Starting phenix.real_space_refine on Wed Sep 17 12:20:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rz9_19607/09_2025/8rz9_19607.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rz9_19607/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8rz9_19607/09_2025/8rz9_19607.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rz9_19607/09_2025/8rz9_19607.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8rz9_19607/09_2025/8rz9_19607.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rz9_19607/09_2025/8rz9_19607.map" } resolution = 3.02 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.39, per 1000 atoms: 0.28 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: 1.04 Conformation dependent library (CDL) restraints added in 367.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.29 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: 1.62 Time building geometry restraints manager: 1.31 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: 2.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.670 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.170 ------------------------------------------------------------------------------- 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 : 0.015 0.781 8718 Z= 1.263 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.70 (0.24), 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 ARG 0.050 0.002 ARG B 573 TYR 0.029 0.004 TYR A 570 PHE 0.019 0.004 PHE B 936 TRP 0.017 0.004 TRP B 562 HIS 0.016 0.002 HIS B 729 Details of bonding type rmsd covalent geometry : bond 0.01036 ( 8716) covalent geometry : angle 1.26065 (11773) hydrogen bonds : bond 0.15434 ( 477) hydrogen bonds : angle 7.01008 ( 1404) Misc. bond : bond 0.72766 ( 2) *********************** 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 : 0.340 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: 0.1206 time to fit residues: 37.9506 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 : 0.356 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 38 optimal weight: 0.2980 chunk 61 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4197 r_free = 0.4197 target = 0.159254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.140550 restraints weight = 12607.517| |-----------------------------------------------------------------------------| r_work (start): 0.3971 rms_B_bonded: 2.05 r_work: 0.3874 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3729 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8718 Z= 0.196 Angle : 0.684 13.378 11773 Z= 0.355 Chirality : 0.045 0.227 1357 Planarity : 0.004 0.043 1489 Dihedral : 8.753 92.960 1219 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 5.41 % Allowed : 23.89 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.79 (0.26), residues: 1049 helix: 0.61 (0.21), residues: 602 sheet: -2.20 (0.46), residues: 97 loop : -1.96 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 638 TYR 0.022 0.002 TYR A 769 PHE 0.010 0.002 PHE B 952 TRP 0.019 0.003 TRP B 807 HIS 0.013 0.001 HIS B 729 Details of bonding type rmsd covalent geometry : bond 0.00432 ( 8716) covalent geometry : angle 0.68385 (11773) hydrogen bonds : bond 0.05330 ( 477) hydrogen bonds : angle 5.34370 ( 1404) Misc. bond : bond 0.00300 ( 2) *********************** 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 264 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 213 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 344 GLN cc_start: 0.7881 (tm-30) cc_final: 0.7611 (tm-30) REVERT: A 592 MET cc_start: 0.8336 (tmm) cc_final: 0.8008 (ptp) REVERT: A 629 GLN cc_start: 0.7571 (OUTLIER) cc_final: 0.6962 (mp10) REVERT: B 553 ASP cc_start: 0.7616 (t0) cc_final: 0.7301 (t0) REVERT: B 688 ILE cc_start: 0.7715 (OUTLIER) cc_final: 0.7329 (mp) REVERT: B 729 HIS cc_start: 0.7290 (t-170) cc_final: 0.6966 (t-170) outliers start: 51 outliers final: 28 residues processed: 243 average time/residue: 0.1186 time to fit residues: 38.1261 Evaluate side-chains 232 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 202 time to evaluate : 0.326 ------------------------------------------------------------------------------- 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 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 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 640 LEU 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 83 optimal weight: 0.6980 chunk 94 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 20 optimal weight: 10.0000 chunk 63 optimal weight: 2.9990 chunk 75 optimal weight: 7.9990 chunk 66 optimal weight: 0.0670 chunk 58 optimal weight: 0.0370 overall best weight: 0.3996 ------------------------------------------------------------------------------- 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 = 0.4212 r_free = 0.4212 target = 0.160305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.142002 restraints weight = 12450.145| |-----------------------------------------------------------------------------| r_work (start): 0.3984 rms_B_bonded: 2.05 r_work: 0.3888 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3745 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8718 Z= 0.154 Angle : 0.621 12.716 11773 Z= 0.321 Chirality : 0.043 0.233 1357 Planarity : 0.004 0.051 1489 Dihedral : 7.040 58.000 1193 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 6.05 % Allowed : 23.78 % Favored : 70.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.26), residues: 1049 helix: 0.84 (0.22), residues: 600 sheet: -2.08 (0.48), residues: 90 loop : -1.76 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 638 TYR 0.015 0.001 TYR A 769 PHE 0.017 0.001 PHE B1007 TRP 0.009 0.002 TRP B 807 HIS 0.004 0.001 HIS B 729 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 8716) covalent geometry : angle 0.62053 (11773) hydrogen bonds : bond 0.04837 ( 477) hydrogen bonds : angle 5.02851 ( 1404) Misc. bond : bond 0.00215 ( 2) *********************** 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 261 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 204 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 369 ASP cc_start: 0.5992 (OUTLIER) cc_final: 0.5752 (m-30) REVERT: A 592 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.8037 (ptp) REVERT: A 629 GLN cc_start: 0.7594 (OUTLIER) cc_final: 0.6976 (mp10) REVERT: A 778 CYS cc_start: 0.8153 (t) cc_final: 0.7936 (t) REVERT: B 553 ASP cc_start: 0.7652 (t0) cc_final: 0.7200 (t0) REVERT: B 688 ILE cc_start: 0.7627 (OUTLIER) cc_final: 0.7159 (mp) REVERT: B 729 HIS cc_start: 0.7193 (t-170) cc_final: 0.6824 (t-90) REVERT: B 917 GLN cc_start: 0.8633 (OUTLIER) cc_final: 0.8366 (mt0) outliers start: 57 outliers final: 33 residues processed: 234 average time/residue: 0.1165 time to fit residues: 36.3939 Evaluate side-chains 238 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 200 time to evaluate : 0.387 ------------------------------------------------------------------------------- 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 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 796 THR 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 A residue 849 LEU Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 663 ILE 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 68 optimal weight: 0.9990 chunk 84 optimal weight: 0.5980 chunk 72 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 63 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 81 optimal weight: 0.6980 chunk 14 optimal weight: 0.0020 chunk 48 optimal weight: 1.9990 overall best weight: 0.5388 ------------------------------------------------------------------------------- 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 549 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.159549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.141096 restraints weight = 12706.797| |-----------------------------------------------------------------------------| r_work (start): 0.3976 rms_B_bonded: 2.08 r_work: 0.3877 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3732 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8718 Z= 0.167 Angle : 0.616 12.685 11773 Z= 0.317 Chirality : 0.043 0.215 1357 Planarity : 0.004 0.047 1489 Dihedral : 6.868 57.443 1191 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 5.94 % Allowed : 25.69 % Favored : 68.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.26), residues: 1049 helix: 0.83 (0.21), residues: 602 sheet: -2.03 (0.48), residues: 92 loop : -1.74 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 752 TYR 0.020 0.002 TYR A 769 PHE 0.012 0.001 PHE B 814 TRP 0.009 0.002 TRP B 807 HIS 0.009 0.001 HIS B 781 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 8716) covalent geometry : angle 0.61557 (11773) hydrogen bonds : bond 0.04657 ( 477) hydrogen bonds : angle 4.92086 ( 1404) Misc. bond : bond 0.00192 ( 2) *********************** 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 258 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 202 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 369 ASP cc_start: 0.6032 (OUTLIER) cc_final: 0.5788 (m-30) REVERT: A 584 ILE cc_start: 0.7315 (OUTLIER) cc_final: 0.7072 (tp) REVERT: A 592 MET cc_start: 0.8321 (OUTLIER) cc_final: 0.8031 (ptp) REVERT: A 629 GLN cc_start: 0.7663 (OUTLIER) cc_final: 0.6941 (mp10) REVERT: A 691 ILE cc_start: 0.7877 (mt) cc_final: 0.7588 (mt) REVERT: A 778 CYS cc_start: 0.8127 (t) cc_final: 0.7895 (t) REVERT: B 553 ASP cc_start: 0.7566 (t0) cc_final: 0.7126 (t0) REVERT: B 688 ILE cc_start: 0.7581 (OUTLIER) cc_final: 0.7093 (mp) REVERT: B 729 HIS cc_start: 0.7237 (t-170) cc_final: 0.6832 (t-170) REVERT: B 839 LYS cc_start: 0.8282 (tppp) cc_final: 0.8023 (tttm) REVERT: B 946 TYR cc_start: 0.7416 (m-80) cc_final: 0.7208 (m-80) REVERT: B 1084 LYS cc_start: 0.7918 (ttmm) cc_final: 0.7616 (mtpp) outliers start: 56 outliers final: 38 residues processed: 235 average time/residue: 0.1143 time to fit residues: 35.9478 Evaluate side-chains 242 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 199 time to evaluate : 0.325 ------------------------------------------------------------------------------- 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 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 796 THR 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 552 THR Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 611 ILE 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 850 THR Chi-restraints excluded: chain B residue 885 SER Chi-restraints excluded: chain B residue 889 GLU 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 8 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 chunk 57 optimal weight: 0.2980 chunk 33 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 64 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 82 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.159572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.141186 restraints weight = 12616.310| |-----------------------------------------------------------------------------| r_work (start): 0.3977 rms_B_bonded: 2.06 r_work: 0.3880 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3734 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8718 Z= 0.170 Angle : 0.612 11.521 11773 Z= 0.318 Chirality : 0.044 0.218 1357 Planarity : 0.004 0.045 1489 Dihedral : 6.869 57.656 1191 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 6.16 % Allowed : 25.80 % Favored : 68.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.26), residues: 1049 helix: 0.84 (0.21), residues: 602 sheet: -1.97 (0.48), residues: 92 loop : -1.75 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 711 TYR 0.020 0.001 TYR A 769 PHE 0.022 0.001 PHE B1007 TRP 0.007 0.001 TRP A 345 HIS 0.003 0.001 HIS B 984 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 8716) covalent geometry : angle 0.61184 (11773) hydrogen bonds : bond 0.04564 ( 477) hydrogen bonds : angle 4.86745 ( 1404) Misc. bond : bond 0.00204 ( 2) *********************** 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 258 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 200 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 GLN cc_start: 0.7865 (tm-30) cc_final: 0.7651 (tm-30) REVERT: A 369 ASP cc_start: 0.6049 (OUTLIER) cc_final: 0.5825 (m-30) REVERT: A 584 ILE cc_start: 0.7290 (OUTLIER) cc_final: 0.7053 (tp) REVERT: A 592 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.8041 (ptt) REVERT: A 629 GLN cc_start: 0.7685 (OUTLIER) cc_final: 0.6978 (mp10) REVERT: A 691 ILE cc_start: 0.7888 (mt) cc_final: 0.7541 (mt) REVERT: A 778 CYS cc_start: 0.8109 (t) cc_final: 0.7883 (t) REVERT: B 553 ASP cc_start: 0.7519 (t0) cc_final: 0.7109 (t0) REVERT: B 688 ILE cc_start: 0.7558 (OUTLIER) cc_final: 0.7065 (mp) REVERT: B 729 HIS cc_start: 0.7426 (t-170) cc_final: 0.7020 (t-170) REVERT: B 839 LYS cc_start: 0.8312 (tppp) cc_final: 0.8028 (tttm) REVERT: B 917 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.8377 (mt0) REVERT: B 1084 LYS cc_start: 0.7922 (ttmm) cc_final: 0.7622 (mtpp) outliers start: 58 outliers final: 41 residues processed: 236 average time/residue: 0.1107 time to fit residues: 35.1690 Evaluate side-chains 243 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 196 time to evaluate : 0.353 ------------------------------------------------------------------------------- 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 658 GLU 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 796 THR 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 A residue 849 LEU Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 611 ILE 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 785 ILE Chi-restraints excluded: chain B residue 788 ASN Chi-restraints excluded: chain B residue 808 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 1059 ILE 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 9 optimal weight: 0.4980 chunk 15 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 69 optimal weight: 0.0060 chunk 82 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 83 optimal weight: 0.5980 chunk 54 optimal weight: 0.9980 chunk 74 optimal weight: 20.0000 chunk 53 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 overall best weight: 0.5596 ------------------------------------------------------------------------------- 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 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 731 GLN B 944 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.159536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.141073 restraints weight = 12624.861| |-----------------------------------------------------------------------------| r_work (start): 0.3977 rms_B_bonded: 2.08 r_work: 0.3881 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3735 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8718 Z= 0.166 Angle : 0.609 10.760 11773 Z= 0.315 Chirality : 0.044 0.190 1357 Planarity : 0.004 0.045 1489 Dihedral : 6.890 57.717 1191 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 6.37 % Allowed : 26.65 % Favored : 66.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.26), residues: 1049 helix: 0.92 (0.21), residues: 601 sheet: -1.88 (0.49), residues: 92 loop : -1.77 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 340 TYR 0.019 0.001 TYR A 769 PHE 0.011 0.001 PHE B 571 TRP 0.006 0.001 TRP B 562 HIS 0.004 0.001 HIS B 781 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 8716) covalent geometry : angle 0.60933 (11773) hydrogen bonds : bond 0.04510 ( 477) hydrogen bonds : angle 4.81626 ( 1404) Misc. bond : bond 0.00256 ( 2) *********************** 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 255 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 195 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 301 LYS cc_start: 0.7924 (OUTLIER) cc_final: 0.7713 (mppt) REVERT: A 344 GLN cc_start: 0.7866 (tm-30) cc_final: 0.7512 (tm-30) REVERT: A 369 ASP cc_start: 0.6046 (OUTLIER) cc_final: 0.5832 (m-30) REVERT: A 562 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.6800 (mp0) REVERT: A 584 ILE cc_start: 0.7263 (OUTLIER) cc_final: 0.7025 (tp) REVERT: A 592 MET cc_start: 0.8333 (OUTLIER) cc_final: 0.8042 (ptt) REVERT: A 629 GLN cc_start: 0.7693 (OUTLIER) cc_final: 0.6982 (mp10) REVERT: A 691 ILE cc_start: 0.7949 (mt) cc_final: 0.7578 (mt) REVERT: A 719 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.8019 (mp) REVERT: A 778 CYS cc_start: 0.8119 (t) cc_final: 0.7890 (t) REVERT: B 688 ILE cc_start: 0.7546 (OUTLIER) cc_final: 0.7067 (mp) REVERT: B 729 HIS cc_start: 0.7527 (t-170) cc_final: 0.7148 (t-170) REVERT: B 839 LYS cc_start: 0.8316 (tppp) cc_final: 0.8026 (tttm) REVERT: B 917 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.8362 (mt0) REVERT: B 1084 LYS cc_start: 0.7976 (ttmm) cc_final: 0.7670 (mtpp) outliers start: 60 outliers final: 41 residues processed: 233 average time/residue: 0.1180 time to fit residues: 36.2533 Evaluate side-chains 242 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 192 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 LYS 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 584 ILE 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 687 LEU Chi-restraints excluded: chain A residue 698 GLU Chi-restraints excluded: chain A residue 719 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 561 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 611 ILE 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 46 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 96 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.158607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.140212 restraints weight = 12701.009| |-----------------------------------------------------------------------------| r_work (start): 0.3966 rms_B_bonded: 2.09 r_work: 0.3869 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3721 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8718 Z= 0.195 Angle : 0.640 10.790 11773 Z= 0.329 Chirality : 0.045 0.200 1357 Planarity : 0.004 0.046 1489 Dihedral : 6.973 57.356 1191 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 6.37 % Allowed : 27.49 % Favored : 66.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.26), residues: 1049 helix: 0.83 (0.21), residues: 601 sheet: -1.73 (0.49), residues: 94 loop : -1.77 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 340 TYR 0.025 0.002 TYR B 946 PHE 0.009 0.001 PHE B 571 TRP 0.010 0.002 TRP B 807 HIS 0.004 0.001 HIS B 984 Details of bonding type rmsd covalent geometry : bond 0.00436 ( 8716) covalent geometry : angle 0.64022 (11773) hydrogen bonds : bond 0.04537 ( 477) hydrogen bonds : angle 4.85584 ( 1404) Misc. bond : bond 0.00267 ( 2) *********************** 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 258 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 198 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 301 LYS cc_start: 0.8029 (OUTLIER) cc_final: 0.7785 (mppt) REVERT: A 344 GLN cc_start: 0.7869 (tm-30) cc_final: 0.7505 (tm-30) REVERT: A 369 ASP cc_start: 0.6002 (OUTLIER) cc_final: 0.5789 (m-30) REVERT: A 562 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.6843 (mp0) REVERT: A 584 ILE cc_start: 0.7257 (OUTLIER) cc_final: 0.7022 (tp) REVERT: A 592 MET cc_start: 0.8347 (OUTLIER) cc_final: 0.8054 (ptt) REVERT: A 629 GLN cc_start: 0.7744 (OUTLIER) cc_final: 0.7028 (mp10) REVERT: A 729 MET cc_start: 0.7755 (mmp) cc_final: 0.7442 (mmp) REVERT: A 778 CYS cc_start: 0.8159 (t) cc_final: 0.7941 (t) REVERT: B 533 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7579 (mm-30) REVERT: B 589 GLU cc_start: 0.8317 (pm20) cc_final: 0.7970 (pm20) REVERT: B 688 ILE cc_start: 0.7524 (OUTLIER) cc_final: 0.7070 (mp) REVERT: B 729 HIS cc_start: 0.7569 (t-170) cc_final: 0.7180 (t-170) REVERT: B 839 LYS cc_start: 0.8333 (tppp) cc_final: 0.8044 (tttm) REVERT: B 917 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.8385 (mt0) REVERT: B 1084 LYS cc_start: 0.7985 (ttmm) cc_final: 0.7681 (mtpp) outliers start: 60 outliers final: 44 residues processed: 235 average time/residue: 0.1143 time to fit residues: 35.8515 Evaluate side-chains 248 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 196 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 LYS 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 698 GLU Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 736 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 A residue 849 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 611 ILE 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 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 913 THR Chi-restraints excluded: chain B residue 914 ILE 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 74 optimal weight: 20.0000 chunk 1 optimal weight: 0.6980 chunk 71 optimal weight: 4.9990 chunk 88 optimal weight: 0.5980 chunk 77 optimal weight: 0.9980 chunk 89 optimal weight: 0.4980 chunk 45 optimal weight: 0.3980 chunk 78 optimal weight: 0.6980 chunk 86 optimal weight: 0.3980 chunk 81 optimal weight: 0.9980 chunk 76 optimal weight: 6.9990 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.159699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.141533 restraints weight = 12370.480| |-----------------------------------------------------------------------------| r_work (start): 0.3982 rms_B_bonded: 2.04 r_work: 0.3887 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3741 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8718 Z= 0.163 Angle : 0.628 10.846 11773 Z= 0.323 Chirality : 0.044 0.230 1357 Planarity : 0.004 0.045 1489 Dihedral : 6.955 58.596 1191 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 6.37 % Allowed : 27.49 % Favored : 66.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.26), residues: 1049 helix: 0.93 (0.21), residues: 599 sheet: -1.71 (0.50), residues: 94 loop : -1.69 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 340 TYR 0.022 0.001 TYR B 629 PHE 0.010 0.001 PHE B 571 TRP 0.010 0.002 TRP B 807 HIS 0.003 0.001 HIS B 984 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 8716) covalent geometry : angle 0.62841 (11773) hydrogen bonds : bond 0.04396 ( 477) hydrogen bonds : angle 4.81840 ( 1404) Misc. bond : bond 0.00204 ( 2) *********************** 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 254 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 194 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 301 LYS cc_start: 0.7956 (OUTLIER) cc_final: 0.7747 (mppt) REVERT: A 562 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.6869 (mp0) REVERT: A 584 ILE cc_start: 0.7235 (OUTLIER) cc_final: 0.6999 (tp) REVERT: A 592 MET cc_start: 0.8334 (OUTLIER) cc_final: 0.8040 (ptt) REVERT: A 629 GLN cc_start: 0.7694 (OUTLIER) cc_final: 0.6996 (mp10) REVERT: A 778 CYS cc_start: 0.8067 (t) cc_final: 0.7867 (t) REVERT: B 533 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7468 (mm-30) REVERT: B 555 LYS cc_start: 0.8007 (ptpp) cc_final: 0.7634 (ptpp) REVERT: B 589 GLU cc_start: 0.8244 (pm20) cc_final: 0.7970 (pm20) REVERT: B 688 ILE cc_start: 0.7514 (OUTLIER) cc_final: 0.7062 (mp) REVERT: B 839 LYS cc_start: 0.8302 (tppp) cc_final: 0.8004 (tttm) REVERT: B 889 GLU cc_start: 0.7530 (pt0) cc_final: 0.6161 (mt-10) REVERT: B 890 ARG cc_start: 0.6727 (OUTLIER) cc_final: 0.6345 (ttm170) REVERT: B 917 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.8398 (mt0) REVERT: B 1084 LYS cc_start: 0.7974 (ttmm) cc_final: 0.7671 (mtpp) outliers start: 60 outliers final: 42 residues processed: 230 average time/residue: 0.1195 time to fit residues: 36.2250 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 : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 LYS 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 409 GLN Chi-restraints excluded: chain A residue 431 LEU 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 688 MET Chi-restraints excluded: chain A residue 736 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 542 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 641 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 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 1066 ARG 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 2 optimal weight: 5.9990 chunk 1 optimal weight: 0.0050 chunk 3 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 29 optimal weight: 0.0470 chunk 38 optimal weight: 0.9980 chunk 5 optimal weight: 0.0980 chunk 52 optimal weight: 0.9980 chunk 76 optimal weight: 7.9990 overall best weight: 0.3692 ------------------------------------------------------------------------------- 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 731 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.160376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.142104 restraints weight = 12485.487| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 2.07 r_work: 0.3893 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3747 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 8718 Z= 0.149 Angle : 0.624 10.652 11773 Z= 0.323 Chirality : 0.044 0.313 1357 Planarity : 0.004 0.044 1489 Dihedral : 6.845 59.531 1189 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 6.05 % Allowed : 27.49 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.26), residues: 1049 helix: 0.92 (0.21), residues: 599 sheet: -1.84 (0.47), residues: 106 loop : -1.64 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 340 TYR 0.019 0.001 TYR B 946 PHE 0.010 0.001 PHE B 571 TRP 0.011 0.001 TRP B 807 HIS 0.028 0.001 HIS B 729 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 8716) covalent geometry : angle 0.62407 (11773) hydrogen bonds : bond 0.04325 ( 477) hydrogen bonds : angle 4.83190 ( 1404) Misc. bond : bond 0.00248 ( 2) *********************** 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 250 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 193 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 ASP cc_start: 0.6842 (p0) cc_final: 0.6275 (p0) REVERT: A 562 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.6867 (mp0) REVERT: A 584 ILE cc_start: 0.7228 (OUTLIER) cc_final: 0.6998 (tp) REVERT: A 592 MET cc_start: 0.8342 (OUTLIER) cc_final: 0.8052 (ptt) REVERT: A 629 GLN cc_start: 0.7666 (OUTLIER) cc_final: 0.6977 (mp10) REVERT: A 778 CYS cc_start: 0.8053 (t) cc_final: 0.7852 (t) REVERT: B 555 LYS cc_start: 0.8013 (ptpp) cc_final: 0.7641 (ptpp) REVERT: B 688 ILE cc_start: 0.7530 (OUTLIER) cc_final: 0.7073 (mp) REVERT: B 702 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7619 (tt) REVERT: B 839 LYS cc_start: 0.8308 (tppp) cc_final: 0.8014 (tttm) REVERT: B 917 GLN cc_start: 0.8626 (OUTLIER) cc_final: 0.8366 (mt0) REVERT: B 1084 LYS cc_start: 0.7994 (ttmm) cc_final: 0.7698 (mtpp) outliers start: 57 outliers final: 45 residues processed: 227 average time/residue: 0.1233 time to fit residues: 36.7412 Evaluate side-chains 243 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 191 time to evaluate : 0.337 ------------------------------------------------------------------------------- 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 409 GLN Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 437 VAL 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 768 GLU 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 561 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 611 ILE 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 702 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 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 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 1081 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 41 optimal weight: 0.7980 chunk 9 optimal weight: 0.3980 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.3980 chunk 59 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 91 optimal weight: 0.4980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 731 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.159785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.141648 restraints weight = 12535.062| |-----------------------------------------------------------------------------| r_work (start): 0.3982 rms_B_bonded: 2.07 r_work: 0.3885 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3741 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 8718 Z= 0.171 Angle : 0.649 11.834 11773 Z= 0.337 Chirality : 0.046 0.342 1357 Planarity : 0.005 0.045 1489 Dihedral : 6.897 59.588 1189 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 5.41 % Allowed : 27.92 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.26), residues: 1049 helix: 0.90 (0.21), residues: 599 sheet: -1.82 (0.47), residues: 106 loop : -1.64 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 389 TYR 0.020 0.001 TYR B 946 PHE 0.009 0.001 PHE B 571 TRP 0.019 0.002 TRP A 345 HIS 0.031 0.001 HIS B 729 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 8716) covalent geometry : angle 0.64934 (11773) hydrogen bonds : bond 0.04418 ( 477) hydrogen bonds : angle 4.87809 ( 1404) Misc. bond : bond 0.00240 ( 2) ********************** 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 244 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 193 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 562 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.6806 (mp0) REVERT: A 584 ILE cc_start: 0.7230 (OUTLIER) cc_final: 0.7000 (tp) REVERT: A 592 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.8046 (ptt) REVERT: A 629 GLN cc_start: 0.7689 (OUTLIER) cc_final: 0.7018 (mp10) REVERT: A 778 CYS cc_start: 0.8076 (t) cc_final: 0.7869 (t) REVERT: B 555 LYS cc_start: 0.8044 (ptpp) cc_final: 0.7669 (ptpp) REVERT: B 688 ILE cc_start: 0.7538 (OUTLIER) cc_final: 0.7093 (mp) REVERT: B 839 LYS cc_start: 0.8298 (tppp) cc_final: 0.7986 (tttm) REVERT: B 894 ILE cc_start: 0.8395 (mt) cc_final: 0.8185 (mt) REVERT: B 917 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.8376 (mt0) REVERT: B 994 LEU cc_start: 0.6109 (tp) cc_final: 0.5354 (tp) REVERT: B 1084 LYS cc_start: 0.8007 (ttmm) cc_final: 0.7719 (mtpp) outliers start: 51 outliers final: 44 residues processed: 223 average time/residue: 0.1271 time to fit residues: 37.1066 Evaluate side-chains 242 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 192 time to evaluate : 0.376 ------------------------------------------------------------------------------- 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 409 GLN Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 437 VAL 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 768 GLU 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 561 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 611 ILE 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 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 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 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 1081 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 73 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 54 optimal weight: 0.0010 chunk 42 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 14 optimal weight: 0.0870 chunk 55 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 overall best weight: 0.5164 ------------------------------------------------------------------------------- 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 731 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.159623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.141589 restraints weight = 12601.425| |-----------------------------------------------------------------------------| r_work (start): 0.3983 rms_B_bonded: 2.07 r_work: 0.3885 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3741 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 8718 Z= 0.168 Angle : 0.649 12.184 11773 Z= 0.335 Chirality : 0.045 0.303 1357 Planarity : 0.004 0.045 1489 Dihedral : 6.935 59.905 1189 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 5.84 % Allowed : 27.39 % Favored : 66.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.26), residues: 1049 helix: 0.88 (0.21), residues: 600 sheet: -1.82 (0.47), residues: 106 loop : -1.70 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 389 TYR 0.021 0.001 TYR B 946 PHE 0.021 0.001 PHE A 725 TRP 0.025 0.002 TRP A 345 HIS 0.029 0.001 HIS B 729 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 8716) covalent geometry : angle 0.64854 (11773) hydrogen bonds : bond 0.04381 ( 477) hydrogen bonds : angle 4.87619 ( 1404) Misc. bond : bond 0.00162 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2695.09 seconds wall clock time: 46 minutes 58.63 seconds (2818.63 seconds total)