Starting phenix.real_space_refine on Tue Aug 4 22:37:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8huj_35041/08_2026/8huj_35041.cif Found real_map, /net/cci-nas-00/data/ceres_data/8huj_35041/08_2026/8huj_35041.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8huj_35041/08_2026/8huj_35041.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8huj_35041/08_2026/8huj_35041.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8huj_35041/08_2026/8huj_35041.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8huj_35041/08_2026/8huj_35041.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8huj_35041/08_2026/8huj_35041.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8huj_35041/08_2026/8huj_35041.cif" } resolution = 3.76 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 99 5.49 5 Mg 3 5.21 5 S 35 5.16 5 C 4108 2.51 5 N 1261 2.21 5 O 1637 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7143 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3067 Classifications: {'peptide': 383} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 372} Chain: "B" Number of atoms: 1951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1951 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 5, 'TRANS': 232} Chain: "C" Number of atoms: 2121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 2121 Classifications: {'RNAv2': 99} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 3, 'rna3p_pur': 44, 'rna3p_pyr': 41} Link IDs: {'rna2p': 14, 'rna3p': 84} Chain breaks: 2 Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3, 'water': 1} Link IDs: {None: 3} Time building chain proxies: 1.21, per 1000 atoms: 0.17 Number of scatterers: 7143 At special positions: 0 Unit cell: (100.98, 94.095, 119.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 35 16.00 P 99 15.00 Mg 3 11.99 O 1637 8.00 N 1261 7.00 C 4108 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.41 Conformation dependent library (CDL) restraints added in 246.1 milliseconds 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1186 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 3 sheets defined 65.1% alpha, 6.9% beta 37 base pairs and 55 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 34 through 38 removed outlier: 4.101A pdb=" N ASN A 38 " --> pdb=" O ASP A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 51 Processing helix chain 'A' and resid 56 through 62 Processing helix chain 'A' and resid 63 through 69 removed outlier: 3.564A pdb=" N GLY A 69 " --> pdb=" O PRO A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 94 removed outlier: 4.207A pdb=" N PHE A 86 " --> pdb=" O LYS A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 123 Processing helix chain 'A' and resid 139 through 150 Processing helix chain 'A' and resid 158 through 167 Processing helix chain 'A' and resid 183 through 191 Processing helix chain 'A' and resid 192 through 203 Processing helix chain 'A' and resid 217 through 228 removed outlier: 3.585A pdb=" N LYS A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 246 Processing helix chain 'A' and resid 257 through 269 removed outlier: 4.416A pdb=" N ASP A 261 " --> pdb=" O GLU A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 295 removed outlier: 3.570A pdb=" N ASP A 286 " --> pdb=" O ARG A 282 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 329 through 336 Processing helix chain 'A' and resid 354 through 361 removed outlier: 3.926A pdb=" N HIS A 358 " --> pdb=" O GLU A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 365 removed outlier: 3.555A pdb=" N ARG A 365 " --> pdb=" O ARG A 362 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 362 through 365' Processing helix chain 'A' and resid 377 through 379 No H-bonds generated for 'chain 'A' and resid 377 through 379' Processing helix chain 'A' and resid 380 through 391 Processing helix chain 'A' and resid 401 through 406 removed outlier: 4.310A pdb=" N LEU A 405 " --> pdb=" O ASN A 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 771 Processing helix chain 'B' and resid 775 through 785 removed outlier: 3.714A pdb=" N LEU B 779 " --> pdb=" O MET B 775 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS B 781 " --> pdb=" O GLN B 777 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLN B 782 " --> pdb=" O GLN B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 790 through 808 Processing helix chain 'B' and resid 811 through 822 removed outlier: 3.574A pdb=" N LEU B 822 " --> pdb=" O MET B 818 " (cutoff:3.500A) Processing helix chain 'B' and resid 838 through 852 Processing helix chain 'B' and resid 853 through 871 removed outlier: 3.807A pdb=" N ASP B 858 " --> pdb=" O ASP B 854 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N GLU B 859 " --> pdb=" O LYS B 855 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS B 866 " --> pdb=" O GLU B 862 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N GLU B 867 " --> pdb=" O LYS B 863 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N MET B 868 " --> pdb=" O LYS B 864 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP B 869 " --> pdb=" O GLN B 865 " (cutoff:3.500A) Processing helix chain 'B' and resid 873 through 908 removed outlier: 3.609A pdb=" N LEU B 908 " --> pdb=" O GLU B 904 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 926 removed outlier: 3.591A pdb=" N MET B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL B 921 " --> pdb=" O HIS B 917 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS B 922 " --> pdb=" O ASP B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 928 through 947 removed outlier: 5.967A pdb=" N LYS B 944 " --> pdb=" O THR B 940 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ASP B 945 " --> pdb=" O THR B 941 " (cutoff:3.500A) Processing helix chain 'B' and resid 948 through 950 No H-bonds generated for 'chain 'B' and resid 948 through 950' Processing helix chain 'B' and resid 951 through 969 removed outlier: 3.570A pdb=" N PHE B 959 " --> pdb=" O MET B 955 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASN B 960 " --> pdb=" O ASP B 956 " (cutoff:3.500A) Processing helix chain 'B' and resid 972 through 988 Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133 removed outlier: 6.462A pdb=" N HIS A 132 " --> pdb=" O VAL A 156 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LEU A 104 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N ASP A 182 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LEU A 106 " --> pdb=" O ASP A 182 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N PHE A 179 " --> pdb=" O VAL A 210 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N LEU A 212 " --> pdb=" O PHE A 179 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LEU A 181 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL A 72 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N SER A 213 " --> pdb=" O VAL A 72 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ALA A 74 " --> pdb=" O SER A 213 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 300 through 301 removed outlier: 6.490A pdb=" N SER A 300 " --> pdb=" O ILE A 327 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ALA A 275 " --> pdb=" O LEU A 326 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N THR A 328 " --> pdb=" O ALA A 275 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ILE A 277 " --> pdb=" O THR A 328 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 827 through 828 269 hydrogen bonds defined for protein. 792 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 93 hydrogen bonds 146 hydrogen bond angles 0 basepair planarities 37 basepair parallelities 55 stacking parallelities Total time for adding SS restraints: 1.01 Time building geometry restraints manager: 0.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1756 1.33 - 1.46: 1895 1.46 - 1.58: 3551 1.58 - 1.70: 195 1.70 - 1.82: 60 Bond restraints: 7457 Sorted by residual: bond pdb=" N VAL B 835 " pdb=" CA VAL B 835 " ideal model delta sigma weight residual 1.455 1.493 -0.038 1.32e-02 5.74e+03 8.07e+00 bond pdb=" N THR B 829 " pdb=" CA THR B 829 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.23e-02 6.61e+03 6.87e+00 bond pdb=" N MET A 187 " pdb=" CA MET A 187 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.21e-02 6.83e+03 6.79e+00 bond pdb=" N LYS A 369 " pdb=" CA LYS A 369 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.19e-02 7.06e+03 6.73e+00 bond pdb=" N VAL A 180 " pdb=" CA VAL A 180 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.19e-02 7.06e+03 6.41e+00 ... (remaining 7452 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 9901 1.97 - 3.93: 549 3.93 - 5.90: 67 5.90 - 7.87: 9 7.87 - 9.83: 1 Bond angle restraints: 10527 Sorted by residual: angle pdb=" CA PHE B 839 " pdb=" CB PHE B 839 " pdb=" CG PHE B 839 " ideal model delta sigma weight residual 113.80 119.00 -5.20 1.00e+00 1.00e+00 2.70e+01 angle pdb=" N ARG A 368 " pdb=" CA ARG A 368 " pdb=" C ARG A 368 " ideal model delta sigma weight residual 111.28 106.15 5.13 1.09e+00 8.42e-01 2.22e+01 angle pdb=" CA VAL B 835 " pdb=" C VAL B 835 " pdb=" O VAL B 835 " ideal model delta sigma weight residual 121.92 117.02 4.90 1.17e+00 7.31e-01 1.75e+01 angle pdb=" N LYS A 369 " pdb=" CA LYS A 369 " pdb=" C LYS A 369 " ideal model delta sigma weight residual 113.02 107.71 5.31 1.49e+00 4.50e-01 1.27e+01 angle pdb=" C ARG B 892 " pdb=" CA ARG B 892 " pdb=" CB ARG B 892 " ideal model delta sigma weight residual 110.85 116.89 -6.04 1.70e+00 3.46e-01 1.26e+01 ... (remaining 10522 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.18: 3906 31.18 - 62.37: 398 62.37 - 93.55: 45 93.55 - 124.74: 0 124.74 - 155.92: 1 Dihedral angle restraints: 4350 sinusoidal: 2531 harmonic: 1819 Sorted by residual: dihedral pdb=" C4' G C 777 " pdb=" C3' G C 777 " pdb=" C2' G C 777 " pdb=" C1' G C 777 " ideal model delta sinusoidal sigma weight residual 36.34 -42.37 78.71 1 3.10e+00 1.04e-01 8.03e+02 dihedral pdb=" C4' A C 775 " pdb=" C3' A C 775 " pdb=" C2' A C 775 " pdb=" C1' A C 775 " ideal model delta sinusoidal sigma weight residual 36.35 -37.66 74.00 1 3.10e+00 1.04e-01 7.24e+02 dihedral pdb=" C4' A C 772 " pdb=" C3' A C 772 " pdb=" C2' A C 772 " pdb=" C1' A C 772 " ideal model delta sinusoidal sigma weight residual 36.34 -36.43 72.77 1 3.10e+00 1.04e-01 7.03e+02 ... (remaining 4347 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 1052 0.105 - 0.210: 125 0.210 - 0.315: 86 0.315 - 0.420: 1 0.420 - 0.525: 11 Chirality restraints: 1275 Sorted by residual: chirality pdb=" C3' U C 778 " pdb=" C4' U C 778 " pdb=" O3' U C 778 " pdb=" C2' U C 778 " both_signs ideal model delta sigma weight residual False -2.50 -1.97 -0.53 2.00e-01 2.50e+01 6.89e+00 chirality pdb=" P G C 766 " pdb=" OP1 G C 766 " pdb=" OP2 G C 766 " pdb=" O5' G C 766 " both_signs ideal model delta sigma weight residual True 2.17 -2.69 -0.52 2.00e-01 2.50e+01 6.78e+00 chirality pdb=" P G C 689 " pdb=" OP1 G C 689 " pdb=" OP2 G C 689 " pdb=" O5' G C 689 " both_signs ideal model delta sigma weight residual True 2.17 -2.67 -0.50 2.00e-01 2.50e+01 6.25e+00 ... (remaining 1272 not shown) Planarity restraints: 979 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 158 " -0.014 2.00e-02 2.50e+03 2.74e-02 7.48e+00 pdb=" C THR A 158 " 0.047 2.00e-02 2.50e+03 pdb=" O THR A 158 " -0.017 2.00e-02 2.50e+03 pdb=" N PRO A 159 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 64 " 0.032 5.00e-02 4.00e+02 4.84e-02 3.74e+00 pdb=" N PRO A 65 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 65 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 65 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 86 " 0.013 2.00e-02 2.50e+03 1.39e-02 3.37e+00 pdb=" CG PHE A 86 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE A 86 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE A 86 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE A 86 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 86 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 86 " 0.002 2.00e-02 2.50e+03 ... (remaining 976 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 829 2.74 - 3.28: 7178 3.28 - 3.82: 13651 3.82 - 4.36: 15716 4.36 - 4.90: 22689 Nonbonded interactions: 60063 Sorted by model distance: nonbonded pdb=" O ASP A 348 " pdb=" NH1 ARG A 359 " model vdw 2.203 3.120 nonbonded pdb=" O CYS B 936 " pdb=" OG1 THR B 940 " model vdw 2.209 3.040 nonbonded pdb=" O ILE A 246 " pdb=" NE2 GLN A 248 " model vdw 2.244 3.120 nonbonded pdb=" O2 C C 746 " pdb=" N6 A C 750 " model vdw 2.249 3.120 nonbonded pdb=" N GLU A 379 " pdb=" OE1 GLU A 379 " model vdw 2.278 3.120 ... (remaining 60058 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 group one per residue 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: 0.150 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: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.930 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 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 0.038 7457 Z= 0.300 Angle : 0.931 9.832 10527 Z= 0.499 Chirality : 0.098 0.525 1275 Planarity : 0.004 0.048 979 Dihedral : 21.571 155.919 3164 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.51 % Allowed : 26.21 % Favored : 71.27 % 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: -0.39 (0.34), residues: 617 helix: 0.44 (0.28), residues: 340 sheet: -0.76 (0.64), residues: 61 loop : -1.08 (0.43), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 190 TYR 0.009 0.002 TYR A 170 PHE 0.032 0.003 PHE A 86 TRP 0.010 0.002 TRP A 287 HIS 0.003 0.001 HIS A 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.30 ( 7457) covalent geometry : angle 0.93146 / 0.50 (10527) hydrogen bonds : bond 0.17853 / 12.31 ( 362) hydrogen bonds : angle 6.49450 / 4.54 ( 938) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.159 Fit side-chains revert: symmetry clash REVERT: A 178 MET cc_start: 0.5083 (mtm) cc_final: 0.4264 (mtm) REVERT: A 228 MET cc_start: 0.4751 (tmm) cc_final: 0.4451 (tmm) REVERT: B 845 ASN cc_start: 0.8227 (OUTLIER) cc_final: 0.7996 (t0) REVERT: B 890 ILE cc_start: 0.8839 (mm) cc_final: 0.8495 (mm) outliers start: 14 outliers final: 5 residues processed: 75 average time/residue: 0.0700 time to fit residues: 6.9726 Evaluate side-chains 66 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 HIS Chi-restraints excluded: chain A residue 368 ARG Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 845 ASN Chi-restraints excluded: chain B residue 893 ARG 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: 5.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 8.9990 chunk 61 optimal weight: 9.9990 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 GLN B 777 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.103895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.073989 restraints weight = 22337.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.074255 restraints weight = 12595.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.074739 restraints weight = 9804.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.075163 restraints weight = 8252.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.075084 restraints weight = 7338.169| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 7457 Z= 0.226 Angle : 1.016 14.618 10527 Z= 0.438 Chirality : 0.078 0.701 1275 Planarity : 0.004 0.043 979 Dihedral : 17.839 160.867 1872 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.95 % Allowed : 25.67 % Favored : 70.38 % 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: 0.03 (0.34), residues: 617 helix: 0.66 (0.27), residues: 362 sheet: -0.92 (0.59), residues: 68 loop : -0.66 (0.51), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 362 TYR 0.015 0.002 TYR A 48 PHE 0.035 0.003 PHE B 977 TRP 0.012 0.002 TRP A 287 HIS 0.003 0.001 HIS B 927 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.23 ( 7457) covalent geometry : angle 1.01642 / 0.44 (10527) hydrogen bonds : bond 0.06638 / 4.02 ( 362) hydrogen bonds : angle 4.48530 / 3.11 ( 938) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 65 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 178 MET cc_start: 0.4981 (mtm) cc_final: 0.4718 (mtm) REVERT: A 187 MET cc_start: 0.6114 (tmm) cc_final: 0.5547 (ppp) REVERT: A 228 MET cc_start: 0.4864 (tmm) cc_final: 0.4442 (tmm) REVERT: A 258 TRP cc_start: 0.8140 (m-10) cc_final: 0.7931 (m-10) REVERT: A 293 HIS cc_start: 0.7864 (t-90) cc_final: 0.7614 (t-90) REVERT: B 853 LYS cc_start: 0.7186 (OUTLIER) cc_final: 0.6765 (ptpt) REVERT: B 890 ILE cc_start: 0.8758 (mm) cc_final: 0.8450 (mm) outliers start: 22 outliers final: 13 residues processed: 83 average time/residue: 0.0752 time to fit residues: 8.5378 Evaluate side-chains 74 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 853 LYS Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 893 ARG Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 975 ILE Chi-restraints excluded: chain B residue 981 ASP Chi-restraints excluded: chain B residue 982 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 1 optimal weight: 9.9990 chunk 43 optimal weight: 6.9990 chunk 7 optimal weight: 40.0000 chunk 44 optimal weight: 1.9990 chunk 21 optimal weight: 0.3980 chunk 52 optimal weight: 0.9990 chunk 10 optimal weight: 9.9990 chunk 55 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 chunk 58 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.107747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.078643 restraints weight = 22606.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.079396 restraints weight = 12218.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.081347 restraints weight = 8872.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.080967 restraints weight = 7418.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.080800 restraints weight = 6425.705| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7457 Z= 0.127 Angle : 0.812 13.838 10527 Z= 0.344 Chirality : 0.063 0.470 1275 Planarity : 0.004 0.040 979 Dihedral : 17.102 161.328 1864 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 3.59 % Allowed : 26.21 % Favored : 70.20 % 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: 0.52 (0.34), residues: 617 helix: 1.30 (0.28), residues: 362 sheet: -0.84 (0.60), residues: 66 loop : -1.00 (0.46), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 161 TYR 0.007 0.001 TYR B 815 PHE 0.031 0.002 PHE B 977 TRP 0.010 0.001 TRP A 287 HIS 0.003 0.001 HIS A 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.13 ( 7457) covalent geometry : angle 0.81245 / 0.34 (10527) hydrogen bonds : bond 0.05901 / 3.89 ( 362) hydrogen bonds : angle 3.78126 / 2.61 ( 938) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 0.191 Fit side-chains REVERT: A 149 MET cc_start: 0.1928 (ptt) cc_final: 0.0816 (mtm) REVERT: A 181 LEU cc_start: 0.7423 (OUTLIER) cc_final: 0.7048 (tp) REVERT: A 187 MET cc_start: 0.6425 (tmm) cc_final: 0.5870 (ppp) REVERT: A 193 LYS cc_start: 0.4894 (OUTLIER) cc_final: 0.4604 (tptt) REVERT: A 229 ARG cc_start: 0.6189 (ptp-170) cc_final: 0.5206 (mmp-170) REVERT: A 293 HIS cc_start: 0.7781 (t-90) cc_final: 0.7489 (t70) REVERT: A 366 PHE cc_start: 0.3547 (OUTLIER) cc_final: 0.3244 (p90) REVERT: B 853 LYS cc_start: 0.7211 (OUTLIER) cc_final: 0.6827 (ptpt) REVERT: B 855 LYS cc_start: 0.7347 (mmtm) cc_final: 0.6851 (mttm) REVERT: B 890 ILE cc_start: 0.8670 (mm) cc_final: 0.8377 (mm) REVERT: B 893 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.8171 (ttm-80) REVERT: B 986 ARG cc_start: 0.7465 (OUTLIER) cc_final: 0.7031 (ttt-90) outliers start: 20 outliers final: 6 residues processed: 96 average time/residue: 0.1074 time to fit residues: 13.3496 Evaluate side-chains 77 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 853 LYS Chi-restraints excluded: chain B residue 893 ARG Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 918 ASP Chi-restraints excluded: chain B residue 936 CYS Chi-restraints excluded: chain B residue 986 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 chunk 68 optimal weight: 20.0000 chunk 51 optimal weight: 20.0000 chunk 49 optimal weight: 8.9990 chunk 3 optimal weight: 0.0980 chunk 36 optimal weight: 0.9980 chunk 66 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 65 optimal weight: 9.9990 overall best weight: 5.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 960 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.103490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.073120 restraints weight = 22688.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.073874 restraints weight = 12580.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.074354 restraints weight = 9824.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.074439 restraints weight = 8320.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.074410 restraints weight = 7377.209| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 7457 Z= 0.221 Angle : 0.927 17.600 10527 Z= 0.396 Chirality : 0.068 0.514 1275 Planarity : 0.004 0.038 979 Dihedral : 17.191 161.805 1862 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 5.75 % Allowed : 25.85 % Favored : 68.40 % 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: 0.55 (0.35), residues: 617 helix: 1.19 (0.27), residues: 357 sheet: -0.90 (0.62), residues: 67 loop : -0.59 (0.49), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 362 TYR 0.016 0.002 TYR A 48 PHE 0.037 0.003 PHE B 977 TRP 0.009 0.002 TRP A 287 HIS 0.003 0.001 HIS B 927 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.22 ( 7457) covalent geometry : angle 0.92662 / 0.40 (10527) hydrogen bonds : bond 0.06306 / 4.03 ( 362) hydrogen bonds : angle 4.00827 / 2.79 ( 938) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 61 time to evaluate : 0.214 Fit side-chains REVERT: A 178 MET cc_start: 0.5212 (mtm) cc_final: 0.4356 (mtm) REVERT: A 181 LEU cc_start: 0.7534 (OUTLIER) cc_final: 0.7190 (tp) REVERT: A 187 MET cc_start: 0.6569 (tmm) cc_final: 0.6084 (ppp) REVERT: A 193 LYS cc_start: 0.4875 (OUTLIER) cc_final: 0.4653 (tptt) REVERT: A 293 HIS cc_start: 0.7817 (t-90) cc_final: 0.7602 (t-90) REVERT: B 791 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.8036 (tt0) REVERT: B 855 LYS cc_start: 0.7300 (mmtm) cc_final: 0.6927 (mttm) REVERT: B 986 ARG cc_start: 0.7522 (OUTLIER) cc_final: 0.6985 (ttt-90) outliers start: 32 outliers final: 20 residues processed: 86 average time/residue: 0.0871 time to fit residues: 10.0734 Evaluate side-chains 84 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 60 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 TRP Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 353 ARG Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 791 GLU Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 857 ASP Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 918 ASP Chi-restraints excluded: chain B residue 936 CYS Chi-restraints excluded: chain B residue 981 ASP Chi-restraints excluded: chain B residue 982 VAL Chi-restraints excluded: chain B residue 986 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 42 optimal weight: 0.8980 chunk 51 optimal weight: 10.0000 chunk 16 optimal weight: 0.0870 chunk 67 optimal weight: 30.0000 chunk 45 optimal weight: 8.9990 chunk 55 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 36 optimal weight: 9.9990 chunk 46 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 overall best weight: 2.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 248 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.105417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.073355 restraints weight = 22244.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.075676 restraints weight = 10906.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.076849 restraints weight = 7552.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.078103 restraints weight = 6206.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.077881 restraints weight = 5440.026| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7457 Z= 0.140 Angle : 0.824 15.998 10527 Z= 0.349 Chirality : 0.062 0.426 1275 Planarity : 0.003 0.039 979 Dihedral : 16.947 159.169 1858 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 5.57 % Allowed : 26.75 % Favored : 67.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.65 (0.35), residues: 617 helix: 1.44 (0.28), residues: 359 sheet: -0.97 (0.61), residues: 68 loop : -0.88 (0.47), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 362 TYR 0.008 0.001 TYR A 48 PHE 0.026 0.002 PHE B 977 TRP 0.011 0.002 TRP A 287 HIS 0.002 0.001 HIS A 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 ( 7457) covalent geometry : angle 0.82419 / 0.35 (10527) hydrogen bonds : bond 0.05868 / 3.82 ( 362) hydrogen bonds : angle 3.69999 / 2.57 ( 938) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 67 time to evaluate : 0.237 Fit side-chains revert: symmetry clash REVERT: A 149 MET cc_start: 0.1907 (ptt) cc_final: 0.0688 (mtm) REVERT: A 178 MET cc_start: 0.4997 (mtm) cc_final: 0.4222 (mtm) REVERT: A 181 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7321 (tp) REVERT: A 187 MET cc_start: 0.6485 (tmm) cc_final: 0.5994 (ppp) REVERT: A 366 PHE cc_start: 0.3432 (OUTLIER) cc_final: 0.3192 (p90) REVERT: B 855 LYS cc_start: 0.7297 (mmtm) cc_final: 0.6878 (mttm) REVERT: B 986 ARG cc_start: 0.7460 (OUTLIER) cc_final: 0.7022 (ttt-90) outliers start: 31 outliers final: 21 residues processed: 90 average time/residue: 0.0926 time to fit residues: 11.0212 Evaluate side-chains 85 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 61 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 TRP Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 869 ASP Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 889 ASP Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 918 ASP Chi-restraints excluded: chain B residue 936 CYS Chi-restraints excluded: chain B residue 962 MET Chi-restraints excluded: chain B residue 981 ASP Chi-restraints excluded: chain B residue 982 VAL Chi-restraints excluded: chain B residue 986 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 6 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 41 optimal weight: 9.9990 chunk 7 optimal weight: 0.0670 chunk 27 optimal weight: 7.9990 chunk 58 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 49 optimal weight: 40.0000 overall best weight: 3.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.104660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.072149 restraints weight = 22471.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.074370 restraints weight = 11174.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.075673 restraints weight = 7718.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.076326 restraints weight = 6419.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.076580 restraints weight = 5887.857| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7457 Z= 0.170 Angle : 0.858 16.471 10527 Z= 0.365 Chirality : 0.063 0.435 1275 Planarity : 0.004 0.038 979 Dihedral : 17.013 160.429 1858 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 5.75 % Allowed : 26.03 % Favored : 68.22 % 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: 0.70 (0.35), residues: 617 helix: 1.45 (0.28), residues: 359 sheet: -0.86 (0.61), residues: 68 loop : -0.86 (0.48), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 362 TYR 0.011 0.002 TYR A 48 PHE 0.024 0.002 PHE B 977 TRP 0.010 0.001 TRP A 287 HIS 0.002 0.001 HIS A 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.17 ( 7457) covalent geometry : angle 0.85763 / 0.37 (10527) hydrogen bonds : bond 0.06017 / 3.90 ( 362) hydrogen bonds : angle 3.75548 / 2.62 ( 938) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 64 time to evaluate : 0.222 Fit side-chains REVERT: A 149 MET cc_start: 0.1824 (ptt) cc_final: 0.0487 (mtm) REVERT: A 178 MET cc_start: 0.5143 (mtm) cc_final: 0.4935 (mtm) REVERT: A 181 LEU cc_start: 0.7686 (OUTLIER) cc_final: 0.7315 (tp) REVERT: A 258 TRP cc_start: 0.8246 (m-10) cc_final: 0.7972 (m-10) REVERT: B 791 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7924 (tt0) REVERT: B 855 LYS cc_start: 0.7188 (mmtm) cc_final: 0.6847 (mttm) REVERT: B 986 ARG cc_start: 0.7476 (OUTLIER) cc_final: 0.7046 (ttt-90) outliers start: 32 outliers final: 24 residues processed: 88 average time/residue: 0.0878 time to fit residues: 10.4603 Evaluate side-chains 90 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 63 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 353 ARG Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 772 THR Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 791 GLU Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 869 ASP Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 889 ASP Chi-restraints excluded: chain B residue 890 ILE Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 918 ASP Chi-restraints excluded: chain B residue 936 CYS Chi-restraints excluded: chain B residue 962 MET Chi-restraints excluded: chain B residue 981 ASP Chi-restraints excluded: chain B residue 982 VAL Chi-restraints excluded: chain B residue 986 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 40 optimal weight: 0.0980 chunk 61 optimal weight: 9.9990 chunk 59 optimal weight: 0.2980 chunk 28 optimal weight: 20.0000 chunk 1 optimal weight: 7.9990 chunk 3 optimal weight: 0.0570 chunk 51 optimal weight: 7.9990 chunk 9 optimal weight: 20.0000 chunk 11 optimal weight: 20.0000 chunk 24 optimal weight: 2.9990 chunk 34 optimal weight: 20.0000 overall best weight: 2.2902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.105963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.073734 restraints weight = 22473.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.075939 restraints weight = 11076.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.077274 restraints weight = 7652.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.077923 restraints weight = 6348.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.078195 restraints weight = 5823.047| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7457 Z= 0.137 Angle : 0.815 15.829 10527 Z= 0.346 Chirality : 0.060 0.409 1275 Planarity : 0.003 0.039 979 Dihedral : 16.961 159.223 1858 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 4.31 % Allowed : 27.83 % Favored : 67.86 % 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: 0.84 (0.35), residues: 617 helix: 1.59 (0.28), residues: 359 sheet: -0.56 (0.66), residues: 61 loop : -0.95 (0.45), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 362 TYR 0.007 0.001 TYR A 48 PHE 0.056 0.002 PHE B 977 TRP 0.021 0.002 TRP A 27 HIS 0.002 0.001 HIS B 927 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 ( 7457) covalent geometry : angle 0.81481 / 0.35 (10527) hydrogen bonds : bond 0.05760 / 3.76 ( 362) hydrogen bonds : angle 3.60757 / 2.49 ( 938) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 65 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 149 MET cc_start: 0.1642 (ptt) cc_final: 0.0390 (mtm) REVERT: A 181 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.7083 (tp) REVERT: A 187 MET cc_start: 0.6532 (tmm) cc_final: 0.6273 (tmm) REVERT: B 855 LYS cc_start: 0.7131 (mmtm) cc_final: 0.6793 (mttm) REVERT: B 986 ARG cc_start: 0.7476 (OUTLIER) cc_final: 0.7029 (ttt-90) outliers start: 24 outliers final: 18 residues processed: 83 average time/residue: 0.0812 time to fit residues: 9.1461 Evaluate side-chains 84 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 64 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 772 THR Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 869 ASP Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 918 ASP Chi-restraints excluded: chain B residue 936 CYS Chi-restraints excluded: chain B residue 981 ASP Chi-restraints excluded: chain B residue 982 VAL Chi-restraints excluded: chain B residue 986 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 34 optimal weight: 20.0000 chunk 43 optimal weight: 3.9990 chunk 28 optimal weight: 20.0000 chunk 31 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 24 optimal weight: 0.0770 chunk 12 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 65 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 overall best weight: 2.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.106203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.076533 restraints weight = 22178.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.077284 restraints weight = 11942.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.078347 restraints weight = 9131.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.078179 restraints weight = 7830.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.078267 restraints weight = 6936.140| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7457 Z= 0.130 Angle : 0.803 15.283 10527 Z= 0.340 Chirality : 0.059 0.400 1275 Planarity : 0.003 0.039 979 Dihedral : 16.958 159.351 1858 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 5.39 % Allowed : 27.11 % Favored : 67.50 % 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: 0.95 (0.35), residues: 617 helix: 1.69 (0.28), residues: 359 sheet: -0.50 (0.67), residues: 61 loop : -0.95 (0.46), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 877 TYR 0.008 0.001 TYR A 48 PHE 0.045 0.002 PHE B 977 TRP 0.013 0.002 TRP A 27 HIS 0.002 0.001 HIS B 927 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 ( 7457) covalent geometry : angle 0.80251 / 0.34 (10527) hydrogen bonds : bond 0.05679 / 3.73 ( 362) hydrogen bonds : angle 3.53771 / 2.44 ( 938) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 66 time to evaluate : 0.219 Fit side-chains revert: symmetry clash REVERT: A 127 MET cc_start: 0.7157 (mmm) cc_final: 0.6941 (mmm) REVERT: A 143 GLU cc_start: 0.2390 (OUTLIER) cc_final: 0.2019 (mt-10) REVERT: A 149 MET cc_start: 0.1539 (ptt) cc_final: 0.0249 (mtm) REVERT: A 178 MET cc_start: 0.5279 (mtm) cc_final: 0.4370 (mtm) REVERT: A 181 LEU cc_start: 0.7500 (OUTLIER) cc_final: 0.7088 (tp) REVERT: A 187 MET cc_start: 0.6563 (tmm) cc_final: 0.6221 (tmm) REVERT: A 257 GLU cc_start: 0.7461 (pm20) cc_final: 0.7152 (pm20) REVERT: A 366 PHE cc_start: 0.3371 (OUTLIER) cc_final: 0.3128 (p90) REVERT: B 791 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7997 (tt0) REVERT: B 834 THR cc_start: 0.8746 (OUTLIER) cc_final: 0.8532 (m) REVERT: B 855 LYS cc_start: 0.7138 (mmtm) cc_final: 0.6816 (mttm) REVERT: B 986 ARG cc_start: 0.7449 (OUTLIER) cc_final: 0.7029 (ttt-90) outliers start: 30 outliers final: 20 residues processed: 90 average time/residue: 0.0833 time to fit residues: 10.1764 Evaluate side-chains 88 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 62 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 GLU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 772 THR Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 791 GLU Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 889 ASP Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 918 ASP Chi-restraints excluded: chain B residue 936 CYS Chi-restraints excluded: chain B residue 962 MET Chi-restraints excluded: chain B residue 981 ASP Chi-restraints excluded: chain B residue 982 VAL Chi-restraints excluded: chain B residue 986 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 2.9990 chunk 7 optimal weight: 0.0670 chunk 56 optimal weight: 9.9990 chunk 66 optimal weight: 9.9990 chunk 41 optimal weight: 9.9990 chunk 64 optimal weight: 20.0000 chunk 1 optimal weight: 4.9990 chunk 59 optimal weight: 8.9990 chunk 21 optimal weight: 30.0000 chunk 62 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 overall best weight: 4.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.104672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.072386 restraints weight = 22129.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.074533 restraints weight = 11035.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.075845 restraints weight = 7687.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 64)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.076505 restraints weight = 6397.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.076594 restraints weight = 5849.323| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7457 Z= 0.181 Angle : 0.859 15.993 10527 Z= 0.367 Chirality : 0.062 0.424 1275 Planarity : 0.004 0.037 979 Dihedral : 17.093 159.866 1858 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 6.10 % Allowed : 26.39 % Favored : 67.50 % 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: 0.83 (0.35), residues: 617 helix: 1.65 (0.28), residues: 353 sheet: -0.56 (0.65), residues: 62 loop : -1.04 (0.45), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 362 TYR 0.013 0.002 TYR A 48 PHE 0.047 0.002 PHE B 977 TRP 0.041 0.004 TRP A 27 HIS 0.003 0.001 HIS B 927 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.18 ( 7457) covalent geometry : angle 0.85949 / 0.37 (10527) hydrogen bonds : bond 0.06199 / 4.07 ( 362) hydrogen bonds : angle 3.70988 / 2.56 ( 938) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 59 time to evaluate : 0.178 Fit side-chains REVERT: A 127 MET cc_start: 0.7159 (mmm) cc_final: 0.6940 (mmm) REVERT: A 143 GLU cc_start: 0.2498 (OUTLIER) cc_final: 0.2093 (mt-10) REVERT: A 149 MET cc_start: 0.1869 (ptt) cc_final: 0.0511 (mtm) REVERT: A 181 LEU cc_start: 0.7610 (OUTLIER) cc_final: 0.7112 (tp) REVERT: A 187 MET cc_start: 0.6668 (tmm) cc_final: 0.6366 (tmm) REVERT: A 366 PHE cc_start: 0.3393 (OUTLIER) cc_final: 0.3174 (p90) REVERT: B 776 PHE cc_start: 0.7766 (t80) cc_final: 0.7367 (t80) REVERT: B 791 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.8032 (tt0) REVERT: B 855 LYS cc_start: 0.7075 (mmtm) cc_final: 0.6748 (mttm) REVERT: B 986 ARG cc_start: 0.7504 (OUTLIER) cc_final: 0.7061 (ttt-90) outliers start: 34 outliers final: 27 residues processed: 87 average time/residue: 0.0896 time to fit residues: 10.4788 Evaluate side-chains 88 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 56 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 143 GLU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 772 THR Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 791 GLU Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 869 ASP Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 889 ASP Chi-restraints excluded: chain B residue 890 ILE Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 918 ASP Chi-restraints excluded: chain B residue 936 CYS Chi-restraints excluded: chain B residue 962 MET Chi-restraints excluded: chain B residue 981 ASP Chi-restraints excluded: chain B residue 982 VAL Chi-restraints excluded: chain B residue 986 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 9 optimal weight: 7.9990 chunk 13 optimal weight: 9.9990 chunk 7 optimal weight: 0.9980 chunk 65 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 66 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 68 optimal weight: 9.9990 chunk 18 optimal weight: 8.9990 chunk 40 optimal weight: 8.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 374 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.103606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.073539 restraints weight = 22245.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.074339 restraints weight = 12490.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.076341 restraints weight = 9315.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.075714 restraints weight = 7965.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.075639 restraints weight = 6800.671| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 7457 Z= 0.223 Angle : 0.918 16.633 10527 Z= 0.394 Chirality : 0.066 0.501 1275 Planarity : 0.004 0.036 979 Dihedral : 17.296 161.294 1858 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 5.92 % Allowed : 26.39 % Favored : 67.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.55 (0.35), residues: 617 helix: 1.26 (0.27), residues: 359 sheet: -0.36 (0.67), residues: 58 loop : -0.98 (0.46), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 362 TYR 0.015 0.002 TYR A 48 PHE 0.057 0.003 PHE B 977 TRP 0.031 0.003 TRP A 27 HIS 0.003 0.001 HIS B 927 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.22 ( 7457) covalent geometry : angle 0.91778 / 0.39 (10527) hydrogen bonds : bond 0.06672 / 4.36 ( 362) hydrogen bonds : angle 3.91114 / 2.71 ( 938) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 59 time to evaluate : 0.239 Fit side-chains REVERT: A 181 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.7240 (tt) REVERT: A 187 MET cc_start: 0.6587 (tmm) cc_final: 0.6305 (tmm) REVERT: B 791 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.8022 (tt0) REVERT: B 855 LYS cc_start: 0.7029 (mmtm) cc_final: 0.6705 (mttm) REVERT: B 986 ARG cc_start: 0.7499 (OUTLIER) cc_final: 0.7066 (ttt-90) outliers start: 33 outliers final: 23 residues processed: 86 average time/residue: 0.0861 time to fit residues: 10.0078 Evaluate side-chains 84 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 58 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 772 THR Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 791 GLU Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 869 ASP Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 889 ASP Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 918 ASP Chi-restraints excluded: chain B residue 936 CYS Chi-restraints excluded: chain B residue 962 MET Chi-restraints excluded: chain B residue 981 ASP Chi-restraints excluded: chain B residue 982 VAL Chi-restraints excluded: chain B residue 986 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 43 optimal weight: 3.9990 chunk 8 optimal weight: 10.0000 chunk 22 optimal weight: 0.9980 chunk 28 optimal weight: 20.0000 chunk 58 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 68 optimal weight: 20.0000 chunk 48 optimal weight: 20.0000 chunk 13 optimal weight: 9.9990 chunk 50 optimal weight: 20.0000 chunk 32 optimal weight: 3.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.105942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.073966 restraints weight = 22020.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.076135 restraints weight = 10749.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.077484 restraints weight = 7399.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.078221 restraints weight = 6135.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.078487 restraints weight = 5585.946| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7457 Z= 0.136 Angle : 0.814 15.418 10527 Z= 0.347 Chirality : 0.061 0.584 1275 Planarity : 0.003 0.038 979 Dihedral : 17.052 167.524 1858 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 4.13 % Allowed : 28.90 % Favored : 66.97 % 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: 0.80 (0.35), residues: 617 helix: 1.54 (0.28), residues: 359 sheet: -0.48 (0.70), residues: 55 loop : -0.96 (0.45), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 362 TYR 0.009 0.001 TYR A 267 PHE 0.048 0.003 PHE B 977 TRP 0.012 0.002 TRP A 287 HIS 0.002 0.001 HIS A 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 ( 7457) covalent geometry : angle 0.81435 / 0.35 (10527) hydrogen bonds : bond 0.05935 / 3.89 ( 362) hydrogen bonds : angle 3.61766 / 2.48 ( 938) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1310.20 seconds wall clock time: 23 minutes 17.65 seconds (1397.65 seconds total)