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/1yab.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1yab/1yab.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 { model { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/1yab.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/1yab.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1yab/1yab.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1yab/1yab.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 { 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: 2831 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1401 Classifications: {'peptide': 85} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 81} Chain: "B" Number of atoms: 1430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 1430 Classifications: {'peptide': 87} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 82} Time building chain proxies: 0.62, per 1000 atoms: 0.22 Number of scatterers: 2831 At special positions: 0 Unit cell: (100.173, 100.173, 87.853, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 4 16.00 O 257 8.00 N 229 7.00 C 865 6.00 H 1476 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: 0.77 Conformation dependent library (CDL) restraints added in 85.7 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 320 Time building geometry restraints manager: 0.88 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: 1476 1.15 - 1.32: 248 1.32 - 1.49: 442 1.49 - 1.66: 665 1.66 - 1.83: 8 Bond restraints: 2839 Sorted by residual: bond pdb=" NH1 ARG B 87 " pdb="HH12 ARG B 87 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N VAL A 114 " pdb=" H VAL A 114 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N HIS A 100 " pdb=" H HIS A 100 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.44e+01 bond pdb=" N LYS B 108 " pdb=" H LYS B 108 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.44e+01 bond pdb=" N LEU A 75 " pdb=" H LEU A 75 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.44e+01 ... (remaining 2834 not shown) Histogram of bond angle deviations from ideal: 97.32 - 104.19: 59 104.19 - 111.07: 3254 111.07 - 117.94: 912 117.94 - 124.81: 926 124.81 - 131.69: 70 Bond angle restraints: 5221 Sorted by residual: angle pdb=" N LYS B 70 " pdb=" CA LYS B 70 " pdb=" C LYS B 70 " ideal model delta sigma weight residual 112.92 102.67 10.25 1.23e+00 6.61e-01 6.95e+01 angle pdb=" CA ASN B 134 " pdb=" C ASN B 134 " pdb=" N PHE B 135 " ideal model delta sigma weight residual 115.55 123.69 -8.14 1.33e+00 5.65e-01 3.75e+01 angle pdb=" C ASN B 134 " pdb=" N PHE B 135 " pdb=" CA PHE B 135 " ideal model delta sigma weight residual 121.54 131.60 -10.06 1.91e+00 2.74e-01 2.77e+01 angle pdb=" C VAL A 81 " pdb=" CA VAL A 81 " pdb=" CB VAL A 81 " ideal model delta sigma weight residual 110.91 104.61 6.30 1.24e+00 6.50e-01 2.58e+01 angle pdb=" N ASP B 132 " pdb=" CA ASP B 132 " pdb=" C ASP B 132 " ideal model delta sigma weight residual 110.80 120.70 -9.90 2.13e+00 2.20e-01 2.16e+01 ... (remaining 5216 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.86: 1127 25.86 - 51.72: 116 51.72 - 77.58: 21 77.58 - 103.44: 5 103.44 - 129.30: 1 Dihedral angle restraints: 1270 sinusoidal: 764 harmonic: 506 Sorted by residual: dihedral pdb=" CA ASN B 134 " pdb=" C ASN B 134 " pdb=" N PHE B 135 " pdb=" CA PHE B 135 " ideal model delta harmonic sigma weight residual 180.00 50.70 129.30 0 5.00e+00 4.00e-02 6.69e+02 dihedral pdb=" C ASP B 132 " pdb=" N ASP B 132 " pdb=" CA ASP B 132 " pdb=" CB ASP B 132 " ideal model delta harmonic sigma weight residual -122.60 -139.66 17.06 0 2.50e+00 1.60e-01 4.66e+01 dihedral pdb=" N ASP B 132 " pdb=" C ASP B 132 " pdb=" CA ASP B 132 " pdb=" CB ASP B 132 " ideal model delta harmonic sigma weight residual 122.80 139.34 -16.54 0 2.50e+00 1.60e-01 4.38e+01 ... (remaining 1267 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.134: 186 0.134 - 0.267: 45 0.267 - 0.401: 3 0.401 - 0.534: 2 0.534 - 0.667: 2 Chirality restraints: 238 Sorted by residual: chirality pdb=" CA PHE B 135 " pdb=" N PHE B 135 " pdb=" C PHE B 135 " pdb=" CB PHE B 135 " both_signs ideal model delta sigma weight residual False 2.51 1.84 0.67 2.00e-01 2.50e+01 1.11e+01 chirality pdb=" CA ASP B 132 " pdb=" N ASP B 132 " pdb=" C ASP B 132 " pdb=" CB ASP B 132 " both_signs ideal model delta sigma weight residual False 2.51 1.87 0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" CA ASP A 132 " pdb=" N ASP A 132 " pdb=" C ASP A 132 " pdb=" CB ASP A 132 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.69e+00 ... (remaining 235 not shown) Planarity restraints: 394 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 134 " -0.004 2.00e-02 2.50e+03 1.16e-02 2.03e+00 pdb=" CG ASN A 134 " -0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN A 134 " 0.016 2.00e-02 2.50e+03 pdb=" ND2 ASN A 134 " -0.002 2.00e-02 2.50e+03 pdb="HD21 ASN A 134 " -0.009 2.00e-02 2.50e+03 pdb="HD22 ASN A 134 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 135 " 0.003 2.00e-02 2.50e+03 6.76e-03 1.37e+00 pdb=" CG PHE B 135 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 PHE B 135 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE B 135 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE B 135 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B 135 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 135 " 0.000 2.00e-02 2.50e+03 pdb=" HD1 PHE B 135 " -0.006 2.00e-02 2.50e+03 pdb=" HD2 PHE B 135 " 0.014 2.00e-02 2.50e+03 pdb=" HE1 PHE B 135 " 0.010 2.00e-02 2.50e+03 pdb=" HE2 PHE B 135 " -0.009 2.00e-02 2.50e+03 pdb=" HZ PHE B 135 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 134 " -0.003 2.00e-02 2.50e+03 9.20e-03 1.27e+00 pdb=" CG ASN B 134 " -0.012 2.00e-02 2.50e+03 pdb=" OD1 ASN B 134 " 0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN B 134 " -0.002 2.00e-02 2.50e+03 pdb="HD21 ASN B 134 " -0.007 2.00e-02 2.50e+03 pdb="HD22 ASN B 134 " 0.012 2.00e-02 2.50e+03 ... (remaining 391 not shown) Histogram of nonbonded interaction distances: 1.15 - 1.84: 90 1.84 - 2.53: 2680 2.53 - 3.22: 8880 3.22 - 3.91: 12220 3.91 - 4.60: 18232 Nonbonded interactions: 42102 Sorted by model distance: nonbonded pdb=" HG3 ARG A 89 " pdb="HH11 ARG A 89 " model vdw 1.154 2.270 nonbonded pdb=" HA GLU A 147 " pdb=" HB2 GLU A 150 " model vdw 1.325 2.440 nonbonded pdb="HH22 ARG A 94 " pdb="HD12 ILE A 104 " model vdw 1.340 2.270 nonbonded pdb=" O LEU A 74 " pdb=" H ASP A 76 " model vdw 1.363 1.850 nonbonded pdb=" HA2 GLY B 126 " pdb=" H THR B 140 " model vdw 1.423 2.270 ... (remaining 42097 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 4 15.91 1 O 257 7.97 1 N 229 6.97 1 C 865 5.97 1 H 1476 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: 1476 of 2831 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 2831 n_use_u_iso = 2831 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 = 2831 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (2831 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 2831 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 = "1yab_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1476 occupancy sum: 1476.00 (% of total atoms 52.17) Rotatable: count: 514 occupancy sum: 514.00 (% of total atoms 18.17) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.40 - 19.90 A, n_refl.=7246 (all), 4.69 % free)-------------| | | | r_work= 0.4059 r_free= 0.4598 coordinate error (max.-lik. estimate): 0.43 A | | | | normalized target function (ml) (work): 5.289039 | | target function (ml) not normalized (work): 36526.102154 | | target function (ml) not normalized (free): 1841.689129 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 19.90 - 4.27 1.00 3512 170 0.3818 0.4405 5.9303 6.0787| | 2: 4.27 - 3.40 1.00 3394 170 0.4725 0.5140 4.6255 4.7548| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 19.90 - 4.27 3512 170 0.47 53.91 0.97 0.49 32804.81| | 2: 4.27 - 3.40 3394 170 0.71 34.58 1.68 1.01 2345.12| |alpha: min = 0.49 max = 1.01 mean = 0.75| |beta: min = 2345.12 max = 32804.81 mean = 17835.19| |figures of merit: min = 0.00 max = 1.00 mean = 0.59| |phase err.(work): min = 0.00 max = 89.99 mean = 44.41| |phase err.(test): min = 0.00 max = 89.81 mean = 43.07| |-----------------------------------------------------------------------------| ----------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 0.080 1363 Z= 0.849 Angle : 1.971 12.009 1839 Z= 1.158 Chirality : 0.128 0.667 238 Planarity : 0.005 0.024 230 Dihedral : 23.170 129.301 543 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 23.72 Ramachandran Plot: Outliers : 8.33 % Allowed : 10.12 % Favored : 81.55 % Rotamer: Outliers : 24.68 % Allowed : 21.52 % Favored : 53.80 % Cbeta Deviations : 2.50 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.61 % Twisted Proline : 0.00 % Twisted General : 1.83 % 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: -4.61 (0.52), residues: 168 helix: -4.84 (0.42), residues: 40 sheet: -3.56 (1.49), residues: 10 loop : -2.51 (0.48), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 94 PHE 0.008 0.003 PHE B 135 HIS 0.002 0.001 HIS A 100 Individual atomic B min max mean iso aniso Overall: 93.69 154.06 112.45 1.19 1355 0 Protein: 93.69 154.06 112.45 1.19 1355 0 Chain A: 94.35 154.06 112.30 N/A 669 0 Chain B: 93.69 153.95 112.61 N/A 686 0 Histogram: Values Number of atoms 93.69 - 99.73 219 99.73 - 105.76 346 105.76 - 111.80 259 111.80 - 117.84 158 117.84 - 123.88 111 123.88 - 129.91 104 129.91 - 135.95 47 135.95 - 141.99 29 141.99 - 148.02 23 148.02 - 154.06 59 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 3 ************************* |--(resolution: 3.40 - 19.90 A, n_refl.=7246 (all), 4.69 % free)-------------| | | | r_work= 0.4059 r_free= 0.4598 coordinate error (max.-lik. estimate): 0.43 A | | | | normalized target function (ml) (work): 5.289039 | | target function (ml) not normalized (work): 36526.102154 | | target function (ml) not normalized (free): 1841.689129 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.4088 0.4059 0.4598 n_refl.: 7246 re-set all scales: r(all,work,free)=0.4088 0.4059 0.4598 n_refl.: 7246 remove outliers: r(all,work,free)=0.4086 0.4057 0.4598 n_refl.: 7245 overall B=-8.40 to atoms: r(all,work,free)=0.3843 0.3813 0.4380 n_refl.: 7245 bulk-solvent and scaling: r(all,work,free)=0.2258 0.2228 0.2845 n_refl.: 7245 remove outliers: r(all,work,free)=0.2258 0.2228 0.2845 n_refl.: 7245 ======================== 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 19.902-13.063 90.91 91 9 0.1925 763.916 733.811 1.338 0.999 0.338 12.965-10.793 93.40 95 4 0.1555 722.206 703.625 1.337 0.998 0.330 10.793-8.919 99.47 176 10 0.1458 676.649 670.817 1.301 0.998 0.327 8.905-7.374 99.69 313 12 0.2067 409.798 395.940 1.152 0.996 0.300 7.364-6.089 99.82 547 20 0.2513 296.258 285.152 1.064 0.993 0.273 6.087-5.031 100.00 938 48 0.2290 234.401 224.135 0.961 0.989 0.215 5.030-4.158 99.88 1640 78 0.1969 247.791 238.471 0.978 0.983 0.155 4.156-3.397 99.85 3105 159 0.2879 111.432 103.442 1.032 0.973 0.058 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0577 b_overall=3.6281 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 15.015255 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.185064 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2533 0.2829 0.0296 0.003 0.7 6.4 2.4 20.3 0 0.125 0.2499 0.2808 0.0309 0.003 0.7 6.4 2.4 20.9 0 0.250 0.2453 0.2825 0.0372 0.003 0.7 7.8 3.0 21.5 0 0.500 0.2379 0.2819 0.0440 0.004 0.8 10.3 3.6 20.9 0 1.000 0.2310 0.2816 0.0506 0.006 1.0 13.5 4.8 21.5 0 2.000 0.2277 0.2769 0.0492 0.007 1.0 15.6 4.8 22.8 0 3.000 0.2238 0.2757 0.0520 0.009 1.2 16.3 4.8 24.1 0 4.000 0.2233 0.2758 0.0525 0.010 1.2 17.3 5.4 24.1 0 5.000 0.2216 0.2767 0.0551 0.012 1.3 19.1 5.4 24.7 0 6.000 0.2206 0.2773 0.0567 0.013 1.4 20.5 4.2 25.9 0 7.000 0.2187 0.2757 0.0570 0.015 1.4 21.2 4.2 26.6 0 8.000 0.2175 0.2757 0.0582 0.016 1.5 23.4 4.8 27.2 0 9.000 0.2172 0.2759 0.0587 0.017 1.6 23.7 5.4 27.2 0 10.000 0.2194 0.2764 0.0570 0.014 1.4 21.9 4.2 26.6 0 7.508 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2533 0.2829 0.0296 0.003 0.7 6.4 2.4 20.3 0 0.125 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 25.33 28.29 2.96 0.822 103.807 0.185 0.064 25.45 28.37 2.92 2.039 103.910 0.006 0.064 24.93 28.04 3.11 2.122 103.931 0.023 0.061 24.08 27.59 3.52 3.397 104.208 0.093 0.057 22.78 27.10 4.32 8.048 105.538 0.185 0.051 22.47 27.01 4.54 9.466 106.011 0.278 0.050 22.28 26.98 4.70 10.498 106.361 0.370 0.049 22.11 26.89 4.79 11.449 106.709 0.463 0.048 21.78 26.73 4.95 13.278 107.483 0.555 0.047 21.69 26.71 5.02 13.925 107.702 0.648 0.046 21.61 26.70 5.09 14.483 107.892 0.740 0.046 21.53 26.69 5.16 15.105 108.119 0.833 0.045 21.49 26.68 5.19 15.449 108.227 0.925 0.045 max suggested for this run: 20.76 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.925 Accepted refinement result: 21.49 26.68 5.19 15.449 108.227 0.925 0.045 Individual atomic B min max mean iso aniso Overall: 81.05 180.66 113.29 12.57 1355 0 Protein: 81.05 180.66 113.29 12.57 1355 0 Chain A: 81.33 180.66 114.22 N/A 669 0 Chain B: 81.05 178.29 112.38 N/A 686 0 Histogram: Values Number of atoms 81.05 - 91.01 254 91.01 - 100.97 209 100.97 - 110.93 228 110.93 - 120.90 210 120.90 - 130.86 155 130.86 - 140.82 132 140.82 - 150.78 86 150.78 - 160.74 40 160.74 - 170.70 26 170.70 - 180.66 15 =========================== Idealize ADP of riding H ========================== r_work=0.2149 r_free=0.2668 r_work=0.2126 r_free=0.2680 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.40 - 19.90 A, n_refl.=7245 (all), 4.69 % free)-------------| | | | r_work= 0.2126 r_free= 0.2680 coordinate error (max.-lik. estimate): 0.39 A | | | | normalized target function (ls_wunit_k1) (work): 0.044237 | | target function (ls_wunit_k1) not normalized (work): 305.453410 | | target function (ls_wunit_k1) not normalized (free): 28.027589 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2153 0.2126 0.2680 n_refl.: 7245 re-set all scales: r(all,work,free)=0.3877 0.3851 0.4352 n_refl.: 7245 remove outliers: r(all,work,free)=0.3877 0.3851 0.4352 n_refl.: 7245 overall B=0.00 to atoms: r(all,work,free)=0.3877 0.3851 0.4352 n_refl.: 7245 bulk-solvent and scaling: r(all,work,free)=0.2133 0.2106 0.2667 n_refl.: 7245 remove outliers: r(all,work,free)=0.2133 0.2106 0.2667 n_refl.: 7245 ======================== 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 19.902-13.063 90.91 91 9 0.1707 480.012 461.268 1.339 1.001 0.334 12.965-10.793 95.19 95 4 0.1127 453.804 451.963 1.359 1.000 0.330 10.793-8.919 99.47 176 10 0.1385 425.178 423.698 1.266 1.000 0.309 8.905-7.374 99.69 313 12 0.1831 257.500 251.769 1.119 0.998 0.290 7.364-6.089 99.82 547 20 0.2160 186.156 182.608 1.042 0.995 0.250 6.087-5.031 100.00 938 48 0.2147 147.287 142.799 0.950 0.991 0.200 5.030-4.158 99.88 1640 78 0.1824 155.701 150.785 0.983 0.986 0.140 4.156-3.397 99.85 3105 159 0.3011 70.019 64.426 1.054 0.978 0.040 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0265 b_overall=0.6317 ============================ 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 = 4.919171 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.040233 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2056 0.2668 0.0611 0.003 0.6 5.7 3.0 15.2 0 0.125 0.2011 0.2657 0.0646 0.003 0.7 6.0 3.0 16.5 0 0.250 0.1965 0.2664 0.0699 0.004 0.7 7.8 3.6 18.4 0 0.500 0.1928 0.2623 0.0695 0.007 0.9 11.3 3.6 19.6 0 1.000 0.1899 0.2582 0.0683 0.011 1.2 16.6 4.8 24.1 0 2.000 0.1884 0.2586 0.0702 0.015 1.5 18.8 4.8 27.2 0 3.000 0.1875 0.2606 0.0731 0.019 1.7 21.2 4.8 29.1 0 4.000 0.1872 0.2595 0.0723 0.022 1.9 22.3 5.4 27.8 0 5.000 0.1866 0.2605 0.0740 0.025 2.1 21.9 5.4 28.5 0 6.000 0.1863 0.2613 0.0750 0.028 2.3 23.4 6.0 30.4 0 7.000 0.1860 0.2602 0.0741 0.031 2.4 25.5 6.5 31.0 0 8.000 0.1856 0.2600 0.0744 0.034 2.6 26.5 7.1 31.0 0 9.000 0.1859 0.2603 0.0743 0.036 2.7 26.9 7.1 31.0 0 10.000 0.1892 0.2583 0.0691 0.013 1.3 16.6 4.2 25.3 0 2.460 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1899 0.2582 0.0683 0.011 1.2 16.6 4.8 24.1 0 2.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 18.99 25.82 6.83 18.763 125.193 0.040 4.884 25.73 30.13 4.41 13.911 135.519 0.001 4.997 23.51 28.40 4.89 14.132 133.490 0.005 4.954 20.35 26.42 6.07 16.678 128.962 0.020 4.885 19.22 25.69 6.46 17.654 127.106 0.040 4.857 18.97 25.40 6.43 18.141 127.068 0.060 4.848 18.83 25.32 6.49 18.433 127.017 0.080 4.844 18.77 25.26 6.49 18.674 127.157 0.101 4.842 18.72 25.24 6.52 18.894 127.291 0.121 4.841 18.69 25.21 6.52 19.087 127.400 0.141 4.840 18.67 25.21 6.54 19.272 127.507 0.161 4.839 18.65 25.20 6.55 19.433 127.598 0.181 4.839 18.64 25.21 6.57 19.580 127.683 0.201 4.839 max suggested for this run: 25.04 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.005 Accepted refinement result: 23.51 28.40 4.89 14.132 133.490 0.005 4.954 Individual atomic B min max mean iso aniso Overall: 94.16 185.40 130.62 5.74 1355 0 Protein: 94.16 185.40 130.62 5.74 1355 0 Chain A: 97.18 185.40 132.48 N/A 669 0 Chain B: 94.16 183.85 128.81 N/A 686 0 Histogram: Values Number of atoms 94.16 - 103.29 25 103.29 - 112.41 179 112.41 - 121.54 256 121.54 - 130.66 306 130.66 - 139.78 238 139.78 - 148.91 155 148.91 - 158.03 81 158.03 - 167.16 39 167.16 - 176.28 54 176.28 - 185.40 22 =========================== Idealize ADP of riding H ========================== r_work=0.2351 r_free=0.2840 r_work=0.2419 r_free=0.2859 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.40 - 19.90 A, n_refl.=7245 (all), 4.69 % free)-------------| | | | r_work= 0.2419 r_free= 0.2859 coordinate error (max.-lik. estimate): 0.17 A | | | | normalized target function (ml) (work): 4.968185 | | target function (ml) not normalized (work): 34305.319166 | | target function (ml) not normalized (free): 1741.473583 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2441 0.2419 0.2859 n_refl.: 7245 re-set all scales: r(all,work,free)=0.4510 0.4491 0.4853 n_refl.: 7245 remove outliers: r(all,work,free)=0.4510 0.4491 0.4853 n_refl.: 7245 overall B=-25.95 to atoms: r(all,work,free)=0.3737 0.3716 0.4141 n_refl.: 7245 bulk-solvent and scaling: r(all,work,free)=0.2231 0.2207 0.2713 n_refl.: 7245 remove outliers: r(all,work,free)=0.2231 0.2207 0.2713 n_refl.: 7245 ======================== 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 19.902-13.063 90.91 91 9 0.1490 420.240 408.324 1.530 1.005 0.344 12.965-10.793 93.40 95 4 0.1112 397.295 392.362 1.534 1.003 0.346 10.793-8.919 99.47 176 10 0.1443 372.234 371.798 1.402 1.002 0.332 8.905-7.374 99.69 313 12 0.1940 225.435 219.423 1.190 1.000 0.310 7.364-6.089 99.82 547 20 0.2433 162.975 157.352 1.076 0.996 0.267 6.087-5.031 100.00 938 48 0.2461 128.947 122.844 0.998 0.990 0.211 5.030-4.158 99.88 1640 78 0.2056 136.313 130.787 1.002 0.981 0.151 4.156-3.397 99.85 3105 159 0.2840 61.300 56.247 1.018 0.969 0.032 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1458 b_overall=8.9574 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.2207 r_free=0.2713 After: r_work=0.2208 r_free=0.2713 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 4.253204 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.040834 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2257 0.2711 0.0454 0.006 1.0 20.9 4.2 22.8 0 0.125 0.2240 0.2700 0.0460 0.006 1.0 19.8 4.2 22.8 0 0.250 0.2224 0.2715 0.0491 0.007 1.1 20.2 4.2 23.4 0 0.500 0.2188 0.2716 0.0528 0.011 1.2 20.9 4.2 23.4 0 1.000 0.2115 0.2739 0.0624 0.021 1.7 25.8 5.4 24.7 0 2.000 0.2086 0.2762 0.0676 0.024 2.2 29.7 6.0 25.3 0 3.000 0.2070 0.2764 0.0693 0.026 2.4 31.5 7.1 24.7 0 4.000 0.2050 0.2763 0.0713 0.030 2.6 32.9 7.1 25.9 0 5.000 0.2036 0.2778 0.0742 0.033 2.9 35.8 7.7 26.6 0 6.000 0.2029 0.2799 0.0770 0.037 3.2 38.2 7.7 29.7 0 7.000 0.2015 0.2791 0.0776 0.041 3.3 41.4 7.1 28.5 0 8.000 0.2000 0.2777 0.0778 0.044 3.6 43.9 7.1 29.7 0 9.000 0.2002 0.2810 0.0807 0.047 3.8 47.8 7.7 30.4 0 10.000 0.2115 0.2736 0.0621 0.021 1.7 26.2 5.4 25.3 0 2.127 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2240 0.2700 0.0460 0.006 1.0 19.8 4.2 22.8 0 0.250 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 22.40 27.00 4.60 19.442 118.353 0.041 4.834 25.77 29.90 4.13 13.987 125.512 0.001 4.898 23.09 27.74 4.64 15.168 122.907 0.005 4.834 20.50 25.77 5.27 18.040 121.756 0.020 4.755 20.16 25.69 5.53 18.757 121.437 0.041 4.746 20.14 25.83 5.69 19.038 120.943 0.061 4.749 20.07 25.84 5.78 19.339 121.212 0.082 4.747 20.03 25.88 5.85 19.632 121.465 0.102 4.745 20.00 25.90 5.90 19.910 121.680 0.123 4.744 19.98 25.91 5.93 20.157 121.856 0.143 4.743 19.97 25.92 5.95 20.367 121.995 0.163 4.743 19.96 25.92 5.96 20.550 122.109 0.184 4.742 19.96 25.93 5.98 20.717 122.206 0.204 4.742 max suggested for this run: 23.67 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.041 Accepted refinement result: 20.16 25.69 5.53 18.757 121.437 0.041 4.746 Individual atomic B min max mean iso aniso Overall: 67.02 182.37 111.12 10.90 1355 0 Protein: 67.02 182.37 111.12 10.90 1355 0 Chain A: 67.02 178.57 112.93 N/A 669 0 Chain B: 67.79 182.37 109.36 N/A 686 0 Histogram: Values Number of atoms 67.02 - 78.55 48 78.55 - 90.09 211 90.09 - 101.62 266 101.62 - 113.16 267 113.16 - 124.69 209 124.69 - 136.23 134 136.23 - 147.76 115 147.76 - 159.30 71 159.30 - 170.83 27 170.83 - 182.37 7 =========================== Idealize ADP of riding H ========================== r_work=0.2016 r_free=0.2569 r_work=0.2004 r_free=0.2578 ----------X-ray data---------- |--(resolution: 3.40 - 19.90 A, n_refl.=7245 (all), 4.69 % free)-------------| | | | r_work= 0.2004 r_free= 0.2578 coordinate error (max.-lik. estimate): 0.16 A | | | | normalized target function (ml) (work): 4.743765 | | target function (ml) not normalized (work): 32755.700339 | | target function (ml) not normalized (free): 1680.065183 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 19.90 - 4.27 0.99 3511 170 0.1856 0.2396 5.1625 5.4216| | 2: 4.27 - 3.40 1.00 3394 170 0.2413 0.3087 4.3106 4.4612| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 19.90 - 4.27 3511 170 0.79 26.61 0.99 0.79 6519.15| | 2: 4.27 - 3.40 3394 170 0.77 29.31 1.05 0.83 1242.53| |alpha: min = 0.79 max = 0.83 mean = 0.81| |beta: min = 1242.53 max = 6519.15 mean = 3925.54| |figures of merit: min = 0.00 max = 1.00 mean = 0.78| |phase err.(work): min = 0.00 max = 89.78 mean = 27.94| |phase err.(test): min = 0.00 max = 89.60 mean = 27.96| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2032 0.2004 0.2578 n_refl.: 7245 re-set all scales: r(all,work,free)=0.3750 0.3727 0.4184 n_refl.: 7245 remove outliers: r(all,work,free)=0.3750 0.3727 0.4184 n_refl.: 7245 overall B=0.00 to atoms: r(all,work,free)=0.3750 0.3727 0.4184 n_refl.: 7245 bulk-solvent and scaling: r(all,work,free)=0.1994 0.1965 0.2547 n_refl.: 7245 remove outliers: r(all,work,free)=0.1994 0.1965 0.2547 n_refl.: 7245 ======================== 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 19.902-13.063 90.91 91 9 0.1576 512.799 495.445 1.475 1.000 0.344 12.965-10.793 95.19 95 4 0.1065 484.800 478.406 1.456 0.999 0.340 10.793-8.919 99.47 176 10 0.1229 454.219 455.100 1.327 0.999 0.319 8.905-7.374 99.69 313 12 0.1840 275.088 267.675 1.141 0.997 0.290 7.364-6.089 99.82 547 20 0.2232 198.871 192.397 1.050 0.995 0.250 6.087-5.031 100.00 938 48 0.2218 157.348 150.783 0.967 0.993 0.190 5.030-4.158 99.88 1640 78 0.1765 166.336 160.571 0.995 0.989 0.120 4.156-3.397 99.85 3105 159 0.2474 74.801 69.347 1.059 0.984 0.030 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0610 b_overall=1.9547 ================= 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 : 0.4059 0.4598 0.014 1.971 93.7 154.1 112.5 0 0.000 1_bss: 0.2228 0.2845 0.014 1.971 85.3 145.7 104.1 0 0.000 1_settarget: 0.2228 0.2845 0.014 1.971 85.3 145.7 104.1 0 0.000 1_weight: 0.2228 0.2845 0.014 1.971 85.3 145.7 104.1 0 0.000 1_xyzrec: 0.2533 0.2829 0.003 0.686 85.3 145.7 104.1 0 0.262 1_adp: 0.2149 0.2668 0.003 0.686 81.1 180.7 113.3 0 0.262 1_regHadp: 0.2126 0.2680 0.003 0.686 81.1 180.7 113.3 0 0.262 2_bss: 0.2106 0.2667 0.003 0.686 81.1 180.7 113.3 0 0.262 2_settarget: 0.2106 0.2667 0.003 0.686 81.1 180.7 113.3 0 0.262 2_updatecdl: 0.2106 0.2667 0.003 0.751 81.1 180.7 113.3 0 0.262 2_weight: 0.2106 0.2667 0.003 0.751 81.1 180.7 113.3 0 0.262 2_xyzrec: 0.1899 0.2582 0.011 1.227 81.1 180.7 113.3 0 0.278 2_adp: 0.2351 0.2840 0.011 1.227 94.2 185.4 130.6 0 0.278 2_regHadp: 0.2419 0.2859 0.011 1.227 94.2 185.4 130.6 0 0.278 3_bss: 0.2207 0.2713 0.011 1.227 68.2 159.5 104.7 0 0.278 3_settarget: 0.2207 0.2713 0.011 1.227 68.2 159.5 104.7 0 0.278 3_updatecdl: 0.2207 0.2713 0.011 1.274 68.2 159.5 104.7 0 0.278 3_setrh: 0.2208 0.2713 0.011 1.274 68.2 159.5 104.7 0 0.278 3_weight: 0.2208 0.2713 0.011 1.274 68.2 159.5 104.7 0 0.278 3_xyzrec: 0.2240 0.2700 0.006 1.039 68.2 159.5 104.7 0 0.282 3_adp: 0.2016 0.2569 0.006 1.039 67.0 182.4 111.1 0 0.282 3_regHadp: 0.2004 0.2578 0.006 1.039 67.0 182.4 111.1 0 0.282 end: 0.1965 0.2547 0.006 1.039 67.0 182.4 111.1 0 0.282 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V1/1yab_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V1/1yab_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.4400 Refinement macro-cycles (run) : 130.0300 Write final files (write_after_run_outputs) : 17.2700 Total : 150.7400 Total CPU time: 2.79 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:25:31 PDT -0700 (1716251131.29 s) Start R-work = 0.2228, R-free = 0.2845 Final R-work = 0.1965, R-free = 0.2547 =============================================================================== Job complete usr+sys time: 183.05 seconds wall clock time: 9 minutes 49.58 seconds (589.58 seconds total)