Starting phenix.real_space_refine on Sat Sep 12 00:15:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bkp_12213/09_2026/7bkp_12213_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bkp_12213/09_2026/7bkp_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 { model { file = "/net/cci-nas-00/data/ceres_data/7bkp_12213/09_2026/7bkp_12213_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bkp_12213/09_2026/7bkp_12213_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7bkp_12213/09_2026/7bkp_12213.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bkp_12213/09_2026/7bkp_12213.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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: 2.24, per 1000 atoms: 0.18 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: 1.02 Conformation dependent library (CDL) restraints added in 357.7 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: 1.97 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: 2.76 Time building geometry restraints manager: 1.44 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: 22221 4.41 - 8.82: 30 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=" O5' C Z 11 " pdb=" C5' C Z 11 " pdb=" C4' C Z 11 " ideal model delta sigma weight residual 109.40 114.19 -4.79 8.00e-01 1.56e+00 3.59e+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: 787 0.066 - 0.133: 197 0.133 - 0.199: 10 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.740 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: 0.070 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 16.640 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 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 : 0.010 0.080 6321 Z= 0.534 Angle : 1.243 55.577 8641 Z= 0.687 Chirality : 0.052 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.008 0.001 ARG A 890 TYR 0.013 0.001 TYR A 381 PHE 0.012 0.001 PHE A 675 TRP 0.013 0.001 TRP A 737 HIS 0.004 0.001 HIS A 753 Details of bonding type rmsd/Z covalent geometry : bond 0.00943 / 0.53 ( 6317) covalent geometry : angle 0.87587 / 0.67 ( 8635) hydrogen bonds : bond 0.14508 / 9.75 ( 319) hydrogen bonds : angle 5.12703 / 3.61 ( 881) metal coordination : bond 0.04667 / 2.34 ( 4) metal coordination : angle 33.48281 / 14.12 ( 6) *********************** 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 : 0.374 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 103 average time/residue: 1.5465 time to fit residues: 165.6041 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 : 0.319 ------------------------------------------------------------------------------- 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 49 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 448 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.121840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.087329 restraints weight = 18528.788| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 1.81 r_work: 0.2957 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6321 Z= 0.143 Angle : 0.630 16.522 8641 Z= 0.331 Chirality : 0.040 0.156 995 Planarity : 0.004 0.038 991 Dihedral : 14.871 83.426 1210 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.29 % Favored : 94.42 % Rotamer: Outliers : 1.62 % Allowed : 11.02 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.32), residues: 681 helix: 1.07 (0.27), residues: 349 sheet: -0.97 (0.48), residues: 103 loop : -2.63 (0.39), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 860 TYR 0.011 0.001 TYR A 312 PHE 0.010 0.001 PHE A 680 TRP 0.010 0.001 TRP A 737 HIS 0.002 0.001 HIS A 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 ( 6317) covalent geometry : angle 0.59116 / 0.33 ( 8635) hydrogen bonds : bond 0.06689 / 4.53 ( 319) hydrogen bonds : angle 4.32174 / 3.03 ( 881) metal coordination : bond 0.01493 / 0.75 ( 4) metal coordination : angle 8.33846 / 3.93 ( 6) *********************** 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 53 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.311 Fit side-chains revert: symmetry clash REVERT: A 468 ARG cc_start: 0.7836 (ttp-170) cc_final: 0.7455 (tpt170) REVERT: A 871 HIS cc_start: 0.7767 (t-90) cc_final: 0.7547 (t70) outliers start: 10 outliers final: 5 residues processed: 49 average time/residue: 1.1246 time to fit residues: 58.4038 Evaluate side-chains 46 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 571 MET Chi-restraints excluded: chain A residue 822 ARG Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 882 LEU 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 0 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 506 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.120644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.086431 restraints weight = 18765.139| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.81 r_work: 0.2944 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6321 Z= 0.136 Angle : 0.545 9.024 8641 Z= 0.297 Chirality : 0.040 0.137 995 Planarity : 0.004 0.040 991 Dihedral : 14.652 75.491 1209 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.29 % Favored : 94.57 % Rotamer: Outliers : 1.30 % Allowed : 11.51 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.34), residues: 681 helix: 1.98 (0.28), residues: 339 sheet: -0.41 (0.54), residues: 94 loop : -2.41 (0.39), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 860 TYR 0.013 0.001 TYR A 312 PHE 0.011 0.001 PHE A 680 TRP 0.010 0.001 TRP A 737 HIS 0.002 0.001 HIS A 604 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 ( 6317) covalent geometry : angle 0.53029 / 0.30 ( 8635) hydrogen bonds : bond 0.06031 / 4.06 ( 319) hydrogen bonds : angle 4.03471 / 2.82 ( 881) metal coordination : bond 0.01091 / 0.55 ( 4) metal coordination : angle 4.72891 / 2.19 ( 6) *********************** 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 46 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: A 468 ARG cc_start: 0.7796 (ttp-170) cc_final: 0.7407 (tpt170) outliers start: 8 outliers final: 3 residues processed: 43 average time/residue: 1.2434 time to fit residues: 56.3302 Evaluate side-chains 38 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 616 ASP 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 35 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 69 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 812 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.118201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.083475 restraints weight = 18854.405| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 1.82 r_work: 0.2890 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6321 Z= 0.181 Angle : 0.570 10.633 8641 Z= 0.315 Chirality : 0.041 0.141 995 Planarity : 0.004 0.036 991 Dihedral : 14.518 81.736 1209 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.87 % Favored : 93.98 % Rotamer: Outliers : 1.13 % Allowed : 11.18 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.34), residues: 681 helix: 2.05 (0.28), residues: 340 sheet: -0.41 (0.55), residues: 96 loop : -2.30 (0.39), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 599 TYR 0.014 0.002 TYR A 312 PHE 0.012 0.001 PHE A 680 TRP 0.011 0.001 TRP A 737 HIS 0.003 0.001 HIS A 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.18 ( 6317) covalent geometry : angle 0.55405 / 0.31 ( 8635) hydrogen bonds : bond 0.06701 / 4.51 ( 319) hydrogen bonds : angle 4.09594 / 2.86 ( 881) metal coordination : bond 0.01011 / 0.51 ( 4) metal coordination : angle 5.03868 / 2.45 ( 6) *********************** 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: 7 poor density : 39 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 43 average time/residue: 1.2392 time to fit residues: 56.2022 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 : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 616 ASP Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 902 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 30 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 18 optimal weight: 0.0980 chunk 32 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.118467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.083767 restraints weight = 18914.189| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 1.83 r_work: 0.2897 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6321 Z= 0.167 Angle : 0.554 9.158 8641 Z= 0.307 Chirality : 0.040 0.141 995 Planarity : 0.004 0.040 991 Dihedral : 14.351 80.601 1209 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.34), residues: 681 helix: 2.19 (0.28), residues: 339 sheet: -0.19 (0.56), residues: 94 loop : -2.32 (0.39), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 599 TYR 0.013 0.002 TYR A 312 PHE 0.011 0.001 PHE A 680 TRP 0.011 0.001 TRP A 737 HIS 0.002 0.001 HIS A 921 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 ( 6317) covalent geometry : angle 0.54151 / 0.31 ( 8635) hydrogen bonds : bond 0.06435 / 4.33 ( 319) hydrogen bonds : angle 4.04616 / 2.82 ( 881) metal coordination : bond 0.00935 / 0.47 ( 4) metal coordination : angle 4.41059 / 2.12 ( 6) *********************** 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 46 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.328 Fit side-chains REVERT: A 468 ARG cc_start: 0.7693 (mtm-85) cc_final: 0.7365 (tpt170) outliers start: 8 outliers final: 5 residues processed: 43 average time/residue: 1.1284 time to fit residues: 51.3549 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 : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 616 ASP Chi-restraints excluded: chain A residue 625 SER 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 25 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 61 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.119071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.084155 restraints weight = 18901.353| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 1.85 r_work: 0.2903 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6321 Z= 0.133 Angle : 0.514 8.256 8641 Z= 0.284 Chirality : 0.039 0.139 995 Planarity : 0.003 0.033 991 Dihedral : 14.191 74.037 1209 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.73 % Favored : 94.13 % Rotamer: Outliers : 0.65 % Allowed : 11.83 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.34), residues: 681 helix: 2.39 (0.28), residues: 338 sheet: -0.29 (0.56), residues: 96 loop : -2.19 (0.39), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 860 TYR 0.011 0.001 TYR A 312 PHE 0.011 0.001 PHE A 680 TRP 0.009 0.001 TRP A 737 HIS 0.002 0.001 HIS A 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 6317) covalent geometry : angle 0.50328 / 0.28 ( 8635) hydrogen bonds : bond 0.05769 / 3.87 ( 319) hydrogen bonds : angle 3.92675 / 2.74 ( 881) metal coordination : bond 0.00752 / 0.38 ( 4) metal coordination : angle 3.90306 / 1.90 ( 6) *********************** 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 42 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 468 ARG cc_start: 0.7677 (mtm-85) cc_final: 0.7358 (tpt170) outliers start: 4 outliers final: 4 residues processed: 40 average time/residue: 1.2406 time to fit residues: 52.3371 Evaluate side-chains 41 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 620 MET Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 956 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 21 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.118206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.083072 restraints weight = 18930.684| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 1.86 r_work: 0.2887 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 6321 Z= 0.161 Angle : 0.531 8.881 8641 Z= 0.295 Chirality : 0.040 0.138 995 Planarity : 0.004 0.043 991 Dihedral : 14.199 74.002 1209 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.81 % Allowed : 11.35 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.34), residues: 681 helix: 2.37 (0.28), residues: 339 sheet: -0.09 (0.56), residues: 94 loop : -2.16 (0.39), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 860 TYR 0.012 0.001 TYR A 312 PHE 0.011 0.001 PHE A 680 TRP 0.009 0.001 TRP A 737 HIS 0.003 0.001 HIS A 921 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 ( 6317) covalent geometry : angle 0.52006 / 0.29 ( 8635) hydrogen bonds : bond 0.06118 / 4.11 ( 319) hydrogen bonds : angle 3.95375 / 2.76 ( 881) metal coordination : bond 0.00817 / 0.41 ( 4) metal coordination : angle 4.15787 / 2.03 ( 6) *********************** 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 43 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 468 ARG cc_start: 0.7703 (mtm-85) cc_final: 0.7354 (tpt170) outliers start: 5 outliers final: 5 residues processed: 41 average time/residue: 1.2910 time to fit residues: 55.7387 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 : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 620 MET Chi-restraints excluded: chain A residue 841 THR 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 12 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.118634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.083612 restraints weight = 18932.187| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 1.85 r_work: 0.2895 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.2947 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= 0.144 Angle : 0.517 8.179 8641 Z= 0.287 Chirality : 0.039 0.137 995 Planarity : 0.003 0.035 991 Dihedral : 14.152 74.124 1209 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.58 % Favored : 94.27 % Rotamer: Outliers : 1.13 % Allowed : 11.35 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.34), residues: 681 helix: 2.45 (0.28), residues: 338 sheet: -0.23 (0.55), residues: 96 loop : -2.08 (0.39), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 599 TYR 0.012 0.001 TYR A 312 PHE 0.011 0.001 PHE A 374 TRP 0.009 0.001 TRP A 737 HIS 0.003 0.001 HIS A 921 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 6317) covalent geometry : angle 0.50723 / 0.29 ( 8635) hydrogen bonds : bond 0.05871 / 3.94 ( 319) hydrogen bonds : angle 3.90842 / 2.73 ( 881) metal coordination : bond 0.00775 / 0.39 ( 4) metal coordination : angle 3.82541 / 1.87 ( 6) *********************** 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 45 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.346 Fit side-chains revert: symmetry clash REVERT: A 468 ARG cc_start: 0.7674 (mtm-85) cc_final: 0.7317 (tpt170) outliers start: 7 outliers final: 4 residues processed: 44 average time/residue: 1.2720 time to fit residues: 58.9949 Evaluate side-chains 41 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 956 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 65 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 18 optimal weight: 0.0060 chunk 29 optimal weight: 0.6980 chunk 68 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 22 optimal weight: 0.0000 chunk 62 optimal weight: 4.9990 chunk 37 optimal weight: 0.0570 overall best weight: 0.3318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.122733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.088315 restraints weight = 18860.651| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.86 r_work: 0.2973 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.3043 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= 0.099 Angle : 0.466 6.169 8641 Z= 0.256 Chirality : 0.038 0.140 995 Planarity : 0.003 0.044 991 Dihedral : 13.999 73.729 1209 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 1.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 0.16 % Allowed : 12.32 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.35), residues: 681 helix: 2.75 (0.29), residues: 339 sheet: -0.35 (0.52), residues: 105 loop : -1.93 (0.40), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 728 TYR 0.010 0.001 TYR A1000 PHE 0.012 0.001 PHE A 680 TRP 0.007 0.001 TRP A 737 HIS 0.003 0.001 HIS A 759 Details of bonding type rmsd/Z covalent geometry : bond 0.00200 / 0.10 ( 6317) covalent geometry : angle 0.46012 / 0.26 ( 8635) hydrogen bonds : bond 0.04460 / 2.99 ( 319) hydrogen bonds : angle 3.61837 / 2.52 ( 881) metal coordination : bond 0.00519 / 0.26 ( 4) metal coordination : angle 2.89715 / 1.42 ( 6) *********************** 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 39 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 38 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 468 ARG cc_start: 0.7636 (mtm-85) cc_final: 0.7270 (tpt170) outliers start: 1 outliers final: 1 residues processed: 39 average time/residue: 1.1951 time to fit residues: 49.1568 Evaluate side-chains 38 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 37 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 841 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 63 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 50 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 56 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.121289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.086819 restraints weight = 19826.092| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 1.85 r_work: 0.2965 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.3066 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= 0.100 Angle : 0.458 6.897 8641 Z= 0.252 Chirality : 0.037 0.135 995 Planarity : 0.003 0.032 991 Dihedral : 14.019 73.848 1209 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 1.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 0.32 % Allowed : 12.64 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.35), residues: 681 helix: 2.79 (0.29), residues: 341 sheet: -0.37 (0.52), residues: 105 loop : -1.85 (0.41), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 860 TYR 0.009 0.001 TYR A1000 PHE 0.011 0.001 PHE A 680 TRP 0.006 0.001 TRP A 737 HIS 0.002 0.001 HIS A 604 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.10 ( 6317) covalent geometry : angle 0.45056 / 0.25 ( 8635) hydrogen bonds : bond 0.04521 / 3.03 ( 319) hydrogen bonds : angle 3.57823 / 2.50 ( 881) metal coordination : bond 0.00537 / 0.27 ( 4) metal coordination : angle 3.18932 / 1.59 ( 6) ********************** 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 39 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 37 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 468 ARG cc_start: 0.7593 (mtm-85) cc_final: 0.7246 (tpt170) outliers start: 2 outliers final: 1 residues processed: 39 average time/residue: 1.2200 time to fit residues: 50.3057 Evaluate side-chains 38 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 37 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 841 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 325 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.121575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.087253 restraints weight = 19652.201| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 1.83 r_work: 0.2971 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6321 Z= 0.097 Angle : 0.455 6.638 8641 Z= 0.250 Chirality : 0.037 0.137 995 Planarity : 0.003 0.042 991 Dihedral : 13.991 73.915 1209 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 1.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.32 % Allowed : 12.80 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.35), residues: 681 helix: 2.83 (0.29), residues: 341 sheet: -0.32 (0.52), residues: 105 loop : -1.81 (0.41), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 860 TYR 0.009 0.001 TYR A1000 PHE 0.011 0.001 PHE A 680 TRP 0.007 0.001 TRP A 737 HIS 0.002 0.001 HIS A 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.10 ( 6317) covalent geometry : angle 0.44820 / 0.25 ( 8635) hydrogen bonds : bond 0.04422 / 2.97 ( 319) hydrogen bonds : angle 3.53960 / 2.47 ( 881) metal coordination : bond 0.00534 / 0.27 ( 4) metal coordination : angle 3.06128 / 1.53 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4036.33 seconds wall clock time: 69 minutes 2.29 seconds (4142.29 seconds total)