Starting phenix.refine on Mon May 20 17:17:05 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=True 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/2fdq/2fdq.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/2fdq/2fdq.mtz" 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" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls occupancies group_anomalous \ den } main { nqh_flips = False max_number_of_iterations = 100 nproc = 20 } modify_start_model { modify { selection = element H occupancies { set = 1 } } } pdb_interpretation { ramachandran_plot_restraints { enabled = True } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = true optimize_adp_weight = true } } Starting job =============================================================================== Symmetric amino acids flipped 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: 1.47, per 1000 atoms: 0.35 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: 2.72 Conformation dependent library (CDL) restraints added in 279.1 milliseconds 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 486 Time building geometry restraints manager: 2.03 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 { ramachandran_plot_restraints { enabled = True } 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 ============================ Update phi&psi targets =========================== 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 14.022219 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 0.1653 0.2100 0.0448 0.014 1.2 11.5 0.0 1.8 0 7.011 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 16.53 21.00 4.48 1.305 30.879 0.452 0.032 16.43 21.16 4.74 1.848 31.018 0.014 0.032 15.89 20.91 5.01 1.816 31.029 0.056 0.029 15.08 20.54 5.46 2.858 31.189 0.226 0.027 14.10 20.19 6.09 5.414 31.586 0.452 0.023 13.69 20.07 6.38 6.764 31.984 0.678 0.022 13.50 20.06 6.56 7.545 32.200 0.904 0.021 13.35 20.08 6.73 8.193 32.386 1.129 0.021 13.03 20.11 7.08 9.722 32.912 1.355 0.020 12.94 20.15 7.21 10.258 33.071 1.581 0.020 12.86 20.19 7.33 10.800 33.238 1.807 0.019 12.82 20.21 7.39 11.043 33.292 2.033 0.019 12.55 20.42 7.87 12.867 33.956 2.259 0.018 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.226 Accepted refinement result: 15.08 20.54 5.46 2.858 31.189 0.226 0.027 Individual atomic B min max mean iso aniso Overall: 16.74 81.18 31.26 2.77 2088 0 Protein: 16.74 81.18 31.26 2.77 2088 0 Chain A: 20.77 67.26 34.48 N/A 696 0 Chain B: 18.91 60.58 30.21 N/A 696 0 Chain C: 16.74 81.18 29.11 N/A 696 0 Histogram: Values Number of atoms 16.74 - 23.18 256 23.18 - 29.63 739 29.63 - 36.07 635 36.07 - 42.52 267 42.52 - 48.96 126 48.96 - 55.41 55 55.41 - 61.85 8 61.85 - 68.30 1 68.30 - 74.74 0 74.74 - 81.18 1 =========================== Idealize ADP of riding H ========================== r_work=0.1508 r_free=0.2054 r_work=0.1489 r_free=0.2042 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.50 - 24.56 A, n_refl.=3900 (all), 4.54 % free)-------------| | | | r_work= 0.1489 r_free= 0.2042 coordinate error (max.-lik. estimate): 0.25 A | | | | normalized target function (ls_wunit_k1) (work): 0.025902 | | target function (ls_wunit_k1) not normalized (work): 96.432467 | | target function (ls_wunit_k1) not normalized (free): 8.953902 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1515 0.1489 0.2042 n_refl.: 3900 re-set all scales: r(all,work,free)=0.3098 0.3052 0.3918 n_refl.: 3900 remove outliers: r(all,work,free)=0.3098 0.3052 0.3918 n_refl.: 3900 overall B=6.25 to atoms: r(all,work,free)=0.3318 0.3272 0.4138 n_refl.: 3900 bulk-solvent and scaling: r(all,work,free)=0.1519 0.1496 0.1985 n_refl.: 3900 remove outliers: r(all,work,free)=0.1519 0.1496 0.1985 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 0.1082 610.732 608.229 1.091 1.004 0.337 11.543-9.422 100.00 94 5 0.0974 597.430 589.761 1.153 1.002 0.335 9.405-7.656 100.00 172 7 0.1042 481.480 477.453 1.132 1.000 0.352 7.645-6.234 100.00 300 18 0.1513 352.631 351.090 1.068 0.998 0.348 6.230-5.074 100.00 574 24 0.1658 306.114 300.783 0.982 0.992 0.342 5.067-4.130 100.00 1040 46 0.1447 338.986 336.144 1.017 0.986 0.287 4.129-3.498 99.54 1446 73 0.1692 271.498 265.660 1.026 0.976 0.134 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0417 b_overall=2.3435 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.621490 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.039817 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 0.1601 0.1984 0.0383 0.004 0.5 3.1 0.0 0.5 0 0.081 0.1469 0.2081 0.0612 0.008 0.8 6.7 0.0 2.7 0 0.243 0.1387 0.2125 0.0738 0.014 1.2 9.6 0.0 4.6 0 0.486 0.1342 0.2151 0.0809 0.018 1.4 14.4 0.0 4.6 0 0.730 0.1309 0.2176 0.0867 0.022 1.7 15.6 1.2 5.0 0 0.973 0.1279 0.2199 0.0920 0.025 1.9 17.3 1.2 5.5 0 1.216 0.1260 0.2221 0.0961 0.028 2.1 18.3 1.2 6.4 0 1.459 0.1241 0.2231 0.0990 0.031 2.2 20.2 1.2 6.8 0 1.703 0.1332 0.2159 0.0827 0.020 1.5 15.4 0.8 5.0 0 0.811 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1601 0.1984 0.0383 0.004 0.5 3.1 0.0 0.5 0 0.081 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 16.01 19.84 3.83 5.041 41.113 0.040 5.563 17.04 20.41 3.37 5.312 42.940 0.001 5.626 15.64 19.59 3.95 4.951 41.612 0.005 5.537 14.13 19.20 5.07 6.254 41.870 0.020 5.432 13.59 19.22 5.63 7.751 42.261 0.040 5.390 13.44 19.33 5.89 8.376 42.369 0.060 5.378 13.31 19.38 6.07 9.065 42.549 0.080 5.366 13.20 19.41 6.21 9.699 42.718 0.100 5.358 13.14 19.45 6.31 10.126 42.828 0.119 5.352 13.02 19.53 6.51 11.053 43.075 0.139 5.342 12.93 19.61 6.68 11.860 43.284 0.159 5.335 12.81 19.76 6.96 13.119 43.608 0.179 5.325 12.78 19.81 7.04 13.504 43.703 0.199 5.323 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: 14.13 19.20 5.07 6.254 41.870 0.020 5.432 Individual atomic B min max mean iso aniso Overall: 17.99 132.56 39.02 5.90 2088 0 Protein: 17.99 132.56 39.02 5.90 2088 0 Chain A: 22.15 103.59 45.43 N/A 696 0 Chain B: 20.75 82.05 36.35 N/A 696 0 Chain C: 17.99 132.56 35.29 N/A 696 0 Histogram: Values Number of atoms 17.99 - 29.45 479 29.45 - 40.90 864 40.90 - 52.36 443 52.36 - 63.82 201 63.82 - 75.28 88 75.28 - 86.73 9 86.73 - 98.19 2 98.19 - 109.65 1 109.65 - 121.10 0 121.10 - 132.56 1 =========================== Idealize ADP of riding H ========================== r_work=0.1413 r_free=0.1920 r_work=0.1399 r_free=0.1916 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.50 - 24.56 A, n_refl.=3900 (all), 4.54 % free)-------------| | | | r_work= 0.1399 r_free= 0.1916 coordinate error (max.-lik. estimate): 0.25 A | | | | normalized target function (ml) (work): 5.421554 | | target function (ml) not normalized (work): 20184.444914 | | target function (ml) not normalized (free): 1066.454660 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1423 0.1399 0.1916 n_refl.: 3900 re-set all scales: r(all,work,free)=0.3273 0.3227 0.4076 n_refl.: 3900 remove outliers: r(all,work,free)=0.3273 0.3227 0.4076 n_refl.: 3900 overall B=0.00 to atoms: r(all,work,free)=0.3273 0.3227 0.4076 n_refl.: 3900 bulk-solvent and scaling: r(all,work,free)=0.1416 0.1392 0.1904 n_refl.: 3900 remove outliers: r(all,work,free)=0.1416 0.1392 0.1904 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 0.1162 610.732 608.990 1.089 1.015 0.340 11.543-9.422 100.00 94 5 0.1021 597.430 591.015 1.170 1.012 0.345 9.405-7.656 100.00 172 7 0.0999 481.480 477.429 1.136 1.008 0.350 7.645-6.234 100.00 300 18 0.1385 352.631 349.524 1.060 1.004 0.350 6.230-5.074 100.00 574 24 0.1505 306.114 302.067 0.974 0.995 0.350 5.067-4.130 100.00 1040 46 0.1338 338.986 334.507 0.994 0.983 0.300 4.129-3.498 99.54 1446 73 0.1558 271.498 265.135 1.004 0.967 0.150 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0577 b_overall=5.1223 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1392 r_free=0.1904 After: r_work=0.1393 r_free=0.1905 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.443461 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.037276 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 0.1395 0.1904 0.0510 0.003 0.5 2.9 0.0 0.5 0 0.072 0.1340 0.1884 0.0544 0.008 0.7 3.6 0.0 0.5 0 0.217 0.1228 0.1910 0.0682 0.012 1.3 8.2 0.0 1.4 0 0.433 0.1202 0.1939 0.0737 0.014 1.5 9.6 0.0 2.7 0 0.650 0.1182 0.1955 0.0773 0.017 1.6 11.8 0.0 3.2 0 0.866 0.1163 0.1988 0.0826 0.019 1.7 12.5 0.0 4.1 0 1.083 0.1153 0.1987 0.0834 0.022 1.8 12.2 0.0 4.1 0 1.299 0.1139 0.2023 0.0884 0.023 2.0 12.7 0.0 4.1 0 1.516 0.1193 0.1944 0.0751 0.014 1.6 10.3 0.0 2.7 0 0.722 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1395 0.1904 0.0510 0.003 0.5 2.9 0.0 0.5 0 0.072 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.95 19.04 5.10 7.273 43.725 0.037 5.421 16.50 19.69 3.19 6.998 46.709 0.001 5.585 15.00 19.23 4.23 7.010 44.671 0.005 5.498 13.42 19.19 5.78 7.031 44.521 0.019 5.379 12.70 19.50 6.79 9.005 44.762 0.037 5.318 12.63 19.51 6.88 9.432 44.613 0.056 5.310 12.51 19.68 7.18 10.183 44.804 0.075 5.298 12.46 19.78 7.31 10.606 44.908 0.093 5.293 12.42 19.89 7.48 11.085 45.047 0.112 5.288 12.38 19.98 7.60 11.472 45.162 0.130 5.285 12.35 20.06 7.71 11.808 45.259 0.149 5.282 12.33 20.14 7.80 12.101 45.346 0.168 5.280 12.32 20.20 7.88 12.351 45.421 0.186 5.278 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.019 Accepted refinement result: 13.42 19.19 5.78 7.031 44.521 0.019 5.379 Individual atomic B min max mean iso aniso Overall: 12.99 155.39 40.61 7.09 2088 0 Protein: 12.99 155.39 40.61 7.09 2088 0 Chain A: 21.34 119.51 49.90 N/A 696 0 Chain B: 18.77 85.33 36.56 N/A 696 0 Chain C: 12.99 155.39 35.37 N/A 696 0 Histogram: Values Number of atoms 12.99 - 27.23 382 27.23 - 41.47 926 41.47 - 55.71 429 55.71 - 69.95 227 69.95 - 84.19 97 84.19 - 98.43 19 98.43 - 112.67 6 112.67 - 126.91 1 126.91 - 141.15 0 141.15 - 155.39 1 =========================== Idealize ADP of riding H ========================== r_work=0.1342 r_free=0.1919 r_work=0.1339 r_free=0.1926 ----------X-ray data---------- |--(resolution: 3.50 - 24.56 A, n_refl.=3900 (all), 4.54 % free)-------------| | | | r_work= 0.1339 r_free= 0.1926 coordinate error (max.-lik. estimate): 0.26 A | | | | normalized target function (ml) (work): 5.377484 | | target function (ml) not normalized (work): 20020.371167 | | target function (ml) not normalized (free): 1079.387898 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1339 0.1926 5.3775 6.0982| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 0.95 10.53 1.00 1.11 6243.76| |alpha: min = 1.04 max = 1.18 mean = 1.11| |beta: min = 3959.04 max = 13319.49 mean = 6243.76| |figures of merit: min = 0.04 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 87.11 mean = 10.53| |phase err.(test): min = 0.00 max = 63.99 mean = 10.14| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1366 0.1339 0.1926 n_refl.: 3900 re-set all scales: r(all,work,free)=0.3263 0.3214 0.4103 n_refl.: 3900 remove outliers: r(all,work,free)=0.3263 0.3214 0.4103 n_refl.: 3900 overall B=0.00 to atoms: r(all,work,free)=0.3263 0.3214 0.4103 n_refl.: 3900 bulk-solvent and scaling: r(all,work,free)=0.1364 0.1337 0.1921 n_refl.: 3900 remove outliers: r(all,work,free)=0.1364 0.1337 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 0.1186 543.954 541.942 1.077 1.027 0.340 11.543-9.422 100.00 94 5 0.1015 532.106 527.343 1.160 1.023 0.345 9.405-7.656 100.00 172 7 0.1021 428.835 425.379 1.129 1.017 0.350 7.645-6.234 100.00 300 18 0.1384 314.074 311.628 1.056 1.011 0.350 6.230-5.074 100.00 574 24 0.1454 272.643 269.508 0.968 0.998 0.340 5.067-4.130 100.00 1040 46 0.1277 301.921 298.114 1.002 0.981 0.300 4.129-3.498 99.54 1446 73 0.1461 241.812 236.813 1.019 0.957 0.153 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0577 b_overall=4.8829 ================= 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_updatephipsi: 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: 0.1653 0.2100 0.014 1.240 21.7 56.7 30.6 0 0.270 1_adp: 0.1508 0.2054 0.014 1.240 16.7 81.2 31.3 0 0.270 1_regHadp: 0.1489 0.2042 0.014 1.240 16.7 81.2 31.3 0 0.270 2_bss: 0.1496 0.1985 0.014 1.240 23.0 87.4 37.5 0 0.270 2_settarget: 0.1496 0.1985 0.014 1.240 23.0 87.4 37.5 0 0.270 2_updatephipsi: 0.1496 0.1985 0.014 1.240 23.0 87.4 37.5 0 0.270 2_updatecdl: 0.1496 0.1985 0.014 1.259 23.0 87.4 37.5 0 0.270 2_weight: 0.1496 0.1985 0.014 1.259 23.0 87.4 37.5 0 0.270 2_xyzrec: 0.1601 0.1984 0.004 0.521 23.0 87.4 37.5 0 0.308 2_adp: 0.1413 0.1920 0.004 0.521 18.0 132.6 39.0 0 0.308 2_regHadp: 0.1399 0.1916 0.004 0.521 18.0 132.6 39.0 0 0.308 3_bss: 0.1392 0.1904 0.004 0.521 18.0 132.6 39.0 0 0.308 3_settarget: 0.1392 0.1904 0.004 0.521 18.0 132.6 39.0 0 0.308 3_updatephipsi: 0.1392 0.1904 0.004 0.521 18.0 132.6 39.0 0 0.308 3_updatecdl: 0.1392 0.1904 0.004 0.547 18.0 132.6 39.0 0 0.308 3_setrh: 0.1393 0.1905 0.004 0.547 18.0 132.6 39.0 0 0.308 3_weight: 0.1393 0.1905 0.004 0.547 18.0 132.6 39.0 0 0.308 3_xyzrec: 0.1395 0.1904 0.003 0.515 18.0 132.6 39.0 0 0.309 3_adp: 0.1342 0.1919 0.003 0.515 13.0 155.4 40.6 0 0.309 3_regHadp: 0.1339 0.1926 0.003 0.515 13.0 155.4 40.6 0 0.309 end: 0.1337 0.1921 0.003 0.515 13.0 155.4 40.6 0 0.309 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V2/2fdq_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V2/2fdq_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 6.1600 Refinement macro-cycles (run) : 159.4800 Write final files (write_after_run_outputs) : 15.8700 Total : 181.5100 Total CPU time: 3.52 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:28:22 PDT -0700 (1716251302.26 s) Start R-work = 0.2170, R-free = 0.1921 Final R-work = 0.1337, R-free = 0.1921 =============================================================================== Job complete usr+sys time: 222.77 seconds wall clock time: 11 minutes 51.68 seconds (711.68 seconds total)