Starting phenix.real_space_refine on Sat Jul 26 13:52:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rz9_19607/07_2025/8rz9_19607.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rz9_19607/07_2025/8rz9_19607.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rz9_19607/07_2025/8rz9_19607.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rz9_19607/07_2025/8rz9_19607.map" model { file = "/net/cci-nas-00/data/ceres_data/8rz9_19607/07_2025/8rz9_19607.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rz9_19607/07_2025/8rz9_19607.cif" } resolution = 3.02 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 44 5.16 5 C 5433 2.51 5 N 1470 2.21 5 O 1616 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 8571 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4232 Classifications: {'peptide': 534} Link IDs: {'PTRANS': 16, 'TRANS': 517} Chain breaks: 4 Chain: "B" Number of atoms: 4275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4275 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 15, 'TRANS': 517} Chain breaks: 3 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N THR A 320 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 THR A 320 " occ=0.00 residue: pdb=" N GLY A 322 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY A 322 " occ=0.00 residue: pdb=" N SER A 323 " occ=0.00 ... (4 atoms not shown) pdb=" OG SER A 323 " occ=0.00 Time building chain proxies: 5.54, per 1000 atoms: 0.65 Number of scatterers: 8571 At special positions: 0 Unit cell: (74.9644, 106.047, 146.272, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 44 16.00 P 6 15.00 Mg 2 11.99 O 1616 8.00 N 1470 7.00 C 5433 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.42 Conformation dependent library (CDL) restraints added in 1.1 seconds 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2028 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 6 sheets defined 60.4% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 303 through 311 Processing helix chain 'A' and resid 325 through 331 Processing helix chain 'A' and resid 335 through 348 Processing helix chain 'A' and resid 352 through 369 removed outlier: 3.590A pdb=" N ILE A 356 " --> pdb=" O ASP A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 378 removed outlier: 3.611A pdb=" N ARG A 373 " --> pdb=" O ASP A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 396 Processing helix chain 'A' and resid 400 through 424 Proline residue: A 415 - end of helix Processing helix chain 'A' and resid 429 through 457 Proline residue: A 439 - end of helix removed outlier: 4.808A pdb=" N LYS A 449 " --> pdb=" O SER A 445 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N PHE A 450 " --> pdb=" O ASP A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 503 Processing helix chain 'A' and resid 553 through 586 removed outlier: 3.772A pdb=" N GLU A 569 " --> pdb=" O LYS A 565 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N GLU A 580 " --> pdb=" O ALA A 576 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ASN A 583 " --> pdb=" O LYS A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 615 removed outlier: 3.654A pdb=" N ALA A 615 " --> pdb=" O VAL A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 692 removed outlier: 3.746A pdb=" N GLY A 692 " --> pdb=" O MET A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 739 removed outlier: 3.798A pdb=" N THR A 732 " --> pdb=" O GLU A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 773 Processing helix chain 'A' and resid 786 through 788 No H-bonds generated for 'chain 'A' and resid 786 through 788' Processing helix chain 'A' and resid 789 through 794 Processing helix chain 'A' and resid 826 through 834 removed outlier: 3.512A pdb=" N VAL A 830 " --> pdb=" O PHE A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 851 Processing helix chain 'A' and resid 852 through 855 removed outlier: 3.774A pdb=" N GLN A 855 " --> pdb=" O GLU A 852 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 852 through 855' Processing helix chain 'B' and resid 538 through 545 Processing helix chain 'B' and resid 559 through 565 removed outlier: 3.565A pdb=" N VAL B 563 " --> pdb=" O SER B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 582 Processing helix chain 'B' and resid 586 through 602 removed outlier: 3.941A pdb=" N ILE B 590 " --> pdb=" O LYS B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 616 Processing helix chain 'B' and resid 620 through 630 removed outlier: 3.686A pdb=" N GLY B 624 " --> pdb=" O ASP B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 655 removed outlier: 3.651A pdb=" N VAL B 642 " --> pdb=" O PHE B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 660 Processing helix chain 'B' and resid 665 through 679 Proline residue: B 676 - end of helix Processing helix chain 'B' and resid 681 through 689 removed outlier: 4.058A pdb=" N TYR B 685 " --> pdb=" O PRO B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 697 removed outlier: 3.802A pdb=" N ALA B 694 " --> pdb=" O ASN B 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 708 Processing helix chain 'B' and resid 709 through 737 removed outlier: 4.067A pdb=" N ARG B 715 " --> pdb=" O LEU B 711 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLN B 731 " --> pdb=" O ARG B 727 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLU B 732 " --> pdb=" O MET B 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 782 through 816 Processing helix chain 'B' and resid 817 through 844 removed outlier: 3.857A pdb=" N VAL B 825 " --> pdb=" O LEU B 821 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLY B 844 " --> pdb=" O VAL B 840 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 872 Processing helix chain 'B' and resid 897 through 900 Processing helix chain 'B' and resid 901 through 919 Processing helix chain 'B' and resid 950 through 966 Processing helix chain 'B' and resid 982 through 1000 Processing helix chain 'B' and resid 1011 through 1016 removed outlier: 4.126A pdb=" N CYS B1015 " --> pdb=" O TYR B1011 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU B1016 " --> pdb=" O PRO B1012 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1011 through 1016' Processing helix chain 'B' and resid 1016 through 1021 removed outlier: 4.271A pdb=" N ASN B1020 " --> pdb=" O GLU B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1068 through 1076 Processing helix chain 'B' and resid 1079 through 1103 Processing sheet with id=AA1, first strand: chain 'A' and resid 512 through 513 Processing sheet with id=AA2, first strand: chain 'A' and resid 653 through 656 removed outlier: 7.013A pdb=" N VAL A 655 " --> pdb=" O LYS A 635 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N LYS A 635 " --> pdb=" O VAL A 655 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 708 through 711 removed outlier: 6.482A pdb=" N LEU A 709 " --> pdb=" O ILE A 746 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N HIS A 665 " --> pdb=" O PHE A 780 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N PHE A 664 " --> pdb=" O ASN A 798 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N LEU A 800 " --> pdb=" O PHE A 664 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ILE A 666 " --> pdb=" O LEU A 800 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N VAL A 802 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N THR A 668 " --> pdb=" O VAL A 802 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N ALA A 804 " --> pdb=" O THR A 668 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ASN A 799 " --> pdb=" O LYS A 818 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LYS A 818 " --> pdb=" O ASN A 799 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N HIS A 801 " --> pdb=" O GLN A 816 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N GLN A 816 " --> pdb=" O HIS A 801 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N THR A 803 " --> pdb=" O LEU A 814 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 769 through 772 removed outlier: 6.966A pdb=" N ARG B 779 " --> pdb=" O VAL B 771 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 880 through 885 removed outlier: 4.978A pdb=" N ASN B 880 " --> pdb=" O ASN B 861 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASN B 861 " --> pdb=" O ASN B 880 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 935 through 938 removed outlier: 6.050A pdb=" N PHE B 936 " --> pdb=" O ILE B 973 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N ASP B 975 " --> pdb=" O PHE B 936 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ARG B 938 " --> pdb=" O ASP B 975 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL B 972 " --> pdb=" O LEU B1006 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N VAL B1008 " --> pdb=" O VAL B 972 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU B 974 " --> pdb=" O VAL B1008 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N GLN B1058 " --> pdb=" O GLY B1031 " (cutoff:3.500A) removed outlier: 8.787A pdb=" N LEU B1033 " --> pdb=" O LEU B1056 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N LEU B1056 " --> pdb=" O LEU B1033 " (cutoff:3.500A) 477 hydrogen bonds defined for protein. 1404 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.35 Time building geometry restraints manager: 2.78 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: 2.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 22.620 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.510 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.24), residues: 1049 helix: -0.15 (0.20), residues: 597 sheet: -2.23 (0.47), residues: 99 loop : -2.39 (0.30), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.004 TRP B 562 HIS 0.016 0.002 HIS B 729 PHE 0.019 0.004 PHE B 936 TYR 0.029 0.004 TYR A 570 ARG 0.050 0.002 ARG B 573 Details of bonding type rmsd hydrogen bonds : bond 0.15434 ( 477) hydrogen bonds : angle 7.01008 ( 1404) covalent geometry : bond 0.01036 ( 8716) covalent geometry : angle 1.26065 (11773) 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 : 0.839 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: 0.2545 time to fit residues: 80.0236 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 : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 LYS Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 384 PHE Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain B residue 675 ILE Chi-restraints excluded: chain B residue 686 LEU Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 779 ARG Chi-restraints excluded: chain B residue 822 CYS Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 925 GLU Chi-restraints excluded: chain B residue 999 ARG Chi-restraints excluded: chain B residue 1033 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 27 optimal weight: 0.0670 chunk 54 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 83 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 chunk 96 optimal weight: 0.7980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 596 ASN ** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 684 HIS B 827 HIS B 944 ASN B1088 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.159644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.140976 restraints weight = 12481.385| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 2.04 r_work: 0.3883 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3739 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8718 Z= 0.181 Angle : 0.671 13.009 11773 Z= 0.349 Chirality : 0.045 0.213 1357 Planarity : 0.004 0.042 1489 Dihedral : 8.781 93.647 1219 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 5.52 % Allowed : 23.78 % Favored : 70.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.26), residues: 1049 helix: 0.66 (0.21), residues: 602 sheet: -2.28 (0.46), residues: 99 loop : -1.94 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP B 807 HIS 0.014 0.001 HIS B 729 PHE 0.011 0.001 PHE B 952 TYR 0.020 0.002 TYR A 769 ARG 0.006 0.001 ARG A 638 Details of bonding type rmsd hydrogen bonds : bond 0.05273 ( 477) hydrogen bonds : angle 5.33691 ( 1404) covalent geometry : bond 0.00393 ( 8716) covalent geometry : angle 0.67053 (11773) Misc. bond : bond 0.00307 ( 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 262 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 210 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 344 GLN cc_start: 0.7903 (tm-30) cc_final: 0.7664 (tm-30) REVERT: A 592 MET cc_start: 0.8329 (tmm) cc_final: 0.7999 (ptp) REVERT: A 629 GLN cc_start: 0.7536 (OUTLIER) cc_final: 0.6966 (mp10) REVERT: B 553 ASP cc_start: 0.7595 (t0) cc_final: 0.7165 (t0) REVERT: B 688 ILE cc_start: 0.7722 (OUTLIER) cc_final: 0.7329 (mp) REVERT: B 729 HIS cc_start: 0.7269 (t-170) cc_final: 0.6956 (t-170) outliers start: 52 outliers final: 29 residues processed: 241 average time/residue: 0.2469 time to fit residues: 78.8491 Evaluate side-chains 231 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 200 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 339 GLN Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 629 GLN Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 698 GLU Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 799 ASN Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain B residue 675 ILE Chi-restraints excluded: chain B residue 686 LEU Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 822 CYS Chi-restraints excluded: chain B residue 840 VAL Chi-restraints excluded: chain B residue 885 SER Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 1033 LEU Chi-restraints excluded: chain B residue 1066 ARG Chi-restraints excluded: chain B residue 1072 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 102 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 54 optimal weight: 0.8980 chunk 85 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 94 optimal weight: 0.7980 chunk 87 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 566 ASN A 613 ASN B 684 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.158318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.140004 restraints weight = 12630.329| |-----------------------------------------------------------------------------| r_work (start): 0.3958 rms_B_bonded: 2.05 r_work: 0.3861 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3717 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8718 Z= 0.200 Angle : 0.652 12.544 11773 Z= 0.340 Chirality : 0.045 0.205 1357 Planarity : 0.005 0.056 1489 Dihedral : 7.162 57.660 1193 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 6.69 % Allowed : 23.04 % Favored : 70.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.26), residues: 1049 helix: 0.73 (0.21), residues: 601 sheet: -2.22 (0.46), residues: 97 loop : -1.81 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 807 HIS 0.005 0.001 HIS B 781 PHE 0.018 0.002 PHE B1007 TYR 0.021 0.002 TYR A 769 ARG 0.005 0.000 ARG A 638 Details of bonding type rmsd hydrogen bonds : bond 0.05050 ( 477) hydrogen bonds : angle 5.10830 ( 1404) covalent geometry : bond 0.00444 ( 8716) covalent geometry : angle 0.65244 (11773) Misc. bond : bond 0.00515 ( 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 273 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 210 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 344 GLN cc_start: 0.7836 (tm-30) cc_final: 0.7454 (tm-30) REVERT: A 369 ASP cc_start: 0.5893 (OUTLIER) cc_final: 0.5635 (m-30) REVERT: A 592 MET cc_start: 0.8358 (OUTLIER) cc_final: 0.8059 (ptp) REVERT: A 629 GLN cc_start: 0.7663 (OUTLIER) cc_final: 0.6998 (mp10) REVERT: A 778 CYS cc_start: 0.8170 (t) cc_final: 0.7941 (t) REVERT: B 553 ASP cc_start: 0.7559 (t0) cc_final: 0.7193 (t0) REVERT: B 688 ILE cc_start: 0.7630 (OUTLIER) cc_final: 0.7168 (mp) REVERT: B 729 HIS cc_start: 0.7202 (t-170) cc_final: 0.6826 (t-90) REVERT: B 839 LYS cc_start: 0.8318 (tppp) cc_final: 0.8049 (tttm) REVERT: B 917 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.8403 (mt0) REVERT: B 975 ASP cc_start: 0.7441 (t70) cc_final: 0.6803 (m-30) outliers start: 63 outliers final: 41 residues processed: 244 average time/residue: 0.2388 time to fit residues: 77.2562 Evaluate side-chains 249 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 203 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 339 GLN Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 404 CYS Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 629 GLN Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 698 GLU Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 799 ASN Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain B residue 675 ILE Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 753 MET Chi-restraints excluded: chain B residue 788 ASN Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 822 CYS Chi-restraints excluded: chain B residue 840 VAL Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 885 SER Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 913 THR Chi-restraints excluded: chain B residue 914 ILE Chi-restraints excluded: chain B residue 917 GLN Chi-restraints excluded: chain B residue 1033 LEU Chi-restraints excluded: chain B residue 1066 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 66 optimal weight: 1.9990 chunk 27 optimal weight: 0.0970 chunk 37 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 549 GLN 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 = 0.158902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.140304 restraints weight = 12586.905| |-----------------------------------------------------------------------------| r_work (start): 0.3964 rms_B_bonded: 2.07 r_work: 0.3866 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3719 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8718 Z= 0.181 Angle : 0.635 12.028 11773 Z= 0.329 Chirality : 0.044 0.203 1357 Planarity : 0.005 0.049 1489 Dihedral : 6.956 58.036 1191 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 5.94 % Allowed : 25.37 % Favored : 68.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.26), residues: 1049 helix: 0.75 (0.21), residues: 602 sheet: -2.21 (0.45), residues: 99 loop : -1.79 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 807 HIS 0.006 0.001 HIS B 781 PHE 0.012 0.001 PHE B 571 TYR 0.021 0.001 TYR A 769 ARG 0.004 0.000 ARG B 779 Details of bonding type rmsd hydrogen bonds : bond 0.04763 ( 477) hydrogen bonds : angle 4.99067 ( 1404) covalent geometry : bond 0.00401 ( 8716) covalent geometry : angle 0.63496 (11773) Misc. bond : bond 0.00052 ( 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 263 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 207 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 GLU cc_start: 0.8278 (tt0) cc_final: 0.7882 (pt0) REVERT: A 369 ASP cc_start: 0.6039 (OUTLIER) cc_final: 0.5800 (m-30) REVERT: A 562 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.6811 (mp0) REVERT: A 584 ILE cc_start: 0.7315 (OUTLIER) cc_final: 0.7087 (tp) REVERT: A 592 MET cc_start: 0.8342 (OUTLIER) cc_final: 0.8052 (ptt) REVERT: A 629 GLN cc_start: 0.7678 (OUTLIER) cc_final: 0.6991 (mp10) REVERT: A 691 ILE cc_start: 0.7880 (mt) cc_final: 0.7598 (mt) REVERT: A 778 CYS cc_start: 0.8070 (t) cc_final: 0.7849 (t) REVERT: B 553 ASP cc_start: 0.7537 (t0) cc_final: 0.7130 (t0) REVERT: B 688 ILE cc_start: 0.7635 (OUTLIER) cc_final: 0.7161 (mp) REVERT: B 729 HIS cc_start: 0.7306 (t-170) cc_final: 0.6896 (t-170) REVERT: B 839 LYS cc_start: 0.8337 (tppp) cc_final: 0.8076 (tttm) REVERT: B 1084 LYS cc_start: 0.8004 (ttmm) cc_final: 0.7672 (mtpp) outliers start: 56 outliers final: 39 residues processed: 239 average time/residue: 0.2353 time to fit residues: 75.0760 Evaluate side-chains 250 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 205 time to evaluate : 0.935 ------------------------------------------------------------------------------- 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 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 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 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 584 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain B residue 675 ILE Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 753 MET Chi-restraints excluded: chain B residue 788 ASN Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 822 CYS Chi-restraints excluded: chain B residue 885 SER Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 1033 LEU Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1066 ARG Chi-restraints excluded: chain B residue 1072 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 85 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 ASN B 944 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.158051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.139623 restraints weight = 12512.550| |-----------------------------------------------------------------------------| r_work (start): 0.3955 rms_B_bonded: 2.05 r_work: 0.3857 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3711 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8718 Z= 0.206 Angle : 0.646 11.879 11773 Z= 0.335 Chirality : 0.045 0.196 1357 Planarity : 0.005 0.050 1489 Dihedral : 7.044 57.836 1191 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 6.79 % Allowed : 26.43 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.26), residues: 1049 helix: 0.71 (0.21), residues: 602 sheet: -2.16 (0.46), residues: 99 loop : -1.79 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 562 HIS 0.005 0.001 HIS B1088 PHE 0.022 0.002 PHE B1007 TYR 0.024 0.002 TYR A 769 ARG 0.004 0.000 ARG A 752 Details of bonding type rmsd hydrogen bonds : bond 0.04748 ( 477) hydrogen bonds : angle 4.95488 ( 1404) covalent geometry : bond 0.00459 ( 8716) covalent geometry : angle 0.64586 (11773) Misc. bond : bond 0.00199 ( 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 267 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 203 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 301 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7759 (mppt) REVERT: A 358 GLU cc_start: 0.8264 (tt0) cc_final: 0.8063 (tt0) REVERT: A 369 ASP cc_start: 0.5999 (OUTLIER) cc_final: 0.5761 (m-30) REVERT: A 562 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.6547 (mt-10) REVERT: A 584 ILE cc_start: 0.7295 (OUTLIER) cc_final: 0.7063 (tp) REVERT: A 592 MET cc_start: 0.8333 (OUTLIER) cc_final: 0.8037 (ptt) REVERT: A 629 GLN cc_start: 0.7754 (OUTLIER) cc_final: 0.7040 (mp10) REVERT: A 778 CYS cc_start: 0.8066 (t) cc_final: 0.7840 (t) REVERT: B 553 ASP cc_start: 0.7528 (t0) cc_final: 0.6366 (t0) REVERT: B 555 LYS cc_start: 0.8051 (ptpp) cc_final: 0.7183 (ptpp) REVERT: B 688 ILE cc_start: 0.7578 (OUTLIER) cc_final: 0.7081 (mp) REVERT: B 729 HIS cc_start: 0.7520 (t-170) cc_final: 0.7123 (t-170) REVERT: B 839 LYS cc_start: 0.8331 (tppp) cc_final: 0.8054 (tttm) REVERT: B 917 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.8373 (mt0) REVERT: B 1084 LYS cc_start: 0.7937 (ttmm) cc_final: 0.7643 (mtpp) outliers start: 64 outliers final: 42 residues processed: 242 average time/residue: 0.2422 time to fit residues: 78.0919 Evaluate side-chains 247 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 197 time to evaluate : 0.744 ------------------------------------------------------------------------------- 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 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 584 ILE Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 629 GLN Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 698 GLU Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 799 ASN Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain B residue 675 ILE Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 753 MET Chi-restraints excluded: chain B residue 788 ASN Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 822 CYS Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 885 SER Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 913 THR Chi-restraints excluded: chain B residue 917 GLN Chi-restraints excluded: chain B residue 1033 LEU Chi-restraints excluded: chain B residue 1066 ARG Chi-restraints excluded: chain B residue 1072 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 83 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 22 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 73 optimal weight: 5.9990 chunk 91 optimal weight: 0.6980 chunk 84 optimal weight: 0.2980 chunk 70 optimal weight: 0.1980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 731 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.159635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.141245 restraints weight = 12461.595| |-----------------------------------------------------------------------------| r_work (start): 0.3979 rms_B_bonded: 2.06 r_work: 0.3881 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3736 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.2454 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= 0.160 Angle : 0.617 11.049 11773 Z= 0.318 Chirality : 0.043 0.180 1357 Planarity : 0.004 0.048 1489 Dihedral : 6.895 59.286 1191 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 6.48 % Allowed : 27.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.26), residues: 1049 helix: 0.85 (0.22), residues: 602 sheet: -1.91 (0.49), residues: 92 loop : -1.74 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 562 HIS 0.005 0.001 HIS B 781 PHE 0.011 0.001 PHE B 571 TYR 0.018 0.001 TYR A 769 ARG 0.003 0.000 ARG A 752 Details of bonding type rmsd hydrogen bonds : bond 0.04497 ( 477) hydrogen bonds : angle 4.85981 ( 1404) covalent geometry : bond 0.00357 ( 8716) covalent geometry : angle 0.61699 (11773) Misc. bond : bond 0.00176 ( 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 265 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 204 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 ASP cc_start: 0.6038 (OUTLIER) cc_final: 0.5818 (m-30) REVERT: A 584 ILE cc_start: 0.7245 (OUTLIER) cc_final: 0.7008 (tp) REVERT: A 592 MET cc_start: 0.8323 (OUTLIER) cc_final: 0.8026 (ptt) REVERT: A 629 GLN cc_start: 0.7695 (OUTLIER) cc_final: 0.6993 (mp10) REVERT: A 778 CYS cc_start: 0.8101 (t) cc_final: 0.7884 (t) REVERT: B 555 LYS cc_start: 0.8069 (ptpp) cc_final: 0.7699 (ptpp) REVERT: B 688 ILE cc_start: 0.7551 (OUTLIER) cc_final: 0.7076 (mp) REVERT: B 729 HIS cc_start: 0.7601 (t-170) cc_final: 0.7200 (t-170) REVERT: B 839 LYS cc_start: 0.8306 (tppp) cc_final: 0.8051 (tttm) REVERT: B 917 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.8369 (mt0) REVERT: B 1084 LYS cc_start: 0.7948 (ttmm) cc_final: 0.7636 (mtpp) outliers start: 61 outliers final: 46 residues processed: 238 average time/residue: 0.2437 time to fit residues: 77.2018 Evaluate side-chains 253 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 201 time to evaluate : 0.869 ------------------------------------------------------------------------------- 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 369 ASP Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 404 CYS Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 629 GLN Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 799 ASN Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain B residue 552 THR 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 656 ILE Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain B residue 675 ILE Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 731 GLN Chi-restraints excluded: chain B residue 753 MET Chi-restraints excluded: chain B residue 788 ASN Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 822 CYS Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 885 SER Chi-restraints excluded: chain B residue 890 ARG Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 913 THR Chi-restraints excluded: chain B residue 917 GLN Chi-restraints excluded: chain B residue 1005 THR Chi-restraints excluded: chain B residue 1033 LEU Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1066 ARG Chi-restraints excluded: chain B residue 1072 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 55 optimal weight: 0.0670 chunk 3 optimal weight: 0.9980 chunk 102 optimal weight: 0.2980 overall best weight: 0.6718 ------------------------------------------------------------------------------- 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 = 0.4196 r_free = 0.4196 target = 0.158717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.140464 restraints weight = 12486.335| |-----------------------------------------------------------------------------| r_work (start): 0.3975 rms_B_bonded: 2.05 r_work: 0.3878 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3734 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8718 Z= 0.188 Angle : 0.640 11.342 11773 Z= 0.330 Chirality : 0.045 0.223 1357 Planarity : 0.004 0.049 1489 Dihedral : 6.945 59.266 1191 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 6.90 % Allowed : 26.86 % Favored : 66.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.26), residues: 1049 helix: 0.86 (0.21), residues: 603 sheet: -1.76 (0.49), residues: 94 loop : -1.76 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 579 HIS 0.004 0.001 HIS B 984 PHE 0.009 0.001 PHE B 571 TYR 0.021 0.001 TYR A 769 ARG 0.005 0.000 ARG A 340 Details of bonding type rmsd hydrogen bonds : bond 0.04532 ( 477) hydrogen bonds : angle 4.88275 ( 1404) covalent geometry : bond 0.00421 ( 8716) covalent geometry : angle 0.64046 (11773) Misc. bond : bond 0.00247 ( 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 264 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 199 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 301 LYS cc_start: 0.7965 (OUTLIER) cc_final: 0.7733 (mppt) REVERT: A 344 GLN cc_start: 0.7820 (tm-30) cc_final: 0.7466 (tm-30) REVERT: A 369 ASP cc_start: 0.6002 (OUTLIER) cc_final: 0.5779 (m-30) REVERT: A 562 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.6800 (mt-10) REVERT: A 584 ILE cc_start: 0.7266 (OUTLIER) cc_final: 0.7035 (tp) REVERT: A 592 MET cc_start: 0.8329 (OUTLIER) cc_final: 0.8031 (ptt) REVERT: A 629 GLN cc_start: 0.7739 (OUTLIER) cc_final: 0.7039 (mp10) REVERT: A 778 CYS cc_start: 0.8066 (t) cc_final: 0.7839 (t) REVERT: B 533 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7571 (mm-30) REVERT: B 555 LYS cc_start: 0.8085 (ptpp) cc_final: 0.7608 (ptpp) REVERT: B 589 GLU cc_start: 0.8334 (pm20) cc_final: 0.7950 (pm20) REVERT: B 688 ILE cc_start: 0.7498 (OUTLIER) cc_final: 0.7024 (mp) REVERT: B 839 LYS cc_start: 0.8323 (tppp) cc_final: 0.8022 (tttm) REVERT: B 889 GLU cc_start: 0.7463 (mt-10) cc_final: 0.6927 (pt0) REVERT: B 917 GLN cc_start: 0.8670 (OUTLIER) cc_final: 0.8376 (mt0) REVERT: B 1084 LYS cc_start: 0.7974 (ttmm) cc_final: 0.7662 (mtpp) outliers start: 65 outliers final: 48 residues processed: 236 average time/residue: 0.2458 time to fit residues: 76.5459 Evaluate side-chains 250 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 194 time to evaluate : 0.874 ------------------------------------------------------------------------------- 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 330 LEU Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 404 CYS Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 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 581 ILE 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 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 800 LEU 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 648 LEU Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain B residue 675 ILE Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 753 MET Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 822 CYS Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 885 SER Chi-restraints excluded: chain B residue 890 ARG Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 913 THR Chi-restraints excluded: chain B residue 917 GLN Chi-restraints excluded: chain B residue 1005 THR Chi-restraints excluded: chain B residue 1033 LEU Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1066 ARG Chi-restraints excluded: chain B residue 1072 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 101 optimal weight: 0.2980 chunk 20 optimal weight: 9.9990 chunk 104 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 91 optimal weight: 0.6980 chunk 5 optimal weight: 0.1980 chunk 1 optimal weight: 0.5980 chunk 58 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 102 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 729 HIS ** 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 = 0.4207 r_free = 0.4207 target = 0.159753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.141668 restraints weight = 12598.158| |-----------------------------------------------------------------------------| r_work (start): 0.3984 rms_B_bonded: 2.07 r_work: 0.3886 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3742 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.2697 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= 0.160 Angle : 0.624 10.878 11773 Z= 0.323 Chirality : 0.044 0.221 1357 Planarity : 0.004 0.046 1489 Dihedral : 6.886 59.520 1191 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 6.05 % Allowed : 28.24 % Favored : 65.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.26), residues: 1049 helix: 0.95 (0.22), residues: 600 sheet: -1.85 (0.46), residues: 106 loop : -1.70 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 579 HIS 0.024 0.001 HIS B 729 PHE 0.011 0.001 PHE B 571 TYR 0.023 0.001 TYR B 629 ARG 0.005 0.000 ARG A 340 Details of bonding type rmsd hydrogen bonds : bond 0.04434 ( 477) hydrogen bonds : angle 4.87347 ( 1404) covalent geometry : bond 0.00356 ( 8716) covalent geometry : angle 0.62449 (11773) Misc. bond : bond 0.00171 ( 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 258 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 201 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 369 ASP cc_start: 0.6020 (OUTLIER) cc_final: 0.5816 (m-30) REVERT: A 562 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7513 (mp0) REVERT: A 584 ILE cc_start: 0.7234 (OUTLIER) cc_final: 0.7002 (tp) REVERT: A 592 MET cc_start: 0.8348 (OUTLIER) cc_final: 0.8051 (ptt) REVERT: A 629 GLN cc_start: 0.7706 (OUTLIER) cc_final: 0.7022 (mp10) REVERT: A 662 GLN cc_start: 0.6056 (mm110) cc_final: 0.5757 (mm-40) REVERT: A 778 CYS cc_start: 0.8043 (t) cc_final: 0.7831 (t) REVERT: B 532 MET cc_start: 0.5597 (ttt) cc_final: 0.5297 (ttt) REVERT: B 533 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7513 (mm-30) REVERT: B 555 LYS cc_start: 0.8121 (ptpp) cc_final: 0.7651 (ptpp) REVERT: B 589 GLU cc_start: 0.8301 (pm20) cc_final: 0.7976 (pm20) REVERT: B 688 ILE cc_start: 0.7547 (OUTLIER) cc_final: 0.7077 (mp) REVERT: B 731 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.8040 (pm20) REVERT: B 839 LYS cc_start: 0.8313 (tppp) cc_final: 0.8037 (tttm) REVERT: B 889 GLU cc_start: 0.7451 (mt-10) cc_final: 0.6381 (mt-10) REVERT: B 917 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.8388 (mt0) REVERT: B 1084 LYS cc_start: 0.7957 (ttmm) cc_final: 0.7649 (mtpp) outliers start: 57 outliers final: 43 residues processed: 234 average time/residue: 0.2369 time to fit residues: 73.5155 Evaluate side-chains 246 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 195 time to evaluate : 0.855 ------------------------------------------------------------------------------- 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 369 ASP Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 404 CYS Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 562 GLU Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 629 GLN Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain A residue 796 THR 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 656 ILE Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain B residue 675 ILE Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 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 1005 THR Chi-restraints excluded: chain B residue 1033 LEU Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1066 ARG Chi-restraints excluded: chain B residue 1072 VAL Chi-restraints excluded: chain B residue 1081 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 74 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 22 optimal weight: 6.9990 chunk 62 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 101 optimal weight: 0.7980 chunk 88 optimal weight: 0.5980 chunk 70 optimal weight: 0.2980 chunk 12 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 ASN ** B 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.158949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.140652 restraints weight = 12575.452| |-----------------------------------------------------------------------------| r_work (start): 0.3974 rms_B_bonded: 2.07 r_work: 0.3876 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3730 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 8718 Z= 0.188 Angle : 0.655 10.586 11773 Z= 0.340 Chirality : 0.046 0.348 1357 Planarity : 0.005 0.048 1489 Dihedral : 6.898 59.555 1189 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 5.84 % Allowed : 29.30 % Favored : 64.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.26), residues: 1049 helix: 0.84 (0.21), residues: 600 sheet: -1.84 (0.47), residues: 106 loop : -1.69 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 807 HIS 0.029 0.001 HIS B 729 PHE 0.010 0.001 PHE B 571 TYR 0.021 0.002 TYR A 769 ARG 0.005 0.000 ARG A 389 Details of bonding type rmsd hydrogen bonds : bond 0.04519 ( 477) hydrogen bonds : angle 4.93425 ( 1404) covalent geometry : bond 0.00422 ( 8716) covalent geometry : angle 0.65527 (11773) Misc. bond : bond 0.00188 ( 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 252 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 197 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 301 LYS cc_start: 0.7946 (OUTLIER) cc_final: 0.7735 (mppt) REVERT: A 344 GLN cc_start: 0.7831 (tm-30) cc_final: 0.7413 (tm-30) REVERT: A 562 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7565 (mp0) REVERT: A 584 ILE cc_start: 0.7239 (OUTLIER) cc_final: 0.7007 (tp) REVERT: A 592 MET cc_start: 0.8346 (OUTLIER) cc_final: 0.8068 (ptt) REVERT: A 629 GLN cc_start: 0.7740 (OUTLIER) cc_final: 0.7038 (mp10) REVERT: A 729 MET cc_start: 0.7844 (mmp) cc_final: 0.7630 (mmm) REVERT: A 778 CYS cc_start: 0.8044 (t) cc_final: 0.7829 (t) REVERT: B 533 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7558 (mm-30) REVERT: B 589 GLU cc_start: 0.8304 (pm20) cc_final: 0.7987 (pm20) REVERT: B 688 ILE cc_start: 0.7572 (OUTLIER) cc_final: 0.7113 (mp) REVERT: B 839 LYS cc_start: 0.8297 (tppp) cc_final: 0.8017 (tttm) REVERT: B 889 GLU cc_start: 0.7521 (mt-10) cc_final: 0.6617 (mt-10) REVERT: B 917 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.8405 (mt0) REVERT: B 994 LEU cc_start: 0.6207 (tp) cc_final: 0.5444 (tp) REVERT: B 1084 LYS cc_start: 0.7975 (ttmm) cc_final: 0.7667 (mtpp) outliers start: 55 outliers final: 44 residues processed: 230 average time/residue: 0.2485 time to fit residues: 75.3600 Evaluate side-chains 245 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 194 time to evaluate : 0.986 ------------------------------------------------------------------------------- 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 417 VAL Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 562 GLU Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 629 GLN Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain A residue 796 THR 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 648 LEU Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain B residue 675 ILE Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 753 MET Chi-restraints excluded: chain B residue 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 1072 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 59 optimal weight: 0.5980 chunk 2 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 76 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 52 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 ASN B 731 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.158920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.140730 restraints weight = 12538.839| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 2.08 r_work: 0.3877 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3732 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 8718 Z= 0.187 Angle : 0.668 11.326 11773 Z= 0.345 Chirality : 0.046 0.282 1357 Planarity : 0.005 0.048 1489 Dihedral : 6.965 58.810 1189 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 5.84 % Allowed : 29.09 % Favored : 65.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.26), residues: 1049 helix: 0.83 (0.21), residues: 600 sheet: -1.81 (0.47), residues: 106 loop : -1.63 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 807 HIS 0.023 0.001 HIS B 729 PHE 0.010 0.001 PHE B 652 TYR 0.020 0.001 TYR A 769 ARG 0.005 0.000 ARG A 340 Details of bonding type rmsd hydrogen bonds : bond 0.04522 ( 477) hydrogen bonds : angle 4.95176 ( 1404) covalent geometry : bond 0.00420 ( 8716) covalent geometry : angle 0.66791 (11773) Misc. bond : bond 0.00200 ( 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 253 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 198 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 301 LYS cc_start: 0.7943 (OUTLIER) cc_final: 0.7708 (mppt) REVERT: A 344 GLN cc_start: 0.7814 (tm-30) cc_final: 0.7401 (tm-30) REVERT: A 464 GLU cc_start: 0.7664 (pm20) cc_final: 0.7419 (mp0) REVERT: A 562 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7542 (mp0) REVERT: A 584 ILE cc_start: 0.7245 (OUTLIER) cc_final: 0.7013 (tp) REVERT: A 592 MET cc_start: 0.8344 (OUTLIER) cc_final: 0.8069 (ptt) REVERT: A 608 PHE cc_start: 0.8259 (m-10) cc_final: 0.7886 (m-80) REVERT: A 629 GLN cc_start: 0.7762 (OUTLIER) cc_final: 0.7064 (mp10) REVERT: A 778 CYS cc_start: 0.8047 (t) cc_final: 0.7832 (t) REVERT: B 688 ILE cc_start: 0.7591 (OUTLIER) cc_final: 0.7156 (mp) REVERT: B 839 LYS cc_start: 0.8294 (tppp) cc_final: 0.8004 (tttm) REVERT: B 917 GLN cc_start: 0.8671 (OUTLIER) cc_final: 0.8382 (mt0) REVERT: B 994 LEU cc_start: 0.6192 (tp) cc_final: 0.5411 (tp) REVERT: B 1084 LYS cc_start: 0.7989 (ttmm) cc_final: 0.7679 (mtpp) outliers start: 55 outliers final: 44 residues processed: 233 average time/residue: 0.2490 time to fit residues: 76.9863 Evaluate side-chains 247 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 196 time to evaluate : 0.844 ------------------------------------------------------------------------------- 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 417 VAL 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 736 LEU Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain B residue 675 ILE Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 731 GLN Chi-restraints excluded: chain B residue 753 MET Chi-restraints excluded: chain B residue 788 ASN Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 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 1072 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 26 optimal weight: 0.6980 chunk 85 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 chunk 98 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 39 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 ASN ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 731 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.158980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.140705 restraints weight = 12611.374| |-----------------------------------------------------------------------------| r_work (start): 0.3974 rms_B_bonded: 2.07 r_work: 0.3876 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3730 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.107 8718 Z= 0.221 Angle : 1.041 59.200 11773 Z= 0.590 Chirality : 0.055 1.057 1357 Planarity : 0.005 0.050 1489 Dihedral : 6.975 58.821 1189 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 19.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 6.05 % Allowed : 29.51 % Favored : 64.44 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.26), residues: 1049 helix: 0.82 (0.21), residues: 600 sheet: -1.81 (0.47), residues: 106 loop : -1.63 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 807 HIS 0.022 0.001 HIS B 729 PHE 0.009 0.001 PHE B 652 TYR 0.020 0.001 TYR A 769 ARG 0.006 0.000 ARG B 593 Details of bonding type rmsd hydrogen bonds : bond 0.04531 ( 477) hydrogen bonds : angle 4.96361 ( 1404) covalent geometry : bond 0.00485 ( 8716) covalent geometry : angle 1.04083 (11773) Misc. bond : bond 0.00262 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5579.49 seconds wall clock time: 95 minutes 53.41 seconds (5753.41 seconds total)