Starting phenix.refine on Mon May 20 17:17:06 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/2pej.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/2pej/2pej.mtz Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- optimize_xyz=true optimize_adp=true main.number_of_mac=3 main.max_number_of_iterations=100 main.nproc=20 nonbonded_weight=100 modify_start_model.modify.selection=element H modify_start_model.modify.occupancies.set=1 strategy=individual_sites+individual_adp ramachandran_plot_restraints.enabled=True secondary_structure.enabled=False main.nqh_flips=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/2pej.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/2pej.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/2pej/2pej.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/2pej/2pej.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls occupancies group_anomalous \ den } main { nqh_flips = False max_number_of_iterations = 100 nproc = 20 } modify_start_model { modify { selection = element H occupancies { set = 1 } } } pdb_interpretation { ramachandran_plot_restraints { enabled = True } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = true optimize_adp_weight = true } } Starting job =============================================================================== Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 10709 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 1791 Classifications: {'peptide': 109} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 105} Chain: "B" Number of atoms: 1774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1774 Classifications: {'peptide': 108} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 104} Chain: "C" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 1789 Classifications: {'peptide': 109} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 105} Chain: "D" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 1760 Classifications: {'peptide': 107} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 103} Chain: "E" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1808 Classifications: {'peptide': 110} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 106} Chain: "F" Number of atoms: 1787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 1787 Classifications: {'peptide': 109} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 105} Time building chain proxies: 3.26, per 1000 atoms: 0.30 Number of scatterers: 10709 At special positions: 0 Unit cell: (93.4462, 93.4462, 411.544, 90, 90, 90) Space group: P 41 21 2 (No. 92) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 18 16.00 O 986 8.00 N 925 7.00 C 3305 6.00 H 5475 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: 6.74 Conformation dependent library (CDL) restraints added in 1.1 seconds 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1256 Time building geometry restraints manager: 5.34 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: 5475 1.15 - 1.32: 909 1.32 - 1.49: 1985 1.49 - 1.66: 2363 1.66 - 1.83: 36 Bond restraints: 10768 Sorted by residual: bond pdb=" N LEU D 57 " pdb=" H LEU D 57 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" N TYR D 56 " pdb=" H TYR D 56 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N ALA D 79 " pdb=" H ALA D 79 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" NE2 GLN C 37 " pdb="HE21 GLN C 37 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N GLU D 66 " pdb=" H GLU D 66 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 10763 not shown) Histogram of bond angle deviations from ideal: 96.60 - 104.11: 95 104.11 - 111.63: 12425 111.63 - 119.14: 2968 119.14 - 126.66: 4055 126.66 - 134.17: 45 Bond angle restraints: 19588 Sorted by residual: angle pdb=" N PHE C 3 " pdb=" CA PHE C 3 " pdb=" C PHE C 3 " ideal model delta sigma weight residual 111.69 119.66 -7.97 1.23e+00 6.61e-01 4.20e+01 angle pdb=" C HIS A 48 " pdb=" N PRO A 49 " pdb=" CA PRO A 49 " ideal model delta sigma weight residual 119.84 126.47 -6.63 1.25e+00 6.40e-01 2.81e+01 angle pdb=" N GLN E 111 " pdb=" CA GLN E 111 " pdb=" C GLN E 111 " ideal model delta sigma weight residual 108.48 116.85 -8.37 1.65e+00 3.67e-01 2.58e+01 angle pdb=" N LYS D 4 " pdb=" CA LYS D 4 " pdb=" C LYS D 4 " ideal model delta sigma weight residual 112.38 118.50 -6.12 1.22e+00 6.72e-01 2.52e+01 angle pdb=" N ASN F 64 " pdb=" CA ASN F 64 " pdb=" C ASN F 64 " ideal model delta sigma weight residual 107.23 115.01 -7.78 1.67e+00 3.59e-01 2.17e+01 ... (remaining 19583 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 4334 17.94 - 35.88: 348 35.88 - 53.82: 177 53.82 - 71.76: 57 71.76 - 89.70: 14 Dihedral angle restraints: 4930 sinusoidal: 2840 harmonic: 2090 Sorted by residual: dihedral pdb=" CA GLU D 32 " pdb=" C GLU D 32 " pdb=" N THR D 33 " pdb=" CA THR D 33 " ideal model delta harmonic sigma weight residual -180.00 -154.07 -25.93 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA GLU C 2 " pdb=" C GLU C 2 " pdb=" N PHE C 3 " pdb=" CA PHE C 3 " ideal model delta harmonic sigma weight residual -180.00 -157.88 -22.12 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" C GLN D 28 " pdb=" N GLN D 28 " pdb=" CA GLN D 28 " pdb=" CB GLN D 28 " ideal model delta harmonic sigma weight residual -122.60 -133.00 10.40 0 2.50e+00 1.60e-01 1.73e+01 ... (remaining 4927 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 653 0.090 - 0.181: 165 0.181 - 0.271: 24 0.271 - 0.361: 7 0.361 - 0.452: 2 Chirality restraints: 851 Sorted by residual: chirality pdb=" CA GLN D 28 " pdb=" N GLN D 28 " pdb=" C GLN D 28 " pdb=" CB GLN D 28 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.10e+00 chirality pdb=" CA PHE C 3 " pdb=" N PHE C 3 " pdb=" C PHE C 3 " pdb=" CB PHE C 3 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.28e+00 chirality pdb=" CA LEU C 83 " pdb=" N LEU C 83 " pdb=" C LEU C 83 " pdb=" CB LEU C 83 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.70e+00 ... (remaining 848 not shown) Planarity restraints: 1541 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 40 " -0.031 2.00e-02 2.50e+03 1.17e-02 5.43e+00 pdb=" CG TRP D 40 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP D 40 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TRP D 40 " 0.010 2.00e-02 2.50e+03 pdb=" NE1 TRP D 40 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP D 40 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP D 40 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 40 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 40 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP D 40 " -0.004 2.00e-02 2.50e+03 pdb=" HD1 TRP D 40 " -0.006 2.00e-02 2.50e+03 pdb=" HE1 TRP D 40 " -0.005 2.00e-02 2.50e+03 pdb=" HE3 TRP D 40 " 0.014 2.00e-02 2.50e+03 pdb=" HZ2 TRP D 40 " 0.002 2.00e-02 2.50e+03 pdb=" HZ3 TRP D 40 " -0.010 2.00e-02 2.50e+03 pdb=" HH2 TRP D 40 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 40 " 0.029 2.00e-02 2.50e+03 1.03e-02 4.23e+00 pdb=" CG TRP A 40 " -0.009 2.00e-02 2.50e+03 pdb=" CD1 TRP A 40 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TRP A 40 " -0.008 2.00e-02 2.50e+03 pdb=" NE1 TRP A 40 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 40 " -0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP A 40 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 40 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 40 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 40 " 0.006 2.00e-02 2.50e+03 pdb=" HD1 TRP A 40 " 0.004 2.00e-02 2.50e+03 pdb=" HE1 TRP A 40 " -0.002 2.00e-02 2.50e+03 pdb=" HE3 TRP A 40 " -0.015 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 40 " -0.002 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 40 " 0.002 2.00e-02 2.50e+03 pdb=" HH2 TRP A 40 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 56 " 0.007 2.00e-02 2.50e+03 8.98e-03 2.42e+00 pdb=" CG TYR A 56 " -0.009 2.00e-02 2.50e+03 pdb=" CD1 TYR A 56 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR A 56 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 56 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 56 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 56 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 56 " 0.004 2.00e-02 2.50e+03 pdb=" HD1 TYR A 56 " -0.012 2.00e-02 2.50e+03 pdb=" HD2 TYR A 56 " 0.015 2.00e-02 2.50e+03 pdb=" HE1 TYR A 56 " 0.015 2.00e-02 2.50e+03 pdb=" HE2 TYR A 56 " -0.012 2.00e-02 2.50e+03 ... (remaining 1538 not shown) Histogram of nonbonded interaction distances: 0.44 - 1.27: 26 1.27 - 2.10: 1182 2.10 - 2.93: 28699 2.93 - 3.77: 48990 3.77 - 4.60: 78719 Warning: very small nonbonded interaction distances. Nonbonded interactions: 157616 Sorted by model distance: nonbonded pdb=" HE2 LYS E 4 " pdb=" HE2 PHE F 85 " model vdw 0.437 2.270 nonbonded pdb=" HE2 PHE B 3 " pdb=" CE LYS B 4 " model vdw 0.479 2.750 nonbonded pdb=" O LEU A 109 " pdb=" HE3 LYS C 46 " model vdw sym.op. 0.570 2.620 x,y+1,z nonbonded pdb="HD22 LEU E 20 " pdb="HD12 ILE E 50 " model vdw 0.593 2.440 nonbonded pdb="HD23 LEU E 91 " pdb=" HE3 LYS E 95 " model vdw 0.689 2.440 ... (remaining 157611 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 18 15.91 1 O 986 7.97 1 N 925 6.97 1 C 3305 5.97 1 H 5475 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: 5475 of 10709 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 10709 n_use_u_iso = 10709 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 = 10709 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (10709 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 10709 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 = "2pej_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 5475 occupancy sum: 5475.00 (% of total atoms 53.37) Rotatable: count: 1628 occupancy sum: 1628.00 (% of total atoms 15.87) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.40 - 19.99 A, n_refl.=25915 (all), 5.09 % free)------------| | | | r_work= 0.4270 r_free= 0.4614 coordinate error (max.-lik. estimate): 0.19 A | | | | normalized target function (ml) (work): 5.895891 | | target function (ml) not normalized (work): 145015.334724 | | target function (ml) not normalized (free): 7902.559553 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 19.99 - 6.98 0.98 2921 153 0.4360 0.4718 7.382 7.48| | 2: 6.98 - 5.58 1.00 2800 148 0.4215 0.5156 6.69 6.77| | 3: 5.58 - 4.89 0.99 2720 172 0.3241 0.3521 6.1102 6.1196| | 4: 4.89 - 4.45 0.99 2703 139 0.3764 0.4024 5.9987 6.0922| | 5: 4.45 - 4.13 0.99 2734 139 0.4458 0.4594 5.7787 5.9358| | 6: 4.13 - 3.89 0.99 2654 143 0.4796 0.5068 5.5643 5.7591| | 7: 3.89 - 3.70 0.99 2711 136 0.4992 0.5177 5.3566 5.4641| | 8: 3.70 - 3.54 0.99 2685 135 0.4835 0.5326 5.105 5.1893| | 9: 3.54 - 3.40 1.00 2668 154 0.4775 0.4950 4.9066 4.9642| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 19.99 - 6.98 2921 153 0.49 51.09 0.92 0.50 544086.03| | 2: 6.98 - 5.58 2800 148 0.30 66.73 0.95 0.53 214995.99| | 3: 5.58 - 4.89 2720 172 0.69 35.94 1.11 0.64 42450.73| | 4: 4.89 - 4.45 2703 139 0.79 27.26 1.44 0.80 27205.46| | 5: 4.45 - 4.13 2734 139 0.79 26.83 1.66 0.95 19864.90| | 6: 4.13 - 3.89 2654 143 0.78 28.28 1.78 1.04 13980.59| | 7: 3.89 - 3.70 2711 136 0.78 28.46 1.82 1.08 9226.84| | 8: 3.70 - 3.54 2685 135 0.77 29.33 1.76 1.05 6022.37| | 9: 3.54 - 3.40 2668 154 0.81 26.83 1.72 0.96 3599.32| |alpha: min = 0.50 max = 1.08 mean = 0.83| |beta: min = 3599.32 max = 544086.03 mean = 102556.05| |figures of merit: min = 0.00 max = 1.00 mean = 0.69| |phase err.(work): min = 0.00 max = 89.99 mean = 35.92| |phase err.(test): min = 0.00 max = 89.77 mean = 35.86| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.057 5293 Z= 0.622 Angle : 1.400 9.726 7134 Z= 0.922 Chirality : 0.084 0.452 851 Planarity : 0.004 0.013 913 Dihedral : 18.241 89.696 2067 Min Nonbonded Distance : 0.751 Molprobity Statistics. All-atom Clashscore : 33.12 Ramachandran Plot: Outliers : 2.19 % Allowed : 15.16 % Favored : 82.66 % Rotamer: Outliers : 11.77 % Allowed : 11.09 % Favored : 77.13 % Cbeta Deviations : 0.16 % 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: -6.00 (0.23), residues: 640 helix: -3.54 (0.15), residues: 557 sheet: None (None), residues: 0 loop : -4.73 (0.48), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 103 TYR 0.018 0.004 TYR B 56 PHE 0.016 0.002 PHE C 44 TRP 0.026 0.005 TRP D 40 HIS 0.005 0.002 HIS A 101 Individual atomic B min max mean iso aniso Overall: 78.72 190.99 119.02 0.81 5234 0 Protein: 78.72 190.99 119.02 0.81 5234 0 Chain A: 78.72 132.62 102.27 N/A 876 0 Chain B: 94.80 147.44 118.99 N/A 867 0 Chain C: 85.82 131.82 108.29 N/A 876 0 Chain D: 84.11 124.52 104.22 N/A 860 0 Chain E: 118.58 190.99 151.35 N/A 883 0 Chain F: 108.44 147.31 128.51 N/A 872 0 Histogram: Values Number of atoms 78.72 - 89.95 313 89.95 - 101.17 702 101.17 - 112.40 1380 112.40 - 123.63 856 123.63 - 134.86 864 134.86 - 146.08 713 146.08 - 157.31 118 157.31 - 168.54 78 168.54 - 179.76 76 179.76 - 190.99 134 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 3 ************************* |--(resolution: 3.40 - 19.99 A, n_refl.=25915 (all), 5.09 % free)------------| | | | r_work= 0.4270 r_free= 0.4614 coordinate error (max.-lik. estimate): 0.19 A | | | | normalized target function (ml) (work): 5.895891 | | target function (ml) not normalized (work): 145015.334724 | | target function (ml) not normalized (free): 7902.559553 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.4288 0.4270 0.4614 n_refl.: 25915 re-set all scales: r(all,work,free)=0.4288 0.4270 0.4614 n_refl.: 25915 remove outliers: r(all,work,free)=0.4266 0.4247 0.4614 n_refl.: 25903 overall B=-17.33 to atoms: r(all,work,free)=0.3800 0.3778 0.4198 n_refl.: 25903 bulk-solvent and scaling: r(all,work,free)=0.2653 0.2628 0.3103 n_refl.: 25903 remove outliers: r(all,work,free)=0.2653 0.2628 0.3103 n_refl.: 25903 ======================== 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 19.988-16.886 98.02 93 6 0.4981 1064.578 868.154 1.015 0.889 0.304 16.855-15.102 97.06 96 3 0.3850 1222.025 1136.069 1.082 0.884 0.305 15.055-13.543 96.90 117 8 0.3123 1277.787 1208.209 1.082 0.887 0.296 13.531-12.124 98.40 177 8 0.2353 1772.472 1690.272 1.270 0.886 0.298 12.122-10.863 98.00 231 14 0.2470 1913.581 1885.994 1.269 0.887 0.253 10.859-9.734 96.81 316 18 0.2173 1837.359 1794.637 1.328 0.888 0.250 9.728-8.719 98.71 440 18 0.2370 1558.782 1516.125 1.331 0.888 0.242 8.719-7.816 98.08 582 32 0.2649 1152.027 1095.392 1.318 0.888 0.235 7.812-7.000 98.44 835 46 0.3179 832.644 767.986 1.214 0.888 0.227 6.996-6.272 99.42 1131 61 0.3629 543.615 499.913 1.102 0.888 0.210 6.270-5.619 99.76 1581 82 0.3397 434.382 397.799 0.922 0.888 0.170 5.619-5.035 99.26 2133 136 0.2723 456.309 441.157 0.978 0.887 0.145 5.034-4.511 99.59 2966 163 0.2174 514.948 493.021 1.118 0.887 0.133 4.511-4.041 99.19 4079 206 0.2150 428.987 409.503 1.196 0.886 0.102 4.041-3.621 99.33 5632 291 0.2586 273.439 257.563 1.179 0.885 0.034 3.621-3.400 99.53 4175 227 0.2771 176.375 161.769 1.056 0.884 0.036 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9964 b_overall=0.3094 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update phi&psi targets =========================== 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 15.888090 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.199475 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 0.2780 0.3218 0.0438 0.004 0.6 5.5 0.2 9.9 0 0.125 0.2755 0.3209 0.0454 0.004 0.6 5.7 0.0 9.9 0 0.250 0.2722 0.3182 0.0460 0.004 0.6 5.9 0.0 9.6 0 0.500 0.2697 0.3170 0.0473 0.004 0.7 6.2 0.2 9.6 0 1.000 0.2657 0.3141 0.0484 0.006 0.8 9.7 0.2 9.6 0 2.000 0.2633 0.3135 0.0503 0.007 0.9 12.4 0.2 10.9 0 3.000 0.2610 0.3117 0.0508 0.009 1.0 14.5 0.2 11.1 0 4.000 0.2594 0.3105 0.0511 0.010 1.1 17.2 0.2 11.8 0 5.000 0.2574 0.3099 0.0525 0.011 1.1 18.8 0.0 11.9 0 6.000 0.2557 0.3096 0.0539 0.013 1.2 21.2 0.0 12.1 0 7.000 0.2548 0.3102 0.0553 0.014 1.3 22.9 0.0 12.8 0 8.000 0.2544 0.3093 0.0550 0.015 1.4 25.6 0.0 13.3 0 9.000 0.2532 0.3089 0.0557 0.016 1.5 27.0 0.0 13.1 0 10.000 0.2560 0.3106 0.0546 0.014 1.3 24.0 0.0 12.8 0 7.944 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2722 0.3182 0.0460 0.004 0.6 5.9 0.0 9.6 0 0.500 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 27.22 31.82 4.60 0.568 101.402 0.199 0.085 27.27 31.86 4.59 1.734 101.460 0.006 0.085 26.94 31.62 4.68 1.878 101.467 0.025 0.083 26.34 31.17 4.83 3.056 101.509 0.100 0.079 25.46 30.48 5.02 8.170 102.594 0.199 0.074 25.27 30.36 5.10 9.901 103.078 0.299 0.073 25.21 30.48 5.28 9.219 103.028 0.399 0.073 24.90 30.30 5.40 13.173 104.036 0.499 0.070 24.85 30.29 5.44 13.905 104.238 0.598 0.070 24.81 30.29 5.47 14.516 104.406 0.698 0.070 24.75 30.25 5.50 15.409 104.675 0.798 0.069 24.71 30.24 5.53 16.041 104.864 0.898 0.069 24.66 30.22 5.57 16.832 105.099 0.997 0.069 max suggested for this run: 20.28 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.997 Accepted refinement result: 24.66 30.22 5.57 16.832 105.099 0.997 0.069 Individual atomic B min max mean iso aniso Overall: 56.39 218.67 109.26 12.97 5234 0 Protein: 56.39 218.67 109.26 12.97 5234 0 Chain A: 56.39 175.98 92.30 N/A 876 0 Chain B: 73.20 175.74 109.23 N/A 867 0 Chain C: 64.28 186.25 99.59 N/A 876 0 Chain D: 63.09 182.53 94.99 N/A 860 0 Chain E: 96.25 218.67 141.56 N/A 883 0 Chain F: 87.53 183.52 117.37 N/A 872 0 Histogram: Values Number of atoms 56.39 - 72.62 352 72.62 - 88.85 1023 88.85 - 105.08 1177 105.08 - 121.31 1128 121.31 - 137.53 709 137.53 - 153.76 431 153.76 - 169.99 289 169.99 - 186.22 78 186.22 - 202.44 32 202.44 - 218.67 15 =========================== Idealize ADP of riding H ========================== r_work=0.2466 r_free=0.3022 r_work=0.2453 r_free=0.3007 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.40 - 19.99 A, n_refl.=25903 (all), 5.09 % free)------------| | | | r_work= 0.2453 r_free= 0.3007 coordinate error (max.-lik. estimate): 0.35 A | | | | normalized target function (ls_wunit_k1) (work): 0.067008 | | target function (ls_wunit_k1) not normalized (work): 1647.319349 | | target function (ls_wunit_k1) not normalized (free): 138.592571 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2481 0.2453 0.3007 n_refl.: 25903 re-set all scales: r(all,work,free)=0.3696 0.3669 0.4163 n_refl.: 25903 remove outliers: r(all,work,free)=0.3696 0.3669 0.4163 n_refl.: 25903 overall B=-0.34 to atoms: r(all,work,free)=0.3687 0.3660 0.4155 n_refl.: 25903 bulk-solvent and scaling: r(all,work,free)=0.2446 0.2415 0.3008 n_refl.: 25903 remove outliers: r(all,work,free)=0.2446 0.2415 0.3008 n_refl.: 25903 ======================== 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 19.988-16.886 98.02 93 6 0.4854 793.074 657.992 0.797 0.984 0.282 16.855-15.102 97.06 96 3 0.3672 910.367 841.092 0.850 0.980 0.284 15.055-13.543 96.90 117 8 0.3014 951.908 908.244 0.891 0.982 0.278 13.531-12.124 98.40 177 8 0.2084 1320.431 1270.703 1.025 0.982 0.273 12.122-10.863 98.00 231 14 0.2068 1425.553 1414.164 1.056 0.983 0.235 10.859-9.734 96.81 316 18 0.1751 1368.769 1353.319 1.118 0.986 0.230 9.728-8.719 98.71 440 18 0.1919 1161.239 1146.079 1.124 0.986 0.225 8.719-7.816 98.08 582 32 0.2098 858.221 837.133 1.121 0.987 0.220 7.812-7.000 98.44 835 46 0.2500 620.291 592.283 1.041 0.988 0.199 6.996-6.272 99.42 1131 61 0.3017 404.975 384.417 0.956 0.989 0.180 6.270-5.619 99.76 1581 82 0.3105 323.600 302.991 0.830 0.991 0.150 5.619-5.035 99.26 2133 136 0.2444 339.935 328.462 0.872 0.993 0.120 5.034-4.511 99.59 2966 163 0.2055 383.619 370.744 0.984 0.995 0.090 4.511-4.041 99.19 4079 206 0.2081 319.581 308.720 1.052 0.998 0.070 4.041-3.621 99.33 5632 291 0.2699 203.703 191.948 1.030 1.001 0.025 3.621-3.400 99.53 4175 227 0.3074 131.393 118.356 0.905 1.004 0.020 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-1.1610 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 6.477103 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.041794 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 0.2457 0.3009 0.0552 0.002 0.5 5.0 0.0 6.5 0 0.125 0.2426 0.2971 0.0545 0.003 0.6 5.8 0.0 6.5 0 0.250 0.2376 0.2937 0.0561 0.004 0.6 7.1 0.0 7.8 0 0.500 0.2335 0.2901 0.0566 0.006 0.8 10.9 0.0 9.9 0 1.000 0.2295 0.2877 0.0582 0.010 1.1 16.0 0.2 11.3 0 2.000 0.2273 0.2859 0.0586 0.014 1.3 20.2 0.8 12.1 0 3.000 0.2258 0.2848 0.0590 0.017 1.6 22.9 1.6 11.8 0 4.000 0.2265 0.2871 0.0607 0.023 1.7 19.0 0.6 9.9 0 5.000 0.2254 0.2866 0.0611 0.025 1.8 20.3 0.9 9.9 0 6.000 0.2218 0.2841 0.0622 0.025 2.1 32.1 2.5 16.6 0 7.000 0.2209 0.2830 0.0622 0.028 2.3 35.5 2.8 18.1 0 8.000 0.2200 0.2829 0.0629 0.030 2.4 37.4 3.4 20.0 0 9.000 0.2193 0.2828 0.0635 0.032 2.5 37.5 3.4 20.1 0 10.000 0.2269 0.2853 0.0584 0.015 1.4 21.1 0.8 11.9 0 3.239 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2426 0.2971 0.0545 0.003 0.6 5.8 0.0 6.5 0 0.250 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 24.26 29.71 5.45 18.599 120.954 0.042 5.896 27.99 32.12 4.13 15.101 127.832 0.001 5.949 26.64 30.97 4.33 15.307 126.547 0.005 5.924 25.03 29.75 4.72 17.483 124.307 0.021 5.878 24.33 29.37 5.04 18.739 122.939 0.042 5.860 24.08 29.25 5.17 19.199 122.499 0.063 5.854 23.97 29.21 5.24 19.467 122.373 0.084 5.852 23.93 29.18 5.26 19.746 122.454 0.104 5.850 23.77 29.13 5.36 19.663 122.198 0.125 5.847 23.74 29.13 5.39 19.790 122.236 0.146 5.846 23.72 29.12 5.40 19.886 122.261 0.167 5.846 23.70 29.12 5.41 19.984 122.304 0.188 5.845 23.69 29.11 5.42 20.073 122.346 0.209 5.845 max suggested for this run: 24.19 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.209 Accepted refinement result: 23.69 29.11 5.42 20.073 122.346 0.209 5.845 Individual atomic B min max mean iso aniso Overall: 51.06 217.72 111.77 16.57 5234 0 Protein: 51.06 217.72 111.77 16.57 5234 0 Chain A: 51.06 180.86 95.18 N/A 876 0 Chain B: 67.87 183.46 111.86 N/A 867 0 Chain C: 60.16 193.66 101.56 N/A 876 0 Chain D: 57.76 182.26 97.98 N/A 860 0 Chain E: 90.92 217.72 143.55 N/A 883 0 Chain F: 82.20 186.02 120.02 N/A 872 0 Histogram: Values Number of atoms 51.06 - 67.72 179 67.72 - 84.39 750 84.39 - 101.06 1127 101.06 - 117.72 1179 117.72 - 134.39 877 134.39 - 151.06 588 151.06 - 167.72 342 167.72 - 184.39 127 184.39 - 201.06 48 201.06 - 217.72 17 =========================== Idealize ADP of riding H ========================== r_work=0.2369 r_free=0.2911 r_work=0.2374 r_free=0.2911 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.40 - 19.99 A, n_refl.=25903 (all), 5.09 % free)------------| | | | r_work= 0.2374 r_free= 0.2911 coordinate error (max.-lik. estimate): 0.34 A | | | | normalized target function (ml) (work): 5.844443 | | target function (ml) not normalized (work): 143679.796076 | | target function (ml) not normalized (free): 7890.407871 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2402 0.2374 0.2911 n_refl.: 25903 re-set all scales: r(all,work,free)=0.3736 0.3712 0.4164 n_refl.: 25903 remove outliers: r(all,work,free)=0.3736 0.3712 0.4164 n_refl.: 25903 overall B=-0.75 to atoms: r(all,work,free)=0.3714 0.3690 0.4145 n_refl.: 25903 bulk-solvent and scaling: r(all,work,free)=0.2402 0.2374 0.2926 n_refl.: 25903 remove outliers: r(all,work,free)=0.2402 0.2374 0.2926 n_refl.: 25903 ======================== 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 19.988-16.886 98.02 93 6 0.4889 793.074 660.845 0.754 0.976 0.270 16.855-15.102 97.06 96 3 0.3855 910.367 827.122 0.812 0.972 0.270 15.055-13.543 96.90 117 8 0.3174 951.908 897.725 0.839 0.976 0.257 13.531-12.124 98.40 177 8 0.2300 1320.431 1256.894 0.967 0.975 0.247 12.122-10.863 98.00 231 14 0.2296 1425.553 1404.277 1.054 0.976 0.230 10.859-9.734 96.81 316 18 0.1965 1368.769 1347.587 1.114 0.979 0.225 9.728-8.719 98.71 440 18 0.2089 1161.239 1139.320 1.123 0.980 0.220 8.719-7.816 98.08 582 32 0.2433 858.221 823.873 1.126 0.982 0.221 7.812-7.000 98.44 835 46 0.2873 620.291 580.276 1.048 0.983 0.201 6.996-6.272 99.42 1131 61 0.3300 404.975 378.580 0.991 0.985 0.185 6.270-5.619 99.76 1581 82 0.3300 323.600 300.310 0.861 0.987 0.151 5.619-5.035 99.26 2133 136 0.2440 339.935 326.202 0.886 0.990 0.115 5.034-4.511 99.59 2966 163 0.1861 383.619 371.418 0.990 0.994 0.085 4.511-4.041 99.19 4079 206 0.1781 319.581 309.184 1.067 0.997 0.071 4.041-3.621 99.33 5632 291 0.2302 203.703 193.236 1.064 1.002 0.020 3.621-3.400 99.53 4175 227 0.2684 131.393 119.979 0.921 1.006 0.010 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-2.6947 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.2374 r_free=0.2926 After: r_work=0.2374 r_free=0.2926 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 7.040974 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.038187 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 0.2376 0.2926 0.0550 0.002 0.6 6.2 0.0 6.8 0 0.125 0.2374 0.2924 0.0550 0.003 0.6 6.2 0.0 6.8 0 0.250 0.2368 0.2919 0.0551 0.003 0.6 6.2 0.0 6.8 0 0.500 0.2331 0.2892 0.0561 0.008 0.8 7.9 0.0 7.0 0 1.000 0.2273 0.2856 0.0583 0.010 1.3 14.1 0.0 7.5 0 2.000 0.2249 0.2843 0.0594 0.013 1.7 18.7 0.0 8.4 0 3.000 0.2238 0.2837 0.0599 0.015 1.8 21.6 0.2 9.9 0 4.000 0.2226 0.2834 0.0607 0.017 2.0 23.9 0.8 10.6 0 5.000 0.2219 0.2830 0.0611 0.020 2.3 24.0 0.8 9.9 0 6.000 0.2209 0.2830 0.0620 0.022 2.5 24.8 0.6 9.7 0 7.000 0.2198 0.2824 0.0625 0.025 2.6 27.8 1.2 10.8 0 8.000 0.2188 0.2824 0.0636 0.027 2.9 34.0 2.3 13.0 0 9.000 0.2183 0.2824 0.0641 0.029 3.1 35.1 2.3 13.1 0 10.000 0.2242 0.2841 0.0598 0.014 1.7 20.8 0.0 8.9 0 3.520 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2368 0.2919 0.0551 0.003 0.6 6.2 0.0 6.8 0 0.500 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 23.68 29.19 5.51 20.139 122.672 0.038 5.845 30.11 33.82 3.70 16.448 132.679 0.001 5.965 28.31 32.31 4.00 17.029 131.300 0.005 5.953 26.02 30.58 4.57 18.487 127.291 0.019 5.906 24.77 29.78 5.01 18.522 124.851 0.038 5.870 24.23 29.36 5.13 18.982 123.904 0.057 5.851 23.94 29.17 5.23 19.374 123.474 0.076 5.842 23.83 29.08 5.25 19.667 123.519 0.095 5.838 23.69 29.04 5.35 19.935 123.295 0.115 5.834 23.62 29.00 5.38 20.142 123.295 0.134 5.832 23.58 28.98 5.41 20.326 123.376 0.153 5.831 23.54 28.97 5.42 20.501 123.458 0.172 5.830 23.52 28.94 5.43 20.660 123.536 0.191 5.829 max suggested for this run: 24.53 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.191 Accepted refinement result: 23.52 28.94 5.43 20.660 123.536 0.191 5.829 Individual atomic B min max mean iso aniso Overall: 47.88 224.88 112.78 18.52 5234 0 Protein: 47.88 224.88 112.78 18.52 5234 0 Chain A: 47.88 188.25 95.50 N/A 876 0 Chain B: 62.55 200.15 112.95 N/A 867 0 Chain C: 56.35 201.00 102.49 N/A 876 0 Chain D: 52.01 199.58 98.99 N/A 860 0 Chain E: 85.17 224.88 144.61 N/A 883 0 Chain F: 76.45 194.03 121.69 N/A 872 0 Histogram: Values Number of atoms 47.88 - 65.58 130 65.58 - 83.28 725 83.28 - 100.98 1158 100.98 - 118.68 1256 118.68 - 136.38 865 136.38 - 154.08 590 154.08 - 171.78 319 171.78 - 189.48 122 189.48 - 207.18 56 207.18 - 224.88 13 =========================== Idealize ADP of riding H ========================== r_work=0.2352 r_free=0.2894 r_work=0.2355 r_free=0.2895 ----------X-ray data---------- |--(resolution: 3.40 - 19.99 A, n_refl.=25903 (all), 5.09 % free)------------| | | | r_work= 0.2355 r_free= 0.2895 coordinate error (max.-lik. estimate): 0.35 A | | | | normalized target function (ml) (work): 5.829317 | | target function (ml) not normalized (work): 143307.921742 | | target function (ml) not normalized (free): 7879.507692 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 19.99 - 6.98 0.98 2910 153 0.2532 0.3013 7.1283 7.2703| | 2: 6.98 - 5.58 1.00 2800 148 0.3339 0.4129 6.504 6.6269| | 3: 5.58 - 4.89 0.99 2720 172 0.2308 0.2824 6.0456 6.13| | 4: 4.89 - 4.45 0.99 2703 139 0.1733 0.2004 5.8404 5.9644| | 5: 4.45 - 4.13 0.99 2734 139 0.1684 0.2198 5.6714 5.8766| | 6: 4.13 - 3.89 0.99 2654 143 0.2002 0.2821 5.5435 5.7752| | 7: 3.89 - 3.70 0.99 2711 136 0.2190 0.2772 5.3821 5.5921| | 8: 3.70 - 3.54 0.99 2684 135 0.2547 0.3127 5.2025 5.2896| | 9: 3.54 - 3.40 1.00 2668 154 0.2527 0.3032 5.0038 5.1014| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 19.99 - 6.98 2910 153 0.72 31.17 0.99 0.99 299410.14| | 2: 6.98 - 5.58 2800 148 0.51 50.20 1.00 0.96 130765.27| | 3: 5.58 - 4.89 2720 172 0.76 29.10 1.00 0.97 38167.38| | 4: 4.89 - 4.45 2703 139 0.86 20.68 1.01 1.01 23311.20| | 5: 4.45 - 4.13 2734 139 0.86 20.27 1.02 1.03 17496.49| | 6: 4.13 - 3.89 2654 143 0.83 23.40 1.05 1.04 13752.55| | 7: 3.89 - 3.70 2711 136 0.81 25.40 1.03 1.02 10513.09| | 8: 3.70 - 3.54 2684 135 0.79 28.21 1.00 0.98 7447.79| | 9: 3.54 - 3.40 2668 154 0.81 26.35 0.99 0.92 4868.99| |alpha: min = 0.92 max = 1.04 mean = 0.99| |beta: min = 4868.99 max = 299410.14 mean = 63051.89| |figures of merit: min = 0.00 max = 1.00 mean = 0.77| |phase err.(work): min = 0.00 max = 89.99 mean = 28.42| |phase err.(test): min = 0.00 max = 89.90 mean = 28.74| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2383 0.2355 0.2895 n_refl.: 25903 re-set all scales: r(all,work,free)=0.3761 0.3737 0.4184 n_refl.: 25903 remove outliers: r(all,work,free)=0.3761 0.3737 0.4184 n_refl.: 25903 overall B=-1.04 to atoms: r(all,work,free)=0.3730 0.3706 0.4157 n_refl.: 25903 bulk-solvent and scaling: r(all,work,free)=0.2380 0.2352 0.2890 n_refl.: 25903 remove outliers: r(all,work,free)=0.2380 0.2352 0.2890 n_refl.: 25903 ======================== 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 19.988-16.886 98.02 93 6 0.4898 793.074 660.795 0.755 0.978 0.270 16.855-15.102 97.06 96 3 0.3879 910.367 823.650 0.812 0.973 0.270 15.055-13.543 96.90 117 8 0.3209 951.908 896.754 0.848 0.977 0.260 13.531-12.124 98.40 177 8 0.2306 1320.431 1255.467 0.993 0.976 0.257 12.122-10.863 98.00 231 14 0.2331 1425.553 1403.603 1.064 0.978 0.236 10.859-9.734 96.81 316 18 0.1995 1368.769 1345.989 1.120 0.981 0.231 9.728-8.719 98.71 440 18 0.2126 1161.239 1136.899 1.125 0.981 0.226 8.719-7.816 98.08 582 32 0.2456 858.221 822.979 1.127 0.983 0.221 7.812-7.000 98.44 835 46 0.2975 620.291 577.289 1.051 0.984 0.201 6.996-6.272 99.42 1131 61 0.3348 404.975 377.171 0.999 0.986 0.181 6.270-5.619 99.76 1581 82 0.3350 323.600 298.961 0.863 0.988 0.151 5.619-5.035 99.26 2133 136 0.2416 339.935 326.268 0.890 0.991 0.116 5.034-4.511 99.59 2966 163 0.1799 383.619 372.128 0.994 0.994 0.086 4.511-4.041 99.19 4079 206 0.1709 319.581 309.913 1.081 0.998 0.071 4.041-3.621 99.33 5632 291 0.2191 203.703 194.223 1.091 1.002 0.015 3.621-3.400 99.53 4175 227 0.2602 131.393 120.562 0.936 1.006 0.010 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-3.7143 ================= 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 : 0.4270 0.4614 0.010 1.400 78.7 191.0 119.0 0 0.000 1_bss: 0.2628 0.3103 0.010 1.400 61.4 173.7 101.7 0 0.000 1_settarget: 0.2628 0.3103 0.010 1.400 61.4 173.7 101.7 0 0.000 1_updatephipsi: 0.2628 0.3103 0.010 1.400 61.4 173.7 101.7 0 0.000 1_weight: 0.2628 0.3103 0.010 1.400 61.4 173.7 101.7 0 0.000 1_xyzrec: 0.2722 0.3182 0.004 0.636 61.4 173.7 101.7 0 0.196 1_adp: 0.2466 0.3022 0.004 0.636 56.4 218.7 109.3 0 0.196 1_regHadp: 0.2453 0.3007 0.004 0.636 56.4 218.7 109.3 0 0.196 2_bss: 0.2415 0.3008 0.004 0.636 56.1 218.3 108.9 0 0.196 2_settarget: 0.2415 0.3008 0.004 0.636 56.1 218.3 108.9 0 0.196 2_updatephipsi: 0.2415 0.3008 0.004 0.636 56.1 218.3 108.9 0 0.196 2_updatecdl: 0.2415 0.3008 0.004 0.664 56.1 218.3 108.9 0 0.196 2_weight: 0.2415 0.3008 0.004 0.664 56.1 218.3 108.9 0 0.196 2_xyzrec: 0.2426 0.2971 0.003 0.553 56.1 218.3 108.9 0 0.252 2_adp: 0.2369 0.2911 0.003 0.553 51.1 217.7 111.8 0 0.252 2_regHadp: 0.2374 0.2911 0.003 0.553 51.1 217.7 111.8 0 0.252 3_bss: 0.2374 0.2926 0.003 0.553 50.3 217.0 111.0 0 0.252 3_settarget: 0.2374 0.2926 0.003 0.553 50.3 217.0 111.0 0 0.252 3_updatephipsi: 0.2374 0.2926 0.003 0.553 50.3 217.0 111.0 0 0.252 3_updatecdl: 0.2374 0.2926 0.003 0.572 50.3 217.0 111.0 0 0.252 3_setrh: 0.2374 0.2926 0.003 0.572 50.3 217.0 111.0 0 0.252 3_weight: 0.2374 0.2926 0.003 0.572 50.3 217.0 111.0 0 0.252 3_xyzrec: 0.2368 0.2919 0.003 0.565 50.3 217.0 111.0 0 0.252 3_adp: 0.2352 0.2894 0.003 0.565 47.9 224.9 112.8 0 0.252 3_regHadp: 0.2355 0.2895 0.003 0.565 47.9 224.9 112.8 0 0.252 end: 0.2352 0.2890 0.003 0.565 46.8 223.8 111.7 0 0.252 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V2/2pej_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V2/2pej_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 15.8300 Refinement macro-cycles (run) : 408.4200 Write final files (write_after_run_outputs) : 23.6600 Total : 447.9100 Total CPU time: 8.42 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:38:54 PDT -0700 (1716251934.31 s) Start R-work = 0.2628, R-free = 0.3103 Final R-work = 0.2352, R-free = 0.2890 =============================================================================== Job complete usr+sys time: 537.17 seconds wall clock time: 22 minutes 23.26 seconds (1343.26 seconds total)