Starting phenix.refine on Mon May 20 17:17:05 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=True 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 { ramachandran_plot_restraints { enabled = True } 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: 1.54, per 1000 atoms: 0.44 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: 2.15 Conformation dependent library (CDL) restraints added in 466.8 milliseconds 414 Ramachandran restraints generated. 207 Oldfield, 0 Emsley, 207 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 396 Time building geometry restraints manager: 1.76 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 { ramachandran_plot_restraints { enabled = True } 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 ============================ Update phi&psi targets =========================== 414 Ramachandran restraints generated. 207 Oldfield, 0 Emsley, 207 emsley8k and 0 Phi/Psi/2. ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 14.578902 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 0.1855 0.2439 0.0584 0.013 1.5 22.0 0.5 8.0 0 7.289 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 18.55 24.39 5.84 1.179 57.497 0.257 0.040 18.58 24.45 5.88 2.519 57.663 0.008 0.040 18.34 24.41 6.08 2.409 57.670 0.032 0.039 17.74 24.32 6.58 2.977 57.774 0.129 0.037 17.09 24.32 7.22 5.178 58.200 0.257 0.035 16.88 24.35 7.46 5.835 58.341 0.386 0.034 16.73 24.31 7.57 6.468 58.515 0.515 0.033 16.57 24.23 7.66 7.319 58.795 0.643 0.033 16.50 24.22 7.72 7.724 58.906 0.772 0.032 16.45 24.23 7.78 8.070 59.002 0.901 0.032 16.40 24.24 7.83 8.380 59.089 1.029 0.032 16.37 24.24 7.87 8.637 59.159 1.158 0.032 16.33 24.23 7.89 8.914 59.240 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: 18.58 24.45 5.88 2.519 57.663 0.008 0.040 Individual atomic B min max mean iso aniso Overall: 30.46 111.24 58.23 1.76 1750 0 Protein: 30.46 111.24 58.18 1.76 1730 0 Other: 50.41 75.23 62.58 N/A 20 0 Chain A: 30.46 111.24 58.23 N/A 1750 0 Histogram: Values Number of atoms 30.46 - 38.53 244 38.53 - 46.61 281 46.61 - 54.69 343 54.69 - 62.77 238 62.77 - 70.85 238 70.85 - 78.92 134 78.92 - 87.00 124 87.00 - 95.08 90 95.08 - 103.16 52 103.16 - 111.24 6 =========================== Idealize ADP of riding H ========================== r_work=0.1858 r_free=0.2445 r_work=0.1857 r_free=0.2439 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.50 - 29.97 A, n_refl.=4182 (all), 10.02 % free)-------------| | | | r_work= 0.1857 r_free= 0.2439 coordinate error (max.-lik. estimate): 0.39 A | | | | normalized target function (ls_wunit_k1) (work): 0.040365 | | target function (ls_wunit_k1) not normalized (work): 151.895298 | | target function (ls_wunit_k1) not normalized (free): 30.442708 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1916 0.1857 0.2439 n_refl.: 4182 re-set all scales: r(all,work,free)=0.3605 0.3550 0.4072 n_refl.: 4182 remove outliers: r(all,work,free)=0.3605 0.3550 0.4072 n_refl.: 4182 overall B=0.00 to atoms: r(all,work,free)=0.3605 0.3550 0.4072 n_refl.: 4182 bulk-solvent and scaling: r(all,work,free)=0.1900 0.1840 0.2427 n_refl.: 4182 remove outliers: r(all,work,free)=0.1900 0.1840 0.2427 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 0.2367 687.189 652.921 1.244 1.000 0.349 12.881-10.207 97.06 88 11 0.1540 954.246 924.339 1.383 1.001 0.340 10.181-8.045 98.52 181 19 0.1400 766.704 768.098 1.292 1.000 0.330 8.023-6.324 96.77 350 40 0.2018 471.028 464.232 1.088 0.997 0.320 6.311-4.969 96.87 696 77 0.1803 429.346 420.539 0.970 0.991 0.240 4.967-3.908 95.56 1374 153 0.1728 405.742 397.543 1.014 0.981 0.140 3.907-3.500 91.76 983 109 0.2179 298.785 286.129 1.058 0.972 0.057 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=5.6755 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 414 Ramachandran restraints generated. 207 Oldfield, 0 Emsley, 207 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 3.265022 wxc_scale = 0.091 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.053340 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 0.2119 0.2445 0.0325 0.002 0.8 4.3 0.0 5.3 0 0.030 0.2050 0.2431 0.0381 0.003 0.8 5.4 0.0 5.9 0 0.089 0.2001 0.2440 0.0439 0.003 0.8 6.3 0.0 5.9 0 0.179 0.1971 0.2452 0.0481 0.004 0.9 6.8 0.0 5.9 0 0.268 0.1940 0.2444 0.0504 0.005 1.0 8.3 0.0 6.4 0 0.358 0.1920 0.2428 0.0508 0.006 1.0 10.3 0.0 6.4 0 0.447 0.1892 0.2423 0.0531 0.007 1.1 11.4 0.0 6.9 0 0.536 0.1886 0.2416 0.0530 0.008 1.1 12.6 0.0 7.4 0 0.626 0.1953 0.2439 0.0486 0.005 0.9 7.1 0.0 5.9 0 0.298 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2119 0.2445 0.0325 0.002 0.8 4.3 0.0 5.3 0 0.030 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 21.19 24.45 3.25 8.566 63.641 0.053 6.100 21.71 25.29 3.57 9.322 64.571 0.002 6.120 20.82 24.90 4.08 9.115 64.285 0.007 6.090 19.43 24.31 4.88 9.632 64.552 0.027 6.042 19.04 24.20 5.16 10.267 64.750 0.053 6.030 18.97 24.21 5.24 10.524 64.787 0.080 6.027 18.81 24.22 5.41 11.102 65.052 0.107 6.023 18.73 24.23 5.50 11.524 65.227 0.133 6.020 18.65 24.24 5.59 11.914 65.386 0.160 6.019 18.58 24.25 5.67 12.455 65.597 0.187 6.017 18.57 24.25 5.69 12.534 65.628 0.213 6.016 18.52 24.26 5.74 12.940 65.775 0.240 6.015 18.47 24.25 5.79 13.413 65.942 0.267 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: 0.053 Accepted refinement result: 19.04 24.20 5.16 10.267 64.750 0.053 6.030 Individual atomic B min max mean iso aniso Overall: 26.03 134.33 60.46 7.61 1750 0 Protein: 26.03 134.33 60.44 7.62 1730 0 Other: 45.41 79.20 61.80 N/A 20 0 Chain A: 26.03 134.33 60.46 N/A 1750 0 Histogram: Values Number of atoms 26.03 - 36.86 167 36.86 - 47.69 383 47.69 - 58.52 370 58.52 - 69.35 292 69.35 - 80.18 204 80.18 - 91.01 177 91.01 - 101.84 114 101.84 - 112.67 32 112.67 - 123.50 10 123.50 - 134.33 1 =========================== Idealize ADP of riding H ========================== r_work=0.1904 r_free=0.2420 r_work=0.1885 r_free=0.2421 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.50 - 29.97 A, n_refl.=4182 (all), 10.02 % free)-------------| | | | r_work= 0.1885 r_free= 0.2421 coordinate error (max.-lik. estimate): 0.39 A | | | | normalized target function (ml) (work): 6.024938 | | target function (ml) not normalized (work): 22671.842234 | | target function (ml) not normalized (free): 2590.958086 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1939 0.1885 0.2421 n_refl.: 4182 re-set all scales: r(all,work,free)=0.3656 0.3604 0.4092 n_refl.: 4182 remove outliers: r(all,work,free)=0.3656 0.3604 0.4092 n_refl.: 4182 overall B=3.34 to atoms: r(all,work,free)=0.3768 0.3716 0.4208 n_refl.: 4182 bulk-solvent and scaling: r(all,work,free)=0.1928 0.1872 0.2430 n_refl.: 4182 remove outliers: r(all,work,free)=0.1928 0.1872 0.2430 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 0.2441 687.189 636.397 1.226 1.040 0.358 12.881-10.207 97.06 88 11 0.1631 954.246 936.382 1.313 1.034 0.343 10.181-8.045 98.52 181 19 0.1532 766.704 765.423 1.242 1.026 0.336 8.023-6.324 96.77 350 40 0.2169 471.028 463.429 1.086 1.012 0.315 6.311-4.969 96.87 696 77 0.1952 429.346 416.877 0.973 0.988 0.243 4.967-3.908 95.56 1374 153 0.1682 405.742 392.886 1.036 0.950 0.134 3.907-3.500 91.76 983 109 0.2089 298.785 282.697 1.131 0.914 0.075 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=5.8423 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 414 Ramachandran restraints generated. 207 Oldfield, 0 Emsley, 207 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1872 r_free=0.2430 After: r_work=0.1872 r_free=0.2428 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 3.902138 wxc_scale = 0.022 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.049723 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 0.1872 0.2428 0.0556 0.002 0.8 4.3 0.0 5.3 0 0.008 0.1872 0.2428 0.0556 0.002 0.8 4.3 0.0 5.3 0 0.025 0.1872 0.2428 0.0556 0.002 0.8 4.3 0.0 5.3 0 0.050 0.1872 0.2428 0.0556 0.002 0.8 4.3 0.0 5.3 0 0.076 0.1872 0.2428 0.0556 0.002 0.8 4.3 0.0 5.3 0 0.101 0.1872 0.2428 0.0556 0.002 0.8 4.3 0.0 5.3 0 0.126 0.1872 0.2428 0.0556 0.002 0.8 4.3 0.0 5.3 0 0.151 0.1872 0.2428 0.0556 0.002 0.8 4.3 0.0 5.3 0 0.176 0.1872 0.2428 0.0556 0.002 0.8 4.3 0.0 5.3 0 0.084 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1872 0.2428 0.0556 0.002 0.8 4.3 0.0 5.3 0 0.008 0.1872 0.2428 0.0556 0.002 0.8 4.3 0.0 5.3 0 0.025 0.1872 0.2428 0.0556 0.002 0.8 4.3 0.0 5.3 0 0.050 0.1872 0.2428 0.0556 0.002 0.8 4.3 0.0 5.3 0 0.076 0.1872 0.2428 0.0556 0.002 0.8 4.3 0.0 5.3 0 0.101 0.1872 0.2428 0.0556 0.002 0.8 4.3 0.0 5.3 0 0.126 0.1872 0.2428 0.0556 0.002 0.8 4.3 0.0 5.3 0 0.151 0.1872 0.2428 0.0556 0.002 0.8 4.3 0.0 5.3 0 0.176 0.1872 0.2428 0.0556 0.002 0.8 4.3 0.0 5.3 0 0.084 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 18.72 24.28 5.56 10.432 69.687 0.050 6.024 21.38 25.20 3.83 9.613 72.995 0.001 6.092 20.79 25.11 4.32 9.813 72.225 0.006 6.079 18.89 24.28 5.39 10.292 69.593 0.025 6.029 18.61 24.28 5.67 10.520 69.620 0.050 6.021 18.37 24.28 5.91 10.965 69.512 0.075 6.014 17.98 24.42 6.43 11.730 69.831 0.099 6.007 17.85 24.53 6.67 12.320 70.110 0.124 6.007 17.77 24.60 6.82 12.722 70.295 0.149 6.006 17.73 24.63 6.90 13.027 70.425 0.174 6.005 17.69 24.67 6.98 13.305 70.541 0.199 6.005 17.66 24.68 7.02 13.532 70.632 0.224 6.005 17.64 24.72 7.08 13.784 70.740 0.249 6.005 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.075 Accepted refinement result: 18.37 24.28 5.91 10.965 69.512 0.075 6.014 Individual atomic B min max mean iso aniso Overall: 24.96 139.19 63.44 8.49 1750 0 Protein: 24.96 139.19 63.43 8.48 1730 0 Other: 44.19 82.61 64.49 N/A 20 0 Chain A: 24.96 139.19 63.44 N/A 1750 0 Histogram: Values Number of atoms 24.96 - 36.39 101 36.39 - 47.81 346 47.81 - 59.23 401 59.23 - 70.65 319 70.65 - 82.08 231 82.08 - 93.50 182 93.50 - 104.92 120 104.92 - 116.34 39 116.34 - 127.76 10 127.76 - 139.19 1 =========================== Idealize ADP of riding H ========================== r_work=0.1837 r_free=0.2428 r_work=0.1834 r_free=0.2429 ----------X-ray data---------- |--(resolution: 3.50 - 29.97 A, n_refl.=4182 (all), 10.02 % free)-------------| | | | r_work= 0.1834 r_free= 0.2429 coordinate error (max.-lik. estimate): 0.37 A | | | | normalized target function (ml) (work): 6.013253 | | target function (ml) not normalized (work): 22627.870034 | | target function (ml) not normalized (free): 2592.119115 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1912 0.2371 6.2717 6.427| | 2: 5.04 - 4.01 0.96 1235 137 0.1642 0.2279 5.9628 6.1116| | 3: 4.00 - 3.50 0.92 1176 131 0.1950 0.2750 5.769 5.9874| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 0.83 21.39 1.00 0.99 45534.82| | 2: 5.04 - 4.01 1235 137 0.85 21.26 1.00 0.99 32500.57| | 3: 4.00 - 3.50 1176 131 0.82 24.65 1.00 0.96 22073.15| |alpha: min = 0.96 max = 0.99 mean = 0.98| |beta: min = 22073.15 max = 45534.82 mean = 33924.88| |figures of merit: min = 0.00 max = 1.00 mean = 0.83| |phase err.(work): min = 0.00 max = 89.87 mean = 22.37| |phase err.(test): min = 0.00 max = 88.47 mean = 21.86| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1894 0.1834 0.2429 n_refl.: 4182 re-set all scales: r(all,work,free)=0.3739 0.3685 0.4191 n_refl.: 4182 remove outliers: r(all,work,free)=0.3739 0.3685 0.4191 n_refl.: 4182 overall B=0.00 to atoms: r(all,work,free)=0.3739 0.3685 0.4191 n_refl.: 4182 bulk-solvent and scaling: r(all,work,free)=0.1895 0.1837 0.2411 n_refl.: 4182 remove outliers: r(all,work,free)=0.1895 0.1837 0.2411 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 0.2500 687.189 642.088 1.191 1.028 0.349 12.881-10.207 97.06 88 11 0.1642 954.246 936.187 1.329 1.023 0.340 10.181-8.045 98.52 181 19 0.1525 766.704 764.424 1.254 1.017 0.330 8.023-6.324 96.77 350 40 0.2151 471.028 463.432 1.109 1.007 0.320 6.311-4.969 96.87 696 77 0.1930 429.346 416.545 0.976 0.987 0.240 4.967-3.908 95.56 1374 153 0.1635 405.742 393.342 1.035 0.956 0.140 3.907-3.500 91.76 983 109 0.2004 298.785 283.638 1.119 0.928 0.082 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=5.5185 ================= 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_updatephipsi: 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: 0.1855 0.2439 0.013 1.455 29.0 112.0 57.9 0 0.297 1_adp: 0.1858 0.2445 0.013 1.455 30.5 111.2 58.2 0 0.297 1_regHadp: 0.1857 0.2439 0.013 1.455 30.5 111.2 58.2 0 0.297 2_bss: 0.1840 0.2427 0.013 1.455 30.5 111.2 58.2 0 0.297 2_settarget: 0.1840 0.2427 0.013 1.455 30.5 111.2 58.2 0 0.297 2_updatephipsi: 0.1840 0.2427 0.013 1.455 30.5 111.2 58.2 0 0.297 2_updatecdl: 0.1840 0.2427 0.013 1.478 30.5 111.2 58.2 0 0.297 2_weight: 0.1840 0.2427 0.013 1.478 30.5 111.2 58.2 0 0.297 2_xyzrec: 0.2119 0.2445 0.002 0.770 30.5 111.2 58.2 0 0.307 2_adp: 0.1904 0.2420 0.002 0.770 26.0 134.3 60.5 0 0.307 2_regHadp: 0.1885 0.2421 0.002 0.770 26.0 134.3 60.5 0 0.307 3_bss: 0.1872 0.2430 0.002 0.770 29.4 137.7 63.8 0 0.307 3_settarget: 0.1872 0.2430 0.002 0.770 29.4 137.7 63.8 0 0.307 3_updatephipsi: 0.1872 0.2430 0.002 0.770 29.4 137.7 63.8 0 0.307 3_updatecdl: 0.1872 0.2430 0.002 0.805 29.4 137.7 63.8 0 0.307 3_setrh: 0.1872 0.2428 0.002 0.805 29.4 137.7 63.8 0 0.307 3_weight: 0.1872 0.2428 0.002 0.805 29.4 137.7 63.8 0 0.307 3_xyzrec: 0.1872 0.2428 0.002 0.805 29.4 137.7 63.8 0 0.307 3_adp: 0.1837 0.2428 0.002 0.805 25.0 139.2 63.4 0 0.307 3_regHadp: 0.1834 0.2429 0.002 0.805 25.0 139.2 63.4 0 0.307 end: 0.1837 0.2411 0.002 0.805 25.0 139.2 63.4 0 0.307 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V2/1u87_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V2/1u87_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 5.1000 Refinement macro-cycles (run) : 166.0400 Write final files (write_after_run_outputs) : 16.8600 Total : 188.0000 Total CPU time: 3.60 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:28:49 PDT -0700 (1716251329.92 s) Start R-work = 0.2217, R-free = 0.2255 Final R-work = 0.1837, R-free = 0.2411 =============================================================================== Job complete usr+sys time: 230.32 seconds wall clock time: 12 minutes 20.57 seconds (740.57 seconds total)