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/2h1g.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/2h1g/2h1g.mtz Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- optimize_xyz=true optimize_adp=true main.number_of_mac=3 main.max_number_of_iterations=100 main.nproc=20 nonbonded_weight=100 modify_start_model.modify.selection=element H modify_start_model.modify.occupancies.set=1 strategy=individual_sites+individual_adp ramachandran_plot_restraints.enabled=False secondary_structure.enabled=False main.nqh_flips=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/2h1g/2h1g.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/2h1g/2h1g.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/2h1g.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/2h1g.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls occupancies group_anomalous \ den } main { nqh_flips = False max_number_of_iterations = 100 nproc = 20 } modify_start_model { modify { selection = element H occupancies { set = 1 } } } pdb_interpretation { nonbonded_weight = 100 } target_weights { optimize_xyz_weight = true optimize_adp_weight = true } } Starting job =============================================================================== Symmetric amino acids flipped None Time to flip residues: 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 4293 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 2139 Classifications: {'peptide': 136} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 127} Chain: "B" Number of atoms: 2154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 2154 Classifications: {'peptide': 137} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 128} Time building chain proxies: 0.85, per 1000 atoms: 0.20 Number of scatterers: 4293 At special positions: 0 Unit cell: (47.031, 59.522, 109.562, 90, 90, 90) Space group: P 21 21 21 (No. 19) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 O 405 8.00 N 349 7.00 C 1391 6.00 H 2138 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: 1.05 Conformation dependent library (CDL) restraints added in 136.4 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 506 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.16: 2140 1.16 - 1.33: 536 1.33 - 1.51: 996 1.51 - 1.68: 655 1.68 - 1.86: 20 Bond restraints: 4347 Sorted by residual: bond pdb=" N LYS B 89 " pdb=" H LYS B 89 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N ASP A 41 " pdb=" H ASP A 41 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N MET A 164 " pdb=" H MET A 164 " 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 B 166 " pdb=" H HIS B 166 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" NE1 TRP B 70 " pdb=" HE1 TRP B 70 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 4342 not shown) Histogram of bond angle deviations from ideal: 98.40 - 106.27: 294 106.27 - 114.14: 5068 114.14 - 122.01: 1765 122.01 - 129.88: 740 129.88 - 137.75: 22 Bond angle restraints: 7889 Sorted by residual: angle pdb=" N TRP B 73 " pdb=" CA TRP B 73 " pdb=" C TRP B 73 " ideal model delta sigma weight residual 111.82 119.27 -7.45 1.16e+00 7.43e-01 4.13e+01 angle pdb=" N ASP A 41 " pdb=" CA ASP A 41 " pdb=" C ASP A 41 " ideal model delta sigma weight residual 110.23 118.37 -8.14 1.45e+00 4.76e-01 3.15e+01 angle pdb=" N ASP B 41 " pdb=" CA ASP B 41 " pdb=" C ASP B 41 " ideal model delta sigma weight residual 110.24 118.13 -7.89 1.41e+00 5.03e-01 3.13e+01 angle pdb=" O VAL A 137 " pdb=" C VAL A 137 " pdb=" N SER A 138 " ideal model delta sigma weight residual 122.72 129.05 -6.33 1.18e+00 7.18e-01 2.88e+01 angle pdb=" C LYS B 173 " pdb=" N PRO B 174 " pdb=" CA PRO B 174 " ideal model delta sigma weight residual 119.84 126.44 -6.60 1.25e+00 6.40e-01 2.79e+01 ... (remaining 7884 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 1802 17.76 - 35.52: 158 35.52 - 53.28: 75 53.28 - 71.04: 15 71.04 - 88.80: 5 Dihedral angle restraints: 2055 sinusoidal: 1106 harmonic: 949 Sorted by residual: dihedral pdb=" C SER B 138 " pdb=" N SER B 138 " pdb=" CA SER B 138 " pdb=" CB SER B 138 " ideal model delta harmonic sigma weight residual -122.60 -144.10 21.50 0 2.50e+00 1.60e-01 7.39e+01 dihedral pdb=" N SER B 138 " pdb=" C SER B 138 " pdb=" CA SER B 138 " pdb=" CB SER B 138 " ideal model delta harmonic sigma weight residual 122.80 143.41 -20.61 0 2.50e+00 1.60e-01 6.80e+01 dihedral pdb=" CA PRO B 139 " pdb=" C PRO B 139 " pdb=" N LEU B 140 " pdb=" CA LEU B 140 " ideal model delta harmonic sigma weight residual -180.00 -150.85 -29.15 0 5.00e+00 4.00e-02 3.40e+01 ... (remaining 2052 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.153: 264 0.153 - 0.305: 60 0.305 - 0.456: 4 0.456 - 0.607: 2 0.607 - 0.759: 1 Chirality restraints: 331 Sorted by residual: chirality pdb=" CA SER B 138 " pdb=" N SER B 138 " pdb=" C SER B 138 " pdb=" CB SER B 138 " both_signs ideal model delta sigma weight residual False 2.51 1.75 0.76 2.00e-01 2.50e+01 1.44e+01 chirality pdb=" CA VAL B 137 " pdb=" N VAL B 137 " pdb=" C VAL B 137 " pdb=" CB VAL B 137 " both_signs ideal model delta sigma weight residual False 2.44 2.91 -0.47 2.00e-01 2.50e+01 5.54e+00 chirality pdb=" CA MET A 169 " pdb=" N MET A 169 " pdb=" C MET A 169 " pdb=" CB MET A 169 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.34e+00 ... (remaining 328 not shown) Planarity restraints: 641 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 73 " 0.047 2.00e-02 2.50e+03 1.93e-02 1.48e+01 pdb=" CG TRP B 73 " 0.014 2.00e-02 2.50e+03 pdb=" CD1 TRP B 73 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP B 73 " -0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP B 73 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TRP B 73 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP B 73 " -0.019 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 73 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 73 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP B 73 " 0.010 2.00e-02 2.50e+03 pdb=" HD1 TRP B 73 " -0.004 2.00e-02 2.50e+03 pdb=" HE1 TRP B 73 " -0.025 2.00e-02 2.50e+03 pdb=" HE3 TRP B 73 " -0.040 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 73 " 0.005 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 73 " -0.001 2.00e-02 2.50e+03 pdb=" HH2 TRP B 73 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 135 " -0.025 2.00e-02 2.50e+03 2.02e-02 1.23e+01 pdb=" CG TYR A 135 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR A 135 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR A 135 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR A 135 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR A 135 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A 135 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 135 " -0.006 2.00e-02 2.50e+03 pdb=" HD1 TYR A 135 " -0.030 2.00e-02 2.50e+03 pdb=" HD2 TYR A 135 " 0.023 2.00e-02 2.50e+03 pdb=" HE1 TYR A 135 " 0.021 2.00e-02 2.50e+03 pdb=" HE2 TYR A 135 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 135 " 0.039 2.00e-02 2.50e+03 1.86e-02 1.03e+01 pdb=" CG TYR B 135 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR B 135 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR B 135 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR B 135 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR B 135 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR B 135 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 135 " 0.034 2.00e-02 2.50e+03 pdb=" HD1 TYR B 135 " 0.009 2.00e-02 2.50e+03 pdb=" HD2 TYR B 135 " -0.009 2.00e-02 2.50e+03 pdb=" HE1 TYR B 135 " -0.019 2.00e-02 2.50e+03 pdb=" HE2 TYR B 135 " -0.000 2.00e-02 2.50e+03 ... (remaining 638 not shown) Histogram of nonbonded interaction distances: 1.38 - 2.03: 214 2.03 - 2.67: 5966 2.67 - 3.31: 13281 3.31 - 3.96: 18109 3.96 - 4.60: 27063 Nonbonded interactions: 64633 Sorted by model distance: nonbonded pdb="HD12 LEU B 145 " pdb=" HB3 LYS B 154 " model vdw 1.385 2.440 nonbonded pdb="HD21 ASN B 44 " pdb=" HB3 SER B 58 " model vdw 1.410 2.270 nonbonded pdb=" HH TYR A 88 " pdb=" OE1 GLU A 97 " model vdw 1.440 1.850 nonbonded pdb=" OD1 ASP A 49 " pdb=" H ASN A 51 " model vdw 1.472 1.850 nonbonded pdb=" OD1 ASP B 49 " pdb=" H ASN B 51 " model vdw 1.500 1.850 ... (remaining 64628 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 10 15.96 2 O 405 7.97 1 N 349 6.97 1 C 1391 5.97 2 H 2138 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: 2138 of 4293 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 4293 n_use_u_iso = 4293 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 = 4293 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (4293 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 4293 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 = "2h1g_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 2138 occupancy sum: 2138.00 (% of total atoms 49.80) Rotatable: count: 610 occupancy sum: 610.00 (% of total atoms 14.21) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.10 - 36.90 A, n_refl.=5695 (all), 5.23 % free)-------------| | | | r_work= 0.3523 r_free= 0.3456 coordinate error (max.-lik. estimate): 0.23 A | | | | normalized target function (ml) (work): 6.129983 | | target function (ml) not normalized (work): 33083.515704 | | target function (ml) not normalized (free): 1923.593214 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 36.90 - 3.91 0.97 2809 138 0.3665 0.3354 6.3578 6.4558| | 2: 3.91 - 3.10 0.94 2588 160 0.3327 0.3587 5.8828 6.4544| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 36.90 - 3.91 2809 138 0.76 28.35 0.89 0.78 61335.00| | 2: 3.91 - 3.10 2588 160 0.88 18.54 1.37 1.02 18111.74| |alpha: min = 0.10 max = 1.08 mean = 0.90| |beta: min = 12794.24 max = 259712.65 mean = 40608.33| |figures of merit: min = 0.00 max = 1.00 mean = 0.82| |phase err.(work): min = 0.00 max = 89.81 mean = 23.65| |phase err.(test): min = 0.00 max = 89.70 mean = 22.17| |-----------------------------------------------------------------------------| ----------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 : 0.024 0.153 2209 Z= 1.362 Angle : 2.035 10.752 2998 Z= 1.276 Chirality : 0.130 0.759 331 Planarity : 0.006 0.021 386 Dihedral : 17.709 88.802 808 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 1.49 % Allowed : 4.83 % Favored : 93.68 % Rotamer: Outliers : 6.69 % Allowed : 12.55 % Favored : 80.75 % Cbeta Deviations : 0.79 % Peptide Plane: Cis-proline : 18.75 % 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: -2.93 (0.45), residues: 269 helix: -2.28 (0.39), residues: 93 sheet: -1.31 (0.58), residues: 77 loop : -1.82 (0.56), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 129 TYR 0.040 0.010 TYR B 135 PHE 0.021 0.006 PHE A 91 TRP 0.027 0.008 TRP B 73 HIS 0.010 0.006 HIS A 90 Individual atomic B min max mean iso aniso Overall: 2.00 37.24 13.06 1.53 2155 0 Protein: 2.00 37.24 13.06 1.53 2155 0 Chain A: 2.00 33.66 13.04 N/A 1073 0 Chain B: 2.00 37.24 13.09 N/A 1082 0 Histogram: Values Number of atoms 2.00 - 5.52 154 5.52 - 9.05 509 9.05 - 12.57 430 12.57 - 16.10 443 16.10 - 19.62 315 19.62 - 23.14 170 23.14 - 26.67 71 26.67 - 30.19 32 30.19 - 33.72 26 33.72 - 37.24 5 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 3 ************************* |--(resolution: 3.10 - 36.90 A, n_refl.=5695 (all), 5.23 % free)-------------| | | | r_work= 0.3523 r_free= 0.3456 coordinate error (max.-lik. estimate): 0.23 A | | | | normalized target function (ml) (work): 6.129983 | | target function (ml) not normalized (work): 33083.515704 | | target function (ml) not normalized (free): 1923.593214 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3517 0.3523 0.3456 n_refl.: 5695 re-set all scales: r(all,work,free)=0.3517 0.3523 0.3456 n_refl.: 5695 remove outliers: r(all,work,free)=0.3515 0.3522 0.3456 n_refl.: 5694 overall B=1.09 to atoms: r(all,work,free)=0.3563 0.3570 0.3478 n_refl.: 5694 bulk-solvent and scaling: r(all,work,free)=0.1927 0.1895 0.2493 n_refl.: 5694 remove outliers: r(all,work,free)=0.1927 0.1895 0.2493 n_refl.: 5694 ======================== 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 36.902-12.728 94.29 95 4 0.2921 541.895 491.160 0.931 1.188 0.390 12.598-9.947 96.15 96 4 0.1369 773.478 775.898 1.022 1.165 0.399 9.931-7.830 97.01 189 6 0.1608 683.507 672.379 1.067 1.151 0.409 7.826-6.174 96.81 381 14 0.2165 462.055 446.916 0.988 1.121 0.461 6.172-4.868 97.27 748 36 0.1786 518.967 507.654 0.949 1.073 0.470 4.862-3.836 96.79 1456 84 0.1625 627.947 611.330 1.027 0.996 0.471 3.836-3.102 94.30 2431 150 0.2128 446.506 421.037 1.121 0.883 0.195 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=4.9144 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 14.962826 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.982810 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 0.2090 0.2525 0.0436 0.003 0.7 3.0 0.7 4.6 0 0.125 0.2068 0.2511 0.0443 0.003 0.7 2.3 0.7 4.6 0 0.250 0.2026 0.2506 0.0480 0.004 0.7 2.6 0.7 4.6 0 0.500 0.1956 0.2495 0.0538 0.004 0.7 2.6 0.7 4.6 0 1.000 0.1860 0.2515 0.0655 0.006 0.8 3.3 1.1 4.6 0 2.000 0.1793 0.2466 0.0673 0.007 0.9 3.7 1.1 4.2 0 3.000 0.1743 0.2488 0.0745 0.008 0.9 4.7 1.1 5.9 0 4.000 0.1721 0.2491 0.0770 0.010 1.0 4.9 1.1 7.1 0 5.000 0.1701 0.2485 0.0783 0.011 1.1 5.6 1.5 7.1 0 6.000 0.1686 0.2485 0.0799 0.013 1.2 6.1 1.5 7.5 0 7.000 0.1672 0.2482 0.0810 0.014 1.3 5.6 1.5 7.5 0 8.000 0.1660 0.2477 0.0817 0.015 1.3 5.8 1.5 7.9 0 9.000 0.1653 0.2477 0.0823 0.016 1.4 6.3 1.5 8.8 0 10.000 0.1680 0.2481 0.0802 0.013 1.2 6.1 1.5 7.5 0 7.481 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2068 0.2511 0.0443 0.003 0.7 2.3 0.7 4.6 0 0.250 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 20.68 25.11 4.43 1.092 14.008 0.983 0.052 20.82 25.32 4.51 1.805 14.210 0.029 0.053 20.03 25.26 5.22 2.200 14.242 0.123 0.049 19.08 25.19 6.11 3.337 14.252 0.491 0.044 17.99 25.28 7.28 6.392 14.818 0.983 0.040 17.44 25.35 7.90 8.643 15.482 1.474 0.037 17.22 25.42 8.20 9.845 15.817 1.966 0.036 17.00 25.58 8.59 11.334 16.281 2.457 0.035 16.88 26.10 9.22 14.349 17.179 2.948 0.035 16.87 26.22 9.36 14.929 17.323 3.440 0.035 16.85 26.35 9.51 15.529 17.486 3.931 0.035 16.69 26.54 9.86 17.514 18.123 4.423 0.034 16.67 26.58 9.91 17.986 18.253 4.914 0.034 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.123 Accepted refinement result: 20.03 25.26 5.22 2.200 14.242 0.123 0.049 Individual atomic B min max mean iso aniso Overall: 5.70 38.91 14.62 2.10 2155 0 Protein: 5.70 38.91 14.62 2.10 2155 0 Chain A: 5.87 34.64 14.70 N/A 1073 0 Chain B: 5.70 38.91 14.55 N/A 1082 0 Histogram: Values Number of atoms 5.70 - 9.02 315 9.02 - 12.34 598 12.34 - 15.66 452 15.66 - 18.98 348 18.98 - 22.30 222 22.30 - 25.62 117 25.62 - 28.95 46 28.95 - 32.27 33 32.27 - 35.59 19 35.59 - 38.91 5 =========================== Idealize ADP of riding H ========================== r_work=0.2003 r_free=0.2526 r_work=0.1993 r_free=0.2520 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.10 - 36.90 A, n_refl.=5694 (all), 5.23 % free)-------------| | | | r_work= 0.1993 r_free= 0.2520 coordinate error (max.-lik. estimate): 0.36 A | | | | normalized target function (ls_wunit_k1) (work): 0.048442 | | target function (ls_wunit_k1) not normalized (work): 261.390513 | | target function (ls_wunit_k1) not normalized (free): 21.954035 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2021 0.1993 0.2520 n_refl.: 5694 re-set all scales: r(all,work,free)=0.3606 0.3612 0.3544 n_refl.: 5694 remove outliers: r(all,work,free)=0.3606 0.3612 0.3544 n_refl.: 5694 overall B=1.04 to atoms: r(all,work,free)=0.3649 0.3657 0.3564 n_refl.: 5694 bulk-solvent and scaling: r(all,work,free)=0.1996 0.1968 0.2500 n_refl.: 5694 remove outliers: r(all,work,free)=0.1996 0.1968 0.2500 n_refl.: 5694 ======================== 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 36.902-12.728 94.29 95 4 0.2872 391.960 345.023 0.932 1.330 0.410 12.598-9.947 96.15 96 4 0.1352 559.468 545.682 0.940 1.293 0.409 9.931-7.830 97.01 189 6 0.1568 494.390 475.993 0.977 1.266 0.419 7.826-6.174 96.81 381 14 0.2288 334.211 317.690 0.880 1.214 0.441 6.172-4.868 97.27 748 36 0.1874 375.376 364.057 0.878 1.130 0.442 4.862-3.836 96.79 1456 84 0.1743 454.203 440.778 1.023 0.998 0.409 3.836-3.102 94.30 2431 150 0.2189 322.964 310.951 1.257 0.804 0.207 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=4.6637 ============================ 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 = 1.925175 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.123673 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 0.1823 0.2410 0.0587 0.003 0.6 3.3 0.7 2.9 0 0.096 0.1712 0.2425 0.0713 0.006 0.7 3.7 0.7 3.8 0 0.289 0.1636 0.2419 0.0784 0.010 1.0 5.4 1.1 5.0 0 0.578 0.1595 0.2433 0.0838 0.013 1.2 5.6 1.5 6.3 0 0.866 0.1569 0.2434 0.0866 0.016 1.3 6.5 1.5 7.1 0 1.155 0.1545 0.2449 0.0904 0.019 1.5 7.2 1.5 7.1 0 1.444 0.1526 0.2451 0.0925 0.021 1.6 7.5 1.5 7.5 0 1.733 0.1511 0.2452 0.0941 0.023 1.7 7.7 1.5 7.5 0 2.021 0.1593 0.2418 0.0824 0.014 1.2 5.4 1.5 6.3 0 0.963 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1823 0.2410 0.0587 0.003 0.6 3.3 0.7 2.9 0 0.096 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 18.23 24.10 5.87 2.662 17.151 0.124 5.810 18.90 24.46 5.56 2.718 17.426 0.004 5.839 17.69 23.77 6.08 2.918 17.442 0.015 5.776 16.65 23.68 7.03 4.517 17.411 0.062 5.717 15.88 23.48 7.61 7.126 17.911 0.124 5.667 15.69 23.52 7.83 8.277 18.171 0.186 5.653 15.60 23.59 7.98 9.032 18.353 0.247 5.646 15.54 23.64 8.11 9.649 18.502 0.309 5.642 15.49 23.68 8.19 10.189 18.632 0.371 5.638 15.46 23.71 8.25 10.592 18.729 0.433 5.636 15.45 23.75 8.30 10.911 18.808 0.495 5.634 15.44 23.78 8.34 11.179 18.875 0.557 5.633 15.42 23.80 8.38 11.425 18.933 0.618 5.632 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.004 Accepted refinement result: 18.90 24.46 5.56 2.718 17.426 0.004 5.839 Individual atomic B min max mean iso aniso Overall: 9.44 36.10 16.21 1.16 2155 0 Protein: 9.44 36.10 16.21 1.16 2155 0 Chain A: 9.93 32.14 16.37 N/A 1073 0 Chain B: 9.44 36.10 16.05 N/A 1082 0 Histogram: Values Number of atoms 9.44 - 12.10 319 12.10 - 14.77 686 14.77 - 17.43 441 17.43 - 20.10 331 20.10 - 22.77 196 22.77 - 25.43 94 25.43 - 28.10 42 28.10 - 30.76 24 30.76 - 33.43 16 33.43 - 36.10 6 =========================== Idealize ADP of riding H ========================== r_work=0.1890 r_free=0.2446 r_work=0.1895 r_free=0.2444 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.10 - 36.90 A, n_refl.=5694 (all), 5.23 % free)-------------| | | | r_work= 0.1895 r_free= 0.2444 coordinate error (max.-lik. estimate): 0.39 A | | | | normalized target function (ml) (work): 5.840810 | | target function (ml) not normalized (work): 31517.010189 | | target function (ml) not normalized (free): 1849.960723 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1925 0.1895 0.2444 n_refl.: 5694 re-set all scales: r(all,work,free)=0.3644 0.3655 0.3491 n_refl.: 5694 remove outliers: r(all,work,free)=0.3644 0.3655 0.3491 n_refl.: 5694 overall B=0.00 to atoms: r(all,work,free)=0.3644 0.3655 0.3491 n_refl.: 5694 bulk-solvent and scaling: r(all,work,free)=0.1988 0.1962 0.2448 n_refl.: 5694 remove outliers: r(all,work,free)=0.1988 0.1962 0.2448 n_refl.: 5694 ======================== 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 36.902-12.728 94.29 95 4 0.2730 391.960 368.101 1.245 1.045 0.410 12.598-9.947 96.15 96 4 0.1336 559.468 570.266 1.193 1.034 0.410 9.931-7.830 97.01 189 6 0.1457 494.390 494.123 1.219 1.033 0.410 7.826-6.174 96.81 381 14 0.2065 334.211 327.228 1.071 1.026 0.490 6.172-4.868 97.27 748 36 0.1656 375.376 372.621 0.996 1.013 0.490 4.862-3.836 96.79 1456 84 0.1701 454.203 438.955 1.015 0.992 0.470 3.836-3.102 94.30 2431 150 0.2316 322.964 305.471 1.016 0.961 0.150 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=5.4203 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1962 r_free=0.2448 After: r_work=0.1963 r_free=0.2448 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.872387 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.103707 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 0.1961 0.2449 0.0488 0.003 0.6 4.0 0.7 2.9 0 0.094 0.1893 0.2439 0.0546 0.009 0.8 4.2 0.7 3.3 0 0.281 0.1775 0.2450 0.0676 0.013 1.4 7.7 1.1 4.6 0 0.562 0.1745 0.2449 0.0704 0.015 1.5 7.7 1.1 4.6 0 0.843 0.1712 0.2459 0.0747 0.020 1.7 10.7 1.5 5.0 0 1.123 0.1702 0.2465 0.0764 0.020 1.8 10.5 1.5 5.4 0 1.404 0.1677 0.2441 0.0764 0.024 1.9 10.5 1.5 6.3 0 1.685 0.1656 0.2456 0.0800 0.026 2.2 11.9 1.9 6.3 0 1.966 0.1736 0.2444 0.0707 0.016 1.6 8.2 1.1 4.6 0 0.936 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1961 0.2449 0.0488 0.003 0.6 4.0 0.7 2.9 0 0.094 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 19.61 24.49 4.88 2.502 17.842 0.104 5.847 20.02 25.02 5.00 2.621 18.135 0.003 5.866 19.17 24.27 5.10 2.609 17.904 0.013 5.822 18.05 23.82 5.78 4.180 17.981 0.052 5.753 17.34 23.52 6.18 6.421 18.381 0.104 5.705 17.17 23.49 6.32 7.398 18.615 0.156 5.692 17.08 23.49 6.42 8.086 18.784 0.207 5.684 17.04 23.49 6.46 8.480 18.881 0.259 5.681 17.00 23.51 6.51 8.828 18.967 0.311 5.678 16.97 23.53 6.57 9.256 19.073 0.363 5.675 16.94 23.55 6.61 9.652 19.169 0.415 5.672 16.93 23.55 6.63 9.950 19.242 0.467 5.670 16.91 23.58 6.67 10.296 19.327 0.519 5.668 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.052 Accepted refinement result: 18.05 23.82 5.78 4.180 17.981 0.052 5.753 Individual atomic B min max mean iso aniso Overall: 4.44 45.66 16.48 4.07 2155 0 Protein: 4.44 45.66 16.48 4.07 2155 0 Chain A: 4.93 41.92 16.86 N/A 1073 0 Chain B: 4.44 45.66 16.11 N/A 1082 0 Histogram: Values Number of atoms 4.44 - 8.56 185 8.56 - 12.68 537 12.68 - 16.80 571 16.80 - 20.93 404 20.93 - 25.05 203 25.05 - 29.17 119 29.17 - 33.30 71 33.30 - 37.42 39 37.42 - 41.54 19 41.54 - 45.66 7 =========================== Idealize ADP of riding H ========================== r_work=0.1805 r_free=0.2382 r_work=0.1793 r_free=0.2383 ----------X-ray data---------- |--(resolution: 3.10 - 36.90 A, n_refl.=5694 (all), 5.23 % free)-------------| | | | r_work= 0.1793 r_free= 0.2383 coordinate error (max.-lik. estimate): 0.31 A | | | | normalized target function (ml) (work): 5.746187 | | target function (ml) not normalized (work): 31006.425412 | | target function (ml) not normalized (free): 1873.770891 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 36.90 - 3.91 0.97 2808 138 0.1611 0.1934 5.7939 6.1888| | 2: 3.91 - 3.10 0.94 2588 160 0.2045 0.2956 5.6944 6.3732| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 36.90 - 3.91 2808 138 0.92 12.78 0.99 1.02 12516.26| | 2: 3.91 - 3.10 2588 160 0.92 14.92 1.02 1.04 11732.39| |alpha: min = 0.88 max = 1.20 mean = 1.03| |beta: min = 7027.24 max = 21939.09 mean = 12140.30| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.98 mean = 13.80| |phase err.(test): min = 0.00 max = 89.52 mean = 13.50| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1824 0.1793 0.2383 n_refl.: 5694 re-set all scales: r(all,work,free)=0.3564 0.3574 0.3451 n_refl.: 5694 remove outliers: r(all,work,free)=0.3564 0.3574 0.3451 n_refl.: 5694 overall B=0.00 to atoms: r(all,work,free)=0.3564 0.3574 0.3451 n_refl.: 5694 bulk-solvent and scaling: r(all,work,free)=0.1810 0.1777 0.2390 n_refl.: 5694 remove outliers: r(all,work,free)=0.1810 0.1777 0.2390 n_refl.: 5694 ======================== 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 36.902-12.728 94.29 95 4 0.2767 391.960 361.723 1.203 1.073 0.410 12.598-9.947 96.15 96 4 0.1331 559.468 567.001 1.168 1.059 0.410 9.931-7.830 97.01 189 6 0.1417 494.390 495.042 1.227 1.055 0.433 7.826-6.174 96.81 381 14 0.1981 334.211 328.585 1.047 1.043 0.458 6.172-4.868 97.27 748 36 0.1546 375.376 370.691 0.981 1.021 0.460 4.862-3.836 96.79 1456 84 0.1535 454.203 442.873 1.038 0.989 0.460 3.836-3.102 94.30 2431 150 0.2041 322.964 307.747 1.064 0.939 0.140 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=4.4321 ================= 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 : 0.3523 0.3456 0.024 2.035 2.0 37.2 13.1 0 0.000 1_bss: 0.1895 0.2493 0.024 2.035 3.1 38.3 14.2 0 0.000 1_settarget: 0.1895 0.2493 0.024 2.035 3.1 38.3 14.2 0 0.000 1_weight: 0.1895 0.2493 0.024 2.035 3.1 38.3 14.2 0 0.000 1_xyzrec: 0.2068 0.2511 0.003 0.677 3.1 38.3 14.2 0 0.147 1_adp: 0.2003 0.2526 0.003 0.677 5.7 38.9 14.6 0 0.147 1_regHadp: 0.1993 0.2520 0.003 0.677 5.7 38.9 14.6 0 0.147 2_bss: 0.1968 0.2500 0.003 0.677 6.7 39.9 15.7 0 0.147 2_settarget: 0.1968 0.2500 0.003 0.677 6.7 39.9 15.7 0 0.147 2_updatecdl: 0.1968 0.2500 0.003 0.705 6.7 39.9 15.7 0 0.147 2_weight: 0.1968 0.2500 0.003 0.705 6.7 39.9 15.7 0 0.147 2_xyzrec: 0.1823 0.2410 0.003 0.569 6.7 39.9 15.7 0 0.231 2_adp: 0.1890 0.2446 0.003 0.569 9.4 36.1 16.2 0 0.231 2_regHadp: 0.1895 0.2444 0.003 0.569 9.4 36.1 16.2 0 0.231 3_bss: 0.1962 0.2448 0.003 0.569 9.4 36.1 16.2 0 0.231 3_settarget: 0.1962 0.2448 0.003 0.569 9.4 36.1 16.2 0 0.231 3_updatecdl: 0.1962 0.2448 0.003 0.611 9.4 36.1 16.2 0 0.231 3_setrh: 0.1963 0.2448 0.003 0.611 9.4 36.1 16.2 0 0.231 3_weight: 0.1963 0.2448 0.003 0.611 9.4 36.1 16.2 0 0.231 3_xyzrec: 0.1961 0.2449 0.003 0.577 9.4 36.1 16.2 0 0.232 3_adp: 0.1805 0.2382 0.003 0.577 4.4 45.7 16.5 0 0.232 3_regHadp: 0.1793 0.2383 0.003 0.577 4.4 45.7 16.5 0 0.232 end: 0.1777 0.2390 0.003 0.577 4.4 45.7 16.5 0 0.232 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V1/2h1g_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V1/2h1g_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 5.5800 Refinement macro-cycles (run) : 161.1800 Write final files (write_after_run_outputs) : 19.3000 Total : 186.0600 Total CPU time: 3.41 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:27:07 PDT -0700 (1716251227.71 s) Start R-work = 0.1895, R-free = 0.2493 Final R-work = 0.1777, R-free = 0.2390 =============================================================================== Job complete usr+sys time: 222.91 seconds wall clock time: 11 minutes 22.90 seconds (682.90 seconds total)