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/2fdq.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/2fdq/2fdq.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 { model { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/2fdq.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/2fdq.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/2fdq/2fdq.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/2fdq/2fdq.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 { nonbonded_weight = 100 } target_weights { optimize_xyz_weight = true optimize_adp_weight = true } } Starting job =============================================================================== Symmetric amino acids flipped Residue "B TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 4164 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 1388 Classifications: {'peptide': 86} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 83} Chain: "B" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 1388 Classifications: {'peptide': 86} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 83} Chain: "C" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 1388 Classifications: {'peptide': 86} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 83} Time building chain proxies: 0.95, per 1000 atoms: 0.23 Number of scatterers: 4164 At special positions: 0 Unit cell: (49.11, 49.11, 130.48, 90, 90, 90) Space group: P 41 (No. 76) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 9 16.00 O 411 8.00 N 342 7.00 C 1326 6.00 H 2076 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: 0.98 Conformation dependent library (CDL) restraints added in 131.1 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 486 Time building geometry restraints manager: 1.15 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: 2076 1.15 - 1.33: 551 1.33 - 1.50: 695 1.50 - 1.68: 863 1.68 - 1.85: 18 Bond restraints: 4203 Sorted by residual: bond pdb=" N LYS A 18 " pdb=" H LYS A 18 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N THR C 35 " pdb=" H THR C 35 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N THR B 64 " pdb=" H THR B 64 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N GLY A 63 " pdb=" H GLY A 63 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N PHE B 5 " pdb=" H PHE B 5 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 4198 not shown) Histogram of bond angle deviations from ideal: 99.00 - 106.00: 110 106.00 - 113.00: 4926 113.00 - 119.99: 1188 119.99 - 126.99: 1387 126.99 - 133.98: 24 Bond angle restraints: 7635 Sorted by residual: angle pdb=" N GLU C 23 " pdb=" CA GLU C 23 " pdb=" C GLU C 23 " ideal model delta sigma weight residual 111.40 103.42 7.98 1.22e+00 6.72e-01 4.28e+01 angle pdb=" N TRP A 58 " pdb=" CA TRP A 58 " pdb=" C TRP A 58 " ideal model delta sigma weight residual 111.36 104.39 6.97 1.09e+00 8.42e-01 4.09e+01 angle pdb=" N LYS C 13 " pdb=" CA LYS C 13 " pdb=" C LYS C 13 " ideal model delta sigma weight residual 113.15 105.67 7.48 1.19e+00 7.06e-01 3.95e+01 angle pdb=" N LYS B 82 " pdb=" CA LYS B 82 " pdb=" C LYS B 82 " ideal model delta sigma weight residual 111.03 104.08 6.95 1.11e+00 8.12e-01 3.92e+01 angle pdb=" N LEU C 61 " pdb=" CA LEU C 61 " pdb=" C LEU C 61 " ideal model delta sigma weight residual 113.18 120.69 -7.51 1.21e+00 6.83e-01 3.85e+01 ... (remaining 7630 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 1730 17.57 - 35.13: 129 35.13 - 52.70: 61 52.70 - 70.26: 22 70.26 - 87.83: 5 Dihedral angle restraints: 1947 sinusoidal: 1056 harmonic: 891 Sorted by residual: dihedral pdb=" CB GLU C 42 " pdb=" CG GLU C 42 " pdb=" CD GLU C 42 " pdb=" OE1 GLU C 42 " ideal model delta sinusoidal sigma weight residual 0.00 87.83 -87.83 1 3.00e+01 1.11e-03 1.03e+01 dihedral pdb=" CB MET C 24 " pdb=" CG MET C 24 " pdb=" SD MET C 24 " pdb=" CE MET C 24 " ideal model delta sinusoidal sigma weight residual -60.00 -118.10 58.10 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" CB MET B 24 " pdb=" CG MET B 24 " pdb=" SD MET B 24 " pdb=" CE MET B 24 " ideal model delta sinusoidal sigma weight residual -60.00 -113.30 53.30 3 1.50e+01 4.44e-03 9.19e+00 ... (remaining 1944 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.054: 129 0.054 - 0.107: 96 0.107 - 0.160: 47 0.160 - 0.213: 12 0.213 - 0.266: 7 Chirality restraints: 291 Sorted by residual: chirality pdb=" CA VAL B 36 " pdb=" N VAL B 36 " pdb=" C VAL B 36 " pdb=" CB VAL B 36 " both_signs ideal model delta sigma weight residual False 2.44 2.71 -0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CA VAL A 77 " pdb=" N VAL A 77 " pdb=" C VAL A 77 " pdb=" CB VAL A 77 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CA LEU C 61 " pdb=" N LEU C 61 " pdb=" C LEU C 61 " pdb=" CB LEU C 61 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.65e+00 ... (remaining 288 not shown) Planarity restraints: 612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 55 " -0.115 2.00e-02 2.50e+03 3.52e-02 4.95e+01 pdb=" CG TRP B 55 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TRP B 55 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP B 55 " 0.021 2.00e-02 2.50e+03 pdb=" NE1 TRP B 55 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP B 55 " 0.009 2.00e-02 2.50e+03 pdb=" CE3 TRP B 55 " 0.025 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 55 " -0.011 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 55 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP B 55 " -0.008 2.00e-02 2.50e+03 pdb=" HD1 TRP B 55 " 0.031 2.00e-02 2.50e+03 pdb=" HE1 TRP B 55 " -0.005 2.00e-02 2.50e+03 pdb=" HE3 TRP B 55 " 0.044 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 55 " -0.029 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 55 " -0.006 2.00e-02 2.50e+03 pdb=" HH2 TRP B 55 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 28 " 0.097 2.00e-02 2.50e+03 3.78e-02 4.30e+01 pdb=" CG TYR C 28 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR C 28 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR C 28 " -0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR C 28 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR C 28 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR C 28 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR C 28 " 0.063 2.00e-02 2.50e+03 pdb=" HD1 TYR C 28 " -0.029 2.00e-02 2.50e+03 pdb=" HD2 TYR C 28 " -0.036 2.00e-02 2.50e+03 pdb=" HE1 TYR C 28 " -0.011 2.00e-02 2.50e+03 pdb=" HE2 TYR C 28 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 73 " 0.098 2.00e-02 2.50e+03 3.77e-02 4.27e+01 pdb=" CG TYR B 73 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR B 73 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR B 73 " -0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR B 73 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR B 73 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR B 73 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR B 73 " 0.059 2.00e-02 2.50e+03 pdb=" HD1 TYR B 73 " -0.033 2.00e-02 2.50e+03 pdb=" HD2 TYR B 73 " -0.037 2.00e-02 2.50e+03 pdb=" HE1 TYR B 73 " -0.008 2.00e-02 2.50e+03 pdb=" HE2 TYR B 73 " -0.004 2.00e-02 2.50e+03 ... (remaining 609 not shown) Histogram of nonbonded interaction distances: 1.32 - 1.98: 274 1.98 - 2.63: 5256 2.63 - 3.29: 13422 3.29 - 3.94: 17161 3.94 - 4.60: 25648 Nonbonded interactions: 61761 Sorted by model distance: nonbonded pdb=" HE ARG B 43 " pdb=" OD1 ASP B 56 " model vdw 1.324 1.850 nonbonded pdb=" HB2 ALA A 8 " pdb="HG23 ILE A 74 " model vdw 1.348 2.440 nonbonded pdb=" OE2 GLU B 23 " pdb=" HZ3 LYS B 83 " model vdw 1.372 1.850 nonbonded pdb=" HG2 LYS B 81 " pdb="HD11 ILE B 86 " model vdw 1.385 2.440 nonbonded pdb=" O LYS A 7 " pdb=" H GLU A 11 " model vdw 1.421 1.850 ... (remaining 61756 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 9 15.91 1 O 411 7.97 1 N 342 6.97 1 C 1326 5.97 1 H 2076 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: 2076 of 4164 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 4164 n_use_u_iso = 4164 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 = 4164 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (4164 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 4164 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 = "2fdq_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 2076 occupancy sum: 2076.00 (% of total atoms 49.86) Rotatable: count: 531 occupancy sum: 531.00 (% of total atoms 12.75) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.50 - 24.56 A, n_refl.=3901 (all), 4.54 % free)-------------| | | | r_work= 0.3367 r_free= 0.3847 coordinate error (max.-lik. estimate): 0.79 A | | | | normalized target function (ml) (work): 5.414009 | | target function (ml) not normalized (work): 20161.769398 | | target function (ml) not normalized (free): 955.736830 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 24.56 - 3.50 1.00 3724 177 0.3367 0.3847 5.414 5.3996| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 24.56 - 3.50 3724 177 0.80 27.40 1.00 0.42 10659.71| |alpha: min = 0.23 max = 0.54 mean = 0.42| |beta: min = 3856.36 max = 48303.69 mean = 10659.71| |figures of merit: min = 0.00 max = 1.00 mean = 0.80| |phase err.(work): min = 0.00 max = 89.81 mean = 27.40| |phase err.(test): min = 0.00 max = 88.12 mean = 26.74| |-----------------------------------------------------------------------------| ----------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 : 0.009 0.063 2127 Z= 0.545 Angle : 1.450 14.176 2844 Z= 0.982 Chirality : 0.089 0.266 291 Planarity : 0.007 0.042 363 Dihedral : 15.771 87.829 822 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 36.98 Ramachandran Plot: Outliers : 5.56 % Allowed : 25.79 % Favored : 68.65 % Rotamer: Outliers : 0.91 % Allowed : 6.39 % Favored : 92.69 % 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: -6.58 (0.37), residues: 252 helix: -4.70 (0.19), residues: 156 sheet: None (None), residues: 0 loop : -3.42 (0.60), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.002 ARG C 43 TYR 0.079 0.021 TYR C 28 PHE 0.033 0.008 PHE C 49 TRP 0.078 0.015 TRP B 55 HIS 0.003 0.002 HIS A 30 Individual atomic B min max mean iso aniso Overall: 20.45 55.43 29.36 1.83 2088 0 Protein: 20.45 55.43 29.36 1.83 2088 0 Chain A: 20.45 53.24 31.53 N/A 696 0 Chain B: 20.45 55.43 28.80 N/A 696 0 Chain C: 20.45 53.74 27.73 N/A 696 0 Histogram: Values Number of atoms 20.45 - 23.95 483 23.95 - 27.45 430 27.45 - 30.94 501 30.94 - 34.44 253 34.44 - 37.94 186 37.94 - 41.44 93 41.44 - 44.94 81 44.94 - 48.43 32 48.43 - 51.93 25 51.93 - 55.43 4 |-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: 3.50 - 24.56 A, n_refl.=3901 (all), 4.54 % free)-------------| | | | r_work= 0.3367 r_free= 0.3847 coordinate error (max.-lik. estimate): 0.79 A | | | | normalized target function (ml) (work): 5.414009 | | target function (ml) not normalized (work): 20161.769398 | | target function (ml) not normalized (free): 955.736830 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3389 0.3367 0.3847 n_refl.: 3901 re-set all scales: r(all,work,free)=0.3389 0.3367 0.3847 n_refl.: 3901 remove outliers: r(all,work,free)=0.3390 0.3368 0.3847 n_refl.: 3900 overall B=1.29 to atoms: r(all,work,free)=0.3430 0.3408 0.3898 n_refl.: 3900 bulk-solvent and scaling: r(all,work,free)=0.2158 0.2170 0.1921 n_refl.: 3900 remove outliers: r(all,work,free)=0.2158 0.2170 0.1921 n_refl.: 3900 ======================== 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 24.555-11.554 100.00 97 4 0.1718 879.253 859.871 1.015 1.135 0.339 11.543-9.422 100.00 94 5 0.1500 860.103 832.148 1.071 1.117 0.339 9.405-7.656 100.00 172 7 0.1517 693.173 674.933 1.053 1.097 0.354 7.645-6.234 100.00 300 18 0.2153 507.673 488.103 1.003 1.068 0.357 6.230-5.074 100.00 574 24 0.2379 440.704 420.298 0.982 1.023 0.356 5.067-4.130 100.00 1040 46 0.2173 488.029 470.997 1.068 0.957 0.285 4.129-3.498 99.54 1446 73 0.2378 390.867 374.550 1.143 0.872 0.156 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=5.8065 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 14.112766 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.451772 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 0.1642 0.2170 0.0528 0.014 1.2 12.7 2.4 1.4 0 7.056 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 16.42 21.70 5.28 1.305 30.879 0.452 0.031 16.33 21.91 5.57 1.854 31.018 0.014 0.031 15.80 21.62 5.82 1.819 31.030 0.056 0.029 14.96 21.24 6.28 2.892 31.213 0.226 0.026 14.00 20.83 6.82 5.417 31.612 0.452 0.023 13.63 20.62 7.00 6.676 31.975 0.678 0.022 13.45 20.61 7.15 7.355 32.152 0.904 0.021 13.27 20.58 7.31 8.191 32.412 1.129 0.021 13.03 20.59 7.55 9.390 32.806 1.355 0.020 12.92 20.63 7.71 10.090 33.039 1.581 0.020 12.83 20.68 7.85 10.645 33.215 1.807 0.019 12.80 20.71 7.91 10.871 33.262 2.033 0.019 12.57 20.90 8.33 12.493 33.858 2.259 0.019 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.056 Accepted refinement result: 15.80 21.62 5.82 1.819 31.030 0.056 0.029 Individual atomic B min max mean iso aniso Overall: 18.29 64.29 30.95 1.70 2088 0 Protein: 18.29 64.29 30.95 1.70 2088 0 Chain A: 22.26 56.80 33.51 N/A 696 0 Chain B: 20.76 54.63 30.19 N/A 696 0 Chain C: 18.29 64.29 29.13 N/A 696 0 Histogram: Values Number of atoms 18.29 - 22.89 103 22.89 - 27.49 595 27.49 - 32.09 647 32.09 - 36.69 385 36.69 - 41.29 206 41.29 - 45.89 88 45.89 - 50.49 45 50.49 - 55.09 17 55.09 - 59.69 1 59.69 - 64.29 1 =========================== Idealize ADP of riding H ========================== r_work=0.1580 r_free=0.2162 r_work=0.1568 r_free=0.2153 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.50 - 24.56 A, n_refl.=3900 (all), 4.54 % free)-------------| | | | r_work= 0.1568 r_free= 0.2153 coordinate error (max.-lik. estimate): 0.26 A | | | | normalized target function (ls_wunit_k1) (work): 0.028806 | | target function (ls_wunit_k1) not normalized (work): 107.245337 | | target function (ls_wunit_k1) not normalized (free): 9.620622 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1596 0.1568 0.2153 n_refl.: 3900 re-set all scales: r(all,work,free)=0.3121 0.3075 0.3945 n_refl.: 3900 remove outliers: r(all,work,free)=0.3121 0.3075 0.3945 n_refl.: 3900 overall B=6.46 to atoms: r(all,work,free)=0.3343 0.3298 0.4167 n_refl.: 3900 bulk-solvent and scaling: r(all,work,free)=0.1592 0.1568 0.2092 n_refl.: 3900 remove outliers: r(all,work,free)=0.1592 0.1568 0.2092 n_refl.: 3900 ======================== 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 24.555-11.554 100.00 97 4 0.1118 613.451 604.173 1.077 1.011 0.343 11.543-9.422 100.00 94 5 0.0970 600.090 595.119 1.158 1.008 0.345 9.405-7.656 100.00 172 7 0.1062 483.624 481.400 1.115 1.006 0.342 7.645-6.234 100.00 300 18 0.1527 354.201 350.077 1.055 1.002 0.357 6.230-5.074 100.00 574 24 0.1719 307.477 302.510 0.976 0.995 0.351 5.067-4.130 100.00 1040 46 0.1538 340.495 337.446 1.001 0.987 0.286 4.129-3.498 99.54 1446 73 0.1791 272.706 265.707 1.008 0.975 0.125 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0417 b_overall=3.4103 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.705410 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.039723 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 0.1682 0.2067 0.0385 0.004 0.5 2.4 0.0 0.5 0 0.085 0.1540 0.2180 0.0640 0.008 0.8 7.2 1.6 2.7 0 0.256 0.1456 0.2204 0.0748 0.014 1.2 13.2 3.2 4.1 0 0.512 0.1416 0.2236 0.0820 0.019 1.5 15.6 5.2 4.6 0 0.767 0.1378 0.2272 0.0894 0.023 1.8 20.4 5.6 4.6 0 1.023 0.1359 0.2288 0.0929 0.026 1.9 20.9 6.0 4.6 0 1.279 0.1331 0.2294 0.0963 0.030 2.2 22.3 6.0 4.6 0 1.535 0.1311 0.2299 0.0988 0.033 2.4 24.5 5.6 5.0 0 1.791 0.1399 0.2243 0.0844 0.020 1.6 17.1 5.2 4.6 0 0.853 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1682 0.2067 0.0385 0.004 0.5 2.4 0.0 0.5 0 0.085 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 16.82 20.67 3.85 4.679 40.809 0.040 5.615 17.23 20.82 3.59 4.913 41.780 0.001 5.638 15.96 20.14 4.18 4.774 41.101 0.005 5.561 14.52 19.67 5.14 6.171 41.520 0.020 5.466 14.10 19.70 5.59 7.246 41.796 0.040 5.434 13.86 19.76 5.90 8.101 42.058 0.060 5.416 13.67 19.80 6.13 8.957 42.309 0.079 5.402 13.60 19.84 6.23 9.338 42.407 0.099 5.396 13.49 19.85 6.37 10.034 42.599 0.119 5.387 13.44 19.88 6.44 10.394 42.695 0.139 5.383 13.40 19.89 6.50 10.723 42.781 0.159 5.379 13.32 19.95 6.62 11.293 42.931 0.179 5.373 13.30 19.96 6.66 11.535 42.991 0.199 5.371 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.020 Accepted refinement result: 14.52 19.67 5.14 6.171 41.520 0.020 5.466 Individual atomic B min max mean iso aniso Overall: 19.75 122.05 38.83 5.29 2088 0 Protein: 19.75 122.05 38.83 5.29 2088 0 Chain A: 24.26 99.76 44.48 N/A 696 0 Chain B: 22.84 78.17 36.51 N/A 696 0 Chain C: 19.75 122.05 35.50 N/A 696 0 Histogram: Values Number of atoms 19.75 - 29.98 482 29.98 - 40.21 834 40.21 - 50.44 458 50.44 - 60.67 207 60.67 - 70.90 93 70.90 - 81.13 8 81.13 - 91.36 4 91.36 - 101.59 1 101.59 - 111.82 0 111.82 - 122.05 1 =========================== Idealize ADP of riding H ========================== r_work=0.1452 r_free=0.1967 r_work=0.1435 r_free=0.1968 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.50 - 24.56 A, n_refl.=3900 (all), 4.54 % free)-------------| | | | r_work= 0.1435 r_free= 0.1968 coordinate error (max.-lik. estimate): 0.24 A | | | | normalized target function (ml) (work): 5.453595 | | target function (ml) not normalized (work): 20303.733618 | | target function (ml) not normalized (free): 1071.686717 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1460 0.1435 0.1968 n_refl.: 3900 re-set all scales: r(all,work,free)=0.3285 0.3238 0.4100 n_refl.: 3900 remove outliers: r(all,work,free)=0.3285 0.3238 0.4100 n_refl.: 3900 overall B=0.00 to atoms: r(all,work,free)=0.3285 0.3238 0.4100 n_refl.: 3900 bulk-solvent and scaling: r(all,work,free)=0.1448 0.1424 0.1943 n_refl.: 3900 remove outliers: r(all,work,free)=0.1448 0.1424 0.1943 n_refl.: 3900 ======================== 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 24.555-11.554 100.00 97 4 0.1137 548.541 547.582 1.123 1.022 0.340 11.543-9.422 100.00 94 5 0.0978 536.593 529.235 1.219 1.018 0.350 9.405-7.656 100.00 172 7 0.0980 432.451 429.243 1.180 1.013 0.350 7.645-6.234 100.00 300 18 0.1410 316.722 313.803 1.098 1.007 0.350 6.230-5.074 100.00 574 24 0.1467 274.942 271.123 1.003 0.996 0.350 5.067-4.130 100.00 1040 46 0.1397 304.467 300.067 1.025 0.980 0.304 4.129-3.498 99.54 1446 73 0.1628 243.851 237.809 1.041 0.960 0.144 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=5.8279 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1424 r_free=0.1943 After: r_work=0.1424 r_free=0.1943 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.488216 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.038306 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 0.1424 0.1940 0.0516 0.003 0.5 2.6 0.0 0.5 0 0.074 0.1367 0.1943 0.0576 0.008 0.7 3.6 0.0 0.5 0 0.223 0.1266 0.1983 0.0717 0.013 1.3 7.9 0.8 0.9 0 0.446 0.1232 0.2041 0.0809 0.014 1.5 10.6 0.8 2.7 0 0.670 0.1210 0.2071 0.0861 0.018 1.6 12.5 1.2 3.2 0 0.893 0.1197 0.2091 0.0894 0.021 1.7 13.2 1.2 3.2 0 1.116 0.1193 0.2063 0.0870 0.020 1.7 11.5 1.2 2.7 0 1.339 0.1160 0.2119 0.0959 0.024 2.1 14.4 1.2 3.7 0 1.563 0.1222 0.2057 0.0834 0.015 1.6 11.0 0.8 3.2 0 0.744 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1424 0.1940 0.0516 0.003 0.5 2.6 0.0 0.5 0 0.074 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 14.24 19.40 5.16 6.952 43.414 0.038 5.338 16.65 19.97 3.32 6.620 46.742 0.001 5.484 14.98 19.37 4.39 6.636 44.076 0.005 5.392 13.43 19.45 6.02 6.930 44.210 0.019 5.277 12.89 19.68 6.79 8.306 44.284 0.038 5.233 12.70 19.86 7.16 9.193 44.444 0.057 5.216 12.59 20.01 7.42 9.931 44.645 0.077 5.206 12.51 20.16 7.65 10.545 44.819 0.096 5.199 12.46 20.28 7.81 11.058 44.969 0.115 5.194 12.43 20.38 7.95 11.450 45.087 0.134 5.190 12.40 20.45 8.05 11.796 45.192 0.153 5.188 12.38 20.52 8.14 12.114 45.286 0.172 5.186 12.36 20.57 8.20 12.372 45.362 0.192 5.184 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.005 Accepted refinement result: 14.98 19.37 4.39 6.636 44.076 0.005 5.392 Individual atomic B min max mean iso aniso Overall: 19.62 117.05 40.15 3.38 2088 0 Protein: 19.62 117.05 40.15 3.38 2088 0 Chain A: 28.91 94.76 48.44 N/A 696 0 Chain B: 23.82 73.17 36.63 N/A 696 0 Chain C: 19.62 117.05 35.37 N/A 696 0 Histogram: Values Number of atoms 19.62 - 29.37 327 29.37 - 39.11 847 39.11 - 48.85 460 48.85 - 58.59 301 58.59 - 68.34 114 68.34 - 78.08 34 78.08 - 87.82 2 87.82 - 97.57 2 97.57 - 107.31 0 107.31 - 117.05 1 =========================== Idealize ADP of riding H ========================== r_work=0.1498 r_free=0.1937 r_work=0.1510 r_free=0.1936 ----------X-ray data---------- |--(resolution: 3.50 - 24.56 A, n_refl.=3900 (all), 4.54 % free)-------------| | | | r_work= 0.1510 r_free= 0.1936 coordinate error (max.-lik. estimate): 0.24 A | | | | normalized target function (ml) (work): 5.399688 | | target function (ml) not normalized (work): 20103.039793 | | target function (ml) not normalized (free): 1032.711824 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 24.56 - 3.50 1.00 3723 177 0.1510 0.1936 5.3997 5.8345| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 24.56 - 3.50 3723 177 0.94 12.84 1.00 0.97 6372.67| |alpha: min = 0.91 max = 1.03 mean = 0.97| |beta: min = 4956.74 max = 10157.53 mean = 6372.67| |figures of merit: min = 0.03 max = 1.00 mean = 0.94| |phase err.(work): min = 0.00 max = 87.40 mean = 12.84| |phase err.(test): min = 0.00 max = 85.41 mean = 12.46| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1530 0.1510 0.1936 n_refl.: 3900 re-set all scales: r(all,work,free)=0.3360 0.3316 0.4127 n_refl.: 3900 remove outliers: r(all,work,free)=0.3360 0.3316 0.4127 n_refl.: 3900 overall B=0.00 to atoms: r(all,work,free)=0.3360 0.3316 0.4127 n_refl.: 3900 bulk-solvent and scaling: r(all,work,free)=0.1531 0.1512 0.1927 n_refl.: 3900 remove outliers: r(all,work,free)=0.1531 0.1512 0.1927 n_refl.: 3900 ======================== 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 24.555-11.554 100.00 97 4 0.1124 548.541 550.592 1.132 1.008 0.340 11.543-9.422 100.00 94 5 0.0939 536.593 527.135 1.224 1.006 0.355 9.405-7.656 100.00 172 7 0.1016 432.451 429.302 1.195 1.003 0.360 7.645-6.234 100.00 300 18 0.1475 316.722 313.547 1.106 1.000 0.360 6.230-5.074 100.00 574 24 0.1571 274.942 270.645 1.003 0.994 0.360 5.067-4.130 100.00 1040 46 0.1500 304.467 300.319 1.020 0.985 0.310 4.129-3.498 99.54 1446 73 0.1749 243.851 236.991 1.020 0.973 0.160 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=6.0842 ================= 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 : 0.3367 0.3847 0.009 1.450 20.4 55.4 29.4 0 0.000 1_bss: 0.2170 0.1921 0.009 1.450 21.7 56.7 30.6 0 0.000 1_settarget: 0.2170 0.1921 0.009 1.450 21.7 56.7 30.6 0 0.000 1_weight: 0.2170 0.1921 0.009 1.450 21.7 56.7 30.6 0 0.000 1_xyzrec: 0.1642 0.2170 0.014 1.210 21.7 56.7 30.6 0 0.268 1_adp: 0.1580 0.2162 0.014 1.210 18.3 64.3 30.9 0 0.268 1_regHadp: 0.1568 0.2153 0.014 1.210 18.3 64.3 30.9 0 0.268 2_bss: 0.1568 0.2092 0.014 1.210 24.8 70.8 37.4 0 0.268 2_settarget: 0.1568 0.2092 0.014 1.210 24.8 70.8 37.4 0 0.268 2_updatecdl: 0.1568 0.2092 0.014 1.247 24.8 70.8 37.4 0 0.268 2_weight: 0.1568 0.2092 0.014 1.247 24.8 70.8 37.4 0 0.268 2_xyzrec: 0.1682 0.2067 0.004 0.504 24.8 70.8 37.4 0 0.325 2_adp: 0.1452 0.1967 0.004 0.504 19.8 122.1 38.8 0 0.325 2_regHadp: 0.1435 0.1968 0.004 0.504 19.8 122.1 38.8 0 0.325 3_bss: 0.1424 0.1943 0.004 0.504 19.8 122.1 38.8 0 0.325 3_settarget: 0.1424 0.1943 0.004 0.504 19.8 122.1 38.8 0 0.325 3_updatecdl: 0.1424 0.1943 0.004 0.567 19.8 122.1 38.8 0 0.325 3_setrh: 0.1424 0.1943 0.004 0.567 19.8 122.1 38.8 0 0.325 3_weight: 0.1424 0.1943 0.004 0.567 19.8 122.1 38.8 0 0.325 3_xyzrec: 0.1424 0.1940 0.003 0.499 19.8 122.1 38.8 0 0.325 3_adp: 0.1498 0.1937 0.003 0.499 19.6 117.1 40.1 0 0.325 3_regHadp: 0.1510 0.1936 0.003 0.499 19.6 117.1 40.1 0 0.325 end: 0.1512 0.1927 0.003 0.499 19.6 117.1 40.1 0 0.325 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V1/2fdq_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V1/2fdq_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 5.0100 Refinement macro-cycles (run) : 144.4900 Write final files (write_after_run_outputs) : 16.1700 Total : 165.6700 Total CPU time: 3.08 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:25:33 PDT -0700 (1716251133.01 s) Start R-work = 0.2170, R-free = 0.1921 Final R-work = 0.1512, R-free = 0.1927 =============================================================================== Job complete usr+sys time: 197.04 seconds wall clock time: 9 minutes 40.42 seconds (580.42 seconds total)