Starting phenix.refine on Wed Apr 10 15:59:19 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, 1TT8_complete.pdb Found miller_array, 1TT8.mtz Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- optimize_adp=true optimize_xyz=true hydrogens.refine=riding nproc=20 main.max_number_of_iterations=50 main.number_of_m=5 refine.adp.individual.aniso=not element H refine.adp.individual.iso=element H Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "1TT8_complete.pdb" } default_model = "1TT8_complete.pdb" miller_array { file = "1TT8.mtz" } default_miller_array = "1TT8.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { adp { individual { isotropic = element H anisotropic = not element H } } } main { number_of_macro_cycles = 5 max_number_of_iterations = 50 nproc = 20 } hydrogens { refine = individual *riding Auto } target_weights { optimize_xyz_weight = true optimize_adp_weight = true } } Starting job =============================================================================== Symmetric amino acids flipped None Time to flip residues: 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3804 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 2676 Classifications: {'peptide': 164} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 13, 'TRANS': 150} Chain: "A" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 1128 Unusual residues: {'PHB': 1} Classifications: {'undetermined': 1, 'water': 371} Link IDs: {None: 371} Time building chain proxies: 0.72, per 1000 atoms: 0.19 Number of scatterers: 3804 At special positions: 0 Unit cell: (31.315, 33.849, 39.776, 67.57, 87.83, 65.66) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 2 16.00 O 614 8.00 N 226 7.00 C 854 6.00 H 2108 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.82 Conformation dependent library (CDL) restraints added in 82.6 milliseconds Time building geometry restraints manager: 1.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.85 - 1.03: 1010 1.03 - 1.22: 1146 1.22 - 1.40: 481 1.40 - 1.59: 822 1.59 - 1.78: 4 Bond restraints: 3463 Sorted by residual: bond pdb=" NH1 ARG A 141 " pdb="HH11 ARG A 141 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" NH2 ARG A 72 " pdb="HH22 ARG A 72 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.44e+01 bond pdb=" N LEU A 25 " pdb=" H LEU A 25 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.44e+01 bond pdb=" NH2 ARG A 51 " pdb="HH21 ARG A 51 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.44e+01 bond pdb=" N SER A 122 " pdb=" H SER A 122 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.44e+01 ... (remaining 3458 not shown) Histogram of bond angle deviations from ideal: 95.90 - 103.77: 44 103.77 - 111.64: 3372 111.64 - 119.51: 932 119.51 - 127.38: 948 127.38 - 135.25: 27 Bond angle restraints: 5323 Sorted by residual: angle pdb=" CD2 HIS A 2 " pdb=" NE2 HIS A 2 " pdb=" CE1 HIS A 2 " ideal model delta sigma weight residual 109.00 101.20 7.80 1.00e+00 1.00e+00 6.09e+01 angle pdb=" CB GLN A 23 " pdb=" CG GLN A 23 " pdb=" CD GLN A 23 " ideal model delta sigma weight residual 112.60 99.94 12.66 1.70e+00 3.46e-01 5.54e+01 angle pdb=" CG HIS A 2 " pdb=" CD2 HIS A 2 " pdb=" NE2 HIS A 2 " ideal model delta sigma weight residual 107.20 114.58 -7.38 1.00e+00 1.00e+00 5.44e+01 angle pdb=" CB HIS A 2 " pdb=" CG HIS A 2 " pdb=" ND1 HIS A 2 " ideal model delta sigma weight residual 122.70 131.93 -9.23 1.50e+00 4.44e-01 3.79e+01 angle pdb=" NE ARG A 51 " pdb=" CZ ARG A 51 " pdb=" NH2 ARG A 51 " ideal model delta sigma weight residual 119.20 114.22 4.98 9.00e-01 1.23e+00 3.06e+01 ... (remaining 5318 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.17: 858 17.17 - 34.34: 63 34.34 - 51.51: 20 51.51 - 68.67: 7 68.67 - 85.84: 6 Dihedral angle restraints: 954 sinusoidal: 719 harmonic: 235 Sorted by residual: dihedral pdb=" CA ILE A 78 " pdb=" C ILE A 78 " pdb=" N LEU A 79 " pdb=" CA LEU A 79 " ideal model delta harmonic sigma weight residual 180.00 156.66 23.34 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA ASP A 32 " pdb=" C ASP A 32 " pdb=" N SER A 33 " pdb=" CA SER A 33 " ideal model delta harmonic sigma weight residual 180.00 163.38 16.62 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CA SER A 142 " pdb=" C SER A 142 " pdb=" N ARG A 143 " pdb=" CA ARG A 143 " ideal model delta harmonic sigma weight residual 180.00 163.41 16.59 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 951 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 140 0.084 - 0.167: 52 0.167 - 0.251: 13 0.251 - 0.335: 2 0.335 - 0.419: 1 Chirality restraints: 208 Sorted by residual: chirality pdb=" CA GLU A 52 " pdb=" N GLU A 52 " pdb=" C GLU A 52 " pdb=" CB GLU A 52 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.38e+00 chirality pdb=" CG LEU A 124 " pdb=" CB LEU A 124 " pdb=" CD1 LEU A 124 " pdb=" CD2 LEU A 124 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA SER A 1 " pdb=" N SER A 1 " pdb=" C SER A 1 " pdb=" CB SER A 1 " both_signs ideal model delta sigma weight residual False 2.57 2.31 0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 205 not shown) Planarity restraints: 384 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 PHB A 400 " -0.018 2.00e-02 2.50e+03 4.22e-02 5.34e+01 pdb=" C1' PHB A 400 " -0.048 2.00e-02 2.50e+03 pdb=" C2 PHB A 400 " 0.001 2.00e-02 2.50e+03 pdb=" C3 PHB A 400 " 0.010 2.00e-02 2.50e+03 pdb=" C4 PHB A 400 " 0.050 2.00e-02 2.50e+03 pdb=" C5 PHB A 400 " -0.013 2.00e-02 2.50e+03 pdb=" C6 PHB A 400 " 0.023 2.00e-02 2.50e+03 pdb=" O4 PHB A 400 " 0.009 2.00e-02 2.50e+03 pdb=" H2 PHB A 400 " 0.007 2.00e-02 2.50e+03 pdb=" H3 PHB A 400 " -0.014 2.00e-02 2.50e+03 pdb=" H5 PHB A 400 " -0.090 2.00e-02 2.50e+03 pdb=" H6 PHB A 400 " 0.084 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 157 " 0.001 2.00e-02 2.50e+03 3.71e-02 4.12e+01 pdb=" CG PHE A 157 " 0.013 2.00e-02 2.50e+03 pdb=" CD1 PHE A 157 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE A 157 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE A 157 " 0.024 2.00e-02 2.50e+03 pdb=" CE2 PHE A 157 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 157 " -0.013 2.00e-02 2.50e+03 pdb=" HD1 PHE A 157 " -0.067 2.00e-02 2.50e+03 pdb=" HD2 PHE A 157 " 0.024 2.00e-02 2.50e+03 pdb=" HE1 PHE A 157 " 0.086 2.00e-02 2.50e+03 pdb=" HE2 PHE A 157 " -0.009 2.00e-02 2.50e+03 pdb=" HZ PHE A 157 " -0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 54 " 0.039 2.00e-02 2.50e+03 3.33e-02 3.33e+01 pdb=" CG PHE A 54 " 0.013 2.00e-02 2.50e+03 pdb=" CD1 PHE A 54 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE A 54 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 54 " 0.018 2.00e-02 2.50e+03 pdb=" CE2 PHE A 54 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 54 " -0.006 2.00e-02 2.50e+03 pdb=" HD1 PHE A 54 " -0.074 2.00e-02 2.50e+03 pdb=" HD2 PHE A 54 " -0.012 2.00e-02 2.50e+03 pdb=" HE1 PHE A 54 " 0.066 2.00e-02 2.50e+03 pdb=" HE2 PHE A 54 " 0.005 2.00e-02 2.50e+03 pdb=" HZ PHE A 54 " -0.030 2.00e-02 2.50e+03 ... (remaining 381 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.10: 744 2.10 - 2.73: 7591 2.73 - 3.35: 14491 3.35 - 3.98: 22059 3.98 - 4.60: 31810 Nonbonded interactions: 76695 Sorted by model distance: nonbonded pdb=" HZ1 LYS A 36 " pdb=" O HOH A 744 " model vdw 1.481 1.850 nonbonded pdb="HE21 GLN A 107 " pdb=" O HOH A 498 " model vdw 1.506 1.850 nonbonded pdb=" HG SER A 147 " pdb=" O HOH A 480 " model vdw 1.511 1.850 nonbonded pdb=" HG1 THR A 125 " pdb=" O HOH A 447 " model vdw 1.546 1.850 nonbonded pdb=" HG SER A 33 " pdb=" O LEU A 114 " model vdw 1.611 1.850 ... (remaining 76690 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 5 Type Number sf(0) Gaussians S 2 15.96 2 O 614 7.97 2 N 226 6.98 3 C 854 5.99 3 H 2108 1.00 3 sf(0) = scattering factor at diffraction angle 0. =========================== Regularize ADP if needed ========================== ========================== Anomalous scatterer groups ========================= All atoms refined with f_prime=0 and f_double_prime=0. ====================== Modifying start model if requested ===================== n_use = 3804 n_use_u_iso = 2166 n_use_u_aniso = 1638 n_grad_site = 0 n_grad_u_iso = 0 n_grad_u_aniso = 0 n_grad_occupancy = 0 n_grad_fp = 0 n_grad_fdp = 0 total number of scatterers = 3804 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (3804 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 2108 aniso = 1696) group_adp = False (0 atoms in 0 groups) tls = False (0 atoms in 0 groups) occupancies = True (24 atoms) group_anomalous = False ============================ Non-default parameters =========================== A complete record of all parameters was written to the .eff file above. Below are only the non-defaults. #phil __ON__ refinement { electron_density_maps { map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT" mtz_label_phases = "PH2FOFCWT" fill_missing_f_obs = True } map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT_no_fill" mtz_label_phases = "PH2FOFCWT_no_fill" } map_coefficients { map_type = "mFo-DFc" mtz_label_amplitudes = "FOFCWT" mtz_label_phases = "PHFOFCWT" } map_coefficients { map_type = "anomalous" mtz_label_amplitudes = "ANOM" mtz_label_phases = "PANOM" } map { map_type = "2mFo-DFc" fill_missing_f_obs = True } map { map_type = "2mFo-DFc" } map { map_type = "mFo-DFc" } } refine { adp { individual { isotropic = element H anisotropic = not element H } } } main { number_of_macro_cycles = 5 max_number_of_iterations = 50 nproc = 20 } hydrogens { refine = individual *riding Auto } pdb_interpretation { c_beta_restraints = False } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } output { prefix = "1TT8_complete_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 2108 occupancy sum: 2108.00 (% of total atoms 55.56) Rotatable: count: 380 occupancy sum: 380.00 (% of total atoms 10.01) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 1.00 - 11.67 A, n_refl.=63699 (all), 3.42 % free)------------| | | | r_work= 0.1365 r_free= 0.1457 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 2.272750 | | target function (ml) not normalized (work): 139826.411924 | | target function (ml) not normalized (free): 4934.998882 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 11.67 - 2.51 0.97 4346 161 0.1488 0.1641 4.0479 4.0555| | 2: 2.51 - 1.99 0.97 4357 144 0.1206 0.1241 3.3864 3.4175| | 3: 1.99 - 1.74 0.96 4342 135 0.1164 0.1476 2.8334 2.9325| | 4: 1.74 - 1.58 0.95 4231 186 0.1212 0.1332 2.4884 2.5293| | 5: 1.58 - 1.47 0.94 4201 153 0.1209 0.1093 2.29 2.218| | 6: 1.47 - 1.38 0.93 4208 148 0.1263 0.1245 2.1185 2.0902| | 7: 1.38 - 1.31 0.92 4116 126 0.1306 0.1518 2.038 2.0614| | 8: 1.31 - 1.26 0.91 4066 145 0.1362 0.1374 1.9942 2.0258| | 9: 1.26 - 1.21 0.90 4027 140 0.1381 0.1362 1.9366 1.9136| | 10: 1.21 - 1.17 0.90 4029 150 0.1361 0.1575 1.8745 1.9374| | 11: 1.17 - 1.13 0.89 3976 128 0.1318 0.1194 1.8099 1.7081| | 12: 1.13 - 1.10 0.87 3945 132 0.1412 0.1205 1.7489 1.6568| | 13: 1.10 - 1.07 0.84 3725 140 0.1664 0.1643 1.7353 1.709| | 14: 1.07 - 1.04 0.77 3442 125 0.1919 0.1873 1.7086 1.6152| | 15: 1.04 - 1.02 0.69 3106 102 0.2428 0.2278 1.7169 1.651| | 16: 1.02 - 1.00 0.32 1406 61 0.2976 0.3925 1.7728 1.9021| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 11.67 - 2.51 4346 161 0.90 17.35 0.99 0.47 489.00| | 2: 2.51 - 1.99 4357 144 0.90 18.01 0.99 0.48 207.79| | 3: 1.99 - 1.74 4342 135 0.94 12.55 1.03 0.50 52.29| | 4: 1.74 - 1.58 4231 186 0.94 11.97 1.04 0.50 25.49| | 5: 1.58 - 1.47 4201 153 0.95 11.35 1.04 0.50 15.39| | 6: 1.47 - 1.38 4208 148 0.95 11.51 1.04 0.50 10.64| | 7: 1.38 - 1.31 4116 126 0.95 11.27 1.04 0.50 8.53| | 8: 1.31 - 1.26 4066 145 0.95 11.25 1.05 0.50 7.46| | 9: 1.26 - 1.21 4027 140 0.95 11.70 1.04 0.51 6.69| | 10: 1.21 - 1.17 4029 150 0.95 11.40 1.03 0.51 5.85| | 11: 1.17 - 1.13 3976 128 0.95 11.03 1.01 0.50 4.98| | 12: 1.13 - 1.10 3945 132 0.95 11.80 0.99 0.49 4.21| | 13: 1.10 - 1.07 3725 140 0.94 13.06 0.96 0.48 3.80| | 14: 1.07 - 1.04 3442 125 0.92 15.75 0.94 0.46 3.88| | 15: 1.04 - 1.02 3106 102 0.88 20.31 0.90 0.44 4.59| | 16: 1.02 - 1.00 1406 61 0.83 25.59 0.86 0.40 5.84| |alpha: min = 0.40 max = 0.51 mean = 0.49| |beta: min = 3.80 max = 489.00 mean = 59.77| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.85 mean = 13.53| |phase err.(test): min = 0.00 max = 87.64 mean = 13.50| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 0.075 1355 Z= 1.096 Angle : 2.081 12.656 1840 Z= 1.294 Chirality : 0.095 0.419 208 Planarity : 0.011 0.058 234 Dihedral : 14.925 85.843 520 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.07 % Allowed : 2.07 % Favored : 95.86 % Cbeta Deviations : 0.65 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.64), residues: 162 helix: -2.80 (0.62), residues: 34 sheet: 0.56 (0.65), residues: 53 loop : -0.06 (0.77), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.003 ARG A 145 TYR 0.024 0.008 TYR A 13 PHE 0.037 0.014 PHE A 38 TRP 0.012 0.004 TRP A 87 HIS 0.016 0.011 HIS A 2 Individual atomic B min max mean iso aniso Overall: 4.71 74.28 15.45 3.03 0 1696 Protein: 4.71 70.18 10.80 3.04 0 1315 Water: 6.57 74.28 32.13 N/A 0 371 Other: 6.33 8.30 7.08 N/A 0 10 Chain A: 4.71 74.28 15.45 N/A 0 1696 Histogram: Values Number of atoms 4.71 - 11.67 988 11.67 - 18.62 319 18.62 - 25.58 114 25.58 - 32.54 83 32.54 - 39.50 75 39.50 - 46.45 57 46.45 - 53.41 28 53.41 - 60.37 23 60.37 - 67.32 5 67.32 - 74.28 4 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.00 - 11.67 A, n_refl.=63699 (all), 3.42 % free)------------| | | | r_work= 0.1365 r_free= 0.1457 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 2.272750 | | target function (ml) not normalized (work): 139826.411924 | | target function (ml) not normalized (free): 4934.998882 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1369 0.1366 0.1458 n_refl.: 63699 re-set all scales: r(all,work,free)=0.1369 0.1366 0.1458 n_refl.: 63699 remove outliers: r(all,work,free)=0.1363 0.1360 0.1458 n_refl.: 63691 overall B=0.21 to atoms: r(all,work,free)=0.1376 0.1373 0.1477 n_refl.: 63691 bulk-solvent and scaling: r(all,work,free)=0.1309 0.1306 0.1382 n_refl.: 63691 remove outliers: r(all,work,free)=0.1306 0.1303 0.1379 n_refl.: 63670 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 9.517-7.089 77.69 91 3 0.2029 145.653 141.260 0.939 0.999 0.295 7.071-6.186 97.09 94 6 0.1881 127.520 125.212 0.969 0.997 0.270 6.180-5.403 98.12 153 4 0.1700 126.784 125.141 0.996 0.999 0.231 5.400-4.722 98.70 220 8 0.1492 176.574 177.266 1.032 0.999 0.226 4.720-4.127 99.14 337 10 0.1289 207.262 206.969 0.997 1.000 0.206 4.123-3.607 98.83 491 15 0.1259 185.501 184.801 0.979 1.000 0.189 3.606-3.152 98.34 745 27 0.1316 158.055 156.908 0.962 1.000 0.129 3.152-2.756 98.30 1120 38 0.1333 114.418 113.108 0.924 1.001 0.019 2.755-2.408 98.05 1641 67 0.1316 90.313 89.349 0.913 1.001 0.000 2.408-2.105 97.52 2466 85 0.1178 82.466 81.259 0.955 1.002 0.000 2.105-1.840 96.44 3682 111 0.1136 66.286 65.571 0.997 1.003 0.000 1.840-1.608 95.62 5401 213 0.1158 42.992 42.546 1.006 1.004 0.000 1.608-1.405 93.99 8009 294 0.1168 30.703 30.385 1.014 1.006 0.000 1.405-1.228 91.46 11706 393 0.1280 23.092 22.705 1.021 1.009 0.000 1.228-1.074 87.95 16773 584 0.1406 17.432 17.030 0.995 1.012 0.000 1.074-0.997 60.43 8566 317 0.2078 11.247 10.780 0.908 1.016 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0792 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1303 r_free=0.1379 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1303 r_free=0.1379 ========================= Local real-space refinement ========================= Before: r_work=0.1303 r_free=0.1379 29 residues out of total 145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 26 time to evaluate : 0.124 outliers start: 3 outliers final: 1 residues processed: 28 average time/residue: 1.5515 time to fit residues: 44.1426 After: r_work=0.1312 r_free=0.1415 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 16.899969 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 217.932894 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1572 0.1663 0.0091 0.003 0.6 3.0 0.0 0.7 0 0.125 0.1533 0.1635 0.0102 0.003 0.7 3.0 0.0 0.7 0 0.250 0.1474 0.1588 0.0114 0.003 0.7 3.0 0.0 0.7 0 0.500 0.1430 0.1568 0.0138 0.004 0.7 2.6 0.0 0.7 0 1.000 0.1379 0.1541 0.0162 0.005 0.8 2.2 0.0 0.7 0 2.000 0.1359 0.1537 0.0178 0.005 0.8 2.2 0.0 0.7 0 3.000 0.1344 0.1536 0.0192 0.006 0.9 3.0 0.0 0.7 0 4.000 0.1327 0.1526 0.0199 0.007 0.9 3.3 0.0 0.7 0 5.000 0.1316 0.1521 0.0205 0.008 1.0 3.7 0.0 0.7 0 6.000 0.1312 0.1525 0.0213 0.009 1.0 3.7 0.0 0.7 0 7.000 0.1312 0.1533 0.0222 0.009 1.0 3.7 0.0 0.7 0 8.000 0.1305 0.1532 0.0228 0.010 1.0 4.1 0.0 0.7 0 9.000 0.1295 0.1529 0.0234 0.011 1.1 4.8 0.0 0.7 0 10.000 0.1306 0.1532 0.0225 0.010 1.0 4.1 0.0 0.7 0 8.450 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1316 0.1521 0.0205 0.008 1.0 3.7 0.0 0.7 0 6.000 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.1316 r_free=0.1521 29 residues out of total 145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 28 time to evaluate : 0.126 outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.1044 After: r_work=0.1316 r_free=0.1521 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.16 15.21 2.05 1.895 17.532 217.933 0.018 13.18 15.23 2.05 1.702 17.531 6.538 0.018 13.18 15.28 2.10 1.547 17.531 27.242 0.018 13.79 16.98 3.19 3.111 18.067 108.966 0.017 12.93 16.33 3.40 3.842 18.254 217.933 0.015 12.76 16.36 3.60 4.616 18.431 326.899 0.014 12.87 16.47 3.60 5.894 18.738 435.866 0.014 12.81 16.58 3.78 6.144 18.812 544.832 0.014 12.58 16.23 3.65 5.640 18.679 653.799 0.013 12.45 16.14 3.69 5.355 18.609 762.765 0.013 12.46 16.21 3.75 5.659 18.692 871.732 0.013 12.52 16.50 3.98 5.821 18.746 980.698 0.013 12.48 16.43 3.95 6.001 18.770 1089.664 0.013 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 6.538 Accepted refinement result: 13.18 15.23 2.05 1.702 17.531 6.538 0.018 Individual atomic B min max mean iso aniso Overall: 5.00 74.48 15.65 2.70 0 1696 Protein: 5.00 67.34 11.01 2.71 0 1315 Water: 6.77 74.48 32.34 N/A 0 371 Other: 6.58 8.38 7.27 N/A 0 10 Chain A: 5.00 74.48 15.65 N/A 0 1696 Histogram: Values Number of atoms 5.00 - 11.95 991 11.95 - 18.90 320 18.90 - 25.85 111 25.85 - 32.80 84 32.80 - 39.74 74 39.74 - 46.69 56 46.69 - 53.64 31 53.64 - 60.59 20 60.59 - 67.54 6 67.54 - 74.48 3 =========================== Idealize ADP of riding H ========================== r_work=0.1318 r_free=0.1523 r_work=0.1311 r_free=0.1512 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1311 r_free = 0.1512 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1309 r_free = 0.1505 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.00 - 9.52 A, n_refl.=63670 (all), 3.42 % free)-------------| | | | r_work= 0.1309 r_free= 0.1505 coordinate error (max.-lik. estimate): 0.06 A | | | | normalized target function (ls_wunit_k1) (work): 0.017858 | | target function (ls_wunit_k1) not normalized (work): 1098.151035 | | target function (ls_wunit_k1) not normalized (free): 61.921718 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1315 0.1309 0.1505 n_refl.: 63670 re-set all scales: r(all,work,free)=0.1387 0.1379 0.1605 n_refl.: 63670 remove outliers: r(all,work,free)=0.1387 0.1379 0.1605 n_refl.: 63670 overall B=0.01 to atoms: r(all,work,free)=0.1388 0.1380 0.1606 n_refl.: 63670 bulk-solvent and scaling: r(all,work,free)=0.1313 0.1307 0.1502 n_refl.: 63670 remove outliers: r(all,work,free)=0.1313 0.1307 0.1502 n_refl.: 63670 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 9.517-7.089 77.69 91 3 0.1782 145.653 145.837 0.996 0.957 0.323 7.071-6.186 97.09 94 6 0.1523 127.520 126.124 1.014 0.956 0.289 6.180-5.403 98.12 153 4 0.1473 126.784 125.852 1.012 0.957 0.255 5.400-4.722 98.70 220 8 0.1090 176.574 178.056 1.047 0.958 0.246 4.720-4.127 99.14 337 10 0.0961 207.262 207.401 1.012 0.958 0.240 4.123-3.607 98.83 491 15 0.0964 185.501 185.353 0.995 0.958 0.188 3.606-3.152 98.34 745 27 0.1060 158.055 157.730 0.980 0.958 0.136 3.152-2.756 98.30 1120 38 0.1200 114.418 113.499 0.940 0.958 0.034 2.755-2.408 98.05 1641 67 0.1230 90.313 89.702 0.928 0.958 0.000 2.408-2.105 97.52 2466 85 0.1163 82.466 81.276 0.976 0.959 0.000 2.105-1.840 96.44 3682 111 0.1160 66.286 65.395 1.021 0.959 0.000 1.840-1.608 95.62 5401 213 0.1257 42.992 42.378 1.025 0.960 0.000 1.608-1.405 93.99 8009 294 0.1304 30.703 30.256 1.033 0.961 0.000 1.405-1.228 91.46 11706 393 0.1444 23.092 22.583 1.046 0.962 0.000 1.228-1.074 87.95 16773 584 0.1529 17.432 16.979 1.025 0.964 0.000 1.074-0.997 60.43 8566 317 0.2143 11.247 10.727 0.946 0.966 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9743 b_overall=0.0100 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1307 r_free=0.1502 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 GLN Total number of N/Q/H flips: 1 r_work=0.1309 r_free=0.1502 ========================= Local real-space refinement ========================= Before: r_work=0.1309 r_free=0.1502 31 residues out of total 145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 30 time to evaluate : 0.162 outliers start: 1 outliers final: 1 residues processed: 31 average time/residue: 3.1582 time to fit residues: 99.3705 After: r_work=0.1313 r_free=0.1500 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 18.923899 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 206.501886 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1626 0.1783 0.0158 0.002 0.6 1.9 0.0 0.7 0 0.125 0.1585 0.1749 0.0164 0.002 0.6 1.5 0.0 0.7 0 0.250 0.1494 0.1665 0.0171 0.002 0.6 1.9 0.0 0.7 0 0.500 0.1418 0.1596 0.0178 0.003 0.6 1.9 0.0 0.7 0 1.000 0.1353 0.1546 0.0193 0.004 0.7 2.6 0.0 0.7 0 2.000 0.1329 0.1536 0.0207 0.005 0.8 2.6 0.0 0.7 0 3.000 0.1311 0.1532 0.0221 0.006 0.8 2.6 0.0 0.7 0 4.000 0.1297 0.1524 0.0227 0.007 0.9 3.0 0.0 0.7 0 5.000 0.1290 0.1524 0.0233 0.007 0.9 3.0 0.0 0.7 0 6.000 0.1285 0.1526 0.0242 0.008 1.0 3.3 0.0 0.7 0 7.000 0.1280 0.1527 0.0247 0.009 1.0 3.3 0.0 0.7 0 8.000 0.1276 0.1527 0.0252 0.009 1.0 3.3 0.0 0.7 0 9.000 0.1272 0.1526 0.0254 0.010 1.1 3.3 0.0 0.7 0 10.000 0.1275 0.1531 0.0256 0.010 1.0 3.3 0.0 0.7 0 9.462 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1290 0.1524 0.0233 0.007 0.9 3.0 0.0 0.7 0 6.000 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.1290 r_free=0.1524 30 residues out of total 145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 29 time to evaluate : 0.223 outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.2099 After: r_work=0.1290 r_free=0.1524 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.90 15.24 2.33 4.030 19.634 206.502 0.017 12.90 15.24 2.33 4.030 19.634 6.195 0.017 12.96 15.35 2.40 3.977 19.634 25.813 0.017 13.56 17.01 3.45 3.856 20.315 103.251 0.016 12.68 16.20 3.52 3.665 20.328 206.502 0.014 12.64 16.32 3.68 4.250 20.670 309.753 0.013 12.44 16.21 3.77 4.124 20.636 413.004 0.013 12.46 16.43 3.97 4.516 20.799 516.255 0.013 12.20 16.03 3.83 4.077 20.637 619.506 0.012 12.22 16.18 3.96 4.304 20.738 722.757 0.012 12.18 16.19 4.01 4.294 20.745 826.008 0.012 12.14 16.25 4.12 4.212 20.719 929.258 0.012 12.12 16.33 4.21 4.089 20.671 1032.509 0.012 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 6.195 Accepted refinement result: 12.90 15.24 2.33 4.030 19.634 6.195 0.017 Individual atomic B min max mean iso aniso Overall: 5.01 74.49 15.66 2.70 0 1696 Protein: 5.01 67.35 11.02 2.71 0 1315 Water: 6.78 74.49 32.35 N/A 0 371 Other: 6.59 8.39 7.28 N/A 0 10 Chain A: 5.01 74.49 15.66 N/A 0 1696 Histogram: Values Number of atoms 5.01 - 11.96 991 11.96 - 18.91 320 18.91 - 25.86 111 25.86 - 32.81 84 32.81 - 39.75 74 39.75 - 46.70 56 46.70 - 53.65 31 53.65 - 60.60 20 60.60 - 67.55 6 67.55 - 74.49 3 =========================== Idealize ADP of riding H ========================== r_work=0.1290 r_free=0.1524 r_work=0.1290 r_free=0.1524 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1290 r_free = 0.1524 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1290 r_free = 0.1524 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.00 - 9.52 A, n_refl.=63670 (all), 3.42 % free)-------------| | | | r_work= 0.1290 r_free= 0.1524 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ls_wunit_k1) (work): 0.016940 | | target function (ls_wunit_k1) not normalized (work): 1041.699884 | | target function (ls_wunit_k1) not normalized (free): 64.451086 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1298 0.1290 0.1524 n_refl.: 63670 re-set all scales: r(all,work,free)=0.1375 0.1366 0.1631 n_refl.: 63670 remove outliers: r(all,work,free)=0.1375 0.1366 0.1631 n_refl.: 63670 overall B=0.01 to atoms: r(all,work,free)=0.1376 0.1367 0.1632 n_refl.: 63670 bulk-solvent and scaling: r(all,work,free)=0.1298 0.1290 0.1524 n_refl.: 63670 remove outliers: r(all,work,free)=0.1298 0.1290 0.1524 n_refl.: 63670 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 9.517-7.089 77.69 91 3 0.1669 145.653 146.335 1.001 0.958 0.339 7.071-6.186 97.09 94 6 0.1386 127.520 127.088 1.024 0.957 0.280 6.180-5.403 98.12 153 4 0.1405 126.784 126.052 1.011 0.958 0.263 5.400-4.722 98.70 220 8 0.1015 176.574 178.043 1.051 0.959 0.257 4.720-4.127 99.14 337 10 0.0884 207.262 207.398 1.009 0.959 0.253 4.123-3.607 98.83 491 15 0.0915 185.501 185.340 0.994 0.959 0.200 3.606-3.152 98.34 745 27 0.1009 158.055 157.906 0.981 0.958 0.160 3.152-2.756 98.30 1120 38 0.1181 114.418 113.466 0.939 0.958 0.015 2.755-2.408 98.05 1641 67 0.1217 90.313 89.744 0.928 0.958 0.000 2.408-2.105 97.52 2466 85 0.1172 82.466 81.279 0.977 0.958 0.000 2.105-1.840 96.44 3682 111 0.1149 66.286 65.438 1.022 0.958 0.000 1.840-1.608 95.62 5401 213 0.1251 42.992 42.370 1.027 0.958 0.000 1.608-1.405 93.99 8009 294 0.1292 30.703 30.258 1.038 0.957 0.000 1.405-1.228 91.46 11706 393 0.1436 23.092 22.584 1.051 0.957 0.000 1.228-1.074 87.95 16773 584 0.1524 17.432 16.977 1.033 0.957 0.000 1.074-0.997 60.43 8566 317 0.2138 11.247 10.723 0.955 0.958 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9743 b_overall=0.0088 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1290 r_free=0.1524 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1290 r_free=0.1524 ========================= Local real-space refinement ========================= Before: r_work=0.1290 r_free=0.1524 30 residues out of total 145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 29 time to evaluate : 0.233 outliers start: 1 outliers final: 1 residues processed: 30 average time/residue: 2.3550 time to fit residues: 71.7506 After: r_work=0.1295 r_free=0.1516 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.441328 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 6.192900 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1338 0.1517 0.0178 0.004 0.7 2.6 0.0 0.7 0 0.072 0.1290 0.1460 0.0170 0.006 0.9 3.7 0.0 0.7 0 0.216 0.1268 0.1436 0.0168 0.008 1.0 3.3 0.0 0.7 0 0.432 0.1259 0.1429 0.0170 0.009 1.1 3.7 0.0 0.7 0 0.649 0.1254 0.1422 0.0168 0.011 1.2 4.1 0.0 0.7 0 0.865 0.1250 0.1417 0.0167 0.012 1.2 4.5 0.0 0.7 0 1.081 0.1247 0.1413 0.0166 0.013 1.3 5.2 0.0 0.7 0 1.297 0.1242 0.1410 0.0167 0.013 1.3 4.8 0.0 0.7 0 1.513 0.1256 0.1427 0.0171 0.010 1.1 3.7 0.0 0.7 0 0.721 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1242 0.1410 0.0167 0.013 1.3 4.8 0.0 0.7 0 1.513 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.1242 r_free=0.1410 29 residues out of total 145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 28 time to evaluate : 0.164 outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.1235 After: r_work=0.1242 r_free=0.1410 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.42 14.10 1.67 4.031 19.644 6.193 2.916 12.43 14.10 1.68 4.028 19.644 0.186 2.916 12.47 14.19 1.72 3.995 19.646 0.774 2.917 12.40 14.49 2.09 3.990 19.647 3.096 2.908 12.37 14.84 2.48 4.017 19.643 6.193 2.911 12.32 15.07 2.75 4.060 19.636 9.289 2.910 12.25 15.07 2.83 4.077 19.635 12.386 2.904 12.18 14.96 2.78 4.087 19.631 15.482 2.896 12.12 14.90 2.78 4.087 19.631 18.579 2.891 12.09 14.92 2.83 4.087 19.631 21.675 2.890 12.06 14.81 2.75 4.095 19.629 24.772 2.884 12.07 14.91 2.85 4.102 19.635 27.868 2.886 12.03 14.83 2.80 4.104 19.638 30.965 2.882 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 0.186 Accepted refinement result: 12.43 14.10 1.68 4.028 19.644 0.186 2.916 Individual atomic B min max mean iso aniso Overall: 5.03 74.50 15.67 2.69 0 1696 Protein: 5.03 67.19 11.02 2.70 0 1315 Water: 6.78 74.50 32.36 N/A 0 371 Other: 6.60 8.39 7.29 N/A 0 10 Chain A: 5.03 74.50 15.67 N/A 0 1696 Histogram: Values Number of atoms 5.03 - 11.98 991 11.98 - 18.92 320 18.92 - 25.87 112 25.87 - 32.82 84 32.82 - 39.77 73 39.77 - 46.71 56 46.71 - 53.66 31 53.66 - 60.61 20 60.61 - 67.56 6 67.56 - 74.50 3 =========================== Idealize ADP of riding H ========================== r_work=0.1243 r_free=0.1410 r_work=0.1243 r_free=0.1410 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1243 r_free = 0.1410 target_work(ml) = 2.916 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1243 r_free = 0.1411 target_work(ml) = 2.916 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.00 - 9.52 A, n_refl.=63670 (all), 3.42 % free)-------------| | | | r_work= 0.1243 r_free= 0.1411 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 2.916277 | | target function (ml) not normalized (work): 179336.469354 | | target function (ml) not normalized (free): 6431.223401 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1249 0.1243 0.1411 n_refl.: 63670 re-set all scales: r(all,work,free)=0.1337 0.1330 0.1528 n_refl.: 63670 remove outliers: r(all,work,free)=0.1337 0.1330 0.1528 n_refl.: 63670 overall B=-0.00 to atoms: r(all,work,free)=0.1336 0.1329 0.1527 n_refl.: 63670 bulk-solvent and scaling: r(all,work,free)=0.1247 0.1241 0.1412 n_refl.: 63670 remove outliers: r(all,work,free)=0.1247 0.1241 0.1412 n_refl.: 63669 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 9.517-7.089 77.69 91 3 0.1868 145.653 145.999 1.008 0.951 0.266 7.071-6.186 97.09 94 6 0.1747 127.520 125.690 1.020 0.950 0.263 6.180-5.403 98.12 153 4 0.1749 126.784 124.560 1.009 0.951 0.251 5.400-4.722 98.70 220 8 0.1249 176.574 177.752 1.052 0.951 0.242 4.720-4.127 99.14 337 10 0.1093 207.262 206.860 1.009 0.952 0.229 4.123-3.607 98.83 491 15 0.1097 185.501 184.844 0.999 0.951 0.221 3.606-3.152 98.34 745 27 0.1262 158.055 156.803 0.982 0.951 0.160 3.152-2.756 98.30 1120 38 0.1319 114.418 112.793 0.943 0.951 0.010 2.755-2.408 98.05 1641 67 0.1362 90.313 89.202 0.936 0.951 0.000 2.408-2.105 97.52 2466 85 0.1201 82.466 81.109 0.983 0.951 0.000 2.105-1.840 96.44 3682 111 0.1102 66.286 65.474 1.031 0.951 0.000 1.840-1.608 95.62 5401 213 0.1096 42.992 42.508 1.037 0.950 0.000 1.608-1.405 93.98 8008 294 0.1075 30.704 30.358 1.050 0.950 0.000 1.405-1.228 91.46 11706 393 0.1201 23.092 22.681 1.065 0.950 0.000 1.228-1.074 87.95 16773 584 0.1325 17.432 17.046 1.049 0.950 0.000 1.074-0.997 60.43 8566 317 0.1988 11.247 10.779 0.960 0.952 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9743 b_overall=-0.0163 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1241 r_free=0.1412 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1241 r_free=0.1412 ========================= Local real-space refinement ========================= Before: r_work=0.1241 r_free=0.1412 28 residues out of total 145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 27 time to evaluate : 0.213 outliers start: 1 outliers final: 1 residues processed: 28 average time/residue: 2.5041 time to fit residues: 71.2912 After: r_work=0.1247 r_free=0.1418 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.366127 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 5.518873 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1328 0.1482 0.0155 0.004 0.8 3.0 0.0 0.7 0 0.068 0.1281 0.1441 0.0160 0.007 0.9 2.6 0.0 1.4 0 0.205 0.1262 0.1424 0.0162 0.009 1.1 3.0 0.0 1.4 0 0.410 0.1252 0.1416 0.0164 0.011 1.2 3.3 0.0 1.4 0 0.615 0.1247 0.1410 0.0163 0.012 1.2 3.3 0.0 1.4 0 0.820 0.1244 0.1406 0.0162 0.013 1.3 4.1 0.0 1.4 0 1.025 0.1241 0.1405 0.0164 0.014 1.3 4.5 0.0 1.4 0 1.230 0.1239 0.1404 0.0165 0.015 1.4 4.8 0.0 1.4 0 1.434 0.1250 0.1412 0.0162 0.011 1.2 3.3 0.0 1.4 0 0.683 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1239 0.1404 0.0165 0.015 1.4 4.8 0.0 1.4 0 1.434 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.1239 r_free=0.1404 30 residues out of total 145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 28 time to evaluate : 0.228 outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.2004 After: r_work=0.1239 r_free=0.1404 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.39 14.04 1.65 4.027 19.640 5.519 2.909 12.39 14.04 1.65 4.027 19.640 0.166 2.909 12.43 14.12 1.69 3.994 19.641 0.690 2.911 12.35 14.35 2.00 3.993 19.637 2.759 2.899 12.35 14.75 2.39 4.017 19.640 5.519 2.906 12.28 14.85 2.57 4.041 19.634 8.278 2.904 12.20 14.92 2.72 4.071 19.625 11.038 2.898 12.15 14.93 2.77 4.076 19.627 13.797 2.895 12.11 14.83 2.72 4.095 19.623 16.557 2.887 12.05 14.73 2.69 4.091 19.621 19.316 2.882 12.01 14.66 2.65 4.097 19.618 22.075 2.877 11.99 14.66 2.67 4.099 19.619 24.835 2.876 11.99 14.71 2.72 4.105 19.621 27.594 2.877 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 0.166 Accepted refinement result: 12.39 14.04 1.65 4.027 19.640 0.166 2.909 Individual atomic B min max mean iso aniso Overall: 5.02 74.50 15.66 2.69 0 1696 Protein: 5.02 67.19 11.02 2.70 0 1315 Water: 6.78 74.50 32.35 N/A 0 371 Other: 6.60 8.38 7.29 N/A 0 10 Chain A: 5.02 74.50 15.66 N/A 0 1696 Histogram: Values Number of atoms 5.02 - 11.97 991 11.97 - 18.92 320 18.92 - 25.87 112 25.87 - 32.81 84 32.81 - 39.76 73 39.76 - 46.71 56 46.71 - 53.66 31 53.66 - 60.60 20 60.60 - 67.55 6 67.55 - 74.50 3 =========================== Idealize ADP of riding H ========================== r_work=0.1239 r_free=0.1404 r_work=0.1239 r_free=0.1404 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1239 r_free = 0.1404 target_work(ml) = 2.909 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1239 r_free = 0.1404 target_work(ml) = 2.909 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.00 - 9.52 A, n_refl.=63669 (all), 3.42 % free)-------------| | | | r_work= 0.1239 r_free= 0.1404 coordinate error (max.-lik. estimate): 0.06 A | | | | normalized target function (ml) (work): 2.909204 | | target function (ml) not normalized (work): 178898.607485 | | target function (ml) not normalized (free): 6421.374275 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1244 0.1239 0.1404 n_refl.: 63669 re-set all scales: r(all,work,free)=0.1335 0.1328 0.1518 n_refl.: 63669 remove outliers: r(all,work,free)=0.1335 0.1328 0.1518 n_refl.: 63669 overall B=-0.00 to atoms: r(all,work,free)=0.1334 0.1328 0.1517 n_refl.: 63669 bulk-solvent and scaling: r(all,work,free)=0.1244 0.1238 0.1404 n_refl.: 63669 remove outliers: r(all,work,free)=0.1244 0.1238 0.1404 n_refl.: 63669 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 9.517-7.089 77.69 91 3 0.1889 145.653 145.787 1.008 0.950 0.280 7.071-6.186 97.09 94 6 0.1820 127.520 125.505 1.013 0.949 0.278 6.180-5.403 98.12 153 4 0.1786 126.784 124.557 1.005 0.950 0.257 5.400-4.722 98.70 220 8 0.1293 176.574 177.742 1.053 0.951 0.253 4.720-4.127 99.14 337 10 0.1100 207.262 206.715 1.010 0.951 0.246 4.123-3.607 98.83 491 15 0.1113 185.501 184.867 1.000 0.951 0.240 3.606-3.152 98.34 745 27 0.1289 158.055 156.643 0.981 0.950 0.170 3.152-2.756 98.30 1120 38 0.1329 114.418 112.722 0.943 0.951 0.015 2.755-2.408 98.05 1641 67 0.1385 90.313 89.148 0.937 0.950 0.000 2.408-2.105 97.52 2466 85 0.1201 82.466 81.117 0.983 0.950 0.000 2.105-1.840 96.44 3682 111 0.1092 66.286 65.483 1.031 0.950 0.000 1.840-1.608 95.62 5401 213 0.1075 42.992 42.533 1.037 0.950 0.000 1.608-1.405 93.98 8008 294 0.1051 30.704 30.388 1.050 0.950 0.000 1.405-1.228 91.46 11706 393 0.1184 23.092 22.702 1.065 0.950 0.000 1.228-1.074 87.95 16773 584 0.1318 17.432 17.058 1.050 0.950 0.000 1.074-0.997 60.43 8566 317 0.1986 11.247 10.785 0.958 0.952 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9743 b_overall=-0.0149 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1238 r_free=0.1404 After: r_work=0.1240 r_free=0.1405 ================================== NQH flips ================================== r_work=0.1240 r_free=0.1405 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1240 r_free=0.1405 ========================= Local real-space refinement ========================= Before: r_work=0.1240 r_free=0.1405 30 residues out of total 145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 28 time to evaluate : 0.128 outliers start: 2 outliers final: 1 residues processed: 30 average time/residue: 1.5541 time to fit residues: 47.3510 After: r_work=0.1249 r_free=0.1411 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.478374 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 5.217339 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1335 0.1471 0.0136 0.006 0.9 4.1 0.0 1.4 0 0.074 0.1290 0.1431 0.0142 0.007 1.0 4.1 0.0 1.4 0 0.222 0.1273 0.1423 0.0151 0.009 1.1 4.8 0.0 1.4 0 0.444 0.1263 0.1421 0.0158 0.010 1.2 5.2 0.0 0.7 0 0.665 0.1254 0.1417 0.0162 0.012 1.3 5.2 0.0 0.7 0 0.887 0.1250 0.1415 0.0165 0.013 1.4 5.2 0.0 0.7 0 1.109 0.1246 0.1414 0.0167 0.015 1.4 5.2 0.0 0.7 0 1.331 0.1244 0.1412 0.0168 0.015 1.4 5.2 0.0 0.7 0 1.552 0.1259 0.1418 0.0160 0.011 1.3 4.8 0.0 0.7 0 0.739 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1244 0.1412 0.0168 0.015 1.4 5.2 0.0 0.7 0 1.552 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.1244 r_free=0.1412 29 residues out of total 145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 28 time to evaluate : 0.115 outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.1013 After: r_work=0.1244 r_free=0.1412 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.44 14.12 1.68 4.027 19.635 5.217 2.914 12.44 14.12 1.68 4.025 19.635 0.157 2.914 12.49 14.20 1.71 3.993 19.637 0.652 2.916 12.40 14.43 2.02 3.993 19.632 2.609 2.904 12.41 14.84 2.43 4.013 19.639 5.217 2.909 12.35 15.03 2.68 4.065 19.624 7.826 2.910 12.28 15.05 2.77 4.079 19.623 10.435 2.904 12.22 15.02 2.80 4.088 19.623 13.043 2.897 12.15 14.87 2.72 4.105 19.620 15.652 2.889 12.11 14.89 2.78 4.093 19.619 18.261 2.887 12.05 14.74 2.69 4.098 19.614 20.869 2.880 12.04 14.74 2.70 4.102 19.615 23.478 2.878 12.03 14.77 2.74 4.114 19.619 26.087 2.878 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 0.157 Accepted refinement result: 12.44 14.12 1.68 4.025 19.635 0.157 2.914 Individual atomic B min max mean iso aniso Overall: 5.02 74.49 15.66 2.67 0 1696 Protein: 5.02 67.07 11.02 2.68 0 1315 Water: 6.78 74.49 32.35 N/A 0 371 Other: 6.60 8.38 7.28 N/A 0 10 Chain A: 5.02 74.49 15.66 N/A 0 1696 Histogram: Values Number of atoms 5.02 - 11.97 991 11.97 - 18.92 321 18.92 - 25.86 111 25.86 - 32.81 84 32.81 - 39.76 73 39.76 - 46.71 56 46.71 - 53.65 31 53.65 - 60.60 20 60.60 - 67.55 6 67.55 - 74.49 3 =========================== Idealize ADP of riding H ========================== r_work=0.1244 r_free=0.1412 r_work=0.1244 r_free=0.1412 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1244 r_free = 0.1412 target_work(ml) = 2.914 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1244 r_free = 0.1413 target_work(ml) = 2.914 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.00 - 9.52 A, n_refl.=63669 (all), 3.42 % free)-------------| | | | r_work= 0.1244 r_free= 0.1413 coordinate error (max.-lik. estimate): 0.06 A | | | | normalized target function (ml) (work): 2.914413 | | target function (ml) not normalized (work): 179218.913695 | | target function (ml) not normalized (free): 6432.394449 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 9.52 - 2.50 0.98 4377 161 0.1316 0.1648 4.5843 4.7139| | 2: 2.50 - 1.99 0.97 4338 145 0.1195 0.1240 4.0565 4.099| | 3: 1.99 - 1.74 0.96 4348 134 0.1092 0.1300 3.502 3.5685| | 4: 1.74 - 1.58 0.95 4233 186 0.1068 0.1185 3.1189 3.1554| | 5: 1.58 - 1.47 0.94 4185 154 0.1043 0.1030 2.8901 2.873| | 6: 1.47 - 1.38 0.93 4208 147 0.1109 0.1201 2.7425 2.8002| | 7: 1.38 - 1.31 0.92 4124 125 0.1183 0.1414 2.6909 2.7219| | 8: 1.31 - 1.26 0.91 4047 145 0.1195 0.1399 2.6322 2.773| | 9: 1.26 - 1.21 0.90 4023 141 0.1248 0.1280 2.5738 2.6182| | 10: 1.21 - 1.17 0.89 4034 150 0.1252 0.1513 2.5168 2.664| | 11: 1.17 - 1.13 0.89 3965 128 0.1232 0.1139 2.4521 2.3702| | 12: 1.13 - 1.10 0.87 3945 131 0.1349 0.1267 2.4041 2.4179| | 13: 1.10 - 1.07 0.84 3724 141 0.1609 0.1732 2.408 2.4169| | 14: 1.07 - 1.04 0.77 3439 125 0.1761 0.1898 2.383 2.3269| | 15: 1.04 - 1.02 0.69 3099 102 0.2108 0.2043 2.3899 2.346| | 16: 1.02 - 1.00 0.32 1405 60 0.2586 0.3578 2.4623 2.6299| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 9.52 - 2.50 4377 161 0.90 16.69 1.00 1.04 1822.73| | 2: 2.50 - 1.99 4338 145 0.90 17.22 1.00 1.06 783.48| | 3: 1.99 - 1.74 4348 134 0.94 11.91 1.00 1.07 202.70| | 4: 1.74 - 1.58 4233 186 0.95 11.18 1.00 1.07 95.42| | 5: 1.58 - 1.47 4185 154 0.95 10.47 1.00 1.06 56.33| | 6: 1.47 - 1.38 4208 147 0.95 10.89 1.00 1.05 40.80| | 7: 1.38 - 1.31 4124 125 0.95 10.97 1.00 1.05 34.10| | 8: 1.31 - 1.26 4047 145 0.95 11.27 1.01 1.05 31.02| | 9: 1.26 - 1.21 4023 141 0.94 11.90 1.01 1.07 28.25| | 10: 1.21 - 1.17 4034 150 0.95 11.57 1.02 1.08 24.41| | 11: 1.17 - 1.13 3965 128 0.95 11.04 1.00 1.08 20.59| | 12: 1.13 - 1.10 3945 131 0.95 11.69 0.98 1.06 17.21| | 13: 1.10 - 1.07 3724 141 0.94 13.33 0.97 1.04 16.08| | 14: 1.07 - 1.04 3439 125 0.91 16.55 1.03 1.03 16.58| | 15: 1.04 - 1.02 3099 102 0.88 20.80 0.98 1.01 19.47| | 16: 1.02 - 1.00 1405 60 0.83 25.49 0.93 0.95 23.98| |alpha: min = 0.95 max = 1.08 mean = 1.05| |beta: min = 16.08 max = 1822.73 mean = 226.17| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.85 mean = 13.31| |phase err.(test): min = 0.00 max = 85.24 mean = 13.38| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1250 0.1244 0.1413 n_refl.: 63669 re-set all scales: r(all,work,free)=0.1340 0.1334 0.1525 n_refl.: 63669 remove outliers: r(all,work,free)=0.1340 0.1334 0.1525 n_refl.: 63669 overall B=-0.00 to atoms: r(all,work,free)=0.1340 0.1333 0.1525 n_refl.: 63669 bulk-solvent and scaling: r(all,work,free)=0.1250 0.1244 0.1412 n_refl.: 63669 remove outliers: r(all,work,free)=0.1250 0.1244 0.1412 n_refl.: 63669 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 9.517-7.089 77.69 91 3 0.1876 145.653 145.942 1.008 0.950 0.280 7.071-6.186 97.09 94 6 0.1856 127.520 125.195 1.010 0.948 0.279 6.180-5.403 98.12 153 4 0.1805 126.784 124.324 1.004 0.949 0.261 5.400-4.722 98.70 220 8 0.1319 176.574 177.565 1.053 0.950 0.255 4.720-4.127 99.14 337 10 0.1123 207.262 206.719 1.009 0.950 0.251 4.123-3.607 98.83 491 15 0.1108 185.501 184.901 1.001 0.950 0.237 3.606-3.152 98.34 745 27 0.1290 158.055 156.497 0.982 0.950 0.190 3.152-2.756 98.30 1120 38 0.1328 114.418 112.757 0.944 0.950 0.024 2.755-2.408 98.05 1641 67 0.1384 90.313 89.132 0.938 0.949 0.000 2.408-2.105 97.52 2466 85 0.1202 82.466 81.100 0.984 0.950 0.000 2.105-1.840 96.44 3682 111 0.1100 66.286 65.482 1.031 0.949 0.000 1.840-1.608 95.62 5401 213 0.1085 42.992 42.520 1.037 0.949 0.000 1.608-1.405 93.98 8008 294 0.1061 30.704 30.379 1.051 0.949 0.000 1.405-1.228 91.46 11706 393 0.1192 23.092 22.697 1.066 0.949 0.000 1.228-1.074 87.95 16773 584 0.1324 17.432 17.055 1.050 0.950 0.000 1.074-0.997 60.43 8566 317 0.1989 11.247 10.783 0.958 0.952 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9743 b_overall=-0.0142 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.1365 0.1457 0.017 2.081 4.7 74.3 15.4 1113 0.000 1_bss: 0.1303 0.1379 0.017 2.081 4.9 74.5 15.7 1113 0.000 1_settarget: 0.1303 0.1379 0.017 2.081 4.9 74.5 15.7 1113 0.000 1_nqh: 0.1303 0.1379 0.017 2.081 4.9 74.5 15.7 1113 0.000 1_realsrl: 0.1312 0.1415 0.017 2.081 4.9 74.5 15.7 1113 0.055 1_weight: 0.1312 0.1415 0.017 2.081 4.9 74.5 15.7 1113 0.055 1_xyzrec: 0.1316 0.1521 0.008 0.952 4.9 74.5 15.7 1113 0.157 1_realsrl2: 0.1316 0.1521 0.008 0.952 4.9 74.5 15.7 1113 0.157 1_adp: 0.1318 0.1523 0.008 0.952 5.0 74.5 15.7 1113 0.157 1_regHadp: 0.1311 0.1512 0.008 0.952 5.0 74.5 15.7 1113 0.157 1_occ: 0.1309 0.1505 0.008 0.952 5.0 74.5 15.7 1113 0.157 2_bss: 0.1307 0.1502 0.008 0.952 5.0 74.5 15.7 1113 0.157 2_settarget: 0.1307 0.1502 0.008 0.952 5.0 74.5 15.7 1113 0.157 2_updatecdl: 0.1307 0.1502 0.008 0.958 5.0 74.5 15.7 1113 0.157 2_nqh: 0.1309 0.1502 0.008 0.958 5.0 74.5 15.7 1113 0.160 2_realsrl: 0.1313 0.1500 0.008 0.959 5.0 74.5 15.7 1113 0.158 2_weight: 0.1313 0.1500 0.008 0.959 5.0 74.5 15.7 1113 0.158 2_xyzrec: 0.1290 0.1524 0.007 0.921 5.0 74.5 15.7 1113 0.179 2_realsrl2: 0.1290 0.1524 0.007 0.921 5.0 74.5 15.7 1113 0.179 2_adp: 0.1290 0.1524 0.007 0.921 5.0 74.5 15.7 1113 0.179 2_regHadp: 0.1290 0.1524 0.007 0.921 5.0 74.5 15.7 1113 0.179 2_occ: 0.1290 0.1524 0.007 0.921 5.0 74.5 15.7 1113 0.179 3_bss: 0.1290 0.1524 0.007 0.921 5.0 74.5 15.7 1113 0.179 3_settarget: 0.1290 0.1524 0.007 0.921 5.0 74.5 15.7 1113 0.179 3_updatecdl: 0.1290 0.1524 0.007 0.926 5.0 74.5 15.7 1113 0.179 3_nqh: 0.1290 0.1524 0.007 0.926 5.0 74.5 15.7 1113 0.179 3_realsrl: 0.1295 0.1516 0.007 0.927 5.0 74.5 15.7 1113 0.179 3_weight: 0.1295 0.1516 0.007 0.927 5.0 74.5 15.7 1113 0.179 3_xyzrec: 0.1242 0.1410 0.013 1.332 5.0 74.5 15.7 1113 0.166 3_realsrl2: 0.1242 0.1410 0.013 1.332 5.0 74.5 15.7 1113 0.166 3_adp: 0.1243 0.1410 0.013 1.332 5.0 74.5 15.7 1113 0.166 3_regHadp: 0.1243 0.1410 0.013 1.332 5.0 74.5 15.7 1113 0.166 3_occ: 0.1243 0.1411 0.013 1.332 5.0 74.5 15.7 1113 0.166 4_bss: 0.1241 0.1412 0.013 1.332 5.0 74.5 15.7 1113 0.166 4_settarget: 0.1241 0.1412 0.013 1.332 5.0 74.5 15.7 1113 0.166 4_updatecdl: 0.1241 0.1412 0.013 1.329 5.0 74.5 15.7 1113 0.166 4_nqh: 0.1241 0.1412 0.013 1.329 5.0 74.5 15.7 1113 0.166 4_realsrl: 0.1247 0.1418 0.013 1.329 5.0 74.5 15.7 1113 0.167 4_weight: 0.1247 0.1418 0.013 1.329 5.0 74.5 15.7 1113 0.167 4_xyzrec: 0.1239 0.1404 0.015 1.386 5.0 74.5 15.7 1113 0.173 4_realsrl2: 0.1239 0.1404 0.015 1.386 5.0 74.5 15.7 1113 0.173 4_adp: 0.1239 0.1404 0.015 1.386 5.0 74.5 15.7 1113 0.173 4_regHadp: 0.1239 0.1404 0.015 1.386 5.0 74.5 15.7 1113 0.173 4_occ: 0.1239 0.1404 0.015 1.386 5.0 74.5 15.7 1113 0.173 5_bss: 0.1238 0.1404 0.015 1.386 5.0 74.5 15.7 1113 0.173 5_settarget: 0.1238 0.1404 0.015 1.386 5.0 74.5 15.7 1113 0.173 5_updatecdl: 0.1238 0.1404 0.015 1.387 5.0 74.5 15.7 1113 0.173 5_setrh: 0.1240 0.1405 0.015 1.387 5.0 74.5 15.7 1113 0.172 5_nqh: 0.1240 0.1405 0.015 1.387 5.0 74.5 15.7 1113 0.172 5_realsrl: 0.1249 0.1411 0.015 1.387 5.0 74.5 15.7 1113 0.172 5_weight: 0.1249 0.1411 0.015 1.387 5.0 74.5 15.7 1113 0.172 5_xyzrec: 0.1244 0.1412 0.015 1.437 5.0 74.5 15.7 1113 0.172 5_realsrl2: 0.1244 0.1412 0.015 1.437 5.0 74.5 15.7 1113 0.172 5_adp: 0.1244 0.1412 0.015 1.437 5.0 74.5 15.7 1113 0.172 5_regHadp: 0.1244 0.1412 0.015 1.437 5.0 74.5 15.7 1113 0.172 5_occ: 0.1244 0.1413 0.015 1.437 5.0 74.5 15.7 1113 0.172 end: 0.1244 0.1412 0.015 1.437 5.0 74.5 15.7 1113 0.172 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/highres/finalised/1TT8_complete_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/highres/finalised/1TT8_complete_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 2.8700 Refinement macro-cycles (run) : 1219.6300 Write final files (write_after_run_outputs) : 44.9000 Total : 1267.4000 Total CPU time: 21.42 minutes =========================== phenix.refine: finished =========================== # Date 2024-04-10 Time 16:31:12 PDT -0700 (1712791872.58 s) Start R-work = 0.1303, R-free = 0.1379 Final R-work = 0.1244, R-free = 0.1412 =============================================================================== Job complete usr+sys time: 1362.94 seconds wall clock time: 33 minutes 12.54 seconds (1992.54 seconds total)