Starting phenix.real_space_refine on Wed Jul 30 14:59:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bkp_12213/07_2025/7bkp_12213_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bkp_12213/07_2025/7bkp_12213.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7bkp_12213/07_2025/7bkp_12213.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bkp_12213/07_2025/7bkp_12213.map" model { file = "/net/cci-nas-00/data/ceres_data/7bkp_12213/07_2025/7bkp_12213_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bkp_12213/07_2025/7bkp_12213_trim.cif" } resolution = 2.8 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= 0.000 sd= 0.002 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: 8 Type Number sf(0) Gaussians Zn 1 6.06 5 P 31 5.49 5 Mg 1 5.21 5 S 34 5.16 5 C 3779 2.51 5 N 1073 2.21 5 O 1243 1.98 5 H 5956 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12118 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 11183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 689, 11183 Classifications: {'peptide': 689} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 667} Chain breaks: 3 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'TYR:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "Z" Number of atoms: 439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 439 Classifications: {'RNA': 14} Modifications used: {'3*END': 1, 'rna3p_pur': 3, 'rna3p_pyr': 11} Link IDs: {'rna3p': 13} Chain: "X" Number of atoms: 463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 463 Classifications: {'RNA': 14} Modifications used: {'3*END': 1, 'rna3p_pur': 11, 'rna3p_pyr': 3} Link IDs: {'rna3p': 13} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9390 SG CYS A 907 78.511 39.319 39.138 1.00 41.60 S ATOM 9436 SG CYS A 910 81.648 40.313 39.827 1.00 44.18 S ATOM 10206 SG CYS A 962 80.682 39.924 43.276 1.00 44.38 S ATOM 10238 SG CYS A 964 80.394 41.880 40.841 1.00 45.58 S Time building chain proxies: 6.47, per 1000 atoms: 0.53 Number of scatterers: 12118 At special positions: 0 Unit cell: (103.2, 89.44, 71.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 S 34 16.00 P 31 15.00 Mg 1 11.99 O 1243 8.00 N 1073 7.00 C 3779 6.00 H 5956 1.00 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=0, symmetry=0 Time building additional restraints: 3.12 Conformation dependent library (CDL) restraints added in 853.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1101 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 910 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 964 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 962 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 907 " Number of angles added : 6 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1318 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 5 sheets defined 56.0% alpha, 11.0% beta 14 base pairs and 22 stacking pairs defined. Time for finding SS restraints: 5.79 Creating SS restraints... Processing helix chain 'A' and resid 310 through 322 removed outlier: 3.928A pdb=" N VAL A 316 " --> pdb=" O TYR A 312 " (cutoff:3.500A) Proline residue: A 319 - end of helix Processing helix chain 'A' and resid 335 through 354 removed outlier: 3.542A pdb=" N VAL A 339 " --> pdb=" O GLY A 335 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA A 354 " --> pdb=" O LYS A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 377 Processing helix chain 'A' and resid 378 through 383 Processing helix chain 'A' and resid 396 through 399 Processing helix chain 'A' and resid 400 through 408 Processing helix chain 'A' and resid 415 through 427 Processing helix chain 'A' and resid 434 through 438 Processing helix chain 'A' and resid 445 through 449 Processing helix chain 'A' and resid 453 through 475 removed outlier: 4.176A pdb=" N LYS A 474 " --> pdb=" O ASN A 470 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN A 475 " --> pdb=" O ASP A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 514 Processing helix chain 'A' and resid 525 through 533 Processing helix chain 'A' and resid 548 through 565 removed outlier: 4.351A pdb=" N LYS A 552 " --> pdb=" O GLU A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 594 Processing helix chain 'A' and resid 598 through 618 removed outlier: 3.531A pdb=" N THR A 617 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 643 removed outlier: 3.979A pdb=" N ALA A 623 " --> pdb=" O ARG A 619 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE A 630 " --> pdb=" O HIS A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 682 Processing helix chain 'A' and resid 683 through 692 removed outlier: 3.747A pdb=" N GLU A 692 " --> pdb=" O LYS A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 716 removed outlier: 3.519A pdb=" N SER A 715 " --> pdb=" O GLN A 711 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLU A 716 " --> pdb=" O PHE A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 741 removed outlier: 3.704A pdb=" N THR A 731 " --> pdb=" O THR A 727 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASN A 741 " --> pdb=" O TRP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 748 removed outlier: 4.349A pdb=" N ALA A 745 " --> pdb=" O ASN A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 781 Processing helix chain 'A' and resid 790 through 793 Processing helix chain 'A' and resid 812 through 822 Processing helix chain 'A' and resid 839 through 863 removed outlier: 3.647A pdb=" N LYS A 852 " --> pdb=" O ASP A 848 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN A 863 " --> pdb=" O ASN A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 891 removed outlier: 3.924A pdb=" N ARG A 890 " --> pdb=" O MET A 886 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER A 891 " --> pdb=" O LYS A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 899 through 902 Processing helix chain 'A' and resid 932 through 937 removed outlier: 3.538A pdb=" N LYS A 936 " --> pdb=" O THR A 932 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLY A 937 " --> pdb=" O PRO A 933 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 932 through 937' Processing helix chain 'A' and resid 944 through 949 Processing helix chain 'A' and resid 1002 through 1006 Processing sheet with id=AA1, first strand: chain 'A' and resid 326 through 329 removed outlier: 6.583A pdb=" N ILE A 326 " --> pdb=" O GLY A 487 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N THR A 489 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ILE A 328 " --> pdb=" O THR A 489 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL A 360 " --> pdb=" O ILE A 411 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N SER A 413 " --> pdb=" O VAL A 360 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N VAL A 362 " --> pdb=" O SER A 413 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 537 through 543 removed outlier: 6.076A pdb=" N CYS A 537 " --> pdb=" O TYR A 830 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N LEU A 832 " --> pdb=" O CYS A 537 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LYS A 539 " --> pdb=" O LEU A 832 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N THR A 834 " --> pdb=" O LYS A 539 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N VAL A 541 " --> pdb=" O THR A 834 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL A 804 " --> pdb=" O VAL A 831 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N VAL A 833 " --> pdb=" O VAL A 804 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ARG A 806 " --> pdb=" O VAL A 833 " (cutoff:3.500A) removed outlier: 8.585A pdb=" N SER A 835 " --> pdb=" O ARG A 806 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLY A 721 " --> pdb=" O LEU A 786 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N ALA A 788 " --> pdb=" O GLY A 721 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ILE A 723 " --> pdb=" O ALA A 788 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 913 through 916 removed outlier: 7.233A pdb=" N LEU A 913 " --> pdb=" O CYS A 907 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N CYS A 907 " --> pdb=" O LEU A 913 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N CYS A 915 " --> pdb=" O LEU A 905 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 920 through 923 Processing sheet with id=AA5, first strand: chain 'A' and resid 940 through 941 removed outlier: 6.762A pdb=" N ILE A 960 " --> pdb=" O TRP A 968 " (cutoff:3.500A) 282 hydrogen bonds defined for protein. 807 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 37 hydrogen bonds 74 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 22 stacking parallelities Total time for adding SS restraints: 5.22 Time building geometry restraints manager: 3.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 5946 1.04 - 1.24: 618 1.24 - 1.44: 2066 1.44 - 1.63: 3589 1.63 - 1.83: 54 Bond restraints: 12273 Sorted by residual: bond pdb=" C4 ATP A1102 " pdb=" C5 ATP A1102 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.40e+01 bond pdb=" C5 ATP A1102 " pdb=" C6 ATP A1102 " ideal model delta sigma weight residual 1.409 1.473 -0.064 1.00e-02 1.00e+04 4.05e+01 bond pdb=" C5 ATP A1102 " pdb=" N7 ATP A1102 " ideal model delta sigma weight residual 1.387 1.338 0.049 1.00e-02 1.00e+04 2.42e+01 bond pdb=" C4 ATP A1102 " pdb=" N9 ATP A1102 " ideal model delta sigma weight residual 1.374 1.327 0.047 1.00e-02 1.00e+04 2.22e+01 bond pdb=" C8 ATP A1102 " pdb=" N7 ATP A1102 " ideal model delta sigma weight residual 1.310 1.354 -0.044 1.00e-02 1.00e+04 1.90e+01 ... (remaining 12268 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.41: 22223 4.41 - 8.82: 28 8.82 - 13.23: 4 13.23 - 17.64: 1 17.64 - 22.05: 2 Bond angle restraints: 22258 Sorted by residual: angle pdb=" PB ATP A1102 " pdb=" O3B ATP A1102 " pdb=" PG ATP A1102 " ideal model delta sigma weight residual 139.87 117.82 22.05 1.00e+00 1.00e+00 4.86e+02 angle pdb=" PA ATP A1102 " pdb=" O3A ATP A1102 " pdb=" PB ATP A1102 " ideal model delta sigma weight residual 136.83 117.22 19.61 1.00e+00 1.00e+00 3.85e+02 angle pdb=" C5 ATP A1102 " pdb=" C4 ATP A1102 " pdb=" N3 ATP A1102 " ideal model delta sigma weight residual 126.80 118.91 7.89 1.00e+00 1.00e+00 6.22e+01 angle pdb=" N3 ATP A1102 " pdb=" C4 ATP A1102 " pdb=" N9 ATP A1102 " ideal model delta sigma weight residual 127.04 135.16 -8.12 1.15e+00 7.59e-01 5.00e+01 angle pdb=" N1 ATP A1102 " pdb=" C2 ATP A1102 " pdb=" N3 ATP A1102 " ideal model delta sigma weight residual 128.69 123.57 5.12 1.00e+00 1.00e+00 2.62e+01 ... (remaining 22253 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.84: 5543 35.84 - 71.67: 196 71.67 - 107.51: 14 107.51 - 143.35: 0 143.35 - 179.18: 9 Dihedral angle restraints: 5762 sinusoidal: 3461 harmonic: 2301 Sorted by residual: dihedral pdb=" CA SER A 995 " pdb=" C SER A 995 " pdb=" N PRO A 996 " pdb=" CA PRO A 996 " ideal model delta harmonic sigma weight residual 180.00 153.54 26.46 0 5.00e+00 4.00e-02 2.80e+01 dihedral pdb=" CA ASN A 549 " pdb=" C ASN A 549 " pdb=" N PRO A 550 " pdb=" CA PRO A 550 " ideal model delta harmonic sigma weight residual -180.00 -159.76 -20.24 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" C LYS A 451 " pdb=" N LYS A 451 " pdb=" CA LYS A 451 " pdb=" CB LYS A 451 " ideal model delta harmonic sigma weight residual -122.60 -131.97 9.37 0 2.50e+00 1.60e-01 1.40e+01 ... (remaining 5759 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 816 0.066 - 0.133: 172 0.133 - 0.199: 6 0.199 - 0.265: 0 0.265 - 0.332: 1 Chirality restraints: 995 Sorted by residual: chirality pdb=" CA LYS A 451 " pdb=" N LYS A 451 " pdb=" C LYS A 451 " pdb=" CB LYS A 451 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" C2' ATP A1102 " pdb=" C1' ATP A1102 " pdb=" C3' ATP A1102 " pdb=" O2' ATP A1102 " both_signs ideal model delta sigma weight residual False -2.68 -2.52 -0.16 2.00e-01 2.50e+01 6.73e-01 chirality pdb=" C4' C Z 11 " pdb=" C5' C Z 11 " pdb=" O4' C Z 11 " pdb=" C3' C Z 11 " both_signs ideal model delta sigma weight residual False -2.50 -2.34 -0.16 2.00e-01 2.50e+01 6.21e-01 ... (remaining 992 not shown) Planarity restraints: 1677 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 450 " 0.206 2.00e-02 2.50e+03 2.43e-01 8.87e+02 pdb=" CG ASN A 450 " -0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN A 450 " -0.197 2.00e-02 2.50e+03 pdb=" ND2 ASN A 450 " -0.001 2.00e-02 2.50e+03 pdb="HD21 ASN A 450 " 0.373 2.00e-02 2.50e+03 pdb="HD22 ASN A 450 " -0.366 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 890 " -0.020 9.50e-02 1.11e+02 2.06e-02 8.65e+00 pdb=" NE ARG A 890 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A 890 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 890 " -0.046 2.00e-02 2.50e+03 pdb=" NH2 ARG A 890 " -0.007 2.00e-02 2.50e+03 pdb="HH11 ARG A 890 " 0.021 2.00e-02 2.50e+03 pdb="HH12 ARG A 890 " 0.008 2.00e-02 2.50e+03 pdb="HH21 ARG A 890 " 0.023 2.00e-02 2.50e+03 pdb="HH22 ARG A 890 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 995 " -0.025 5.00e-02 4.00e+02 3.82e-02 2.34e+00 pdb=" N PRO A 996 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 996 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 996 " -0.021 5.00e-02 4.00e+02 ... (remaining 1674 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 540 2.18 - 2.79: 23935 2.79 - 3.39: 29666 3.39 - 4.00: 40602 4.00 - 4.60: 64294 Nonbonded interactions: 159037 Sorted by model distance: nonbonded pdb=" OE1 GLU A 671 " pdb=" H GLU A 671 " model vdw 1.577 2.450 nonbonded pdb=" HE2 HIS A 347 " pdb=" OG SER A 439 " model vdw 1.627 2.450 nonbonded pdb=" OE1 GLU A 842 " pdb=" H GLU A 842 " model vdw 1.645 2.450 nonbonded pdb=" HG1 THR A 727 " pdb=" OG SER A 730 " model vdw 1.684 2.450 nonbonded pdb=" O LYS A 750 " pdb=" H ASN A 784 " model vdw 1.699 2.450 ... (remaining 159032 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=1.00 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: 1.360 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: 0.200 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 39.840 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 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 : 0.009 0.080 6321 Z= 0.422 Angle : 1.215 55.577 8641 Z= 0.578 Chirality : 0.049 0.332 995 Planarity : 0.004 0.038 991 Dihedral : 15.132 82.134 2655 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.46 % Favored : 93.25 % Rotamer: Outliers : 0.32 % Allowed : 4.21 % Favored : 95.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -2.15 (0.29), residues: 681 helix: -0.48 (0.25), residues: 353 sheet: -1.22 (0.48), residues: 103 loop : -2.94 (0.36), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 737 HIS 0.004 0.001 HIS A 753 PHE 0.012 0.001 PHE A 675 TYR 0.013 0.001 TYR A 381 ARG 0.008 0.001 ARG A 890 Details of bonding type rmsd hydrogen bonds : bond 0.14508 ( 319) hydrogen bonds : angle 5.12703 ( 881) metal coordination : bond 0.04667 ( 4) metal coordination : angle 33.48281 ( 6) covalent geometry : bond 0.00940 ( 6317) covalent geometry : angle 0.83608 ( 8635) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 337 is missing expected H atoms. Skipping. Residue TYR 696 is missing expected H atoms. Skipping. Residue TYR 954 is missing expected H atoms. Skipping. Evaluate side-chains 103 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 101 time to evaluate : 0.890 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 103 average time/residue: 3.3011 time to fit residues: 352.8535 Evaluate side-chains 44 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 43 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 625 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 21 optimal weight: 0.2980 chunk 33 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.123711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.089734 restraints weight = 18529.402| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 1.80 r_work: 0.3003 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6321 Z= 0.114 Angle : 0.562 12.691 8641 Z= 0.284 Chirality : 0.039 0.143 995 Planarity : 0.004 0.048 991 Dihedral : 14.621 73.611 1210 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.14 % Favored : 94.57 % Rotamer: Outliers : 1.30 % Allowed : 10.86 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.04 (0.33), residues: 681 helix: 1.58 (0.28), residues: 346 sheet: -0.57 (0.53), residues: 94 loop : -2.27 (0.39), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 737 HIS 0.003 0.001 HIS A 604 PHE 0.010 0.001 PHE A 680 TYR 0.011 0.001 TYR A 312 ARG 0.003 0.000 ARG A 860 Details of bonding type rmsd hydrogen bonds : bond 0.05080 ( 319) hydrogen bonds : angle 3.91195 ( 881) metal coordination : bond 0.01354 ( 4) metal coordination : angle 7.21028 ( 6) covalent geometry : bond 0.00233 ( 6317) covalent geometry : angle 0.52912 ( 8635) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 337 is missing expected H atoms. Skipping. Residue TYR 696 is missing expected H atoms. Skipping. Residue TYR 954 is missing expected H atoms. Skipping. Evaluate side-chains 50 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 1.016 Fit side-chains revert: symmetry clash REVERT: A 468 ARG cc_start: 0.7713 (ttp-170) cc_final: 0.7343 (tpt170) outliers start: 8 outliers final: 3 residues processed: 46 average time/residue: 2.6606 time to fit residues: 129.4652 Evaluate side-chains 41 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 571 MET Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 902 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 23 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.119671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.085048 restraints weight = 18905.039| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 1.82 r_work: 0.2918 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6321 Z= 0.146 Angle : 0.543 11.625 8641 Z= 0.286 Chirality : 0.040 0.137 995 Planarity : 0.003 0.040 991 Dihedral : 14.214 78.980 1209 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.87 % Favored : 93.98 % Rotamer: Outliers : 1.13 % Allowed : 11.51 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.34), residues: 681 helix: 2.30 (0.29), residues: 339 sheet: -0.23 (0.55), residues: 94 loop : -2.14 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 737 HIS 0.002 0.001 HIS A 974 PHE 0.011 0.001 PHE A 680 TYR 0.012 0.001 TYR A 312 ARG 0.002 0.000 ARG A 728 Details of bonding type rmsd hydrogen bonds : bond 0.05644 ( 319) hydrogen bonds : angle 3.82921 ( 881) metal coordination : bond 0.00910 ( 4) metal coordination : angle 5.66989 ( 6) covalent geometry : bond 0.00324 ( 6317) covalent geometry : angle 0.52175 ( 8635) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 337 is missing expected H atoms. Skipping. Residue TYR 696 is missing expected H atoms. Skipping. Residue TYR 954 is missing expected H atoms. Skipping. Evaluate side-chains 45 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.878 Fit side-chains revert: symmetry clash REVERT: A 468 ARG cc_start: 0.7778 (ttp-170) cc_final: 0.7357 (tpt170) outliers start: 7 outliers final: 2 residues processed: 40 average time/residue: 2.7696 time to fit residues: 116.5918 Evaluate side-chains 40 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 38 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 902 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 5 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 17 optimal weight: 0.0370 chunk 41 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.120539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.085937 restraints weight = 18756.503| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 1.85 r_work: 0.2935 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6321 Z= 0.117 Angle : 0.496 8.736 8641 Z= 0.264 Chirality : 0.039 0.136 995 Planarity : 0.003 0.032 991 Dihedral : 14.070 73.804 1209 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 1.40 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.14 % Favored : 94.71 % Rotamer: Outliers : 0.97 % Allowed : 11.67 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.92 (0.35), residues: 681 helix: 2.58 (0.29), residues: 340 sheet: -0.19 (0.55), residues: 94 loop : -2.04 (0.40), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 737 HIS 0.002 0.001 HIS A 921 PHE 0.010 0.001 PHE A 680 TYR 0.011 0.001 TYR A 312 ARG 0.002 0.000 ARG A 599 Details of bonding type rmsd hydrogen bonds : bond 0.04778 ( 319) hydrogen bonds : angle 3.65658 ( 881) metal coordination : bond 0.00739 ( 4) metal coordination : angle 4.19088 ( 6) covalent geometry : bond 0.00247 ( 6317) covalent geometry : angle 0.48356 ( 8635) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 337 is missing expected H atoms. Skipping. Residue TYR 696 is missing expected H atoms. Skipping. Residue TYR 954 is missing expected H atoms. Skipping. Evaluate side-chains 46 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.884 Fit side-chains revert: symmetry clash REVERT: A 468 ARG cc_start: 0.7714 (ttp-170) cc_final: 0.7295 (tpt170) outliers start: 6 outliers final: 2 residues processed: 44 average time/residue: 2.6487 time to fit residues: 122.5964 Evaluate side-chains 39 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 37 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 880 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 42 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.117668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.082785 restraints weight = 18873.081| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 1.84 r_work: 0.2882 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6321 Z= 0.171 Angle : 0.549 9.707 8641 Z= 0.295 Chirality : 0.041 0.138 995 Planarity : 0.004 0.039 991 Dihedral : 14.154 73.595 1209 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.87 % Favored : 93.98 % Rotamer: Outliers : 1.30 % Allowed : 11.99 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.85 (0.34), residues: 681 helix: 2.51 (0.28), residues: 338 sheet: -0.05 (0.56), residues: 94 loop : -2.10 (0.39), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 737 HIS 0.003 0.001 HIS A 921 PHE 0.011 0.001 PHE A 374 TYR 0.013 0.001 TYR A 312 ARG 0.003 0.000 ARG A 599 Details of bonding type rmsd hydrogen bonds : bond 0.06019 ( 319) hydrogen bonds : angle 3.85818 ( 881) metal coordination : bond 0.00868 ( 4) metal coordination : angle 4.57034 ( 6) covalent geometry : bond 0.00383 ( 6317) covalent geometry : angle 0.53533 ( 8635) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 337 is missing expected H atoms. Skipping. Residue TYR 696 is missing expected H atoms. Skipping. Residue TYR 954 is missing expected H atoms. Skipping. Evaluate side-chains 47 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 308 GLN cc_start: 0.7847 (OUTLIER) cc_final: 0.7187 (mp10) REVERT: A 468 ARG cc_start: 0.7827 (ttp-170) cc_final: 0.7389 (tpt170) outliers start: 8 outliers final: 3 residues processed: 46 average time/residue: 2.7562 time to fit residues: 133.3072 Evaluate side-chains 40 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 GLN Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 956 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 50 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 21 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.120208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.085931 restraints weight = 20010.287| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 1.84 r_work: 0.2947 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6321 Z= 0.107 Angle : 0.485 7.353 8641 Z= 0.259 Chirality : 0.038 0.136 995 Planarity : 0.003 0.032 991 Dihedral : 14.057 73.775 1209 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 1.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 0.65 % Allowed : 12.80 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.06 (0.35), residues: 681 helix: 2.71 (0.29), residues: 341 sheet: -0.13 (0.55), residues: 94 loop : -2.01 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 737 HIS 0.002 0.001 HIS A 447 PHE 0.011 0.001 PHE A 680 TYR 0.009 0.001 TYR A1000 ARG 0.002 0.000 ARG A 860 Details of bonding type rmsd hydrogen bonds : bond 0.04602 ( 319) hydrogen bonds : angle 3.59110 ( 881) metal coordination : bond 0.00631 ( 4) metal coordination : angle 3.47232 ( 6) covalent geometry : bond 0.00223 ( 6317) covalent geometry : angle 0.47616 ( 8635) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 337 is missing expected H atoms. Skipping. Residue TYR 696 is missing expected H atoms. Skipping. Residue TYR 954 is missing expected H atoms. Skipping. Evaluate side-chains 43 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 1.169 Fit side-chains revert: symmetry clash REVERT: A 468 ARG cc_start: 0.7658 (ttp-170) cc_final: 0.7250 (tpt170) outliers start: 4 outliers final: 2 residues processed: 43 average time/residue: 3.4848 time to fit residues: 157.5191 Evaluate side-chains 40 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 38 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 880 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 46 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 3 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.118127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.083520 restraints weight = 19868.421| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 1.85 r_work: 0.2900 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6321 Z= 0.150 Angle : 0.520 8.769 8641 Z= 0.280 Chirality : 0.040 0.138 995 Planarity : 0.003 0.037 991 Dihedral : 14.112 73.762 1209 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.02 % Favored : 93.83 % Rotamer: Outliers : 1.46 % Allowed : 12.16 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.01 (0.34), residues: 681 helix: 2.65 (0.28), residues: 340 sheet: -0.08 (0.55), residues: 94 loop : -2.01 (0.40), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 737 HIS 0.003 0.001 HIS A 921 PHE 0.010 0.001 PHE A 374 TYR 0.013 0.001 TYR A 312 ARG 0.002 0.000 ARG A 599 Details of bonding type rmsd hydrogen bonds : bond 0.05536 ( 319) hydrogen bonds : angle 3.74970 ( 881) metal coordination : bond 0.00770 ( 4) metal coordination : angle 4.10323 ( 6) covalent geometry : bond 0.00331 ( 6317) covalent geometry : angle 0.50886 ( 8635) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 337 is missing expected H atoms. Skipping. Residue TYR 696 is missing expected H atoms. Skipping. Residue TYR 954 is missing expected H atoms. Skipping. Evaluate side-chains 47 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 1.364 Fit side-chains revert: symmetry clash REVERT: A 308 GLN cc_start: 0.7836 (OUTLIER) cc_final: 0.7178 (mp10) REVERT: A 468 ARG cc_start: 0.7745 (ttp-170) cc_final: 0.7316 (tpt170) outliers start: 9 outliers final: 5 residues processed: 45 average time/residue: 3.6771 time to fit residues: 175.6896 Evaluate side-chains 44 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 GLN Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 880 SER Chi-restraints excluded: chain A residue 956 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 2 optimal weight: 0.6980 chunk 32 optimal weight: 5.9990 chunk 54 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.119019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.084533 restraints weight = 19937.492| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 1.85 r_work: 0.2916 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6321 Z= 0.131 Angle : 0.500 7.940 8641 Z= 0.268 Chirality : 0.039 0.137 995 Planarity : 0.003 0.033 991 Dihedral : 14.086 73.887 1209 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 1.30 % Allowed : 12.32 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.10 (0.35), residues: 681 helix: 2.72 (0.28), residues: 340 sheet: -0.07 (0.55), residues: 94 loop : -1.97 (0.40), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 737 HIS 0.002 0.001 HIS A 753 PHE 0.010 0.001 PHE A 680 TYR 0.010 0.001 TYR A 312 ARG 0.003 0.000 ARG A 860 Details of bonding type rmsd hydrogen bonds : bond 0.05082 ( 319) hydrogen bonds : angle 3.67233 ( 881) metal coordination : bond 0.00731 ( 4) metal coordination : angle 3.74049 ( 6) covalent geometry : bond 0.00283 ( 6317) covalent geometry : angle 0.49022 ( 8635) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 337 is missing expected H atoms. Skipping. Residue TYR 696 is missing expected H atoms. Skipping. Residue TYR 954 is missing expected H atoms. Skipping. Evaluate side-chains 46 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.972 Fit side-chains revert: symmetry clash REVERT: A 308 GLN cc_start: 0.7904 (OUTLIER) cc_final: 0.7263 (mp10) REVERT: A 468 ARG cc_start: 0.7737 (ttp-170) cc_final: 0.7305 (tpt170) outliers start: 8 outliers final: 4 residues processed: 44 average time/residue: 2.7144 time to fit residues: 126.4094 Evaluate side-chains 42 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 GLN Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 880 SER Chi-restraints excluded: chain A residue 956 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 37 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 54 optimal weight: 0.3980 chunk 35 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.120327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.085947 restraints weight = 19783.803| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.83 r_work: 0.2951 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6321 Z= 0.106 Angle : 0.472 7.251 8641 Z= 0.252 Chirality : 0.038 0.134 995 Planarity : 0.003 0.034 991 Dihedral : 14.031 73.778 1209 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 0.97 % Allowed : 12.48 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.28 (0.35), residues: 681 helix: 2.88 (0.29), residues: 340 sheet: -0.33 (0.51), residues: 105 loop : -1.79 (0.41), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 737 HIS 0.002 0.001 HIS A 753 PHE 0.010 0.001 PHE A 680 TYR 0.009 0.001 TYR A 312 ARG 0.002 0.000 ARG A 860 Details of bonding type rmsd hydrogen bonds : bond 0.04456 ( 319) hydrogen bonds : angle 3.53163 ( 881) metal coordination : bond 0.00623 ( 4) metal coordination : angle 3.38742 ( 6) covalent geometry : bond 0.00224 ( 6317) covalent geometry : angle 0.46371 ( 8635) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 337 is missing expected H atoms. Skipping. Residue TYR 696 is missing expected H atoms. Skipping. Residue TYR 954 is missing expected H atoms. Skipping. Evaluate side-chains 44 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.916 Fit side-chains revert: symmetry clash REVERT: A 308 GLN cc_start: 0.7885 (OUTLIER) cc_final: 0.7244 (mp10) REVERT: A 468 ARG cc_start: 0.7700 (ttp-170) cc_final: 0.7271 (tpt170) outliers start: 6 outliers final: 4 residues processed: 44 average time/residue: 2.6222 time to fit residues: 121.7154 Evaluate side-chains 42 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 GLN Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 880 SER Chi-restraints excluded: chain A residue 956 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 9 optimal weight: 0.1980 chunk 44 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.120334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.085888 restraints weight = 19739.466| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.84 r_work: 0.2944 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6321 Z= 0.109 Angle : 0.471 7.126 8641 Z= 0.251 Chirality : 0.038 0.134 995 Planarity : 0.003 0.032 991 Dihedral : 13.996 73.778 1209 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.81 % Allowed : 12.48 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.40 (0.35), residues: 681 helix: 2.97 (0.29), residues: 340 sheet: -0.27 (0.51), residues: 105 loop : -1.72 (0.42), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 737 HIS 0.002 0.001 HIS A 753 PHE 0.009 0.001 PHE A 680 TYR 0.009 0.001 TYR A 312 ARG 0.002 0.000 ARG A 310 Details of bonding type rmsd hydrogen bonds : bond 0.04413 ( 319) hydrogen bonds : angle 3.48336 ( 881) metal coordination : bond 0.00597 ( 4) metal coordination : angle 3.34226 ( 6) covalent geometry : bond 0.00234 ( 6317) covalent geometry : angle 0.46300 ( 8635) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 337 is missing expected H atoms. Skipping. Residue TYR 696 is missing expected H atoms. Skipping. Residue TYR 954 is missing expected H atoms. Skipping. Evaluate side-chains 43 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 1.111 Fit side-chains revert: symmetry clash REVERT: A 308 GLN cc_start: 0.7974 (OUTLIER) cc_final: 0.7411 (mp10) REVERT: A 468 ARG cc_start: 0.7686 (ttp-170) cc_final: 0.7259 (tpt170) outliers start: 5 outliers final: 5 residues processed: 43 average time/residue: 3.2496 time to fit residues: 148.1274 Evaluate side-chains 43 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 GLN Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 880 SER Chi-restraints excluded: chain A residue 956 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 17 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.122173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.088006 restraints weight = 19823.276| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 1.85 r_work: 0.2985 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6321 Z= 0.093 Angle : 0.451 6.313 8641 Z= 0.239 Chirality : 0.038 0.138 995 Planarity : 0.003 0.032 991 Dihedral : 13.941 73.748 1209 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.81 % Allowed : 12.64 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.55 (0.35), residues: 681 helix: 3.12 (0.29), residues: 340 sheet: -0.32 (0.51), residues: 105 loop : -1.61 (0.42), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 737 HIS 0.002 0.001 HIS A 604 PHE 0.011 0.001 PHE A 680 TYR 0.008 0.001 TYR A1000 ARG 0.002 0.000 ARG A 860 Details of bonding type rmsd hydrogen bonds : bond 0.03835 ( 319) hydrogen bonds : angle 3.33138 ( 881) metal coordination : bond 0.00519 ( 4) metal coordination : angle 2.95399 ( 6) covalent geometry : bond 0.00197 ( 6317) covalent geometry : angle 0.44449 ( 8635) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8719.18 seconds wall clock time: 155 minutes 46.54 seconds (9346.54 seconds total)