Starting phenix.real_space_refine on Tue Jul 29 17:16:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oma_16972/07_2025/8oma_16972.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oma_16972/07_2025/8oma_16972.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8oma_16972/07_2025/8oma_16972.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oma_16972/07_2025/8oma_16972.map" model { file = "/net/cci-nas-00/data/ceres_data/8oma_16972/07_2025/8oma_16972.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oma_16972/07_2025/8oma_16972.cif" } resolution = 3.29 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= 0.024 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 40 5.49 5 Mg 1 5.21 5 S 52 5.16 5 C 7099 2.51 5 N 1952 2.21 5 O 2235 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 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: 11379 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 351 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "D" Number of atoms: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 346 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "A" Number of atoms: 5990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 760, 5990 Classifications: {'peptide': 760} Link IDs: {'PTRANS': 21, 'TRANS': 738} Chain breaks: 4 Chain: "B" Number of atoms: 4629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4629 Classifications: {'peptide': 577} Link IDs: {'PTRANS': 17, 'TRANS': 559} Chain breaks: 2 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.88, per 1000 atoms: 0.60 Number of scatterers: 11379 At special positions: 0 Unit cell: (94.1626, 107.876, 173.698, 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 52 16.00 P 40 15.00 Mg 1 11.99 O 2235 8.00 N 1952 7.00 C 7099 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.88 Conformation dependent library (CDL) restraints added in 1.4 seconds 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2530 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 9 sheets defined 58.3% alpha, 8.9% beta 17 base pairs and 29 stacking pairs defined. Time for finding SS restraints: 3.59 Creating SS restraints... Processing helix chain 'A' and resid 184 through 193 removed outlier: 3.655A pdb=" N GLN A 193 " --> pdb=" O ALA A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 220 removed outlier: 4.023A pdb=" N LYS A 212 " --> pdb=" O GLY A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 232 Processing helix chain 'A' and resid 236 through 245 Processing helix chain 'A' and resid 247 through 251 removed outlier: 4.069A pdb=" N GLY A 250 " --> pdb=" O GLY A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 262 Proline residue: A 259 - end of helix Processing helix chain 'A' and resid 263 through 277 Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 303 through 310 Processing helix chain 'A' and resid 325 through 331 Processing helix chain 'A' and resid 335 through 348 Processing helix chain 'A' and resid 352 through 369 removed outlier: 3.597A pdb=" N ILE A 356 " --> pdb=" O ASP A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 379 removed outlier: 3.631A pdb=" N ASP A 379 " --> pdb=" O THR A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 396 Processing helix chain 'A' and resid 400 through 423 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: 4.778A pdb=" N LYS A 449 " --> pdb=" O SER A 445 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N PHE A 450 " --> pdb=" O ASP A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 465 Processing helix chain 'A' and resid 475 through 504 removed outlier: 3.647A pdb=" N GLY A 504 " --> pdb=" O ALA A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 587 removed outlier: 4.769A pdb=" N GLU A 580 " --> pdb=" O ALA A 576 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ASN A 583 " --> pdb=" O LYS A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 615 removed outlier: 3.578A pdb=" N ALA A 615 " --> pdb=" O VAL A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 692 Processing helix chain 'A' and resid 723 through 739 Processing helix chain 'A' and resid 756 through 773 Processing helix chain 'A' and resid 786 through 793 Processing helix chain 'A' and resid 826 through 834 removed outlier: 3.616A 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 879 through 894 Processing helix chain 'A' and resid 900 through 919 Processing helix chain 'A' and resid 920 through 930 removed outlier: 3.716A pdb=" N ILE A 926 " --> pdb=" O PHE A 922 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 545 Processing helix chain 'B' and resid 559 through 565 Processing helix chain 'B' and resid 569 through 581 Processing helix chain 'B' and resid 586 through 602 Processing helix chain 'B' and resid 606 through 615 Processing helix chain 'B' and resid 622 through 630 Processing helix chain 'B' and resid 634 through 663 removed outlier: 3.588A pdb=" N PHE B 638 " --> pdb=" O SER B 634 " (cutoff:3.500A) Proline residue: B 657 - end of helix Processing helix chain 'B' and resid 665 through 679 removed outlier: 3.954A pdb=" N ILE B 672 " --> pdb=" O LEU B 668 " (cutoff:3.500A) Proline residue: B 676 - end of helix Processing helix chain 'B' and resid 682 through 688 removed outlier: 3.676A pdb=" N LEU B 686 " --> pdb=" O VAL B 682 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS B 687 " --> pdb=" O GLU B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 697 Processing helix chain 'B' and resid 705 through 708 removed outlier: 4.255A pdb=" N ASP B 708 " --> pdb=" O ASP B 705 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 705 through 708' Processing helix chain 'B' and resid 709 through 738 removed outlier: 3.707A pdb=" N ARG B 715 " --> pdb=" O LEU B 711 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLN B 731 " --> pdb=" O ARG B 727 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N GLU B 732 " --> pdb=" O MET B 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 762 Processing helix chain 'B' and resid 782 through 817 removed outlier: 4.049A pdb=" N HIS B 817 " --> pdb=" O LYS B 813 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 844 removed outlier: 3.763A pdb=" N GLY B 844 " --> pdb=" O VAL B 840 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 871 Processing helix chain 'B' and resid 901 through 919 Processing helix chain 'B' and resid 944 through 948 Processing helix chain 'B' and resid 950 through 966 Processing helix chain 'B' and resid 982 through 1000 Processing helix chain 'B' and resid 1016 through 1021 removed outlier: 3.547A 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 1111 removed outlier: 3.588A pdb=" N LEU B1083 " --> pdb=" O PRO B1079 " (cutoff:3.500A) Processing helix chain 'B' and resid 1115 through 1124 Processing sheet with id=AA1, first strand: chain 'A' and resid 223 through 227 removed outlier: 5.959A pdb=" N CYS A 199 " --> pdb=" O THR A 225 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ARG A 227 " --> pdb=" O CYS A 199 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N LEU A 201 " --> pdb=" O ARG A 227 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N MET A 152 " --> pdb=" O PRO A 202 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N VAL A 147 " --> pdb=" O VAL A 166 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL A 166 " --> pdb=" O VAL A 147 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN A 160 " --> pdb=" O SER A 153 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 513 through 516 Processing sheet with id=AA3, first strand: chain 'A' and resid 539 through 541 Processing sheet with id=AA4, first strand: chain 'A' and resid 632 through 635 removed outlier: 3.698A pdb=" N SER A 699 " --> pdb=" O LYS A 635 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 708 through 711 removed outlier: 7.381A pdb=" N ASN A 799 " --> pdb=" O LYS A 818 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N LYS A 818 " --> pdb=" O ASN A 799 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N HIS A 801 " --> pdb=" O GLN A 816 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N GLN A 816 " --> pdb=" O HIS A 801 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N THR A 803 " --> pdb=" O LEU A 814 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU A 814 " --> pdb=" O THR A 803 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 754 through 756 Processing sheet with id=AA7, first strand: chain 'B' and resid 880 through 882 removed outlier: 5.673A pdb=" N ASN B 880 " --> pdb=" O ASN B 861 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ASN B 861 " --> pdb=" O ASN B 880 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 892 through 895 removed outlier: 5.821A pdb=" N ILE B 893 " --> pdb=" O TYR B1028 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N MET B1030 " --> pdb=" O ILE B 893 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N THR B 895 " --> pdb=" O MET B1030 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N PHE B1032 " --> pdb=" O THR B 895 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N GLN B1058 " --> pdb=" O GLY B1031 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N LEU B1033 " --> pdb=" O LEU B1056 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N LEU B1056 " --> pdb=" O LEU B1033 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 935 through 937 removed outlier: 3.510A pdb=" N LEU B 974 " --> pdb=" O LEU B1006 " (cutoff:3.500A) 598 hydrogen bonds defined for protein. 1722 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 42 hydrogen bonds 84 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 29 stacking parallelities Total time for adding SS restraints: 4.45 Time building geometry restraints manager: 3.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3522 1.34 - 1.48: 2877 1.48 - 1.61: 5153 1.61 - 1.75: 2 1.75 - 1.88: 84 Bond restraints: 11638 Sorted by residual: bond pdb=" CA SER A 637 " pdb=" CB SER A 637 " ideal model delta sigma weight residual 1.529 1.460 0.069 1.66e-02 3.63e+03 1.73e+01 bond pdb=" CE1 HIS B 864 " pdb=" NE2 HIS B 864 " ideal model delta sigma weight residual 1.321 1.354 -0.033 1.00e-02 1.00e+04 1.09e+01 bond pdb=" CA SER B 920 " pdb=" CB SER B 920 " ideal model delta sigma weight residual 1.528 1.480 0.048 1.48e-02 4.57e+03 1.07e+01 bond pdb=" CG MET B 953 " pdb=" SD MET B 953 " ideal model delta sigma weight residual 1.803 1.884 -0.081 2.50e-02 1.60e+03 1.04e+01 bond pdb=" CD ARG B 938 " pdb=" NE ARG B 938 " ideal model delta sigma weight residual 1.458 1.419 0.039 1.40e-02 5.10e+03 7.95e+00 ... (remaining 11633 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 13515 1.80 - 3.59: 2090 3.59 - 5.39: 222 5.39 - 7.18: 23 7.18 - 8.98: 6 Bond angle restraints: 15856 Sorted by residual: angle pdb=" C5' ATP B2000 " pdb=" O5' ATP B2000 " pdb=" PA ATP B2000 " ideal model delta sigma weight residual 121.27 113.20 8.07 1.00e+00 1.00e+00 6.50e+01 angle pdb=" N THR B 951 " pdb=" CA THR B 951 " pdb=" CB THR B 951 " ideal model delta sigma weight residual 109.72 117.37 -7.65 1.70e+00 3.46e-01 2.02e+01 angle pdb=" C ARG A 711 " pdb=" CA ARG A 711 " pdb=" CB ARG A 711 " ideal model delta sigma weight residual 111.70 117.20 -5.50 1.31e+00 5.83e-01 1.77e+01 angle pdb=" C PRO A 652 " pdb=" CA PRO A 652 " pdb=" CB PRO A 652 " ideal model delta sigma weight residual 111.23 106.06 5.17 1.28e+00 6.10e-01 1.63e+01 angle pdb=" N GLY A 692 " pdb=" CA GLY A 692 " pdb=" C GLY A 692 " ideal model delta sigma weight residual 114.95 109.31 5.64 1.41e+00 5.03e-01 1.60e+01 ... (remaining 15851 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 5764 17.96 - 35.92: 869 35.92 - 53.88: 323 53.88 - 71.85: 66 71.85 - 89.81: 18 Dihedral angle restraints: 7040 sinusoidal: 3145 harmonic: 3895 Sorted by residual: dihedral pdb=" CA GLY A 504 " pdb=" C GLY A 504 " pdb=" N LEU A 505 " pdb=" CA LEU A 505 " ideal model delta harmonic sigma weight residual 180.00 -152.34 -27.66 0 5.00e+00 4.00e-02 3.06e+01 dihedral pdb=" CA MET B 728 " pdb=" C MET B 728 " pdb=" N HIS B 729 " pdb=" CA HIS B 729 " ideal model delta harmonic sigma weight residual 180.00 155.28 24.72 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA SER B1067 " pdb=" C SER B1067 " pdb=" N TYR B1068 " pdb=" CA TYR B1068 " ideal model delta harmonic sigma weight residual -180.00 -155.91 -24.09 0 5.00e+00 4.00e-02 2.32e+01 ... (remaining 7037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1034 0.076 - 0.152: 625 0.152 - 0.228: 128 0.228 - 0.304: 25 0.304 - 0.380: 7 Chirality restraints: 1819 Sorted by residual: chirality pdb=" CA ARG A 171 " pdb=" N ARG A 171 " pdb=" C ARG A 171 " pdb=" CB ARG A 171 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.62e+00 chirality pdb=" CG LEU B 640 " pdb=" CB LEU B 640 " pdb=" CD1 LEU B 640 " pdb=" CD2 LEU B 640 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" CB THR B 951 " pdb=" CA THR B 951 " pdb=" OG1 THR B 951 " pdb=" CG2 THR B 951 " both_signs ideal model delta sigma weight residual False 2.55 2.20 0.36 2.00e-01 2.50e+01 3.15e+00 ... (remaining 1816 not shown) Planarity restraints: 1897 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 938 " 0.406 9.50e-02 1.11e+02 1.82e-01 2.25e+01 pdb=" NE ARG B 938 " -0.034 2.00e-02 2.50e+03 pdb=" CZ ARG B 938 " 0.020 2.00e-02 2.50e+03 pdb=" NH1 ARG B 938 " -0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG B 938 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 991 " -0.032 2.00e-02 2.50e+03 1.72e-02 5.92e+00 pdb=" CG TYR B 991 " 0.017 2.00e-02 2.50e+03 pdb=" CD1 TYR B 991 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR B 991 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR B 991 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR B 991 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR B 991 " -0.008 2.00e-02 2.50e+03 pdb=" OH TYR B 991 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B1007 " 0.027 2.00e-02 2.50e+03 1.78e-02 5.55e+00 pdb=" CG PHE B1007 " -0.013 2.00e-02 2.50e+03 pdb=" CD1 PHE B1007 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE B1007 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 PHE B1007 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B1007 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B1007 " 0.023 2.00e-02 2.50e+03 ... (remaining 1894 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 86 2.48 - 3.09: 8207 3.09 - 3.69: 19419 3.69 - 4.30: 27120 4.30 - 4.90: 42534 Nonbonded interactions: 97366 Sorted by model distance: nonbonded pdb=" O2G ATP B2000 " pdb="MG MG B2001 " model vdw 1.878 2.170 nonbonded pdb=" OG SER B 903 " pdb="MG MG B2001 " model vdw 2.000 2.170 nonbonded pdb=" OG1 THR A 335 " pdb=" OD2 ASP A 603 " model vdw 2.112 3.040 nonbonded pdb=" O LYS A 565 " pdb=" OG1 THR A 568 " model vdw 2.174 3.040 nonbonded pdb=" OD1 ASN A 186 " pdb=" NE2 GLN A 348 " model vdw 2.178 3.120 ... (remaining 97361 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=0.03 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.000 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: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 30.470 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 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 : 0.011 0.890 11639 Z= 0.963 Angle : 1.304 8.981 15856 Z= 0.857 Chirality : 0.094 0.380 1819 Planarity : 0.007 0.182 1897 Dihedral : 19.919 89.807 4510 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 28.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 2.97 % Allowed : 22.71 % Favored : 74.32 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.22), residues: 1321 helix: 0.08 (0.18), residues: 716 sheet: -2.00 (0.41), residues: 145 loop : -2.34 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.005 TRP A 764 HIS 0.016 0.003 HIS B 647 PHE 0.027 0.005 PHE B1007 TYR 0.032 0.005 TYR B 991 ARG 0.025 0.002 ARG B 938 Details of bonding type rmsd hydrogen bonds : bond 0.13805 ( 640) hydrogen bonds : angle 6.35725 ( 1806) covalent geometry : bond 0.00765 (11638) covalent geometry : angle 1.30443 (15856) Misc. bond : bond 0.89030 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 217 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LYS cc_start: 0.6314 (OUTLIER) cc_final: 0.5035 (ttpp) REVERT: A 245 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7459 (tm) REVERT: A 253 MET cc_start: 0.8246 (tpp) cc_final: 0.5575 (tpp) REVERT: A 324 GLN cc_start: 0.8416 (mp10) cc_final: 0.8190 (mp10) REVERT: A 348 GLN cc_start: 0.7119 (OUTLIER) cc_final: 0.6843 (pt0) REVERT: A 466 HIS cc_start: 0.7335 (p90) cc_final: 0.7118 (p-80) REVERT: A 572 GLU cc_start: 0.9114 (pt0) cc_final: 0.8822 (pp20) REVERT: A 594 THR cc_start: 0.8824 (OUTLIER) cc_final: 0.8454 (t) REVERT: A 631 ARG cc_start: 0.8460 (ttp-170) cc_final: 0.8260 (ttp80) REVERT: A 638 ARG cc_start: 0.5886 (ptm-80) cc_final: 0.5583 (ptm-80) REVERT: A 729 MET cc_start: 0.5867 (OUTLIER) cc_final: 0.5528 (ttt) REVERT: A 743 SER cc_start: 0.7606 (t) cc_final: 0.7318 (t) REVERT: A 786 GLU cc_start: 0.7791 (tt0) cc_final: 0.7491 (tm-30) REVERT: A 815 TYR cc_start: 0.7436 (m-10) cc_final: 0.7129 (m-10) REVERT: B 549 GLN cc_start: 0.8411 (pt0) cc_final: 0.7890 (pt0) REVERT: B 557 LYS cc_start: 0.8175 (tptm) cc_final: 0.6044 (ptmm) REVERT: B 617 LYS cc_start: 0.8716 (tptp) cc_final: 0.7859 (mmtm) REVERT: B 781 HIS cc_start: 0.8721 (t70) cc_final: 0.8307 (t70) REVERT: B 796 ARG cc_start: 0.7896 (ptm-80) cc_final: 0.7559 (ptm-80) REVERT: B 892 MET cc_start: 0.8939 (ttm) cc_final: 0.8609 (ttm) outliers start: 35 outliers final: 17 residues processed: 236 average time/residue: 0.2935 time to fit residues: 92.3753 Evaluate side-chains 214 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 192 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 926 ILE Chi-restraints excluded: chain B residue 692 GLN Chi-restraints excluded: chain B residue 812 GLU Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 866 VAL Chi-restraints excluded: chain B residue 938 ARG Chi-restraints excluded: chain B residue 1027 ASN Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain B residue 1060 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 0.0670 chunk 102 optimal weight: 7.9990 chunk 56 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 105 optimal weight: 0.9990 chunk 40 optimal weight: 0.2980 chunk 64 optimal weight: 0.3980 chunk 78 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 GLN ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 593 GLN B 647 HIS B 729 HIS B 880 ASN ** B 898 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 908 GLN B1010 HIS B1120 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4950 r_free = 0.4950 target = 0.222666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4621 r_free = 0.4621 target = 0.189228 restraints weight = 18396.789| |-----------------------------------------------------------------------------| r_work (start): 0.4562 rms_B_bonded: 3.67 r_work: 0.4430 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.4430 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4428 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4428 r_free = 0.4428 target_work(ls_wunit_k1) = 0.171 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4428 r_free = 0.4428 target_work(ls_wunit_k1) = 0.171 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4428 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5810 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11639 Z= 0.165 Angle : 0.673 9.935 15856 Z= 0.363 Chirality : 0.043 0.201 1819 Planarity : 0.004 0.071 1897 Dihedral : 18.113 87.107 1900 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 19.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 3.14 % Allowed : 21.53 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.23), residues: 1321 helix: 0.42 (0.18), residues: 725 sheet: -1.93 (0.40), residues: 169 loop : -1.76 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 764 HIS 0.007 0.001 HIS B 729 PHE 0.044 0.002 PHE A 286 TYR 0.013 0.001 TYR B 877 ARG 0.003 0.000 ARG A 638 Details of bonding type rmsd hydrogen bonds : bond 0.04720 ( 640) hydrogen bonds : angle 4.98817 ( 1806) covalent geometry : bond 0.00352 (11638) covalent geometry : angle 0.67252 (15856) Misc. bond : bond 0.00408 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 204 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 GLU cc_start: 0.7576 (mt-10) cc_final: 0.7208 (mt-10) REVERT: A 229 LYS cc_start: 0.4717 (OUTLIER) cc_final: 0.3979 (ttpp) REVERT: A 253 MET cc_start: 0.7037 (tpp) cc_final: 0.4887 (tpp) REVERT: A 324 GLN cc_start: 0.7587 (mp10) cc_final: 0.7309 (mp10) REVERT: A 386 ASP cc_start: 0.6325 (t0) cc_final: 0.6100 (t0) REVERT: A 480 GLU cc_start: 0.8355 (pp20) cc_final: 0.7959 (pp20) REVERT: A 572 GLU cc_start: 0.8050 (pt0) cc_final: 0.7833 (pp20) REVERT: A 594 THR cc_start: 0.8077 (OUTLIER) cc_final: 0.7807 (t) REVERT: A 631 ARG cc_start: 0.7446 (ttp-170) cc_final: 0.7160 (ptm160) REVERT: A 743 SER cc_start: 0.6639 (t) cc_final: 0.6408 (t) REVERT: A 813 MET cc_start: 0.6272 (mmp) cc_final: 0.6042 (mmp) REVERT: A 815 TYR cc_start: 0.6746 (m-10) cc_final: 0.6247 (m-10) REVERT: A 846 GLN cc_start: 0.7023 (mm-40) cc_final: 0.6808 (mm-40) REVERT: B 549 GLN cc_start: 0.7159 (pt0) cc_final: 0.6491 (pt0) REVERT: B 577 LYS cc_start: 0.7186 (tttt) cc_final: 0.6892 (ttmm) REVERT: B 578 LYS cc_start: 0.7641 (tttt) cc_final: 0.7126 (tmtt) REVERT: B 584 LEU cc_start: 0.7712 (mt) cc_final: 0.7357 (mt) REVERT: B 640 LEU cc_start: 0.5149 (OUTLIER) cc_final: 0.4857 (mp) REVERT: B 796 ARG cc_start: 0.7716 (ptm-80) cc_final: 0.7256 (ptm-80) REVERT: B 839 LYS cc_start: 0.6981 (mttt) cc_final: 0.6676 (tptp) REVERT: B 892 MET cc_start: 0.7756 (ttm) cc_final: 0.7314 (ttm) REVERT: B 925 GLU cc_start: 0.7139 (mm-30) cc_final: 0.6903 (mm-30) REVERT: B 938 ARG cc_start: 0.6198 (OUTLIER) cc_final: 0.5944 (tpm170) REVERT: B 964 ARG cc_start: 0.7664 (mtt180) cc_final: 0.7393 (ptt-90) outliers start: 37 outliers final: 18 residues processed: 222 average time/residue: 0.2669 time to fit residues: 81.2168 Evaluate side-chains 216 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 194 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain B residue 555 LYS Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain B residue 802 ASP Chi-restraints excluded: chain B residue 827 HIS Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 938 ARG Chi-restraints excluded: chain B residue 1034 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 128 optimal weight: 0.9990 chunk 76 optimal weight: 0.0980 chunk 4 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 134 optimal weight: 7.9990 chunk 60 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 chunk 80 optimal weight: 0.5980 chunk 84 optimal weight: 0.9980 chunk 106 optimal weight: 0.8980 chunk 56 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 GLN ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 HIS B 684 HIS B 817 HIS ** B 898 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4927 r_free = 0.4927 target = 0.220482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.186442 restraints weight = 18641.311| |-----------------------------------------------------------------------------| r_work (start): 0.4536 rms_B_bonded: 3.79 r_work: 0.4402 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.4402 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4412 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4412 r_free = 0.4412 target_work(ls_wunit_k1) = 0.170 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4412 r_free = 0.4412 target_work(ls_wunit_k1) = 0.170 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4412 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5850 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11639 Z= 0.169 Angle : 0.644 7.423 15856 Z= 0.350 Chirality : 0.043 0.227 1819 Planarity : 0.005 0.074 1897 Dihedral : 17.832 80.709 1873 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 19.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 3.31 % Allowed : 23.31 % Favored : 73.39 % 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: -0.60 (0.23), residues: 1321 helix: 0.64 (0.19), residues: 724 sheet: -1.46 (0.43), residues: 158 loop : -1.64 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 764 HIS 0.011 0.002 HIS B 684 PHE 0.048 0.002 PHE A 286 TYR 0.013 0.002 TYR A 769 ARG 0.006 0.000 ARG B1101 Details of bonding type rmsd hydrogen bonds : bond 0.04442 ( 640) hydrogen bonds : angle 4.82957 ( 1806) covalent geometry : bond 0.00362 (11638) covalent geometry : angle 0.64440 (15856) Misc. bond : bond 0.00347 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 196 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7424 (mt-10) REVERT: A 253 MET cc_start: 0.6995 (tpp) cc_final: 0.5159 (tpp) REVERT: A 324 GLN cc_start: 0.7626 (mp10) cc_final: 0.7286 (mp10) REVERT: A 344 GLN cc_start: 0.6073 (tm-30) cc_final: 0.5680 (tm-30) REVERT: A 386 ASP cc_start: 0.6399 (t0) cc_final: 0.6181 (t0) REVERT: A 431 LEU cc_start: 0.7178 (tp) cc_final: 0.6905 (tp) REVERT: A 450 PHE cc_start: 0.4722 (t80) cc_final: 0.3909 (t80) REVERT: A 453 MET cc_start: 0.6815 (tpp) cc_final: 0.6526 (tpp) REVERT: A 480 GLU cc_start: 0.8181 (pp20) cc_final: 0.7904 (pp20) REVERT: A 481 LEU cc_start: 0.7967 (mt) cc_final: 0.7734 (mt) REVERT: A 535 ASN cc_start: 0.6611 (OUTLIER) cc_final: 0.5961 (t0) REVERT: A 572 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7867 (pt0) REVERT: A 631 ARG cc_start: 0.7503 (ttp-170) cc_final: 0.7236 (ptm160) REVERT: A 659 LYS cc_start: 0.7453 (tptp) cc_final: 0.7247 (tptm) REVERT: A 743 SER cc_start: 0.6670 (t) cc_final: 0.6436 (t) REVERT: A 786 GLU cc_start: 0.6650 (pt0) cc_final: 0.6368 (tm-30) REVERT: A 815 TYR cc_start: 0.6912 (m-10) cc_final: 0.6348 (m-10) REVERT: A 846 GLN cc_start: 0.7158 (mm-40) cc_final: 0.6898 (mm-40) REVERT: B 549 GLN cc_start: 0.7290 (pt0) cc_final: 0.6487 (pt0) REVERT: B 615 LEU cc_start: 0.8148 (mt) cc_final: 0.7814 (mm) REVERT: B 617 LYS cc_start: 0.7937 (tptp) cc_final: 0.7339 (mmtm) REVERT: B 631 LYS cc_start: 0.8097 (mptt) cc_final: 0.7882 (mptt) REVERT: B 679 LEU cc_start: 0.5668 (OUTLIER) cc_final: 0.5194 (mt) REVERT: B 796 ARG cc_start: 0.7754 (ptm-80) cc_final: 0.7295 (ptm-80) REVERT: B 892 MET cc_start: 0.7808 (ttm) cc_final: 0.7387 (ttm) REVERT: B 925 GLU cc_start: 0.7161 (mm-30) cc_final: 0.6902 (mm-30) REVERT: B 964 ARG cc_start: 0.7683 (mtt180) cc_final: 0.7394 (ptt-90) REVERT: B 1094 GLU cc_start: 0.7422 (mt-10) cc_final: 0.7113 (mt-10) outliers start: 39 outliers final: 19 residues processed: 219 average time/residue: 0.2692 time to fit residues: 80.7380 Evaluate side-chains 206 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 184 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 535 ASN Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 726 MET Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain B residue 802 ASP Chi-restraints excluded: chain B residue 827 HIS Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 1034 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 13 optimal weight: 0.0770 chunk 116 optimal weight: 0.6980 chunk 68 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 95 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 829 HIS B 647 HIS ** B 880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 898 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4920 r_free = 0.4920 target = 0.219896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.186036 restraints weight = 18396.299| |-----------------------------------------------------------------------------| r_work (start): 0.4528 rms_B_bonded: 3.73 r_work: 0.4395 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.4395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5866 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11639 Z= 0.165 Angle : 0.633 7.701 15856 Z= 0.344 Chirality : 0.043 0.200 1819 Planarity : 0.005 0.076 1897 Dihedral : 17.650 76.399 1864 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 18.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 4.41 % Allowed : 23.64 % Favored : 71.95 % 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: -0.48 (0.23), residues: 1321 helix: 0.73 (0.19), residues: 725 sheet: -1.54 (0.42), residues: 158 loop : -1.53 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 764 HIS 0.005 0.001 HIS B1010 PHE 0.051 0.002 PHE A 286 TYR 0.016 0.002 TYR B 877 ARG 0.009 0.000 ARG B 573 Details of bonding type rmsd hydrogen bonds : bond 0.04293 ( 640) hydrogen bonds : angle 4.71427 ( 1806) covalent geometry : bond 0.00354 (11638) covalent geometry : angle 0.63294 (15856) Misc. bond : bond 0.00254 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 191 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 ARG cc_start: 0.8349 (ptp90) cc_final: 0.8037 (ptp90) REVERT: A 172 LYS cc_start: 0.7931 (mptt) cc_final: 0.7643 (mmtm) REVERT: A 253 MET cc_start: 0.7009 (tpp) cc_final: 0.5345 (tpp) REVERT: A 271 SER cc_start: 0.4280 (OUTLIER) cc_final: 0.3098 (t) REVERT: A 279 LEU cc_start: 0.4890 (OUTLIER) cc_final: 0.4620 (mp) REVERT: A 334 LYS cc_start: 0.6706 (mtmm) cc_final: 0.6361 (mtmm) REVERT: A 380 LEU cc_start: 0.5524 (OUTLIER) cc_final: 0.4885 (mt) REVERT: A 386 ASP cc_start: 0.6378 (t0) cc_final: 0.6161 (t0) REVERT: A 409 GLN cc_start: 0.5599 (OUTLIER) cc_final: 0.4957 (tt0) REVERT: A 413 GLN cc_start: 0.5686 (OUTLIER) cc_final: 0.3527 (mm-40) REVERT: A 431 LEU cc_start: 0.7227 (tp) cc_final: 0.6924 (tp) REVERT: A 480 GLU cc_start: 0.8123 (pp20) cc_final: 0.7859 (pp20) REVERT: A 481 LEU cc_start: 0.7927 (mt) cc_final: 0.7657 (mt) REVERT: A 535 ASN cc_start: 0.6560 (OUTLIER) cc_final: 0.5900 (t0) REVERT: A 631 ARG cc_start: 0.7596 (ttp-170) cc_final: 0.7353 (ptm160) REVERT: A 659 LYS cc_start: 0.7521 (tptp) cc_final: 0.7104 (ttmm) REVERT: A 846 GLN cc_start: 0.7176 (mm-40) cc_final: 0.6879 (mm-40) REVERT: B 549 GLN cc_start: 0.7309 (pt0) cc_final: 0.6783 (pt0) REVERT: B 615 LEU cc_start: 0.8093 (mt) cc_final: 0.7801 (mm) REVERT: B 617 LYS cc_start: 0.8076 (tptp) cc_final: 0.7431 (mmtm) REVERT: B 631 LYS cc_start: 0.8035 (mptt) cc_final: 0.7788 (mptt) REVERT: B 672 ILE cc_start: 0.2437 (OUTLIER) cc_final: 0.2237 (mt) REVERT: B 796 ARG cc_start: 0.7784 (ptm-80) cc_final: 0.7306 (ptm-80) REVERT: B 839 LYS cc_start: 0.7006 (mttt) cc_final: 0.6757 (mttt) REVERT: B 892 MET cc_start: 0.7859 (ttm) cc_final: 0.7440 (ttm) REVERT: B 925 GLU cc_start: 0.7144 (mm-30) cc_final: 0.6893 (mm-30) REVERT: B 964 ARG cc_start: 0.7675 (mtt180) cc_final: 0.7357 (ptt-90) REVERT: B 1094 GLU cc_start: 0.7384 (mt-10) cc_final: 0.7016 (mt-10) REVERT: B 1098 ASN cc_start: 0.7879 (m-40) cc_final: 0.7675 (p0) outliers start: 52 outliers final: 26 residues processed: 226 average time/residue: 0.2848 time to fit residues: 87.9337 Evaluate side-chains 213 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 180 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 413 GLN Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 535 ASN Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 726 MET Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain B residue 684 HIS Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain B residue 802 ASP Chi-restraints excluded: chain B residue 827 HIS Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 938 ARG Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 1034 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 3 optimal weight: 0.9990 chunk 100 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 102 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 25 optimal weight: 0.0970 chunk 44 optimal weight: 1.9990 chunk 131 optimal weight: 0.4980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 GLN ** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 ASN ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 639 HIS ** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 HIS ** B 864 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 898 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4898 r_free = 0.4898 target = 0.217838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.184566 restraints weight = 18353.920| |-----------------------------------------------------------------------------| r_work (start): 0.4508 rms_B_bonded: 3.64 r_work: 0.4378 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.4378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5894 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11639 Z= 0.186 Angle : 0.654 7.630 15856 Z= 0.357 Chirality : 0.044 0.212 1819 Planarity : 0.005 0.076 1897 Dihedral : 17.576 76.509 1862 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 20.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 5.17 % Allowed : 23.98 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.23), residues: 1321 helix: 0.65 (0.19), residues: 727 sheet: -1.41 (0.45), residues: 139 loop : -1.70 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 764 HIS 0.006 0.001 HIS B 729 PHE 0.024 0.002 PHE A 436 TYR 0.023 0.002 TYR A 815 ARG 0.005 0.000 ARG B 573 Details of bonding type rmsd hydrogen bonds : bond 0.04398 ( 640) hydrogen bonds : angle 4.75076 ( 1806) covalent geometry : bond 0.00400 (11638) covalent geometry : angle 0.65351 (15856) Misc. bond : bond 0.00218 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 187 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 ARG cc_start: 0.8326 (ptp90) cc_final: 0.8055 (ptp90) REVERT: A 172 LYS cc_start: 0.7895 (mptt) cc_final: 0.7628 (mmtm) REVERT: A 243 ARG cc_start: 0.8304 (ttt90) cc_final: 0.7826 (mtp-110) REVERT: A 271 SER cc_start: 0.4327 (OUTLIER) cc_final: 0.2876 (p) REVERT: A 380 LEU cc_start: 0.5583 (OUTLIER) cc_final: 0.4982 (mt) REVERT: A 409 GLN cc_start: 0.5727 (OUTLIER) cc_final: 0.5372 (tt0) REVERT: A 413 GLN cc_start: 0.5720 (OUTLIER) cc_final: 0.3905 (mm-40) REVERT: A 431 LEU cc_start: 0.7264 (tp) cc_final: 0.6955 (tp) REVERT: A 480 GLU cc_start: 0.8132 (pp20) cc_final: 0.7759 (pp20) REVERT: A 481 LEU cc_start: 0.7995 (mt) cc_final: 0.7690 (mt) REVERT: A 535 ASN cc_start: 0.6540 (OUTLIER) cc_final: 0.5754 (t0) REVERT: A 631 ARG cc_start: 0.7748 (ttp-170) cc_final: 0.7436 (ptm160) REVERT: A 659 LYS cc_start: 0.7591 (tptp) cc_final: 0.7185 (tptm) REVERT: A 660 ASP cc_start: 0.7521 (t0) cc_final: 0.7191 (t70) REVERT: A 661 LYS cc_start: 0.7849 (OUTLIER) cc_final: 0.7394 (ptmm) REVERT: A 779 MET cc_start: 0.6384 (mtm) cc_final: 0.5602 (ttm) REVERT: A 786 GLU cc_start: 0.6695 (pt0) cc_final: 0.6348 (tm-30) REVERT: A 805 LEU cc_start: 0.6187 (OUTLIER) cc_final: 0.5817 (tt) REVERT: A 815 TYR cc_start: 0.7145 (m-80) cc_final: 0.6610 (m-10) REVERT: A 846 GLN cc_start: 0.7233 (mm-40) cc_final: 0.6913 (mm-40) REVERT: B 549 GLN cc_start: 0.7365 (pt0) cc_final: 0.6802 (pt0) REVERT: B 615 LEU cc_start: 0.8184 (mt) cc_final: 0.7844 (mm) REVERT: B 617 LYS cc_start: 0.8055 (tptp) cc_final: 0.7476 (mmtm) REVERT: B 631 LYS cc_start: 0.8093 (mptt) cc_final: 0.7833 (mptt) REVERT: B 672 ILE cc_start: 0.2442 (OUTLIER) cc_final: 0.2225 (mt) REVERT: B 679 LEU cc_start: 0.6041 (OUTLIER) cc_final: 0.5562 (mt) REVERT: B 704 LYS cc_start: 0.6492 (OUTLIER) cc_final: 0.6069 (mtpp) REVERT: B 779 ARG cc_start: 0.5987 (mmm160) cc_final: 0.5685 (mmm160) REVERT: B 781 HIS cc_start: 0.8046 (t70) cc_final: 0.7652 (t-90) REVERT: B 796 ARG cc_start: 0.7790 (ptm-80) cc_final: 0.7309 (ptm-80) REVERT: B 839 LYS cc_start: 0.7111 (mttt) cc_final: 0.6622 (mttt) REVERT: B 892 MET cc_start: 0.7818 (ttm) cc_final: 0.7503 (ttm) REVERT: B 925 GLU cc_start: 0.7112 (mm-30) cc_final: 0.6906 (mm-30) REVERT: B 964 ARG cc_start: 0.7676 (mtt180) cc_final: 0.7314 (ptt-90) REVERT: B 1094 GLU cc_start: 0.7363 (mt-10) cc_final: 0.6928 (mt-10) REVERT: B 1103 ARG cc_start: 0.7295 (mtt90) cc_final: 0.7015 (mtt90) outliers start: 61 outliers final: 35 residues processed: 233 average time/residue: 0.2804 time to fit residues: 89.2805 Evaluate side-chains 227 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 182 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 324 GLN Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 413 GLN Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 535 ASN Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 661 LYS Chi-restraints excluded: chain A residue 726 MET Chi-restraints excluded: chain A residue 747 ILE Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 882 LYS Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 684 HIS Chi-restraints excluded: chain B residue 704 LYS Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 802 ASP Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 938 ARG Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain B residue 1058 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 110 optimal weight: 0.9980 chunk 131 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 113 optimal weight: 0.7980 chunk 48 optimal weight: 0.4980 chunk 116 optimal weight: 0.6980 chunk 123 optimal weight: 3.9990 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 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 HIS ** B 864 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 898 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 908 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 = 0.4901 r_free = 0.4901 target = 0.218245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.184295 restraints weight = 18592.083| |-----------------------------------------------------------------------------| r_work (start): 0.4505 rms_B_bonded: 3.81 r_work: 0.4367 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.4367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5911 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11639 Z= 0.170 Angle : 0.655 7.666 15856 Z= 0.355 Chirality : 0.044 0.299 1819 Planarity : 0.005 0.078 1897 Dihedral : 17.484 74.814 1862 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 19.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 4.75 % Allowed : 24.49 % Favored : 70.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.23), residues: 1321 helix: 0.76 (0.19), residues: 726 sheet: -1.38 (0.45), residues: 139 loop : -1.60 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 807 HIS 0.011 0.001 HIS B 729 PHE 0.027 0.002 PHE B 571 TYR 0.016 0.002 TYR A 815 ARG 0.004 0.000 ARG B 573 Details of bonding type rmsd hydrogen bonds : bond 0.04305 ( 640) hydrogen bonds : angle 4.71333 ( 1806) covalent geometry : bond 0.00367 (11638) covalent geometry : angle 0.65523 (15856) Misc. bond : bond 0.00211 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 184 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 LYS cc_start: 0.7850 (mptt) cc_final: 0.7567 (mmtm) REVERT: A 253 MET cc_start: 0.7090 (tpp) cc_final: 0.5002 (tpp) REVERT: A 271 SER cc_start: 0.4478 (OUTLIER) cc_final: 0.3059 (p) REVERT: A 380 LEU cc_start: 0.5565 (OUTLIER) cc_final: 0.4936 (mt) REVERT: A 397 GLN cc_start: 0.7138 (mp10) cc_final: 0.6888 (mp10) REVERT: A 409 GLN cc_start: 0.5592 (OUTLIER) cc_final: 0.4754 (mt0) REVERT: A 413 GLN cc_start: 0.5640 (OUTLIER) cc_final: 0.3789 (mm-40) REVERT: A 431 LEU cc_start: 0.7321 (tp) cc_final: 0.7009 (tp) REVERT: A 450 PHE cc_start: 0.4971 (t80) cc_final: 0.4735 (t80) REVERT: A 480 GLU cc_start: 0.8176 (pp20) cc_final: 0.7779 (pp20) REVERT: A 481 LEU cc_start: 0.8005 (mt) cc_final: 0.7673 (mt) REVERT: A 535 ASN cc_start: 0.6533 (OUTLIER) cc_final: 0.5790 (t0) REVERT: A 631 ARG cc_start: 0.7697 (ttp-170) cc_final: 0.7394 (ptm160) REVERT: A 659 LYS cc_start: 0.7554 (tptp) cc_final: 0.7148 (tptm) REVERT: A 660 ASP cc_start: 0.7592 (t0) cc_final: 0.7191 (t70) REVERT: A 661 LYS cc_start: 0.7830 (OUTLIER) cc_final: 0.7390 (ptmm) REVERT: A 779 MET cc_start: 0.6415 (mtm) cc_final: 0.5578 (ttm) REVERT: A 786 GLU cc_start: 0.6636 (pt0) cc_final: 0.6316 (tm-30) REVERT: A 805 LEU cc_start: 0.6089 (OUTLIER) cc_final: 0.5729 (tt) REVERT: A 815 TYR cc_start: 0.7091 (m-80) cc_final: 0.6610 (m-10) REVERT: A 846 GLN cc_start: 0.7229 (mm-40) cc_final: 0.6896 (mm-40) REVERT: B 549 GLN cc_start: 0.7417 (pt0) cc_final: 0.6843 (pt0) REVERT: B 606 SER cc_start: 0.6972 (t) cc_final: 0.6768 (t) REVERT: B 617 LYS cc_start: 0.8013 (tptp) cc_final: 0.7423 (mmtm) REVERT: B 631 LYS cc_start: 0.8007 (mptt) cc_final: 0.7718 (mptt) REVERT: B 632 LYS cc_start: 0.8351 (tptt) cc_final: 0.8021 (tptp) REVERT: B 672 ILE cc_start: 0.2267 (OUTLIER) cc_final: 0.2012 (mt) REVERT: B 679 LEU cc_start: 0.6099 (OUTLIER) cc_final: 0.5746 (mm) REVERT: B 704 LYS cc_start: 0.6520 (OUTLIER) cc_final: 0.6123 (mtpp) REVERT: B 779 ARG cc_start: 0.6121 (mmm160) cc_final: 0.5717 (mmm160) REVERT: B 781 HIS cc_start: 0.8026 (t70) cc_final: 0.7671 (t-90) REVERT: B 796 ARG cc_start: 0.7773 (ptm-80) cc_final: 0.7303 (ptm-80) REVERT: B 839 LYS cc_start: 0.6893 (mttt) cc_final: 0.6621 (mttt) REVERT: B 852 GLN cc_start: 0.7406 (mt0) cc_final: 0.7124 (mt0) REVERT: B 892 MET cc_start: 0.7802 (ttm) cc_final: 0.7514 (ttm) REVERT: B 925 GLU cc_start: 0.7171 (mm-30) cc_final: 0.6927 (mm-30) REVERT: B 1094 GLU cc_start: 0.7406 (mt-10) cc_final: 0.7053 (mt-10) REVERT: B 1098 ASN cc_start: 0.7886 (m-40) cc_final: 0.7674 (p0) REVERT: B 1103 ARG cc_start: 0.7327 (mtt90) cc_final: 0.7026 (mtt90) outliers start: 56 outliers final: 30 residues processed: 222 average time/residue: 0.2938 time to fit residues: 88.8658 Evaluate side-chains 217 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 177 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 413 GLN Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 535 ASN Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 661 LYS Chi-restraints excluded: chain A residue 707 CYS Chi-restraints excluded: chain A residue 747 ILE Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 882 LYS Chi-restraints excluded: chain A residue 926 ILE Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 684 HIS Chi-restraints excluded: chain B residue 704 LYS Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain B residue 802 ASP Chi-restraints excluded: chain B residue 827 HIS Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 938 ARG Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain B residue 1058 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 56 optimal weight: 0.5980 chunk 105 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 119 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 27 optimal weight: 0.0980 chunk 83 optimal weight: 0.7980 chunk 133 optimal weight: 2.9990 chunk 10 optimal weight: 0.4980 chunk 67 optimal weight: 0.5980 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 324 GLN ** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 602 HIS B 647 HIS ** B 864 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 898 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4911 r_free = 0.4911 target = 0.219059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.185428 restraints weight = 18646.030| |-----------------------------------------------------------------------------| r_work (start): 0.4530 rms_B_bonded: 3.79 r_work: 0.4399 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.4399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5885 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11639 Z= 0.155 Angle : 0.651 8.284 15856 Z= 0.350 Chirality : 0.043 0.234 1819 Planarity : 0.004 0.078 1897 Dihedral : 17.380 73.861 1862 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 19.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 4.58 % Allowed : 24.83 % Favored : 70.59 % 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: -0.35 (0.23), residues: 1321 helix: 0.85 (0.19), residues: 726 sheet: -1.42 (0.45), residues: 139 loop : -1.54 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 807 HIS 0.011 0.001 HIS B 729 PHE 0.020 0.002 PHE B 571 TYR 0.015 0.002 TYR A 522 ARG 0.025 0.001 ARG A 524 Details of bonding type rmsd hydrogen bonds : bond 0.04162 ( 640) hydrogen bonds : angle 4.67788 ( 1806) covalent geometry : bond 0.00332 (11638) covalent geometry : angle 0.65072 (15856) Misc. bond : bond 0.00219 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 185 time to evaluate : 2.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 MET cc_start: 0.7015 (tpp) cc_final: 0.5018 (tpp) REVERT: A 271 SER cc_start: 0.4456 (OUTLIER) cc_final: 0.3036 (p) REVERT: A 380 LEU cc_start: 0.5435 (OUTLIER) cc_final: 0.4845 (mt) REVERT: A 397 GLN cc_start: 0.7133 (mp10) cc_final: 0.6825 (mp10) REVERT: A 409 GLN cc_start: 0.5589 (OUTLIER) cc_final: 0.5382 (tt0) REVERT: A 413 GLN cc_start: 0.5558 (OUTLIER) cc_final: 0.3777 (mm-40) REVERT: A 431 LEU cc_start: 0.7362 (tp) cc_final: 0.7048 (tp) REVERT: A 480 GLU cc_start: 0.8154 (pp20) cc_final: 0.7738 (pp20) REVERT: A 481 LEU cc_start: 0.7977 (mt) cc_final: 0.7650 (mt) REVERT: A 514 ASP cc_start: 0.7254 (OUTLIER) cc_final: 0.6942 (p0) REVERT: A 535 ASN cc_start: 0.6657 (OUTLIER) cc_final: 0.5930 (t0) REVERT: A 613 ASN cc_start: 0.7908 (OUTLIER) cc_final: 0.7551 (m-40) REVERT: A 631 ARG cc_start: 0.7664 (ttp-170) cc_final: 0.7273 (ptm-80) REVERT: A 659 LYS cc_start: 0.7417 (tptp) cc_final: 0.7009 (tptm) REVERT: A 660 ASP cc_start: 0.7537 (t0) cc_final: 0.7126 (t70) REVERT: A 661 LYS cc_start: 0.7777 (OUTLIER) cc_final: 0.7336 (ptmm) REVERT: A 743 SER cc_start: 0.6402 (t) cc_final: 0.5858 (m) REVERT: A 779 MET cc_start: 0.6351 (mtm) cc_final: 0.5529 (ttm) REVERT: A 786 GLU cc_start: 0.6490 (pt0) cc_final: 0.6192 (tm-30) REVERT: A 805 LEU cc_start: 0.6076 (OUTLIER) cc_final: 0.5713 (tt) REVERT: A 815 TYR cc_start: 0.6995 (m-80) cc_final: 0.6524 (m-10) REVERT: A 846 GLN cc_start: 0.7186 (mm-40) cc_final: 0.6851 (mm-40) REVERT: B 549 GLN cc_start: 0.7445 (pt0) cc_final: 0.7079 (pt0) REVERT: B 606 SER cc_start: 0.6990 (t) cc_final: 0.6779 (t) REVERT: B 617 LYS cc_start: 0.7908 (tptp) cc_final: 0.7388 (mmtm) REVERT: B 623 ARG cc_start: 0.0399 (OUTLIER) cc_final: -0.3252 (mmm160) REVERT: B 631 LYS cc_start: 0.8011 (mptt) cc_final: 0.7687 (mptt) REVERT: B 632 LYS cc_start: 0.8325 (tptt) cc_final: 0.8028 (tptp) REVERT: B 672 ILE cc_start: 0.2231 (OUTLIER) cc_final: 0.1990 (mt) REVERT: B 679 LEU cc_start: 0.6123 (OUTLIER) cc_final: 0.5804 (mm) REVERT: B 704 LYS cc_start: 0.6361 (OUTLIER) cc_final: 0.5998 (mtpp) REVERT: B 779 ARG cc_start: 0.6281 (mmm160) cc_final: 0.6045 (mmm160) REVERT: B 781 HIS cc_start: 0.7995 (t70) cc_final: 0.7709 (t70) REVERT: B 796 ARG cc_start: 0.7803 (ptm-80) cc_final: 0.7389 (ptm-80) REVERT: B 839 LYS cc_start: 0.6874 (mttt) cc_final: 0.6429 (mttt) REVERT: B 852 GLN cc_start: 0.7359 (mt0) cc_final: 0.7108 (mt0) REVERT: B 892 MET cc_start: 0.7742 (ttm) cc_final: 0.7368 (ttm) REVERT: B 893 ILE cc_start: 0.8046 (mt) cc_final: 0.7688 (mm) REVERT: B 925 GLU cc_start: 0.7186 (mm-30) cc_final: 0.6948 (mm-30) REVERT: B 964 ARG cc_start: 0.7584 (mtt180) cc_final: 0.7227 (ptt-90) REVERT: B 1028 TYR cc_start: 0.8335 (m-80) cc_final: 0.8079 (m-80) REVERT: B 1094 GLU cc_start: 0.7372 (mt-10) cc_final: 0.7022 (mt-10) REVERT: B 1103 ARG cc_start: 0.7263 (mtt90) cc_final: 0.6954 (mtt90) outliers start: 54 outliers final: 35 residues processed: 220 average time/residue: 0.4013 time to fit residues: 121.4766 Evaluate side-chains 227 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 179 time to evaluate : 1.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 324 GLN Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 413 GLN Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 514 ASP Chi-restraints excluded: chain A residue 535 ASN Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 613 ASN Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 661 LYS Chi-restraints excluded: chain A residue 707 CYS Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 882 LYS Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 914 GLU Chi-restraints excluded: chain A residue 926 ILE Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 623 ARG Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 680 SER Chi-restraints excluded: chain B residue 684 HIS Chi-restraints excluded: chain B residue 704 LYS Chi-restraints excluded: chain B residue 738 LYS Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 802 ASP Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 938 ARG Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain B residue 1058 GLN Chi-restraints excluded: chain B residue 1059 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 55 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 126 optimal weight: 0.0370 chunk 69 optimal weight: 0.9990 chunk 125 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 75 optimal weight: 5.9990 chunk 46 optimal weight: 0.5980 chunk 47 optimal weight: 0.5980 chunk 82 optimal weight: 0.5980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 GLN ** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 829 HIS B 551 GLN B 582 GLN B 647 HIS B 861 ASN ** B 864 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 898 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4912 r_free = 0.4912 target = 0.219070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.185251 restraints weight = 18488.747| |-----------------------------------------------------------------------------| r_work (start): 0.4527 rms_B_bonded: 3.78 r_work: 0.4393 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.4393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5890 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11639 Z= 0.154 Angle : 0.654 9.287 15856 Z= 0.352 Chirality : 0.043 0.232 1819 Planarity : 0.005 0.077 1897 Dihedral : 17.349 73.478 1862 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 19.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 4.75 % Allowed : 24.83 % Favored : 70.42 % 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 (0.23), residues: 1321 helix: 0.89 (0.19), residues: 726 sheet: -1.40 (0.45), residues: 139 loop : -1.55 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 807 HIS 0.010 0.001 HIS B1010 PHE 0.019 0.002 PHE B 571 TYR 0.014 0.002 TYR B 818 ARG 0.019 0.000 ARG A 524 Details of bonding type rmsd hydrogen bonds : bond 0.04148 ( 640) hydrogen bonds : angle 4.67781 ( 1806) covalent geometry : bond 0.00331 (11638) covalent geometry : angle 0.65438 (15856) Misc. bond : bond 0.00210 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 186 time to evaluate : 3.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 MET cc_start: 0.6989 (tpp) cc_final: 0.5093 (tpp) REVERT: A 271 SER cc_start: 0.4446 (OUTLIER) cc_final: 0.3047 (p) REVERT: A 334 LYS cc_start: 0.6704 (mtmm) cc_final: 0.6420 (mtmm) REVERT: A 380 LEU cc_start: 0.5479 (OUTLIER) cc_final: 0.4888 (mt) REVERT: A 413 GLN cc_start: 0.5497 (OUTLIER) cc_final: 0.3744 (mm-40) REVERT: A 431 LEU cc_start: 0.7370 (tp) cc_final: 0.7052 (tp) REVERT: A 480 GLU cc_start: 0.8118 (pp20) cc_final: 0.7704 (pp20) REVERT: A 481 LEU cc_start: 0.7994 (mt) cc_final: 0.7672 (mt) REVERT: A 514 ASP cc_start: 0.7142 (OUTLIER) cc_final: 0.6883 (p0) REVERT: A 535 ASN cc_start: 0.6672 (OUTLIER) cc_final: 0.5961 (t0) REVERT: A 555 LYS cc_start: 0.8379 (mptt) cc_final: 0.8083 (mptt) REVERT: A 613 ASN cc_start: 0.7951 (OUTLIER) cc_final: 0.7577 (m-40) REVERT: A 631 ARG cc_start: 0.7647 (ttp-170) cc_final: 0.7263 (ptm-80) REVERT: A 659 LYS cc_start: 0.7339 (tptp) cc_final: 0.6922 (mmmm) REVERT: A 660 ASP cc_start: 0.7551 (t0) cc_final: 0.7038 (t70) REVERT: A 684 VAL cc_start: 0.3207 (OUTLIER) cc_final: 0.2113 (t) REVERT: A 743 SER cc_start: 0.6416 (t) cc_final: 0.5842 (m) REVERT: A 779 MET cc_start: 0.6426 (mtm) cc_final: 0.5601 (ttm) REVERT: A 786 GLU cc_start: 0.6463 (pt0) cc_final: 0.6150 (tm-30) REVERT: A 805 LEU cc_start: 0.6066 (OUTLIER) cc_final: 0.5698 (tt) REVERT: A 815 TYR cc_start: 0.6977 (m-80) cc_final: 0.6499 (m-10) REVERT: A 846 GLN cc_start: 0.7207 (mm-40) cc_final: 0.6859 (mm-40) REVERT: B 549 GLN cc_start: 0.7473 (pt0) cc_final: 0.7102 (pt0) REVERT: B 606 SER cc_start: 0.6968 (t) cc_final: 0.6759 (t) REVERT: B 617 LYS cc_start: 0.7896 (tptp) cc_final: 0.7391 (mmtm) REVERT: B 623 ARG cc_start: 0.0435 (OUTLIER) cc_final: -0.2056 (mmt90) REVERT: B 632 LYS cc_start: 0.8231 (tptt) cc_final: 0.7915 (tptp) REVERT: B 672 ILE cc_start: 0.2182 (OUTLIER) cc_final: 0.1965 (mt) REVERT: B 679 LEU cc_start: 0.6205 (OUTLIER) cc_final: 0.5884 (mm) REVERT: B 704 LYS cc_start: 0.6370 (OUTLIER) cc_final: 0.6011 (mtpp) REVERT: B 747 VAL cc_start: 0.1443 (OUTLIER) cc_final: 0.0907 (p) REVERT: B 779 ARG cc_start: 0.6387 (mmm160) cc_final: 0.6177 (mmm160) REVERT: B 781 HIS cc_start: 0.7940 (t70) cc_final: 0.7709 (t70) REVERT: B 796 ARG cc_start: 0.7804 (ptm-80) cc_final: 0.7392 (ptm-80) REVERT: B 839 LYS cc_start: 0.6848 (mttt) cc_final: 0.6392 (mttt) REVERT: B 852 GLN cc_start: 0.7362 (mt0) cc_final: 0.7107 (mt0) REVERT: B 892 MET cc_start: 0.7771 (ttm) cc_final: 0.7357 (ttm) REVERT: B 893 ILE cc_start: 0.8044 (mt) cc_final: 0.7695 (mm) REVERT: B 925 GLU cc_start: 0.7190 (mm-30) cc_final: 0.6953 (mm-30) REVERT: B 1028 TYR cc_start: 0.8354 (m-80) cc_final: 0.8082 (m-80) REVERT: B 1094 GLU cc_start: 0.7454 (mt-10) cc_final: 0.7095 (mt-10) REVERT: B 1103 ARG cc_start: 0.7245 (mtt90) cc_final: 0.6949 (mtt90) outliers start: 56 outliers final: 37 residues processed: 221 average time/residue: 0.6032 time to fit residues: 186.3723 Evaluate side-chains 228 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 178 time to evaluate : 2.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 324 GLN Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 413 GLN Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 514 ASP Chi-restraints excluded: chain A residue 535 ASN Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 613 ASN Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 707 CYS Chi-restraints excluded: chain A residue 747 ILE Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 813 MET Chi-restraints excluded: chain A residue 882 LYS Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 914 GLU Chi-restraints excluded: chain A residue 926 ILE Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 623 ARG Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 680 SER Chi-restraints excluded: chain B residue 684 HIS Chi-restraints excluded: chain B residue 704 LYS Chi-restraints excluded: chain B residue 738 LYS Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain B residue 802 ASP Chi-restraints excluded: chain B residue 827 HIS Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 938 ARG Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 1015 CYS Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain B residue 1058 GLN Chi-restraints excluded: chain B residue 1059 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 32 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 0.0370 chunk 87 optimal weight: 0.4980 chunk 109 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 116 optimal weight: 0.6980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 GLN ** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 HIS B 861 ASN ** B 864 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 898 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4911 r_free = 0.4911 target = 0.218991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.185270 restraints weight = 18576.752| |-----------------------------------------------------------------------------| r_work (start): 0.4527 rms_B_bonded: 3.76 r_work: 0.4392 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.4392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5896 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11639 Z= 0.159 Angle : 0.667 10.513 15856 Z= 0.357 Chirality : 0.043 0.225 1819 Planarity : 0.005 0.077 1897 Dihedral : 17.335 73.093 1862 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 19.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 4.41 % Allowed : 25.00 % Favored : 70.59 % 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: -0.28 (0.23), residues: 1321 helix: 0.93 (0.19), residues: 725 sheet: -1.35 (0.46), residues: 139 loop : -1.58 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 807 HIS 0.009 0.001 HIS B 729 PHE 0.017 0.002 PHE B 571 TYR 0.016 0.002 TYR B 818 ARG 0.015 0.001 ARG A 524 Details of bonding type rmsd hydrogen bonds : bond 0.04155 ( 640) hydrogen bonds : angle 4.70866 ( 1806) covalent geometry : bond 0.00341 (11638) covalent geometry : angle 0.66674 (15856) Misc. bond : bond 0.00219 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 187 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 ARG cc_start: 0.8283 (ptp90) cc_final: 0.7929 (ptp90) REVERT: A 253 MET cc_start: 0.6974 (tpp) cc_final: 0.5138 (tpp) REVERT: A 271 SER cc_start: 0.4455 (OUTLIER) cc_final: 0.3076 (p) REVERT: A 380 LEU cc_start: 0.5519 (OUTLIER) cc_final: 0.4952 (mt) REVERT: A 413 GLN cc_start: 0.5505 (OUTLIER) cc_final: 0.3793 (mm-40) REVERT: A 431 LEU cc_start: 0.7377 (tp) cc_final: 0.7063 (tp) REVERT: A 492 MET cc_start: 0.8652 (ttt) cc_final: 0.8360 (ttt) REVERT: A 535 ASN cc_start: 0.6714 (OUTLIER) cc_final: 0.6008 (t0) REVERT: A 555 LYS cc_start: 0.8386 (mptt) cc_final: 0.8096 (mptt) REVERT: A 613 ASN cc_start: 0.7988 (OUTLIER) cc_final: 0.7620 (m-40) REVERT: A 631 ARG cc_start: 0.7691 (ttp-170) cc_final: 0.7405 (mtm110) REVERT: A 659 LYS cc_start: 0.7357 (tptp) cc_final: 0.6916 (ttmm) REVERT: A 707 CYS cc_start: 0.6583 (OUTLIER) cc_final: 0.6150 (p) REVERT: A 743 SER cc_start: 0.6495 (t) cc_final: 0.5884 (m) REVERT: A 779 MET cc_start: 0.6420 (mtm) cc_final: 0.5625 (ttm) REVERT: A 786 GLU cc_start: 0.6420 (pt0) cc_final: 0.6143 (tm-30) REVERT: A 805 LEU cc_start: 0.6087 (OUTLIER) cc_final: 0.5724 (tt) REVERT: A 815 TYR cc_start: 0.7013 (m-80) cc_final: 0.6534 (m-10) REVERT: A 829 HIS cc_start: 0.7174 (m90) cc_final: 0.6631 (m90) REVERT: A 846 GLN cc_start: 0.7222 (mm-40) cc_final: 0.6885 (mm-40) REVERT: A 914 GLU cc_start: 0.4236 (OUTLIER) cc_final: 0.3770 (pm20) REVERT: B 549 GLN cc_start: 0.7410 (pt0) cc_final: 0.7043 (pt0) REVERT: B 599 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.6926 (tt0) REVERT: B 615 LEU cc_start: 0.7967 (mt) cc_final: 0.7729 (mm) REVERT: B 617 LYS cc_start: 0.7906 (tptp) cc_final: 0.7413 (mmtm) REVERT: B 623 ARG cc_start: 0.0444 (OUTLIER) cc_final: -0.2237 (mmp-170) REVERT: B 632 LYS cc_start: 0.8253 (tptt) cc_final: 0.7918 (tptp) REVERT: B 672 ILE cc_start: 0.2312 (OUTLIER) cc_final: 0.2083 (mt) REVERT: B 679 LEU cc_start: 0.6365 (OUTLIER) cc_final: 0.6051 (mm) REVERT: B 704 LYS cc_start: 0.6415 (OUTLIER) cc_final: 0.6065 (mtpp) REVERT: B 796 ARG cc_start: 0.7822 (ptm-80) cc_final: 0.7406 (ptm-80) REVERT: B 839 LYS cc_start: 0.6763 (mttt) cc_final: 0.6296 (mttt) REVERT: B 852 GLN cc_start: 0.7352 (mt0) cc_final: 0.7113 (mt0) REVERT: B 892 MET cc_start: 0.7722 (ttm) cc_final: 0.7326 (ttm) REVERT: B 893 ILE cc_start: 0.8093 (mt) cc_final: 0.7784 (mm) REVERT: B 925 GLU cc_start: 0.7015 (mm-30) cc_final: 0.6809 (mm-30) REVERT: B 1028 TYR cc_start: 0.8380 (m-80) cc_final: 0.8129 (m-80) REVERT: B 1094 GLU cc_start: 0.7483 (mt-10) cc_final: 0.7094 (mt-10) REVERT: B 1103 ARG cc_start: 0.7255 (mtt90) cc_final: 0.6948 (mtt90) outliers start: 52 outliers final: 35 residues processed: 222 average time/residue: 0.3040 time to fit residues: 91.5442 Evaluate side-chains 228 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 180 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 324 GLN Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 413 GLN Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 514 ASP Chi-restraints excluded: chain A residue 535 ASN Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 613 ASN Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 672 MET Chi-restraints excluded: chain A residue 707 CYS Chi-restraints excluded: chain A residue 747 ILE Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 813 MET Chi-restraints excluded: chain A residue 882 LYS Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 914 GLU Chi-restraints excluded: chain A residue 926 ILE Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 623 ARG Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 680 SER Chi-restraints excluded: chain B residue 684 HIS Chi-restraints excluded: chain B residue 704 LYS Chi-restraints excluded: chain B residue 738 LYS Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain B residue 802 ASP Chi-restraints excluded: chain B residue 827 HIS Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 1015 CYS Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain B residue 1058 GLN Chi-restraints excluded: chain B residue 1059 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 19 optimal weight: 0.6980 chunk 71 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 83 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 97 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 26 optimal weight: 0.3980 chunk 29 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 GLN ** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 HIS ** B 864 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 898 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4908 r_free = 0.4908 target = 0.218468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.184663 restraints weight = 18390.190| |-----------------------------------------------------------------------------| r_work (start): 0.4511 rms_B_bonded: 3.74 r_work: 0.4375 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.4375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5913 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11639 Z= 0.165 Angle : 0.684 9.632 15856 Z= 0.365 Chirality : 0.044 0.221 1819 Planarity : 0.005 0.078 1897 Dihedral : 17.325 72.988 1862 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 20.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 4.24 % Allowed : 26.10 % Favored : 69.66 % 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: -0.34 (0.23), residues: 1321 helix: 0.89 (0.19), residues: 731 sheet: -1.34 (0.47), residues: 136 loop : -1.65 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 764 HIS 0.010 0.001 HIS B 781 PHE 0.032 0.002 PHE B 784 TYR 0.016 0.002 TYR B 818 ARG 0.014 0.001 ARG A 524 Details of bonding type rmsd hydrogen bonds : bond 0.04244 ( 640) hydrogen bonds : angle 4.74552 ( 1806) covalent geometry : bond 0.00355 (11638) covalent geometry : angle 0.68369 (15856) Misc. bond : bond 0.00207 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 180 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 MET cc_start: 0.7026 (tpp) cc_final: 0.5196 (tpp) REVERT: A 271 SER cc_start: 0.4469 (OUTLIER) cc_final: 0.3064 (p) REVERT: A 380 LEU cc_start: 0.5575 (OUTLIER) cc_final: 0.4999 (mt) REVERT: A 413 GLN cc_start: 0.5426 (OUTLIER) cc_final: 0.3727 (mm-40) REVERT: A 431 LEU cc_start: 0.7439 (tp) cc_final: 0.7124 (tp) REVERT: A 492 MET cc_start: 0.8657 (ttt) cc_final: 0.8375 (ttt) REVERT: A 535 ASN cc_start: 0.6725 (OUTLIER) cc_final: 0.6077 (t0) REVERT: A 555 LYS cc_start: 0.8391 (mptt) cc_final: 0.8108 (mptt) REVERT: A 613 ASN cc_start: 0.7995 (OUTLIER) cc_final: 0.7610 (m-40) REVERT: A 631 ARG cc_start: 0.7669 (ttp-170) cc_final: 0.7371 (mtm110) REVERT: A 661 LYS cc_start: 0.7762 (ttmt) cc_final: 0.7333 (ptmm) REVERT: A 684 VAL cc_start: 0.3249 (OUTLIER) cc_final: 0.2288 (t) REVERT: A 707 CYS cc_start: 0.6571 (OUTLIER) cc_final: 0.6292 (p) REVERT: A 779 MET cc_start: 0.6441 (mtm) cc_final: 0.5648 (ttm) REVERT: A 786 GLU cc_start: 0.6464 (pt0) cc_final: 0.6177 (tm-30) REVERT: A 805 LEU cc_start: 0.6114 (OUTLIER) cc_final: 0.5746 (tt) REVERT: A 815 TYR cc_start: 0.7071 (m-80) cc_final: 0.6585 (m-10) REVERT: A 829 HIS cc_start: 0.7183 (m90) cc_final: 0.6641 (m90) REVERT: A 846 GLN cc_start: 0.7225 (mm-40) cc_final: 0.6968 (mm-40) REVERT: A 850 GLU cc_start: 0.7044 (mm-30) cc_final: 0.6491 (mm-30) REVERT: B 549 GLN cc_start: 0.7411 (pt0) cc_final: 0.7049 (pt0) REVERT: B 599 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6901 (tt0) REVERT: B 615 LEU cc_start: 0.7983 (mt) cc_final: 0.7751 (mm) REVERT: B 617 LYS cc_start: 0.7875 (tptp) cc_final: 0.7407 (mmtm) REVERT: B 623 ARG cc_start: 0.0360 (OUTLIER) cc_final: -0.3116 (mmt-90) REVERT: B 632 LYS cc_start: 0.8185 (tptt) cc_final: 0.7843 (tptp) REVERT: B 672 ILE cc_start: 0.2299 (OUTLIER) cc_final: 0.2057 (mt) REVERT: B 704 LYS cc_start: 0.6375 (OUTLIER) cc_final: 0.6030 (mtpp) REVERT: B 729 HIS cc_start: 0.6858 (m-70) cc_final: 0.6550 (m170) REVERT: B 796 ARG cc_start: 0.7811 (ptm-80) cc_final: 0.7392 (ptm-80) REVERT: B 839 LYS cc_start: 0.6769 (mttt) cc_final: 0.6294 (mttt) REVERT: B 892 MET cc_start: 0.7709 (ttm) cc_final: 0.7225 (ttm) REVERT: B 893 ILE cc_start: 0.8122 (mt) cc_final: 0.7781 (mm) REVERT: B 964 ARG cc_start: 0.7630 (mtt180) cc_final: 0.7334 (ptt-90) REVERT: B 1028 TYR cc_start: 0.8409 (m-80) cc_final: 0.8102 (m-80) REVERT: B 1094 GLU cc_start: 0.7537 (mt-10) cc_final: 0.7127 (mt-10) REVERT: B 1103 ARG cc_start: 0.7250 (mtt90) cc_final: 0.6972 (mtt90) outliers start: 50 outliers final: 36 residues processed: 214 average time/residue: 0.2830 time to fit residues: 82.9540 Evaluate side-chains 225 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 177 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 324 GLN Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 413 GLN Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 514 ASP Chi-restraints excluded: chain A residue 535 ASN Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 613 ASN Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 672 MET Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 707 CYS Chi-restraints excluded: chain A residue 747 ILE Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 813 MET Chi-restraints excluded: chain A residue 882 LYS Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 914 GLU Chi-restraints excluded: chain A residue 926 ILE Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 623 ARG Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 680 SER Chi-restraints excluded: chain B residue 684 HIS Chi-restraints excluded: chain B residue 704 LYS Chi-restraints excluded: chain B residue 738 LYS Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 802 ASP Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 1015 CYS Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain B residue 1058 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 119 optimal weight: 0.0980 chunk 124 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 128 optimal weight: 0.8980 chunk 63 optimal weight: 0.5980 chunk 80 optimal weight: 0.1980 chunk 72 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 107 optimal weight: 0.6980 chunk 105 optimal weight: 0.6980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 GLN ** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 HIS B 852 GLN ** B 864 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4916 r_free = 0.4916 target = 0.219309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.185687 restraints weight = 18345.346| |-----------------------------------------------------------------------------| r_work (start): 0.4520 rms_B_bonded: 3.75 r_work: 0.4385 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.4385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5891 moved from start: 0.3733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 11639 Z= 0.156 Angle : 0.687 10.669 15856 Z= 0.365 Chirality : 0.044 0.328 1819 Planarity : 0.005 0.078 1897 Dihedral : 17.269 72.264 1862 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 19.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 3.81 % Allowed : 26.95 % Favored : 69.24 % 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: -0.29 (0.24), residues: 1321 helix: 0.92 (0.19), residues: 732 sheet: -1.35 (0.47), residues: 136 loop : -1.62 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 807 HIS 0.013 0.001 HIS B 729 PHE 0.017 0.002 PHE B 571 TYR 0.015 0.002 TYR A 299 ARG 0.013 0.001 ARG A 524 Details of bonding type rmsd hydrogen bonds : bond 0.04202 ( 640) hydrogen bonds : angle 4.74897 ( 1806) covalent geometry : bond 0.00337 (11638) covalent geometry : angle 0.68685 (15856) Misc. bond : bond 0.00216 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7742.35 seconds wall clock time: 141 minutes 15.20 seconds (8475.20 seconds total)