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/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=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/2h1g.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/2h1g.pdb" 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" } 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: 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: 1.78, per 1000 atoms: 0.41 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: 2.82 Conformation dependent library (CDL) restraints added in 501.6 milliseconds 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 506 Time building geometry restraints manager: 2.46 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 { ramachandran_plot_restraints { enabled = True } 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 ============================ Update phi&psi targets =========================== 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 14.717551 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 0.2524 0.0435 0.004 0.7 2.6 0.0 4.6 0 0.125 0.2062 0.2512 0.0449 0.003 0.7 2.1 0.0 4.6 0 0.250 0.2018 0.2495 0.0477 0.003 0.7 1.9 0.0 4.6 0 0.500 0.1947 0.2479 0.0532 0.004 0.7 1.6 0.0 4.6 0 1.000 0.1866 0.2492 0.0626 0.006 0.8 2.8 0.0 4.6 0 2.000 0.1821 0.2487 0.0666 0.007 0.9 3.7 0.0 5.4 0 3.000 0.1746 0.2468 0.0722 0.009 1.0 3.7 0.0 5.4 0 4.000 0.1745 0.2486 0.0741 0.010 1.1 5.1 0.0 6.7 0 5.000 0.1704 0.2472 0.0768 0.011 1.1 4.4 0.0 7.1 0 6.000 0.1694 0.2485 0.0791 0.013 1.2 5.1 0.0 7.9 0 7.000 0.1676 0.2464 0.0788 0.014 1.3 4.9 0.0 7.5 0 8.000 0.1663 0.2469 0.0806 0.015 1.3 5.1 0.0 7.5 0 9.000 0.1650 0.2470 0.0820 0.016 1.4 5.8 0.0 7.9 0 10.000 0.1687 0.2475 0.0788 0.013 1.2 4.7 0.0 7.1 0 7.359 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1947 0.2479 0.0532 0.004 0.7 1.6 0.0 4.6 0 1.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 19.47 24.79 5.32 1.092 14.008 0.983 0.046 19.64 25.07 5.43 1.799 14.208 0.029 0.047 18.93 25.02 6.09 2.128 14.238 0.123 0.043 17.94 24.96 7.02 3.376 14.285 0.491 0.039 16.98 24.96 7.98 6.143 14.804 0.983 0.035 16.58 24.96 8.39 7.791 15.252 1.474 0.034 16.37 25.05 8.68 8.869 15.539 1.966 0.033 16.09 25.33 9.24 11.706 16.379 2.457 0.032 16.01 25.43 9.42 12.525 16.591 2.948 0.031 15.98 25.42 9.44 13.064 16.731 3.440 0.031 15.93 25.47 9.53 13.868 16.964 3.931 0.031 15.91 25.56 9.64 14.416 17.101 4.423 0.031 15.90 25.57 9.67 14.871 17.223 4.914 0.031 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.029 Accepted refinement result: 19.64 25.07 5.43 1.799 14.208 0.029 0.047 Individual atomic B min max mean iso aniso Overall: 6.95 36.64 14.55 1.20 2155 0 Protein: 6.95 36.64 14.55 1.20 2155 0 Chain A: 6.95 32.68 14.54 N/A 1073 0 Chain B: 7.32 36.64 14.57 N/A 1082 0 Histogram: Values Number of atoms 6.95 - 9.92 391 9.92 - 12.89 606 12.89 - 15.86 417 15.86 - 18.83 345 18.83 - 21.80 208 21.80 - 24.77 98 24.77 - 27.74 47 27.74 - 30.71 24 30.71 - 33.68 15 33.68 - 36.64 4 =========================== Idealize ADP of riding H ========================== r_work=0.1964 r_free=0.2507 r_work=0.1962 r_free=0.2500 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.10 - 36.90 A, n_refl.=5694 (all), 5.23 % free)-------------| | | | r_work= 0.1962 r_free= 0.2500 coordinate error (max.-lik. estimate): 0.37 A | | | | normalized target function (ls_wunit_k1) (work): 0.046598 | | target function (ls_wunit_k1) not normalized (work): 251.443780 | | target function (ls_wunit_k1) not normalized (free): 21.570638 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1990 0.1962 0.2500 n_refl.: 5694 re-set all scales: r(all,work,free)=0.3587 0.3592 0.3526 n_refl.: 5694 remove outliers: r(all,work,free)=0.3587 0.3592 0.3526 n_refl.: 5694 overall B=1.18 to atoms: r(all,work,free)=0.3635 0.3642 0.3550 n_refl.: 5694 bulk-solvent and scaling: r(all,work,free)=0.2036 0.2010 0.2509 n_refl.: 5694 remove outliers: r(all,work,free)=0.2036 0.2010 0.2509 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 0.2803 392.001 365.099 1.242 1.044 0.410 12.598-9.947 96.15 96 4 0.1291 559.526 570.520 1.200 1.034 0.409 9.931-7.830 97.01 189 6 0.1493 494.442 492.718 1.217 1.033 0.408 7.826-6.174 96.81 381 14 0.2160 334.246 327.396 1.081 1.025 0.477 6.172-4.868 97.27 748 36 0.1792 375.415 370.384 0.990 1.013 0.475 4.862-3.836 96.79 1456 84 0.1746 454.251 439.783 1.017 0.993 0.462 3.836-3.102 94.30 2431 150 0.2338 322.998 305.411 1.017 0.963 0.175 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=5.3036 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.896344 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.115591 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 0.1963 0.2439 0.0476 0.003 0.6 2.8 0.0 3.3 0 0.095 0.1844 0.2422 0.0577 0.006 0.8 3.7 0.0 4.6 0 0.284 0.1786 0.2453 0.0667 0.010 1.0 5.1 0.0 5.4 0 0.569 0.1744 0.2442 0.0698 0.014 1.2 6.3 0.0 5.0 0 0.853 0.1708 0.2437 0.0729 0.017 1.4 7.0 0.0 5.4 0 1.138 0.1671 0.2398 0.0727 0.020 1.6 7.0 0.0 7.1 0 1.422 0.1648 0.2407 0.0759 0.023 1.7 7.9 0.0 7.9 0 1.707 0.1634 0.2418 0.0784 0.025 1.8 8.9 0.4 7.5 0 1.991 0.1733 0.2439 0.0706 0.015 1.3 6.3 0.0 5.0 0 0.948 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1963 0.2439 0.0476 0.003 0.6 2.8 0.0 3.3 0 0.095 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 19.63 24.39 4.76 2.321 17.195 0.116 5.848 19.75 24.96 5.21 2.582 17.401 0.003 5.853 19.08 24.30 5.22 2.553 17.261 0.014 5.816 17.74 23.95 6.22 4.990 17.452 0.058 5.733 17.33 23.82 6.49 6.507 17.770 0.116 5.706 17.14 23.78 6.64 7.596 18.015 0.173 5.692 17.03 23.81 6.78 8.376 18.192 0.231 5.685 16.91 23.84 6.92 9.639 18.484 0.289 5.675 16.89 23.88 6.99 10.107 18.592 0.347 5.672 16.86 23.91 7.04 10.461 18.673 0.405 5.670 16.85 23.94 7.09 10.746 18.739 0.462 5.669 16.84 23.95 7.11 10.984 18.795 0.520 5.668 16.84 23.97 7.14 11.219 18.849 0.578 5.667 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.014 Accepted refinement result: 19.08 24.30 5.22 2.553 17.261 0.014 5.816 Individual atomic B min max mean iso aniso Overall: 6.90 39.16 15.86 1.81 2155 0 Protein: 6.90 39.16 15.86 1.81 2155 0 Chain A: 7.23 35.20 15.98 N/A 1073 0 Chain B: 6.90 39.16 15.75 N/A 1082 0 Histogram: Values Number of atoms 6.90 - 10.13 180 10.13 - 13.35 682 13.35 - 16.58 489 16.58 - 19.81 361 19.81 - 23.03 216 23.03 - 26.26 126 26.26 - 29.48 45 29.48 - 32.71 32 32.71 - 35.93 19 35.93 - 39.16 5 =========================== Idealize ADP of riding H ========================== r_work=0.1908 r_free=0.2430 r_work=0.1904 r_free=0.2429 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.10 - 36.90 A, n_refl.=5694 (all), 5.23 % free)-------------| | | | r_work= 0.1904 r_free= 0.2429 coordinate error (max.-lik. estimate): 0.33 A | | | | normalized target function (ml) (work): 5.813534 | | target function (ml) not normalized (work): 31369.832072 | | target function (ml) not normalized (free): 1852.731224 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1932 0.1904 0.2429 n_refl.: 5694 re-set all scales: r(all,work,free)=0.3594 0.3605 0.3456 n_refl.: 5694 remove outliers: r(all,work,free)=0.3594 0.3605 0.3456 n_refl.: 5694 overall B=0.00 to atoms: r(all,work,free)=0.3594 0.3605 0.3456 n_refl.: 5694 bulk-solvent and scaling: r(all,work,free)=0.1923 0.1895 0.2427 n_refl.: 5694 remove outliers: r(all,work,free)=0.1923 0.1895 0.2427 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 0.2827 392.001 365.388 1.247 1.045 0.410 12.598-9.947 96.15 96 4 0.1307 559.526 571.103 1.201 1.035 0.410 9.931-7.830 97.01 189 6 0.1461 494.442 494.066 1.218 1.034 0.410 7.826-6.174 96.81 381 14 0.1988 334.246 328.089 1.075 1.027 0.490 6.172-4.868 97.27 748 36 0.1631 375.415 370.875 0.985 1.014 0.490 4.862-3.836 96.79 1456 84 0.1632 454.251 440.325 1.016 0.995 0.480 3.836-3.102 94.30 2431 150 0.2225 322.998 307.565 1.014 0.964 0.130 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=5.3750 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1895 r_free=0.2427 After: r_work=0.1896 r_free=0.2428 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.780458 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.112540 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 0.1895 0.2426 0.0530 0.003 0.6 2.8 0.0 3.3 0 0.089 0.1853 0.2410 0.0557 0.007 0.7 3.3 0.0 3.3 0 0.267 0.1736 0.2384 0.0648 0.013 1.3 6.1 0.0 4.2 0 0.534 0.1690 0.2410 0.0720 0.015 1.5 9.6 0.4 4.6 0 0.801 0.1663 0.2401 0.0739 0.018 1.6 10.5 0.4 5.0 0 1.068 0.1654 0.2384 0.0731 0.020 1.6 9.6 0.4 5.0 0 1.335 0.1632 0.2409 0.0777 0.022 1.8 10.3 0.4 6.7 0 1.602 0.1611 0.2412 0.0801 0.025 2.0 11.4 0.4 6.7 0 1.869 0.1678 0.2405 0.0728 0.016 1.6 10.3 0.4 5.0 0 0.890 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1895 0.2426 0.0530 0.003 0.6 2.8 0.0 3.3 0 0.089 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 18.95 24.26 5.30 2.675 17.441 0.113 5.811 19.62 24.86 5.24 2.733 17.719 0.003 5.847 18.56 24.10 5.54 2.741 17.677 0.014 5.788 17.65 24.00 6.35 4.356 17.618 0.056 5.731 16.95 23.86 6.91 6.792 18.036 0.113 5.683 16.77 23.91 7.14 7.860 18.268 0.169 5.671 16.68 23.98 7.30 8.624 18.445 0.225 5.664 16.63 24.01 7.38 9.175 18.573 0.281 5.660 16.60 24.06 7.46 9.603 18.676 0.338 5.657 16.59 24.10 7.51 9.916 18.753 0.394 5.656 16.57 24.13 7.56 10.228 18.828 0.450 5.654 16.57 24.17 7.60 10.458 18.885 0.506 5.654 16.56 24.18 7.62 10.642 18.933 0.563 5.653 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.014 Accepted refinement result: 18.56 24.10 5.54 2.741 17.677 0.014 5.788 Individual atomic B min max mean iso aniso Overall: 5.87 43.99 16.34 2.48 2155 0 Protein: 5.87 43.99 16.34 2.48 2155 0 Chain A: 7.50 39.63 16.67 N/A 1073 0 Chain B: 5.87 43.99 16.00 N/A 1082 0 Histogram: Values Number of atoms 5.87 - 9.68 141 9.68 - 13.49 715 13.49 - 17.31 564 17.31 - 21.12 336 21.12 - 24.93 188 24.93 - 28.74 109 28.74 - 32.56 48 32.56 - 36.37 31 36.37 - 40.18 19 40.18 - 43.99 4 =========================== Idealize ADP of riding H ========================== r_work=0.1856 r_free=0.2410 r_work=0.1853 r_free=0.2408 ----------X-ray data---------- |--(resolution: 3.10 - 36.90 A, n_refl.=5694 (all), 5.23 % free)-------------| | | | r_work= 0.1853 r_free= 0.2408 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ml) (work): 5.785862 | | target function (ml) not normalized (work): 31220.512473 | | target function (ml) not normalized (free): 1854.713219 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1653 0.1973 5.818 6.1623| | 2: 3.91 - 3.10 0.94 2588 160 0.2130 0.2963 5.751 6.277| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 0.91 13.19 0.99 1.02 13249.49| | 2: 3.91 - 3.10 2588 160 0.90 16.13 1.01 1.03 13213.64| |alpha: min = 0.87 max = 1.19 mean = 1.02| |beta: min = 8215.97 max = 22942.54 mean = 13232.30| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.86 mean = 14.60| |phase err.(test): min = 0.00 max = 89.55 mean = 14.46| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1882 0.1853 0.2408 n_refl.: 5694 re-set all scales: r(all,work,free)=0.3591 0.3602 0.3455 n_refl.: 5694 remove outliers: r(all,work,free)=0.3591 0.3602 0.3455 n_refl.: 5694 overall B=0.00 to atoms: r(all,work,free)=0.3591 0.3602 0.3455 n_refl.: 5694 bulk-solvent and scaling: r(all,work,free)=0.1857 0.1828 0.2396 n_refl.: 5694 remove outliers: r(all,work,free)=0.1857 0.1828 0.2396 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 0.2870 392.001 358.051 1.136 1.118 0.410 12.598-9.947 96.15 96 4 0.1307 559.526 565.640 1.113 1.101 0.410 9.931-7.830 97.01 189 6 0.1477 494.442 493.261 1.164 1.093 0.433 7.826-6.174 96.81 381 14 0.1955 334.246 327.385 1.015 1.074 0.480 6.172-4.868 97.27 748 36 0.1601 375.415 370.827 0.954 1.043 0.480 4.862-3.836 96.79 1456 84 0.1579 454.251 442.537 1.023 0.995 0.480 3.836-3.102 94.30 2431 150 0.2114 322.998 308.129 1.066 0.922 0.140 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=5.2324 ================= 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_updatephipsi: 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: 0.1947 0.2479 0.004 0.741 3.1 38.3 14.2 0 0.154 1_adp: 0.1964 0.2507 0.004 0.741 7.0 36.6 14.6 0 0.154 1_regHadp: 0.1962 0.2500 0.004 0.741 7.0 36.6 14.6 0 0.154 2_bss: 0.2010 0.2509 0.004 0.741 8.1 37.8 15.7 0 0.154 2_settarget: 0.2010 0.2509 0.004 0.741 8.1 37.8 15.7 0 0.154 2_updatephipsi: 0.2010 0.2509 0.004 0.741 8.1 37.8 15.7 0 0.154 2_updatecdl: 0.2010 0.2509 0.004 0.771 8.1 37.8 15.7 0 0.154 2_weight: 0.2010 0.2509 0.004 0.771 8.1 37.8 15.7 0 0.154 2_xyzrec: 0.1963 0.2439 0.003 0.575 8.1 37.8 15.7 0 0.251 2_adp: 0.1908 0.2430 0.003 0.575 6.9 39.2 15.9 0 0.251 2_regHadp: 0.1904 0.2429 0.003 0.575 6.9 39.2 15.9 0 0.251 3_bss: 0.1895 0.2427 0.003 0.575 6.9 39.2 15.9 0 0.251 3_settarget: 0.1895 0.2427 0.003 0.575 6.9 39.2 15.9 0 0.251 3_updatephipsi: 0.1895 0.2427 0.003 0.575 6.9 39.2 15.9 0 0.251 3_updatecdl: 0.1895 0.2427 0.003 0.599 6.9 39.2 15.9 0 0.251 3_setrh: 0.1896 0.2428 0.003 0.599 6.9 39.2 15.9 0 0.250 3_weight: 0.1896 0.2428 0.003 0.599 6.9 39.2 15.9 0 0.250 3_xyzrec: 0.1895 0.2426 0.003 0.580 6.9 39.2 15.9 0 0.251 3_adp: 0.1856 0.2410 0.003 0.580 5.9 44.0 16.3 0 0.251 3_regHadp: 0.1853 0.2408 0.003 0.580 5.9 44.0 16.3 0 0.251 end: 0.1828 0.2396 0.003 0.580 5.9 44.0 16.3 0 0.251 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V2/2h1g_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V2/2h1g_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 6.5900 Refinement macro-cycles (run) : 189.0400 Write final files (write_after_run_outputs) : 20.8900 Total : 216.5200 Total CPU time: 4.15 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:30:17 PDT -0700 (1716251417.39 s) Start R-work = 0.1895, R-free = 0.2493 Final R-work = 0.1828, R-free = 0.2396 =============================================================================== Job complete usr+sys time: 269.37 seconds wall clock time: 13 minutes 49.04 seconds (829.04 seconds total)