Starting phenix.real_space_refine on Wed Mar 4 09:22:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bkp_12213/03_2026/7bkp_12213_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bkp_12213/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7bkp_12213/03_2026/7bkp_12213.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bkp_12213/03_2026/7bkp_12213.map" model { file = "/net/cci-nas-00/data/ceres_data/7bkp_12213/03_2026/7bkp_12213_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bkp_12213/03_2026/7bkp_12213_trim.cif" } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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: 2.52, per 1000 atoms: 0.21 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: 1.14 Conformation dependent library (CDL) restraints added in 434.3 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: 2.31 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: 3.05 Time building geometry restraints manager: 1.58 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: 2.110 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: 0.050 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 18.810 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.670 ------------------------------------------------------------------------------- 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 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 covalent geometry : bond 0.00940 ( 6317) covalent geometry : angle 0.83608 ( 8635) hydrogen bonds : bond 0.14508 ( 319) hydrogen bonds : angle 5.12703 ( 881) metal coordination : bond 0.04667 ( 4) metal coordination : angle 33.48281 ( 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 : 0.340 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 103 average time/residue: 1.7034 time to fit residues: 181.3824 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 : 0.314 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 448 HIS A 506 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.121367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.087068 restraints weight = 18665.130| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.81 r_work: 0.2961 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.2102 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 : 0.580 12.460 8641 Z= 0.300 Chirality : 0.040 0.140 995 Planarity : 0.004 0.043 991 Dihedral : 14.664 73.667 1210 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.14 % Favored : 94.57 % Rotamer: Outliers : 1.46 % Allowed : 10.70 % 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: -0.12 (0.33), residues: 681 helix: 1.62 (0.28), residues: 339 sheet: -0.54 (0.53), residues: 94 loop : -2.41 (0.38), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 860 TYR 0.012 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 604 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 6317) covalent geometry : angle 0.55416 ( 8635) hydrogen bonds : bond 0.05629 ( 319) hydrogen bonds : angle 4.05385 ( 881) metal coordination : bond 0.01327 ( 4) metal coordination : angle 6.47479 ( 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 50 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: A 468 ARG cc_start: 0.7770 (ttp-170) cc_final: 0.7359 (tpt170) outliers start: 9 outliers final: 3 residues processed: 46 average time/residue: 1.2338 time to fit residues: 59.4978 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 : 0.336 ------------------------------------------------------------------------------- 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 0 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 chunk 45 optimal weight: 0.4980 chunk 7 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3595 r_free = 0.3595 target = 0.124067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.090231 restraints weight = 18936.650| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.82 r_work: 0.3013 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6321 Z= 0.099 Angle : 0.480 9.239 8641 Z= 0.250 Chirality : 0.038 0.140 995 Planarity : 0.003 0.037 991 Dihedral : 14.131 73.715 1209 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 1.15 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.14 % Favored : 94.71 % Rotamer: Outliers : 0.49 % Allowed : 11.35 % Favored : 88.17 % 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: 0.77 (0.35), residues: 681 helix: 2.48 (0.29), residues: 342 sheet: -0.34 (0.55), residues: 93 loop : -2.14 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 860 TYR 0.009 0.001 TYR A 631 PHE 0.012 0.001 PHE A 680 TRP 0.007 0.001 TRP A 737 HIS 0.002 0.001 HIS A 604 Details of bonding type rmsd covalent geometry : bond 0.00210 ( 6317) covalent geometry : angle 0.46547 ( 8635) hydrogen bonds : bond 0.04145 ( 319) hydrogen bonds : angle 3.53606 ( 881) metal coordination : bond 0.00701 ( 4) metal coordination : angle 4.53230 ( 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 44 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 468 ARG cc_start: 0.7721 (ttp-170) cc_final: 0.7316 (tpt170) outliers start: 3 outliers final: 2 residues processed: 42 average time/residue: 1.2637 time to fit residues: 55.8611 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 : 0.356 ------------------------------------------------------------------------------- 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 35 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 56 optimal weight: 8.9990 chunk 16 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 overall best weight: 2.5786 ------------------------------------------------------------------------------- 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 = 0.3505 r_free = 0.3505 target = 0.117353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.082239 restraints weight = 19145.714| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 1.86 r_work: 0.2871 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6321 Z= 0.183 Angle : 0.582 10.473 8641 Z= 0.313 Chirality : 0.041 0.140 995 Planarity : 0.004 0.034 991 Dihedral : 14.188 73.750 1209 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.31 % Favored : 93.54 % 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: 0.72 (0.34), residues: 681 helix: 2.37 (0.28), residues: 339 sheet: -0.12 (0.56), residues: 94 loop : -2.12 (0.39), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 860 TYR 0.016 0.002 TYR A 312 PHE 0.010 0.001 PHE A 374 TRP 0.011 0.001 TRP A 737 HIS 0.004 0.001 HIS A 921 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 6317) covalent geometry : angle 0.56802 ( 8635) hydrogen bonds : bond 0.06499 ( 319) hydrogen bonds : angle 3.96037 ( 881) metal coordination : bond 0.00940 ( 4) metal coordination : angle 4.87305 ( 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 49 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.324 Fit side-chains REVERT: A 308 GLN cc_start: 0.7874 (OUTLIER) cc_final: 0.7308 (mp10) outliers start: 8 outliers final: 4 residues processed: 45 average time/residue: 1.2910 time to fit residues: 60.9100 Evaluate side-chains 41 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 GLN Chi-restraints excluded: chain A residue 384 LYS Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 860 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 30 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 18 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 34 optimal weight: 8.9990 chunk 47 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.120209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.085317 restraints weight = 19084.353| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 1.86 r_work: 0.2926 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.2957 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= 0.115 Angle : 0.495 8.159 8641 Z= 0.265 Chirality : 0.039 0.136 995 Planarity : 0.003 0.034 991 Dihedral : 14.073 73.710 1209 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 1.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % 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 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: 0.98 (0.35), residues: 681 helix: 2.61 (0.29), residues: 341 sheet: -0.27 (0.55), residues: 96 loop : -1.96 (0.40), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 860 TYR 0.010 0.001 TYR A 312 PHE 0.010 0.001 PHE A 680 TRP 0.008 0.001 TRP A 737 HIS 0.002 0.001 HIS A 447 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 6317) covalent geometry : angle 0.48447 ( 8635) hydrogen bonds : bond 0.04847 ( 319) hydrogen bonds : angle 3.66163 ( 881) metal coordination : bond 0.00690 ( 4) metal coordination : angle 3.82375 ( 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 44 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 468 ARG cc_start: 0.7634 (mtm-85) cc_final: 0.7291 (tpt170) outliers start: 6 outliers final: 2 residues processed: 44 average time/residue: 1.2658 time to fit residues: 58.2698 Evaluate side-chains 38 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 36 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 61 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 = 0.3521 r_free = 0.3521 target = 0.118608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.084104 restraints weight = 19792.486| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 1.84 r_work: 0.2912 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.3095 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= 0.138 Angle : 0.514 8.562 8641 Z= 0.275 Chirality : 0.039 0.137 995 Planarity : 0.003 0.035 991 Dihedral : 14.081 73.870 1209 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.73 % Favored : 94.13 % Rotamer: Outliers : 1.46 % Allowed : 11.99 % 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 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: 0.99 (0.34), residues: 681 helix: 2.63 (0.29), residues: 340 sheet: -0.09 (0.56), residues: 94 loop : -2.02 (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 0.008 0.001 TRP A 737 HIS 0.002 0.001 HIS A 921 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 6317) covalent geometry : angle 0.50365 ( 8635) hydrogen bonds : bond 0.05278 ( 319) hydrogen bonds : angle 3.70843 ( 881) metal coordination : bond 0.00739 ( 4) metal coordination : angle 3.97931 ( 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 45 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 468 ARG cc_start: 0.7651 (mtm-85) cc_final: 0.7291 (tpt170) outliers start: 9 outliers final: 4 residues processed: 42 average time/residue: 1.3452 time to fit residues: 59.2541 Evaluate side-chains 39 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 21 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3553 r_free = 0.3553 target = 0.121118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.086663 restraints weight = 19869.099| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 1.85 r_work: 0.2959 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.3191 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= 0.102 Angle : 0.470 7.094 8641 Z= 0.250 Chirality : 0.038 0.136 995 Planarity : 0.003 0.032 991 Dihedral : 14.005 73.670 1209 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 1.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % 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 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: 1.23 (0.35), residues: 681 helix: 2.86 (0.29), residues: 340 sheet: -0.25 (0.52), residues: 103 loop : -1.88 (0.41), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 860 TYR 0.009 0.001 TYR A1000 PHE 0.010 0.001 PHE A 680 TRP 0.007 0.001 TRP A 737 HIS 0.002 0.001 HIS A 753 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 6317) covalent geometry : angle 0.46198 ( 8635) hydrogen bonds : bond 0.04321 ( 319) hydrogen bonds : angle 3.51301 ( 881) metal coordination : bond 0.00566 ( 4) metal coordination : angle 3.30944 ( 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 41 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.314 Fit side-chains revert: symmetry clash REVERT: A 308 GLN cc_start: 0.7813 (OUTLIER) cc_final: 0.7162 (mp10) REVERT: A 468 ARG cc_start: 0.7579 (mtm-85) cc_final: 0.7221 (tpt170) outliers start: 4 outliers final: 3 residues processed: 40 average time/residue: 1.2516 time to fit residues: 52.5634 Evaluate side-chains 39 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.335 ------------------------------------------------------------------------------- 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 880 SER 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: 3.9990 chunk 27 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- 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 = 0.3499 r_free = 0.3499 target = 0.117212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.082663 restraints weight = 19804.667| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 1.82 r_work: 0.2881 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.3220 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= 0.188 Angle : 0.560 9.541 8641 Z= 0.301 Chirality : 0.041 0.140 995 Planarity : 0.004 0.036 991 Dihedral : 14.163 73.720 1209 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.31 % Favored : 93.54 % Rotamer: Outliers : 1.13 % Allowed : 12.16 % 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 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: 0.99 (0.34), residues: 681 helix: 2.57 (0.28), residues: 340 sheet: -0.02 (0.56), residues: 94 loop : -1.97 (0.40), residues: 247 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 0.013 0.001 PHE A 374 TRP 0.010 0.001 TRP A 737 HIS 0.003 0.001 HIS A 921 Details of bonding type rmsd covalent geometry : bond 0.00423 ( 6317) covalent geometry : angle 0.54813 ( 8635) hydrogen bonds : bond 0.06201 ( 319) hydrogen bonds : angle 3.85921 ( 881) metal coordination : bond 0.00855 ( 4) metal coordination : angle 4.45209 ( 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 43 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.329 Fit side-chains REVERT: A 308 GLN cc_start: 0.7867 (OUTLIER) cc_final: 0.7235 (mp10) REVERT: A 468 ARG cc_start: 0.7728 (mtm-85) cc_final: 0.7375 (tpt170) outliers start: 7 outliers final: 5 residues processed: 42 average time/residue: 1.1920 time to fit residues: 52.7017 Evaluate side-chains 41 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.325 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 65 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 37 optimal weight: 0.0570 overall best weight: 2.4106 ------------------------------------------------------------------------------- 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 = 0.3506 r_free = 0.3506 target = 0.117690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.083164 restraints weight = 19724.583| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 1.83 r_work: 0.2898 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 6321 Z= 0.165 Angle : 0.536 8.770 8641 Z= 0.289 Chirality : 0.040 0.139 995 Planarity : 0.003 0.036 991 Dihedral : 14.200 74.085 1209 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.87 % Favored : 93.98 % Rotamer: Outliers : 0.97 % Allowed : 12.32 % 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 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: 1.01 (0.34), residues: 681 helix: 2.59 (0.28), residues: 339 sheet: -0.02 (0.55), residues: 94 loop : -1.92 (0.40), residues: 248 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 covalent geometry : bond 0.00365 ( 6317) covalent geometry : angle 0.52505 ( 8635) hydrogen bonds : bond 0.05757 ( 319) hydrogen bonds : angle 3.81457 ( 881) metal coordination : bond 0.00815 ( 4) metal coordination : angle 4.10772 ( 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 42 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.308 Fit side-chains revert: symmetry clash REVERT: A 308 GLN cc_start: 0.7920 (OUTLIER) cc_final: 0.7274 (mp10) outliers start: 6 outliers final: 5 residues processed: 41 average time/residue: 1.2805 time to fit residues: 54.9784 Evaluate side-chains 42 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.256 ------------------------------------------------------------------------------- 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 63 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- 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 = 0.3532 r_free = 0.3532 target = 0.119530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.084615 restraints weight = 19126.790| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 1.86 r_work: 0.2911 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.3368 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= 0.124 Angle : 0.497 7.852 8641 Z= 0.266 Chirality : 0.039 0.136 995 Planarity : 0.003 0.035 991 Dihedral : 14.126 73.862 1209 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.73 % Favored : 94.13 % 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 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: 1.21 (0.35), residues: 681 helix: 2.76 (0.28), residues: 340 sheet: -0.05 (0.55), residues: 94 loop : -1.82 (0.41), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 310 TYR 0.010 0.001 TYR A 312 PHE 0.010 0.001 PHE A 680 TRP 0.008 0.001 TRP A 737 HIS 0.002 0.001 HIS A 753 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 6317) covalent geometry : angle 0.48741 ( 8635) hydrogen bonds : bond 0.04934 ( 319) hydrogen bonds : angle 3.64519 ( 881) metal coordination : bond 0.00694 ( 4) metal coordination : angle 3.64718 ( 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 41 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.339 Fit side-chains REVERT: A 308 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7363 (mp10) outliers start: 5 outliers final: 4 residues processed: 41 average time/residue: 1.2650 time to fit residues: 54.4289 Evaluate side-chains 41 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.244 ------------------------------------------------------------------------------- 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 38 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- 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 = 0.3566 r_free = 0.3566 target = 0.122004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.087423 restraints weight = 18950.044| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 1.86 r_work: 0.2963 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.3476 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= 0.097 Angle : 0.460 6.332 8641 Z= 0.245 Chirality : 0.038 0.140 995 Planarity : 0.003 0.032 991 Dihedral : 14.025 73.740 1209 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 1.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % 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 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: 1.43 (0.35), residues: 681 helix: 3.00 (0.29), residues: 340 sheet: -0.31 (0.51), residues: 105 loop : -1.68 (0.42), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 860 TYR 0.008 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 753 Details of bonding type rmsd covalent geometry : bond 0.00204 ( 6317) covalent geometry : angle 0.45315 ( 8635) hydrogen bonds : bond 0.04010 ( 319) hydrogen bonds : angle 3.40554 ( 881) metal coordination : bond 0.00529 ( 4) metal coordination : angle 2.95087 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3962.85 seconds wall clock time: 67 minutes 41.32 seconds (4061.32 seconds total)