Starting phenix.real_space_refine on Thu Jul 2 19:20:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hud_35035/07_2026/8hud_35035_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hud_35035/07_2026/8hud_35035.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hud_35035/07_2026/8hud_35035.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hud_35035/07_2026/8hud_35035.map" model { file = "/net/cci-nas-00/data/ceres_data/8hud_35035/07_2026/8hud_35035_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hud_35035/07_2026/8hud_35035_neut.cif" } resolution = 3.43 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= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1238 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 106 5.49 5 S 26 5.16 5 C 5114 2.51 5 N 1515 2.21 5 O 1909 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8670 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 767, 6406 Classifications: {'peptide': 767} Link IDs: {'PTRANS': 14, 'TRANS': 752} Chain breaks: 6 Chain: "B" Number of atoms: 1526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1526 Classifications: {'RNA': 72} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 33, 'rna3p_pyr': 34} Link IDs: {'rna2p': 5, 'rna3p': 66} Chain: "C" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 574 Classifications: {'DNA': 28} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 27} Chain: "D" Number of atoms: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 164 Classifications: {'DNA': 8} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 7} Time building chain proxies: 1.69, per 1000 atoms: 0.19 Number of scatterers: 8670 At special positions: 0 Unit cell: (82, 105.78, 134.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 26 16.00 P 106 15.00 O 1909 8.00 N 1515 7.00 C 5114 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 816 " - pdb=" SG CYS A 976 " distance=2.08 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: 0.93 Conformation dependent library (CDL) restraints added in 226.7 milliseconds 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1462 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 7 sheets defined 46.5% alpha, 10.3% beta 40 base pairs and 65 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 38 through 71 Processing helix chain 'A' and resid 82 through 93 removed outlier: 3.928A pdb=" N THR A 92 " --> pdb=" O ASN A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 108 Processing helix chain 'A' and resid 127 through 140 removed outlier: 3.500A pdb=" N LYS A 140 " --> pdb=" O GLU A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 155 Processing helix chain 'A' and resid 178 through 196 Processing helix chain 'A' and resid 201 through 213 Processing helix chain 'A' and resid 250 through 255 removed outlier: 3.606A pdb=" N LYS A 253 " --> pdb=" O ILE A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 286 removed outlier: 3.748A pdb=" N GLN A 275 " --> pdb=" O SER A 271 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU A 286 " --> pdb=" O ASP A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 308 Processing helix chain 'A' and resid 312 through 322 Processing helix chain 'A' and resid 345 through 358 removed outlier: 4.281A pdb=" N THR A 356 " --> pdb=" O LYS A 352 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ILE A 357 " --> pdb=" O GLU A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 379 Processing helix chain 'A' and resid 381 through 392 Processing helix chain 'A' and resid 397 through 411 Processing helix chain 'A' and resid 412 through 415 Processing helix chain 'A' and resid 422 through 436 Proline residue: A 431 - end of helix Processing helix chain 'A' and resid 439 through 445 Processing helix chain 'A' and resid 454 through 460 Processing helix chain 'A' and resid 466 through 470 Processing helix chain 'A' and resid 476 through 495 Processing helix chain 'A' and resid 685 through 700 Processing helix chain 'A' and resid 845 through 858 Processing helix chain 'A' and resid 871 through 884 removed outlier: 4.037A pdb=" N ARG A 875 " --> pdb=" O PRO A 871 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASP A 876 " --> pdb=" O LYS A 872 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N MET A 877 " --> pdb=" O THR A 873 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU A 878 " --> pdb=" O TYR A 874 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR A 883 " --> pdb=" O LYS A 879 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR A 884 " --> pdb=" O ILE A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 898 Processing helix chain 'A' and resid 931 through 935 removed outlier: 3.735A pdb=" N GLY A 935 " --> pdb=" O HIS A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 995 Processing helix chain 'A' and resid 1007 through 1011 Processing helix chain 'A' and resid 1027 through 1031 removed outlier: 3.651A pdb=" N GLU A1031 " --> pdb=" O LYS A1028 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 267 through 268 removed outlier: 3.543A pdb=" N ALA A 267 " --> pdb=" O HIS A 419 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 291 through 292 removed outlier: 3.517A pdb=" N LYS A 287 " --> pdb=" O SER A 329 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER A 329 " --> pdb=" O LYS A 287 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 332 through 333 removed outlier: 4.376A pdb=" N ARG A 332 " --> pdb=" O ILE A 340 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 916 through 923 removed outlier: 6.575A pdb=" N LYS A 837 " --> pdb=" O SER A 921 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N GLN A 923 " --> pdb=" O ILE A 835 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N ILE A 835 " --> pdb=" O GLN A 923 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLY A 827 " --> pdb=" O ILE A 838 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 945 " --> pdb=" O ILE A 928 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 964 through 970 removed outlier: 3.948A pdb=" N TYR A 957 " --> pdb=" O THR A1013 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N THR A1013 " --> pdb=" O TYR A 957 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 964 through 970 Processing sheet with id=AA7, first strand: chain 'A' and resid 1074 through 1075 removed outlier: 3.804A pdb=" N ILE A1074 " --> pdb=" O ILE A1048 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE A1048 " --> pdb=" O ILE A1074 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER A1039 " --> pdb=" O GLU A1049 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N LYS A1051 " --> pdb=" O PHE A1037 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N PHE A1037 " --> pdb=" O LYS A1051 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY A1083 " --> pdb=" O GLN A1025 " (cutoff:3.500A) 267 hydrogen bonds defined for protein. 759 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 102 hydrogen bonds 204 hydrogen bond angles 0 basepair planarities 40 basepair parallelities 65 stacking parallelities Total time for adding SS restraints: 2.01 Time building geometry restraints manager: 1.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2247 1.34 - 1.46: 2793 1.46 - 1.59: 3756 1.59 - 1.71: 211 1.71 - 1.84: 41 Bond restraints: 9048 Sorted by residual: bond pdb=" O3' DG C 10 " pdb=" P DC C 11 " ideal model delta sigma weight residual 1.607 1.672 -0.065 1.50e-02 4.44e+03 1.86e+01 bond pdb=" O3' DG D 6 " pdb=" P DC D 7 " ideal model delta sigma weight residual 1.607 1.660 -0.053 1.50e-02 4.44e+03 1.25e+01 bond pdb=" CA ARG A1071 " pdb=" C ARG A1071 " ideal model delta sigma weight residual 1.524 1.482 0.042 1.31e-02 5.83e+03 1.05e+01 bond pdb=" C3' DG C 7 " pdb=" C2' DG C 7 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.70e+00 bond pdb=" O3' U B 32 " pdb=" P G B 33 " ideal model delta sigma weight residual 1.607 1.652 -0.045 1.50e-02 4.44e+03 9.13e+00 ... (remaining 9043 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 12233 2.21 - 4.42: 360 4.42 - 6.63: 39 6.63 - 8.85: 7 8.85 - 11.06: 4 Bond angle restraints: 12643 Sorted by residual: angle pdb=" N ILE A 200 " pdb=" CA ILE A 200 " pdb=" C ILE A 200 " ideal model delta sigma weight residual 109.58 116.95 -7.37 1.29e+00 6.01e-01 3.26e+01 angle pdb=" C SER A 839 " pdb=" CA SER A 839 " pdb=" CB SER A 839 " ideal model delta sigma weight residual 109.37 118.96 -9.59 1.91e+00 2.74e-01 2.52e+01 angle pdb=" O4' DC C 11 " pdb=" C4' DC C 11 " pdb=" C3' DC C 11 " ideal model delta sigma weight residual 106.00 102.99 3.01 6.00e-01 2.78e+00 2.51e+01 angle pdb=" O4' DT C 26 " pdb=" C4' DT C 26 " pdb=" C3' DT C 26 " ideal model delta sigma weight residual 106.00 103.01 2.99 6.00e-01 2.78e+00 2.49e+01 angle pdb=" CA PHE A 344 " pdb=" CB PHE A 344 " pdb=" CG PHE A 344 " ideal model delta sigma weight residual 113.80 118.73 -4.93 1.00e+00 1.00e+00 2.43e+01 ... (remaining 12638 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 4362 17.77 - 35.54: 694 35.54 - 53.31: 295 53.31 - 71.08: 122 71.08 - 88.85: 25 Dihedral angle restraints: 5498 sinusoidal: 3218 harmonic: 2280 Sorted by residual: dihedral pdb=" CB CYS A 816 " pdb=" SG CYS A 816 " pdb=" SG CYS A 976 " pdb=" CB CYS A 976 " ideal model delta sinusoidal sigma weight residual -86.00 -29.71 -56.29 1 1.00e+01 1.00e-02 4.27e+01 dihedral pdb=" CA GLY A1030 " pdb=" C GLY A1030 " pdb=" N GLU A1031 " pdb=" CA GLU A1031 " ideal model delta harmonic sigma weight residual 180.00 155.55 24.45 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA TYR A 158 " pdb=" C TYR A 158 " pdb=" N HIS A 159 " pdb=" CA HIS A 159 " ideal model delta harmonic sigma weight residual 180.00 -162.50 -17.50 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 5495 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1195 0.070 - 0.141: 177 0.141 - 0.211: 49 0.211 - 0.281: 9 0.281 - 0.352: 2 Chirality restraints: 1432 Sorted by residual: chirality pdb=" C3' DG C 10 " pdb=" C4' DG C 10 " pdb=" O3' DG C 10 " pdb=" C2' DG C 10 " both_signs ideal model delta sigma weight residual False -2.73 -2.38 -0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" CA ILE A1053 " pdb=" N ILE A1053 " pdb=" C ILE A1053 " pdb=" CB ILE A1053 " both_signs ideal model delta sigma weight residual False 2.43 2.75 -0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" C3' U B 44 " pdb=" C4' U B 44 " pdb=" O3' U B 44 " pdb=" C2' U B 44 " both_signs ideal model delta sigma weight residual False -2.48 -2.75 0.28 2.00e-01 2.50e+01 1.92e+00 ... (remaining 1429 not shown) Planarity restraints: 1206 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC D 7 " 0.006 2.00e-02 2.50e+03 2.05e-02 9.49e+00 pdb=" N1 DC D 7 " 0.024 2.00e-02 2.50e+03 pdb=" C2 DC D 7 " -0.028 2.00e-02 2.50e+03 pdb=" O2 DC D 7 " -0.001 2.00e-02 2.50e+03 pdb=" N3 DC D 7 " 0.023 2.00e-02 2.50e+03 pdb=" C4 DC D 7 " -0.016 2.00e-02 2.50e+03 pdb=" N4 DC D 7 " -0.000 2.00e-02 2.50e+03 pdb=" C5 DC D 7 " 0.023 2.00e-02 2.50e+03 pdb=" C6 DC D 7 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B 32 " -0.019 2.00e-02 2.50e+03 1.83e-02 7.56e+00 pdb=" N1 U B 32 " 0.008 2.00e-02 2.50e+03 pdb=" C2 U B 32 " 0.043 2.00e-02 2.50e+03 pdb=" O2 U B 32 " -0.010 2.00e-02 2.50e+03 pdb=" N3 U B 32 " -0.017 2.00e-02 2.50e+03 pdb=" C4 U B 32 " -0.011 2.00e-02 2.50e+03 pdb=" O4 U B 32 " -0.004 2.00e-02 2.50e+03 pdb=" C5 U B 32 " 0.013 2.00e-02 2.50e+03 pdb=" C6 U B 32 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG D 8 " -0.004 2.00e-02 2.50e+03 1.58e-02 7.51e+00 pdb=" N9 DG D 8 " -0.001 2.00e-02 2.50e+03 pdb=" C8 DG D 8 " -0.001 2.00e-02 2.50e+03 pdb=" N7 DG D 8 " -0.000 2.00e-02 2.50e+03 pdb=" C5 DG D 8 " 0.031 2.00e-02 2.50e+03 pdb=" C6 DG D 8 " -0.001 2.00e-02 2.50e+03 pdb=" O6 DG D 8 " 0.000 2.00e-02 2.50e+03 pdb=" N1 DG D 8 " -0.029 2.00e-02 2.50e+03 pdb=" C2 DG D 8 " -0.015 2.00e-02 2.50e+03 pdb=" N2 DG D 8 " 0.030 2.00e-02 2.50e+03 pdb=" N3 DG D 8 " -0.010 2.00e-02 2.50e+03 pdb=" C4 DG D 8 " -0.000 2.00e-02 2.50e+03 ... (remaining 1203 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 2295 2.81 - 3.33: 7622 3.33 - 3.85: 14998 3.85 - 4.38: 17138 4.38 - 4.90: 26612 Nonbonded interactions: 68665 Sorted by model distance: nonbonded pdb=" O GLY A 131 " pdb=" OD1 ASN A 135 " model vdw 2.284 3.040 nonbonded pdb=" OD2 ASP A 954 " pdb=" OH TYR A 988 " model vdw 2.290 3.040 nonbonded pdb=" OG SER A 268 " pdb=" OD1 ASP A 374 " model vdw 2.294 3.040 nonbonded pdb=" OH TYR A 234 " pdb=" O4 U B 64 " model vdw 2.316 3.040 nonbonded pdb=" O ASP A 360 " pdb=" OG SER A 363 " model vdw 2.337 3.040 ... (remaining 68660 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: 4.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.140 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 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 : 0.005 0.065 9049 Z= 0.360 Angle : 0.842 11.058 12645 Z= 0.581 Chirality : 0.059 0.352 1432 Planarity : 0.004 0.046 1206 Dihedral : 20.890 88.851 4033 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.83 % Favored : 90.17 % Rotamer: Outliers : 0.56 % Allowed : 23.22 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.31), residues: 753 helix: 0.44 (0.29), residues: 319 sheet: -1.73 (0.68), residues: 52 loop : -2.05 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 314 TYR 0.036 0.002 TYR A 272 PHE 0.032 0.002 PHE A 344 TRP 0.012 0.002 TRP A1067 HIS 0.009 0.002 HIS A 973 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.36 ( 9048) covalent geometry : angle 0.83782 / 0.58 (12643) SS BOND : bond 0.04955 / 2.61 ( 1) SS BOND : angle 6.97606 / 3.96 ( 2) hydrogen bonds : bond 0.15082 / 9.93 ( 363) hydrogen bonds : angle 6.62569 / 4.75 ( 963) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 88 time to evaluate : 0.172 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 90 average time/residue: 0.1023 time to fit residues: 12.5991 Evaluate side-chains 70 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.1980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 GLN A 327 GLN A 392 GLN A 705 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.194939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.168234 restraints weight = 14060.113| |-----------------------------------------------------------------------------| r_work (start): 0.4077 rms_B_bonded: 1.80 r_work: 0.3900 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9049 Z= 0.151 Angle : 0.563 5.936 12645 Z= 0.329 Chirality : 0.041 0.231 1432 Planarity : 0.004 0.041 1206 Dihedral : 20.264 78.855 2323 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 3.64 % Allowed : 23.36 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.30), residues: 753 helix: 0.83 (0.29), residues: 319 sheet: -1.41 (0.75), residues: 49 loop : -1.92 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 51 TYR 0.012 0.001 TYR A1081 PHE 0.019 0.002 PHE A 134 TRP 0.010 0.002 TRP A1067 HIS 0.006 0.001 HIS A 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.15 ( 9048) covalent geometry : angle 0.56266 / 0.33 (12643) SS BOND : bond 0.00536 / 0.28 ( 1) SS BOND : angle 2.43967 / 1.31 ( 2) hydrogen bonds : bond 0.05534 / 3.76 ( 363) hydrogen bonds : angle 4.62094 / 3.36 ( 963) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 77 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 PHE cc_start: 0.6342 (m-80) cc_final: 0.6085 (m-80) REVERT: A 327 GLN cc_start: 0.6057 (OUTLIER) cc_final: 0.5095 (pm20) REVERT: A 347 TYR cc_start: 0.6316 (OUTLIER) cc_final: 0.5221 (m-80) REVERT: A 981 TYR cc_start: 0.5842 (OUTLIER) cc_final: 0.4357 (m-80) REVERT: A 992 LEU cc_start: 0.6161 (mt) cc_final: 0.5885 (mt) outliers start: 26 outliers final: 8 residues processed: 96 average time/residue: 0.0875 time to fit residues: 11.9000 Evaluate side-chains 76 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 342 HIS Chi-restraints excluded: chain A residue 347 TYR Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 849 CYS Chi-restraints excluded: chain A residue 981 TYR Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 987 THR Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1074 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 6 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 83 optimal weight: 9.9990 chunk 8 optimal weight: 0.9990 chunk 67 optimal weight: 0.2980 chunk 14 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 312 ASN A 327 GLN A 410 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.195678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.164484 restraints weight = 14373.334| |-----------------------------------------------------------------------------| r_work (start): 0.4071 rms_B_bonded: 2.25 r_work: 0.3949 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9049 Z= 0.141 Angle : 0.526 5.743 12645 Z= 0.310 Chirality : 0.040 0.198 1432 Planarity : 0.003 0.037 1206 Dihedral : 20.095 80.035 2323 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 3.78 % Allowed : 22.66 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.31), residues: 753 helix: 1.02 (0.29), residues: 320 sheet: -1.52 (0.66), residues: 62 loop : -1.95 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 56 TYR 0.013 0.001 TYR A 874 PHE 0.013 0.001 PHE A 277 TRP 0.008 0.001 TRP A1067 HIS 0.005 0.001 HIS A 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 ( 9048) covalent geometry : angle 0.52540 / 0.31 (12643) SS BOND : bond 0.00226 / 0.12 ( 1) SS BOND : angle 1.07442 / 0.60 ( 2) hydrogen bonds : bond 0.05063 / 3.47 ( 363) hydrogen bonds : angle 4.36191 / 3.16 ( 963) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 73 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 PHE cc_start: 0.6493 (m-80) cc_final: 0.6093 (m-80) REVERT: A 318 LYS cc_start: 0.8421 (pttp) cc_final: 0.8125 (tptt) REVERT: A 347 TYR cc_start: 0.6389 (OUTLIER) cc_final: 0.5506 (m-80) REVERT: A 981 TYR cc_start: 0.5734 (OUTLIER) cc_final: 0.4256 (m-80) REVERT: A 992 LEU cc_start: 0.6246 (mt) cc_final: 0.5974 (mt) outliers start: 27 outliers final: 11 residues processed: 93 average time/residue: 0.0875 time to fit residues: 11.7728 Evaluate side-chains 83 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 347 TYR Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 849 CYS Chi-restraints excluded: chain A residue 981 TYR Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 987 THR Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1074 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 1 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 78 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 24 optimal weight: 0.1980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 ASN ** A 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.195715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.168563 restraints weight = 14701.175| |-----------------------------------------------------------------------------| r_work (start): 0.4127 rms_B_bonded: 2.06 r_work: 0.3931 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9049 Z= 0.131 Angle : 0.519 10.935 12645 Z= 0.300 Chirality : 0.039 0.202 1432 Planarity : 0.003 0.033 1206 Dihedral : 19.954 80.737 2323 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 3.36 % Allowed : 22.80 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.31), residues: 753 helix: 1.13 (0.29), residues: 320 sheet: -1.56 (0.70), residues: 55 loop : -1.93 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 829 TYR 0.016 0.001 TYR A 341 PHE 0.013 0.001 PHE A 277 TRP 0.007 0.001 TRP A 68 HIS 0.009 0.001 HIS A 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 ( 9048) covalent geometry : angle 0.51860 / 0.30 (12643) SS BOND : bond 0.00136 / 0.07 ( 1) SS BOND : angle 0.77715 / 0.43 ( 2) hydrogen bonds : bond 0.04588 / 3.14 ( 363) hydrogen bonds : angle 4.23057 / 3.09 ( 963) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 68 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 PHE cc_start: 0.6474 (m-80) cc_final: 0.6042 (m-80) REVERT: A 347 TYR cc_start: 0.6315 (OUTLIER) cc_final: 0.5830 (m-80) REVERT: A 981 TYR cc_start: 0.5711 (OUTLIER) cc_final: 0.4268 (m-80) REVERT: A 992 LEU cc_start: 0.6245 (mt) cc_final: 0.5961 (mt) outliers start: 24 outliers final: 9 residues processed: 86 average time/residue: 0.0818 time to fit residues: 10.2620 Evaluate side-chains 77 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 347 TYR Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 849 CYS Chi-restraints excluded: chain A residue 981 TYR Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 987 THR Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1074 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 2 optimal weight: 0.6980 chunk 79 optimal weight: 9.9990 chunk 18 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 39 optimal weight: 3.9990 chunk 80 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.195398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.168308 restraints weight = 14531.191| |-----------------------------------------------------------------------------| r_work (start): 0.4122 rms_B_bonded: 2.07 r_work: 0.3925 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9049 Z= 0.131 Angle : 0.508 6.786 12645 Z= 0.295 Chirality : 0.039 0.178 1432 Planarity : 0.003 0.030 1206 Dihedral : 19.841 80.942 2323 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % Rotamer: Outliers : 3.36 % Allowed : 23.50 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.31), residues: 753 helix: 1.18 (0.29), residues: 320 sheet: -1.11 (0.66), residues: 61 loop : -1.99 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 56 TYR 0.015 0.001 TYR A 128 PHE 0.013 0.001 PHE A 277 TRP 0.007 0.001 TRP A1067 HIS 0.005 0.001 HIS A 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 ( 9048) covalent geometry : angle 0.50836 / 0.30 (12643) SS BOND : bond 0.00005 / 0.00 ( 1) SS BOND : angle 0.50976 / 0.29 ( 2) hydrogen bonds : bond 0.04458 / 3.06 ( 363) hydrogen bonds : angle 4.12385 / 3.00 ( 963) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 74 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 PHE cc_start: 0.6574 (m-80) cc_final: 0.6095 (m-80) REVERT: A 347 TYR cc_start: 0.6402 (OUTLIER) cc_final: 0.5926 (m-80) REVERT: A 403 LYS cc_start: 0.7897 (mmtt) cc_final: 0.7396 (ttpt) REVERT: A 981 TYR cc_start: 0.5751 (OUTLIER) cc_final: 0.4235 (m-80) REVERT: A 992 LEU cc_start: 0.6326 (mt) cc_final: 0.6058 (mt) outliers start: 24 outliers final: 13 residues processed: 92 average time/residue: 0.0767 time to fit residues: 10.1188 Evaluate side-chains 83 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 347 TYR Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 849 CYS Chi-restraints excluded: chain A residue 981 TYR Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 987 THR Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1074 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 11 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 53 optimal weight: 0.4980 chunk 26 optimal weight: 6.9990 chunk 76 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 138 GLN A 148 GLN ** A 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.189603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.158063 restraints weight = 14750.130| |-----------------------------------------------------------------------------| r_work (start): 0.4000 rms_B_bonded: 2.29 r_work: 0.3858 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 9049 Z= 0.233 Angle : 0.631 8.906 12645 Z= 0.357 Chirality : 0.045 0.204 1432 Planarity : 0.004 0.034 1206 Dihedral : 19.913 79.653 2323 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.49 % Favored : 89.51 % Rotamer: Outliers : 5.45 % Allowed : 23.08 % Favored : 71.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.30), residues: 753 helix: 0.90 (0.29), residues: 321 sheet: -1.16 (0.74), residues: 50 loop : -2.20 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 55 TYR 0.019 0.002 TYR A1014 PHE 0.021 0.002 PHE A 277 TRP 0.008 0.002 TRP A 68 HIS 0.006 0.002 HIS A 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.23 ( 9048) covalent geometry : angle 0.63130 / 0.36 (12643) SS BOND : bond 0.00318 / 0.17 ( 1) SS BOND : angle 0.51092 / 0.26 ( 2) hydrogen bonds : bond 0.05836 / 3.99 ( 363) hydrogen bonds : angle 4.43187 / 3.23 ( 963) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 75 time to evaluate : 0.173 Fit side-chains revert: symmetry clash REVERT: A 55 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.8163 (ptp90) REVERT: A 219 TYR cc_start: 0.7707 (p90) cc_final: 0.7340 (p90) REVERT: A 347 TYR cc_start: 0.6613 (OUTLIER) cc_final: 0.5707 (m-80) REVERT: A 357 ILE cc_start: 0.7863 (OUTLIER) cc_final: 0.7556 (pt) REVERT: A 369 LEU cc_start: 0.7030 (OUTLIER) cc_final: 0.6614 (tt) REVERT: A 403 LYS cc_start: 0.7960 (mmtt) cc_final: 0.7492 (mmtm) REVERT: A 707 LYS cc_start: 0.7959 (mmtm) cc_final: 0.7529 (mmtt) REVERT: A 981 TYR cc_start: 0.5989 (OUTLIER) cc_final: 0.4316 (m-80) REVERT: A 986 GLU cc_start: 0.6857 (OUTLIER) cc_final: 0.6074 (mp0) outliers start: 39 outliers final: 20 residues processed: 108 average time/residue: 0.0703 time to fit residues: 11.0119 Evaluate side-chains 96 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 70 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ARG Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 347 TYR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 849 CYS Chi-restraints excluded: chain A residue 981 TYR Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 984 ASP Chi-restraints excluded: chain A residue 986 GLU Chi-restraints excluded: chain A residue 987 THR Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1074 ILE Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1103 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 41 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 chunk 33 optimal weight: 0.9980 chunk 12 optimal weight: 0.2980 chunk 55 optimal weight: 0.0970 chunk 80 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 7 optimal weight: 0.3980 chunk 42 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 2 optimal weight: 0.2980 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 342 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.196382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.169099 restraints weight = 14886.167| |-----------------------------------------------------------------------------| r_work (start): 0.4143 rms_B_bonded: 1.96 r_work: 0.3962 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9049 Z= 0.123 Angle : 0.523 6.961 12645 Z= 0.305 Chirality : 0.039 0.183 1432 Planarity : 0.003 0.027 1206 Dihedral : 19.789 81.172 2323 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 3.08 % Allowed : 25.17 % Favored : 71.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.30), residues: 753 helix: 1.08 (0.29), residues: 320 sheet: -1.91 (0.63), residues: 64 loop : -1.88 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 60 TYR 0.021 0.001 TYR A 128 PHE 0.011 0.001 PHE A 277 TRP 0.009 0.001 TRP A1067 HIS 0.003 0.001 HIS A 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 ( 9048) covalent geometry : angle 0.52250 / 0.30 (12643) SS BOND : bond 0.00059 / 0.03 ( 1) SS BOND : angle 0.79488 / 0.43 ( 2) hydrogen bonds : bond 0.04437 / 3.00 ( 363) hydrogen bonds : angle 4.20508 / 3.09 ( 963) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 75 time to evaluate : 0.199 Fit side-chains revert: symmetry clash REVERT: A 134 PHE cc_start: 0.6499 (m-80) cc_final: 0.5957 (m-80) REVERT: A 347 TYR cc_start: 0.6428 (OUTLIER) cc_final: 0.5677 (m-80) REVERT: A 403 LYS cc_start: 0.7906 (mmtt) cc_final: 0.7530 (ttpt) REVERT: A 410 ASN cc_start: 0.7610 (t0) cc_final: 0.7376 (t0) REVERT: A 707 LYS cc_start: 0.7937 (mmtm) cc_final: 0.7526 (mmtt) REVERT: A 981 TYR cc_start: 0.5991 (OUTLIER) cc_final: 0.4404 (m-80) REVERT: A 986 GLU cc_start: 0.6819 (OUTLIER) cc_final: 0.6023 (mp0) outliers start: 22 outliers final: 12 residues processed: 92 average time/residue: 0.0696 time to fit residues: 9.3927 Evaluate side-chains 84 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 347 TYR Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 849 CYS Chi-restraints excluded: chain A residue 981 TYR Chi-restraints excluded: chain A residue 986 GLU Chi-restraints excluded: chain A residue 987 THR Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1074 ILE Chi-restraints excluded: chain A residue 1103 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 84 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 64 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 83 optimal weight: 10.0000 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 ASN ** A 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.194794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.167326 restraints weight = 14626.595| |-----------------------------------------------------------------------------| r_work (start): 0.4123 rms_B_bonded: 1.95 r_work: 0.3942 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9049 Z= 0.151 Angle : 0.530 5.865 12645 Z= 0.310 Chirality : 0.041 0.175 1432 Planarity : 0.003 0.027 1206 Dihedral : 19.702 81.147 2323 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 3.92 % Allowed : 23.92 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.30), residues: 753 helix: 1.11 (0.29), residues: 319 sheet: -1.50 (0.68), residues: 58 loop : -1.94 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 51 TYR 0.018 0.002 TYR A 128 PHE 0.014 0.002 PHE A 277 TRP 0.008 0.001 TRP A1067 HIS 0.002 0.001 HIS A 936 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 ( 9048) covalent geometry : angle 0.53007 / 0.31 (12643) SS BOND : bond 0.00118 / 0.06 ( 1) SS BOND : angle 0.31766 / 0.18 ( 2) hydrogen bonds : bond 0.04630 / 3.18 ( 363) hydrogen bonds : angle 4.19339 / 3.07 ( 963) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 69 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.8181 (ptp90) REVERT: A 357 ILE cc_start: 0.7707 (OUTLIER) cc_final: 0.7444 (pt) REVERT: A 403 LYS cc_start: 0.7956 (mmtt) cc_final: 0.7554 (mmtm) REVERT: A 707 LYS cc_start: 0.7994 (mmtm) cc_final: 0.7526 (mmtt) REVERT: A 981 TYR cc_start: 0.6024 (OUTLIER) cc_final: 0.4444 (m-80) REVERT: A 986 GLU cc_start: 0.6809 (OUTLIER) cc_final: 0.6044 (mp0) outliers start: 28 outliers final: 17 residues processed: 92 average time/residue: 0.0847 time to fit residues: 11.1461 Evaluate side-chains 89 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 68 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ARG Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 347 TYR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain A residue 981 TYR Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 986 GLU Chi-restraints excluded: chain A residue 987 THR Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1074 ILE Chi-restraints excluded: chain A residue 1103 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 64 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 47 optimal weight: 3.9990 chunk 65 optimal weight: 0.4980 chunk 15 optimal weight: 0.6980 chunk 51 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 20 optimal weight: 0.0980 chunk 54 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.196105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.168919 restraints weight = 14556.305| |-----------------------------------------------------------------------------| r_work (start): 0.4142 rms_B_bonded: 1.94 r_work: 0.3962 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9049 Z= 0.127 Angle : 0.521 11.796 12645 Z= 0.303 Chirality : 0.039 0.185 1432 Planarity : 0.003 0.063 1206 Dihedral : 19.676 81.961 2323 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 3.22 % Allowed : 24.34 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.30), residues: 753 helix: 1.14 (0.29), residues: 319 sheet: -1.82 (0.74), residues: 52 loop : -1.85 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 56 TYR 0.023 0.001 TYR A 128 PHE 0.011 0.001 PHE A 277 TRP 0.009 0.001 TRP A1067 HIS 0.003 0.001 HIS A 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.13 ( 9048) covalent geometry : angle 0.52092 / 0.30 (12643) SS BOND : bond 0.00020 / 0.01 ( 1) SS BOND : angle 0.48076 / 0.26 ( 2) hydrogen bonds : bond 0.04281 / 2.93 ( 363) hydrogen bonds : angle 4.06793 / 2.97 ( 963) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 73 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.8170 (ptp90) REVERT: A 134 PHE cc_start: 0.6758 (t80) cc_final: 0.6211 (m-80) REVERT: A 328 TYR cc_start: 0.4674 (OUTLIER) cc_final: 0.2990 (t80) REVERT: A 357 ILE cc_start: 0.7693 (OUTLIER) cc_final: 0.7433 (pt) REVERT: A 403 LYS cc_start: 0.7909 (mmtt) cc_final: 0.7520 (mmtm) REVERT: A 707 LYS cc_start: 0.7949 (mmtm) cc_final: 0.7521 (mmtt) REVERT: A 981 TYR cc_start: 0.5930 (OUTLIER) cc_final: 0.4409 (m-80) outliers start: 23 outliers final: 17 residues processed: 90 average time/residue: 0.0851 time to fit residues: 10.8508 Evaluate side-chains 90 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 69 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ARG Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 328 TYR Chi-restraints excluded: chain A residue 347 TYR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 981 TYR Chi-restraints excluded: chain A residue 987 THR Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1053 ILE Chi-restraints excluded: chain A residue 1074 ILE Chi-restraints excluded: chain A residue 1103 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 57 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 43 optimal weight: 0.0010 chunk 39 optimal weight: 3.9990 chunk 65 optimal weight: 0.0070 chunk 35 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 overall best weight: 0.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 312 ASN ** A 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.197831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.170893 restraints weight = 14817.029| |-----------------------------------------------------------------------------| r_work (start): 0.4159 rms_B_bonded: 1.97 r_work: 0.3978 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 9049 Z= 0.117 Angle : 0.488 9.342 12645 Z= 0.287 Chirality : 0.038 0.165 1432 Planarity : 0.003 0.065 1206 Dihedral : 19.577 82.231 2323 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 2.80 % Allowed : 25.03 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.31), residues: 753 helix: 1.28 (0.29), residues: 319 sheet: -1.70 (0.75), residues: 52 loop : -1.74 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 829 TYR 0.021 0.001 TYR A 128 PHE 0.017 0.001 PHE A 364 TRP 0.010 0.001 TRP A1067 HIS 0.006 0.001 HIS A 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.12 ( 9048) covalent geometry : angle 0.48792 / 0.29 (12643) SS BOND : bond 0.00049 / 0.03 ( 1) SS BOND : angle 0.56251 / 0.30 ( 2) hydrogen bonds : bond 0.03964 / 2.69 ( 363) hydrogen bonds : angle 3.92359 / 2.86 ( 963) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 76 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.8164 (ptp90) REVERT: A 328 TYR cc_start: 0.5176 (OUTLIER) cc_final: 0.3151 (t80) REVERT: A 357 ILE cc_start: 0.7645 (OUTLIER) cc_final: 0.7364 (pt) REVERT: A 403 LYS cc_start: 0.7898 (mmtt) cc_final: 0.7516 (mmtm) REVERT: A 707 LYS cc_start: 0.7960 (mmtm) cc_final: 0.7528 (mmtt) REVERT: A 959 ASN cc_start: 0.7021 (m-40) cc_final: 0.6769 (m110) REVERT: A 981 TYR cc_start: 0.5862 (OUTLIER) cc_final: 0.4403 (m-80) REVERT: A 986 GLU cc_start: 0.6912 (OUTLIER) cc_final: 0.6127 (mp0) outliers start: 20 outliers final: 14 residues processed: 93 average time/residue: 0.0809 time to fit residues: 10.6583 Evaluate side-chains 89 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 70 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ARG Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 328 TYR Chi-restraints excluded: chain A residue 347 TYR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 981 TYR Chi-restraints excluded: chain A residue 986 GLU Chi-restraints excluded: chain A residue 987 THR Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1074 ILE Chi-restraints excluded: chain A residue 1103 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 58 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 59 optimal weight: 0.4980 chunk 15 optimal weight: 0.8980 chunk 75 optimal weight: 0.0770 chunk 76 optimal weight: 9.9990 chunk 79 optimal weight: 10.0000 chunk 11 optimal weight: 0.9980 chunk 4 optimal weight: 0.0970 chunk 83 optimal weight: 9.9990 chunk 67 optimal weight: 0.1980 overall best weight: 0.3336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 312 ASN ** A 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.198385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.171524 restraints weight = 14570.310| |-----------------------------------------------------------------------------| r_work (start): 0.4165 rms_B_bonded: 1.93 r_work: 0.3984 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 9049 Z= 0.112 Angle : 0.496 9.975 12645 Z= 0.291 Chirality : 0.038 0.162 1432 Planarity : 0.003 0.061 1206 Dihedral : 19.561 81.941 2323 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 2.66 % Allowed : 25.45 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.31), residues: 753 helix: 1.22 (0.29), residues: 320 sheet: -1.59 (0.76), residues: 52 loop : -1.77 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 314 TYR 0.033 0.001 TYR A 128 PHE 0.025 0.001 PHE A 134 TRP 0.010 0.001 TRP A1067 HIS 0.003 0.000 HIS A 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.11 ( 9048) covalent geometry : angle 0.49617 / 0.29 (12643) SS BOND : bond 0.00044 / 0.02 ( 1) SS BOND : angle 0.54894 / 0.29 ( 2) hydrogen bonds : bond 0.03887 / 2.62 ( 363) hydrogen bonds : angle 3.88896 / 2.83 ( 963) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1818.30 seconds wall clock time: 32 minutes 1.07 seconds (1921.07 seconds total)