Starting phenix.refine on Mon May 20 17:17:06 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=True 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 { 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: 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: 0.97, per 1000 atoms: 0.34 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: 1.37 Conformation dependent library (CDL) restraints added in 156.5 milliseconds 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 320 Time building geometry restraints manager: 1.44 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 { ramachandran_plot_restraints { enabled = True } 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 ============================ Update phi&psi targets =========================== 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 14.664544 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 0.2453 0.2866 0.0413 0.004 0.9 8.5 1.2 24.7 0 0.125 0.2512 0.2849 0.0337 0.003 0.8 9.2 1.2 20.9 0 0.250 0.2462 0.2843 0.0381 0.004 0.8 10.6 1.2 21.5 0 0.500 0.2381 0.2830 0.0449 0.004 0.9 11.7 1.2 22.8 0 1.000 0.2317 0.2826 0.0509 0.006 1.0 14.2 1.2 22.8 0 2.000 0.2283 0.2793 0.0510 0.008 1.1 15.9 1.2 23.4 0 3.000 0.2257 0.2782 0.0525 0.009 1.2 18.1 1.2 24.7 0 4.000 0.2246 0.2804 0.0559 0.011 1.3 19.5 1.2 25.3 0 5.000 0.2222 0.2797 0.0575 0.012 1.4 19.1 1.8 25.9 0 6.000 0.2208 0.2777 0.0569 0.014 1.4 21.2 2.4 27.2 0 7.000 0.2194 0.2778 0.0584 0.015 1.5 21.9 2.4 27.2 0 8.000 0.2183 0.2777 0.0594 0.017 1.6 22.7 2.4 27.2 0 9.000 0.2176 0.2768 0.0592 0.018 1.6 22.7 2.4 27.8 0 10.000 0.2200 0.2784 0.0584 0.014 1.5 20.2 2.4 27.2 0 7.332 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2512 0.2849 0.0337 0.003 0.8 9.2 1.2 20.9 0 0.250 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 25.12 28.49 3.37 0.822 103.807 0.185 0.062 25.27 28.55 3.28 2.039 103.904 0.006 0.063 24.74 28.26 3.51 2.107 103.910 0.023 0.060 23.91 27.79 3.88 3.338 104.148 0.093 0.056 22.71 27.19 4.48 7.830 105.388 0.185 0.050 22.41 26.99 4.57 9.365 105.880 0.278 0.049 22.23 26.88 4.65 10.458 106.240 0.370 0.048 22.11 26.81 4.70 11.255 106.502 0.463 0.047 21.92 26.74 4.82 12.350 106.927 0.555 0.047 21.73 26.68 4.95 13.501 107.373 0.648 0.046 21.60 26.65 5.05 14.490 107.745 0.740 0.045 21.54 26.63 5.10 14.997 107.914 0.833 0.045 21.51 26.61 5.11 15.327 108.010 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: 21.51 26.61 5.11 15.327 108.010 0.925 0.045 Individual atomic B min max mean iso aniso Overall: 81.13 184.67 112.84 12.52 1355 0 Protein: 81.13 184.67 112.84 12.52 1355 0 Chain A: 81.33 184.67 113.83 N/A 669 0 Chain B: 81.13 179.91 111.86 N/A 686 0 Histogram: Values Number of atoms 81.13 - 91.48 275 91.48 - 101.84 230 101.84 - 112.19 240 112.19 - 122.54 205 122.54 - 132.90 136 132.90 - 143.25 119 143.25 - 153.61 78 153.61 - 163.96 44 163.96 - 174.31 19 174.31 - 184.67 9 =========================== Idealize ADP of riding H ========================== r_work=0.2151 r_free=0.2661 r_work=0.2134 r_free=0.2677 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.40 - 19.90 A, n_refl.=7245 (all), 4.69 % free)-------------| | | | r_work= 0.2134 r_free= 0.2677 coordinate error (max.-lik. estimate): 0.38 A | | | | normalized target function (ls_wunit_k1) (work): 0.043982 | | target function (ls_wunit_k1) not normalized (work): 303.698790 | | target function (ls_wunit_k1) not normalized (free): 28.614018 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2160 0.2134 0.2677 n_refl.: 7245 re-set all scales: r(all,work,free)=0.3862 0.3839 0.4288 n_refl.: 7245 remove outliers: r(all,work,free)=0.3862 0.3839 0.4288 n_refl.: 7245 overall B=0.00 to atoms: r(all,work,free)=0.3862 0.3839 0.4288 n_refl.: 7245 bulk-solvent and scaling: r(all,work,free)=0.2127 0.2100 0.2653 n_refl.: 7245 remove outliers: r(all,work,free)=0.2127 0.2100 0.2653 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 0.1586 482.896 464.782 1.389 0.995 0.344 12.965-10.793 95.19 95 4 0.1135 456.531 454.552 1.326 0.994 0.330 10.793-8.919 99.47 176 10 0.1324 427.732 426.770 1.241 0.995 0.305 8.905-7.374 99.69 313 12 0.1787 259.047 253.928 1.094 0.993 0.290 7.364-6.089 99.82 547 20 0.2187 187.274 184.029 1.016 0.992 0.250 6.087-5.031 100.00 938 48 0.2167 148.172 143.128 0.925 0.989 0.190 5.030-4.158 99.88 1640 78 0.1821 156.637 151.647 0.960 0.986 0.130 4.156-3.397 99.85 3105 159 0.3025 70.440 65.033 1.031 0.982 0.045 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9978 b_overall=0.1322 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 4.528312 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.039768 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 0.2088 0.2633 0.0545 0.003 0.6 7.4 1.2 13.9 0 0.125 0.2029 0.2653 0.0624 0.003 0.7 8.1 1.2 16.5 0 0.250 0.1977 0.2645 0.0667 0.005 0.8 9.6 1.8 17.7 0 0.500 0.1940 0.2624 0.0684 0.007 0.9 13.5 1.8 19.6 0 1.000 0.1908 0.2614 0.0706 0.012 1.2 14.5 1.8 22.8 0 2.000 0.1896 0.2595 0.0699 0.016 1.5 17.3 1.8 24.7 0 3.000 0.1888 0.2601 0.0714 0.020 1.7 19.8 2.4 27.2 0 4.000 0.1880 0.2596 0.0715 0.024 1.9 23.0 3.0 27.2 0 5.000 0.1879 0.2626 0.0748 0.027 2.1 24.1 3.0 30.4 0 6.000 0.1873 0.2631 0.0758 0.030 2.3 24.4 3.6 31.6 0 7.000 0.1865 0.2646 0.0781 0.033 2.5 25.1 3.6 32.3 0 8.000 0.1862 0.2626 0.0763 0.035 2.6 27.3 4.2 32.3 0 9.000 0.1861 0.2650 0.0790 0.038 2.8 28.3 3.6 28.5 0 10.000 0.1904 0.2611 0.0708 0.013 1.3 14.9 1.8 22.8 0 2.264 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2088 0.2633 0.0545 0.003 0.6 7.4 1.2 13.9 0 0.125 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 20.88 26.33 5.45 18.685 124.634 0.040 4.953 26.33 29.78 3.45 13.844 133.796 0.001 5.046 24.88 28.25 3.37 14.599 132.543 0.005 5.014 22.14 26.62 4.48 16.974 129.053 0.020 4.945 21.05 26.12 5.07 17.676 127.098 0.040 4.919 20.75 25.96 5.22 18.150 126.757 0.060 4.912 20.63 25.96 5.33 18.612 127.032 0.080 4.907 20.33 25.63 5.29 18.667 126.786 0.099 4.899 20.27 25.58 5.31 18.858 126.846 0.119 4.897 20.21 25.56 5.35 19.075 126.983 0.139 4.896 20.18 25.55 5.37 19.288 127.130 0.159 4.894 20.15 25.55 5.40 19.489 127.263 0.179 4.893 20.13 25.54 5.41 19.678 127.389 0.199 4.892 max suggested for this run: 24.93 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.199 Accepted refinement result: 20.13 25.54 5.41 19.678 127.389 0.199 4.892 Individual atomic B min max mean iso aniso Overall: 76.13 201.77 118.59 18.30 1355 0 Protein: 76.13 201.77 118.59 18.30 1355 0 Chain A: 76.96 198.81 119.92 N/A 669 0 Chain B: 76.13 201.77 117.30 N/A 686 0 Histogram: Values Number of atoms 76.13 - 88.69 189 88.69 - 101.26 194 101.26 - 113.82 261 113.82 - 126.38 237 126.38 - 138.95 162 138.95 - 151.51 123 151.51 - 164.08 116 164.08 - 176.64 47 176.64 - 189.20 21 189.20 - 201.77 5 =========================== Idealize ADP of riding H ========================== r_work=0.2013 r_free=0.2554 r_work=0.2021 r_free=0.2553 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.40 - 19.90 A, n_refl.=7245 (all), 4.69 % free)-------------| | | | r_work= 0.2021 r_free= 0.2553 coordinate error (max.-lik. estimate): 0.23 A | | | | normalized target function (ml) (work): 4.890596 | | target function (ml) not normalized (work): 33769.566705 | | target function (ml) not normalized (free): 1725.633445 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2047 0.2021 0.2553 n_refl.: 7245 re-set all scales: r(all,work,free)=0.3918 0.3896 0.4332 n_refl.: 7245 remove outliers: r(all,work,free)=0.3918 0.3896 0.4332 n_refl.: 7245 overall B=-7.28 to atoms: r(all,work,free)=0.3688 0.3665 0.4119 n_refl.: 7245 bulk-solvent and scaling: r(all,work,free)=0.2030 0.2003 0.2551 n_refl.: 7245 remove outliers: r(all,work,free)=0.2030 0.2003 0.2551 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 0.1689 482.896 464.372 1.526 0.980 0.346 12.965-10.793 95.19 95 4 0.1252 456.531 451.281 1.406 0.980 0.324 10.793-8.919 99.47 176 10 0.1247 427.732 426.504 1.337 0.981 0.316 8.905-7.374 99.69 313 12 0.1891 259.047 252.527 1.157 0.981 0.288 7.364-6.089 99.82 547 20 0.2179 187.274 181.807 1.066 0.982 0.240 6.087-5.031 100.00 938 48 0.2229 148.172 142.360 0.961 0.984 0.191 5.030-4.158 99.88 1640 78 0.1817 156.637 150.901 0.979 0.986 0.120 4.156-3.397 99.85 3105 159 0.2511 70.440 65.136 1.025 0.991 0.034 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0577 b_overall=3.1422 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.2003 r_free=0.2551 After: r_work=0.2003 r_free=0.2552 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 5.053278 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.037712 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 0.2002 0.2549 0.0548 0.003 0.7 7.8 1.2 13.9 0 0.125 0.1999 0.2550 0.0551 0.003 0.7 7.4 1.2 13.9 0 0.250 0.1984 0.2560 0.0576 0.005 0.7 8.1 1.2 13.9 0 0.500 0.1894 0.2564 0.0670 0.010 1.2 12.4 1.2 12.7 0 1.000 0.1858 0.2551 0.0693 0.012 1.6 26.9 1.2 16.5 0 2.000 0.1838 0.2521 0.0683 0.015 1.8 27.3 1.8 19.6 0 3.000 0.1823 0.2524 0.0701 0.019 2.1 30.8 1.8 20.3 0 4.000 0.1818 0.2535 0.0718 0.022 2.3 33.6 2.4 20.9 0 5.000 0.1807 0.2526 0.0719 0.024 2.6 32.2 2.4 20.9 0 6.000 0.1807 0.2537 0.0730 0.026 2.7 32.6 2.4 20.9 0 7.000 0.1805 0.2511 0.0706 0.029 2.9 35.8 2.4 24.7 0 8.000 0.1798 0.2503 0.0705 0.030 3.0 32.9 2.4 23.4 0 9.000 0.1804 0.2469 0.0665 0.033 3.1 38.9 3.0 31.0 0 10.000 0.1851 0.2563 0.0712 0.013 1.8 25.1 1.2 15.8 0 2.527 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1999 0.2550 0.0551 0.003 0.7 7.4 1.2 13.9 0 0.250 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 19.99 25.50 5.51 21.592 123.771 0.038 4.893 26.39 30.12 3.73 16.567 133.489 0.001 5.023 26.04 29.96 3.92 17.276 134.128 0.005 5.022 22.49 27.29 4.80 18.246 128.634 0.019 4.960 21.18 26.38 5.19 18.595 126.691 0.038 4.922 20.60 25.88 5.28 18.905 125.853 0.057 4.903 20.35 25.68 5.33 19.132 125.680 0.075 4.895 20.19 25.62 5.43 19.322 125.850 0.094 4.890 19.98 25.46 5.48 19.610 125.636 0.113 4.883 19.86 25.41 5.54 19.967 125.512 0.132 4.880 19.79 25.37 5.57 20.248 125.493 0.151 4.878 19.74 25.36 5.62 20.453 125.658 0.170 4.877 19.71 25.35 5.64 20.651 125.476 0.189 4.876 max suggested for this run: 24.75 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.189 Accepted refinement result: 19.71 25.35 5.64 20.651 125.476 0.189 4.876 Individual atomic B min max mean iso aniso Overall: 64.54 204.07 114.88 19.73 1355 0 Protein: 64.54 204.07 114.88 19.73 1355 0 Chain A: 66.21 204.07 116.42 N/A 669 0 Chain B: 64.54 204.00 113.38 N/A 686 0 Histogram: Values Number of atoms 64.54 - 78.49 92 78.49 - 92.45 201 92.45 - 106.40 296 106.40 - 120.35 271 120.35 - 134.31 177 134.31 - 148.26 126 148.26 - 162.21 118 162.21 - 176.16 49 176.16 - 190.12 18 190.12 - 204.07 7 =========================== Idealize ADP of riding H ========================== r_work=0.1971 r_free=0.2535 r_work=0.1973 r_free=0.2534 ----------X-ray data---------- |--(resolution: 3.40 - 19.90 A, n_refl.=7245 (all), 4.69 % free)-------------| | | | r_work= 0.1973 r_free= 0.2534 coordinate error (max.-lik. estimate): 0.17 A | | | | normalized target function (ml) (work): 4.876430 | | target function (ml) not normalized (work): 33671.751774 | | target function (ml) not normalized (free): 1723.207732 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1847 0.2383 5.307 5.5507| | 2: 4.27 - 3.40 1.00 3394 170 0.2321 0.2958 4.431 4.5858| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 26.54 1.00 0.93 8676.49| | 2: 4.27 - 3.40 3394 170 0.79 27.95 1.03 0.98 1544.36| |alpha: min = 0.93 max = 0.98 mean = 0.95| |beta: min = 1544.36 max = 8676.49 mean = 5170.85| |figures of merit: min = 0.00 max = 1.00 mean = 0.79| |phase err.(work): min = 0.00 max = 89.96 mean = 27.23| |phase err.(test): min = 0.00 max = 89.56 mean = 27.64| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2001 0.1973 0.2534 n_refl.: 7245 re-set all scales: r(all,work,free)=0.3773 0.3749 0.4215 n_refl.: 7245 remove outliers: r(all,work,free)=0.3773 0.3749 0.4215 n_refl.: 7245 overall B=-3.62 to atoms: r(all,work,free)=0.3658 0.3634 0.4110 n_refl.: 7245 bulk-solvent and scaling: r(all,work,free)=0.1987 0.1961 0.2495 n_refl.: 7245 remove outliers: r(all,work,free)=0.1987 0.1961 0.2495 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 0.1679 482.896 463.011 1.497 0.975 0.345 12.965-10.793 95.19 95 4 0.1230 456.531 449.935 1.383 0.977 0.322 10.793-8.919 99.47 176 10 0.1295 427.732 425.223 1.312 0.978 0.313 8.905-7.374 99.69 313 12 0.1881 259.047 251.862 1.133 0.980 0.284 7.364-6.089 99.82 547 20 0.2175 187.274 181.787 1.054 0.983 0.245 6.087-5.031 100.00 938 48 0.2200 148.172 142.597 0.942 0.988 0.196 5.030-4.158 99.88 1640 78 0.1761 156.637 151.687 0.955 0.995 0.115 4.156-3.397 99.85 3105 159 0.2407 70.440 66.140 1.014 1.007 0.032 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0265 b_overall=1.3245 ================= 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_updatephipsi: 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: 0.2512 0.2849 0.003 0.766 85.3 145.7 104.1 0 0.264 1_adp: 0.2151 0.2661 0.003 0.766 81.1 184.7 112.8 0 0.264 1_regHadp: 0.2134 0.2677 0.003 0.766 81.1 184.7 112.8 0 0.264 2_bss: 0.2100 0.2653 0.003 0.766 81.1 184.7 112.8 0 0.264 2_settarget: 0.2100 0.2653 0.003 0.766 81.1 184.7 112.8 0 0.264 2_updatephipsi: 0.2100 0.2653 0.003 0.766 81.1 184.7 112.8 0 0.264 2_updatecdl: 0.2100 0.2653 0.004 0.819 81.1 184.7 112.8 0 0.264 2_weight: 0.2100 0.2653 0.004 0.819 81.1 184.7 112.8 0 0.264 2_xyzrec: 0.2088 0.2633 0.003 0.647 81.1 184.7 112.8 0 0.342 2_adp: 0.2013 0.2554 0.003 0.647 76.1 201.8 118.6 0 0.342 2_regHadp: 0.2021 0.2553 0.003 0.647 76.1 201.8 118.6 0 0.342 3_bss: 0.2003 0.2551 0.003 0.647 68.9 194.5 111.3 0 0.342 3_settarget: 0.2003 0.2551 0.003 0.647 68.9 194.5 111.3 0 0.342 3_updatephipsi: 0.2003 0.2551 0.003 0.647 68.9 194.5 111.3 0 0.342 3_updatecdl: 0.2003 0.2551 0.003 0.665 68.9 194.5 111.3 0 0.342 3_setrh: 0.2003 0.2552 0.003 0.665 68.9 194.5 111.3 0 0.342 3_weight: 0.2003 0.2552 0.003 0.665 68.9 194.5 111.3 0 0.342 3_xyzrec: 0.1999 0.2550 0.003 0.653 68.9 194.5 111.3 0 0.343 3_adp: 0.1971 0.2535 0.003 0.653 64.5 204.1 114.9 0 0.343 3_regHadp: 0.1973 0.2534 0.003 0.653 64.5 204.1 114.9 0 0.343 end: 0.1961 0.2495 0.003 0.653 60.9 200.5 111.3 0 0.343 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V2/1yab_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V2/1yab_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.1200 Refinement macro-cycles (run) : 146.7700 Write final files (write_after_run_outputs) : 17.6800 Total : 168.5700 Total CPU time: 3.24 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:28:42 PDT -0700 (1716251322.93 s) Start R-work = 0.2228, R-free = 0.2845 Final R-work = 0.1961, R-free = 0.2495 =============================================================================== Job complete usr+sys time: 210.81 seconds wall clock time: 12 minutes 20.18 seconds (740.18 seconds total)