Starting phenix.real_space_refine on Wed Aug 5 19:57:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8oma_16972/08_2026/8oma_16972.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oma_16972/08_2026/8oma_16972.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8oma_16972/08_2026/8oma_16972.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oma_16972/08_2026/8oma_16972.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8oma_16972/08_2026/8oma_16972.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8oma_16972/08_2026/8oma_16972.cif" model { file = "/net/cci-nas-00/data/ceres_data/8oma_16972/08_2026/8oma_16972.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oma_16972/08_2026/8oma_16972.cif" } 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-2.2rc3-6140/lib/python3.11/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: 2.46, per 1000 atoms: 0.22 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: 1.01 Conformation dependent library (CDL) restraints added in 522.3 milliseconds 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: 2.24 Time building geometry restraints manager: 1.34 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: 13540 1.80 - 3.59: 2070 3.59 - 5.39: 217 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: 5744 17.96 - 35.92: 858 35.92 - 53.88: 307 53.88 - 71.85: 53 71.85 - 89.81: 16 Dihedral angle restraints: 6978 sinusoidal: 3083 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 6975 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1036 0.076 - 0.152: 623 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: 2.160 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.460 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7000 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= 0.969 Angle : 1.298 8.981 15856 Z= 0.858 Chirality : 0.094 0.380 1819 Planarity : 0.007 0.182 1897 Dihedral : 19.476 89.807 4448 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 are 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/Z covalent geometry : bond 0.00769 / 0.51 (11638) covalent geometry : angle 1.29796 / 0.86 (15856) hydrogen bonds : bond 0.13805 / 15.42 ( 640) hydrogen bonds : angle 6.35725 / 7.26 ( 1806) Misc. bond : bond 0.89030 / 44.51 ( 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 : 0.389 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: 0.8245 (tpp) cc_final: 0.5576 (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: 0.6844 (pt0) REVERT: A 466 HIS cc_start: 0.7335 (p90) cc_final: 0.7119 (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: 0.7895 (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: 0.1405 time to fit residues: 44.8429 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 : 0.385 ------------------------------------------------------------------------------- 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... ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 GLN ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 593 GLN B 647 HIS B 729 HIS ** B 731 GLN ** 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** B1010 HIS B1120 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4907 r_free = 0.4907 target = 0.214801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.180363 restraints weight = 18428.452| |-----------------------------------------------------------------------------| r_work (start): 0.4529 rms_B_bonded: 3.96 r_work: 0.4376 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.4376 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4375 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4375 r_free = 0.4375 target_work(ls_wunit_k1) = 0.168 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4375 r_free = 0.4375 target_work(ls_wunit_k1) = 0.168 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.4375 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5930 moved from start: 0.1271 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= 0.196 Angle : 0.721 9.655 15856 Z= 0.388 Chirality : 0.046 0.202 1819 Planarity : 0.005 0.069 1897 Dihedral : 17.424 62.948 1838 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 20.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 3.31 % Allowed : 22.12 % Favored : 74.58 % 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 are not related in a simple way. whole: -1.10 (0.23), residues: 1321 helix: 0.25 (0.18), residues: 724 sheet: -1.80 (0.41), residues: 162 loop : -1.84 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 979 TYR 0.015 0.002 TYR B 877 PHE 0.044 0.002 PHE A 286 TRP 0.010 0.001 TRP A 764 HIS 0.009 0.001 HIS B 729 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.20 (11638) covalent geometry : angle 0.72102 / 0.39 (15856) hydrogen bonds : bond 0.05105 / 5.56 ( 640) hydrogen bonds : angle 5.12855 / 5.99 ( 1806) Misc. bond : bond 0.00698 / 0.35 ( 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 244 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 205 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7315 (mt-10) REVERT: A 229 LYS cc_start: 0.4693 (OUTLIER) cc_final: 0.3886 (ttpp) REVERT: A 253 MET cc_start: 0.7104 (tpp) cc_final: 0.4521 (tpp) REVERT: A 324 GLN cc_start: 0.7660 (mp10) cc_final: 0.7349 (mp10) REVERT: A 386 ASP cc_start: 0.6534 (t0) cc_final: 0.6303 (t0) REVERT: A 594 THR cc_start: 0.8112 (OUTLIER) cc_final: 0.7865 (t) REVERT: A 631 ARG cc_start: 0.7654 (ttp-170) cc_final: 0.7351 (ptm160) REVERT: A 659 LYS cc_start: 0.7639 (tptp) cc_final: 0.7437 (tppp) REVERT: A 743 SER cc_start: 0.6820 (t) cc_final: 0.6588 (t) REVERT: A 815 TYR cc_start: 0.6880 (m-10) cc_final: 0.6435 (m-10) REVERT: B 549 GLN cc_start: 0.7265 (pt0) cc_final: 0.6521 (pt0) REVERT: B 555 LYS cc_start: 0.6929 (OUTLIER) cc_final: 0.6640 (mtpp) REVERT: B 577 LYS cc_start: 0.7255 (tttt) cc_final: 0.6955 (ttmm) REVERT: B 578 LYS cc_start: 0.7663 (tttt) cc_final: 0.7141 (tmtt) REVERT: B 584 LEU cc_start: 0.7737 (mt) cc_final: 0.7368 (mt) REVERT: B 599 GLU cc_start: 0.7079 (tt0) cc_final: 0.6787 (tt0) REVERT: B 640 LEU cc_start: 0.5283 (OUTLIER) cc_final: 0.4975 (mp) REVERT: B 779 ARG cc_start: 0.6585 (mmm-85) cc_final: 0.6297 (mmm-85) REVERT: B 781 HIS cc_start: 0.7702 (t70) cc_final: 0.6967 (t70) REVERT: B 796 ARG cc_start: 0.7777 (ptm-80) cc_final: 0.7359 (ptm-80) REVERT: B 839 LYS cc_start: 0.6984 (mttt) cc_final: 0.6673 (tptp) REVERT: B 892 MET cc_start: 0.7862 (ttm) cc_final: 0.7417 (ttm) REVERT: B 938 ARG cc_start: 0.6371 (OUTLIER) cc_final: 0.6044 (tpm170) REVERT: B 964 ARG cc_start: 0.7731 (mtt180) cc_final: 0.7474 (ptt-90) REVERT: B 1030 MET cc_start: 0.7221 (mmm) cc_final: 0.7016 (mmm) outliers start: 39 outliers final: 21 residues processed: 226 average time/residue: 0.1260 time to fit residues: 39.6529 Evaluate side-chains 208 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 182 time to evaluate : 0.386 ------------------------------------------------------------------------------- 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 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 662 GLN Chi-restraints excluded: chain A residue 729 MET 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: 0.9980 chunk 109 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 77 optimal weight: 9.9990 chunk 121 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 344 GLN A 395 GLN ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 424 HIS A 451 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4853 r_free = 0.4853 target = 0.209845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.176360 restraints weight = 18443.545| |-----------------------------------------------------------------------------| r_work (start): 0.4477 rms_B_bonded: 4.04 r_work: 0.4313 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.4313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6011 moved from start: 0.1774 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= 0.268 Angle : 0.748 7.224 15856 Z= 0.409 Chirality : 0.047 0.241 1819 Planarity : 0.005 0.081 1897 Dihedral : 17.247 61.177 1814 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 23.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 4.58 % Allowed : 22.03 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.23), residues: 1321 helix: 0.10 (0.18), residues: 726 sheet: -1.91 (0.41), residues: 155 loop : -1.86 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 373 TYR 0.016 0.002 TYR B 877 PHE 0.038 0.003 PHE A 436 TRP 0.015 0.002 TRP A 764 HIS 0.011 0.002 HIS B 684 Details of bonding type rmsd/Z covalent geometry : bond 0.00570 / 0.27 (11638) covalent geometry : angle 0.74802 / 0.41 (15856) hydrogen bonds : bond 0.05230 / 5.61 ( 640) hydrogen bonds : angle 5.16307 / 5.98 ( 1806) Misc. bond : bond 0.00221 / 0.11 ( 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 248 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 194 time to evaluate : 0.367 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: A 172 LYS cc_start: 0.7687 (mmtm) cc_final: 0.7474 (mmtm) REVERT: A 188 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7545 (mt-10) REVERT: A 229 LYS cc_start: 0.4660 (OUTLIER) cc_final: 0.3843 (tmtt) REVERT: A 245 LEU cc_start: 0.5947 (OUTLIER) cc_final: 0.5520 (tm) REVERT: A 271 SER cc_start: 0.4372 (OUTLIER) cc_final: 0.3300 (t) REVERT: A 324 GLN cc_start: 0.7614 (mp10) cc_final: 0.7228 (mp10) REVERT: A 386 ASP cc_start: 0.6576 (t0) cc_final: 0.6366 (t0) REVERT: A 431 LEU cc_start: 0.7285 (tp) cc_final: 0.6962 (tp) REVERT: A 480 GLU cc_start: 0.8324 (pp20) cc_final: 0.7965 (pp20) REVERT: A 535 ASN cc_start: 0.6560 (OUTLIER) cc_final: 0.5714 (t0) REVERT: A 594 THR cc_start: 0.8134 (OUTLIER) cc_final: 0.7805 (t) REVERT: A 631 ARG cc_start: 0.7825 (ttp-170) cc_final: 0.7456 (ptm160) REVERT: A 659 LYS cc_start: 0.7812 (tptp) cc_final: 0.7442 (tppp) REVERT: A 660 ASP cc_start: 0.7749 (t0) cc_final: 0.7293 (t0) REVERT: A 661 LYS cc_start: 0.7775 (ttmt) cc_final: 0.7236 (ptmm) REVERT: A 786 GLU cc_start: 0.6926 (pt0) cc_final: 0.6504 (tm-30) REVERT: A 811 LEU cc_start: 0.7073 (OUTLIER) cc_final: 0.6300 (tt) REVERT: A 813 MET cc_start: 0.7125 (mmp) cc_final: 0.6919 (mmp) REVERT: A 815 TYR cc_start: 0.7188 (m-10) cc_final: 0.6693 (m-80) REVERT: A 829 HIS cc_start: 0.6872 (t70) cc_final: 0.6629 (t70) REVERT: B 549 GLN cc_start: 0.7344 (pt0) cc_final: 0.6522 (pt0) REVERT: B 577 LYS cc_start: 0.7076 (tttt) cc_final: 0.6808 (ttmm) REVERT: B 584 LEU cc_start: 0.8196 (mt) cc_final: 0.7899 (mt) REVERT: B 615 LEU cc_start: 0.8203 (mt) cc_final: 0.7883 (mm) REVERT: B 640 LEU cc_start: 0.5276 (OUTLIER) cc_final: 0.5001 (mp) REVERT: B 796 ARG cc_start: 0.7864 (ptm-80) cc_final: 0.7431 (ptm-80) REVERT: B 839 LYS cc_start: 0.7063 (mttt) cc_final: 0.6545 (tptp) REVERT: B 892 MET cc_start: 0.7919 (ttm) cc_final: 0.7385 (ttm) REVERT: B 925 GLU cc_start: 0.7095 (mm-30) cc_final: 0.6854 (mm-30) REVERT: B 938 ARG cc_start: 0.6391 (OUTLIER) cc_final: 0.6079 (tpm170) REVERT: B 964 ARG cc_start: 0.7784 (mtt180) cc_final: 0.7452 (ptt-90) REVERT: B 1030 MET cc_start: 0.7407 (mmm) cc_final: 0.7166 (mmm) REVERT: B 1084 LYS cc_start: 0.6854 (mmtm) cc_final: 0.6643 (mmtm) REVERT: B 1094 GLU cc_start: 0.7540 (mt-10) cc_final: 0.7056 (mt-10) outliers start: 54 outliers final: 26 residues processed: 230 average time/residue: 0.1101 time to fit residues: 35.8069 Evaluate side-chains 215 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 181 time to evaluate : 0.398 ------------------------------------------------------------------------------- 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 260 GLU Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 299 TYR Chi-restraints excluded: chain A residue 311 ASN 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 467 GLU Chi-restraints excluded: chain A residue 535 ASN 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 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 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 802 ASP Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 938 ARG Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 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: 0.9980 chunk 55 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 1 optimal weight: 50.0000 chunk 7 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 344 GLN A 395 GLN ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 GLN ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 846 GLN B 647 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** ** 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 = 0.4892 r_free = 0.4892 target = 0.217326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.183003 restraints weight = 18671.176| |-----------------------------------------------------------------------------| r_work (start): 0.4484 rms_B_bonded: 3.78 r_work: 0.4350 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.4350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6009 moved from start: 0.2080 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= 0.196 Angle : 0.689 7.607 15856 Z= 0.375 Chirality : 0.045 0.232 1819 Planarity : 0.005 0.083 1897 Dihedral : 17.186 59.509 1811 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 21.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 4.49 % Allowed : 23.98 % Favored : 71.53 % 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 are not related in a simple way. whole: -1.03 (0.23), residues: 1321 helix: 0.29 (0.19), residues: 722 sheet: -1.84 (0.41), residues: 158 loop : -1.74 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 482 TYR 0.021 0.002 TYR B 877 PHE 0.026 0.002 PHE A 436 TRP 0.009 0.001 TRP A 764 HIS 0.005 0.001 HIS B1029 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.20 (11638) covalent geometry : angle 0.68875 / 0.37 (15856) hydrogen bonds : bond 0.04800 / 5.18 ( 640) hydrogen bonds : angle 5.00381 / 5.80 ( 1806) Misc. bond : bond 0.00575 / 0.29 ( 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 248 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 195 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 LYS cc_start: 0.7681 (mmtm) cc_final: 0.7452 (mmtm) REVERT: A 188 GLU cc_start: 0.7676 (mt-10) cc_final: 0.7400 (mt-10) REVERT: A 245 LEU cc_start: 0.5822 (OUTLIER) cc_final: 0.5538 (tm) REVERT: A 253 MET cc_start: 0.7024 (tpp) cc_final: 0.4978 (tpp) REVERT: A 271 SER cc_start: 0.4422 (OUTLIER) cc_final: 0.2981 (p) REVERT: A 324 GLN cc_start: 0.7608 (mp10) cc_final: 0.7211 (mp10) REVERT: A 386 ASP cc_start: 0.6472 (t0) cc_final: 0.6262 (t0) REVERT: A 409 GLN cc_start: 0.5556 (OUTLIER) cc_final: 0.5272 (tt0) REVERT: A 413 GLN cc_start: 0.5906 (OUTLIER) cc_final: 0.4069 (mm-40) REVERT: A 431 LEU cc_start: 0.7310 (tp) cc_final: 0.7008 (tp) REVERT: A 535 ASN cc_start: 0.6628 (OUTLIER) cc_final: 0.5818 (t0) REVERT: A 631 ARG cc_start: 0.7640 (ttp-170) cc_final: 0.7398 (ptm160) REVERT: A 786 GLU cc_start: 0.6696 (pt0) cc_final: 0.6455 (tm-30) REVERT: A 811 LEU cc_start: 0.6227 (OUTLIER) cc_final: 0.5621 (tt) REVERT: B 549 GLN cc_start: 0.7334 (pt0) cc_final: 0.6595 (pt0) REVERT: B 584 LEU cc_start: 0.8095 (mt) cc_final: 0.7811 (mt) REVERT: B 599 GLU cc_start: 0.7211 (OUTLIER) cc_final: 0.6856 (tt0) REVERT: B 617 LYS cc_start: 0.7936 (tptp) cc_final: 0.7274 (mmtm) REVERT: B 631 LYS cc_start: 0.8181 (mptt) cc_final: 0.7925 (mptt) REVERT: B 640 LEU cc_start: 0.5393 (OUTLIER) cc_final: 0.5049 (mm) REVERT: B 643 LYS cc_start: 0.6492 (OUTLIER) cc_final: 0.6274 (tppt) REVERT: B 672 ILE cc_start: 0.2637 (OUTLIER) cc_final: 0.2396 (mt) REVERT: B 704 LYS cc_start: 0.6488 (OUTLIER) cc_final: 0.6065 (mtpp) REVERT: B 796 ARG cc_start: 0.7781 (ptm-80) cc_final: 0.7317 (ptm-80) REVERT: B 852 GLN cc_start: 0.7395 (mt0) cc_final: 0.7127 (mt0) REVERT: B 892 MET cc_start: 0.7812 (ttm) cc_final: 0.7485 (ttm) REVERT: B 925 GLU cc_start: 0.7095 (mm-30) cc_final: 0.6849 (mm-30) REVERT: B 964 ARG cc_start: 0.7720 (mtt180) cc_final: 0.7497 (ptp-170) REVERT: B 1091 LYS cc_start: 0.8168 (tppt) cc_final: 0.7898 (tppt) outliers start: 53 outliers final: 26 residues processed: 230 average time/residue: 0.1262 time to fit residues: 39.6463 Evaluate side-chains 221 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 184 time to evaluate : 0.451 ------------------------------------------------------------------------------- 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 409 GLN Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 413 GLN Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 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 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 729 MET 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 599 GLU Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 643 LYS Chi-restraints excluded: chain B residue 649 LYS Chi-restraints excluded: chain B residue 672 ILE 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 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 1034 VAL Chi-restraints excluded: chain B residue 1060 THR 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: 4.9990 chunk 49 optimal weight: 3.9990 chunk 117 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 102 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 129 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 344 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 829 HIS A 846 GLN B 647 HIS B 861 ASN ** B 864 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 898 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4872 r_free = 0.4872 target = 0.215389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.181220 restraints weight = 18504.878| |-----------------------------------------------------------------------------| r_work (start): 0.4463 rms_B_bonded: 3.73 r_work: 0.4325 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.4325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6074 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 11639 Z= 0.225 Angle : 0.730 9.040 15856 Z= 0.392 Chirality : 0.046 0.237 1819 Planarity : 0.005 0.085 1897 Dihedral : 17.072 59.921 1802 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 22.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 5.25 % Allowed : 24.49 % 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 are not related in a simple way. whole: -1.06 (0.23), residues: 1321 helix: 0.25 (0.19), residues: 725 sheet: -1.72 (0.42), residues: 148 loop : -1.80 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 752 TYR 0.019 0.002 TYR B 877 PHE 0.032 0.002 PHE A 436 TRP 0.011 0.002 TRP A 764 HIS 0.008 0.001 HIS B 729 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.22 (11638) covalent geometry : angle 0.72981 / 0.39 (15856) hydrogen bonds : bond 0.04873 / 5.21 ( 640) hydrogen bonds : angle 5.06981 / 5.80 ( 1806) Misc. bond : bond 0.00320 / 0.16 ( 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 254 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 192 time to evaluate : 0.347 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: A 172 LYS cc_start: 0.7724 (mmtm) cc_final: 0.7470 (mmtm) REVERT: A 245 LEU cc_start: 0.5925 (OUTLIER) cc_final: 0.5462 (tm) REVERT: A 253 MET cc_start: 0.7148 (tpp) cc_final: 0.5203 (tpp) REVERT: A 271 SER cc_start: 0.4506 (OUTLIER) cc_final: 0.3385 (t) REVERT: A 324 GLN cc_start: 0.7656 (mp10) cc_final: 0.7230 (mp10) REVERT: A 380 LEU cc_start: 0.5668 (OUTLIER) cc_final: 0.5074 (mt) REVERT: A 386 ASP cc_start: 0.6542 (t0) cc_final: 0.6341 (t0) REVERT: A 413 GLN cc_start: 0.5933 (OUTLIER) cc_final: 0.4072 (mm-40) REVERT: A 431 LEU cc_start: 0.7376 (tp) cc_final: 0.7074 (tp) REVERT: A 449 LYS cc_start: 0.6462 (tptp) cc_final: 0.6187 (tptp) REVERT: A 535 ASN cc_start: 0.6626 (OUTLIER) cc_final: 0.5877 (t0) REVERT: A 631 ARG cc_start: 0.7659 (ttp-170) cc_final: 0.7424 (ptm160) REVERT: A 661 LYS cc_start: 0.7872 (OUTLIER) cc_final: 0.7503 (ptmm) REVERT: A 786 GLU cc_start: 0.6704 (pt0) cc_final: 0.6454 (tm-30) REVERT: A 815 TYR cc_start: 0.7128 (m-10) cc_final: 0.6763 (m-10) REVERT: B 549 GLN cc_start: 0.7371 (pt0) cc_final: 0.6873 (pt0) REVERT: B 599 GLU cc_start: 0.7238 (OUTLIER) cc_final: 0.6708 (tt0) REVERT: B 615 LEU cc_start: 0.8129 (mt) cc_final: 0.7894 (mm) REVERT: B 631 LYS cc_start: 0.8178 (mptt) cc_final: 0.7881 (mptt) REVERT: B 672 ILE cc_start: 0.2493 (OUTLIER) cc_final: 0.2197 (mt) REVERT: B 704 LYS cc_start: 0.6575 (OUTLIER) cc_final: 0.6153 (mtpp) REVERT: B 796 ARG cc_start: 0.7840 (ptm-80) cc_final: 0.7357 (ptm-80) REVERT: B 839 LYS cc_start: 0.6984 (mptt) cc_final: 0.6606 (mttt) REVERT: B 892 MET cc_start: 0.7793 (ttm) cc_final: 0.7509 (ttm) REVERT: B 964 ARG cc_start: 0.7740 (mtt180) cc_final: 0.7436 (ttp-110) REVERT: B 1030 MET cc_start: 0.7406 (mmm) cc_final: 0.7041 (mmm) REVERT: B 1091 LYS cc_start: 0.8154 (tppt) cc_final: 0.7869 (tppt) REVERT: B 1103 ARG cc_start: 0.7346 (mtt90) cc_final: 0.7072 (mtt90) outliers start: 62 outliers final: 33 residues processed: 232 average time/residue: 0.1227 time to fit residues: 39.5916 Evaluate side-chains 228 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 186 time to evaluate : 0.375 ------------------------------------------------------------------------------- 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 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 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 578 VAL 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 707 CYS Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 747 ILE Chi-restraints excluded: chain A residue 807 THR 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 599 GLU Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain B residue 684 HIS Chi-restraints excluded: chain B residue 704 LYS Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 802 ASP Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 938 ARG Chi-restraints excluded: chain B residue 1027 ASN Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain B residue 1058 GLN Chi-restraints excluded: chain B residue 1060 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 0 optimal weight: 20.0000 chunk 114 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 95 optimal weight: 0.3980 chunk 54 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 GLN ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 846 GLN B 647 HIS B 852 GLN ** B 861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4892 r_free = 0.4892 target = 0.217233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.183896 restraints weight = 18519.455| |-----------------------------------------------------------------------------| r_work (start): 0.4493 rms_B_bonded: 3.64 r_work: 0.4355 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.4355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6023 moved from start: 0.2654 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= 0.176 Angle : 0.699 8.425 15856 Z= 0.375 Chirality : 0.045 0.218 1819 Planarity : 0.005 0.086 1897 Dihedral : 17.022 59.866 1802 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 19.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 5.25 % Allowed : 24.75 % 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 are not related in a simple way. whole: -0.87 (0.23), residues: 1321 helix: 0.42 (0.19), residues: 724 sheet: -1.69 (0.44), residues: 138 loop : -1.73 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 406 TYR 0.017 0.002 TYR B 877 PHE 0.021 0.002 PHE A 436 TRP 0.010 0.001 TRP B 807 HIS 0.004 0.001 HIS B 729 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.18 (11638) covalent geometry : angle 0.69873 / 0.37 (15856) hydrogen bonds : bond 0.04633 / 4.97 ( 640) hydrogen bonds : angle 4.96676 / 5.69 ( 1806) Misc. bond : bond 0.00299 / 0.15 ( 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 241 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 179 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 ARG cc_start: 0.8282 (ptp90) cc_final: 0.7978 (ptp90) REVERT: A 253 MET cc_start: 0.7055 (tpp) cc_final: 0.5388 (tpp) REVERT: A 271 SER cc_start: 0.4428 (OUTLIER) cc_final: 0.2969 (p) REVERT: A 324 GLN cc_start: 0.7596 (mp10) cc_final: 0.7057 (mp10) REVERT: A 371 GLU cc_start: 0.6440 (OUTLIER) cc_final: 0.6143 (tt0) REVERT: A 380 LEU cc_start: 0.5568 (OUTLIER) cc_final: 0.4972 (mt) REVERT: A 397 GLN cc_start: 0.7242 (mp10) cc_final: 0.7003 (mp10) REVERT: A 413 GLN cc_start: 0.5773 (OUTLIER) cc_final: 0.4287 (mm110) REVERT: A 431 LEU cc_start: 0.7326 (tp) cc_final: 0.7027 (tp) REVERT: A 462 GLN cc_start: 0.6418 (mp10) cc_final: 0.5923 (mt0) REVERT: A 535 ASN cc_start: 0.6597 (OUTLIER) cc_final: 0.5859 (t0) REVERT: A 631 ARG cc_start: 0.7573 (ttp-170) cc_final: 0.7323 (ptm160) REVERT: A 661 LYS cc_start: 0.7954 (OUTLIER) cc_final: 0.7599 (ptmm) REVERT: B 549 GLN cc_start: 0.7343 (pt0) cc_final: 0.6832 (pt0) REVERT: B 599 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6905 (tt0) REVERT: B 672 ILE cc_start: 0.2590 (OUTLIER) cc_final: 0.2322 (mt) REVERT: B 704 LYS cc_start: 0.6440 (OUTLIER) cc_final: 0.5931 (mtpt) REVERT: B 729 HIS cc_start: 0.7368 (m90) cc_final: 0.7078 (m90) REVERT: B 796 ARG cc_start: 0.7800 (ptm-80) cc_final: 0.7326 (ptm-80) REVERT: B 839 LYS cc_start: 0.6774 (mptt) cc_final: 0.6459 (tptp) REVERT: B 892 MET cc_start: 0.7740 (ttm) cc_final: 0.7445 (ttm) REVERT: B 964 ARG cc_start: 0.7682 (mtt180) cc_final: 0.7375 (ttp-110) REVERT: B 1091 LYS cc_start: 0.8002 (tppt) cc_final: 0.7263 (tppt) REVERT: B 1094 GLU cc_start: 0.7472 (mt-10) cc_final: 0.6952 (mt-10) REVERT: B 1103 ARG cc_start: 0.7298 (mtt90) cc_final: 0.7023 (mtt90) outliers start: 62 outliers final: 39 residues processed: 218 average time/residue: 0.1209 time to fit residues: 37.0501 Evaluate side-chains 224 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 176 time to evaluate : 0.394 ------------------------------------------------------------------------------- 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 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 479 SER Chi-restraints excluded: chain A residue 535 ASN Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 578 VAL 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 672 MET 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 803 THR Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 813 MET 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 672 ILE 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 827 HIS Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 938 ARG Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain B residue 1058 GLN Chi-restraints excluded: chain B residue 1060 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 78 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 46 optimal weight: 0.5980 chunk 21 optimal weight: 0.3980 chunk 123 optimal weight: 0.6980 chunk 27 optimal weight: 0.0470 chunk 71 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 119 optimal weight: 0.6980 chunk 131 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 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** A 846 GLN B 647 HIS ** B 861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4907 r_free = 0.4907 target = 0.219252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.186755 restraints weight = 18652.865| |-----------------------------------------------------------------------------| r_work (start): 0.4509 rms_B_bonded: 3.71 r_work: 0.4373 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.4373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5989 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 11639 Z= 0.158 Angle : 0.699 9.677 15856 Z= 0.369 Chirality : 0.045 0.245 1819 Planarity : 0.005 0.086 1897 Dihedral : 16.941 59.568 1800 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 20.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 4.41 % Allowed : 25.85 % Favored : 69.75 % 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 are not related in a simple way. whole: -0.73 (0.23), residues: 1321 helix: 0.55 (0.19), residues: 725 sheet: -1.68 (0.43), residues: 148 loop : -1.68 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 573 TYR 0.019 0.002 TYR A 769 PHE 0.035 0.002 PHE B 571 TRP 0.009 0.001 TRP B 807 HIS 0.005 0.001 HIS B 729 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.16 (11638) covalent geometry : angle 0.69942 / 0.37 (15856) hydrogen bonds : bond 0.04486 / 4.84 ( 640) hydrogen bonds : angle 4.92264 / 5.65 ( 1806) Misc. bond : bond 0.00344 / 0.17 ( 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 233 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 181 time to evaluate : 0.410 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: 0.8290 (ptp90) cc_final: 0.7987 (ptp90) REVERT: A 271 SER cc_start: 0.4420 (OUTLIER) cc_final: 0.3233 (t) REVERT: A 324 GLN cc_start: 0.7608 (mp10) cc_final: 0.7068 (mp10) REVERT: A 371 GLU cc_start: 0.6372 (OUTLIER) cc_final: 0.6120 (tt0) REVERT: A 380 LEU cc_start: 0.5515 (OUTLIER) cc_final: 0.4894 (mt) REVERT: A 413 GLN cc_start: 0.5611 (OUTLIER) cc_final: 0.4121 (mm110) REVERT: A 431 LEU cc_start: 0.7297 (tp) cc_final: 0.6993 (tp) REVERT: A 462 GLN cc_start: 0.6412 (mp10) cc_final: 0.5846 (mt0) REVERT: A 535 ASN cc_start: 0.6510 (OUTLIER) cc_final: 0.5655 (t0) REVERT: A 613 ASN cc_start: 0.7909 (OUTLIER) cc_final: 0.7606 (t0) REVERT: A 631 ARG cc_start: 0.7570 (ttp-170) cc_final: 0.7196 (ptm-80) REVERT: A 661 LYS cc_start: 0.7961 (ttmt) cc_final: 0.7586 (ptmm) REVERT: A 914 GLU cc_start: 0.4332 (OUTLIER) cc_final: 0.3886 (pm20) REVERT: B 549 GLN cc_start: 0.7344 (pt0) cc_final: 0.6808 (pt0) REVERT: B 599 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6690 (tt0) REVERT: B 617 LYS cc_start: 0.8121 (tppt) cc_final: 0.7410 (mmtm) REVERT: B 629 TYR cc_start: 0.7673 (t80) cc_final: 0.7428 (t80) REVERT: B 631 LYS cc_start: 0.8011 (mptt) cc_final: 0.7713 (mptt) REVERT: B 672 ILE cc_start: 0.2591 (OUTLIER) cc_final: 0.2333 (mt) REVERT: B 704 LYS cc_start: 0.6416 (OUTLIER) cc_final: 0.6055 (mtpp) REVERT: B 892 MET cc_start: 0.7758 (ttm) cc_final: 0.7477 (ttm) REVERT: B 964 ARG cc_start: 0.7696 (mtt180) cc_final: 0.7380 (ttp-110) REVERT: B 1030 MET cc_start: 0.7417 (OUTLIER) cc_final: 0.7146 (mmm) REVERT: B 1091 LYS cc_start: 0.7943 (tppt) cc_final: 0.6989 (tppt) REVERT: B 1094 GLU cc_start: 0.7481 (mt-10) cc_final: 0.6434 (mt-10) REVERT: B 1103 ARG cc_start: 0.7290 (mtt90) cc_final: 0.7009 (mtt90) outliers start: 52 outliers final: 35 residues processed: 217 average time/residue: 0.1225 time to fit residues: 37.3882 Evaluate side-chains 222 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 176 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 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 479 SER Chi-restraints excluded: chain A residue 535 ASN Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 613 ASN Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 672 MET Chi-restraints excluded: chain A residue 707 CYS Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 914 GLU Chi-restraints excluded: chain A residue 926 ILE Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 672 ILE 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 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 1027 ASN Chi-restraints excluded: chain B residue 1030 MET Chi-restraints excluded: chain B residue 1034 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 28 optimal weight: 0.9980 chunk 17 optimal weight: 0.3980 chunk 105 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 61 optimal weight: 0.0970 chunk 56 optimal weight: 0.2980 chunk 108 optimal weight: 0.9990 chunk 129 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 GLN ** 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 647 HIS ** B 861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 864 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 880 ASN ** B 898 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 908 GLN ** 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 = 0.4886 r_free = 0.4886 target = 0.212977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.179666 restraints weight = 18498.278| |-----------------------------------------------------------------------------| r_work (start): 0.4511 rms_B_bonded: 4.09 r_work (final): 0.4511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5818 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 11639 Z= 0.160 Angle : 0.693 10.061 15856 Z= 0.368 Chirality : 0.045 0.228 1819 Planarity : 0.005 0.103 1897 Dihedral : 16.905 59.813 1800 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 19.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 4.32 % Allowed : 26.10 % 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 are not related in a simple way. whole: -0.66 (0.23), residues: 1321 helix: 0.59 (0.19), residues: 726 sheet: -1.69 (0.43), residues: 148 loop : -1.61 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 779 TYR 0.026 0.002 TYR A 815 PHE 0.024 0.002 PHE B 571 TRP 0.009 0.001 TRP B 807 HIS 0.004 0.001 HIS B1029 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 (11638) covalent geometry : angle 0.69320 / 0.37 (15856) hydrogen bonds : bond 0.04426 / 4.78 ( 640) hydrogen bonds : angle 4.87243 / 5.61 ( 1806) Misc. bond : bond 0.00331 / 0.17 ( 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 232 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 181 time to evaluate : 0.407 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 188 GLU cc_start: 0.7551 (mt-10) cc_final: 0.7129 (pt0) REVERT: A 253 MET cc_start: 0.6834 (tpp) cc_final: 0.4773 (tpp) REVERT: A 271 SER cc_start: 0.3911 (OUTLIER) cc_final: 0.2828 (t) REVERT: A 324 GLN cc_start: 0.7494 (mp10) cc_final: 0.6981 (mp10) REVERT: A 344 GLN cc_start: 0.5805 (tm-30) cc_final: 0.5524 (tm-30) REVERT: A 348 GLN cc_start: 0.6102 (OUTLIER) cc_final: 0.5652 (pm20) REVERT: A 371 GLU cc_start: 0.6218 (OUTLIER) cc_final: 0.5959 (tt0) REVERT: A 380 LEU cc_start: 0.4848 (OUTLIER) cc_final: 0.4317 (mt) REVERT: A 413 GLN cc_start: 0.5304 (OUTLIER) cc_final: 0.3563 (mm-40) REVERT: A 431 LEU cc_start: 0.7338 (tp) cc_final: 0.7016 (tp) REVERT: A 481 LEU cc_start: 0.7741 (mm) cc_final: 0.7527 (mm) REVERT: A 535 ASN cc_start: 0.6586 (OUTLIER) cc_final: 0.5527 (t0) REVERT: A 613 ASN cc_start: 0.7777 (OUTLIER) cc_final: 0.7440 (t0) REVERT: A 631 ARG cc_start: 0.7377 (ttp-170) cc_final: 0.6949 (ptm-80) REVERT: A 661 LYS cc_start: 0.7748 (ttmt) cc_final: 0.7341 (ptmm) REVERT: A 902 GLU cc_start: 0.5356 (OUTLIER) cc_final: 0.5142 (mm-30) REVERT: B 543 ARG cc_start: 0.7711 (mtm110) cc_final: 0.7459 (ptm-80) REVERT: B 549 GLN cc_start: 0.7280 (pt0) cc_final: 0.6863 (pt0) REVERT: B 599 GLU cc_start: 0.7039 (OUTLIER) cc_final: 0.6510 (tt0) REVERT: B 615 LEU cc_start: 0.8224 (mt) cc_final: 0.7967 (mm) REVERT: B 629 TYR cc_start: 0.7426 (t80) cc_final: 0.7202 (t80) REVERT: B 631 LYS cc_start: 0.7974 (mptt) cc_final: 0.7649 (mptt) REVERT: B 704 LYS cc_start: 0.6442 (OUTLIER) cc_final: 0.6108 (mtpp) REVERT: B 892 MET cc_start: 0.7023 (ttm) cc_final: 0.6773 (ttm) REVERT: B 964 ARG cc_start: 0.7371 (mtt180) cc_final: 0.7025 (ptt-90) REVERT: B 1091 LYS cc_start: 0.7960 (tppt) cc_final: 0.6932 (tppt) REVERT: B 1094 GLU cc_start: 0.7208 (mt-10) cc_final: 0.6150 (mt-10) REVERT: B 1103 ARG cc_start: 0.7257 (mtt90) cc_final: 0.6979 (mtt90) outliers start: 51 outliers final: 33 residues processed: 215 average time/residue: 0.1158 time to fit residues: 35.1001 Evaluate side-chains 216 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 173 time to evaluate : 0.351 ------------------------------------------------------------------------------- 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 348 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 479 SER Chi-restraints excluded: chain A residue 535 ASN Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 613 ASN Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 672 MET Chi-restraints excluded: chain A residue 707 CYS Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 902 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 640 LEU Chi-restraints excluded: chain B residue 644 THR 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 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 1060 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 134 optimal weight: 3.9990 chunk 114 optimal weight: 0.7980 chunk 90 optimal weight: 0.6980 chunk 132 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 120 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 397 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 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 582 GLN B 647 HIS ** B 861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4894 r_free = 0.4894 target = 0.216991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.182758 restraints weight = 18391.757| |-----------------------------------------------------------------------------| r_work (start): 0.4485 rms_B_bonded: 3.72 r_work: 0.4349 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.4349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6038 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11639 Z= 0.183 Angle : 0.712 11.412 15856 Z= 0.379 Chirality : 0.045 0.269 1819 Planarity : 0.005 0.085 1897 Dihedral : 16.905 59.749 1800 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 20.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 4.15 % Allowed : 26.36 % Favored : 69.49 % 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 are not related in a simple way. whole: -0.69 (0.23), residues: 1321 helix: 0.59 (0.19), residues: 725 sheet: -1.66 (0.45), residues: 139 loop : -1.70 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 573 TYR 0.021 0.002 TYR B 789 PHE 0.024 0.002 PHE B 571 TRP 0.007 0.001 TRP B 807 HIS 0.005 0.001 HIS B1029 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.18 (11638) covalent geometry : angle 0.71214 / 0.38 (15856) hydrogen bonds : bond 0.04492 / 4.83 ( 640) hydrogen bonds : angle 4.89406 / 5.65 ( 1806) Misc. bond : bond 0.00299 / 0.15 ( 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: 49 poor density : 189 time to evaluate : 0.410 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: 0.8279 (ptp90) cc_final: 0.7923 (ptp90) REVERT: A 253 MET cc_start: 0.7149 (tpp) cc_final: 0.4931 (tpp) REVERT: A 271 SER cc_start: 0.4586 (OUTLIER) cc_final: 0.3380 (t) REVERT: A 324 GLN cc_start: 0.7638 (mp10) cc_final: 0.7096 (mp10) REVERT: A 380 LEU cc_start: 0.5643 (OUTLIER) cc_final: 0.5051 (mt) REVERT: A 402 GLN cc_start: 0.6950 (tt0) cc_final: 0.6340 (pm20) REVERT: A 413 GLN cc_start: 0.5551 (OUTLIER) cc_final: 0.4320 (mm110) REVERT: A 431 LEU cc_start: 0.7348 (tp) cc_final: 0.7039 (tp) REVERT: A 535 ASN cc_start: 0.6627 (OUTLIER) cc_final: 0.5846 (t0) REVERT: A 555 LYS cc_start: 0.8286 (mptt) cc_final: 0.7967 (mptt) REVERT: A 631 ARG cc_start: 0.7594 (ttp-170) cc_final: 0.7239 (ptm-80) REVERT: A 661 LYS cc_start: 0.7866 (ttmt) cc_final: 0.7487 (ptmm) REVERT: B 549 GLN cc_start: 0.7393 (pt0) cc_final: 0.7032 (pt0) REVERT: B 599 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6736 (tt0) REVERT: B 615 LEU cc_start: 0.8285 (mt) cc_final: 0.8005 (mm) REVERT: B 617 LYS cc_start: 0.7806 (tptp) cc_final: 0.7350 (mmtm) REVERT: B 623 ARG cc_start: 0.0461 (OUTLIER) cc_final: -0.2410 (mmm160) REVERT: B 629 TYR cc_start: 0.7734 (t80) cc_final: 0.7503 (t80) REVERT: B 631 LYS cc_start: 0.8095 (mptt) cc_final: 0.7799 (mptt) REVERT: B 704 LYS cc_start: 0.6412 (OUTLIER) cc_final: 0.6061 (mtpp) REVERT: B 784 PHE cc_start: 0.8382 (t80) cc_final: 0.8015 (t80) REVERT: B 796 ARG cc_start: 0.7952 (ptm-80) cc_final: 0.7318 (ptm-80) REVERT: B 892 MET cc_start: 0.7827 (ttm) cc_final: 0.7504 (ttm) REVERT: B 964 ARG cc_start: 0.7661 (mtt180) cc_final: 0.7363 (ttp-110) REVERT: B 1030 MET cc_start: 0.7372 (mmm) cc_final: 0.7102 (mmm) REVERT: B 1091 LYS cc_start: 0.7952 (tppt) cc_final: 0.7015 (tppt) REVERT: B 1094 GLU cc_start: 0.7496 (mt-10) cc_final: 0.6460 (mt-10) REVERT: B 1103 ARG cc_start: 0.7295 (mtt90) cc_final: 0.7044 (mtt90) outliers start: 49 outliers final: 31 residues processed: 217 average time/residue: 0.1291 time to fit residues: 38.6181 Evaluate side-chains 217 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 179 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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 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 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 672 MET Chi-restraints excluded: chain A residue 707 CYS Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 914 GLU Chi-restraints excluded: chain A residue 926 ILE Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 623 ARG Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 684 HIS 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 1027 ASN Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain B residue 1058 GLN Chi-restraints excluded: chain B residue 1060 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 57 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 47 optimal weight: 9.9990 chunk 134 optimal weight: 4.9990 chunk 12 optimal weight: 0.3980 chunk 61 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 52 optimal weight: 0.2980 chunk 32 optimal weight: 0.8980 chunk 133 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 729 HIS ** B 861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 898 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4900 r_free = 0.4900 target = 0.217787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.183338 restraints weight = 18511.367| |-----------------------------------------------------------------------------| r_work (start): 0.4489 rms_B_bonded: 3.79 r_work: 0.4349 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.4349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6033 moved from start: 0.3282 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= 0.176 Angle : 0.734 13.503 15856 Z= 0.390 Chirality : 0.047 0.378 1819 Planarity : 0.005 0.086 1897 Dihedral : 16.891 59.911 1800 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 21.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 3.47 % Allowed : 27.20 % Favored : 69.32 % 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 are not related in a simple way. whole: -0.61 (0.23), residues: 1321 helix: 0.64 (0.19), residues: 725 sheet: -1.63 (0.44), residues: 148 loop : -1.60 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 573 TYR 0.018 0.002 TYR A 815 PHE 0.022 0.002 PHE B 571 TRP 0.010 0.001 TRP A 764 HIS 0.012 0.001 HIS B1010 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.18 (11638) covalent geometry : angle 0.73413 / 0.39 (15856) hydrogen bonds : bond 0.04521 / 4.87 ( 640) hydrogen bonds : angle 4.90773 / 5.64 ( 1806) Misc. bond : bond 0.00309 / 0.15 ( 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 227 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 186 time to evaluate : 0.385 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: 0.8252 (ptp90) cc_final: 0.7864 (ptp90) REVERT: A 253 MET cc_start: 0.7134 (tpp) cc_final: 0.4944 (tpp) REVERT: A 271 SER cc_start: 0.4585 (OUTLIER) cc_final: 0.3399 (t) REVERT: A 324 GLN cc_start: 0.7632 (mp10) cc_final: 0.7167 (mp10) REVERT: A 347 LYS cc_start: 0.7731 (tptp) cc_final: 0.7312 (tptp) REVERT: A 380 LEU cc_start: 0.5595 (OUTLIER) cc_final: 0.4980 (mt) REVERT: A 413 GLN cc_start: 0.5500 (OUTLIER) cc_final: 0.3645 (mm-40) REVERT: A 431 LEU cc_start: 0.7371 (tp) cc_final: 0.7049 (tp) REVERT: A 535 ASN cc_start: 0.6668 (OUTLIER) cc_final: 0.5892 (t0) REVERT: A 631 ARG cc_start: 0.7691 (ttp-170) cc_final: 0.7300 (ptm-80) REVERT: A 661 LYS cc_start: 0.7822 (ttmt) cc_final: 0.7445 (ptmm) REVERT: A 786 GLU cc_start: 0.6695 (pt0) cc_final: 0.6359 (tm-30) REVERT: A 815 TYR cc_start: 0.6941 (m-10) cc_final: 0.6215 (m-80) REVERT: A 852 GLU cc_start: 0.7626 (mm-30) cc_final: 0.7330 (mm-30) REVERT: B 549 GLN cc_start: 0.7390 (pt0) cc_final: 0.7036 (pt0) REVERT: B 599 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.6716 (tt0) REVERT: B 615 LEU cc_start: 0.8265 (mt) cc_final: 0.7990 (mm) REVERT: B 617 LYS cc_start: 0.7825 (tptp) cc_final: 0.7308 (mmtm) REVERT: B 623 ARG cc_start: 0.0465 (OUTLIER) cc_final: -0.2423 (mmm160) REVERT: B 629 TYR cc_start: 0.7754 (t80) cc_final: 0.7485 (t80) REVERT: B 704 LYS cc_start: 0.6456 (OUTLIER) cc_final: 0.6131 (mtpp) REVERT: B 781 HIS cc_start: 0.8052 (t70) cc_final: 0.7846 (t70) REVERT: B 796 ARG cc_start: 0.7948 (ptm-80) cc_final: 0.7342 (ptm-80) REVERT: B 964 ARG cc_start: 0.7689 (mtt180) cc_final: 0.7317 (ptt-90) REVERT: B 1010 HIS cc_start: 0.6930 (m90) cc_final: 0.6692 (m90) REVERT: B 1030 MET cc_start: 0.7370 (mmm) cc_final: 0.7129 (mmm) REVERT: B 1091 LYS cc_start: 0.7986 (tppt) cc_final: 0.6990 (tppt) REVERT: B 1094 GLU cc_start: 0.7542 (mt-10) cc_final: 0.6430 (mt-10) REVERT: B 1103 ARG cc_start: 0.7304 (mtt90) cc_final: 0.7036 (mtt90) outliers start: 41 outliers final: 29 residues processed: 210 average time/residue: 0.1293 time to fit residues: 37.1715 Evaluate side-chains 217 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 181 time to evaluate : 0.484 ------------------------------------------------------------------------------- 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 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 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 672 MET Chi-restraints excluded: chain A residue 707 CYS Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 899 MET 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 644 THR 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 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 1060 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 24 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 117 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 395 GLN A 397 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** ** A 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 HIS ** B 861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4891 r_free = 0.4891 target = 0.217061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.182296 restraints weight = 18518.918| |-----------------------------------------------------------------------------| r_work (start): 0.4475 rms_B_bonded: 3.79 r_work: 0.4336 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.4336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6053 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 11639 Z= 0.195 Angle : 0.747 12.263 15856 Z= 0.399 Chirality : 0.047 0.271 1819 Planarity : 0.005 0.085 1897 Dihedral : 16.886 59.599 1800 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 22.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 3.56 % Allowed : 27.03 % 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 are not related in a simple way. whole: -0.67 (0.23), residues: 1321 helix: 0.60 (0.19), residues: 725 sheet: -1.55 (0.46), residues: 139 loop : -1.70 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 573 TYR 0.017 0.002 TYR B 789 PHE 0.027 0.002 PHE B 784 TRP 0.011 0.001 TRP A 764 HIS 0.009 0.001 HIS B1010 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.19 (11638) covalent geometry : angle 0.74681 / 0.40 (15856) hydrogen bonds : bond 0.04665 / 5.05 ( 640) hydrogen bonds : angle 4.99463 / 5.68 ( 1806) Misc. bond : bond 0.00290 / 0.14 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3477.73 seconds wall clock time: 60 minutes 26.71 seconds (3626.71 seconds total)