 Z= 0.338 Chirality : 0.044 0.206 1357 Planarity : 0.005 0.057 1489 Dihedral : 7.161 57.752 1193 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 6.69 % Allowed : 23.46 % Favored : 69.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.26), residues: 1049 helix: 0.74 (0.21), residues: 601 sheet: -2.21 (0.46), residues: 97 loop : -1.82 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 807 HIS 0.005 0.001 HIS B 781 PHE 0.018 0.002 PHE B1007 TYR 0.021 0.002 TYR A 769 ARG 0.005 0.000 ARG A 638 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 206 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 GLN cc_start: 0.7831 (tm-30) cc_final: 0.7442 (tm-30) REVERT: A 369 ASP cc_start: 0.5975 (OUTLIER) cc_final: 0.5734 (m-30) REVERT: A 592 MET cc_start: 0.8344 (OUTLIER) cc_final: 0.8043 (ptp) REVERT: A 629 GLN cc_start: 0.7643 (OUTLIER) cc_final: 0.6979 (mp10) REVERT: A 778 CYS cc_start: 0.8155 (t) cc_final: 0.7925 (t) REVERT: A 819 LYS cc_start: 0.7979 (mmmt) cc_final: 0.7776 (mmtp) REVERT: B 553 ASP cc_start: 0.7574 (t0) cc_final: 0.7204 (t0) REVERT: B 688 ILE cc_start: 0.7633 (OUTLIER) cc_final: 0.7171 (mp) REVERT: B 729 HIS cc_start: 0.7200 (t-170) cc_final: 0.6813 (t-170) REVERT: B 839 LYS cc_start: 0.8305 (tppp) cc_final: 0.8037 (tttm) REVERT: B 889 GLU cc_start: 0.6610 (mt-10) cc_final: 0.6338 (mt-10) REVERT: B 917 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.8378 (mt0) REVERT: B 975 ASP cc_start: 0.7414 (t70) cc_final: 0.6801 (m-30) REVERT: B 1061 ARG cc_start: 0.7767 (ttm110) cc_final: 0.7482 (ttm-80) outliers start: 63 outliers final: 42 residues processed: 240 average time/residue: 0.2383 time to fit residues: 75.6070 Evaluate side-chains 247 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 200 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 339 GLN Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 404 CYS Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 629 GLN Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 698 GLU Chi-restraints excluded: chain A residue 752 ARG Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 799 ASN Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain B residue 675 ILE Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 753 MET Chi-restraints excluded: chain B residue 788 ASN Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 822 CYS Chi-restraints excluded: chain B residue 840 VAL Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 885 SER Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 913 THR Chi-restraints excluded: chain B residue 914 ILE Chi-restraints excluded: chain B residue 917 GLN Chi-restraints excluded: chain B residue 1033 LEU Chi-restraints excluded: chain B residue 1066 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 66 optimal weight: 0.0370 chunk 27 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 68 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 71 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.159697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.141339 restraints weight = 12567.922| |-----------------------------------------------------------------------------| r_work (start): 0.3979 rms_B_bonded: 2.05 r_work: 0.3882 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3737 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8716 Z= 0.224 Angle : 0.620 11.911 11773 Z= 0.320 Chirality : 0.043 0.200 1357 Planarity : 0.004 0.047 1489 Dihedral : 6.863 58.277 1191 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 5.52 % Allowed : 26.01 % Favored : 68.47 % 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: -0.49 (0.26), residues: 1049 helix: 0.80 (0.21), residues: 602 sheet: -2.10 (0.47), residues: 92 loop : -1.74 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 807 HIS 0.004 0.001 HIS A 639 PHE 0.013 0.001 PHE B 571 TYR 0.019 0.001 TYR A 769 ARG 0.004 0.000 ARG B 593 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 205 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 GLU cc_start: 0.8257 (tt0) cc_final: 0.7871 (pt0) REVERT: A 369 ASP cc_start: 0.6012 (OUTLIER) cc_final: 0.5769 (m-30) REVERT: A 562 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.6800 (mt-10) REVERT: A 592 MET cc_start: 0.8316 (OUTLIER) cc_final: 0.8026 (ptt) REVERT: A 629 GLN cc_start: 0.7665 (OUTLIER) cc_final: 0.6964 (mp10) REVERT: A 691 ILE cc_start: 0.7858 (mt) cc_final: 0.7565 (mt) REVERT: A 778 CYS cc_start: 0.8079 (t) cc_final: 0.7862 (t) REVERT: B 553 ASP cc_start: 0.7537 (t0) cc_final: 0.7105 (t0) REVERT: B 628 ILE cc_start: 0.8092 (mt) cc_final: 0.7771 (mt) REVERT: B 688 ILE cc_start: 0.7568 (OUTLIER) cc_final: 0.7084 (mp) REVERT: B 729 HIS cc_start: 0.7161 (t-170) cc_final: 0.6777 (t-170) REVERT: B 839 LYS cc_start: 0.8305 (tppp) cc_final: 0.8045 (tttm) REVERT: B 889 GLU cc_start: 0.6989 (mt-10) cc_final: 0.6627 (mt-10) REVERT: B 1084 LYS cc_start: 0.7983 (ttmm) cc_final: 0.7675 (mtpp) outliers start: 52 outliers final: 34 residues processed: 237 average time/residue: 0.2390 time to fit residues: 75.1211 Evaluate side-chains 239 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 200 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 404 CYS Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 562 GLU Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 629 GLN Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain A residue 799 ASN Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain B residue 675 ILE Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 753 MET Chi-restraints excluded: chain B residue 788 ASN Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 822 CYS Chi-restraints excluded: chain B residue 885 SER Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 1033 LEU Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1066 ARG Chi-restraints excluded: chain B residue 1072 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 85 optimal weight: 0.6980 chunk 104 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 88 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 8 optimal weight: 0.3980 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 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 ASN B 731 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.158701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.140232 restraints weight = 12514.594| |-----------------------------------------------------------------------------| r_work (start): 0.3964 rms_B_bonded: 2.06 r_work: 0.3868 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3722 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8716 Z= 0.269 Angle : 0.631 12.116 11773 Z= 0.327 Chirality : 0.044 0.226 1357 Planarity : 0.005 0.050 1489 Dihedral : 6.925 57.879 1191 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 5.94 % Allowed : 26.86 % Favored : 67.20 % 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: -0.49 (0.26), residues: 1049 helix: 0.80 (0.21), residues: 602 sheet: -2.04 (0.48), residues: 92 loop : -1.74 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 562 HIS 0.004 0.001 HIS B 984 PHE 0.022 0.001 PHE B1007 TYR 0.022 0.002 TYR A 769 ARG 0.004 0.000 ARG A 752 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 206 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 ASP cc_start: 0.5964 (OUTLIER) cc_final: 0.5726 (m-30) REVERT: A 584 ILE cc_start: 0.7305 (OUTLIER) cc_final: 0.7067 (tp) REVERT: A 592 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.8032 (ptt) REVERT: A 629 GLN cc_start: 0.7720 (OUTLIER) cc_final: 0.7009 (mp10) REVERT: A 691 ILE cc_start: 0.7902 (mt) cc_final: 0.7571 (mt) REVERT: A 778 CYS cc_start: 0.8102 (t) cc_final: 0.7867 (t) REVERT: B 555 LYS cc_start: 0.8050 (ptpp) cc_final: 0.7682 (ptpp) REVERT: B 628 ILE cc_start: 0.8128 (mt) cc_final: 0.7816 (mt) REVERT: B 688 ILE cc_start: 0.7542 (OUTLIER) cc_final: 0.7059 (mp) REVERT: B 729 HIS cc_start: 0.7512 (t-170) cc_final: 0.7103 (t-170) REVERT: B 839 LYS cc_start: 0.8325 (tppp) cc_final: 0.8068 (tttm) REVERT: B 917 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.8362 (mt0) REVERT: B 1084 LYS cc_start: 0.7909 (ttmm) cc_final: 0.7611 (mtpp) outliers start: 56 outliers final: 40 residues processed: 240 average time/residue: 0.2231 time to fit residues: 71.3050 Evaluate side-chains 245 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 199 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 404 CYS Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 629 GLN Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 698 GLU Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain A residue 799 ASN Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain B residue 675 ILE Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 731 GLN Chi-restraints excluded: chain B residue 753 MET Chi-restraints excluded: chain B residue 788 ASN Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 822 CYS Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 885 SER Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 913 THR Chi-restraints excluded: chain B residue 917 GLN Chi-restraints excluded: chain B residue 1033 LEU Chi-restraints excluded: chain B residue 1066 ARG Chi-restraints excluded: chain B residue 1072 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 83 optimal weight: 0.1980 chunk 79 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 22 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 84 optimal weight: 0.0770 chunk 70 optimal weight: 0.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 944 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.159445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.140971 restraints weight = 12473.351| |-----------------------------------------------------------------------------| r_work (start): 0.3976 rms_B_bonded: 2.06 r_work: 0.3881 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3735 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8716 Z= 0.231 Angle : 0.619 11.571 11773 Z= 0.319 Chirality : 0.043 0.223 1357 Planarity : 0.004 0.045 1489 Dihedral : 6.863 58.674 1191 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 5.73 % Allowed : 27.71 % Favored : 66.56 % 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: -0.40 (0.26), residues: 1049 helix: 0.87 (0.21), residues: 603 sheet: -1.92 (0.49), residues: 92 loop : -1.72 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 562 HIS 0.005 0.001 HIS B 781 PHE 0.011 0.001 PHE B 571 TYR 0.018 0.001 TYR A 769 ARG 0.003 0.000 ARG A 340 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 198 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 ASP cc_start: 0.6035 (OUTLIER) cc_final: 0.5817 (m-30) REVERT: A 562 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.6824 (mt-10) REVERT: A 584 ILE cc_start: 0.7263 (OUTLIER) cc_final: 0.7027 (tp) REVERT: A 592 MET cc_start: 0.8333 (OUTLIER) cc_final: 0.8040 (ptt) REVERT: A 629 GLN cc_start: 0.7702 (OUTLIER) cc_final: 0.6999 (mp10) REVERT: A 691 ILE cc_start: 0.7920 (mt) cc_final: 0.7577 (mt) REVERT: A 778 CYS cc_start: 0.8061 (t) cc_final: 0.7830 (t) REVERT: B 555 LYS cc_start: 0.8066 (ptpp) cc_final: 0.7689 (ptpp) REVERT: B 628 ILE cc_start: 0.8154 (mt) cc_final: 0.7852 (mt) REVERT: B 688 ILE cc_start: 0.7573 (OUTLIER) cc_final: 0.7089 (mp) REVERT: B 729 HIS cc_start: 0.7558 (t-170) cc_final: 0.7185 (t-170) REVERT: B 839 LYS cc_start: 0.8333 (tppp) cc_final: 0.8057 (tttm) REVERT: B 917 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.8372 (mt0) REVERT: B 1084 LYS cc_start: 0.7968 (ttmm) cc_final: 0.7661 (mtpp) outliers start: 54 outliers final: 39 residues processed: 231 average time/residue: 0.2441 time to fit residues: 74.3717 Evaluate side-chains 245 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 199 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 404 CYS Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 562 GLU Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 629 GLN Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain A residue 799 ASN Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain B residue 557 LYS Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain B residue 675 ILE Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 753 MET Chi-restraints excluded: chain B residue 788 ASN Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 822 CYS Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 885 SER Chi-restraints excluded: chain B residue 890 ARG Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 917 GLN Chi-restraints excluded: chain B residue 1033 LEU Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1066 ARG Chi-restraints excluded: chain B residue 1072 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 3 optimal weight: 0.2980 chunk 102 optimal weight: 0.1980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.158716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.140520 restraints weight = 12525.042| |-----------------------------------------------------------------------------| r_work (start): 0.3970 rms_B_bonded: 2.04 r_work: 0.3873 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3727 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8716 Z= 0.266 Angle : 0.632 10.222 11773 Z= 0.326 Chirality : 0.044 0.202 1357 Planarity : 0.005 0.048 1489 Dihedral : 6.923 58.559 1191 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 6.37 % Allowed : 27.18 % Favored : 66.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.26), residues: 1049 helix: 0.88 (0.21), residues: 602 sheet: -1.86 (0.49), residues: 92 loop : -1.74 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 579 HIS 0.004 0.001 HIS B 984 PHE 0.010 0.001 PHE B 571 TYR 0.021 0.002 TYR A 769 ARG 0.004 0.000 ARG A 340 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 201 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 344 GLN cc_start: 0.7848 (tm-30) cc_final: 0.7501 (tm-30) REVERT: A 369 ASP cc_start: 0.6000 (OUTLIER) cc_final: 0.5789 (m-30) REVERT: A 562 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.6747 (mt-10) REVERT: A 584 ILE cc_start: 0.7254 (OUTLIER) cc_final: 0.7020 (tp) REVERT: A 592 MET cc_start: 0.8326 (OUTLIER) cc_final: 0.8030 (ptt) REVERT: A 629 GLN cc_start: 0.7755 (OUTLIER) cc_final: 0.7036 (mp10) REVERT: A 778 CYS cc_start: 0.8094 (t) cc_final: 0.7866 (t) REVERT: B 533 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7612 (mm-30) REVERT: B 555 LYS cc_start: 0.7964 (ptpp) cc_final: 0.7571 (ptpp) REVERT: B 589 GLU cc_start: 0.8315 (pm20) cc_final: 0.7913 (pm20) REVERT: B 628 ILE cc_start: 0.8104 (OUTLIER) cc_final: 0.7822 (mt) REVERT: B 688 ILE cc_start: 0.7513 (OUTLIER) cc_final: 0.7037 (mp) REVERT: B 839 LYS cc_start: 0.8326 (tppp) cc_final: 0.8070 (tttm) REVERT: B 889 GLU cc_start: 0.7374 (mt-10) cc_final: 0.6918 (pt0) REVERT: B 894 ILE cc_start: 0.8406 (mt) cc_final: 0.8193 (mt) REVERT: B 917 GLN cc_start: 0.8657 (OUTLIER) cc_final: 0.8359 (mt0) REVERT: B 1084 LYS cc_start: 0.7972 (ttmm) cc_final: 0.7661 (mtpp) outliers start: 60 outliers final: 43 residues processed: 236 average time/residue: 0.2521 time to fit residues: 78.7986 Evaluate side-chains 243 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 192 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 404 CYS Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 562 GLU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 629 GLN Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 799 ASN Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 628 ILE Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain B residue 675 ILE Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 753 MET Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 822 CYS Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 885 SER Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 913 THR Chi-restraints excluded: chain B residue 917 GLN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1005 THR Chi-restraints excluded: chain B residue 1033 LEU Chi-restraints excluded: chain B residue 1066 ARG Chi-restraints excluded: chain B residue 1072 VAL Chi-restraints excluded: chain B residue 1081 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 101 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 41 optimal weight: 0.3980 chunk 91 optimal weight: 0.1980 chunk 5 optimal weight: 0.6980 chunk 1 optimal weight: 0.0770 chunk 58 optimal weight: 0.4980 chunk 19 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.3738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 549 GLN ** B 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.160525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.142071 restraints weight = 12647.732| |-----------------------------------------------------------------------------| r_work (start): 0.3996 rms_B_bonded: 2.09 r_work: 0.3898 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3753 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8716 Z= 0.204 Angle : 0.625 10.626 11773 Z= 0.321 Chirality : 0.044 0.260 1357 Planarity : 0.004 0.043 1489 Dihedral : 6.848 59.856 1191 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 6.05 % Allowed : 28.77 % Favored : 65.18 % 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: -0.31 (0.26), residues: 1049 helix: 0.98 (0.21), residues: 602 sheet: -1.98 (0.46), residues: 104 loop : -1.70 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 345 HIS 0.023 0.001 HIS B 729 PHE 0.024 0.001 PHE B1007 TYR 0.017 0.001 TYR B 629 ARG 0.005 0.000 ARG A 340 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 195 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 562 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.6772 (mt-10) REVERT: A 584 ILE cc_start: 0.7249 (OUTLIER) cc_final: 0.7013 (tp) REVERT: A 592 MET cc_start: 0.8326 (OUTLIER) cc_final: 0.8029 (ptt) REVERT: A 629 GLN cc_start: 0.7702 (OUTLIER) cc_final: 0.6995 (mp10) REVERT: A 778 CYS cc_start: 0.8083 (t) cc_final: 0.7868 (t) REVERT: B 533 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7515 (mm-30) REVERT: B 589 GLU cc_start: 0.8284 (pm20) cc_final: 0.7937 (pm20) REVERT: B 628 ILE cc_start: 0.8102 (OUTLIER) cc_final: 0.7835 (mt) REVERT: B 688 ILE cc_start: 0.7510 (OUTLIER) cc_final: 0.7060 (mp) REVERT: B 839 LYS cc_start: 0.8311 (tppp) cc_final: 0.8023 (tttm) REVERT: B 889 GLU cc_start: 0.7268 (mt-10) cc_final: 0.6902 (pt0) REVERT: B 894 ILE cc_start: 0.8382 (mt) cc_final: 0.8169 (mt) REVERT: B 917 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.8386 (mt0) REVERT: B 994 LEU cc_start: 0.6411 (tp) cc_final: 0.5516 (tp) REVERT: B 1084 LYS cc_start: 0.7968 (ttmm) cc_final: 0.7657 (mtpp) outliers start: 57 outliers final: 43 residues processed: 226 average time/residue: 0.2419 time to fit residues: 71.9840 Evaluate side-chains 238 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 188 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 404 CYS Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 562 GLU Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 629 GLN Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain A residue 799 ASN Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 628 ILE Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain B residue 675 ILE Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 753 MET Chi-restraints excluded: chain B residue 788 ASN Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 822 CYS Chi-restraints excluded: chain B residue 885 SER Chi-restraints excluded: chain B residue 890 ARG Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 913 THR Chi-restraints excluded: chain B residue 917 GLN Chi-restraints excluded: chain B residue 1005 THR Chi-restraints excluded: chain B residue 1033 LEU Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1066 ARG Chi-restraints excluded: chain B residue 1072 VAL Chi-restraints excluded: chain B residue 1081 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 74 optimal weight: 20.0000 chunk 87 optimal weight: 0.2980 chunk 55 optimal weight: 0.6980 chunk 22 optimal weight: 10.0000 chunk 62 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 101 optimal weight: 0.6980 chunk 88 optimal weight: 0.5980 chunk 70 optimal weight: 0.3980 chunk 12 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 ASN B 549 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.159953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.141620 restraints weight = 12579.550| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 2.06 r_work: 0.3891 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3747 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 8716 Z= 0.234 Angle : 0.639 11.041 11773 Z= 0.330 Chirality : 0.045 0.308 1357 Planarity : 0.004 0.045 1489 Dihedral : 6.837 59.551 1189 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 6.26 % Allowed : 27.81 % Favored : 65.92 % 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: -0.31 (0.26), residues: 1049 helix: 0.94 (0.21), residues: 600 sheet: -1.79 (0.48), residues: 106 loop : -1.67 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 807 HIS 0.024 0.001 HIS B 729 PHE 0.023 0.001 PHE B1007 TYR 0.018 0.001 TYR A 769 ARG 0.002 0.000 ARG B 979 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 194 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 344 GLN cc_start: 0.7758 (tm-30) cc_final: 0.7390 (tm-30) REVERT: A 562 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.6712 (mt-10) REVERT: A 584 ILE cc_start: 0.7230 (OUTLIER) cc_final: 0.6995 (tp) REVERT: A 592 MET cc_start: 0.8330 (OUTLIER) cc_final: 0.8036 (ptt) REVERT: A 629 GLN cc_start: 0.7727 (OUTLIER) cc_final: 0.7019 (mp10) REVERT: A 773 LYS cc_start: 0.7137 (ttpp) cc_final: 0.6743 (tttm) REVERT: A 778 CYS cc_start: 0.8027 (t) cc_final: 0.7813 (t) REVERT: B 533 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7536 (mm-30) REVERT: B 589 GLU cc_start: 0.8277 (pm20) cc_final: 0.8007 (pm20) REVERT: B 628 ILE cc_start: 0.8110 (OUTLIER) cc_final: 0.7847 (mt) REVERT: B 688 ILE cc_start: 0.7560 (OUTLIER) cc_final: 0.7112 (mp) REVERT: B 839 LYS cc_start: 0.8310 (tppp) cc_final: 0.8022 (tttm) REVERT: B 889 GLU cc_start: 0.7429 (mt-10) cc_final: 0.7118 (pt0) REVERT: B 894 ILE cc_start: 0.8375 (mt) cc_final: 0.8169 (mt) REVERT: B 917 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.8363 (mt0) REVERT: B 994 LEU cc_start: 0.6153 (tp) cc_final: 0.5395 (tp) REVERT: B 1084 LYS cc_start: 0.7979 (ttmm) cc_final: 0.7671 (mtpp) outliers start: 59 outliers final: 43 residues processed: 227 average time/residue: 0.2950 time to fit residues: 88.4247 Evaluate side-chains 241 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 191 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 404 CYS Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 562 GLU Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 629 GLN Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 698 GLU Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 628 ILE Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain B residue 675 ILE Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 753 MET Chi-restraints excluded: chain B residue 788 ASN Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 822 CYS Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 885 SER Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 913 THR Chi-restraints excluded: chain B residue 917 GLN Chi-restraints excluded: chain B residue 1005 THR Chi-restraints excluded: chain B residue 1033 LEU Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1066 ARG Chi-restraints excluded: chain B residue 1072 VAL Chi-restraints excluded: chain B residue 1081 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 59 optimal weight: 0.5980 chunk 2 optimal weight: 5.9990 chunk 20 optimal weight: 20.0000 chunk 76 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 11 optimal weight: 0.2980 chunk 52 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 ASN B 731 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.158423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.140185 restraints weight = 12547.080| |-----------------------------------------------------------------------------| r_work (start): 0.3966 rms_B_bonded: 2.06 r_work: 0.3869 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3723 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 8716 Z= 0.292 Angle : 0.683 12.314 11773 Z= 0.353 Chirality : 0.047 0.236 1357 Planarity : 0.005 0.047 1489 Dihedral : 7.020 59.250 1189 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 17.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 5.41 % Allowed : 28.77 % Favored : 65.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.45 (0.26), residues: 1049 helix: 0.78 (0.21), residues: 604 sheet: -1.78 (0.47), residues: 106 loop : -1.70 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 807 HIS 0.032 0.002 HIS B 729 PHE 0.024 0.002 PHE B1007 TYR 0.023 0.002 TYR A 769 ARG 0.004 0.000 ARG A 711 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 201 time to evaluate : 0.990 Fit side-chains revert: symmetry clash REVERT: A 344 GLN cc_start: 0.7756 (tm-30) cc_final: 0.7351 (tm-30) REVERT: A 464 GLU cc_start: 0.7674 (pm20) cc_final: 0.7411 (mp0) REVERT: A 562 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7448 (mp0) REVERT: A 584 ILE cc_start: 0.7252 (OUTLIER) cc_final: 0.7015 (tp) REVERT: A 592 MET cc_start: 0.8334 (OUTLIER) cc_final: 0.8057 (ptt) REVERT: A 629 GLN cc_start: 0.7786 (OUTLIER) cc_final: 0.7075 (mp10) REVERT: A 773 LYS cc_start: 0.7304 (ttpp) cc_final: 0.6738 (tttm) REVERT: A 778 CYS cc_start: 0.8034 (t) cc_final: 0.7822 (t) REVERT: B 628 ILE cc_start: 0.8170 (OUTLIER) cc_final: 0.7916 (mt) REVERT: B 688 ILE cc_start: 0.7603 (OUTLIER) cc_final: 0.7162 (mp) REVERT: B 839 LYS cc_start: 0.8314 (tppp) cc_final: 0.8003 (tttm) REVERT: B 894 ILE cc_start: 0.8379 (mt) cc_final: 0.8174 (mt) REVERT: B 917 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.8371 (mt0) REVERT: B 994 LEU cc_start: 0.6211 (tp) cc_final: 0.5439 (tp) REVERT: B 1084 LYS cc_start: 0.7994 (ttmm) cc_final: 0.7692 (mtpp) outliers start: 51 outliers final: 41 residues processed: 232 average time/residue: 0.2501 time to fit residues: 77.2799 Evaluate side-chains 247 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 199 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 404 CYS Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 562 GLU Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 629 GLN Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 698 GLU Chi-restraints excluded: chain A residue 768 GLU Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 628 ILE Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain B residue 675 ILE Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 731 GLN Chi-restraints excluded: chain B residue 753 MET Chi-restraints excluded: chain B residue 788 ASN Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 822 CYS Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 885 SER Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 913 THR Chi-restraints excluded: chain B residue 917 GLN Chi-restraints excluded: chain B residue 1005 THR Chi-restraints excluded: chain B residue 1033 LEU Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1066 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 26 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 chunk 95 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 66 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN ** B 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 731 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.158363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.140192 restraints weight = 12621.808| |-----------------------------------------------------------------------------| r_work (start): 0.3970 rms_B_bonded: 2.07 r_work: 0.3873 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3725 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 8716 Z= 0.300 Angle : 0.691 10.339 11773 Z= 0.358 Chirality : 0.047 0.333 1357 Planarity : 0.005 0.049 1489 Dihedral : 7.050 58.561 1189 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 5.20 % Allowed : 29.09 % Favored : 65.71 % 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: -0.47 (0.26), residues: 1049 helix: 0.75 (0.21), residues: 604 sheet: -1.64 (0.50), residues: 94 loop : -1.75 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 807 HIS 0.018 0.001 HIS B 729 PHE 0.024 0.002 PHE B1007 TYR 0.023 0.002 TYR A 769 ARG 0.006 0.000 ARG B 593 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5281.73 seconds wall clock time: 92 minutes 26.12 seconds (5546.12 seconds total)