Starting phenix.refine on Mon May 20 17:16:28 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/1u87.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1u87/1u87.mtz Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- optimize_xyz=true optimize_adp=true main.number_of_mac=3 main.max_number_of_iterations=100 main.nproc=20 nonbonded_weight=100 modify_start_model.modify.selection=element H modify_start_model.modify.occupancies.set=1 strategy=individual_sites+individual_adp ramachandran_plot_restraints.enabled=False secondary_structure.enabled=False main.nqh_flips=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1u87/1u87.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1u87/1u87.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/1u87.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/1u87.pdb" } 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 { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls occupancies group_anomalous \ den } main { nqh_flips = False max_number_of_iterations = 100 nproc = 20 } modify_start_model { modify { selection = element H occupancies { set = 1 } } } pdb_interpretation { nonbonded_weight = 100 } 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: 3506 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 3471 Classifications: {'peptide': 209} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 197} Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'GSH': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.79, per 1000 atoms: 0.23 Number of scatterers: 3506 At special positions: 0 Unit cell: (123.05, 123.05, 72.51, 90, 90, 120) Space group: P 63 2 2 (No. 182) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 O 316 8.00 N 282 7.00 C 1138 6.00 H 1756 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: 0.75 Conformation dependent library (CDL) restraints added in 164.5 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 396 Time building geometry restraints manager: 0.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.15: 1751 1.15 - 1.33: 431 1.33 - 1.50: 638 1.50 - 1.68: 707 1.68 - 1.85: 23 Bond restraints: 3550 Sorted by residual: bond pdb=" N3 GSH A 500 " pdb=" HN3 GSH A 500 " ideal model delta sigma weight residual 0.860 1.020 -0.160 1.00e-02 1.00e+04 2.57e+02 bond pdb=" N2 GSH A 500 " pdb=" HN2 GSH A 500 " ideal model delta sigma weight residual 0.860 1.020 -0.160 1.10e-02 8.26e+03 2.12e+02 bond pdb=" CA2 GSH A 500 " pdb=" HA2 GSH A 500 " ideal model delta sigma weight residual 0.970 1.090 -0.120 1.00e-02 1.00e+04 1.45e+02 bond pdb=" CB2 GSH A 500 " pdb="HB23 GSH A 500 " ideal model delta sigma weight residual 0.970 1.090 -0.120 1.00e-02 1.00e+04 1.45e+02 bond pdb=" CA1 GSH A 500 " pdb=" HA1 GSH A 500 " ideal model delta sigma weight residual 0.970 1.090 -0.120 1.00e-02 1.00e+04 1.44e+02 ... (remaining 3545 not shown) Histogram of bond angle deviations from ideal: 99.31 - 107.06: 254 107.06 - 114.81: 4243 114.81 - 122.56: 1410 122.56 - 130.32: 522 130.32 - 138.07: 15 Bond angle restraints: 6444 Sorted by residual: angle pdb=" N TYR A 164 " pdb=" CA TYR A 164 " pdb=" C TYR A 164 " ideal model delta sigma weight residual 114.31 102.34 11.97 1.29e+00 6.01e-01 8.61e+01 angle pdb="HN11 GSH A 500 " pdb=" N1 GSH A 500 " pdb="HN12 GSH A 500 " ideal model delta sigma weight residual 111.04 138.07 -27.03 3.00e+00 1.11e-01 8.12e+01 angle pdb=" N ASP A 62 " pdb=" CA ASP A 62 " pdb=" C ASP A 62 " ideal model delta sigma weight residual 114.04 103.69 10.35 1.24e+00 6.50e-01 6.97e+01 angle pdb=" CA2 GSH A 500 " pdb=" C2 GSH A 500 " pdb=" O2 GSH A 500 " ideal model delta sigma weight residual 120.61 109.21 11.40 1.39e+00 5.18e-01 6.72e+01 angle pdb=" N GLY A 61 " pdb=" CA GLY A 61 " pdb=" C GLY A 61 " ideal model delta sigma weight residual 115.47 104.89 10.58 1.31e+00 5.83e-01 6.53e+01 ... (remaining 6439 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.48: 1414 13.48 - 26.97: 129 26.97 - 40.45: 71 40.45 - 53.94: 33 53.94 - 67.42: 25 Dihedral angle restraints: 1672 sinusoidal: 918 harmonic: 754 Sorted by residual: dihedral pdb=" CA ASP A 190 " pdb=" CB ASP A 190 " pdb=" CG ASP A 190 " pdb=" OD1 ASP A 190 " ideal model delta sinusoidal sigma weight residual -30.00 -89.11 59.11 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" N HIS A 150 " pdb=" C HIS A 150 " pdb=" CA HIS A 150 " pdb=" CB HIS A 150 " ideal model delta harmonic sigma weight residual 122.80 130.92 -8.12 0 2.50e+00 1.60e-01 1.06e+01 dihedral pdb=" CB MET A 132 " pdb=" CG MET A 132 " pdb=" SD MET A 132 " pdb=" CE MET A 132 " ideal model delta sinusoidal sigma weight residual 180.00 120.60 59.40 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 1669 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 1.084: 254 1.084 - 2.167: 0 2.167 - 3.250: 0 3.250 - 4.334: 0 4.334 - 5.417: 1 Chirality restraints: 255 Sorted by residual: chirality pdb=" CA1 GSH A 500 " pdb=" CB1 GSH A 500 " pdb=" C1 GSH A 500 " pdb=" N1 GSH A 500 " both_signs ideal model delta sigma weight residual False -2.66 2.76 -5.42 2.00e-01 2.50e+01 7.34e+02 chirality pdb=" CA HIS A 150 " pdb=" N HIS A 150 " pdb=" C HIS A 150 " pdb=" CB HIS A 150 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.25e+00 chirality pdb=" CA ILE A 186 " pdb=" N ILE A 186 " pdb=" C ILE A 186 " pdb=" CB ILE A 186 " both_signs ideal model delta sigma weight residual False 2.43 2.75 -0.31 2.00e-01 2.50e+01 2.44e+00 ... (remaining 252 not shown) Planarity restraints: 502 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 GSH A 500 " 0.313 2.00e-02 2.50e+03 2.24e-01 7.49e+02 pdb=" CA2 GSH A 500 " 0.101 2.00e-02 2.50e+03 pdb=" CA3 GSH A 500 " 0.137 2.00e-02 2.50e+03 pdb=" N3 GSH A 500 " 0.034 2.00e-02 2.50e+03 pdb=" O2 GSH A 500 " -0.303 2.00e-02 2.50e+03 pdb=" HN3 GSH A 500 " -0.283 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 156 " -0.131 2.00e-02 2.50e+03 5.15e-02 7.95e+01 pdb=" CG TYR A 156 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR A 156 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR A 156 " 0.030 2.00e-02 2.50e+03 pdb=" CE1 TYR A 156 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR A 156 " 0.013 2.00e-02 2.50e+03 pdb=" CZ TYR A 156 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 156 " -0.089 2.00e-02 2.50e+03 pdb=" HD1 TYR A 156 " 0.040 2.00e-02 2.50e+03 pdb=" HD2 TYR A 156 " 0.047 2.00e-02 2.50e+03 pdb=" HE1 TYR A 156 " 0.015 2.00e-02 2.50e+03 pdb=" HE2 TYR A 156 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 201 " 0.100 2.00e-02 2.50e+03 3.02e-02 3.64e+01 pdb=" CG TRP A 201 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TRP A 201 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP A 201 " -0.019 2.00e-02 2.50e+03 pdb=" NE1 TRP A 201 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP A 201 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 201 " -0.020 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 201 " 0.010 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 201 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 201 " 0.009 2.00e-02 2.50e+03 pdb=" HD1 TRP A 201 " -0.029 2.00e-02 2.50e+03 pdb=" HE1 TRP A 201 " 0.002 2.00e-02 2.50e+03 pdb=" HE3 TRP A 201 " -0.032 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 201 " 0.021 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 201 " -0.007 2.00e-02 2.50e+03 pdb=" HH2 TRP A 201 " 0.021 2.00e-02 2.50e+03 ... (remaining 499 not shown) Histogram of nonbonded interaction distances: 1.18 - 1.87: 142 1.87 - 2.55: 3363 2.55 - 3.23: 10953 3.23 - 3.92: 14318 3.92 - 4.60: 22275 Nonbonded interactions: 51051 Sorted by model distance: nonbonded pdb="HG13 ILE A 109 " pdb=" H ALA A 110 " model vdw 1.183 2.270 nonbonded pdb="HH12 ARG A 103 " pdb="HE21 GLN A 204 " model vdw 1.249 2.100 nonbonded pdb=" HD2 PHE A 122 " pdb=" HE1 MET A 165 " model vdw 1.275 2.270 nonbonded pdb=" HA PHE A 7 " pdb="HD22 LEU A 55 " model vdw 1.279 2.440 nonbonded pdb=" HB3 GLU A 30 " pdb="HD11 LEU A 32 " model vdw 1.331 2.440 ... (remaining 51046 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 14 15.91 1 O 316 7.97 1 N 282 6.97 1 C 1138 5.97 1 H 1756 1.00 1 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 ===================== Setting occupancies to: 1.000: selected atoms: 1756 of 3506 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 3506 n_use_u_iso = 3506 n_use_u_aniso = 0 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 = 3506 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (3506 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 3506 aniso = 0) group_adp = False (0 atoms in 0 groups) tls = False (0 atoms in 0 groups) occupancies = False (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 { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls occupancies group_anomalous den } main { nqh_flips = False max_number_of_iterations = 100 nproc = 20 } modify_start_model { modify { selection = element H occupancies { set = 1 } } } hydrogens { refine = individual *riding Auto } pdb_interpretation { nonbonded_weight = 100 } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } output { prefix = "1u87_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1756 occupancy sum: 1756.00 (% of total atoms 50.11) Rotatable: count: 466 occupancy sum: 466.00 (% of total atoms 13.30) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.50 - 29.97 A, n_refl.=4185 (all), 10.01 % free)-------------| | | | r_work= 0.3292 r_free= 0.3504 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ml) (work): 4.035015 | | target function (ml) not normalized (work): 15195.866676 | | target function (ml) not normalized (free): 1683.480726 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 29.97 - 5.04 0.97 1353 151 0.3689 0.3748 4.5706 4.5071| | 2: 5.04 - 4.01 0.96 1235 137 0.2801 0.3157 3.9206 3.9093| | 3: 4.00 - 3.50 0.92 1178 131 0.3184 0.3512 3.5398 3.5675| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 29.97 - 5.04 1353 151 0.58 43.57 0.90 0.05 1455.33| | 2: 5.04 - 4.01 1235 137 0.71 33.64 1.20 0.06 636.30| | 3: 4.00 - 3.50 1178 131 0.85 21.79 1.27 0.07 174.86| |alpha: min = 0.05 max = 0.07 mean = 0.06| |beta: min = 174.86 max = 1455.33 mean = 786.21| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 89.84 mean = 33.50| |phase err.(test): min = 0.00 max = 88.64 mean = 34.34| |-----------------------------------------------------------------------------| ----------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 : 0.011 0.121 1794 Z= 0.666 Angle : 1.713 19.034 2419 Z= 1.088 Chirality : 0.354 5.417 255 Planarity : 0.012 0.154 305 Dihedral : 17.263 67.421 697 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 38.80 Ramachandran Plot: Outliers : 8.70 % Allowed : 20.29 % Favored : 71.01 % Rotamer: Outliers : 9.57 % Allowed : 6.91 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: -6.40 (0.37), residues: 207 helix: -4.33 (0.27), residues: 104 sheet: None (None), residues: 0 loop : -4.22 (0.45), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 103 TYR 0.107 0.013 TYR A 156 PHE 0.039 0.010 PHE A 179 TRP 0.068 0.013 TRP A 201 HIS 0.001 0.001 HIS A 139 Individual atomic B min max mean iso aniso Overall: 15.03 98.11 43.96 1.66 1750 0 Protein: 15.03 98.11 43.87 1.66 1730 0 Other: 41.47 63.03 52.15 N/A 20 0 Chain A: 15.03 98.11 43.96 N/A 1750 0 Histogram: Values Number of atoms 15.03 - 23.34 283 23.34 - 31.65 247 31.65 - 39.95 311 39.95 - 48.26 195 48.26 - 56.57 287 56.57 - 64.88 141 64.88 - 73.19 115 73.19 - 81.49 109 81.49 - 89.80 54 89.80 - 98.11 8 |-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 3 ************************* |--(resolution: 3.50 - 29.97 A, n_refl.=4185 (all), 10.01 % free)-------------| | | | r_work= 0.3292 r_free= 0.3504 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ml) (work): 4.035015 | | target function (ml) not normalized (work): 15195.866676 | | target function (ml) not normalized (free): 1683.480726 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3311 0.3292 0.3504 n_refl.: 4185 re-set all scales: r(all,work,free)=0.3311 0.3292 0.3504 n_refl.: 4185 remove outliers: r(all,work,free)=0.3322 0.3304 0.3504 n_refl.: 4182 overall B=13.94 to atoms: r(all,work,free)=0.3719 0.3690 0.3993 n_refl.: 4182 bulk-solvent and scaling: r(all,work,free)=0.2220 0.2217 0.2255 n_refl.: 4182 remove outliers: r(all,work,free)=0.2220 0.2217 0.2255 n_refl.: 4182 ======================== 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 29.974-12.976 97.12 91 10 0.2919 1104.388 1001.047 1.273 0.998 0.352 12.881-10.207 97.06 88 11 0.2180 1533.577 1475.189 1.351 0.999 0.334 10.181-8.045 98.52 181 19 0.1853 1232.177 1220.067 1.249 0.998 0.325 8.023-6.324 96.77 350 40 0.2505 756.993 729.392 1.028 0.996 0.298 6.311-4.969 96.87 696 77 0.2091 690.006 669.251 0.952 0.990 0.241 4.967-3.908 95.56 1374 153 0.2087 652.071 626.849 1.012 0.981 0.158 3.907-3.500 91.76 983 109 0.2468 480.180 456.614 1.052 0.972 0.077 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0610 b_overall=3.6244 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 14.623866 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.257357 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 5.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1848 0.2432 0.0584 0.012 1.4 23.1 4.8 8.0 0 7.312 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 18.48 24.32 5.84 1.179 57.497 0.257 0.040 18.52 24.38 5.85 2.559 57.667 0.008 0.040 18.29 24.34 6.06 2.586 57.695 0.032 0.040 17.71 24.25 6.54 2.989 57.772 0.129 0.037 17.05 24.24 7.19 5.213 58.185 0.257 0.035 16.83 24.23 7.40 5.908 58.335 0.386 0.034 16.70 24.25 7.55 6.479 58.500 0.515 0.033 16.52 24.21 7.69 7.330 58.778 0.643 0.033 16.44 24.20 7.76 7.755 58.892 0.772 0.033 16.39 24.19 7.80 8.115 58.991 0.901 0.032 16.34 24.19 7.85 8.453 59.083 1.029 0.032 16.30 24.20 7.90 8.793 59.179 1.158 0.032 16.28 24.22 7.95 8.982 59.228 1.287 0.032 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.008 Accepted refinement result: 18.52 24.38 5.85 2.559 57.667 0.008 0.040 Individual atomic B min max mean iso aniso Overall: 30.52 111.11 58.24 1.75 1750 0 Protein: 30.52 111.11 58.19 1.75 1730 0 Other: 50.41 75.14 62.46 N/A 20 0 Chain A: 30.52 111.11 58.24 N/A 1750 0 Histogram: Values Number of atoms 30.52 - 38.58 246 38.58 - 46.64 280 46.64 - 54.70 340 54.70 - 62.76 243 62.76 - 70.81 237 70.81 - 78.87 132 78.87 - 86.93 124 86.93 - 94.99 91 94.99 - 103.05 51 103.05 - 111.11 6 =========================== Idealize ADP of riding H ========================== r_work=0.1852 r_free=0.2438 r_work=0.1854 r_free=0.2430 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.50 - 29.97 A, n_refl.=4182 (all), 10.02 % free)-------------| | | | r_work= 0.1854 r_free= 0.2430 coordinate error (max.-lik. estimate): 0.39 A | | | | normalized target function (ls_wunit_k1) (work): 0.040449 | | target function (ls_wunit_k1) not normalized (work): 152.207848 | | target function (ls_wunit_k1) not normalized (free): 30.363713 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1912 0.1854 0.2430 n_refl.: 4182 re-set all scales: r(all,work,free)=0.3598 0.3542 0.4072 n_refl.: 4182 remove outliers: r(all,work,free)=0.3598 0.3542 0.4072 n_refl.: 4182 overall B=0.00 to atoms: r(all,work,free)=0.3598 0.3542 0.4072 n_refl.: 4182 bulk-solvent and scaling: r(all,work,free)=0.1898 0.1837 0.2438 n_refl.: 4182 remove outliers: r(all,work,free)=0.1898 0.1837 0.2438 n_refl.: 4182 ======================== 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 29.974-12.976 97.12 91 10 0.2388 687.015 649.986 1.282 0.989 0.352 12.881-10.207 97.06 88 11 0.1576 954.004 923.253 1.375 0.990 0.331 10.181-8.045 98.52 181 19 0.1411 766.510 766.531 1.296 0.990 0.323 8.023-6.324 96.77 350 40 0.2026 470.908 464.329 1.100 0.989 0.320 6.311-4.969 96.87 696 77 0.1797 429.237 420.200 0.981 0.984 0.240 4.967-3.908 95.56 1374 153 0.1717 405.639 397.819 1.021 0.977 0.140 3.907-3.500 91.76 983 109 0.2164 298.709 286.034 1.063 0.971 0.051 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=5.4616 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 3.466952 wxc_scale = 0.103 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.051976 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 5.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2090 0.2491 0.0401 0.003 0.8 5.1 1.4 5.3 0 0.036 0.2034 0.2473 0.0438 0.003 0.8 5.7 2.4 5.3 0 0.107 0.1973 0.2455 0.0482 0.004 0.9 6.0 2.4 5.3 0 0.215 0.1945 0.2468 0.0523 0.005 0.9 6.6 2.4 6.4 0 0.322 0.1915 0.2450 0.0535 0.006 1.0 8.6 2.4 6.4 0 0.429 0.1889 0.2447 0.0558 0.007 1.1 10.8 1.9 7.4 0 0.536 0.1873 0.2446 0.0573 0.008 1.1 12.3 2.4 9.0 0 0.644 0.1864 0.2454 0.0590 0.008 1.2 14.0 3.4 9.0 0 0.751 0.1941 0.2468 0.0528 0.005 0.9 7.4 2.4 6.4 0 0.358 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2090 0.2491 0.0401 0.003 0.8 5.1 1.4 5.3 0 0.036 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 20.90 24.91 4.01 8.565 63.652 0.052 6.099 21.51 25.50 3.98 9.330 64.559 0.002 6.121 20.62 25.17 4.55 9.170 64.103 0.006 6.091 19.38 24.60 5.22 9.409 64.141 0.026 6.048 18.96 24.43 5.47 10.088 64.494 0.052 6.033 18.78 24.39 5.61 10.563 64.709 0.078 6.027 18.67 24.37 5.71 10.983 64.897 0.104 6.024 18.56 24.35 5.79 11.488 65.119 0.130 6.021 18.49 24.35 5.85 11.847 65.265 0.156 6.019 18.44 24.34 5.89 12.118 65.377 0.182 6.017 18.39 24.33 5.93 12.473 65.519 0.208 6.016 18.37 24.32 5.95 12.650 65.591 0.234 6.015 18.33 24.31 5.98 12.948 65.705 0.260 6.014 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.260 Accepted refinement result: 18.33 24.31 5.98 12.948 65.705 0.260 6.014 Individual atomic B min max mean iso aniso Overall: 25.52 149.78 62.35 12.10 1750 0 Protein: 25.52 149.78 62.34 12.13 1730 0 Other: 45.86 90.62 63.53 N/A 20 0 Chain A: 25.52 149.78 62.35 N/A 1750 0 Histogram: Values Number of atoms 25.52 - 37.95 220 37.95 - 50.37 387 50.37 - 62.80 408 62.80 - 75.23 231 75.23 - 87.65 224 87.65 - 100.08 174 100.08 - 112.50 76 112.50 - 124.93 27 124.93 - 137.35 2 137.35 - 149.78 1 =========================== Idealize ADP of riding H ========================== r_work=0.1833 r_free=0.2431 r_work=0.1818 r_free=0.2438 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.50 - 29.97 A, n_refl.=4182 (all), 10.02 % free)-------------| | | | r_work= 0.1818 r_free= 0.2438 coordinate error (max.-lik. estimate): 0.40 A | | | | normalized target function (ml) (work): 6.011145 | | target function (ml) not normalized (work): 22619.939123 | | target function (ml) not normalized (free): 2594.727998 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1880 0.1818 0.2438 n_refl.: 4182 re-set all scales: r(all,work,free)=0.3624 0.3568 0.4101 n_refl.: 4182 remove outliers: r(all,work,free)=0.3624 0.3568 0.4101 n_refl.: 4182 overall B=1.41 to atoms: r(all,work,free)=0.3673 0.3617 0.4150 n_refl.: 4182 bulk-solvent and scaling: r(all,work,free)=0.1868 0.1806 0.2415 n_refl.: 4182 remove outliers: r(all,work,free)=0.1868 0.1806 0.2415 n_refl.: 4182 ======================== 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 29.974-12.976 97.12 91 10 0.2468 687.015 634.673 1.259 1.020 0.358 12.881-10.207 97.06 88 11 0.1572 954.004 935.801 1.343 1.016 0.339 10.181-8.045 98.52 181 19 0.1476 766.510 766.667 1.260 1.011 0.329 8.023-6.324 96.77 350 40 0.2224 470.908 460.824 1.102 1.003 0.308 6.311-4.969 96.87 696 77 0.1917 429.237 416.420 0.960 0.986 0.227 4.967-3.908 95.56 1374 153 0.1592 405.639 393.109 1.021 0.961 0.137 3.907-3.500 91.76 983 109 0.1945 298.709 283.612 1.090 0.938 0.058 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=6.3658 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1806 r_free=0.2415 After: r_work=0.1806 r_free=0.2413 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 4.222567 wxc_scale = 0.023 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.049611 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 5.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1806 0.2413 0.0607 0.003 0.9 5.1 1.4 5.3 0 0.010 0.1806 0.2413 0.0607 0.003 0.9 5.1 1.4 5.3 0 0.029 0.1806 0.2413 0.0607 0.003 0.9 5.1 1.4 5.3 0 0.057 0.1806 0.2413 0.0607 0.003 0.9 5.1 1.4 5.3 0 0.086 0.1806 0.2413 0.0607 0.003 0.9 5.1 1.4 5.3 0 0.115 0.1806 0.2413 0.0607 0.003 0.9 5.1 1.4 5.3 0 0.144 0.1806 0.2413 0.0607 0.003 0.9 5.1 1.4 5.3 0 0.172 0.1806 0.2413 0.0607 0.003 0.9 5.1 1.4 5.3 0 0.201 0.1806 0.2413 0.0607 0.003 0.9 5.1 1.4 5.3 0 0.096 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1806 0.2413 0.0607 0.003 0.9 5.1 1.4 5.3 0 0.010 0.1806 0.2413 0.0607 0.003 0.9 5.1 1.4 5.3 0 0.029 0.1806 0.2413 0.0607 0.003 0.9 5.1 1.4 5.3 0 0.057 0.1806 0.2413 0.0607 0.003 0.9 5.1 1.4 5.3 0 0.086 0.1806 0.2413 0.0607 0.003 0.9 5.1 1.4 5.3 0 0.115 0.1806 0.2413 0.0607 0.003 0.9 5.1 1.4 5.3 0 0.144 0.1806 0.2413 0.0607 0.003 0.9 5.1 1.4 5.3 0 0.172 0.1806 0.2413 0.0607 0.003 0.9 5.1 1.4 5.3 0 0.201 0.1806 0.2413 0.0607 0.003 0.9 5.1 1.4 5.3 0 0.096 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 18.06 24.13 6.07 12.665 69.941 0.050 6.006 20.98 24.97 3.99 11.051 74.340 0.001 6.074 20.19 24.63 4.44 10.761 73.349 0.006 6.057 18.78 24.14 5.37 11.690 70.982 0.025 6.019 18.06 24.00 5.94 12.247 69.784 0.050 6.004 17.88 24.02 6.14 12.612 69.664 0.074 6.002 17.76 23.99 6.24 12.909 69.694 0.099 5.999 17.66 24.01 6.35 13.153 69.705 0.124 5.998 17.59 24.07 6.48 13.400 69.785 0.149 5.997 17.54 24.12 6.58 13.608 69.845 0.174 5.997 17.50 24.17 6.67 13.801 69.918 0.198 5.997 17.46 24.19 6.73 13.974 69.982 0.223 5.996 17.43 24.22 6.78 14.138 70.051 0.248 5.996 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.050 Accepted refinement result: 18.06 24.00 5.94 12.247 69.784 0.050 6.004 Individual atomic B min max mean iso aniso Overall: 23.81 146.19 63.45 9.25 1750 0 Protein: 23.81 146.19 63.45 9.23 1730 0 Other: 42.27 87.03 63.63 N/A 20 0 Chain A: 23.81 146.19 63.45 N/A 1750 0 Histogram: Values Number of atoms 23.81 - 36.05 100 36.05 - 48.29 350 48.29 - 60.53 476 60.53 - 72.77 281 72.77 - 85.00 227 85.00 - 97.24 185 97.24 - 109.48 87 109.48 - 121.72 37 121.72 - 133.96 6 133.96 - 146.19 1 =========================== Idealize ADP of riding H ========================== r_work=0.1806 r_free=0.2400 r_work=0.1810 r_free=0.2402 ----------X-ray data---------- |--(resolution: 3.50 - 29.97 A, n_refl.=4182 (all), 10.02 % free)-------------| | | | r_work= 0.1810 r_free= 0.2402 coordinate error (max.-lik. estimate): 0.37 A | | | | normalized target function (ml) (work): 6.005114 | | target function (ml) not normalized (work): 22597.243374 | | target function (ml) not normalized (free): 2590.622571 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 29.97 - 5.04 0.97 1352 151 0.1909 0.2297 6.2626 6.4043| | 2: 5.04 - 4.01 0.96 1235 137 0.1614 0.2317 5.9539 6.1214| | 3: 4.00 - 3.50 0.92 1176 131 0.1890 0.2721 5.763 5.9919| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 29.97 - 5.04 1352 151 0.84 21.07 1.00 0.99 44132.75| | 2: 5.04 - 4.01 1235 137 0.85 21.25 1.00 0.98 32109.61| | 3: 4.00 - 3.50 1176 131 0.82 24.81 1.01 0.95 22343.83| |alpha: min = 0.95 max = 0.99 mean = 0.97| |beta: min = 22343.83 max = 44132.75 mean = 33377.41| |figures of merit: min = 0.01 max = 1.00 mean = 0.83| |phase err.(work): min = 0.00 max = 89.30 mean = 22.30| |phase err.(test): min = 0.00 max = 86.11 mean = 21.96| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1869 0.1810 0.2402 n_refl.: 4182 re-set all scales: r(all,work,free)=0.3694 0.3640 0.4166 n_refl.: 4182 remove outliers: r(all,work,free)=0.3694 0.3640 0.4166 n_refl.: 4182 overall B=0.00 to atoms: r(all,work,free)=0.3694 0.3640 0.4166 n_refl.: 4182 bulk-solvent and scaling: r(all,work,free)=0.1869 0.1809 0.2405 n_refl.: 4182 remove outliers: r(all,work,free)=0.1869 0.1809 0.2405 n_refl.: 4182 ======================== 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 29.974-12.976 97.12 91 10 0.2455 687.015 637.479 1.223 1.019 0.353 12.881-10.207 97.06 88 11 0.1568 954.004 935.651 1.344 1.016 0.340 10.181-8.045 98.52 181 19 0.1469 766.510 767.275 1.268 1.011 0.340 8.023-6.324 96.77 350 40 0.2203 470.908 462.059 1.104 1.002 0.310 6.311-4.969 96.87 696 77 0.1941 429.237 416.155 0.967 0.986 0.240 4.967-3.908 95.56 1374 153 0.1598 405.639 393.541 1.022 0.961 0.140 3.907-3.500 91.76 983 109 0.1943 298.709 283.631 1.091 0.938 0.061 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=6.2306 ================= 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) ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.3292 0.3504 0.011 1.713 15.0 98.1 44.0 0 0.000 1_bss: 0.2217 0.2255 0.011 1.713 29.0 112.0 57.9 0 0.000 1_settarget: 0.2217 0.2255 0.011 1.713 29.0 112.0 57.9 0 0.000 1_weight: 0.2217 0.2255 0.011 1.713 29.0 112.0 57.9 0 0.000 1_xyzrec: 0.1848 0.2432 0.012 1.417 29.0 112.0 57.9 0 0.304 1_adp: 0.1852 0.2438 0.012 1.417 30.5 111.1 58.2 0 0.304 1_regHadp: 0.1854 0.2430 0.012 1.417 30.5 111.1 58.2 0 0.304 2_bss: 0.1837 0.2438 0.012 1.417 30.5 111.1 58.2 0 0.304 2_settarget: 0.1837 0.2438 0.012 1.417 30.5 111.1 58.2 0 0.304 2_updatecdl: 0.1837 0.2438 0.012 1.458 30.5 111.1 58.2 0 0.304 2_weight: 0.1837 0.2438 0.012 1.458 30.5 111.1 58.2 0 0.304 2_xyzrec: 0.2090 0.2491 0.003 0.789 30.5 111.1 58.2 0 0.307 2_adp: 0.1833 0.2431 0.003 0.789 25.5 149.8 62.4 0 0.307 2_regHadp: 0.1818 0.2438 0.003 0.789 25.5 149.8 62.4 0 0.307 3_bss: 0.1806 0.2415 0.003 0.789 26.9 151.2 63.8 0 0.307 3_settarget: 0.1806 0.2415 0.003 0.789 26.9 151.2 63.8 0 0.307 3_updatecdl: 0.1806 0.2415 0.003 0.853 26.9 151.2 63.8 0 0.307 3_setrh: 0.1806 0.2413 0.003 0.853 26.9 151.2 63.8 0 0.307 3_weight: 0.1806 0.2413 0.003 0.853 26.9 151.2 63.8 0 0.307 3_xyzrec: 0.1806 0.2413 0.003 0.853 26.9 151.2 63.8 0 0.307 3_adp: 0.1806 0.2400 0.003 0.853 23.8 146.2 63.5 0 0.307 3_regHadp: 0.1810 0.2402 0.003 0.853 23.8 146.2 63.5 0 0.307 end: 0.1809 0.2405 0.003 0.853 23.8 146.2 63.5 0 0.307 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V1/1u87_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V1/1u87_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.6500 Refinement macro-cycles (run) : 149.7700 Write final files (write_after_run_outputs) : 16.4100 Total : 170.8300 Total CPU time: 3.16 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:25:47 PDT -0700 (1716251147.28 s) Start R-work = 0.2217, R-free = 0.2255 Final R-work = 0.1809, R-free = 0.2405 =============================================================================== Job complete usr+sys time: 203.02 seconds wall clock time: 9 minutes 59.17 seconds (599.17 seconds total)