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/2yhj.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/2yhj/2yhj.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/2yhj/2yhj.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/2yhj/2yhj.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/2yhj.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/2yhj.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: 8784 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 4392 Classifications: {'peptide': 285} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 277} Chain: "B" Number of atoms: 4392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 4392 Classifications: {'peptide': 285} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 277} Time building chain proxies: 1.55, per 1000 atoms: 0.18 Number of scatterers: 8784 At special positions: 0 Unit cell: (159.697, 159.697, 159.697, 90, 90, 90) Space group: P 21 3 (No. 198) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 4 16.00 O 904 8.00 N 728 7.00 C 2814 6.00 H 4334 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: 2.04 Conformation dependent library (CDL) restraints added in 349.5 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 1052 Time building geometry restraints manager: 2.37 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: 4332 1.15 - 1.31: 765 1.31 - 1.48: 1860 1.48 - 1.64: 1909 1.64 - 1.81: 6 Bond restraints: 8872 Sorted by residual: bond pdb=" N VAL A 100 " pdb=" H VAL A 100 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" N LYS B 46 " pdb=" H LYS B 46 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" NE2 GLN B 140 " pdb="HE22 GLN B 140 " 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 B 292 " pdb=" H ASP B 292 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N ILE A 253 " pdb=" H ILE A 253 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 8867 not shown) Histogram of bond angle deviations from ideal: 97.03 - 104.43: 162 104.43 - 111.82: 9279 111.82 - 119.21: 2643 119.21 - 126.60: 3803 126.60 - 133.99: 71 Bond angle restraints: 15958 Sorted by residual: angle pdb=" N LEU B 37 " pdb=" CA LEU B 37 " pdb=" C LEU B 37 " ideal model delta sigma weight residual 110.14 119.17 -9.03 1.47e+00 4.63e-01 3.78e+01 angle pdb=" N VAL B 89 " pdb=" CA VAL B 89 " pdb=" CB VAL B 89 " ideal model delta sigma weight residual 111.00 117.48 -6.48 1.14e+00 7.69e-01 3.23e+01 angle pdb=" N ILE A 108 " pdb=" CA ILE A 108 " pdb=" C ILE A 108 " ideal model delta sigma weight residual 110.53 115.72 -5.19 9.40e-01 1.13e+00 3.04e+01 angle pdb=" C GLU A 181 " pdb=" N THR A 182 " pdb=" CA THR A 182 " ideal model delta sigma weight residual 120.31 128.30 -7.99 1.52e+00 4.33e-01 2.76e+01 angle pdb=" N ILE A 289 " pdb=" CA ILE A 289 " pdb=" C ILE A 289 " ideal model delta sigma weight residual 108.27 115.35 -7.08 1.37e+00 5.33e-01 2.67e+01 ... (remaining 15953 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 3781 17.72 - 35.43: 252 35.43 - 53.15: 113 53.15 - 70.87: 53 70.87 - 88.58: 11 Dihedral angle restraints: 4210 sinusoidal: 2252 harmonic: 1958 Sorted by residual: dihedral pdb=" C THR B 212 " pdb=" N THR B 212 " pdb=" CA THR B 212 " pdb=" CB THR B 212 " ideal model delta harmonic sigma weight residual -122.00 -135.87 13.87 0 2.50e+00 1.60e-01 3.08e+01 dihedral pdb=" C GLU B 184 " pdb=" N GLU B 184 " pdb=" CA GLU B 184 " pdb=" CB GLU B 184 " ideal model delta harmonic sigma weight residual -122.60 -135.02 12.42 0 2.50e+00 1.60e-01 2.47e+01 dihedral pdb=" C ASN B 86 " pdb=" N ASN B 86 " pdb=" CA ASN B 86 " pdb=" CB ASN B 86 " ideal model delta harmonic sigma weight residual -122.60 -134.99 12.39 0 2.50e+00 1.60e-01 2.46e+01 ... (remaining 4207 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 495 0.107 - 0.213: 154 0.213 - 0.320: 30 0.320 - 0.427: 15 0.427 - 0.533: 6 Chirality restraints: 700 Sorted by residual: chirality pdb=" CA GLU B 184 " pdb=" N GLU B 184 " pdb=" C GLU B 184 " pdb=" CB GLU B 184 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 7.11e+00 chirality pdb=" CA ASN B 86 " pdb=" N ASN B 86 " pdb=" C ASN B 86 " pdb=" CB ASN B 86 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.73e+00 chirality pdb=" CA ASN A 86 " pdb=" N ASN A 86 " pdb=" C ASN A 86 " pdb=" CB ASN A 86 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.28e+00 ... (remaining 697 not shown) Planarity restraints: 1346 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN B 61 " -0.013 2.00e-02 2.50e+03 3.89e-02 2.26e+01 pdb=" CD GLN B 61 " -0.051 2.00e-02 2.50e+03 pdb=" OE1 GLN B 61 " 0.052 2.00e-02 2.50e+03 pdb=" NE2 GLN B 61 " -0.008 2.00e-02 2.50e+03 pdb="HE21 GLN B 61 " 0.050 2.00e-02 2.50e+03 pdb="HE22 GLN B 61 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 264 " -0.005 2.00e-02 2.50e+03 2.57e-02 1.99e+01 pdb=" CG TYR B 264 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 TYR B 264 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR B 264 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B 264 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 264 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR B 264 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 264 " 0.007 2.00e-02 2.50e+03 pdb=" HD1 TYR B 264 " 0.040 2.00e-02 2.50e+03 pdb=" HD2 TYR B 264 " 0.047 2.00e-02 2.50e+03 pdb=" HE1 TYR B 264 " -0.004 2.00e-02 2.50e+03 pdb=" HE2 TYR B 264 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 130 " 0.014 2.00e-02 2.50e+03 2.57e-02 1.99e+01 pdb=" CG TYR B 130 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR B 130 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR B 130 " -0.017 2.00e-02 2.50e+03 pdb=" CE1 TYR B 130 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR B 130 " 0.014 2.00e-02 2.50e+03 pdb=" CZ TYR B 130 " 0.011 2.00e-02 2.50e+03 pdb=" OH TYR B 130 " -0.004 2.00e-02 2.50e+03 pdb=" HD1 TYR B 130 " 0.042 2.00e-02 2.50e+03 pdb=" HD2 TYR B 130 " -0.039 2.00e-02 2.50e+03 pdb=" HE1 TYR B 130 " -0.039 2.00e-02 2.50e+03 pdb=" HE2 TYR B 130 " 0.041 2.00e-02 2.50e+03 ... (remaining 1343 not shown) Histogram of nonbonded interaction distances: 0.90 - 1.64: 26 1.64 - 2.38: 2855 2.38 - 3.12: 27212 3.12 - 3.86: 38333 3.86 - 4.60: 59693 Warning: very small nonbonded interaction distances. Nonbonded interactions: 128119 Sorted by model distance: nonbonded pdb="HH12 ARG A 227 " pdb=" HB2 PRO A 311 " model vdw 0.896 2.270 nonbonded pdb="HH12 ARG B 227 " pdb=" HB2 PRO B 311 " model vdw 0.922 2.270 nonbonded pdb=" HE2 LYS B 257 " pdb=" HA LYS B 283 " model vdw 1.020 2.440 nonbonded pdb=" HE2 LYS A 257 " pdb=" HA LYS A 283 " model vdw 1.026 2.440 nonbonded pdb="HD21 ASN A 36 " pdb=" HE2 LYS B 283 " model vdw 1.089 2.270 ... (remaining 128114 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 904 7.97 1 N 728 6.97 1 C 2814 5.97 1 H 4334 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: 4334 of 8784 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 8784 n_use_u_iso = 8784 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 = 8784 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (8784 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 8784 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 = "2yhj_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 4334 occupancy sum: 4334.00 (% of total atoms 49.51) Rotatable: count: 1252 occupancy sum: 1252.00 (% of total atoms 14.30) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 4.00 - 65.20 A, n_refl.=11707 (all), 4.74 % free)------------| | | | r_work= 0.5891 r_free= 0.4411 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.177790 | | target function (ml) not normalized (work): 46590.717736 | | target function (ml) not normalized (free): 2297.685890 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 65.20 - 6.35 1.00 2869 154 0.5470 0.4516 5.0219 4.6882| | 2: 6.35 - 5.04 1.00 2777 143 0.5707 0.3865 4.0914 4.1453| | 3: 5.04 - 4.40 1.00 2783 123 0.6252 0.4330 3.9538 4.0152| | 4: 4.40 - 4.00 0.99 2723 135 0.6724 0.5113 3.6055 3.6227| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 65.20 - 6.35 2869 154 0.51 50.27 0.85 0.03 2262.31| | 2: 6.35 - 5.04 2777 143 0.43 57.38 2.00 0.04 1473.91| | 3: 5.04 - 4.40 2783 123 0.59 44.81 2.34 0.05 841.25| | 4: 4.40 - 4.00 2723 135 0.61 43.53 2.67 0.06 378.44| |alpha: min = 0.03 max = 0.06 mean = 0.04| |beta: min = 378.44 max = 2262.31 mean = 1251.37| |figures of merit: min = 0.00 max = 1.00 mean = 0.54| |phase err.(work): min = 0.00 max = 89.88 mean = 49.03| |phase err.(test): min = 0.00 max = 89.64 mean = 49.15| |-----------------------------------------------------------------------------| ----------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 : 0.010 0.113 4538 Z= 0.608 Angle : 1.541 9.034 6170 Z= 1.009 Chirality : 0.123 0.533 700 Planarity : 0.007 0.028 792 Dihedral : 15.468 88.583 1622 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.22 % Allowed : 6.83 % Favored : 88.96 % Cbeta Deviations : 2.09 % Peptide Plane: Cis-proline : 0.00 % 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: -0.48 (0.32), residues: 566 helix: -0.38 (0.69), residues: 42 sheet: 0.26 (0.29), residues: 286 loop : -0.96 (0.35), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.002 ARG A 116 TYR 0.045 0.007 TYR B 264 PHE 0.018 0.005 PHE B 316 TRP 0.046 0.009 TRP A 162 HIS 0.008 0.002 HIS A 146 Individual atomic B min max mean iso aniso Overall: 34.09 300.00 115.49 16.58 4450 0 Protein: 34.09 300.00 115.49 16.58 4450 0 Chain A: 34.09 300.00 113.10 N/A 2225 0 Chain B: 38.50 300.00 117.88 N/A 2225 0 Histogram: Values Number of atoms 34.09 - 60.68 195 60.68 - 87.27 913 87.27 - 113.86 1318 113.86 - 140.45 1013 140.45 - 167.04 585 167.04 - 193.64 250 193.64 - 220.23 97 220.23 - 246.82 41 246.82 - 273.41 14 273.41 - 300.00 24 |-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: 4.00 - 65.20 A, n_refl.=11707 (all), 4.74 % free)------------| | | | r_work= 0.5891 r_free= 0.4411 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.177790 | | target function (ml) not normalized (work): 46590.717736 | | target function (ml) not normalized (free): 2297.685890 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.5850 0.5891 0.4411 n_refl.: 11707 re-set all scales: r(all,work,free)=0.5850 0.5891 0.4411 n_refl.: 11707 remove outliers: r(all,work,free)=0.5853 0.5894 0.4411 n_refl.: 11703 overall B=1.75 to atoms: r(all,work,free)=0.5901 0.5942 0.4442 n_refl.: 11703 bulk-solvent and scaling: r(all,work,free)=0.3020 0.2998 0.3469 n_refl.: 11703 remove outliers: r(all,work,free)=0.3020 0.2998 0.3469 n_refl.: 11703 ======================== 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 65.196-20.791 100.00 98 1 0.3727 4797.975 4480.474 1.327 1.203 0.370 20.447-16.215 100.00 96 3 0.3168 3372.726 3174.597 1.053 1.189 0.340 16.132-12.745 100.00 194 11 0.2772 3266.441 3051.447 1.121 1.171 0.329 12.705-10.080 100.00 377 16 0.2682 3068.794 2812.929 1.067 1.142 0.309 10.040-7.926 100.00 749 47 0.2594 2378.704 2226.653 1.035 1.095 0.278 7.906-6.254 99.81 1487 80 0.3015 1468.580 1345.750 1.035 1.018 0.228 6.249-4.933 100.00 3011 157 0.3075 1268.682 1121.341 1.068 0.895 0.177 4.931-4.001 99.68 5136 240 0.3089 1069.236 942.207 1.427 0.716 0.137 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=7.8620 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 14.259442 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.153546 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 5.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.3027 0.3510 0.0483 0.003 0.5 1.4 0.0 3.4 0 0.125 0.3005 0.3505 0.0500 0.003 0.5 1.4 0.0 3.4 0 0.250 0.2968 0.3496 0.0529 0.003 0.6 1.4 0.0 3.2 0 0.500 0.2934 0.3472 0.0538 0.005 0.7 2.4 0.0 3.4 0 1.000 0.2768 0.3588 0.0820 0.005 0.6 3.6 0.2 3.8 0 2.000 0.2733 0.3583 0.0851 0.007 0.8 5.2 0.4 3.8 0 3.000 0.2713 0.3590 0.0877 0.008 0.8 6.3 0.5 4.6 0 4.000 0.2695 0.3595 0.0899 0.009 0.9 8.1 0.9 5.6 0 5.000 0.2680 0.3601 0.0921 0.010 1.0 8.9 0.9 6.8 0 6.000 0.2671 0.3603 0.0932 0.012 1.1 11.7 1.2 8.0 0 7.000 0.2656 0.3588 0.0932 0.013 1.2 12.4 1.4 7.8 0 8.000 0.2646 0.3598 0.0952 0.014 1.2 13.3 2.1 8.2 0 9.000 0.2642 0.3597 0.0955 0.015 1.3 14.5 1.9 9.2 0 10.000 0.2669 0.3596 0.0927 0.012 1.1 11.3 1.6 7.4 0 7.130 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.3027 0.3510 0.0483 0.003 0.5 1.4 0.0 3.4 0 0.125 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 30.27 35.10 4.83 11.856 115.379 0.154 0.117 30.45 33.68 3.23 15.647 119.798 0.005 0.118 30.22 33.61 3.39 15.674 119.738 0.019 0.117 29.47 33.48 4.02 16.054 119.595 0.077 0.112 28.79 33.49 4.70 16.984 119.579 0.154 0.108 28.35 33.53 5.18 17.852 119.602 0.230 0.105 28.05 33.67 5.62 18.616 119.645 0.307 0.103 27.85 33.76 5.91 19.345 119.739 0.384 0.102 27.70 33.84 6.15 20.024 119.858 0.461 0.101 27.58 33.91 6.33 20.570 119.940 0.537 0.101 27.49 33.98 6.49 21.086 120.037 0.614 0.100 27.39 33.93 6.55 21.434 120.107 0.691 0.100 27.25 34.05 6.79 22.362 120.417 0.768 0.099 max suggested for this run: 23.08 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.077 Accepted refinement result: 29.47 33.48 4.02 16.054 119.595 0.077 0.112 Individual atomic B min max mean iso aniso Overall: 38.39 296.75 125.56 12.07 4450 0 Protein: 38.39 296.75 125.56 12.07 4450 0 Chain A: 38.39 296.75 123.34 N/A 2225 0 Chain B: 63.07 296.75 127.78 N/A 2225 0 Histogram: Values Number of atoms 38.39 - 64.23 8 64.23 - 90.06 423 90.06 - 115.90 1555 115.90 - 141.73 1367 141.73 - 167.57 669 167.57 - 193.40 267 193.40 - 219.24 85 219.24 - 245.08 39 245.08 - 270.91 15 270.91 - 296.75 22 =========================== Idealize ADP of riding H ========================== r_work=0.2947 r_free=0.3348 r_work=0.2935 r_free=0.3360 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 4.00 - 65.20 A, n_refl.=11703 (all), 4.74 % free)------------| | | | r_work= 0.2935 r_free= 0.3360 coordinate error (max.-lik. estimate): 0.59 A | | | | normalized target function (ls_wunit_k1) (work): 0.111210 | | target function (ls_wunit_k1) not normalized (work): 1239.763910 | | target function (ls_wunit_k1) not normalized (free): 78.052794 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2955 0.2935 0.3360 n_refl.: 11703 re-set all scales: r(all,work,free)=0.6164 0.6203 0.4641 n_refl.: 11703 remove outliers: r(all,work,free)=0.6164 0.6203 0.4641 n_refl.: 11703 overall B=-2.84 to atoms: r(all,work,free)=0.6090 0.6130 0.4583 n_refl.: 11703 bulk-solvent and scaling: r(all,work,free)=0.2929 0.2909 0.3343 n_refl.: 11703 remove outliers: r(all,work,free)=0.2929 0.2909 0.3343 n_refl.: 11703 ======================== 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 65.196-20.791 100.00 98 1 0.3739 1671.447 1549.054 1.218 1.162 0.370 20.447-16.215 100.00 96 3 0.3134 1174.940 1112.610 0.979 1.151 0.339 16.132-12.745 100.00 194 11 0.2729 1137.914 1064.473 1.032 1.136 0.326 12.705-10.080 100.00 377 16 0.2580 1069.061 989.427 1.034 1.112 0.322 10.040-7.926 100.00 749 47 0.2441 828.657 782.224 0.989 1.074 0.283 7.906-6.254 99.81 1487 80 0.2814 511.602 472.534 0.963 1.012 0.213 6.249-4.933 100.00 3011 157 0.2913 441.964 394.973 1.037 0.912 0.184 4.931-4.001 99.68 5136 240 0.3099 372.484 330.174 1.316 0.766 0.104 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9978 b_overall=0.5947 ============================ 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 = 7.525119 wxc_scale = 0.022 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.074977 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 5.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2958 0.3381 0.0423 0.002 0.4 1.4 0.0 2.4 0 0.016 0.2920 0.3381 0.0461 0.002 0.4 1.5 0.0 2.4 0 0.049 0.2883 0.3374 0.0491 0.002 0.4 1.5 0.0 2.4 0 0.098 0.2856 0.3381 0.0525 0.002 0.4 1.5 0.0 2.4 0 0.148 0.2836 0.3400 0.0564 0.002 0.4 1.4 0.0 2.6 0 0.197 0.2821 0.3416 0.0595 0.002 0.4 1.9 0.0 2.8 0 0.246 0.2813 0.3400 0.0587 0.002 0.5 2.7 0.0 2.8 0 0.295 0.2804 0.3389 0.0585 0.003 0.5 3.5 0.0 2.6 0 0.345 0.2848 0.3384 0.0536 0.002 0.4 1.4 0.0 2.4 0 0.164 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2958 0.3381 0.0423 0.002 0.4 1.4 0.0 2.4 0 0.016 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 29.58 33.81 4.23 19.784 134.013 0.075 6.504 32.30 34.68 2.39 17.291 144.339 0.002 6.522 31.49 34.53 3.04 16.801 143.493 0.009 6.508 29.50 34.13 4.63 18.097 139.980 0.037 6.476 28.60 34.44 5.84 20.146 138.565 0.075 6.467 28.34 34.27 5.93 20.113 137.060 0.112 6.468 28.20 34.25 6.05 20.588 136.874 0.150 6.468 28.12 34.17 6.05 20.930 136.845 0.187 6.467 28.04 34.21 6.17 21.358 137.043 0.225 6.467 28.02 34.20 6.19 21.446 136.994 0.262 6.467 27.96 34.24 6.28 21.770 137.166 0.300 6.466 27.93 34.26 6.33 21.975 137.261 0.337 6.466 27.90 34.30 6.39 22.212 137.383 0.375 6.466 max suggested for this run: 26.80 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.037 Accepted refinement result: 29.50 34.13 4.63 18.097 139.980 0.037 6.476 Individual atomic B min max mean iso aniso Overall: 56.37 288.91 134.50 12.57 4450 0 Protein: 56.37 288.91 134.50 12.57 4450 0 Chain A: 56.37 288.91 132.19 N/A 2225 0 Chain B: 66.75 288.91 136.81 N/A 2225 0 Histogram: Values Number of atoms 56.37 - 79.62 43 79.62 - 102.87 664 102.87 - 126.13 1206 126.13 - 149.38 1254 149.38 - 172.64 821 172.64 - 195.89 295 195.89 - 219.14 97 219.14 - 242.40 33 242.40 - 265.65 15 265.65 - 288.91 22 =========================== Idealize ADP of riding H ========================== r_work=0.2950 r_free=0.3413 r_work=0.2957 r_free=0.3435 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 4.00 - 65.20 A, n_refl.=11703 (all), 4.74 % free)------------| | | | r_work= 0.2957 r_free= 0.3435 coordinate error (max.-lik. estimate): 0.58 A | | | | normalized target function (ml) (work): 6.476636 | | target function (ml) not normalized (work): 72201.543401 | | target function (ml) not normalized (free): 3632.524182 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2979 0.2957 0.3435 n_refl.: 11703 re-set all scales: r(all,work,free)=0.6381 0.6417 0.4841 n_refl.: 11703 remove outliers: r(all,work,free)=0.6381 0.6417 0.4841 n_refl.: 11703 overall B=-15.42 to atoms: r(all,work,free)=0.5986 0.6025 0.4531 n_refl.: 11703 bulk-solvent and scaling: r(all,work,free)=0.2981 0.2958 0.3447 n_refl.: 11703 remove outliers: r(all,work,free)=0.2981 0.2958 0.3447 n_refl.: 11703 ======================== 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 65.196-20.791 100.00 98 1 0.3727 1485.455 1379.695 1.410 1.073 0.372 20.447-16.215 100.00 96 3 0.3173 1044.197 996.169 1.124 1.069 0.339 16.132-12.745 100.00 194 11 0.2793 1011.291 940.330 1.172 1.062 0.330 12.705-10.080 100.00 377 16 0.2566 950.100 880.665 1.161 1.051 0.330 10.040-7.926 100.00 749 47 0.2477 736.448 692.853 1.089 1.032 0.294 7.906-6.254 99.81 1487 80 0.2997 454.673 411.676 1.016 1.002 0.217 6.249-4.933 100.00 3011 157 0.3025 392.784 344.799 0.988 0.952 0.182 4.931-4.001 99.68 5136 240 0.3076 331.036 291.744 1.115 0.879 0.110 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0577 b_overall=6.6575 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.2958 r_free=0.3447 After: r_work=0.2958 r_free=0.3446 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 8.090153 wxc_scale = 0.133 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.080931 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 5.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2955 0.3442 0.0487 0.002 0.4 1.4 0.0 2.4 0 0.125 0.2949 0.3437 0.0489 0.002 0.4 1.3 0.0 2.4 0 0.250 0.2911 0.3436 0.0525 0.005 0.6 1.6 0.0 2.0 0 0.500 0.2811 0.3432 0.0620 0.009 1.1 5.8 0.0 2.2 0 1.000 0.2778 0.3441 0.0663 0.012 1.3 9.6 0.0 2.2 0 2.000 0.2760 0.3460 0.0700 0.014 1.6 18.9 0.2 2.6 0 3.000 0.2742 0.3452 0.0711 0.016 1.8 24.4 0.9 3.6 0 4.000 0.2722 0.3438 0.0716 0.016 1.8 27.5 1.8 6.4 0 5.000 0.2719 0.3482 0.0763 0.020 2.2 30.8 1.9 5.6 0 6.000 0.2710 0.3481 0.0770 0.022 2.3 29.9 1.8 6.0 0 7.000 0.2700 0.3486 0.0786 0.024 2.4 33.7 2.1 8.0 0 8.000 0.2696 0.3493 0.0798 0.024 2.6 39.7 2.7 14.1 0 9.000 0.2691 0.3492 0.0801 0.026 2.7 40.0 3.4 10.6 0 10.000 0.2807 0.3438 0.0631 0.009 1.1 6.5 0.0 2.2 0 1.073 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2949 0.3437 0.0489 0.002 0.4 1.3 0.0 2.4 0 0.250 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 29.49 34.37 4.89 21.189 131.988 0.081 6.362 32.00 34.51 2.51 17.732 139.975 0.002 6.405 31.68 34.48 2.80 17.274 140.523 0.010 6.399 29.30 34.14 4.84 19.211 136.157 0.040 6.363 28.35 34.21 5.86 21.063 134.488 0.081 6.347 28.09 34.20 6.11 21.699 134.210 0.121 6.341 28.08 34.22 6.14 21.961 133.907 0.162 6.341 27.97 34.28 6.31 22.422 134.255 0.202 6.339 27.99 34.29 6.30 22.587 134.182 0.243 6.338 27.91 34.32 6.40 22.997 134.494 0.283 6.337 27.94 34.30 6.35 22.895 134.439 0.324 6.337 27.90 34.33 6.42 23.106 134.603 0.364 6.336 27.86 34.34 6.49 23.420 134.842 0.405 6.335 max suggested for this run: 26.40 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.040 Accepted refinement result: 29.30 34.14 4.84 19.211 136.157 0.040 6.363 Individual atomic B min max mean iso aniso Overall: 63.21 268.49 127.31 11.11 4450 0 Protein: 63.21 268.49 127.31 11.11 4450 0 Chain A: 63.21 268.49 125.71 N/A 2225 0 Chain B: 68.82 268.49 128.91 N/A 2225 0 Histogram: Values Number of atoms 63.21 - 83.73 186 83.73 - 104.26 931 104.26 - 124.79 1162 124.79 - 145.32 1065 145.32 - 165.85 621 165.85 - 186.38 288 186.38 - 206.90 117 206.90 - 227.43 45 227.43 - 247.96 15 247.96 - 268.49 20 =========================== Idealize ADP of riding H ========================== r_work=0.2930 r_free=0.3414 r_work=0.2933 r_free=0.3412 ----------X-ray data---------- |--(resolution: 4.00 - 65.20 A, n_refl.=11703 (all), 4.74 % free)------------| | | | r_work= 0.2933 r_free= 0.3412 coordinate error (max.-lik. estimate): 0.54 A | | | | normalized target function (ml) (work): 6.365584 | | target function (ml) not normalized (work): 70963.535185 | | target function (ml) not normalized (free): 3564.828191 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 65.20 - 6.35 1.00 2866 154 0.2740 0.3311 6.8495 6.8531| | 2: 6.35 - 5.04 1.00 2776 143 0.3058 0.3356 6.3335 6.3948| | 3: 5.04 - 4.40 1.00 2783 123 0.3017 0.3545 6.2702 6.3442| | 4: 4.40 - 4.00 0.99 2723 135 0.3137 0.3595 5.9864 6.0345| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 65.20 - 6.35 2866 154 0.75 30.18 0.97 0.83 131797.36| | 2: 6.35 - 5.04 2776 143 0.63 41.35 1.03 0.84 96606.37| | 3: 5.04 - 4.40 2783 123 0.72 34.52 1.08 0.85 66359.03| | 4: 4.40 - 4.00 2723 135 0.69 37.32 1.03 0.86 41719.24| |alpha: min = 0.83 max = 0.86 mean = 0.85| |beta: min = 41719.24 max = 131797.36 mean = 84695.83| |figures of merit: min = 0.00 max = 1.00 mean = 0.70| |phase err.(work): min = 0.00 max = 89.99 mean = 35.79| |phase err.(test): min = 0.00 max = 89.78 mean = 35.99| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2956 0.2933 0.3412 n_refl.: 11703 re-set all scales: r(all,work,free)=0.6206 0.6242 0.4695 n_refl.: 11703 remove outliers: r(all,work,free)=0.6206 0.6242 0.4695 n_refl.: 11703 overall B=-0.74 to atoms: r(all,work,free)=0.6187 0.6223 0.4680 n_refl.: 11703 bulk-solvent and scaling: r(all,work,free)=0.2967 0.2946 0.3403 n_refl.: 11703 remove outliers: r(all,work,free)=0.2967 0.2946 0.3403 n_refl.: 11703 ======================== 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 65.196-20.791 100.00 98 1 0.3652 1485.455 1383.432 1.338 1.028 0.370 20.447-16.215 100.00 96 3 0.3168 1044.197 997.816 1.045 1.027 0.332 16.132-12.745 100.00 194 11 0.2814 1011.291 937.918 1.099 1.024 0.322 12.705-10.080 100.00 377 16 0.2563 950.100 884.609 1.112 1.020 0.320 10.040-7.926 100.00 749 47 0.2430 736.448 696.903 1.052 1.012 0.281 7.906-6.254 99.81 1487 80 0.2881 454.673 417.586 0.988 0.999 0.221 6.249-4.933 100.00 3011 157 0.3029 392.784 346.482 0.940 0.977 0.171 4.931-4.001 99.68 5136 240 0.3103 331.036 292.734 1.056 0.945 0.091 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-2.5692 ================= 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 : 0.5891 0.4411 0.010 1.541 34.1 300.0 115.5 0 0.000 1_bss: 0.2998 0.3469 0.010 1.541 35.8 301.7 117.2 0 0.000 1_settarget: 0.2998 0.3469 0.010 1.541 35.8 301.7 117.2 0 0.000 1_weight: 0.2998 0.3469 0.010 1.541 35.8 301.7 117.2 0 0.000 1_xyzrec: 0.3027 0.3510 0.003 0.531 35.8 301.7 117.2 0 0.126 1_adp: 0.2947 0.3348 0.003 0.531 38.4 296.7 125.6 0 0.126 1_regHadp: 0.2935 0.3360 0.003 0.531 38.4 296.7 125.6 0 0.126 2_bss: 0.2909 0.3343 0.003 0.531 35.5 293.9 122.7 0 0.126 2_settarget: 0.2909 0.3343 0.003 0.531 35.5 293.9 122.7 0 0.126 2_updatecdl: 0.2909 0.3343 0.003 0.570 35.5 293.9 122.7 0 0.126 2_weight: 0.2909 0.3343 0.003 0.570 35.5 293.9 122.7 0 0.126 2_xyzrec: 0.2958 0.3381 0.002 0.385 35.5 293.9 122.7 0 0.212 2_adp: 0.2950 0.3413 0.002 0.385 56.4 288.9 134.5 0 0.212 2_regHadp: 0.2957 0.3435 0.002 0.385 56.4 288.9 134.5 0 0.212 3_bss: 0.2958 0.3447 0.002 0.385 40.9 273.5 119.1 0 0.212 3_settarget: 0.2958 0.3447 0.002 0.385 40.9 273.5 119.1 0 0.212 3_updatecdl: 0.2958 0.3447 0.002 0.472 40.9 273.5 119.1 0 0.212 3_setrh: 0.2958 0.3446 0.002 0.472 40.9 273.5 119.1 0 0.212 3_weight: 0.2958 0.3446 0.002 0.472 40.9 273.5 119.1 0 0.212 3_xyzrec: 0.2949 0.3437 0.002 0.414 40.9 273.5 119.1 0 0.212 3_adp: 0.2930 0.3414 0.002 0.414 63.2 268.5 127.3 0 0.212 3_regHadp: 0.2933 0.3412 0.002 0.414 63.2 268.5 127.3 0 0.212 end: 0.2946 0.3403 0.002 0.414 62.5 267.7 126.6 0 0.212 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V1/2yhj_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V1/2yhj_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 12.3700 Refinement macro-cycles (run) : 311.4700 Write final files (write_after_run_outputs) : 17.8900 Total : 341.7300 Total CPU time: 6.29 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:35:36 PDT -0700 (1716251736.79 s) Start R-work = 0.2998, R-free = 0.3469 Final R-work = 0.2946, R-free = 0.3403 =============================================================================== Job complete usr+sys time: 397.48 seconds wall clock time: 19 minutes 30.27 seconds (1170.27 seconds total)