Starting phenix.real_space_refine on Wed Sep 25 23:29:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oma_16972/09_2024/8oma_16972.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oma_16972/09_2024/8oma_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oma_16972/09_2024/8oma_16972.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oma_16972/09_2024/8oma_16972.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oma_16972/09_2024/8oma_16972.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oma_16972/09_2024/8oma_16972.cif" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 40 5.49 5 Mg 1 5.21 5 S 52 5.16 5 C 7099 2.51 5 N 1952 2.21 5 O 2235 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 11379 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 351 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "D" Number of atoms: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 346 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "A" Number of atoms: 5990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 760, 5990 Classifications: {'peptide': 760} Link IDs: {'PTRANS': 21, 'TRANS': 738} Chain breaks: 4 Chain: "B" Number of atoms: 4629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4629 Classifications: {'peptide': 577} Link IDs: {'PTRANS': 17, 'TRANS': 559} Chain breaks: 2 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.85, per 1000 atoms: 0.60 Number of scatterers: 11379 At special positions: 0 Unit cell: (94.1626, 107.876, 173.698, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 52 16.00 P 40 15.00 Mg 1 11.99 O 2235 8.00 N 1952 7.00 C 7099 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.88 Conformation dependent library (CDL) restraints added in 1.3 seconds 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2530 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 9 sheets defined 58.3% alpha, 8.9% beta 17 base pairs and 29 stacking pairs defined. Time for finding SS restraints: 3.82 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: 3.96 Time building geometry restraints manager: 3.34 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: 13515 1.80 - 3.59: 2090 3.59 - 5.39: 222 5.39 - 7.18: 23 7.18 - 8.98: 6 Bond angle restraints: 15856 Sorted by residual: angle pdb=" C5' ATP B2000 " pdb=" O5' ATP B2000 " pdb=" PA ATP B2000 " ideal model delta sigma weight residual 121.27 113.20 8.07 1.00e+00 1.00e+00 6.50e+01 angle pdb=" N THR B 951 " pdb=" CA THR B 951 " pdb=" CB THR B 951 " ideal model delta sigma weight residual 109.72 117.37 -7.65 1.70e+00 3.46e-01 2.02e+01 angle pdb=" C ARG A 711 " pdb=" CA ARG A 711 " pdb=" CB ARG A 711 " ideal model delta sigma weight residual 111.70 117.20 -5.50 1.31e+00 5.83e-01 1.77e+01 angle pdb=" C PRO A 652 " pdb=" CA PRO A 652 " pdb=" CB PRO A 652 " ideal model delta sigma weight residual 111.23 106.06 5.17 1.28e+00 6.10e-01 1.63e+01 angle pdb=" N GLY A 692 " pdb=" CA GLY A 692 " pdb=" C GLY A 692 " ideal model delta sigma weight residual 114.95 109.31 5.64 1.41e+00 5.03e-01 1.60e+01 ... (remaining 15851 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 5764 17.96 - 35.92: 869 35.92 - 53.88: 323 53.88 - 71.85: 66 71.85 - 89.81: 18 Dihedral angle restraints: 7040 sinusoidal: 3145 harmonic: 3895 Sorted by residual: dihedral pdb=" CA GLY A 504 " pdb=" C GLY A 504 " pdb=" N LEU A 505 " pdb=" CA LEU A 505 " ideal model delta harmonic sigma weight residual 180.00 -152.34 -27.66 0 5.00e+00 4.00e-02 3.06e+01 dihedral pdb=" CA MET B 728 " pdb=" C MET B 728 " pdb=" N HIS B 729 " pdb=" CA HIS B 729 " ideal model delta harmonic sigma weight residual 180.00 155.28 24.72 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA SER B1067 " pdb=" C SER B1067 " pdb=" N TYR B1068 " pdb=" CA TYR B1068 " ideal model delta harmonic sigma weight residual -180.00 -155.91 -24.09 0 5.00e+00 4.00e-02 2.32e+01 ... (remaining 7037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1034 0.076 - 0.152: 625 0.152 - 0.228: 128 0.228 - 0.304: 25 0.304 - 0.380: 7 Chirality restraints: 1819 Sorted by residual: chirality pdb=" CA ARG A 171 " pdb=" N ARG A 171 " pdb=" C ARG A 171 " pdb=" CB ARG A 171 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.62e+00 chirality pdb=" CG LEU B 640 " pdb=" CB LEU B 640 " pdb=" CD1 LEU B 640 " pdb=" CD2 LEU B 640 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" CB THR B 951 " pdb=" CA THR B 951 " pdb=" OG1 THR B 951 " pdb=" CG2 THR B 951 " both_signs ideal model delta sigma weight residual False 2.55 2.20 0.36 2.00e-01 2.50e+01 3.15e+00 ... (remaining 1816 not shown) Planarity restraints: 1897 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 938 " 0.406 9.50e-02 1.11e+02 1.82e-01 2.25e+01 pdb=" NE ARG B 938 " -0.034 2.00e-02 2.50e+03 pdb=" CZ ARG B 938 " 0.020 2.00e-02 2.50e+03 pdb=" NH1 ARG B 938 " -0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG B 938 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 991 " -0.032 2.00e-02 2.50e+03 1.72e-02 5.92e+00 pdb=" CG TYR B 991 " 0.017 2.00e-02 2.50e+03 pdb=" CD1 TYR B 991 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR B 991 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR B 991 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR B 991 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR B 991 " -0.008 2.00e-02 2.50e+03 pdb=" OH TYR B 991 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B1007 " 0.027 2.00e-02 2.50e+03 1.78e-02 5.55e+00 pdb=" CG PHE B1007 " -0.013 2.00e-02 2.50e+03 pdb=" CD1 PHE B1007 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE B1007 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 PHE B1007 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B1007 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B1007 " 0.023 2.00e-02 2.50e+03 ... (remaining 1894 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 86 2.48 - 3.09: 8207 3.09 - 3.69: 19419 3.69 - 4.30: 27120 4.30 - 4.90: 42534 Nonbonded interactions: 97366 Sorted by model distance: nonbonded pdb=" O2G ATP B2000 " pdb="MG MG B2001 " model vdw 1.878 2.170 nonbonded pdb=" OG SER B 903 " pdb="MG MG B2001 " model vdw 2.000 2.170 nonbonded pdb=" OG1 THR A 335 " pdb=" OD2 ASP A 603 " model vdw 2.112 3.040 nonbonded pdb=" O LYS A 565 " pdb=" OG1 THR A 568 " model vdw 2.174 3.040 nonbonded pdb=" OD1 ASN A 186 " pdb=" NE2 GLN A 348 " model vdw 2.178 3.120 ... (remaining 97361 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.03 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.840 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: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 30.030 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.081 11638 Z= 0.488 Angle : 1.304 8.981 15856 Z= 0.857 Chirality : 0.094 0.380 1819 Planarity : 0.007 0.182 1897 Dihedral : 19.919 89.807 4510 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 28.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 2.97 % Allowed : 22.71 % Favored : 74.32 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.22), residues: 1321 helix: 0.08 (0.18), residues: 716 sheet: -2.00 (0.41), residues: 145 loop : -2.34 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.005 TRP A 764 HIS 0.016 0.003 HIS B 647 PHE 0.027 0.005 PHE B1007 TYR 0.032 0.005 TYR B 991 ARG 0.025 0.002 ARG B 938 *********************** 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 fitting. rotamer outliers: 35 poor density : 217 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LYS cc_start: 0.6314 (OUTLIER) cc_final: 0.5035 (ttpp) REVERT: A 245 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7459 (tm) REVERT: A 253 MET cc_start: 0.8246 (tpp) cc_final: 0.5575 (tpp) REVERT: A 324 GLN cc_start: 0.8416 (mp10) cc_final: 0.8190 (mp10) REVERT: A 348 GLN cc_start: 0.7119 (OUTLIER) cc_final: 0.6843 (pt0) REVERT: A 466 HIS cc_start: 0.7335 (p90) cc_final: 0.7118 (p-80) REVERT: A 572 GLU cc_start: 0.9114 (pt0) cc_final: 0.8822 (pp20) REVERT: A 594 THR cc_start: 0.8824 (OUTLIER) cc_final: 0.8454 (t) REVERT: A 631 ARG cc_start: 0.8460 (ttp-170) cc_final: 0.8260 (ttp80) REVERT: A 638 ARG cc_start: 0.5886 (ptm-80) cc_final: 0.5583 (ptm-80) REVERT: A 729 MET cc_start: 0.5867 (OUTLIER) cc_final: 0.5528 (ttt) REVERT: A 743 SER cc_start: 0.7606 (t) cc_final: 0.7318 (t) REVERT: A 786 GLU cc_start: 0.7791 (tt0) cc_final: 0.7491 (tm-30) REVERT: A 815 TYR cc_start: 0.7436 (m-10) cc_final: 0.7129 (m-10) REVERT: B 549 GLN cc_start: 0.8411 (pt0) cc_final: 0.7890 (pt0) REVERT: B 557 LYS cc_start: 0.8175 (tptm) cc_final: 0.6044 (ptmm) REVERT: B 617 LYS cc_start: 0.8716 (tptp) cc_final: 0.7859 (mmtm) REVERT: B 781 HIS cc_start: 0.8721 (t70) cc_final: 0.8307 (t70) REVERT: B 796 ARG cc_start: 0.7896 (ptm-80) cc_final: 0.7559 (ptm-80) REVERT: B 892 MET cc_start: 0.8939 (ttm) cc_final: 0.8609 (ttm) outliers start: 35 outliers final: 17 residues processed: 236 average time/residue: 0.3010 time to fit residues: 94.4939 Evaluate side-chains 214 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 192 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 926 ILE Chi-restraints excluded: chain B residue 692 GLN Chi-restraints excluded: chain B residue 812 GLU Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 866 VAL Chi-restraints excluded: chain B residue 938 ARG Chi-restraints excluded: chain B residue 1027 ASN Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain B residue 1060 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 0.0670 chunk 102 optimal weight: 7.9990 chunk 56 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 105 optimal weight: 0.9990 chunk 40 optimal weight: 0.2980 chunk 64 optimal weight: 0.3980 chunk 78 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 GLN ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 593 GLN B 647 HIS B 729 HIS B 880 ASN ** B 898 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 908 GLN B1010 HIS B1120 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6821 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11638 Z= 0.226 Angle : 0.673 9.936 15856 Z= 0.363 Chirality : 0.043 0.201 1819 Planarity : 0.004 0.071 1897 Dihedral : 18.113 87.109 1900 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 19.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 3.14 % Allowed : 21.53 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.23), residues: 1321 helix: 0.42 (0.18), residues: 725 sheet: -1.93 (0.40), residues: 169 loop : -1.76 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 764 HIS 0.007 0.001 HIS B 729 PHE 0.044 0.002 PHE A 286 TYR 0.013 0.001 TYR B 877 ARG 0.003 0.000 ARG A 638 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 204 time to evaluate : 1.164 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 229 LYS cc_start: 0.6186 (OUTLIER) cc_final: 0.5170 (ttpp) REVERT: A 253 MET cc_start: 0.7936 (tpp) cc_final: 0.5640 (tpp) REVERT: A 324 GLN cc_start: 0.8431 (mp10) cc_final: 0.8201 (mp10) REVERT: A 364 GLU cc_start: 0.7620 (tt0) cc_final: 0.7158 (pp20) REVERT: A 386 ASP cc_start: 0.6800 (t0) cc_final: 0.6562 (t0) REVERT: A 446 ASP cc_start: 0.8050 (m-30) cc_final: 0.7830 (m-30) REVERT: A 572 GLU cc_start: 0.9067 (pt0) cc_final: 0.8783 (pp20) REVERT: A 631 ARG cc_start: 0.8431 (ttp-170) cc_final: 0.8138 (ptm160) REVERT: A 729 MET cc_start: 0.6102 (OUTLIER) cc_final: 0.5842 (ttt) REVERT: A 813 MET cc_start: 0.7735 (mmp) cc_final: 0.7372 (mmp) REVERT: A 815 TYR cc_start: 0.7094 (m-10) cc_final: 0.6528 (m-10) REVERT: B 549 GLN cc_start: 0.8249 (pt0) cc_final: 0.7717 (pt0) REVERT: B 578 LYS cc_start: 0.8046 (tttt) cc_final: 0.7667 (tmtt) REVERT: B 584 LEU cc_start: 0.8249 (mt) cc_final: 0.8008 (mt) REVERT: B 640 LEU cc_start: 0.6997 (OUTLIER) cc_final: 0.6599 (mp) REVERT: B 796 ARG cc_start: 0.7887 (ptm-80) cc_final: 0.7535 (ptm-80) REVERT: B 839 LYS cc_start: 0.7543 (mttt) cc_final: 0.6920 (tptp) REVERT: B 892 MET cc_start: 0.8977 (ttm) cc_final: 0.8614 (ttm) REVERT: B 925 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7649 (mm-30) outliers start: 37 outliers final: 18 residues processed: 222 average time/residue: 0.2755 time to fit residues: 83.6117 Evaluate side-chains 210 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 189 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 655 VAL 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 582 GLN Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain B residue 802 ASP Chi-restraints excluded: chain B residue 827 HIS Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 1034 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 68 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 33 optimal weight: 0.0870 chunk 122 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 121 optimal weight: 0.8980 chunk 41 optimal weight: 10.0000 chunk 98 optimal weight: 5.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 GLN ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 898 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11638 Z= 0.239 Angle : 0.652 7.454 15856 Z= 0.355 Chirality : 0.043 0.227 1819 Planarity : 0.005 0.074 1897 Dihedral : 17.810 80.569 1871 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 20.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 3.47 % Allowed : 22.97 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.23), residues: 1321 helix: 0.57 (0.19), residues: 724 sheet: -1.48 (0.43), residues: 158 loop : -1.65 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 764 HIS 0.013 0.001 HIS B 684 PHE 0.047 0.002 PHE A 286 TYR 0.014 0.002 TYR A 769 ARG 0.006 0.001 ARG B1101 *********************** 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 237 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 196 time to evaluate : 1.140 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 245 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7509 (tm) REVERT: A 253 MET cc_start: 0.7773 (tpp) cc_final: 0.5739 (tpp) REVERT: A 271 SER cc_start: 0.6542 (OUTLIER) cc_final: 0.5041 (t) REVERT: A 324 GLN cc_start: 0.8489 (mp10) cc_final: 0.8262 (mp10) REVERT: A 386 ASP cc_start: 0.6835 (t0) cc_final: 0.6613 (t0) REVERT: A 450 PHE cc_start: 0.5094 (t80) cc_final: 0.4871 (t80) REVERT: A 535 ASN cc_start: 0.7232 (OUTLIER) cc_final: 0.6131 (t0) REVERT: A 631 ARG cc_start: 0.8480 (ttp-170) cc_final: 0.8219 (ptm160) REVERT: A 813 MET cc_start: 0.7825 (mmp) cc_final: 0.7590 (mmp) REVERT: A 815 TYR cc_start: 0.7267 (m-10) cc_final: 0.6634 (m-10) REVERT: A 838 LYS cc_start: 0.7823 (mtpp) cc_final: 0.7602 (ptmm) REVERT: B 549 GLN cc_start: 0.8285 (pt0) cc_final: 0.7847 (pt0) REVERT: B 617 LYS cc_start: 0.8693 (tptp) cc_final: 0.7856 (mmtm) REVERT: B 640 LEU cc_start: 0.7006 (OUTLIER) cc_final: 0.6777 (mm) REVERT: B 679 LEU cc_start: 0.6820 (OUTLIER) cc_final: 0.6174 (mm) REVERT: B 796 ARG cc_start: 0.7920 (ptm-80) cc_final: 0.7605 (ptm-80) REVERT: B 892 MET cc_start: 0.9029 (ttm) cc_final: 0.8662 (ttm) REVERT: B 925 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7617 (mm-30) outliers start: 41 outliers final: 20 residues processed: 221 average time/residue: 0.2742 time to fit residues: 83.0034 Evaluate side-chains 212 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 187 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 456 THR 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 661 LYS Chi-restraints excluded: chain A residue 726 MET Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain B residue 802 ASP Chi-restraints excluded: chain B residue 827 HIS Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 1034 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 121 optimal weight: 3.9990 chunk 92 optimal weight: 0.3980 chunk 63 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 116 optimal weight: 0.1980 chunk 35 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 829 HIS A 846 GLN B 647 HIS ** B 898 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11638 Z= 0.222 Angle : 0.639 6.997 15856 Z= 0.347 Chirality : 0.043 0.207 1819 Planarity : 0.004 0.077 1897 Dihedral : 17.670 76.359 1867 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 18.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 4.32 % Allowed : 23.22 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.23), residues: 1321 helix: 0.65 (0.19), residues: 726 sheet: -1.51 (0.42), residues: 158 loop : -1.60 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 764 HIS 0.005 0.001 HIS B1010 PHE 0.018 0.002 PHE A 436 TYR 0.016 0.002 TYR B 877 ARG 0.003 0.000 ARG B1101 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 192 time to evaluate : 1.159 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 171 ARG cc_start: 0.8887 (ptp90) cc_final: 0.8661 (ptp90) REVERT: A 253 MET cc_start: 0.7687 (tpp) cc_final: 0.5858 (tpp) REVERT: A 279 LEU cc_start: 0.5624 (OUTLIER) cc_final: 0.5349 (mp) REVERT: A 324 GLN cc_start: 0.8547 (mp10) cc_final: 0.8304 (mp10) REVERT: A 380 LEU cc_start: 0.6612 (OUTLIER) cc_final: 0.6217 (mt) REVERT: A 386 ASP cc_start: 0.6783 (t0) cc_final: 0.6581 (t0) REVERT: A 409 GLN cc_start: 0.6241 (OUTLIER) cc_final: 0.5391 (mt0) REVERT: A 413 GLN cc_start: 0.6782 (OUTLIER) cc_final: 0.4560 (mm-40) REVERT: A 431 LEU cc_start: 0.7594 (tp) cc_final: 0.7358 (tp) REVERT: A 450 PHE cc_start: 0.4958 (t80) cc_final: 0.4680 (t80) REVERT: A 535 ASN cc_start: 0.7251 (OUTLIER) cc_final: 0.6163 (t0) REVERT: A 631 ARG cc_start: 0.8469 (ttp-170) cc_final: 0.8232 (ptm160) REVERT: A 657 PHE cc_start: 0.7107 (OUTLIER) cc_final: 0.6900 (m-80) REVERT: A 786 GLU cc_start: 0.7618 (pt0) cc_final: 0.7128 (tm-30) REVERT: A 813 MET cc_start: 0.7743 (mmp) cc_final: 0.7346 (mmp) REVERT: A 838 LYS cc_start: 0.7829 (mtpp) cc_final: 0.7598 (ptmm) REVERT: B 549 GLN cc_start: 0.8300 (pt0) cc_final: 0.7998 (pt0) REVERT: B 573 ARG cc_start: 0.8212 (ttt180) cc_final: 0.7976 (ttm-80) REVERT: B 617 LYS cc_start: 0.8719 (tptp) cc_final: 0.7874 (mmtm) REVERT: B 672 ILE cc_start: 0.3342 (OUTLIER) cc_final: 0.2683 (mt) REVERT: B 796 ARG cc_start: 0.7945 (ptm-80) cc_final: 0.7579 (ptm-80) REVERT: B 892 MET cc_start: 0.9028 (ttm) cc_final: 0.8675 (ttm) REVERT: B 925 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7605 (mm-30) outliers start: 51 outliers final: 26 residues processed: 229 average time/residue: 0.2879 time to fit residues: 89.3444 Evaluate side-chains 212 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 179 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 413 GLN Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 535 ASN Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 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 657 PHE Chi-restraints excluded: chain A residue 707 CYS Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain B residue 684 HIS Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain B residue 802 ASP Chi-restraints excluded: chain B residue 827 HIS Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 1034 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 108 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 chunk 1 optimal weight: 30.0000 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 111 optimal weight: 0.5980 chunk 90 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 66 optimal weight: 0.8980 chunk 117 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 639 HIS ** A 665 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6893 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11638 Z= 0.244 Angle : 0.650 7.699 15856 Z= 0.354 Chirality : 0.044 0.221 1819 Planarity : 0.004 0.077 1897 Dihedral : 17.559 76.260 1862 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 19.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 4.49 % Allowed : 23.90 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.23), residues: 1321 helix: 0.65 (0.19), residues: 727 sheet: -1.35 (0.45), residues: 146 loop : -1.63 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 764 HIS 0.005 0.001 HIS B1029 PHE 0.026 0.002 PHE B 571 TYR 0.017 0.002 TYR A 815 ARG 0.003 0.000 ARG B 779 *********************** 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 247 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 194 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 ARG cc_start: 0.8902 (ptp90) cc_final: 0.8660 (ptp90) REVERT: A 188 GLU cc_start: 0.8916 (mt-10) cc_final: 0.8689 (pt0) REVERT: A 271 SER cc_start: 0.6614 (OUTLIER) cc_final: 0.4929 (p) REVERT: A 324 GLN cc_start: 0.8525 (mp10) cc_final: 0.8276 (mp10) REVERT: A 380 LEU cc_start: 0.6664 (OUTLIER) cc_final: 0.5993 (mt) REVERT: A 386 ASP cc_start: 0.6887 (t0) cc_final: 0.6686 (t0) REVERT: A 409 GLN cc_start: 0.6352 (OUTLIER) cc_final: 0.5533 (mt0) REVERT: A 413 GLN cc_start: 0.6816 (OUTLIER) cc_final: 0.4551 (mm-40) REVERT: A 431 LEU cc_start: 0.7566 (tp) cc_final: 0.7331 (tp) REVERT: A 450 PHE cc_start: 0.4984 (t80) cc_final: 0.4687 (t80) REVERT: A 535 ASN cc_start: 0.7248 (OUTLIER) cc_final: 0.6012 (t0) REVERT: A 631 ARG cc_start: 0.8475 (ttp-170) cc_final: 0.8231 (ptm160) REVERT: A 657 PHE cc_start: 0.7070 (OUTLIER) cc_final: 0.6832 (m-80) REVERT: A 660 ASP cc_start: 0.8141 (t0) cc_final: 0.7893 (t70) REVERT: A 661 LYS cc_start: 0.8135 (OUTLIER) cc_final: 0.7812 (ptmm) REVERT: A 786 GLU cc_start: 0.7639 (pt0) cc_final: 0.7137 (tm-30) REVERT: A 813 MET cc_start: 0.7766 (mmp) cc_final: 0.7511 (mmp) REVERT: A 815 TYR cc_start: 0.7350 (m-80) cc_final: 0.6878 (m-80) REVERT: B 549 GLN cc_start: 0.8338 (pt0) cc_final: 0.8010 (pt0) REVERT: B 573 ARG cc_start: 0.8211 (ttt180) cc_final: 0.7994 (ttm-80) REVERT: B 615 LEU cc_start: 0.8325 (mt) cc_final: 0.8118 (mm) REVERT: B 617 LYS cc_start: 0.8698 (tptp) cc_final: 0.7923 (mmtm) REVERT: B 631 LYS cc_start: 0.8668 (mptt) cc_final: 0.8398 (mppt) REVERT: B 672 ILE cc_start: 0.3261 (OUTLIER) cc_final: 0.2560 (mt) REVERT: B 679 LEU cc_start: 0.7120 (OUTLIER) cc_final: 0.6554 (mm) REVERT: B 704 LYS cc_start: 0.6600 (OUTLIER) cc_final: 0.6328 (mtpp) REVERT: B 747 VAL cc_start: 0.2293 (OUTLIER) cc_final: 0.2085 (m) REVERT: B 781 HIS cc_start: 0.8903 (t70) cc_final: 0.8677 (t-90) REVERT: B 789 TYR cc_start: 0.8535 (t80) cc_final: 0.8327 (t80) REVERT: B 796 ARG cc_start: 0.7973 (ptm-80) cc_final: 0.7619 (ptm-80) REVERT: B 839 LYS cc_start: 0.7506 (mptt) cc_final: 0.7050 (mttt) REVERT: B 892 MET cc_start: 0.9061 (ttm) cc_final: 0.8781 (ttm) REVERT: B 925 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7580 (mm-30) outliers start: 53 outliers final: 28 residues processed: 232 average time/residue: 0.2796 time to fit residues: 88.2449 Evaluate side-chains 224 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 185 time to evaluate : 1.140 ------------------------------------------------------------------------------- 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 325 SER Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 413 GLN Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 535 ASN Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 657 PHE Chi-restraints excluded: chain A residue 661 LYS Chi-restraints excluded: chain A residue 707 CYS Chi-restraints excluded: chain A residue 882 LYS Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 684 HIS Chi-restraints excluded: chain B residue 704 LYS Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 802 ASP Chi-restraints excluded: chain B residue 827 HIS Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain B residue 1058 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 43 optimal weight: 1.9990 chunk 117 optimal weight: 7.9990 chunk 25 optimal weight: 0.6980 chunk 76 optimal weight: 4.9990 chunk 32 optimal weight: 0.4980 chunk 130 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 125 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6900 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11638 Z= 0.246 Angle : 0.662 8.334 15856 Z= 0.358 Chirality : 0.045 0.295 1819 Planarity : 0.005 0.079 1897 Dihedral : 17.502 75.322 1862 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 20.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 4.41 % Allowed : 24.66 % Favored : 70.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.23), residues: 1321 helix: 0.71 (0.19), residues: 726 sheet: -1.34 (0.45), residues: 146 loop : -1.56 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 764 HIS 0.008 0.001 HIS B 729 PHE 0.043 0.002 PHE A 286 TYR 0.017 0.002 TYR B 877 ARG 0.006 0.000 ARG B1103 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 188 time to evaluate : 1.167 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 171 ARG cc_start: 0.8914 (ptp90) cc_final: 0.8652 (ptp90) REVERT: A 188 GLU cc_start: 0.8907 (mt-10) cc_final: 0.8703 (pt0) REVERT: A 253 MET cc_start: 0.7738 (tpp) cc_final: 0.5400 (tpp) REVERT: A 271 SER cc_start: 0.6644 (OUTLIER) cc_final: 0.4923 (p) REVERT: A 324 GLN cc_start: 0.8558 (mp10) cc_final: 0.8280 (mp10) REVERT: A 356 ILE cc_start: 0.7526 (mm) cc_final: 0.7190 (tt) REVERT: A 380 LEU cc_start: 0.6670 (OUTLIER) cc_final: 0.5977 (mt) REVERT: A 409 GLN cc_start: 0.6387 (OUTLIER) cc_final: 0.5780 (mt0) REVERT: A 413 GLN cc_start: 0.6815 (OUTLIER) cc_final: 0.4571 (mm-40) REVERT: A 431 LEU cc_start: 0.7606 (tp) cc_final: 0.7373 (tp) REVERT: A 450 PHE cc_start: 0.4863 (t80) cc_final: 0.4532 (t80) REVERT: A 535 ASN cc_start: 0.7244 (OUTLIER) cc_final: 0.6001 (t0) REVERT: A 631 ARG cc_start: 0.8460 (ttp-170) cc_final: 0.8153 (ptm-80) REVERT: A 657 PHE cc_start: 0.7175 (OUTLIER) cc_final: 0.6913 (m-80) REVERT: A 661 LYS cc_start: 0.8051 (OUTLIER) cc_final: 0.7758 (ptmm) REVERT: A 786 GLU cc_start: 0.7613 (pt0) cc_final: 0.7112 (tm-30) REVERT: A 790 LEU cc_start: 0.8648 (tt) cc_final: 0.8068 (pp) REVERT: A 815 TYR cc_start: 0.7331 (m-80) cc_final: 0.6742 (m-80) REVERT: B 549 GLN cc_start: 0.8408 (pt0) cc_final: 0.8077 (pt0) REVERT: B 606 SER cc_start: 0.7176 (t) cc_final: 0.6959 (t) REVERT: B 672 ILE cc_start: 0.3149 (OUTLIER) cc_final: 0.2415 (mt) REVERT: B 679 LEU cc_start: 0.7093 (OUTLIER) cc_final: 0.6557 (mm) REVERT: B 704 LYS cc_start: 0.6590 (OUTLIER) cc_final: 0.6045 (mttt) REVERT: B 796 ARG cc_start: 0.7942 (ptm-80) cc_final: 0.7581 (ptm-80) REVERT: B 802 ASP cc_start: 0.6260 (OUTLIER) cc_final: 0.6013 (p0) REVERT: B 839 LYS cc_start: 0.7323 (mptt) cc_final: 0.6701 (tptp) REVERT: B 848 ARG cc_start: 0.8775 (mmm160) cc_final: 0.8468 (mmm160) REVERT: B 852 GLN cc_start: 0.8559 (mt0) cc_final: 0.8322 (mt0) REVERT: B 863 ARG cc_start: 0.4759 (OUTLIER) cc_final: 0.2708 (ttm110) REVERT: B 892 MET cc_start: 0.9031 (ttm) cc_final: 0.8745 (ttm) REVERT: B 925 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7620 (mm-30) REVERT: B 938 ARG cc_start: 0.7406 (tpm170) cc_final: 0.6812 (tpt170) REVERT: B 1091 LYS cc_start: 0.8560 (tppt) cc_final: 0.8360 (tppt) outliers start: 52 outliers final: 29 residues processed: 223 average time/residue: 0.2850 time to fit residues: 86.0396 Evaluate side-chains 219 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 178 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 413 GLN Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 535 ASN Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 657 PHE Chi-restraints excluded: chain A residue 661 LYS Chi-restraints excluded: chain A residue 707 CYS Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 926 ILE Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 684 HIS Chi-restraints excluded: chain B residue 704 LYS Chi-restraints excluded: chain B residue 738 LYS 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 863 ARG Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain B residue 1058 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 0.9990 chunk 74 optimal weight: 6.9990 chunk 95 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 109 optimal weight: 0.7980 chunk 72 optimal weight: 0.5980 chunk 130 optimal weight: 0.9980 chunk 81 optimal weight: 0.0040 chunk 79 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 846 GLN B 582 GLN B 602 HIS B 647 HIS ** B 864 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 898 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6892 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 11638 Z= 0.235 Angle : 0.680 8.845 15856 Z= 0.364 Chirality : 0.044 0.280 1819 Planarity : 0.005 0.078 1897 Dihedral : 17.429 74.582 1862 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 20.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 4.41 % Allowed : 24.83 % Favored : 70.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.23), residues: 1321 helix: 0.77 (0.19), residues: 727 sheet: -1.26 (0.47), residues: 137 loop : -1.62 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 807 HIS 0.007 0.001 HIS B 781 PHE 0.016 0.002 PHE B 571 TYR 0.021 0.002 TYR A 815 ARG 0.012 0.001 ARG A 524 *********************** 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 237 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 185 time to evaluate : 1.183 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 171 ARG cc_start: 0.8891 (ptp90) cc_final: 0.8627 (ptp90) REVERT: A 253 MET cc_start: 0.7627 (tpp) cc_final: 0.5405 (tpp) REVERT: A 271 SER cc_start: 0.6681 (OUTLIER) cc_final: 0.5026 (p) REVERT: A 324 GLN cc_start: 0.8579 (mp10) cc_final: 0.8303 (mp10) REVERT: A 356 ILE cc_start: 0.7521 (mm) cc_final: 0.7189 (tt) REVERT: A 380 LEU cc_start: 0.6672 (OUTLIER) cc_final: 0.5986 (mt) REVERT: A 409 GLN cc_start: 0.6320 (OUTLIER) cc_final: 0.5869 (tt0) REVERT: A 413 GLN cc_start: 0.6736 (OUTLIER) cc_final: 0.4527 (mm-40) REVERT: A 431 LEU cc_start: 0.7649 (tp) cc_final: 0.7421 (tp) REVERT: A 450 PHE cc_start: 0.4784 (t80) cc_final: 0.4508 (t80) REVERT: A 462 GLN cc_start: 0.6451 (mp10) cc_final: 0.6240 (mt0) REVERT: A 535 ASN cc_start: 0.7440 (OUTLIER) cc_final: 0.6214 (t0) REVERT: A 613 ASN cc_start: 0.8185 (OUTLIER) cc_final: 0.7864 (m-40) REVERT: A 631 ARG cc_start: 0.8448 (ttp-170) cc_final: 0.8152 (ptm-80) REVERT: A 657 PHE cc_start: 0.7116 (OUTLIER) cc_final: 0.6842 (m-80) REVERT: A 661 LYS cc_start: 0.8002 (ttmt) cc_final: 0.7701 (ptmm) REVERT: A 786 GLU cc_start: 0.7528 (pt0) cc_final: 0.7038 (tm-30) REVERT: A 815 TYR cc_start: 0.7318 (m-80) cc_final: 0.6759 (m-10) REVERT: B 549 GLN cc_start: 0.8406 (pt0) cc_final: 0.8198 (pt0) REVERT: B 606 SER cc_start: 0.7161 (t) cc_final: 0.6946 (t) REVERT: B 617 LYS cc_start: 0.8612 (tptp) cc_final: 0.7880 (mmtm) REVERT: B 623 ARG cc_start: 0.2736 (OUTLIER) cc_final: -0.0939 (mmp-170) REVERT: B 672 ILE cc_start: 0.3169 (OUTLIER) cc_final: 0.2430 (mt) REVERT: B 679 LEU cc_start: 0.7183 (OUTLIER) cc_final: 0.6677 (mm) REVERT: B 704 LYS cc_start: 0.6519 (OUTLIER) cc_final: 0.6141 (mttt) REVERT: B 796 ARG cc_start: 0.7944 (ptm-80) cc_final: 0.7573 (ptm-80) REVERT: B 802 ASP cc_start: 0.6256 (OUTLIER) cc_final: 0.6001 (p0) REVERT: B 839 LYS cc_start: 0.7369 (mptt) cc_final: 0.6743 (tptp) REVERT: B 852 GLN cc_start: 0.8554 (mt0) cc_final: 0.8324 (mt0) REVERT: B 863 ARG cc_start: 0.4822 (OUTLIER) cc_final: 0.3998 (ttm110) REVERT: B 925 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7601 (mm-30) REVERT: B 1091 LYS cc_start: 0.8529 (tppt) cc_final: 0.8247 (tppt) outliers start: 52 outliers final: 32 residues processed: 224 average time/residue: 0.2822 time to fit residues: 85.8874 Evaluate side-chains 217 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 172 time to evaluate : 1.122 ------------------------------------------------------------------------------- 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 325 SER Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 413 GLN Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 514 ASP Chi-restraints excluded: chain A residue 535 ASN Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 613 ASN Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 657 PHE Chi-restraints excluded: chain A residue 707 CYS Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 882 LYS Chi-restraints excluded: chain A residue 926 ILE Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 623 ARG Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 680 SER Chi-restraints excluded: chain B residue 684 HIS Chi-restraints excluded: chain B residue 704 LYS Chi-restraints excluded: chain B residue 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 863 ARG Chi-restraints excluded: chain B residue 1015 CYS Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain B residue 1058 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 51 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 chunk 64 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 102 optimal weight: 6.9990 chunk 118 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 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** A 846 GLN B 647 HIS ** B 864 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 898 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11638 Z= 0.273 Angle : 0.711 14.683 15856 Z= 0.378 Chirality : 0.046 0.464 1819 Planarity : 0.005 0.079 1897 Dihedral : 17.460 75.013 1862 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 21.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 4.49 % Allowed : 24.83 % Favored : 70.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.24), residues: 1321 helix: 0.74 (0.19), residues: 726 sheet: -1.27 (0.46), residues: 141 loop : -1.61 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 764 HIS 0.008 0.001 HIS B1010 PHE 0.023 0.002 PHE A 436 TYR 0.018 0.002 TYR B1028 ARG 0.017 0.001 ARG A 524 *********************** 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 240 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 187 time to evaluate : 1.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.7967 (tmm) cc_final: 0.7712 (mmm) REVERT: A 253 MET cc_start: 0.7548 (tpp) cc_final: 0.5380 (tpp) REVERT: A 271 SER cc_start: 0.6722 (OUTLIER) cc_final: 0.5051 (p) REVERT: A 324 GLN cc_start: 0.8612 (mp10) cc_final: 0.8318 (mp10) REVERT: A 356 ILE cc_start: 0.7591 (mm) cc_final: 0.7343 (tt) REVERT: A 380 LEU cc_start: 0.6730 (OUTLIER) cc_final: 0.6037 (mt) REVERT: A 409 GLN cc_start: 0.6378 (OUTLIER) cc_final: 0.6046 (tt0) REVERT: A 413 GLN cc_start: 0.6740 (OUTLIER) cc_final: 0.4494 (mm-40) REVERT: A 431 LEU cc_start: 0.7681 (tp) cc_final: 0.7449 (tp) REVERT: A 450 PHE cc_start: 0.4807 (t80) cc_final: 0.4529 (t80) REVERT: A 535 ASN cc_start: 0.7461 (OUTLIER) cc_final: 0.6175 (t0) REVERT: A 572 GLU cc_start: 0.8931 (pt0) cc_final: 0.8731 (pp20) REVERT: A 613 ASN cc_start: 0.8226 (OUTLIER) cc_final: 0.7898 (m-40) REVERT: A 631 ARG cc_start: 0.8451 (ttp-170) cc_final: 0.8157 (mtm110) REVERT: A 743 SER cc_start: 0.7360 (t) cc_final: 0.6796 (m) REVERT: A 786 GLU cc_start: 0.7588 (pt0) cc_final: 0.7082 (tm-30) REVERT: A 815 TYR cc_start: 0.7408 (m-80) cc_final: 0.6842 (m-10) REVERT: B 549 GLN cc_start: 0.8413 (pt0) cc_final: 0.8197 (pt0) REVERT: B 606 SER cc_start: 0.7188 (t) cc_final: 0.6970 (t) REVERT: B 623 ARG cc_start: 0.2713 (OUTLIER) cc_final: -0.1052 (mmp-170) REVERT: B 672 ILE cc_start: 0.3256 (OUTLIER) cc_final: 0.2496 (mt) REVERT: B 679 LEU cc_start: 0.7333 (OUTLIER) cc_final: 0.6799 (mm) REVERT: B 704 LYS cc_start: 0.6595 (OUTLIER) cc_final: 0.6049 (mttt) REVERT: B 796 ARG cc_start: 0.7979 (ptm-80) cc_final: 0.7604 (ptm-80) REVERT: B 802 ASP cc_start: 0.6277 (OUTLIER) cc_final: 0.6015 (p0) REVERT: B 839 LYS cc_start: 0.7298 (mptt) cc_final: 0.6654 (tptp) REVERT: B 852 GLN cc_start: 0.8589 (mt0) cc_final: 0.8354 (mt0) REVERT: B 863 ARG cc_start: 0.4969 (OUTLIER) cc_final: 0.4035 (ttm110) REVERT: B 892 MET cc_start: 0.9007 (ttm) cc_final: 0.8785 (ttt) REVERT: B 893 ILE cc_start: 0.8362 (mt) cc_final: 0.8124 (mm) REVERT: B 925 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7584 (mm-30) REVERT: B 1010 HIS cc_start: 0.7760 (m90) cc_final: 0.7436 (m90) REVERT: B 1091 LYS cc_start: 0.8572 (tppt) cc_final: 0.8297 (tppt) outliers start: 53 outliers final: 33 residues processed: 228 average time/residue: 0.2838 time to fit residues: 88.4037 Evaluate side-chains 229 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 184 time to evaluate : 1.177 ------------------------------------------------------------------------------- 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 325 SER Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 413 GLN Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 535 ASN Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 613 ASN Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 747 ILE Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 882 LYS Chi-restraints excluded: chain A residue 926 ILE Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 623 ARG Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 680 SER Chi-restraints excluded: chain B residue 684 HIS Chi-restraints excluded: chain B residue 704 LYS Chi-restraints excluded: chain B residue 738 LYS Chi-restraints excluded: chain B residue 802 ASP Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 863 ARG Chi-restraints excluded: chain B residue 938 ARG Chi-restraints excluded: chain B residue 1015 CYS Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain B residue 1058 GLN Chi-restraints excluded: chain B residue 1059 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 2.9990 chunk 121 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 0.0870 chunk 95 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 109 optimal weight: 0.0670 chunk 114 optimal weight: 0.7980 chunk 120 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 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** A 829 HIS B 647 HIS B 861 ASN ** B 864 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 898 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6878 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11638 Z= 0.222 Angle : 0.699 14.585 15856 Z= 0.371 Chirality : 0.045 0.468 1819 Planarity : 0.005 0.093 1897 Dihedral : 17.332 72.918 1862 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 20.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 3.90 % Allowed : 25.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.24), residues: 1321 helix: 0.83 (0.19), residues: 727 sheet: -1.27 (0.47), residues: 136 loop : -1.58 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 807 HIS 0.013 0.001 HIS B 729 PHE 0.015 0.002 PHE B 571 TYR 0.019 0.002 TYR B1028 ARG 0.020 0.001 ARG B1103 *********************** 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 223 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 177 time to evaluate : 1.133 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 152 MET cc_start: 0.7937 (tmm) cc_final: 0.7695 (mmm) REVERT: A 171 ARG cc_start: 0.8859 (ptp90) cc_final: 0.8618 (ptp90) REVERT: A 243 ARG cc_start: 0.8390 (ttt90) cc_final: 0.8135 (mtp-110) REVERT: A 253 MET cc_start: 0.7489 (tpp) cc_final: 0.5379 (tpp) REVERT: A 271 SER cc_start: 0.6701 (OUTLIER) cc_final: 0.5053 (p) REVERT: A 356 ILE cc_start: 0.7584 (mm) cc_final: 0.7293 (tt) REVERT: A 371 GLU cc_start: 0.6984 (OUTLIER) cc_final: 0.6777 (tt0) REVERT: A 380 LEU cc_start: 0.6640 (OUTLIER) cc_final: 0.5976 (mt) REVERT: A 409 GLN cc_start: 0.6302 (OUTLIER) cc_final: 0.6029 (tt0) REVERT: A 413 GLN cc_start: 0.6628 (OUTLIER) cc_final: 0.4352 (mm-40) REVERT: A 431 LEU cc_start: 0.7664 (tp) cc_final: 0.7435 (tp) REVERT: A 450 PHE cc_start: 0.4735 (t80) cc_final: 0.4241 (t80) REVERT: A 492 MET cc_start: 0.9351 (ttt) cc_final: 0.9130 (tpt) REVERT: A 535 ASN cc_start: 0.7482 (OUTLIER) cc_final: 0.6327 (t0) REVERT: A 563 TYR cc_start: 0.9105 (t80) cc_final: 0.8762 (t80) REVERT: A 613 ASN cc_start: 0.8195 (OUTLIER) cc_final: 0.7858 (m-40) REVERT: A 631 ARG cc_start: 0.8387 (ttp-170) cc_final: 0.8097 (mtm110) REVERT: A 661 LYS cc_start: 0.7865 (ptmm) cc_final: 0.7633 (ptmm) REVERT: A 684 VAL cc_start: 0.4746 (OUTLIER) cc_final: 0.3190 (t) REVERT: A 779 MET cc_start: 0.8240 (OUTLIER) cc_final: 0.7332 (ttm) REVERT: A 786 GLU cc_start: 0.7456 (pt0) cc_final: 0.6973 (tm-30) REVERT: A 805 LEU cc_start: 0.6439 (OUTLIER) cc_final: 0.6155 (tt) REVERT: A 815 TYR cc_start: 0.7246 (m-80) cc_final: 0.6699 (m-10) REVERT: B 549 GLN cc_start: 0.8432 (pt0) cc_final: 0.8221 (pt0) REVERT: B 617 LYS cc_start: 0.8581 (tptp) cc_final: 0.7911 (mmtm) REVERT: B 623 ARG cc_start: 0.2632 (OUTLIER) cc_final: -0.0670 (mmm-85) REVERT: B 672 ILE cc_start: 0.3188 (OUTLIER) cc_final: 0.2432 (mt) REVERT: B 704 LYS cc_start: 0.6546 (OUTLIER) cc_final: 0.6208 (mtpt) REVERT: B 796 ARG cc_start: 0.7947 (ptm-80) cc_final: 0.7621 (ptm-80) REVERT: B 802 ASP cc_start: 0.6157 (OUTLIER) cc_final: 0.5856 (p0) REVERT: B 839 LYS cc_start: 0.7332 (mptt) cc_final: 0.6703 (tptp) REVERT: B 877 TYR cc_start: 0.8370 (t80) cc_final: 0.8072 (t80) REVERT: B 892 MET cc_start: 0.8830 (ttm) cc_final: 0.8581 (ttt) REVERT: B 893 ILE cc_start: 0.8427 (mt) cc_final: 0.8187 (mm) REVERT: B 925 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7571 (mm-30) REVERT: B 1010 HIS cc_start: 0.7646 (m90) cc_final: 0.7354 (m90) REVERT: B 1091 LYS cc_start: 0.8516 (tppt) cc_final: 0.8243 (tppt) REVERT: B 1101 ARG cc_start: 0.7934 (ttm110) cc_final: 0.7700 (ttm110) outliers start: 46 outliers final: 25 residues processed: 208 average time/residue: 0.2931 time to fit residues: 83.5546 Evaluate side-chains 215 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 176 time to evaluate : 1.240 ------------------------------------------------------------------------------- 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 325 SER Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 413 GLN Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 535 ASN Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 613 ASN Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 882 LYS Chi-restraints excluded: chain A residue 926 ILE Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 623 ARG Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain B residue 680 SER Chi-restraints excluded: chain B residue 684 HIS Chi-restraints excluded: chain B residue 704 LYS Chi-restraints excluded: chain B residue 738 LYS Chi-restraints excluded: chain B residue 802 ASP Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain B residue 1058 GLN Chi-restraints excluded: chain B residue 1059 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 128 optimal weight: 0.0770 chunk 78 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 134 optimal weight: 9.9990 chunk 123 optimal weight: 0.5980 chunk 107 optimal weight: 5.9990 chunk 11 optimal weight: 0.6980 chunk 82 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 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** ** A 846 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 HIS B 852 GLN B 861 ASN ** B 864 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 898 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11638 Z= 0.228 Angle : 0.708 15.130 15856 Z= 0.374 Chirality : 0.045 0.456 1819 Planarity : 0.005 0.080 1897 Dihedral : 17.287 73.323 1862 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 20.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 3.64 % Allowed : 26.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.24), residues: 1321 helix: 0.84 (0.19), residues: 730 sheet: -1.27 (0.47), residues: 135 loop : -1.74 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 807 HIS 0.010 0.001 HIS B 729 PHE 0.015 0.002 PHE B 571 TYR 0.016 0.002 TYR B1028 ARG 0.013 0.001 ARG B 734 ********************** 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 220 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 177 time to evaluate : 1.136 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 152 MET cc_start: 0.7930 (tmm) cc_final: 0.7663 (mmm) REVERT: A 171 ARG cc_start: 0.8872 (ptp90) cc_final: 0.8652 (ptp90) REVERT: A 243 ARG cc_start: 0.8387 (ttt90) cc_final: 0.7911 (mtp-110) REVERT: A 253 MET cc_start: 0.7475 (tpp) cc_final: 0.5419 (tpp) REVERT: A 271 SER cc_start: 0.6710 (OUTLIER) cc_final: 0.5065 (p) REVERT: A 356 ILE cc_start: 0.7618 (mm) cc_final: 0.7318 (tt) REVERT: A 371 GLU cc_start: 0.7107 (OUTLIER) cc_final: 0.6877 (tt0) REVERT: A 413 GLN cc_start: 0.6648 (OUTLIER) cc_final: 0.4406 (mm-40) REVERT: A 431 LEU cc_start: 0.7684 (tp) cc_final: 0.7451 (tp) REVERT: A 450 PHE cc_start: 0.4708 (t80) cc_final: 0.4239 (t80) REVERT: A 492 MET cc_start: 0.9345 (ttt) cc_final: 0.9140 (ttt) REVERT: A 535 ASN cc_start: 0.7477 (OUTLIER) cc_final: 0.6348 (t0) REVERT: A 563 TYR cc_start: 0.9127 (t80) cc_final: 0.8787 (t80) REVERT: A 613 ASN cc_start: 0.8203 (OUTLIER) cc_final: 0.7881 (m-40) REVERT: A 631 ARG cc_start: 0.8387 (ttp-170) cc_final: 0.8099 (mtm110) REVERT: A 661 LYS cc_start: 0.7888 (ptmm) cc_final: 0.7664 (ptmm) REVERT: A 743 SER cc_start: 0.7141 (t) cc_final: 0.6634 (m) REVERT: A 779 MET cc_start: 0.8193 (OUTLIER) cc_final: 0.7307 (ttm) REVERT: A 786 GLU cc_start: 0.7480 (pt0) cc_final: 0.6995 (tm-30) REVERT: A 805 LEU cc_start: 0.6437 (OUTLIER) cc_final: 0.6161 (tt) REVERT: A 815 TYR cc_start: 0.7258 (m-80) cc_final: 0.6697 (m-10) REVERT: A 829 HIS cc_start: 0.8089 (m90) cc_final: 0.7829 (m90) REVERT: B 549 GLN cc_start: 0.8447 (pt0) cc_final: 0.8239 (pt0) REVERT: B 617 LYS cc_start: 0.8564 (tptp) cc_final: 0.7899 (mmtm) REVERT: B 623 ARG cc_start: 0.2668 (OUTLIER) cc_final: -0.0782 (mmm160) REVERT: B 672 ILE cc_start: 0.3291 (OUTLIER) cc_final: 0.2522 (mt) REVERT: B 704 LYS cc_start: 0.6540 (OUTLIER) cc_final: 0.6017 (mttt) REVERT: B 796 ARG cc_start: 0.7954 (ptm-80) cc_final: 0.7572 (ptm-80) REVERT: B 802 ASP cc_start: 0.6155 (OUTLIER) cc_final: 0.5854 (p0) REVERT: B 839 LYS cc_start: 0.7274 (mptt) cc_final: 0.6624 (tptp) REVERT: B 892 MET cc_start: 0.8869 (ttm) cc_final: 0.8623 (ttt) REVERT: B 893 ILE cc_start: 0.8437 (mt) cc_final: 0.8198 (mm) REVERT: B 925 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7406 (mm-30) REVERT: B 947 LYS cc_start: 0.8624 (mtpt) cc_final: 0.8216 (mtpt) REVERT: B 1010 HIS cc_start: 0.7605 (m90) cc_final: 0.7339 (m90) REVERT: B 1091 LYS cc_start: 0.8518 (tppt) cc_final: 0.8244 (tppt) outliers start: 43 outliers final: 27 residues processed: 208 average time/residue: 0.3092 time to fit residues: 89.5648 Evaluate side-chains 215 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 177 time to evaluate : 1.201 ------------------------------------------------------------------------------- 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 325 SER Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 413 GLN Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 535 ASN Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 613 ASN Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 882 LYS Chi-restraints excluded: chain A residue 926 ILE Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 623 ARG Chi-restraints excluded: chain B residue 628 ILE Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain B residue 680 SER Chi-restraints excluded: chain B residue 684 HIS Chi-restraints excluded: chain B residue 704 LYS Chi-restraints excluded: chain B residue 738 LYS Chi-restraints excluded: chain B residue 802 ASP Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 1015 CYS Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain B residue 1059 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 114 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 chunk 98 optimal weight: 0.9980 chunk 15 optimal weight: 8.9990 chunk 29 optimal weight: 0.4980 chunk 107 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 13 optimal weight: 0.0050 chunk 19 optimal weight: 0.7980 chunk 94 optimal weight: 0.8980 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 395 GLN ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 846 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 582 GLN B 647 HIS ** B 880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1029 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4908 r_free = 0.4908 target = 0.218539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.184804 restraints weight = 18196.603| |-----------------------------------------------------------------------------| r_work (start): 0.4508 rms_B_bonded: 3.78 r_work: 0.4366 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.4366 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4365 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4365 r_free = 0.4365 target_work(ls_wunit_k1) = 0.166 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4365 r_free = 0.4365 target_work(ls_wunit_k1) = 0.166 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4365 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5939 moved from start: 0.3985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11638 Z= 0.219 Angle : 0.707 14.817 15856 Z= 0.373 Chirality : 0.045 0.455 1819 Planarity : 0.005 0.081 1897 Dihedral : 17.210 72.642 1862 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 20.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 3.47 % Allowed : 26.44 % Favored : 70.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.24), residues: 1321 helix: 0.88 (0.19), residues: 733 sheet: -1.25 (0.47), residues: 135 loop : -1.71 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 807 HIS 0.012 0.001 HIS B 729 PHE 0.014 0.002 PHE B 571 TYR 0.015 0.002 TYR B 818 ARG 0.016 0.001 ARG B 734 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3163.44 seconds wall clock time: 57 minutes 6.90 seconds (3426.90 seconds total)