Starting phenix.refine on Wed Apr 10 15:59:19 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, 5ZGL_complete.pdb Found miller_array, 5ZGL.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 = "5ZGL_complete.pdb" } default_model = "5ZGL_complete.pdb" miller_array { file = "5ZGL.mtz" } default_miller_array = "5ZGL.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: 152 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 70 Classifications: {'peptide': 7} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 6} Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 70 Classifications: {'peptide': 7} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 6} Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 9 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Time building chain proxies: 0.05, per 1000 atoms: 0.33 Number of scatterers: 152 At special positions: 0 Unit cell: (11.957, 10.141, 21.372, 90, 100.112, 90) Space group: P 1 21 1 (No. 4) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) O 24 8.00 N 14 7.00 C 44 6.00 H 70 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: 0.06 Conformation dependent library (CDL) restraints added in 5.3 milliseconds Time building geometry restraints manager: 0.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.85 - 0.99: 12 0.99 - 1.13: 58 1.13 - 1.28: 16 1.28 - 1.42: 28 1.42 - 1.56: 34 Bond restraints: 148 Sorted by residual: bond pdb=" N GLY B 238 " pdb=" H GLY B 238 " ideal model delta sigma weight residual 0.860 1.020 -0.160 2.00e-02 2.50e+03 6.43e+01 bond pdb=" N GLY A 238 " pdb=" H GLY A 238 " ideal model delta sigma weight residual 0.860 1.020 -0.160 2.00e-02 2.50e+03 6.43e+01 bond pdb=" N TYR B 237 " pdb=" H TYR B 237 " ideal model delta sigma weight residual 0.860 1.020 -0.160 2.00e-02 2.50e+03 6.42e+01 bond pdb=" N GLY B 236 " pdb=" H GLY B 236 " ideal model delta sigma weight residual 0.860 1.020 -0.160 2.00e-02 2.50e+03 6.42e+01 bond pdb=" N SER A 240 " pdb=" H SER A 240 " ideal model delta sigma weight residual 0.860 1.020 -0.160 2.00e-02 2.50e+03 6.42e+01 ... (remaining 143 not shown) Histogram of bond angle deviations from ideal: 103.84 - 108.17: 13 108.17 - 112.50: 112 112.50 - 116.83: 25 116.83 - 121.16: 50 121.16 - 125.49: 42 Bond angle restraints: 242 Sorted by residual: angle pdb=" C GLY A 238 " pdb=" N GLY A 239 " pdb=" CA GLY A 239 " ideal model delta sigma weight residual 121.03 118.74 2.29 1.51e+00 4.39e-01 2.31e+00 angle pdb=" C SER B 240 " pdb=" CA SER B 240 " pdb=" CB SER B 240 " ideal model delta sigma weight residual 110.10 112.97 -2.87 1.90e+00 2.77e-01 2.29e+00 angle pdb=" C SER B 240 " pdb=" CA SER B 240 " pdb=" HA SER B 240 " ideal model delta sigma weight residual 109.00 105.12 3.88 3.00e+00 1.11e-01 1.67e+00 angle pdb=" O SER B 240 " pdb=" C SER B 240 " pdb=" OXT SER B 240 " ideal model delta sigma weight residual 118.00 121.78 -3.78 3.00e+00 1.11e-01 1.59e+00 angle pdb=" CA TYR A 237 " pdb=" CB TYR A 237 " pdb=" CG TYR A 237 " ideal model delta sigma weight residual 113.90 111.69 2.21 1.80e+00 3.09e-01 1.51e+00 ... (remaining 237 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.97: 36 11.97 - 23.94: 2 23.94 - 35.91: 3 35.91 - 47.87: 4 47.87 - 59.84: 11 Dihedral angle restraints: 56 sinusoidal: 34 harmonic: 22 Sorted by residual: dihedral pdb=" CA TYR A 237 " pdb=" C TYR A 237 " pdb=" N GLY A 238 " pdb=" CA GLY A 238 " ideal model delta harmonic sigma weight residual 180.00 158.42 21.58 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA GLY A 239 " pdb=" C GLY A 239 " pdb=" N SER A 240 " pdb=" CA SER A 240 " ideal model delta harmonic sigma weight residual 180.00 169.05 10.95 0 5.00e+00 4.00e-02 4.80e+00 dihedral pdb=" N TYR A 237 " pdb=" CA TYR A 237 " pdb=" CB TYR A 237 " pdb=" CG TYR A 237 " ideal model delta sinusoidal sigma weight residual 60.00 86.25 -26.25 3 1.50e+01 4.44e-03 3.82e+00 ... (remaining 53 not shown) Histogram of chiral volume deviations from ideal: 0.017 - 0.041: 1 0.041 - 0.066: 1 0.066 - 0.091: 0 0.091 - 0.116: 1 0.116 - 0.141: 1 Chirality restraints: 4 Sorted by residual: chirality pdb=" CA TYR B 237 " pdb=" N TYR B 237 " pdb=" C TYR B 237 " pdb=" CB TYR B 237 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.94e-01 chirality pdb=" CA SER B 240 " pdb=" N SER B 240 " pdb=" C SER B 240 " pdb=" CB SER B 240 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 2.85e-01 chirality pdb=" CA TYR A 237 " pdb=" N TYR A 237 " pdb=" C TYR A 237 " pdb=" CB TYR A 237 " both_signs ideal model delta sigma weight residual False 2.51 2.58 -0.07 2.00e-01 2.50e+01 1.08e-01 ... (remaining 1 not shown) Planarity restraints: 28 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 237 " 0.130 2.00e-02 2.50e+03 5.20e-02 8.12e+01 pdb=" CG TYR A 237 " 0.005 2.00e-02 2.50e+03 pdb=" CD1 TYR A 237 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR A 237 " -0.028 2.00e-02 2.50e+03 pdb=" CE1 TYR A 237 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 237 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 237 " 0.010 2.00e-02 2.50e+03 pdb=" OH TYR A 237 " 0.055 2.00e-02 2.50e+03 pdb=" HD1 TYR A 237 " -0.074 2.00e-02 2.50e+03 pdb=" HD2 TYR A 237 " -0.073 2.00e-02 2.50e+03 pdb=" HE1 TYR A 237 " 0.005 2.00e-02 2.50e+03 pdb=" HE2 TYR A 237 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 237 " -0.052 2.00e-02 2.50e+03 2.05e-02 1.26e+01 pdb=" CG TYR B 237 " 0.004 2.00e-02 2.50e+03 pdb=" CD1 TYR B 237 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR B 237 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR B 237 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 237 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 237 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 237 " -0.015 2.00e-02 2.50e+03 pdb=" HD1 TYR B 237 " 0.022 2.00e-02 2.50e+03 pdb=" HD2 TYR B 237 " 0.033 2.00e-02 2.50e+03 pdb=" HE1 TYR B 237 " -0.004 2.00e-02 2.50e+03 pdb=" HE2 TYR B 237 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 236 " -0.006 2.00e-02 2.50e+03 1.27e-02 1.61e+00 pdb=" C GLY A 236 " 0.022 2.00e-02 2.50e+03 pdb=" O GLY A 236 " -0.008 2.00e-02 2.50e+03 pdb=" N TYR A 237 " -0.007 2.00e-02 2.50e+03 ... (remaining 25 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.19: 56 2.19 - 2.77: 335 2.77 - 3.35: 675 3.35 - 3.92: 1101 3.92 - 4.50: 1666 Nonbonded interactions: 3833 Sorted by model distance: nonbonded pdb=" H1 GLY A 234 " pdb=" O SER A 240 " model vdw sym.op. 1.615 1.850 x+1,y,z-1 nonbonded pdb=" H2 GLY A 234 " pdb=" O SER A 240 " model vdw sym.op. 1.675 1.850 x+1,y,z-1 nonbonded pdb=" HH TYR B 237 " pdb=" O HOH B 301 " model vdw 1.712 1.850 nonbonded pdb=" HH TYR A 237 " pdb=" OXT SER B 240 " model vdw 1.762 1.850 nonbonded pdb=" O SER B 240 " pdb=" HG SER B 240 " model vdw sym.op. 1.807 1.850 -x+1,y+1/2,-z+2 ... (remaining 3828 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: 4 Type Number sf(0) Gaussians O 24 7.97 2 N 14 6.98 3 C 44 5.99 3 H 70 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 = 152 n_use_u_iso = 70 n_use_u_aniso = 82 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 = 152 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (152 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 70 aniso = 82) group_adp = False (0 atoms in 0 groups) tls = False (0 atoms in 0 groups) occupancies = True (0 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 = "5ZGL_complete_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 70 occupancy sum: 70.00 (% of total atoms 46.05) Rotatable: count: 10 occupancy sum: 10.00 (% of total atoms 6.58) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 0.95 - 11.77 A, n_refl.=2791 (all), 9.89 % free)-------------| | | | r_work= 0.1208 r_free= 0.1288 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 3.721460 | | target function (ml) not normalized (work): 9359.470812 | | target function (ml) not normalized (free): 1047.581155 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 11.77 - 1.20 0.93 1422 158 0.1144 0.1234 4.0113 4.1118| | 2: 1.20 - 0.95 0.73 1093 118 0.1400 0.1458 3.3444 3.3721| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 11.77 - 1.20 1422 158 0.89 15.71 1.01 4.78 485.85| | 2: 1.20 - 0.95 1093 118 0.91 14.36 0.96 4.74 101.14| |alpha: min = 4.74 max = 4.78 mean = 4.76| |beta: min = 101.14 max = 485.85 mean = 318.66| |figures of merit: min = 0.02 max = 1.00 mean = 0.90| |phase err.(work): min = 0.00 max = 88.01 mean = 15.12| |phase err.(test): min = 0.00 max = 89.34 mean = 15.27| |-----------------------------------------------------------------------------| ----------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 : 0.014 0.053 78 Z= 0.783 Angle : 1.191 3.780 100 Z= 0.598 Chirality : 0.095 0.141 4 Planarity : 0.014 0.047 16 Dihedral : 15.137 55.439 22 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % 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: -4.18 (1.28), residues: 10 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.18 (0.98), residues: 10 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.089 0.026 TYR A 237 Individual atomic B min max mean iso aniso Overall: 3.52 44.26 7.66 1.33 0 82 Protein: 3.52 23.39 6.48 1.33 0 78 Water: 16.92 44.26 30.63 N/A 0 4 Chain A: 3.72 44.26 9.30 N/A 0 42 Chain B: 3.52 37.46 5.93 N/A 0 40 Histogram: Values Number of atoms 3.52 - 7.59 62 7.59 - 11.66 9 11.66 - 15.74 1 15.74 - 19.81 3 19.81 - 23.89 5 23.89 - 27.96 0 27.96 - 32.04 0 32.04 - 36.11 0 36.11 - 40.18 1 40.18 - 44.26 1 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 0.95 - 11.77 A, n_refl.=2791 (all), 9.89 % free)-------------| | | | r_work= 0.1208 r_free= 0.1288 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 3.721460 | | target function (ml) not normalized (work): 9359.470812 | | target function (ml) not normalized (free): 1047.581155 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1216 0.1208 0.1288 n_refl.: 2791 re-set all scales: r(all,work,free)=0.1216 0.1208 0.1288 n_refl.: 2791 remove outliers: r(all,work,free)=0.1224 0.1214 0.1312 n_refl.: 2770 overall B=0.08 to atoms: r(all,work,free)=0.1218 0.1208 0.1306 n_refl.: 2770 bulk-solvent and scaling: r(all,work,free)=0.1110 0.1095 0.1236 n_refl.: 2770 remove outliers: r(all,work,free)=0.1094 0.1079 0.1236 n_refl.: 2763 ======================== 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 11.771-3.014 85.47 90 10 0.1354 33.291 32.191 0.992 1.017 0.000 3.010-2.425 97.09 90 10 0.1182 28.434 28.310 0.993 1.008 0.000 2.414-1.937 93.43 167 18 0.0847 29.902 29.477 0.995 1.007 0.000 1.935-1.553 94.91 318 36 0.1051 18.473 17.841 0.997 1.003 0.000 1.553-1.246 91.70 587 65 0.0989 12.198 11.716 1.001 1.001 0.000 1.245-0.950 74.40 1238 134 0.1102 7.639 7.828 1.007 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0045 b_overall=0.0309 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1079 r_free=0.1236 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1079 r_free=0.1236 ========================= Local real-space refinement ========================= Before: r_work=0.1079 r_free=0.1236 0 residues out of total 4 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0045 After: r_work=0.1079 r_free=0.1236 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 8.038694 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 9.264868 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 0.1611 0.1804 0.0193 0.003 0.7 0.0 0.0 0.0 0 0.125 0.1468 0.1634 0.0166 0.003 0.8 0.0 0.0 0.0 0 0.250 0.1358 0.1501 0.0143 0.003 0.8 0.0 0.0 0.0 0 0.500 0.1264 0.1394 0.0130 0.004 0.9 0.0 0.0 0.0 0 1.000 0.1196 0.1349 0.0153 0.005 0.9 0.0 0.0 0.0 0 2.000 0.1159 0.1331 0.0172 0.006 0.9 0.0 0.0 0.0 0 3.000 0.1137 0.1319 0.0183 0.007 1.0 0.0 0.0 0.0 0 4.000 0.1121 0.1310 0.0189 0.007 1.0 0.0 0.0 0.0 0 5.000 0.1109 0.1301 0.0193 0.008 1.1 0.0 0.0 0.0 0 6.000 0.1097 0.1296 0.0198 0.009 1.1 0.0 0.0 0.0 0 7.000 0.1090 0.1292 0.0202 0.009 1.1 0.0 0.0 0.0 0 8.000 0.1083 0.1289 0.0206 0.010 1.2 0.0 0.0 0.0 0 9.000 0.1076 0.1285 0.0209 0.010 1.2 0.0 0.0 0.0 0 10.000 0.1136 0.1319 0.0183 0.007 1.0 0.0 0.0 0.0 0 4.019 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1076 0.1285 0.0209 0.010 1.2 0.0 0.0 0.0 0 10.000 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.1076 r_free=0.1285 0 residues out of total 4 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.005 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0036 After: r_work=0.1076 r_free=0.1285 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.76 12.85 2.09 0.963 8.475 9.265 0.012 10.76 12.85 2.08 0.962 8.475 0.278 0.012 10.76 12.85 2.08 0.963 8.475 1.158 0.012 10.76 12.85 2.09 0.933 8.473 4.632 0.012 10.68 12.83 2.15 0.976 8.498 9.265 0.011 10.44 12.80 2.36 1.097 8.563 13.897 0.011 10.29 12.78 2.49 1.217 8.609 18.530 0.010 10.17 12.75 2.58 1.300 8.636 23.162 0.010 10.08 12.74 2.66 1.373 8.657 27.795 0.010 10.00 12.73 2.73 1.440 8.674 32.427 0.010 9.95 12.72 2.77 1.492 8.688 37.059 0.009 9.90 12.70 2.80 1.538 8.695 41.692 0.009 9.86 12.70 2.84 1.583 8.708 46.324 0.009 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 41.692 Accepted refinement result: 9.90 12.70 2.80 1.538 8.695 41.692 0.009 Individual atomic B min max mean iso aniso Overall: 3.29 44.66 8.14 1.83 0 82 Protein: 3.29 31.20 6.92 1.83 0 78 Water: 20.06 44.66 31.98 N/A 0 4 Chain A: 3.73 44.66 10.01 N/A 0 42 Chain B: 3.29 39.86 6.18 N/A 0 40 Histogram: Values Number of atoms 3.29 - 7.43 58 7.43 - 11.56 12 11.56 - 15.70 1 15.70 - 19.84 3 19.84 - 23.97 4 23.97 - 28.11 1 28.11 - 32.25 1 32.25 - 36.39 0 36.39 - 40.52 1 40.52 - 44.66 1 =========================== Idealize ADP of riding H ========================== r_work=0.0993 r_free=0.1277 r_work=0.0985 r_free=0.1280 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 0.95 - 11.77 A, n_refl.=2763 (all), 9.88 % free)-------------| | | | r_work= 0.0985 r_free= 0.1280 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.009263 | | target function (ls_wunit_k1) not normalized (work): 23.064542 | | target function (ls_wunit_k1) not normalized (free): 5.219275 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1016 0.0985 0.1280 n_refl.: 2763 re-set all scales: r(all,work,free)=0.1130 0.1109 0.1314 n_refl.: 2763 remove outliers: r(all,work,free)=0.1130 0.1109 0.1314 n_refl.: 2763 overall B=0.05 to atoms: r(all,work,free)=0.1127 0.1106 0.1312 n_refl.: 2763 bulk-solvent and scaling: r(all,work,free)=0.1013 0.0983 0.1277 n_refl.: 2763 remove outliers: r(all,work,free)=0.1013 0.0983 0.1277 n_refl.: 2763 ======================== 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 11.771-3.014 85.47 90 10 0.0935 33.291 32.840 0.987 1.022 0.000 3.010-2.425 97.09 90 10 0.0782 28.434 28.452 0.988 1.014 0.000 2.414-1.937 93.43 167 18 0.0628 29.902 29.765 0.988 1.014 0.000 1.935-1.553 94.91 318 36 0.0841 18.473 17.955 0.990 1.012 0.000 1.553-1.246 91.70 587 65 0.0954 12.198 11.838 0.992 1.012 0.000 1.245-0.950 74.40 1238 134 0.1304 7.639 7.802 0.996 1.011 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0176 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0983 r_free=0.1277 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0983 r_free=0.1277 ========================= Local real-space refinement ========================= Before: r_work=0.0983 r_free=0.1277 0 residues out of total 4 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0051 After: r_work=0.0983 r_free=0.1277 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 8.437449 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 17.270857 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 0.1568 0.1819 0.0251 0.002 0.7 0.0 0.0 0.0 0 0.125 0.1397 0.1641 0.0244 0.003 0.7 0.0 0.0 0.0 0 0.250 0.1251 0.1483 0.0232 0.003 0.7 0.0 0.0 0.0 0 0.500 0.1167 0.1391 0.0224 0.004 0.8 0.0 0.0 0.0 0 1.000 0.1092 0.1341 0.0250 0.004 0.9 0.0 0.0 0.0 0 2.000 0.1056 0.1320 0.0264 0.005 0.9 0.0 0.0 0.0 0 3.000 0.1035 0.1306 0.0271 0.006 1.0 0.0 0.0 0.0 0 4.000 0.1021 0.1296 0.0276 0.006 1.0 0.0 0.0 0.0 0 5.000 0.1010 0.1292 0.0281 0.007 1.0 0.0 0.0 0.0 0 6.000 0.1003 0.1288 0.0285 0.008 1.1 0.0 0.0 0.0 0 7.000 0.0992 0.1284 0.0291 0.008 1.1 0.0 0.0 0.0 0 8.000 0.0989 0.1286 0.0297 0.009 1.1 0.0 0.0 0.0 0 9.000 0.0984 0.1284 0.0299 0.009 1.1 0.0 0.0 0.0 0 10.000 0.1030 0.1302 0.0272 0.006 1.0 0.0 0.0 0.0 0 4.219 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.0992 0.1284 0.0291 0.008 1.1 0.0 0.0 0.0 0 8.000 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.0992 r_free=0.1284 0 residues out of total 4 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0035 After: r_work=0.0992 r_free=0.1284 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.92 12.84 2.91 2.319 9.860 17.271 0.010 9.92 12.84 2.91 2.319 9.860 0.518 0.010 9.92 12.84 2.91 2.319 9.860 2.159 0.010 9.92 12.84 2.91 2.319 9.860 8.635 0.010 9.92 12.84 2.91 2.319 9.860 17.271 0.010 9.93 12.83 2.91 2.319 9.859 25.906 0.010 9.93 12.79 2.86 2.361 9.852 34.542 0.010 9.87 12.86 3.00 2.201 9.937 43.177 0.009 9.80 12.77 2.97 2.399 9.861 51.813 0.009 9.76 12.84 3.08 2.198 9.980 60.448 0.009 9.72 12.84 3.12 2.217 10.000 69.083 0.009 9.67 12.86 3.18 2.246 10.008 77.719 0.009 9.65 12.86 3.20 2.256 10.020 86.354 0.009 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 51.813 Accepted refinement result: 9.80 12.77 2.97 2.399 9.861 51.813 0.009 Individual atomic B min max mean iso aniso Overall: 3.27 44.64 8.19 1.92 0 82 Protein: 3.27 32.19 6.99 1.92 0 78 Water: 19.94 44.64 31.59 N/A 0 4 Chain A: 3.76 44.64 10.04 N/A 0 42 Chain B: 3.27 40.01 6.25 N/A 0 40 Histogram: Values Number of atoms 3.27 - 7.41 59 7.41 - 11.55 11 11.55 - 15.68 1 15.68 - 19.82 2 19.82 - 23.96 5 23.96 - 28.10 1 28.10 - 32.23 1 32.23 - 36.37 0 36.37 - 40.51 1 40.51 - 44.64 1 =========================== Idealize ADP of riding H ========================== r_work=0.0981 r_free=0.1283 r_work=0.0981 r_free=0.1284 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 0.95 - 11.77 A, n_refl.=2763 (all), 9.88 % free)-------------| | | | r_work= 0.0981 r_free= 0.1284 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.009212 | | target function (ls_wunit_k1) not normalized (work): 22.937609 | | target function (ls_wunit_k1) not normalized (free): 5.268045 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1012 0.0981 0.1284 n_refl.: 2763 re-set all scales: r(all,work,free)=0.1127 0.1104 0.1332 n_refl.: 2763 remove outliers: r(all,work,free)=0.1127 0.1104 0.1332 n_refl.: 2763 overall B=0.02 to atoms: r(all,work,free)=0.1126 0.1103 0.1331 n_refl.: 2763 bulk-solvent and scaling: r(all,work,free)=0.1011 0.0979 0.1282 n_refl.: 2763 remove outliers: r(all,work,free)=0.1009 0.0979 0.1268 n_refl.: 2762 ======================== 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 11.771-3.014 85.47 90 10 0.0918 33.291 32.900 0.986 1.024 0.000 3.010-2.425 97.09 90 10 0.0774 28.434 28.591 0.986 1.016 0.000 2.414-1.937 93.43 167 18 0.0609 29.902 29.819 0.987 1.017 0.000 1.935-1.553 94.91 318 36 0.0840 18.473 17.951 0.987 1.016 0.000 1.553-1.246 91.70 587 65 0.0957 12.198 11.845 0.988 1.017 0.000 1.245-0.950 74.35 1238 133 0.1317 7.642 7.805 0.990 1.019 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0046 b_overall=0.0075 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0979 r_free=0.1268 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0979 r_free=0.1268 ========================= Local real-space refinement ========================= Before: r_work=0.0979 r_free=0.1268 0 residues out of total 4 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0050 After: r_work=0.0979 r_free=0.1268 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.885495 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.500915 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 0.1129 0.1361 0.0232 0.003 0.8 0.0 0.0 0.0 0 0.044 0.1030 0.1298 0.0268 0.005 0.9 0.0 0.0 0.0 0 0.133 0.0991 0.1272 0.0281 0.007 0.9 0.0 0.0 0.0 0 0.266 0.0974 0.1264 0.0291 0.008 1.0 0.0 0.0 0.0 0 0.398 0.0963 0.1258 0.0295 0.009 1.1 0.0 0.0 0.0 0 0.531 0.0956 0.1258 0.0302 0.010 1.1 0.0 0.0 0.0 0 0.664 0.0951 0.1249 0.0298 0.010 1.2 0.0 0.0 0.0 0 0.797 0.0947 0.1248 0.0301 0.011 1.2 0.0 0.0 0.0 0 0.930 0.0968 0.1266 0.0297 0.009 1.0 0.0 0.0 0.0 0 0.443 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.0947 0.1248 0.0301 0.011 1.2 0.0 0.0 0.0 0 0.930 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.0947 r_free=0.1248 0 residues out of total 4 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0034 After: r_work=0.0947 r_free=0.1248 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.47 12.48 3.01 2.354 9.870 0.501 1.926 9.53 12.38 2.86 2.337 9.870 0.015 1.926 9.47 12.48 3.01 2.354 9.870 0.063 1.926 9.53 12.27 2.74 2.332 9.866 0.250 1.915 9.80 12.21 2.41 2.329 9.841 0.501 1.911 9.68 12.26 2.58 2.343 9.834 0.751 1.904 9.65 12.28 2.64 2.355 9.826 1.002 1.900 9.63 12.28 2.65 2.366 9.821 1.252 1.897 9.59 12.23 2.64 2.375 9.818 1.503 1.892 9.56 12.18 2.62 2.380 9.818 1.753 1.888 9.54 12.14 2.60 2.384 9.819 2.004 1.886 9.55 12.16 2.62 2.368 9.801 2.254 1.887 9.49 12.17 2.67 2.380 9.808 2.505 1.885 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 2.004 Accepted refinement result: 9.54 12.14 2.60 2.384 9.819 2.004 1.886 Individual atomic B min max mean iso aniso Overall: 3.66 44.60 8.12 1.83 0 82 Protein: 3.66 31.12 6.92 1.83 0 78 Water: 19.85 44.60 31.46 N/A 0 4 Chain A: 3.89 44.60 9.98 N/A 0 42 Chain B: 3.66 39.98 6.16 N/A 0 40 Histogram: Values Number of atoms 3.66 - 7.75 62 7.75 - 11.85 8 11.85 - 15.94 1 15.94 - 20.04 4 20.04 - 24.13 3 24.13 - 28.22 1 28.22 - 32.32 1 32.32 - 36.41 0 36.41 - 40.50 1 40.50 - 44.60 1 =========================== Idealize ADP of riding H ========================== r_work=0.0954 r_free=0.1215 r_work=0.0955 r_free=0.1215 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 0.95 - 11.77 A, n_refl.=2762 (all), 9.85 % free)-------------| | | | r_work= 0.0955 r_free= 0.1215 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 1.886224 | | target function (ml) not normalized (work): 4696.697861 | | target function (ml) not normalized (free): 565.181205 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0982 0.0955 0.1215 n_refl.: 2762 re-set all scales: r(all,work,free)=0.1104 0.1084 0.1285 n_refl.: 2762 remove outliers: r(all,work,free)=0.1104 0.1084 0.1285 n_refl.: 2762 overall B=-0.01 to atoms: r(all,work,free)=0.1104 0.1084 0.1285 n_refl.: 2762 bulk-solvent and scaling: r(all,work,free)=0.0983 0.0957 0.1216 n_refl.: 2762 remove outliers: r(all,work,free)=0.0983 0.0957 0.1216 n_refl.: 2762 ======================== 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 11.771-3.014 85.47 90 10 0.0962 33.291 32.800 0.991 1.019 0.000 3.010-2.425 97.09 90 10 0.0841 28.434 28.497 0.991 1.012 0.000 2.414-1.937 93.43 167 18 0.0689 29.902 29.706 0.990 1.014 0.000 1.935-1.553 94.91 318 36 0.0895 18.473 17.905 0.990 1.015 0.000 1.553-1.246 91.70 587 65 0.1008 12.198 11.755 0.990 1.019 0.000 1.245-0.950 74.35 1238 133 0.1084 7.642 7.783 0.990 1.025 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0167 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0957 r_free=0.1216 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0957 r_free=0.1216 ========================= Local real-space refinement ========================= Before: r_work=0.0957 r_free=0.1216 0 residues out of total 4 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0051 After: r_work=0.0957 r_free=0.1216 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.725536 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.457955 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 0.1151 0.1335 0.0183 0.003 0.8 0.0 0.0 0.0 0 0.036 0.1053 0.1268 0.0215 0.005 0.9 0.0 0.0 0.0 0 0.109 0.1010 0.1237 0.0228 0.007 0.9 0.0 0.0 0.0 0 0.218 0.0989 0.1220 0.0232 0.008 1.0 0.0 0.0 0.0 0 0.326 0.0976 0.1215 0.0239 0.009 1.1 0.0 0.0 0.0 0 0.435 0.0969 0.1212 0.0244 0.010 1.1 0.0 0.0 0.0 0 0.544 0.0961 0.1206 0.0246 0.010 1.2 0.0 0.0 0.0 0 0.653 0.0956 0.1205 0.0248 0.011 1.2 0.0 0.0 0.0 0 0.762 0.0984 0.1218 0.0234 0.008 1.0 0.0 0.0 0.0 0 0.363 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.0956 0.1205 0.0248 0.011 1.2 0.0 0.0 0.0 0 0.762 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.0956 r_free=0.1205 0 residues out of total 4 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.005 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0036 After: r_work=0.0956 r_free=0.1205 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.56 12.05 2.48 2.309 9.761 0.458 1.886 9.56 12.05 2.48 2.309 9.761 0.014 1.886 9.56 12.05 2.48 2.309 9.761 0.057 1.886 9.56 12.05 2.48 2.309 9.761 0.229 1.886 9.57 12.04 2.47 2.308 9.760 0.458 1.886 9.58 12.03 2.45 2.308 9.754 0.687 1.887 9.63 12.01 2.38 2.313 9.735 0.916 1.887 9.61 12.02 2.41 2.316 9.736 1.145 1.886 9.61 12.03 2.42 2.320 9.735 1.374 1.887 9.60 12.03 2.42 2.327 9.733 1.603 1.887 9.58 12.05 2.47 2.347 9.724 1.832 1.885 9.58 12.09 2.51 2.336 9.722 2.061 1.888 9.55 12.08 2.53 2.329 9.742 2.290 1.884 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 0.916 Accepted refinement result: 9.63 12.01 2.38 2.313 9.735 0.916 1.887 Individual atomic B min max mean iso aniso Overall: 3.58 44.59 8.06 1.80 0 82 Protein: 3.58 30.96 6.86 1.80 0 78 Water: 19.83 44.59 31.44 N/A 0 4 Chain A: 3.83 44.59 9.93 N/A 0 42 Chain B: 3.58 39.97 6.11 N/A 0 40 Histogram: Values Number of atoms 3.58 - 7.68 61 7.68 - 11.78 9 11.78 - 15.88 1 15.88 - 19.98 4 19.98 - 24.08 3 24.08 - 28.18 1 28.18 - 32.28 1 32.28 - 36.38 0 36.38 - 40.48 1 40.48 - 44.59 1 =========================== Idealize ADP of riding H ========================== r_work=0.0963 r_free=0.1201 r_work=0.0963 r_free=0.1201 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 0.95 - 11.77 A, n_refl.=2762 (all), 9.85 % free)-------------| | | | r_work= 0.0963 r_free= 0.1201 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 1.887323 | | target function (ml) not normalized (work): 4699.434745 | | target function (ml) not normalized (free): 564.820700 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0987 0.0963 0.1201 n_refl.: 2762 re-set all scales: r(all,work,free)=0.1114 0.1096 0.1276 n_refl.: 2762 remove outliers: r(all,work,free)=0.1114 0.1096 0.1276 n_refl.: 2762 overall B=0.03 to atoms: r(all,work,free)=0.1112 0.1094 0.1274 n_refl.: 2762 bulk-solvent and scaling: r(all,work,free)=0.0984 0.0960 0.1198 n_refl.: 2762 remove outliers: r(all,work,free)=0.0984 0.0960 0.1198 n_refl.: 2762 ======================== 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 11.771-3.014 85.47 90 10 0.0963 33.291 32.784 0.991 1.018 0.000 3.010-2.425 97.09 90 10 0.0843 28.434 28.530 0.992 1.010 0.000 2.414-1.937 93.43 167 18 0.0689 29.902 29.699 0.992 1.011 0.000 1.935-1.553 94.91 318 36 0.0901 18.473 17.911 0.993 1.009 0.000 1.553-1.246 91.70 587 65 0.1005 12.198 11.750 0.995 1.010 0.000 1.245-0.950 74.35 1238 133 0.1091 7.642 7.783 0.998 1.011 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0130 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0960 r_free=0.1198 After: r_work=0.0963 r_free=0.1199 ================================== NQH flips ================================== r_work=0.0963 r_free=0.1199 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0963 r_free=0.1199 ========================= Local real-space refinement ========================= Before: r_work=0.0963 r_free=0.1199 0 residues out of total 4 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.005 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0052 After: r_work=0.0963 r_free=0.1199 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.842145 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.470722 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 0.1153 0.1315 0.0162 0.004 0.9 0.0 0.0 0.0 0 0.042 0.1061 0.1249 0.0187 0.006 0.9 0.0 0.0 0.0 0 0.126 0.1025 0.1227 0.0202 0.007 1.0 0.0 0.0 0.0 0 0.253 0.1007 0.1214 0.0207 0.008 1.1 0.0 0.0 0.0 0 0.379 0.0980 0.1204 0.0224 0.010 1.2 0.0 0.0 0.0 0 0.505 0.0969 0.1200 0.0232 0.011 1.2 0.0 0.0 0.0 0 0.632 0.0963 0.1199 0.0235 0.011 1.2 0.0 0.0 0.0 0 0.758 0.0963 0.1199 0.0236 0.011 1.2 0.0 0.0 0.0 0 0.884 0.0998 0.1209 0.0211 0.009 1.2 0.0 0.0 0.0 0 0.421 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.0963 0.1199 0.0235 0.011 1.2 0.0 0.0 0.0 0 0.758 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.0963 r_free=0.1199 0 residues out of total 4 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.005 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0035 After: r_work=0.0963 r_free=0.1199 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.63 11.99 2.35 2.292 9.739 0.471 1.891 9.63 11.99 2.36 2.292 9.739 0.014 1.891 9.63 11.99 2.36 2.292 9.739 0.059 1.891 9.63 11.99 2.35 2.292 9.739 0.235 1.891 9.63 11.99 2.36 2.292 9.739 0.471 1.891 9.66 11.98 2.33 2.293 9.730 0.706 1.891 9.69 12.00 2.31 2.302 9.711 0.941 1.891 9.69 12.04 2.35 2.308 9.708 1.177 1.891 9.68 12.07 2.39 2.319 9.704 1.412 1.891 9.66 12.08 2.42 2.334 9.699 1.648 1.890 9.66 12.09 2.43 2.332 9.688 1.883 1.892 9.62 12.08 2.46 2.332 9.699 2.118 1.889 9.59 12.10 2.51 2.333 9.716 2.354 1.886 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 0.706 Accepted refinement result: 9.66 11.98 2.33 2.293 9.730 0.706 1.891 Individual atomic B min max mean iso aniso Overall: 3.60 44.62 8.08 1.79 0 82 Protein: 3.60 30.90 6.88 1.79 0 78 Water: 19.85 44.62 31.47 N/A 0 4 Chain A: 3.85 44.62 9.94 N/A 0 42 Chain B: 3.60 40.00 6.13 N/A 0 40 Histogram: Values Number of atoms 3.60 - 7.70 61 7.70 - 11.80 9 11.80 - 15.90 1 15.90 - 20.01 4 20.01 - 24.11 3 24.11 - 28.21 1 28.21 - 32.31 1 32.31 - 36.41 0 36.41 - 40.51 1 40.51 - 44.62 1 =========================== Idealize ADP of riding H ========================== r_work=0.0966 r_free=0.1198 r_work=0.0966 r_free=0.1198 ----------X-ray data---------- |--(resolution: 0.95 - 11.77 A, n_refl.=2762 (all), 9.85 % free)-------------| | | | r_work= 0.0966 r_free= 0.1198 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 1.890955 | | target function (ml) not normalized (work): 4708.476900 | | target function (ml) not normalized (free): 565.169588 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 11.77 - 1.20 0.93 1414 157 0.0920 0.1112 2.2223 2.3963| | 2: 1.20 - 0.95 0.72 1076 115 0.1112 0.1493 1.4555 1.6431| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 11.77 - 1.20 1414 157 0.91 13.36 1.00 1.00 15.88| | 2: 1.20 - 0.95 1076 115 0.93 13.09 0.97 0.96 3.50| |alpha: min = 0.96 max = 1.00 mean = 0.98| |beta: min = 3.50 max = 15.88 mean = 10.53| |figures of merit: min = 0.01 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.51 mean = 13.24| |phase err.(test): min = 0.00 max = 87.83 mean = 14.17| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0990 0.0966 0.1198 n_refl.: 2762 re-set all scales: r(all,work,free)=0.1118 0.1100 0.1277 n_refl.: 2762 remove outliers: r(all,work,free)=0.1118 0.1100 0.1277 n_refl.: 2762 overall B=0.02 to atoms: r(all,work,free)=0.1117 0.1099 0.1276 n_refl.: 2762 bulk-solvent and scaling: r(all,work,free)=0.0989 0.0965 0.1198 n_refl.: 2762 remove outliers: r(all,work,free)=0.0989 0.0965 0.1198 n_refl.: 2762 ======================== 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 11.771-3.014 85.47 90 10 0.0980 33.291 32.770 0.991 1.018 0.000 3.010-2.425 97.09 90 10 0.0852 28.434 28.533 0.991 1.011 0.000 2.414-1.937 93.43 167 18 0.0694 29.902 29.682 0.991 1.012 0.000 1.935-1.553 94.91 318 36 0.0909 18.473 17.917 0.992 1.011 0.000 1.553-1.246 91.70 587 65 0.1009 12.198 11.748 0.993 1.013 0.000 1.245-0.950 74.35 1238 133 0.1092 7.642 7.783 0.995 1.015 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0077 ================= 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 : 0.1208 0.1288 0.014 1.191 3.5 44.3 7.7 12 0.000 1_bss: 0.1079 0.1236 0.014 1.191 3.6 44.3 7.7 12 0.000 1_settarget: 0.1079 0.1236 0.014 1.191 3.6 44.3 7.7 12 0.000 1_nqh: 0.1079 0.1236 0.014 1.191 3.6 44.3 7.7 12 0.000 1_realsrl: 0.1079 0.1236 0.014 1.191 3.6 44.3 7.7 12 0.000 1_weight: 0.1079 0.1236 0.014 1.191 3.6 44.3 7.7 12 0.000 1_xyzrec: 0.1076 0.1285 0.010 1.205 3.6 44.3 7.7 12 0.086 1_realsrl2: 0.1076 0.1285 0.010 1.205 3.6 44.3 7.7 12 0.086 1_adp: 0.0993 0.1277 0.010 1.205 3.3 44.7 8.1 12 0.086 1_regHadp: 0.0985 0.1280 0.010 1.205 3.3 44.7 8.1 12 0.086 2_bss: 0.0983 0.1277 0.010 1.205 3.3 44.7 8.2 12 0.086 2_settarget: 0.0983 0.1277 0.010 1.205 3.3 44.7 8.2 12 0.086 2_updatecdl: 0.0983 0.1277 0.010 1.200 3.3 44.7 8.2 12 0.086 2_nqh: 0.0983 0.1277 0.010 1.200 3.3 44.7 8.2 12 0.086 2_realsrl: 0.0983 0.1277 0.010 1.200 3.3 44.7 8.2 12 0.086 2_weight: 0.0983 0.1277 0.010 1.200 3.3 44.7 8.2 12 0.086 2_xyzrec: 0.0992 0.1284 0.008 1.075 3.3 44.7 8.2 12 0.090 2_realsrl2: 0.0992 0.1284 0.008 1.075 3.3 44.7 8.2 12 0.090 2_adp: 0.0981 0.1283 0.008 1.075 3.3 44.6 8.2 12 0.090 2_regHadp: 0.0981 0.1284 0.008 1.075 3.3 44.6 8.2 12 0.090 3_bss: 0.0979 0.1268 0.008 1.075 3.3 44.7 8.2 12 0.090 3_settarget: 0.0979 0.1268 0.008 1.075 3.3 44.7 8.2 12 0.090 3_updatecdl: 0.0979 0.1268 0.008 1.075 3.3 44.7 8.2 12 0.090 3_nqh: 0.0979 0.1268 0.008 1.075 3.3 44.7 8.2 12 0.090 3_realsrl: 0.0979 0.1268 0.008 1.075 3.3 44.7 8.2 12 0.090 3_weight: 0.0979 0.1268 0.008 1.075 3.3 44.7 8.2 12 0.090 3_xyzrec: 0.0947 0.1248 0.011 1.197 3.3 44.7 8.2 12 0.084 3_realsrl2: 0.0947 0.1248 0.011 1.197 3.3 44.7 8.2 12 0.084 3_adp: 0.0954 0.1215 0.011 1.197 3.7 44.6 8.1 12 0.084 3_regHadp: 0.0955 0.1215 0.011 1.197 3.7 44.6 8.1 12 0.084 4_bss: 0.0957 0.1216 0.011 1.197 3.7 44.6 8.1 12 0.084 4_settarget: 0.0957 0.1216 0.011 1.197 3.7 44.6 8.1 12 0.084 4_updatecdl: 0.0957 0.1216 0.011 1.197 3.7 44.6 8.1 12 0.084 4_nqh: 0.0957 0.1216 0.011 1.197 3.7 44.6 8.1 12 0.084 4_realsrl: 0.0957 0.1216 0.011 1.197 3.7 44.6 8.1 12 0.084 4_weight: 0.0957 0.1216 0.011 1.197 3.7 44.6 8.1 12 0.084 4_xyzrec: 0.0956 0.1205 0.011 1.187 3.7 44.6 8.1 12 0.084 4_realsrl2: 0.0956 0.1205 0.011 1.187 3.7 44.6 8.1 12 0.084 4_adp: 0.0963 0.1201 0.011 1.187 3.6 44.6 8.1 12 0.084 4_regHadp: 0.0963 0.1201 0.011 1.187 3.6 44.6 8.1 12 0.084 5_bss: 0.0960 0.1198 0.011 1.187 3.6 44.6 8.1 12 0.084 5_settarget: 0.0960 0.1198 0.011 1.187 3.6 44.6 8.1 12 0.084 5_updatecdl: 0.0960 0.1198 0.011 1.191 3.6 44.6 8.1 12 0.084 5_setrh: 0.0963 0.1199 0.011 1.191 3.6 44.6 8.1 12 0.084 5_nqh: 0.0963 0.1199 0.011 1.191 3.6 44.6 8.1 12 0.084 5_realsrl: 0.0963 0.1199 0.011 1.191 3.6 44.6 8.1 12 0.084 5_weight: 0.0963 0.1199 0.011 1.191 3.6 44.6 8.1 12 0.084 5_xyzrec: 0.0963 0.1199 0.011 1.199 3.6 44.6 8.1 12 0.084 5_realsrl2: 0.0963 0.1199 0.011 1.199 3.6 44.6 8.1 12 0.084 5_adp: 0.0966 0.1198 0.011 1.199 3.6 44.6 8.1 12 0.084 5_regHadp: 0.0966 0.1198 0.011 1.199 3.6 44.6 8.1 12 0.084 end: 0.0965 0.1198 0.011 1.199 3.6 44.6 8.1 12 0.084 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/highres/finalised/5ZGL_complete_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/highres/finalised/5ZGL_complete_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 0.1300 Refinement macro-cycles (run) : 74.4600 Write final files (write_after_run_outputs) : 4.5200 Total : 79.1100 Total CPU time: 86.01 seconds =========================== phenix.refine: finished =========================== # Date 2024-04-10 Time 16:01:15 PDT -0700 (1712790075.12 s) Start R-work = 0.1079, R-free = 0.1236 Final R-work = 0.0965, R-free = 0.1198 =============================================================================== Job complete usr+sys time: 88.04 seconds wall clock time: 119.25 seconds