Starting phenix.real_space_refine on Sat Aug 23 10:39:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oma_16972/08_2025/8oma_16972.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oma_16972/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8oma_16972/08_2025/8oma_16972.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oma_16972/08_2025/8oma_16972.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8oma_16972/08_2025/8oma_16972.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oma_16972/08_2025/8oma_16972.map" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.024 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 3.01, per 1000 atoms: 0.26 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: 1.08 Conformation dependent library (CDL) restraints added in 513.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.31 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: 2.33 Time building geometry restraints manager: 1.41 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: 2.390 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.560 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.680 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.51 (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 ARG 0.025 0.002 ARG B 938 TYR 0.032 0.005 TYR B 991 PHE 0.027 0.005 PHE B1007 TRP 0.017 0.005 TRP A 764 HIS 0.016 0.003 HIS B 647 Details of bonding type rmsd covalent geometry : bond 0.00765 (11638) covalent geometry : angle 1.30443 (15856) hydrogen bonds : bond 0.13805 ( 640) hydrogen bonds : angle 6.35725 ( 1806) 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 : 0.429 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: 0.1536 time to fit residues: 49.1071 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 : 0.410 ------------------------------------------------------------------------------- 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 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 ** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 HIS B 729 HIS ** 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** B1010 HIS ** B1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1120 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4928 r_free = 0.4928 target = 0.221211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4613 r_free = 0.4613 target = 0.189446 restraints weight = 18416.119| |-----------------------------------------------------------------------------| r_work (start): 0.4541 rms_B_bonded: 3.61 r_work: 0.4407 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.4407 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4404 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4404 r_free = 0.4404 target_work(ls_wunit_k1) = 0.170 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4404 r_free = 0.4404 target_work(ls_wunit_k1) = 0.170 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4404 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5852 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 11639 Z= 0.194 Angle : 0.696 9.755 15856 Z= 0.376 Chirality : 0.044 0.203 1819 Planarity : 0.005 0.073 1897 Dihedral : 18.201 89.228 1900 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 21.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 3.31 % Allowed : 22.37 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.23), residues: 1321 helix: 0.31 (0.18), residues: 725 sheet: -1.78 (0.41), residues: 162 loop : -1.85 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 382 TYR 0.013 0.002 TYR B 877 PHE 0.042 0.002 PHE A 286 TRP 0.009 0.001 TRP A 764 HIS 0.007 0.001 HIS B 729 Details of bonding type rmsd covalent geometry : bond 0.00418 (11638) covalent geometry : angle 0.69574 (15856) hydrogen bonds : bond 0.04868 ( 640) hydrogen bonds : angle 5.05607 ( 1806) Misc. bond : bond 0.00649 ( 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 240 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 201 time to evaluate : 0.267 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: A 188 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7353 (mt-10) REVERT: A 229 LYS cc_start: 0.4730 (OUTLIER) cc_final: 0.3992 (ttpp) REVERT: A 324 GLN cc_start: 0.7584 (mp10) cc_final: 0.7289 (mp10) REVERT: A 386 ASP cc_start: 0.6416 (t0) cc_final: 0.6188 (t0) REVERT: A 468 PHE cc_start: 0.6056 (m-80) cc_final: 0.5848 (m-10) REVERT: A 572 GLU cc_start: 0.8088 (pt0) cc_final: 0.7858 (pp20) REVERT: A 594 THR cc_start: 0.8084 (OUTLIER) cc_final: 0.7815 (t) REVERT: A 631 ARG cc_start: 0.7554 (ttp-170) cc_final: 0.7284 (ptm160) REVERT: A 815 TYR cc_start: 0.6908 (m-10) cc_final: 0.6491 (m-10) REVERT: B 549 GLN cc_start: 0.7242 (pt0) cc_final: 0.6542 (pt0) REVERT: B 555 LYS cc_start: 0.6922 (OUTLIER) cc_final: 0.6643 (mtpp) REVERT: B 577 LYS cc_start: 0.7194 (tttt) cc_final: 0.6903 (ttmm) REVERT: B 578 LYS cc_start: 0.7652 (tttt) cc_final: 0.7138 (tmtt) REVERT: B 584 LEU cc_start: 0.7858 (mt) cc_final: 0.7509 (mt) REVERT: B 640 LEU cc_start: 0.5262 (OUTLIER) cc_final: 0.5029 (mp) REVERT: B 796 ARG cc_start: 0.7737 (ptm-80) cc_final: 0.7323 (ptm-80) REVERT: B 839 LYS cc_start: 0.7015 (mttt) cc_final: 0.6698 (tptp) REVERT: B 892 MET cc_start: 0.7746 (ttm) cc_final: 0.7321 (ttm) REVERT: B 925 GLU cc_start: 0.7134 (mm-30) cc_final: 0.6907 (mm-30) REVERT: B 938 ARG cc_start: 0.6295 (OUTLIER) cc_final: 0.6057 (tpm170) REVERT: B 964 ARG cc_start: 0.7712 (mtt180) cc_final: 0.7444 (ptt-90) outliers start: 39 outliers final: 20 residues processed: 222 average time/residue: 0.1208 time to fit residues: 36.9041 Evaluate side-chains 218 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 193 time to evaluate : 0.399 ------------------------------------------------------------------------------- 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 456 THR Chi-restraints excluded: chain A residue 460 MET 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 561 LEU Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 640 LEU 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 81 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 115 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 chunk 77 optimal weight: 7.9990 chunk 121 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 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** ** A 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 HIS B 684 HIS B 817 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4906 r_free = 0.4906 target = 0.218326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.184968 restraints weight = 18412.911| |-----------------------------------------------------------------------------| r_work (start): 0.4510 rms_B_bonded: 3.69 r_work: 0.4374 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.4374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5903 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11639 Z= 0.195 Angle : 0.672 7.495 15856 Z= 0.365 Chirality : 0.044 0.220 1819 Planarity : 0.005 0.077 1897 Dihedral : 17.898 80.271 1873 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 20.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 4.66 % Allowed : 22.63 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.23), residues: 1321 helix: 0.46 (0.19), residues: 724 sheet: -1.83 (0.41), residues: 165 loop : -1.70 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 752 TYR 0.013 0.002 TYR A 769 PHE 0.049 0.002 PHE A 286 TRP 0.010 0.001 TRP A 764 HIS 0.012 0.002 HIS B 684 Details of bonding type rmsd covalent geometry : bond 0.00417 (11638) covalent geometry : angle 0.67209 (15856) hydrogen bonds : bond 0.04635 ( 640) hydrogen bonds : angle 4.92112 ( 1806) Misc. bond : bond 0.00286 ( 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 250 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 195 time to evaluate : 0.270 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 188 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7499 (mt-10) REVERT: A 245 LEU cc_start: 0.5868 (OUTLIER) cc_final: 0.5544 (tm) REVERT: A 253 MET cc_start: 0.7017 (tpp) cc_final: 0.5086 (tpp) REVERT: A 271 SER cc_start: 0.4376 (OUTLIER) cc_final: 0.2959 (p) REVERT: A 386 ASP cc_start: 0.6467 (t0) cc_final: 0.6261 (t0) REVERT: A 397 GLN cc_start: 0.7206 (mp10) cc_final: 0.7004 (mp10) REVERT: A 409 GLN cc_start: 0.5441 (OUTLIER) cc_final: 0.4456 (mt0) REVERT: A 431 LEU cc_start: 0.7237 (tp) cc_final: 0.6933 (tp) REVERT: A 450 PHE cc_start: 0.4733 (t80) cc_final: 0.4421 (t80) REVERT: A 453 MET cc_start: 0.6823 (tpp) cc_final: 0.6602 (tpp) REVERT: A 535 ASN cc_start: 0.6614 (OUTLIER) cc_final: 0.5901 (t0) REVERT: A 572 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7831 (pt0) REVERT: A 631 ARG cc_start: 0.7542 (ttp-170) cc_final: 0.7268 (ptm160) REVERT: A 661 LYS cc_start: 0.7930 (OUTLIER) cc_final: 0.7583 (ptmm) REVERT: A 786 GLU cc_start: 0.6764 (pt0) cc_final: 0.6436 (tm-30) REVERT: A 811 LEU cc_start: 0.5756 (OUTLIER) cc_final: 0.5346 (tt) REVERT: B 549 GLN cc_start: 0.7327 (pt0) cc_final: 0.6676 (pt0) REVERT: B 615 LEU cc_start: 0.8189 (mt) cc_final: 0.7857 (mm) REVERT: B 617 LYS cc_start: 0.7918 (tptp) cc_final: 0.7316 (mmtm) REVERT: B 631 LYS cc_start: 0.8168 (mptt) cc_final: 0.7965 (mptt) REVERT: B 640 LEU cc_start: 0.5288 (OUTLIER) cc_final: 0.5034 (mm) REVERT: B 679 LEU cc_start: 0.5913 (OUTLIER) cc_final: 0.5475 (mt) REVERT: B 796 ARG cc_start: 0.7825 (ptm-80) cc_final: 0.7398 (ptm-80) REVERT: B 892 MET cc_start: 0.7746 (ttm) cc_final: 0.7337 (ttm) REVERT: B 925 GLU cc_start: 0.7084 (mm-30) cc_final: 0.6831 (mm-30) REVERT: B 964 ARG cc_start: 0.7748 (mtt180) cc_final: 0.7427 (ptt-90) REVERT: B 1091 LYS cc_start: 0.8155 (tppt) cc_final: 0.7531 (tppt) REVERT: B 1094 GLU cc_start: 0.7340 (mt-10) cc_final: 0.6430 (mt-10) outliers start: 55 outliers final: 27 residues processed: 231 average time/residue: 0.1097 time to fit residues: 35.1117 Evaluate side-chains 216 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 180 time to evaluate : 0.270 ------------------------------------------------------------------------------- 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 245 LEU 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 358 GLU Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 457 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 661 LYS Chi-restraints excluded: chain A residue 726 MET Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 679 LEU 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 1060 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 106 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 chunk 1 optimal weight: 30.0000 chunk 7 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 GLN ** 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 A 846 GLN B 647 HIS ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4896 r_free = 0.4896 target = 0.217552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.184376 restraints weight = 18434.515| |-----------------------------------------------------------------------------| r_work (start): 0.4505 rms_B_bonded: 3.62 r_work: 0.4375 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.4375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5896 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11639 Z= 0.184 Angle : 0.658 10.588 15856 Z= 0.357 Chirality : 0.043 0.217 1819 Planarity : 0.005 0.077 1897 Dihedral : 17.720 76.194 1864 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 19.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 5.17 % Allowed : 22.46 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.69 (0.23), residues: 1321 helix: 0.56 (0.19), residues: 725 sheet: -1.54 (0.43), residues: 148 loop : -1.69 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 752 TYR 0.017 0.002 TYR B 877 PHE 0.023 0.002 PHE A 436 TRP 0.009 0.001 TRP A 764 HIS 0.004 0.001 HIS B1029 Details of bonding type rmsd covalent geometry : bond 0.00396 (11638) covalent geometry : angle 0.65808 (15856) hydrogen bonds : bond 0.04446 ( 640) hydrogen bonds : angle 4.85026 ( 1806) Misc. bond : bond 0.00242 ( 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 251 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 190 time to evaluate : 0.416 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: A 171 ARG cc_start: 0.8259 (ptp90) cc_final: 0.7894 (ptp90) REVERT: A 253 MET cc_start: 0.7002 (tpp) cc_final: 0.5386 (tpp) REVERT: A 271 SER cc_start: 0.4321 (OUTLIER) cc_final: 0.2934 (p) REVERT: A 279 LEU cc_start: 0.4954 (OUTLIER) cc_final: 0.4686 (mp) REVERT: A 311 ASN cc_start: 0.8198 (OUTLIER) cc_final: 0.7798 (t0) REVERT: A 380 LEU cc_start: 0.5583 (OUTLIER) cc_final: 0.4939 (mt) REVERT: A 397 GLN cc_start: 0.7163 (mp10) cc_final: 0.6889 (mp10) REVERT: A 413 GLN cc_start: 0.5805 (OUTLIER) cc_final: 0.3950 (mm-40) REVERT: A 431 LEU cc_start: 0.7315 (tp) cc_final: 0.7024 (tp) REVERT: A 450 PHE cc_start: 0.4598 (t80) cc_final: 0.4250 (t80) REVERT: A 535 ASN cc_start: 0.6624 (OUTLIER) cc_final: 0.5874 (t0) REVERT: A 631 ARG cc_start: 0.7687 (ttp-170) cc_final: 0.7395 (ptm160) REVERT: A 661 LYS cc_start: 0.7930 (OUTLIER) cc_final: 0.7582 (ptmm) REVERT: A 743 SER cc_start: 0.6581 (t) cc_final: 0.5976 (m) REVERT: A 779 MET cc_start: 0.6420 (mtm) cc_final: 0.5587 (ttm) REVERT: A 786 GLU cc_start: 0.6619 (pt0) cc_final: 0.6336 (tm-30) REVERT: A 805 LEU cc_start: 0.6068 (OUTLIER) cc_final: 0.5692 (tt) REVERT: B 549 GLN cc_start: 0.7275 (pt0) cc_final: 0.6757 (pt0) REVERT: B 615 LEU cc_start: 0.8168 (mt) cc_final: 0.7865 (mm) REVERT: B 617 LYS cc_start: 0.8033 (tptp) cc_final: 0.7419 (mmtm) REVERT: B 631 LYS cc_start: 0.8142 (mptt) cc_final: 0.7888 (mptt) REVERT: B 640 LEU cc_start: 0.5603 (OUTLIER) cc_final: 0.5270 (mm) REVERT: B 672 ILE cc_start: 0.2481 (OUTLIER) cc_final: 0.2248 (mt) REVERT: B 679 LEU cc_start: 0.6077 (OUTLIER) cc_final: 0.5600 (mt) REVERT: B 704 LYS cc_start: 0.6462 (OUTLIER) cc_final: 0.6019 (mtpp) REVERT: B 796 ARG cc_start: 0.7815 (ptm-80) cc_final: 0.7328 (ptm-80) REVERT: B 839 LYS cc_start: 0.6930 (mptt) cc_final: 0.6564 (mttt) REVERT: B 852 GLN cc_start: 0.7322 (mt0) cc_final: 0.7071 (mt0) REVERT: B 892 MET cc_start: 0.7759 (ttm) cc_final: 0.7338 (ttm) REVERT: B 925 GLU cc_start: 0.7102 (mm-30) cc_final: 0.6838 (mm-30) REVERT: B 964 ARG cc_start: 0.7764 (mtt180) cc_final: 0.7403 (ptt-90) REVERT: B 1091 LYS cc_start: 0.8055 (tppt) cc_final: 0.7758 (tppt) outliers start: 61 outliers final: 31 residues processed: 230 average time/residue: 0.1231 time to fit residues: 39.0623 Evaluate side-chains 221 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 178 time to evaluate : 0.412 ------------------------------------------------------------------------------- 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 311 ASN Chi-restraints excluded: chain A residue 324 GLN Chi-restraints excluded: chain A residue 325 SER 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 524 ARG 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 729 MET 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 B residue 561 LEU Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 644 THR 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 704 LYS 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 1034 VAL Chi-restraints excluded: chain B residue 1058 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 9 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 chunk 117 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 102 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 103 optimal weight: 0.2980 chunk 129 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 GLN ** 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 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 846 GLN B 647 HIS B 692 GLN B 861 ASN ** B 864 HIS ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4835 r_free = 0.4835 target = 0.208338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.174167 restraints weight = 18614.808| |-----------------------------------------------------------------------------| r_work (start): 0.4445 rms_B_bonded: 3.95 r_work: 0.4290 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.4290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6018 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 11639 Z= 0.261 Angle : 0.726 9.179 15856 Z= 0.394 Chirality : 0.046 0.221 1819 Planarity : 0.005 0.081 1897 Dihedral : 17.794 77.083 1862 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 23.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 5.59 % Allowed : 24.07 % Favored : 70.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.93 (0.23), residues: 1321 helix: 0.33 (0.19), residues: 731 sheet: -1.55 (0.45), residues: 138 loop : -1.78 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 573 TYR 0.017 0.002 TYR B 877 PHE 0.039 0.002 PHE A 436 TRP 0.012 0.002 TRP A 764 HIS 0.006 0.001 HIS B1029 Details of bonding type rmsd covalent geometry : bond 0.00556 (11638) covalent geometry : angle 0.72566 (15856) hydrogen bonds : bond 0.04878 ( 640) hydrogen bonds : angle 5.05026 ( 1806) Misc. bond : bond 0.00214 ( 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 251 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 185 time to evaluate : 0.313 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: 0.8303 (ptp90) cc_final: 0.7931 (ptp90) REVERT: A 253 MET cc_start: 0.7150 (tpp) cc_final: 0.5627 (tpp) REVERT: A 271 SER cc_start: 0.4513 (OUTLIER) cc_final: 0.3436 (t) REVERT: A 311 ASN cc_start: 0.8366 (OUTLIER) cc_final: 0.7983 (m-40) REVERT: A 312 LEU cc_start: 0.7452 (OUTLIER) cc_final: 0.7213 (mt) REVERT: A 371 GLU cc_start: 0.6704 (OUTLIER) cc_final: 0.6274 (tt0) REVERT: A 380 LEU cc_start: 0.5797 (OUTLIER) cc_final: 0.5239 (mt) REVERT: A 397 GLN cc_start: 0.7137 (mp10) cc_final: 0.6798 (mp10) REVERT: A 413 GLN cc_start: 0.5840 (OUTLIER) cc_final: 0.3985 (mm-40) REVERT: A 431 LEU cc_start: 0.7463 (tp) cc_final: 0.7158 (tp) REVERT: A 450 PHE cc_start: 0.4589 (t80) cc_final: 0.4173 (t80) REVERT: A 535 ASN cc_start: 0.6581 (OUTLIER) cc_final: 0.5730 (t0) REVERT: A 631 ARG cc_start: 0.7853 (ttp-170) cc_final: 0.7520 (ptm160) REVERT: A 661 LYS cc_start: 0.7843 (OUTLIER) cc_final: 0.7385 (ptmm) REVERT: A 786 GLU cc_start: 0.6825 (pt0) cc_final: 0.6478 (tm-30) REVERT: B 549 GLN cc_start: 0.7449 (pt0) cc_final: 0.6700 (pt0) REVERT: B 599 GLU cc_start: 0.7314 (tt0) cc_final: 0.7010 (tt0) REVERT: B 631 LYS cc_start: 0.8234 (mptt) cc_final: 0.7972 (mptt) REVERT: B 672 ILE cc_start: 0.2587 (OUTLIER) cc_final: 0.2270 (mt) REVERT: B 679 LEU cc_start: 0.6231 (OUTLIER) cc_final: 0.5811 (mt) REVERT: B 704 LYS cc_start: 0.6445 (OUTLIER) cc_final: 0.6062 (mtpp) REVERT: B 779 ARG cc_start: 0.6474 (mmm160) cc_final: 0.6253 (mmm-85) REVERT: B 796 ARG cc_start: 0.7892 (ptm-80) cc_final: 0.7401 (ptm-80) REVERT: B 839 LYS cc_start: 0.6810 (mptt) cc_final: 0.6608 (mttt) REVERT: B 852 GLN cc_start: 0.7485 (mt0) cc_final: 0.7263 (mt0) REVERT: B 892 MET cc_start: 0.7895 (ttm) cc_final: 0.7562 (ttm) REVERT: B 925 GLU cc_start: 0.7092 (mm-30) cc_final: 0.6877 (mm-30) REVERT: B 1094 GLU cc_start: 0.7523 (mt-10) cc_final: 0.7189 (mt-10) REVERT: B 1103 ARG cc_start: 0.7405 (mtt90) cc_final: 0.7136 (mtt90) outliers start: 66 outliers final: 34 residues processed: 232 average time/residue: 0.1222 time to fit residues: 38.9837 Evaluate side-chains 229 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 184 time to evaluate : 0.284 ------------------------------------------------------------------------------- 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 312 LEU Chi-restraints excluded: chain A residue 324 GLN Chi-restraints excluded: chain A residue 371 GLU 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 460 MET 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 599 LEU 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 729 MET Chi-restraints excluded: chain A residue 747 ILE Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 882 LYS Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain B residue 543 ARG Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 644 THR 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 704 LYS 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 1030 MET 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 0 optimal weight: 10.0000 chunk 114 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 18 optimal weight: 0.3980 chunk 69 optimal weight: 2.9990 chunk 17 optimal weight: 0.1980 chunk 23 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 GLN A 395 GLN ** 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 846 GLN B 647 HIS B 861 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4897 r_free = 0.4897 target = 0.218125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.186216 restraints weight = 18520.480| |-----------------------------------------------------------------------------| r_work (start): 0.4515 rms_B_bonded: 3.67 r_work: 0.4382 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.4382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5912 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11639 Z= 0.162 Angle : 0.680 9.336 15856 Z= 0.366 Chirality : 0.043 0.211 1819 Planarity : 0.004 0.082 1897 Dihedral : 17.619 76.311 1862 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 20.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 5.08 % Allowed : 24.58 % Favored : 70.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.62 (0.23), residues: 1321 helix: 0.62 (0.19), residues: 725 sheet: -1.53 (0.44), residues: 148 loop : -1.63 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG A 524 TYR 0.016 0.002 TYR B 789 PHE 0.019 0.002 PHE B 571 TRP 0.011 0.001 TRP B 807 HIS 0.010 0.001 HIS B1010 Details of bonding type rmsd covalent geometry : bond 0.00349 (11638) covalent geometry : angle 0.67993 (15856) hydrogen bonds : bond 0.04400 ( 640) hydrogen bonds : angle 4.87828 ( 1806) Misc. bond : bond 0.00268 ( 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 252 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 192 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 ARG cc_start: 0.8337 (ptp90) cc_final: 0.7979 (ptp90) REVERT: A 271 SER cc_start: 0.4461 (OUTLIER) cc_final: 0.3067 (p) REVERT: A 380 LEU cc_start: 0.5422 (OUTLIER) cc_final: 0.4805 (mt) REVERT: A 397 GLN cc_start: 0.7168 (mp10) cc_final: 0.6809 (mp10) REVERT: A 413 GLN cc_start: 0.5643 (OUTLIER) cc_final: 0.3766 (mm-40) REVERT: A 431 LEU cc_start: 0.7383 (tp) cc_final: 0.7071 (tp) REVERT: A 450 PHE cc_start: 0.4560 (t80) cc_final: 0.4132 (t80) REVERT: A 453 MET cc_start: 0.6564 (tpp) cc_final: 0.6318 (mpp) REVERT: A 514 ASP cc_start: 0.7324 (OUTLIER) cc_final: 0.7015 (p0) REVERT: A 535 ASN cc_start: 0.6610 (OUTLIER) cc_final: 0.5797 (t0) REVERT: A 631 ARG cc_start: 0.7729 (ttp-170) cc_final: 0.7407 (ptm160) REVERT: A 653 ASN cc_start: 0.7245 (t0) cc_final: 0.6986 (t0) REVERT: A 661 LYS cc_start: 0.7785 (OUTLIER) cc_final: 0.7363 (ptmm) REVERT: A 786 GLU cc_start: 0.6532 (pt0) cc_final: 0.6266 (tm-30) REVERT: A 805 LEU cc_start: 0.6117 (OUTLIER) cc_final: 0.5741 (tt) REVERT: A 914 GLU cc_start: 0.4239 (OUTLIER) cc_final: 0.3876 (pm20) REVERT: B 549 GLN cc_start: 0.7384 (pt0) cc_final: 0.6846 (pt0) REVERT: B 577 LYS cc_start: 0.7203 (tttt) cc_final: 0.6863 (ttpp) REVERT: B 599 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.6896 (tt0) REVERT: B 617 LYS cc_start: 0.7929 (tptp) cc_final: 0.7337 (mmtm) REVERT: B 623 ARG cc_start: 0.0430 (OUTLIER) cc_final: -0.2487 (mmm160) REVERT: B 647 HIS cc_start: 0.7296 (OUTLIER) cc_final: 0.7025 (t-90) REVERT: B 672 ILE cc_start: 0.2407 (OUTLIER) cc_final: 0.2165 (mt) REVERT: B 679 LEU cc_start: 0.6310 (OUTLIER) cc_final: 0.6004 (mm) REVERT: B 704 LYS cc_start: 0.6416 (OUTLIER) cc_final: 0.5702 (mttt) REVERT: B 781 HIS cc_start: 0.7949 (t70) cc_final: 0.7668 (t-90) REVERT: B 796 ARG cc_start: 0.7859 (ptm-80) cc_final: 0.7378 (ptm-80) REVERT: B 839 LYS cc_start: 0.6781 (mptt) cc_final: 0.6493 (tptp) REVERT: B 892 MET cc_start: 0.7743 (ttm) cc_final: 0.7438 (ttm) REVERT: B 925 GLU cc_start: 0.7075 (mm-30) cc_final: 0.6839 (mm-30) REVERT: B 939 MET cc_start: 0.7609 (ptm) cc_final: 0.7397 (ptm) REVERT: B 964 ARG cc_start: 0.7714 (mtt180) cc_final: 0.7431 (ttp-110) REVERT: B 1010 HIS cc_start: 0.6944 (m90) cc_final: 0.6715 (m90) REVERT: B 1084 LYS cc_start: 0.6853 (mmtt) cc_final: 0.6634 (mppt) REVERT: B 1091 LYS cc_start: 0.7971 (tppt) cc_final: 0.7081 (tppt) REVERT: B 1094 GLU cc_start: 0.7507 (mt-10) cc_final: 0.6904 (mt-10) REVERT: B 1103 ARG cc_start: 0.7282 (mtt90) cc_final: 0.7015 (mtt90) outliers start: 60 outliers final: 26 residues processed: 234 average time/residue: 0.1199 time to fit residues: 38.8617 Evaluate side-chains 224 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 184 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 380 LEU 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 599 LEU Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 637 SER 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 729 MET Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 914 GLU 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 644 THR Chi-restraints excluded: chain B residue 647 HIS Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 704 LYS Chi-restraints excluded: chain B residue 738 LYS 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 1027 ASN 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 78 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 46 optimal weight: 0.2980 chunk 21 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 108 optimal weight: 0.8980 chunk 119 optimal weight: 0.6980 chunk 131 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 GLN ** A 348 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 ** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 846 GLN B 582 GLN B 647 HIS B 852 GLN ** B 864 HIS ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4888 r_free = 0.4888 target = 0.216732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.182727 restraints weight = 18386.242| |-----------------------------------------------------------------------------| r_work (start): 0.4486 rms_B_bonded: 3.74 r_work: 0.4351 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.4351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5935 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11639 Z= 0.177 Angle : 0.695 8.988 15856 Z= 0.373 Chirality : 0.045 0.276 1819 Planarity : 0.005 0.082 1897 Dihedral : 17.572 75.074 1862 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 21.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 4.83 % Allowed : 25.17 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.24), residues: 1321 helix: 0.71 (0.19), residues: 724 sheet: -1.35 (0.47), residues: 138 loop : -1.60 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A 524 TYR 0.015 0.002 TYR B 789 PHE 0.021 0.002 PHE A 436 TRP 0.009 0.001 TRP B 807 HIS 0.024 0.002 HIS B 647 Details of bonding type rmsd covalent geometry : bond 0.00382 (11638) covalent geometry : angle 0.69467 (15856) hydrogen bonds : bond 0.04367 ( 640) hydrogen bonds : angle 4.86419 ( 1806) Misc. bond : bond 0.00222 ( 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 241 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 184 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 ARG cc_start: 0.8344 (ptp90) cc_final: 0.7982 (ptp90) REVERT: A 253 MET cc_start: 0.7061 (tpp) cc_final: 0.5009 (tpp) REVERT: A 271 SER cc_start: 0.4507 (OUTLIER) cc_final: 0.3107 (p) REVERT: A 380 LEU cc_start: 0.5570 (OUTLIER) cc_final: 0.4973 (mt) REVERT: A 397 GLN cc_start: 0.7090 (mp10) cc_final: 0.6730 (mp10) REVERT: A 413 GLN cc_start: 0.5504 (OUTLIER) cc_final: 0.3642 (mm-40) REVERT: A 431 LEU cc_start: 0.7407 (tp) cc_final: 0.7094 (tp) REVERT: A 450 PHE cc_start: 0.4431 (t80) cc_final: 0.4089 (t80) REVERT: A 453 MET cc_start: 0.6551 (tpp) cc_final: 0.6298 (tpp) REVERT: A 514 ASP cc_start: 0.7084 (OUTLIER) cc_final: 0.6844 (p0) REVERT: A 535 ASN cc_start: 0.6665 (OUTLIER) cc_final: 0.5866 (t0) REVERT: A 631 ARG cc_start: 0.7762 (ttp-170) cc_final: 0.7319 (ptm-80) REVERT: A 661 LYS cc_start: 0.7827 (ttmt) cc_final: 0.7471 (ptmm) REVERT: A 707 CYS cc_start: 0.6623 (OUTLIER) cc_final: 0.6341 (p) REVERT: A 786 GLU cc_start: 0.6569 (pt0) cc_final: 0.6328 (tm-30) REVERT: A 815 TYR cc_start: 0.6987 (m-10) cc_final: 0.6250 (m-80) REVERT: B 549 GLN cc_start: 0.7432 (pt0) cc_final: 0.7055 (pt0) REVERT: B 599 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6686 (tt0) REVERT: B 617 LYS cc_start: 0.7948 (tptp) cc_final: 0.7465 (mmtm) REVERT: B 623 ARG cc_start: 0.0321 (OUTLIER) cc_final: -0.2547 (mmm160) REVERT: B 672 ILE cc_start: 0.2400 (OUTLIER) cc_final: 0.2166 (mt) REVERT: B 679 LEU cc_start: 0.6353 (OUTLIER) cc_final: 0.6042 (mm) REVERT: B 704 LYS cc_start: 0.6431 (OUTLIER) cc_final: 0.6085 (mtpp) REVERT: B 796 ARG cc_start: 0.7845 (ptm-80) cc_final: 0.7366 (ptm-80) REVERT: B 839 LYS cc_start: 0.6775 (OUTLIER) cc_final: 0.6472 (mptt) REVERT: B 925 GLU cc_start: 0.7010 (mm-30) cc_final: 0.6780 (mm-30) REVERT: B 964 ARG cc_start: 0.7706 (mtt180) cc_final: 0.7416 (ttp-110) REVERT: B 1010 HIS cc_start: 0.6888 (m90) cc_final: 0.6639 (m90) REVERT: B 1091 LYS cc_start: 0.8052 (tppt) cc_final: 0.7035 (tppt) REVERT: B 1094 GLU cc_start: 0.7567 (mt-10) cc_final: 0.6421 (mt-10) REVERT: B 1103 ARG cc_start: 0.7288 (mtt90) cc_final: 0.7009 (mtt90) outliers start: 57 outliers final: 38 residues processed: 220 average time/residue: 0.1226 time to fit residues: 37.0865 Evaluate side-chains 225 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 175 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 261 MET 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 356 ILE Chi-restraints excluded: chain A residue 380 LEU 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 469 LEU 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 599 LEU 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 707 CYS Chi-restraints excluded: chain A residue 726 MET Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 747 ILE Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 817 VAL 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 561 LEU 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 644 THR 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 704 LYS Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 839 LYS 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 1027 ASN 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 28 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 96 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 108 optimal weight: 0.6980 chunk 129 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN A 324 GLN ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 395 GLN ** 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 846 GLN B 647 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4887 r_free = 0.4887 target = 0.216371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.182274 restraints weight = 18328.835| |-----------------------------------------------------------------------------| r_work (start): 0.4483 rms_B_bonded: 3.76 r_work: 0.4347 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.4347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5946 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11639 Z= 0.183 Angle : 0.695 8.689 15856 Z= 0.372 Chirality : 0.044 0.259 1819 Planarity : 0.005 0.083 1897 Dihedral : 17.550 72.619 1862 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 22.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 4.83 % Allowed : 25.59 % Favored : 69.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.24), residues: 1321 helix: 0.73 (0.19), residues: 724 sheet: -1.51 (0.45), residues: 146 loop : -1.62 (0.31), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 524 TYR 0.016 0.002 TYR B 818 PHE 0.023 0.002 PHE A 436 TRP 0.009 0.001 TRP B 807 HIS 0.010 0.002 HIS B 729 Details of bonding type rmsd covalent geometry : bond 0.00395 (11638) covalent geometry : angle 0.69459 (15856) hydrogen bonds : bond 0.04377 ( 640) hydrogen bonds : angle 4.87841 ( 1806) Misc. bond : bond 0.00225 ( 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 244 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 187 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 ARG cc_start: 0.8314 (ptp90) cc_final: 0.7969 (ptp90) REVERT: A 215 GLN cc_start: 0.8224 (OUTLIER) cc_final: 0.7630 (tp-100) REVERT: A 253 MET cc_start: 0.7044 (tpp) cc_final: 0.5083 (tpp) REVERT: A 271 SER cc_start: 0.4496 (OUTLIER) cc_final: 0.3079 (p) REVERT: A 380 LEU cc_start: 0.5548 (OUTLIER) cc_final: 0.4945 (mt) REVERT: A 397 GLN cc_start: 0.7101 (mp10) cc_final: 0.6757 (mp10) REVERT: A 413 GLN cc_start: 0.5498 (OUTLIER) cc_final: 0.3590 (mm-40) REVERT: A 431 LEU cc_start: 0.7424 (tp) cc_final: 0.7110 (tp) REVERT: A 450 PHE cc_start: 0.4432 (t80) cc_final: 0.4104 (t80) REVERT: A 453 MET cc_start: 0.6479 (tpp) cc_final: 0.6266 (tpp) REVERT: A 535 ASN cc_start: 0.6707 (OUTLIER) cc_final: 0.5898 (t0) REVERT: A 555 LYS cc_start: 0.8427 (mptt) cc_final: 0.8110 (mptt) REVERT: A 631 ARG cc_start: 0.7723 (ttp-170) cc_final: 0.7320 (ptm-80) REVERT: A 661 LYS cc_start: 0.7848 (ttmt) cc_final: 0.7472 (ptmm) REVERT: A 707 CYS cc_start: 0.6615 (OUTLIER) cc_final: 0.6336 (p) REVERT: A 786 GLU cc_start: 0.6583 (pt0) cc_final: 0.6330 (tm-30) REVERT: A 815 TYR cc_start: 0.6967 (m-10) cc_final: 0.6767 (m-80) REVERT: B 549 GLN cc_start: 0.7424 (pt0) cc_final: 0.7067 (pt0) REVERT: B 577 LYS cc_start: 0.7315 (tttt) cc_final: 0.7029 (ttmm) REVERT: B 599 GLU cc_start: 0.7223 (OUTLIER) cc_final: 0.6890 (tt0) REVERT: B 615 LEU cc_start: 0.8236 (mt) cc_final: 0.7944 (mm) REVERT: B 623 ARG cc_start: 0.0417 (OUTLIER) cc_final: -0.2044 (mmm160) REVERT: B 672 ILE cc_start: 0.2410 (OUTLIER) cc_final: 0.2184 (mt) REVERT: B 679 LEU cc_start: 0.6402 (OUTLIER) cc_final: 0.6076 (mm) REVERT: B 704 LYS cc_start: 0.6409 (OUTLIER) cc_final: 0.5842 (mtpt) REVERT: B 796 ARG cc_start: 0.7847 (ptm-80) cc_final: 0.7361 (ptm-80) REVERT: B 839 LYS cc_start: 0.6727 (OUTLIER) cc_final: 0.6375 (tptp) REVERT: B 892 MET cc_start: 0.7802 (ttm) cc_final: 0.7354 (ttt) REVERT: B 893 ILE cc_start: 0.8072 (mt) cc_final: 0.7714 (mm) REVERT: B 925 GLU cc_start: 0.7000 (mm-30) cc_final: 0.6771 (mm-30) REVERT: B 939 MET cc_start: 0.7661 (ptm) cc_final: 0.7431 (ptm) REVERT: B 964 ARG cc_start: 0.7739 (mtt180) cc_final: 0.7450 (ttp-110) REVERT: B 1010 HIS cc_start: 0.6892 (m90) cc_final: 0.6561 (m90) REVERT: B 1084 LYS cc_start: 0.6903 (mmtt) cc_final: 0.6668 (mppt) REVERT: B 1091 LYS cc_start: 0.7979 (tppt) cc_final: 0.7079 (tppt) REVERT: B 1094 GLU cc_start: 0.7569 (mt-10) cc_final: 0.6945 (mt-10) REVERT: B 1103 ARG cc_start: 0.7297 (mtt90) cc_final: 0.7027 (mtt90) outliers start: 57 outliers final: 36 residues processed: 225 average time/residue: 0.1295 time to fit residues: 39.8101 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 : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 GLN 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 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 599 LEU 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 707 CYS Chi-restraints excluded: chain A residue 726 MET Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 747 ILE Chi-restraints excluded: chain A residue 805 LEU 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 647 HIS 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 704 LYS Chi-restraints excluded: chain B residue 738 LYS Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 827 HIS Chi-restraints excluded: chain B residue 839 LYS 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 1015 CYS Chi-restraints excluded: chain B residue 1027 ASN 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 134 optimal weight: 0.0020 chunk 114 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 122 optimal weight: 0.9980 chunk 120 optimal weight: 0.5980 chunk 69 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN 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 613 ASN ** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 846 GLN B 582 GLN B 647 HIS ** B1027 ASN ** 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 = 0.4889 r_free = 0.4889 target = 0.216648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.182686 restraints weight = 18297.195| |-----------------------------------------------------------------------------| r_work (start): 0.4488 rms_B_bonded: 3.74 r_work: 0.4351 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.4351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5948 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11639 Z= 0.174 Angle : 0.691 8.920 15856 Z= 0.370 Chirality : 0.044 0.251 1819 Planarity : 0.005 0.083 1897 Dihedral : 17.508 72.331 1862 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 21.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 5.08 % Allowed : 25.51 % Favored : 69.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.24), residues: 1321 helix: 0.76 (0.19), residues: 725 sheet: -1.45 (0.45), residues: 145 loop : -1.61 (0.31), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 524 TYR 0.017 0.002 TYR B 818 PHE 0.020 0.002 PHE A 436 TRP 0.009 0.001 TRP B 807 HIS 0.024 0.002 HIS B 647 Details of bonding type rmsd covalent geometry : bond 0.00377 (11638) covalent geometry : angle 0.69067 (15856) hydrogen bonds : bond 0.04337 ( 640) hydrogen bonds : angle 4.89083 ( 1806) Misc. bond : bond 0.00222 ( 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 238 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 178 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 ARG cc_start: 0.8293 (ptp90) cc_final: 0.7913 (ptp90) REVERT: A 215 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7589 (tp-100) REVERT: A 253 MET cc_start: 0.7046 (tpp) cc_final: 0.5198 (tpp) REVERT: A 271 SER cc_start: 0.4575 (OUTLIER) cc_final: 0.3175 (p) REVERT: A 371 GLU cc_start: 0.6678 (OUTLIER) cc_final: 0.6314 (tt0) REVERT: A 380 LEU cc_start: 0.5523 (OUTLIER) cc_final: 0.4943 (mt) REVERT: A 413 GLN cc_start: 0.5490 (OUTLIER) cc_final: 0.3557 (mm-40) REVERT: A 431 LEU cc_start: 0.7433 (tp) cc_final: 0.7122 (tp) REVERT: A 450 PHE cc_start: 0.4456 (t80) cc_final: 0.4145 (t80) REVERT: A 453 MET cc_start: 0.6504 (tpp) cc_final: 0.6273 (tpp) REVERT: A 535 ASN cc_start: 0.6717 (OUTLIER) cc_final: 0.5920 (t0) REVERT: A 631 ARG cc_start: 0.7704 (ttp-170) cc_final: 0.7307 (ptm-80) REVERT: A 661 LYS cc_start: 0.7830 (ttmt) cc_final: 0.7443 (ptmm) REVERT: A 707 CYS cc_start: 0.6630 (OUTLIER) cc_final: 0.6366 (p) REVERT: A 786 GLU cc_start: 0.6555 (pt0) cc_final: 0.6302 (tm-30) REVERT: B 549 GLN cc_start: 0.7451 (pt0) cc_final: 0.7099 (pt0) REVERT: B 577 LYS cc_start: 0.7332 (tttt) cc_final: 0.7046 (ttmm) REVERT: B 588 ARG cc_start: 0.7456 (mtt90) cc_final: 0.7041 (ttt90) REVERT: B 599 GLU cc_start: 0.7222 (OUTLIER) cc_final: 0.6895 (tt0) REVERT: B 615 LEU cc_start: 0.8226 (mt) cc_final: 0.7937 (mm) REVERT: B 617 LYS cc_start: 0.7843 (tptp) cc_final: 0.7367 (mmtm) REVERT: B 623 ARG cc_start: 0.0342 (OUTLIER) cc_final: -0.2595 (mmm160) REVERT: B 672 ILE cc_start: 0.2348 (OUTLIER) cc_final: 0.2109 (mt) REVERT: B 679 LEU cc_start: 0.6512 (OUTLIER) cc_final: 0.6203 (mm) REVERT: B 704 LYS cc_start: 0.6291 (OUTLIER) cc_final: 0.5736 (mtpt) REVERT: B 796 ARG cc_start: 0.7838 (ptm-80) cc_final: 0.7352 (ptm-80) REVERT: B 839 LYS cc_start: 0.6752 (OUTLIER) cc_final: 0.6373 (tptp) REVERT: B 892 MET cc_start: 0.7727 (ttm) cc_final: 0.7400 (ttt) REVERT: B 893 ILE cc_start: 0.8092 (mt) cc_final: 0.7751 (mm) REVERT: B 925 GLU cc_start: 0.6995 (mm-30) cc_final: 0.6778 (mm-30) REVERT: B 939 MET cc_start: 0.7626 (ptm) cc_final: 0.7391 (ptm) REVERT: B 964 ARG cc_start: 0.7712 (mtt180) cc_final: 0.7343 (ptt-90) REVERT: B 1010 HIS cc_start: 0.6973 (m90) cc_final: 0.6619 (m90) REVERT: B 1091 LYS cc_start: 0.7971 (tppt) cc_final: 0.7055 (tppt) REVERT: B 1094 GLU cc_start: 0.7539 (mt-10) cc_final: 0.6911 (mt-10) REVERT: B 1103 ARG cc_start: 0.7277 (mtt90) cc_final: 0.7005 (mtt90) outliers start: 60 outliers final: 37 residues processed: 219 average time/residue: 0.1279 time to fit residues: 38.4637 Evaluate side-chains 225 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 175 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 215 GLN 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 371 GLU Chi-restraints excluded: chain A residue 380 LEU 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 632 ILE Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 707 CYS Chi-restraints excluded: chain A residue 726 MET Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 747 ILE Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 882 LYS 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 647 HIS 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 808 LEU Chi-restraints excluded: chain B residue 839 LYS 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 1015 CYS Chi-restraints excluded: chain B residue 1027 ASN 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 57 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 47 optimal weight: 0.5980 chunk 134 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 133 optimal weight: 0.3980 chunk 107 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN A 324 GLN ** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 395 GLN ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 ASN ** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 HIS ** B 880 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4896 r_free = 0.4896 target = 0.217215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.183130 restraints weight = 18413.790| |-----------------------------------------------------------------------------| r_work (start): 0.4495 rms_B_bonded: 3.78 r_work: 0.4357 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.4357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5935 moved from start: 0.3722 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= 0.168 Angle : 0.692 9.423 15856 Z= 0.370 Chirality : 0.044 0.249 1819 Planarity : 0.005 0.083 1897 Dihedral : 17.462 71.953 1862 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 21.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 4.15 % Allowed : 25.59 % Favored : 70.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.24), residues: 1321 helix: 0.79 (0.19), residues: 726 sheet: -1.42 (0.46), residues: 145 loop : -1.61 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 524 TYR 0.019 0.002 TYR A 815 PHE 0.018 0.002 PHE A 436 TRP 0.010 0.001 TRP B 807 HIS 0.026 0.002 HIS B 647 Details of bonding type rmsd covalent geometry : bond 0.00363 (11638) covalent geometry : angle 0.69160 (15856) hydrogen bonds : bond 0.04297 ( 640) hydrogen bonds : angle 4.89179 ( 1806) Misc. bond : bond 0.00218 ( 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 233 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 184 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 ARG cc_start: 0.8284 (ptp90) cc_final: 0.7888 (ptp90) REVERT: A 188 GLU cc_start: 0.7565 (mt-10) cc_final: 0.7199 (pt0) REVERT: A 253 MET cc_start: 0.7037 (tpp) cc_final: 0.5168 (tpp) REVERT: A 271 SER cc_start: 0.4605 (OUTLIER) cc_final: 0.3221 (p) REVERT: A 380 LEU cc_start: 0.5530 (OUTLIER) cc_final: 0.4927 (mt) REVERT: A 413 GLN cc_start: 0.5473 (OUTLIER) cc_final: 0.3615 (mm-40) REVERT: A 431 LEU cc_start: 0.7426 (tp) cc_final: 0.7113 (tp) REVERT: A 453 MET cc_start: 0.6514 (tpp) cc_final: 0.6293 (tpp) REVERT: A 535 ASN cc_start: 0.6708 (OUTLIER) cc_final: 0.5931 (t0) REVERT: A 555 LYS cc_start: 0.8439 (mptt) cc_final: 0.8118 (mptt) REVERT: A 631 ARG cc_start: 0.7719 (ttp-170) cc_final: 0.7439 (mtm110) REVERT: A 661 LYS cc_start: 0.7842 (ttmt) cc_final: 0.7464 (ptmm) REVERT: A 707 CYS cc_start: 0.6632 (OUTLIER) cc_final: 0.6371 (p) REVERT: A 786 GLU cc_start: 0.6499 (pt0) cc_final: 0.6233 (tm-30) REVERT: A 850 GLU cc_start: 0.7055 (mm-30) cc_final: 0.6515 (mm-30) REVERT: B 549 GLN cc_start: 0.7442 (pt0) cc_final: 0.7075 (pt0) REVERT: B 577 LYS cc_start: 0.7333 (tttt) cc_final: 0.7079 (ttmm) REVERT: B 599 GLU cc_start: 0.7211 (OUTLIER) cc_final: 0.6881 (tt0) REVERT: B 606 SER cc_start: 0.7087 (t) cc_final: 0.6872 (t) REVERT: B 615 LEU cc_start: 0.8255 (mt) cc_final: 0.7957 (mm) REVERT: B 617 LYS cc_start: 0.7826 (tptp) cc_final: 0.7366 (mmtm) REVERT: B 623 ARG cc_start: 0.0210 (OUTLIER) cc_final: -0.2716 (mmm160) REVERT: B 672 ILE cc_start: 0.2281 (OUTLIER) cc_final: 0.2037 (mt) REVERT: B 679 LEU cc_start: 0.6493 (OUTLIER) cc_final: 0.6192 (mm) REVERT: B 704 LYS cc_start: 0.6277 (OUTLIER) cc_final: 0.5692 (mttt) REVERT: B 796 ARG cc_start: 0.7853 (ptm-80) cc_final: 0.7351 (ptm-80) REVERT: B 839 LYS cc_start: 0.6742 (OUTLIER) cc_final: 0.6378 (tptp) REVERT: B 892 MET cc_start: 0.7716 (ttm) cc_final: 0.7360 (ttt) REVERT: B 893 ILE cc_start: 0.8062 (mt) cc_final: 0.7703 (mm) REVERT: B 925 GLU cc_start: 0.7014 (mm-30) cc_final: 0.6790 (mm-30) REVERT: B 939 MET cc_start: 0.7624 (ptm) cc_final: 0.7393 (ptm) REVERT: B 964 ARG cc_start: 0.7700 (mtt180) cc_final: 0.7336 (ptt-90) REVERT: B 1010 HIS cc_start: 0.6934 (m90) cc_final: 0.6604 (m90) REVERT: B 1030 MET cc_start: 0.7410 (mmm) cc_final: 0.7145 (mmm) REVERT: B 1091 LYS cc_start: 0.7954 (tppt) cc_final: 0.7041 (tppt) REVERT: B 1094 GLU cc_start: 0.7504 (mt-10) cc_final: 0.6886 (mt-10) REVERT: B 1103 ARG cc_start: 0.7264 (mtt90) cc_final: 0.6986 (mtt90) outliers start: 49 outliers final: 38 residues processed: 215 average time/residue: 0.1314 time to fit residues: 38.7950 Evaluate side-chains 227 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 178 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 GLU 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 371 GLU Chi-restraints excluded: chain A residue 380 LEU 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 522 TYR 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 707 CYS Chi-restraints excluded: chain A residue 726 MET Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 747 ILE Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 882 LYS 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 647 HIS 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 688 ILE Chi-restraints excluded: chain B residue 704 LYS Chi-restraints excluded: chain B residue 738 LYS Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 839 LYS 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 1015 CYS Chi-restraints excluded: chain B residue 1027 ASN 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 24 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 32 optimal weight: 0.0970 chunk 117 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 48 optimal weight: 0.3980 chunk 5 optimal weight: 0.3980 chunk 10 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 49 optimal weight: 0.0970 overall best weight: 0.3376 ------------------------------------------------------------------------------- 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 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 846 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 HIS ** B 880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 908 GLN ** 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 = 0.4912 r_free = 0.4912 target = 0.218911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.185106 restraints weight = 18418.736| |-----------------------------------------------------------------------------| r_work (start): 0.4511 rms_B_bonded: 3.77 r_work: 0.4371 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.4371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5926 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11639 Z= 0.149 Angle : 0.680 9.070 15856 Z= 0.364 Chirality : 0.044 0.243 1819 Planarity : 0.005 0.084 1897 Dihedral : 17.360 72.428 1862 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 20.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 4.15 % Allowed : 25.93 % Favored : 69.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.24), residues: 1321 helix: 0.86 (0.19), residues: 725 sheet: -1.34 (0.46), residues: 145 loop : -1.59 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 524 TYR 0.023 0.002 TYR A 815 PHE 0.027 0.002 PHE A 450 TRP 0.010 0.001 TRP B 807 HIS 0.024 0.001 HIS B 647 Details of bonding type rmsd covalent geometry : bond 0.00320 (11638) covalent geometry : angle 0.68045 (15856) hydrogen bonds : bond 0.04182 ( 640) hydrogen bonds : angle 4.84136 ( 1806) Misc. bond : bond 0.00225 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3351.14 seconds wall clock time: 58 minutes 22.74 seconds (3502.74 seconds total)