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/1w60.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1w60/1w60.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/1w60/1w60.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1w60/1w60.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/1w60.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/1w60.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: 7874 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 3937 Classifications: {'peptide': 255} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 247} Chain: "B" Number of atoms: 3937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 3937 Classifications: {'peptide': 255} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 247} Time building chain proxies: 1.41, per 1000 atoms: 0.18 Number of scatterers: 7874 At special positions: 0 Unit cell: (82.892, 82.892, 70.859, 90, 90, 120) Space group: P 3 (No. 143) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 O 786 8.00 N 644 7.00 C 2466 6.00 H 3946 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: 1.82 Conformation dependent library (CDL) restraints added in 249.3 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 968 Time building geometry restraints manager: 2.10 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: 3934 1.15 - 1.32: 712 1.32 - 1.49: 1460 1.49 - 1.66: 1768 1.66 - 1.83: 52 Bond restraints: 7926 Sorted by residual: bond pdb=" NE1 TRP B 28 " pdb=" CE2 TRP B 28 " ideal model delta sigma weight residual 1.370 1.483 -0.113 1.10e-02 8.26e+03 1.06e+02 bond pdb=" N SER A 112 " pdb=" H SER A 112 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" ND2 ASN B 107 " pdb="HD22 ASN B 107 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" N GLN B 131 " pdb=" H GLN B 131 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N LEU B 6 " pdb=" H LEU B 6 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 7921 not shown) Histogram of bond angle deviations from ideal: 97.88 - 105.14: 87 105.14 - 112.40: 9571 112.40 - 119.66: 1859 119.66 - 126.92: 2837 126.92 - 134.18: 20 Bond angle restraints: 14374 Sorted by residual: angle pdb=" N ASP B 232 " pdb=" CA ASP B 232 " pdb=" CB ASP B 232 " ideal model delta sigma weight residual 114.17 108.16 6.01 1.14e+00 7.69e-01 2.78e+01 angle pdb=" CD ARG A 64 " pdb=" NE ARG A 64 " pdb=" CZ ARG A 64 " ideal model delta sigma weight residual 124.40 117.23 7.17 1.40e+00 5.10e-01 2.62e+01 angle pdb=" N PRO B 234 " pdb=" CA PRO B 234 " pdb=" CB PRO B 234 " ideal model delta sigma weight residual 103.31 107.82 -4.51 8.90e-01 1.26e+00 2.57e+01 angle pdb=" CD ARG A 61 " pdb=" NE ARG A 61 " pdb=" CZ ARG A 61 " ideal model delta sigma weight residual 124.40 117.32 7.08 1.40e+00 5.10e-01 2.56e+01 angle pdb=" N PRO B 202 " pdb=" CA PRO B 202 " pdb=" CB PRO B 202 " ideal model delta sigma weight residual 103.19 107.64 -4.45 9.00e-01 1.23e+00 2.45e+01 ... (remaining 14369 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 3107 17.84 - 35.68: 335 35.68 - 53.52: 181 53.52 - 71.37: 70 71.37 - 89.21: 19 Dihedral angle restraints: 3712 sinusoidal: 2056 harmonic: 1656 Sorted by residual: dihedral pdb=" CA ASP A 122 " pdb=" C ASP A 122 " pdb=" N VAL A 123 " pdb=" CA VAL A 123 " ideal model delta harmonic sigma weight residual -180.00 -162.23 -17.77 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA ASN A 95 " pdb=" C ASN A 95 " pdb=" N ALA A 96 " pdb=" CA ALA A 96 " ideal model delta harmonic sigma weight residual -180.00 -162.99 -17.01 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA ASP B 122 " pdb=" C ASP B 122 " pdb=" N VAL B 123 " pdb=" CA VAL B 123 " ideal model delta harmonic sigma weight residual -180.00 -163.34 -16.66 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 3709 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 402 0.037 - 0.075: 108 0.075 - 0.112: 81 0.112 - 0.149: 23 0.149 - 0.187: 22 Chirality restraints: 636 Sorted by residual: chirality pdb=" CB THR B 219 " pdb=" CA THR B 219 " pdb=" OG1 THR B 219 " pdb=" CG2 THR B 219 " both_signs ideal model delta sigma weight residual False 2.55 2.74 -0.19 2.00e-01 2.50e+01 8.73e-01 chirality pdb=" CB THR A 219 " pdb=" CA THR A 219 " pdb=" OG1 THR A 219 " pdb=" CG2 THR A 219 " both_signs ideal model delta sigma weight residual False 2.55 2.73 -0.18 2.00e-01 2.50e+01 8.13e-01 chirality pdb=" CB THR B 73 " pdb=" CA THR B 73 " pdb=" OG1 THR B 73 " pdb=" CG2 THR B 73 " both_signs ideal model delta sigma weight residual False 2.55 2.73 -0.18 2.00e-01 2.50e+01 7.95e-01 ... (remaining 633 not shown) Planarity restraints: 1186 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 239 " -0.113 2.00e-02 2.50e+03 4.19e-02 5.26e+01 pdb=" CG TYR B 239 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR B 239 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR B 239 " 0.029 2.00e-02 2.50e+03 pdb=" CE1 TYR B 239 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR B 239 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 239 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR B 239 " -0.043 2.00e-02 2.50e+03 pdb=" HD1 TYR B 239 " 0.037 2.00e-02 2.50e+03 pdb=" HD2 TYR B 239 " 0.052 2.00e-02 2.50e+03 pdb=" HE1 TYR B 239 " -0.002 2.00e-02 2.50e+03 pdb=" HE2 TYR B 239 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 246 " -0.035 2.00e-02 2.50e+03 1.72e-02 6.67e+00 pdb=" CG HIS B 246 " 0.015 2.00e-02 2.50e+03 pdb=" ND1 HIS B 246 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 HIS B 246 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 HIS B 246 " -0.006 2.00e-02 2.50e+03 pdb=" NE2 HIS B 246 " -0.009 2.00e-02 2.50e+03 pdb=" HD1 HIS B 246 " 0.022 2.00e-02 2.50e+03 pdb=" HD2 HIS B 246 " 0.013 2.00e-02 2.50e+03 pdb=" HE1 HIS B 246 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 246 " 0.034 2.00e-02 2.50e+03 1.68e-02 6.34e+00 pdb=" CG HIS A 246 " -0.015 2.00e-02 2.50e+03 pdb=" ND1 HIS A 246 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 HIS A 246 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 HIS A 246 " 0.006 2.00e-02 2.50e+03 pdb=" NE2 HIS A 246 " 0.009 2.00e-02 2.50e+03 pdb=" HD1 HIS A 246 " -0.021 2.00e-02 2.50e+03 pdb=" HD2 HIS A 246 " -0.012 2.00e-02 2.50e+03 pdb=" HE1 HIS A 246 " 0.017 2.00e-02 2.50e+03 ... (remaining 1183 not shown) Histogram of nonbonded interaction distances: 0.94 - 1.67: 63 1.67 - 2.40: 3135 2.40 - 3.13: 24071 3.13 - 3.87: 33793 3.87 - 4.60: 51974 Warning: very small nonbonded interaction distances. Nonbonded interactions: 113036 Sorted by model distance: nonbonded pdb=" O LEU B 182 " pdb=" HG SER B 183 " model vdw 0.936 1.850 nonbonded pdb=" HB2 GLN B 184 " pdb="HG11 VAL B 195 " model vdw 1.002 2.440 nonbonded pdb="HG13 VAL A 188 " pdb=" HB2 ALA B 252 " model vdw sym.op. 1.043 2.440 -x+y+1,-x+1,z nonbonded pdb="HG13 VAL B 195 " pdb=" H THR B 196 " model vdw 1.203 2.270 nonbonded pdb=" HG2 PRO B 140 " pdb=" HG3 GLU B 193 " model vdw 1.204 2.440 ... (remaining 113031 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 32 15.96 2 O 786 7.97 1 N 644 6.97 1 C 2466 5.97 2 H 3946 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: 3946 of 7874 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 7874 n_use_u_iso = 7874 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 = 7874 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (7874 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 7874 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 = "1w60_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 3946 occupancy sum: 3946.00 (% of total atoms 50.11) Rotatable: count: 1214 occupancy sum: 1214.00 (% of total atoms 15.42) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.14 - 25.21 A, n_refl.=9258 (all), 4.80 % free)-------------| | | | r_work= 0.3127 r_free= 0.3555 coordinate error (max.-lik. estimate): 0.43 A | | | | normalized target function (ml) (work): 6.213664 | | target function (ml) not normalized (work): 54767.234476 | | target function (ml) not normalized (free): 2756.138780 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 25.21 - 4.53 0.98 2961 131 0.3221 0.3675 6.7019 6.6358| | 2: 4.52 - 3.60 0.98 2955 140 0.3038 0.3318 6.2193 6.2826| | 3: 3.60 - 3.14 0.97 2898 173 0.3059 0.3697 5.709 5.8225| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 25.21 - 4.53 2961 131 0.65 40.73 0.91 0.65 115062.26| | 2: 4.52 - 3.60 2955 140 0.68 38.46 1.23 0.87 57473.34| | 3: 3.60 - 3.14 2898 173 0.73 34.32 1.19 0.95 19014.54| |alpha: min = 0.65 max = 0.95 mean = 0.83| |beta: min = 19014.54 max = 115062.26 mean = 64174.86| |figures of merit: min = 0.00 max = 0.99 mean = 0.68| |phase err.(work): min = 0.00 max = 89.90 mean = 37.86| |phase err.(test): min = 0.00 max = 88.83 mean = 37.54| |-----------------------------------------------------------------------------| ----------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 : 0.007 0.113 3980 Z= 0.444 Angle : 1.399 7.165 5378 Z= 0.912 Chirality : 0.058 0.187 636 Planarity : 0.003 0.044 692 Dihedral : 23.356 87.623 1492 Min Nonbonded Distance : 1.684 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 2.96 % Allowed : 6.32 % Favored : 90.71 % Rotamer: Outliers : 23.77 % Allowed : 18.39 % Favored : 57.85 % Cbeta Deviations : 0.00 % 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: -3.75 (0.31), residues: 506 helix: -2.40 (0.42), residues: 82 sheet: -1.98 (0.30), residues: 252 loop : -2.98 (0.35), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 61 TYR 0.086 0.005 TYR B 239 PHE 0.018 0.001 PHE B 103 TRP 0.020 0.004 TRP B 28 HIS 0.002 0.001 HIS B 246 Individual atomic B min max mean iso aniso Overall: 2.00 149.48 50.67 9.35 3928 0 Protein: 2.00 149.48 50.67 9.35 3928 0 Chain A: 2.00 149.40 50.68 N/A 1964 0 Chain B: 3.06 149.48 50.65 N/A 1964 0 Histogram: Values Number of atoms 2.00 - 16.75 88 16.75 - 31.50 624 31.50 - 46.24 1249 46.24 - 60.99 942 60.99 - 75.74 488 75.74 - 90.49 299 90.49 - 105.24 135 105.24 - 119.98 34 119.98 - 134.73 25 134.73 - 149.48 44 |-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: 3.14 - 25.21 A, n_refl.=9258 (all), 4.80 % free)-------------| | | | r_work= 0.3127 r_free= 0.3555 coordinate error (max.-lik. estimate): 0.43 A | | | | normalized target function (ml) (work): 6.213664 | | target function (ml) not normalized (work): 54767.234476 | | target function (ml) not normalized (free): 2756.138780 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3149 0.3127 0.3555 n_refl.: 9258 re-set all scales: r(all,work,free)=0.3149 0.3127 0.3555 n_refl.: 9258 remove outliers: r(all,work,free)=0.3148 0.3126 0.3555 n_refl.: 9255 overall B=5.77 to atoms: r(all,work,free)=0.3305 0.3283 0.3719 n_refl.: 9255 bulk-solvent and scaling: r(all,work,free)=0.2347 0.2324 0.2782 n_refl.: 9255 remove outliers: r(all,work,free)=0.2347 0.2324 0.2782 n_refl.: 9255 ======================== 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 25.215-13.182 84.48 95 3 0.2240 720.927 692.011 1.575 1.004 0.382 13.182-10.771 92.52 92 7 0.2328 728.577 659.686 1.354 1.009 0.372 10.742-8.763 94.15 183 10 0.1786 646.556 624.296 1.235 1.006 0.367 8.709-7.139 97.85 350 14 0.1955 566.962 549.169 1.218 1.006 0.361 7.120-5.819 98.85 652 33 0.2417 394.630 369.156 1.076 1.002 0.357 5.810-4.742 98.41 1191 49 0.2078 477.646 452.627 0.970 0.997 0.284 4.737-3.861 98.48 2221 114 0.2121 429.398 408.632 1.018 0.988 0.203 3.860-3.143 97.34 4027 214 0.2781 247.845 230.388 1.027 0.974 0.071 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=4.8102 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 15.341763 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.207977 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 0.2294 0.2747 0.0453 0.003 0.5 2.7 2.0 15.5 0 0.125 0.2241 0.2725 0.0484 0.003 0.5 2.8 2.0 15.9 0 0.250 0.2162 0.2716 0.0554 0.003 0.5 2.7 2.0 15.7 0 0.500 0.2058 0.2714 0.0655 0.003 0.5 3.3 2.6 16.1 0 1.000 0.1956 0.2751 0.0795 0.005 0.7 5.7 3.2 16.8 0 2.000 0.1909 0.2757 0.0848 0.006 0.8 7.4 3.0 17.9 0 3.000 0.1867 0.2760 0.0893 0.007 0.9 9.0 3.2 19.1 0 4.000 0.1837 0.2751 0.0914 0.009 1.0 10.5 3.0 20.0 0 5.000 0.1813 0.2754 0.0940 0.010 1.1 11.2 3.0 21.5 0 6.000 0.1799 0.2737 0.0938 0.011 1.1 12.7 3.0 21.3 0 7.000 0.1783 0.2726 0.0943 0.012 1.2 12.8 3.2 21.1 0 8.000 0.1767 0.2733 0.0966 0.013 1.3 14.1 3.4 22.6 0 9.000 0.1752 0.2735 0.0984 0.014 1.3 14.9 3.4 22.9 0 10.000 0.1790 0.2741 0.0951 0.012 1.2 13.1 3.0 21.1 0 7.671 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2294 0.2747 0.0453 0.003 0.5 2.7 2.0 15.5 0 0.125 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 22.94 27.47 4.53 6.626 55.231 0.208 0.062 23.92 28.17 4.25 6.166 55.923 0.006 0.067 23.66 28.13 4.47 6.101 55.888 0.026 0.065 22.82 27.99 5.17 6.370 55.855 0.104 0.061 22.09 27.87 5.78 7.268 55.934 0.208 0.057 21.63 27.76 6.13 8.157 56.041 0.312 0.055 21.31 27.67 6.35 9.033 56.228 0.416 0.053 21.01 27.64 6.63 10.105 56.545 0.520 0.052 20.84 27.65 6.80 10.757 56.683 0.624 0.051 20.71 27.66 6.95 11.322 56.807 0.728 0.051 20.60 27.66 7.06 11.822 56.921 0.832 0.050 20.52 27.66 7.15 12.275 57.027 0.936 0.050 20.37 27.67 7.30 13.088 57.288 1.040 0.049 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.208 Accepted refinement result: 22.09 27.87 5.78 7.268 55.934 0.208 0.057 Individual atomic B min max mean iso aniso Overall: 18.75 155.23 57.85 7.71 3928 0 Protein: 18.75 155.23 57.85 7.71 3928 0 Chain A: 19.09 155.23 57.83 N/A 1964 0 Chain B: 18.75 151.91 57.87 N/A 1964 0 Histogram: Values Number of atoms 18.75 - 32.40 208 32.40 - 46.04 1128 46.04 - 59.69 1121 59.69 - 73.34 718 73.34 - 86.99 357 86.99 - 100.64 228 100.64 - 114.28 82 114.28 - 127.93 19 127.93 - 141.58 29 141.58 - 155.23 38 =========================== Idealize ADP of riding H ========================== r_work=0.2209 r_free=0.2787 r_work=0.2193 r_free=0.2777 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.14 - 25.21 A, n_refl.=9255 (all), 4.80 % free)-------------| | | | r_work= 0.2193 r_free= 0.2777 coordinate error (max.-lik. estimate): 0.53 A | | | | normalized target function (ls_wunit_k1) (work): 0.056382 | | target function (ls_wunit_k1) not normalized (work): 496.778681 | | target function (ls_wunit_k1) not normalized (free): 44.262559 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2220 0.2193 0.2777 n_refl.: 9255 re-set all scales: r(all,work,free)=0.3289 0.3262 0.3771 n_refl.: 9255 remove outliers: r(all,work,free)=0.3289 0.3262 0.3771 n_refl.: 9255 overall B=0.00 to atoms: r(all,work,free)=0.3289 0.3262 0.3771 n_refl.: 9255 bulk-solvent and scaling: r(all,work,free)=0.2218 0.2191 0.2765 n_refl.: 9255 remove outliers: r(all,work,free)=0.2218 0.2191 0.2765 n_refl.: 9255 ======================== 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 25.215-13.182 84.48 95 3 0.2165 538.986 515.451 1.423 1.015 0.376 13.182-10.771 91.67 92 7 0.2127 544.705 511.428 1.299 1.018 0.370 10.742-8.763 94.15 183 10 0.1668 483.384 465.594 1.189 1.014 0.367 8.709-7.139 97.85 350 14 0.1727 423.877 413.802 1.166 1.012 0.360 7.120-5.819 98.85 652 33 0.2154 295.037 282.122 1.030 1.006 0.340 5.810-4.742 98.41 1191 49 0.1864 357.102 342.060 0.951 0.997 0.300 4.737-3.861 98.48 2221 114 0.1977 321.031 308.633 1.001 0.983 0.230 3.860-3.143 97.34 4027 214 0.2752 185.296 173.814 1.023 0.960 0.050 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0577 b_overall=3.7719 ============================ 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 = 3.704927 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.056516 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 0.2041 0.2732 0.0691 0.002 0.5 3.3 2.2 10.5 0 0.125 0.1978 0.2728 0.0750 0.003 0.5 3.6 2.4 12.1 0 0.250 0.1913 0.2763 0.0850 0.005 0.6 6.5 2.8 13.5 0 0.500 0.1854 0.2773 0.0919 0.008 0.9 9.3 2.8 16.1 0 1.000 0.1792 0.2787 0.0995 0.014 1.3 11.8 3.0 19.5 0 2.000 0.1756 0.2773 0.1016 0.019 1.6 14.5 4.3 20.9 0 3.000 0.1731 0.2776 0.1045 0.024 1.9 16.3 4.2 20.9 0 4.000 0.1709 0.2780 0.1071 0.028 2.1 20.1 4.7 23.3 0 5.000 0.1692 0.2787 0.1094 0.031 2.3 22.6 5.9 24.0 0 6.000 0.1679 0.2797 0.1118 0.035 2.6 24.8 6.7 25.3 0 7.000 0.1667 0.2785 0.1118 0.038 2.8 25.3 6.9 25.3 0 8.000 0.1658 0.2789 0.1131 0.041 2.9 27.3 7.3 25.8 0 9.000 0.1645 0.2799 0.1154 0.044 3.1 28.3 7.3 26.9 0 10.000 0.1799 0.2787 0.0988 0.014 1.2 11.7 3.0 19.5 0 1.852 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1978 0.2728 0.0750 0.003 0.5 3.6 2.4 12.1 0 0.250 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 19.78 27.28 7.50 10.097 62.922 0.057 5.617 23.07 29.11 6.04 9.625 66.378 0.002 5.702 22.27 28.71 6.44 10.067 64.981 0.007 5.683 19.80 27.37 7.57 10.198 62.671 0.028 5.616 19.52 27.34 7.82 10.532 62.567 0.057 5.609 19.25 27.35 8.10 11.135 62.326 0.085 5.601 18.83 27.66 8.83 12.409 62.475 0.113 5.591 18.70 27.69 8.98 12.687 62.659 0.141 5.589 18.61 27.71 9.10 12.953 62.822 0.170 5.586 18.56 27.75 9.19 13.146 62.933 0.198 5.586 18.58 27.63 9.05 12.994 62.865 0.226 5.585 18.46 27.76 9.30 13.534 63.140 0.254 5.584 18.43 27.78 9.34 13.692 63.220 0.283 5.584 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.002 Accepted refinement result: 23.07 29.11 6.04 9.625 66.378 0.002 5.702 Individual atomic B min max mean iso aniso Overall: 40.17 150.23 64.77 3.71 3928 0 Protein: 40.17 150.23 64.77 3.71 3928 0 Chain A: 40.19 150.23 64.80 N/A 1964 0 Chain B: 40.17 146.91 64.74 N/A 1964 0 Histogram: Values Number of atoms 40.17 - 51.18 648 51.18 - 62.18 1531 62.18 - 73.19 862 73.19 - 84.19 465 84.19 - 95.20 194 95.20 - 106.21 106 106.21 - 117.21 35 117.21 - 128.22 25 128.22 - 139.22 30 139.22 - 150.23 32 =========================== Idealize ADP of riding H ========================== r_work=0.2307 r_free=0.2911 r_work=0.2337 r_free=0.2911 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.14 - 25.21 A, n_refl.=9255 (all), 4.80 % free)-------------| | | | r_work= 0.2337 r_free= 0.2911 coordinate error (max.-lik. estimate): 0.40 A | | | | normalized target function (ml) (work): 5.710703 | | target function (ml) not normalized (work): 50317.003728 | | target function (ml) not normalized (free): 2579.532164 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2363 0.2337 0.2911 n_refl.: 9255 re-set all scales: r(all,work,free)=0.3686 0.3663 0.4146 n_refl.: 9255 remove outliers: r(all,work,free)=0.3686 0.3663 0.4146 n_refl.: 9255 overall B=-5.08 to atoms: r(all,work,free)=0.3518 0.3493 0.3978 n_refl.: 9255 bulk-solvent and scaling: r(all,work,free)=0.2333 0.2306 0.2878 n_refl.: 9255 remove outliers: r(all,work,free)=0.2333 0.2306 0.2878 n_refl.: 9255 ======================== 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 25.215-13.182 84.48 95 3 0.1915 474.603 461.987 1.401 1.038 0.380 13.182-10.771 92.52 92 7 0.1892 479.639 453.248 1.248 1.039 0.370 10.742-8.763 94.15 183 10 0.1442 425.643 409.860 1.142 1.033 0.361 8.709-7.139 97.85 350 14 0.1672 373.244 365.418 1.146 1.027 0.357 7.120-5.819 98.85 652 33 0.2293 259.795 246.133 1.016 1.015 0.341 5.810-4.742 98.41 1191 49 0.1991 314.446 298.895 0.983 0.999 0.315 4.737-3.861 98.48 2221 114 0.2136 282.683 269.553 1.040 0.973 0.226 3.860-3.143 97.34 4027 214 0.2939 163.162 149.955 1.088 0.933 0.056 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0610 b_overall=2.2966 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.2306 r_free=0.2878 After: r_work=0.2307 r_free=0.2878 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 3.593507 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.052778 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 0.2311 0.2881 0.0570 0.003 0.5 4.1 2.2 11.9 0 0.125 0.2304 0.2878 0.0574 0.003 0.5 4.1 2.2 11.9 0 0.250 0.2279 0.2870 0.0591 0.006 0.6 4.4 2.2 11.7 0 0.500 0.2167 0.2870 0.0702 0.013 1.3 8.9 2.4 11.9 0 1.000 0.2053 0.2857 0.0804 0.019 2.1 18.3 3.0 14.6 0 2.000 0.2005 0.2858 0.0853 0.023 2.3 25.3 4.2 17.5 0 3.000 0.1964 0.2833 0.0869 0.028 2.9 25.4 3.6 17.0 0 4.000 0.1932 0.2864 0.0932 0.033 3.1 35.8 5.5 23.1 0 5.000 0.1920 0.2844 0.0924 0.033 3.2 32.6 5.3 22.2 0 6.000 0.1891 0.2857 0.0966 0.038 3.6 38.7 5.7 26.7 0 7.000 0.1847 0.2842 0.0994 0.043 4.0 40.0 5.9 25.6 1 8.000 0.1829 0.2861 0.1032 0.048 4.2 42.7 6.1 27.4 3 9.000 0.1811 0.2857 0.1046 0.052 4.5 45.0 6.5 27.8 4 10.000 0.2073 0.2864 0.0791 0.018 2.0 16.4 2.6 14.1 0 1.797 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2304 0.2878 0.0574 0.003 0.5 4.1 2.2 11.9 0 0.250 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 23.04 28.78 5.74 9.622 65.482 0.053 5.581 25.00 31.32 6.32 8.703 71.479 0.002 5.628 22.61 28.80 6.19 9.615 65.414 0.007 5.569 22.29 28.69 6.40 9.868 65.269 0.026 5.559 20.70 28.13 7.44 11.305 65.837 0.053 5.511 20.35 28.08 7.73 12.133 66.337 0.079 5.500 20.12 28.07 7.95 12.990 66.752 0.106 5.494 20.06 28.04 7.99 13.221 66.859 0.132 5.492 20.11 27.98 7.87 13.306 66.864 0.158 5.494 20.06 27.97 7.91 13.608 66.996 0.185 5.493 20.02 27.98 7.96 13.860 67.104 0.211 5.492 19.99 27.97 7.98 14.077 67.193 0.237 5.491 19.97 27.96 7.99 14.261 67.268 0.264 5.490 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.002 Accepted refinement result: 25.00 31.32 6.32 8.703 71.479 0.002 5.628 Individual atomic B min max mean iso aniso Overall: 47.48 140.14 71.71 2.59 3928 0 Protein: 47.48 140.14 71.71 2.59 3928 0 Chain A: 50.13 140.14 71.71 N/A 1964 0 Chain B: 47.48 136.83 71.71 N/A 1964 0 Histogram: Values Number of atoms 47.48 - 56.75 89 56.75 - 66.01 1238 66.01 - 75.28 1582 75.28 - 84.55 648 84.55 - 93.81 201 93.81 - 103.08 65 103.08 - 112.35 29 112.35 - 121.61 21 121.61 - 130.88 29 130.88 - 140.14 26 =========================== Idealize ADP of riding H ========================== r_work=0.2500 r_free=0.3132 r_work=0.2503 r_free=0.3144 ----------X-ray data---------- |--(resolution: 3.14 - 25.21 A, n_refl.=9255 (all), 4.80 % free)-------------| | | | r_work= 0.2503 r_free= 0.3144 coordinate error (max.-lik. estimate): 0.38 A | | | | normalized target function (ml) (work): 5.628567 | | target function (ml) not normalized (work): 49593.306971 | | target function (ml) not normalized (free): 2544.387433 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 25.21 - 4.53 0.98 2958 131 0.2072 0.2696 5.8295 5.948| | 2: 4.52 - 3.60 0.98 2955 140 0.2669 0.3070 5.6928 5.8239| | 3: 3.60 - 3.14 0.97 2898 173 0.3219 0.3959 5.358 5.4904| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 25.21 - 4.53 2958 131 0.83 25.09 0.96 0.95 23400.91| | 2: 4.52 - 3.60 2955 140 0.78 29.91 1.07 1.00 16486.42| | 3: 3.60 - 3.14 2898 173 0.68 38.47 1.13 1.00 10179.44| |alpha: min = 0.95 max = 1.00 mean = 0.98| |beta: min = 10179.44 max = 23400.91 mean = 16733.32| |figures of merit: min = 0.00 max = 1.00 mean = 0.76| |phase err.(work): min = 0.00 max = 89.82 mean = 31.11| |phase err.(test): min = 6.56 max = 88.69 mean = 32.69| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2532 0.2503 0.3144 n_refl.: 9255 re-set all scales: r(all,work,free)=0.4101 0.4076 0.4607 n_refl.: 9255 remove outliers: r(all,work,free)=0.4101 0.4076 0.4607 n_refl.: 9255 overall B=-12.24 to atoms: r(all,work,free)=0.3688 0.3662 0.4205 n_refl.: 9255 bulk-solvent and scaling: r(all,work,free)=0.2429 0.2399 0.3056 n_refl.: 9255 remove outliers: r(all,work,free)=0.2429 0.2399 0.3056 n_refl.: 9255 ======================== 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 25.215-13.182 84.48 95 3 0.1988 474.603 459.844 1.259 1.133 0.385 13.182-10.771 92.52 92 7 0.1876 479.639 450.266 1.131 1.126 0.375 10.742-8.763 94.15 183 10 0.1373 425.643 409.938 1.047 1.111 0.370 8.709-7.139 97.85 350 14 0.1666 373.244 365.474 1.057 1.093 0.372 7.120-5.819 98.85 652 33 0.2345 259.795 245.371 0.960 1.061 0.367 5.810-4.742 98.41 1191 49 0.2077 314.446 299.084 0.967 1.016 0.348 4.737-3.861 98.48 2221 114 0.2294 282.683 268.281 1.054 0.946 0.250 3.860-3.143 97.34 4027 214 0.3029 163.162 149.589 1.203 0.840 0.065 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0577 b_overall=2.6781 ================= 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 : 0.3127 0.3555 0.007 1.399 2.0 149.5 50.7 0 0.000 1_bss: 0.2324 0.2782 0.007 1.399 7.8 155.3 56.4 0 0.000 1_settarget: 0.2324 0.2782 0.007 1.399 7.8 155.3 56.4 0 0.000 1_weight: 0.2324 0.2782 0.007 1.399 7.8 155.3 56.4 0 0.000 1_xyzrec: 0.2294 0.2747 0.003 0.499 7.8 155.3 56.4 0 0.160 1_adp: 0.2209 0.2787 0.003 0.499 18.7 155.2 57.8 0 0.160 1_regHadp: 0.2193 0.2777 0.003 0.499 18.7 155.2 57.8 0 0.160 2_bss: 0.2191 0.2765 0.003 0.499 18.7 155.2 57.8 0 0.160 2_settarget: 0.2191 0.2765 0.003 0.499 18.7 155.2 57.8 0 0.160 2_updatecdl: 0.2191 0.2765 0.003 0.559 18.7 155.2 57.8 0 0.160 2_weight: 0.2191 0.2765 0.003 0.559 18.7 155.2 57.8 0 0.160 2_xyzrec: 0.1978 0.2728 0.003 0.515 18.7 155.2 57.8 0 0.236 2_adp: 0.2307 0.2911 0.003 0.515 40.2 150.2 64.8 0 0.236 2_regHadp: 0.2337 0.2911 0.003 0.515 40.2 150.2 64.8 0 0.236 3_bss: 0.2306 0.2878 0.003 0.515 35.1 145.1 59.7 0 0.236 3_settarget: 0.2306 0.2878 0.003 0.515 35.1 145.1 59.7 0 0.236 3_updatecdl: 0.2306 0.2878 0.003 0.567 35.1 145.1 59.7 0 0.236 3_setrh: 0.2307 0.2878 0.003 0.567 35.1 145.1 59.7 0 0.236 3_weight: 0.2307 0.2878 0.003 0.567 35.1 145.1 59.7 0 0.236 3_xyzrec: 0.2304 0.2878 0.003 0.523 35.1 145.1 59.7 0 0.236 3_adp: 0.2500 0.3132 0.003 0.523 47.5 140.1 71.7 0 0.236 3_regHadp: 0.2503 0.3144 0.003 0.523 47.5 140.1 71.7 0 0.236 end: 0.2399 0.3056 0.003 0.523 35.2 127.9 59.5 0 0.236 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V1/1w60_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V1/1w60_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 8.7200 Refinement macro-cycles (run) : 248.2900 Write final files (write_after_run_outputs) : 24.2100 Total : 281.2200 Total CPU time: 5.14 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:33:16 PDT -0700 (1716251596.09 s) Start R-work = 0.2324, R-free = 0.2782 Final R-work = 0.2399, R-free = 0.3056 =============================================================================== Job complete usr+sys time: 331.81 seconds wall clock time: 17 minutes 22.26 seconds (1042.26 seconds total)