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/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=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/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 { nonbonded_weight = 100 } target_weights { optimize_xyz_weight = true optimize_adp_weight = true } } Starting job =============================================================================== Symmetric amino acids flipped None Time to flip residues: 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 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: 1.83, per 1000 atoms: 0.17 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: 2.74 Conformation dependent library (CDL) restraints added in 455.2 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 1256 Time building geometry restraints manager: 3.23 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 { 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 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 15.947745 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 0.2782 0.3232 0.0451 0.003 0.6 4.8 1.1 9.2 0 0.125 0.2757 0.3217 0.0460 0.003 0.6 4.8 1.1 9.4 0 0.250 0.2730 0.3194 0.0464 0.004 0.6 5.2 1.1 9.0 0 0.500 0.2694 0.3181 0.0486 0.004 0.6 5.9 1.1 9.4 0 1.000 0.2669 0.3155 0.0486 0.006 0.7 11.1 1.7 9.4 0 2.000 0.2641 0.3143 0.0502 0.007 0.8 15.4 2.8 10.6 0 3.000 0.2616 0.3130 0.0514 0.009 1.0 19.6 4.2 11.6 0 4.000 0.2592 0.3118 0.0526 0.010 1.0 23.3 5.0 11.4 0 5.000 0.2573 0.3099 0.0526 0.011 1.1 25.2 5.2 11.9 0 6.000 0.2563 0.3105 0.0542 0.013 1.2 28.5 6.2 11.9 0 7.000 0.2546 0.3097 0.0551 0.014 1.3 29.0 6.1 12.1 0 8.000 0.2535 0.3094 0.0559 0.014 1.3 30.3 6.2 12.6 0 9.000 0.2531 0.3100 0.0568 0.016 1.4 32.8 7.0 12.8 0 10.000 0.2553 0.3105 0.0552 0.014 1.3 30.3 6.6 12.3 0 7.974 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2782 0.3232 0.0451 0.003 0.6 4.8 1.1 9.2 0 0.125 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 27.82 32.32 4.51 0.568 101.402 0.199 0.091 27.86 32.36 4.50 1.759 101.465 0.006 0.091 27.52 32.12 4.60 1.886 101.475 0.025 0.089 26.95 31.70 4.75 3.050 101.525 0.100 0.086 26.06 31.16 5.10 8.488 102.681 0.199 0.079 25.86 31.13 5.27 10.236 103.166 0.299 0.078 25.78 30.94 5.16 9.600 103.180 0.399 0.078 25.47 30.86 5.39 14.066 104.331 0.499 0.075 25.42 30.86 5.45 14.847 104.547 0.598 0.075 25.38 30.84 5.45 15.232 104.647 0.698 0.075 25.29 30.84 5.55 16.530 105.042 0.798 0.074 25.25 30.80 5.55 17.023 105.187 0.898 0.073 25.20 30.81 5.62 18.060 105.499 0.997 0.073 max suggested for this run: 20.28 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.898 Accepted refinement result: 25.25 30.80 5.55 17.023 105.187 0.898 0.073 Individual atomic B min max mean iso aniso Overall: 56.39 223.19 109.44 12.86 5234 0 Protein: 56.39 223.19 109.44 12.86 5234 0 Chain A: 56.39 187.55 92.29 N/A 876 0 Chain B: 72.84 182.16 109.38 N/A 867 0 Chain C: 64.28 186.63 99.98 N/A 876 0 Chain D: 62.80 177.00 95.24 N/A 860 0 Chain E: 96.25 223.19 141.75 N/A 883 0 Chain F: 87.44 192.86 117.49 N/A 872 0 Histogram: Values Number of atoms 56.39 - 73.07 358 73.07 - 89.75 1113 89.75 - 106.43 1178 106.43 - 123.11 1145 123.11 - 139.79 665 139.79 - 156.47 398 156.47 - 173.15 274 173.15 - 189.83 63 189.83 - 206.51 32 206.51 - 223.19 8 =========================== Idealize ADP of riding H ========================== r_work=0.2525 r_free=0.3080 r_work=0.2510 r_free=0.3061 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.40 - 19.99 A, n_refl.=25903 (all), 5.09 % free)------------| | | | r_work= 0.2510 r_free= 0.3061 coordinate error (max.-lik. estimate): 0.37 A | | | | normalized target function (ls_wunit_k1) (work): 0.071565 | | target function (ls_wunit_k1) not normalized (work): 1759.359754 | | target function (ls_wunit_k1) not normalized (free): 142.294748 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2538 0.2510 0.3061 n_refl.: 25903 re-set all scales: r(all,work,free)=0.3723 0.3697 0.4182 n_refl.: 25903 remove outliers: r(all,work,free)=0.3723 0.3697 0.4182 n_refl.: 25903 overall B=-0.31 to atoms: r(all,work,free)=0.3715 0.3689 0.4175 n_refl.: 25903 bulk-solvent and scaling: r(all,work,free)=0.2511 0.2480 0.3077 n_refl.: 25903 remove outliers: r(all,work,free)=0.2511 0.2480 0.3077 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 0.4911 793.644 650.866 0.793 0.977 0.280 16.855-15.102 97.06 96 3 0.3781 911.021 831.253 0.826 0.973 0.273 15.055-13.543 96.90 117 8 0.3038 952.592 904.372 0.845 0.976 0.255 13.531-12.124 98.40 177 8 0.2232 1321.380 1263.637 0.970 0.976 0.247 12.122-10.863 98.00 231 14 0.2200 1426.577 1411.786 1.065 0.977 0.235 10.859-9.734 96.81 316 18 0.1876 1369.753 1351.354 1.127 0.980 0.230 9.728-8.719 98.71 440 18 0.2009 1162.074 1143.732 1.138 0.981 0.227 8.719-7.816 98.08 582 32 0.2193 858.838 836.031 1.133 0.982 0.224 7.812-7.000 98.44 835 46 0.2620 620.737 589.912 1.052 0.984 0.200 6.996-6.272 99.42 1131 61 0.3130 405.266 381.483 0.964 0.986 0.180 6.270-5.619 99.76 1581 82 0.3117 323.833 303.192 0.836 0.988 0.150 5.619-5.035 99.26 2133 136 0.2502 340.179 328.556 0.868 0.991 0.115 5.034-4.511 99.59 2966 163 0.2097 383.894 370.517 0.990 0.995 0.100 4.511-4.041 99.19 4079 206 0.2130 319.810 308.610 1.049 0.999 0.070 4.041-3.621 99.33 5632 291 0.2745 203.849 191.518 1.024 1.004 0.023 3.621-3.400 99.53 4175 227 0.3064 131.488 118.572 0.898 1.009 0.020 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-1.0876 ============================ 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 = 6.802922 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.041866 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 0.2466 0.3022 0.0555 0.002 0.5 4.5 1.1 6.1 0 0.125 0.2420 0.2981 0.0561 0.002 0.5 6.0 1.1 7.3 0 0.250 0.2386 0.2967 0.0581 0.004 0.6 7.3 1.2 8.4 0 0.500 0.2351 0.2930 0.0579 0.006 0.8 12.2 2.0 9.4 0 1.000 0.2321 0.2912 0.0591 0.010 1.0 14.9 3.3 9.9 0 2.000 0.2315 0.2914 0.0598 0.014 1.3 15.8 2.8 9.4 0 3.000 0.2299 0.2899 0.0600 0.020 1.5 18.5 3.0 9.4 0 4.000 0.2264 0.2865 0.0601 0.019 1.7 28.8 6.4 14.3 0 5.000 0.2253 0.2853 0.0600 0.022 1.9 32.9 7.3 14.7 0 6.000 0.2244 0.2845 0.0601 0.024 2.0 34.2 7.5 15.9 0 7.000 0.2234 0.2841 0.0607 0.027 2.2 35.6 8.0 16.2 0 8.000 0.2225 0.2835 0.0609 0.029 2.3 37.4 8.6 17.4 0 9.000 0.2216 0.2831 0.0615 0.031 2.5 39.9 9.5 18.1 0 10.000 0.2305 0.2903 0.0598 0.016 1.4 18.2 3.1 9.4 0 3.401 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2420 0.2981 0.0561 0.002 0.5 6.0 1.1 7.3 0 0.250 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 24.20 29.81 5.61 18.611 121.318 0.042 5.897 28.08 32.32 4.24 15.163 128.333 0.001 5.948 26.68 31.24 4.56 15.348 127.036 0.005 5.924 25.01 29.97 4.97 17.525 124.757 0.021 5.879 24.29 29.51 5.22 18.777 123.331 0.042 5.860 24.04 29.36 5.32 19.199 122.807 0.063 5.855 23.94 29.32 5.37 19.509 122.763 0.084 5.852 23.90 29.30 5.41 19.778 122.829 0.105 5.851 23.74 29.22 5.48 19.718 122.605 0.126 5.847 23.71 29.22 5.51 19.781 122.574 0.147 5.847 23.69 29.20 5.51 19.856 122.587 0.167 5.846 23.67 29.19 5.52 19.956 122.636 0.188 5.846 23.66 29.19 5.53 20.031 122.670 0.209 5.845 max suggested for this run: 24.26 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.209 Accepted refinement result: 23.66 29.19 5.53 20.031 122.670 0.209 5.845 Individual atomic B min max mean iso aniso Overall: 51.08 220.28 111.89 16.29 5234 0 Protein: 51.08 220.28 111.89 16.29 5234 0 Chain A: 51.08 182.23 95.23 N/A 876 0 Chain B: 67.52 186.20 111.87 N/A 867 0 Chain C: 60.18 194.61 101.81 N/A 876 0 Chain D: 57.49 179.22 98.24 N/A 860 0 Chain E: 90.94 220.28 143.62 N/A 883 0 Chain F: 82.13 193.90 120.10 N/A 872 0 Histogram: Values Number of atoms 51.08 - 68.00 184 68.00 - 84.92 750 84.92 - 101.84 1185 101.84 - 118.76 1174 118.76 - 135.68 888 135.68 - 152.60 564 152.60 - 169.52 321 169.52 - 186.44 105 186.44 - 203.36 49 203.36 - 220.28 14 =========================== Idealize ADP of riding H ========================== r_work=0.2366 r_free=0.2919 r_work=0.2371 r_free=0.2918 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.40 - 19.99 A, n_refl.=25903 (all), 5.09 % free)------------| | | | r_work= 0.2371 r_free= 0.2918 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ml) (work): 5.844544 | | target function (ml) not normalized (work): 143682.262441 | | target function (ml) not normalized (free): 7894.660232 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2399 0.2371 0.2918 n_refl.: 25903 re-set all scales: r(all,work,free)=0.3736 0.3711 0.4174 n_refl.: 25903 remove outliers: r(all,work,free)=0.3736 0.3711 0.4174 n_refl.: 25903 overall B=-0.74 to atoms: r(all,work,free)=0.3714 0.3689 0.4156 n_refl.: 25903 bulk-solvent and scaling: r(all,work,free)=0.2394 0.2366 0.2915 n_refl.: 25903 remove outliers: r(all,work,free)=0.2394 0.2366 0.2915 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 0.4873 793.644 657.425 0.748 0.976 0.270 16.855-15.102 97.06 96 3 0.3867 911.021 830.008 0.812 0.971 0.270 15.055-13.543 96.90 117 8 0.3156 952.592 897.555 0.847 0.975 0.260 13.531-12.124 98.40 177 8 0.2281 1321.380 1256.670 0.973 0.974 0.250 12.122-10.863 98.00 231 14 0.2285 1426.577 1407.404 1.054 0.976 0.230 10.859-9.734 96.81 316 18 0.1949 1369.753 1348.555 1.114 0.979 0.230 9.728-8.719 98.71 440 18 0.2065 1162.074 1141.375 1.127 0.980 0.231 8.719-7.816 98.08 582 32 0.2390 858.838 826.019 1.121 0.982 0.211 7.812-7.000 98.44 835 46 0.2847 620.737 582.346 1.047 0.984 0.211 6.996-6.272 99.42 1131 61 0.3290 405.266 377.623 0.984 0.986 0.181 6.270-5.619 99.76 1581 82 0.3279 323.833 300.577 0.858 0.988 0.151 5.619-5.035 99.26 2133 136 0.2411 340.179 327.447 0.882 0.992 0.115 5.034-4.511 99.59 2966 163 0.1855 383.894 371.619 0.997 0.996 0.101 4.511-4.041 99.19 4079 206 0.1800 319.810 309.189 1.060 1.000 0.071 4.041-3.621 99.33 5632 291 0.2327 203.849 193.153 1.057 1.006 0.020 3.621-3.400 99.53 4175 227 0.2655 131.488 120.400 0.914 1.011 0.010 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-2.6367 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.2366 r_free=0.2915 After: r_work=0.2366 r_free=0.2915 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 6.923083 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.037829 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 0.2367 0.2915 0.0548 0.002 0.5 6.4 1.1 7.3 0 0.125 0.2365 0.2913 0.0548 0.002 0.5 6.4 1.1 7.3 0 0.250 0.2358 0.2911 0.0552 0.003 0.5 6.6 1.1 7.2 0 0.500 0.2322 0.2885 0.0563 0.008 0.8 8.3 1.1 6.8 0 1.000 0.2271 0.2851 0.0580 0.011 1.4 16.8 1.2 7.3 0 2.000 0.2254 0.2857 0.0603 0.013 1.6 22.5 3.0 9.6 0 3.000 0.2237 0.2846 0.0609 0.015 1.9 23.8 2.8 9.2 0 4.000 0.2222 0.2844 0.0622 0.019 2.2 29.1 3.8 9.9 0 5.000 0.2218 0.2841 0.0623 0.020 2.3 31.2 5.2 11.6 0 6.000 0.2209 0.2835 0.0626 0.023 2.4 28.3 3.4 9.9 0 7.000 0.2198 0.2836 0.0638 0.025 2.8 33.2 4.8 11.8 0 8.000 0.2190 0.2825 0.0635 0.027 3.0 38.4 6.2 13.7 0 9.000 0.2185 0.2823 0.0638 0.028 3.2 41.0 7.0 14.8 0 10.000 0.2245 0.2846 0.0601 0.014 1.8 21.7 2.3 8.5 0 3.462 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2365 0.2913 0.0548 0.002 0.5 6.4 1.1 7.3 0 0.250 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 23.65 29.13 5.48 20.051 122.899 0.038 5.847 29.27 33.08 3.81 17.479 131.459 0.001 5.965 28.22 32.27 4.05 17.115 131.459 0.005 5.951 26.10 30.55 4.45 18.568 127.719 0.019 5.909 24.74 29.79 5.05 18.370 125.162 0.038 5.871 24.18 29.33 5.15 18.842 124.144 0.057 5.851 23.94 29.17 5.23 19.229 123.894 0.076 5.843 23.76 29.08 5.32 19.568 123.660 0.095 5.838 23.67 29.04 5.38 19.813 123.652 0.113 5.835 23.60 29.03 5.42 20.022 123.678 0.132 5.833 23.57 29.01 5.44 20.208 123.768 0.151 5.831 23.54 29.00 5.46 20.382 123.857 0.170 5.830 23.51 29.00 5.48 20.545 123.942 0.189 5.829 max suggested for this run: 24.58 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.189 Accepted refinement result: 23.51 29.00 5.48 20.545 123.942 0.189 5.829 Individual atomic B min max mean iso aniso Overall: 47.91 224.24 113.29 18.36 5234 0 Protein: 47.91 224.24 113.29 18.36 5234 0 Chain A: 47.91 183.55 96.07 N/A 876 0 Chain B: 62.58 193.49 113.29 N/A 867 0 Chain C: 56.51 202.72 103.15 N/A 876 0 Chain D: 51.75 192.14 99.71 N/A 860 0 Chain E: 85.20 224.24 144.93 N/A 883 0 Chain F: 76.39 198.70 122.11 N/A 872 0 Histogram: Values Number of atoms 47.91 - 65.55 116 65.55 - 83.18 675 83.18 - 100.81 1163 100.81 - 118.44 1251 118.44 - 136.07 919 136.07 - 153.71 583 153.71 - 171.34 335 171.34 - 188.97 119 188.97 - 206.60 58 206.60 - 224.24 15 =========================== Idealize ADP of riding H ========================== r_work=0.2351 r_free=0.2900 r_work=0.2355 r_free=0.2901 ----------X-ray data---------- |--(resolution: 3.40 - 19.99 A, n_refl.=25903 (all), 5.09 % free)------------| | | | r_work= 0.2355 r_free= 0.2901 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ml) (work): 5.829685 | | target function (ml) not normalized (work): 143316.970208 | | target function (ml) not normalized (free): 7881.854413 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2517 0.3003 7.1242 7.2652| | 2: 6.98 - 5.58 1.00 2800 148 0.3329 0.4182 6.5016 6.6314| | 3: 5.58 - 4.89 0.99 2720 172 0.2310 0.2794 6.0506 6.1335| | 4: 4.89 - 4.45 0.99 2703 139 0.1737 0.2087 5.8435 5.9737| | 5: 4.45 - 4.13 0.99 2734 139 0.1716 0.2161 5.6819 5.8824| | 6: 4.13 - 3.89 0.99 2654 143 0.2050 0.2800 5.5586 5.7779| | 7: 3.89 - 3.70 0.99 2711 136 0.2228 0.2899 5.3924 5.6272| | 8: 3.70 - 3.54 0.99 2684 135 0.2515 0.3076 5.1955 5.2771| | 9: 3.54 - 3.40 1.00 2668 154 0.2459 0.2974 4.9768 5.0774| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 0.73 30.78 0.99 1.00 294183.37| | 2: 6.98 - 5.58 2800 148 0.52 49.90 1.00 0.97 129465.29| | 3: 5.58 - 4.89 2720 172 0.76 29.16 1.00 0.99 38711.18| | 4: 4.89 - 4.45 2703 139 0.85 20.80 1.01 1.03 23579.18| | 5: 4.45 - 4.13 2734 139 0.86 20.53 1.02 1.04 17883.94| | 6: 4.13 - 3.89 2654 143 0.83 23.71 1.04 1.05 14085.86| | 7: 3.89 - 3.70 2711 136 0.81 25.71 1.03 1.03 10690.54| | 8: 3.70 - 3.54 2684 135 0.79 27.69 1.01 1.00 7287.66| | 9: 3.54 - 3.40 2668 154 0.83 24.50 1.00 0.95 4439.00| |alpha: min = 0.95 max = 1.05 mean = 1.01| |beta: min = 4439.00 max = 294183.37 mean = 62409.26| |figures of merit: min = 0.00 max = 1.00 mean = 0.77| |phase err.(work): min = 0.00 max = 89.97 mean = 28.20| |phase err.(test): min = 0.00 max = 89.74 mean = 28.53| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2383 0.2355 0.2901 n_refl.: 25903 re-set all scales: r(all,work,free)=0.3784 0.3760 0.4209 n_refl.: 25903 remove outliers: r(all,work,free)=0.3784 0.3760 0.4209 n_refl.: 25903 overall B=-0.98 to atoms: r(all,work,free)=0.3754 0.3730 0.4183 n_refl.: 25903 bulk-solvent and scaling: r(all,work,free)=0.2380 0.2351 0.2906 n_refl.: 25903 remove outliers: r(all,work,free)=0.2380 0.2351 0.2906 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 0.4882 793.644 657.395 0.723 0.975 0.270 16.855-15.102 97.06 96 3 0.3890 911.021 828.799 0.784 0.971 0.270 15.055-13.543 96.90 117 8 0.3176 952.592 896.514 0.810 0.975 0.257 13.531-12.124 98.40 177 8 0.2315 1321.380 1255.300 0.933 0.974 0.247 12.122-10.863 98.00 231 14 0.2327 1426.577 1405.909 1.017 0.976 0.230 10.859-9.734 96.81 316 18 0.1995 1369.753 1347.521 1.075 0.979 0.229 9.728-8.719 98.71 440 18 0.2111 1162.074 1138.557 1.087 0.980 0.227 8.719-7.816 98.08 582 32 0.2441 858.838 823.840 1.088 0.982 0.221 7.812-7.000 98.44 835 46 0.2943 620.737 579.291 1.016 0.984 0.201 6.996-6.272 99.42 1131 61 0.3344 405.266 376.332 0.961 0.986 0.181 6.270-5.619 99.76 1581 82 0.3339 323.833 298.966 0.832 0.989 0.151 5.619-5.035 99.26 2133 136 0.2411 340.179 326.931 0.857 0.992 0.116 5.034-4.511 99.59 2966 163 0.1806 383.894 372.124 0.971 0.997 0.101 4.511-4.041 99.19 4079 206 0.1736 319.810 309.971 1.041 1.001 0.071 4.041-3.621 99.33 5632 291 0.2216 203.849 194.184 1.051 1.007 0.022 3.621-3.400 99.53 4175 227 0.2544 131.488 121.105 0.907 1.012 0.010 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-4.4126 ================= 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_weight: 0.2628 0.3103 0.010 1.400 61.4 173.7 101.7 0 0.000 1_xyzrec: 0.2782 0.3232 0.003 0.560 61.4 173.7 101.7 0 0.188 1_adp: 0.2525 0.3080 0.003 0.560 56.4 223.2 109.4 0 0.188 1_regHadp: 0.2510 0.3061 0.003 0.560 56.4 223.2 109.4 0 0.188 2_bss: 0.2480 0.3077 0.003 0.560 56.1 222.9 109.1 0 0.188 2_settarget: 0.2480 0.3077 0.003 0.560 56.1 222.9 109.1 0 0.188 2_updatecdl: 0.2480 0.3077 0.003 0.635 56.1 222.9 109.1 0 0.188 2_weight: 0.2480 0.3077 0.003 0.635 56.1 222.9 109.1 0 0.188 2_xyzrec: 0.2420 0.2981 0.002 0.516 56.1 222.9 109.1 0 0.227 2_adp: 0.2366 0.2919 0.002 0.516 51.1 220.3 111.9 0 0.227 2_regHadp: 0.2371 0.2918 0.002 0.516 51.1 220.3 111.9 0 0.227 3_bss: 0.2366 0.2915 0.002 0.516 50.3 219.5 111.2 0 0.227 3_settarget: 0.2366 0.2915 0.002 0.516 50.3 219.5 111.2 0 0.227 3_updatecdl: 0.2366 0.2915 0.003 0.550 50.3 219.5 111.2 0 0.227 3_setrh: 0.2366 0.2915 0.003 0.550 50.3 219.5 111.2 0 0.227 3_weight: 0.2366 0.2915 0.003 0.550 50.3 219.5 111.2 0 0.227 3_xyzrec: 0.2365 0.2913 0.002 0.523 50.3 219.5 111.2 0 0.227 3_adp: 0.2351 0.2900 0.002 0.523 47.9 224.2 113.3 0 0.227 3_regHadp: 0.2355 0.2901 0.002 0.523 47.9 224.2 113.3 0 0.227 end: 0.2351 0.2906 0.002 0.523 46.9 223.3 112.3 0 0.227 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V1/2pej_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V1/2pej_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 15.7300 Refinement macro-cycles (run) : 403.1800 Write final files (write_after_run_outputs) : 23.5600 Total : 442.4700 Total CPU time: 8.07 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:38:13 PDT -0700 (1716251893.28 s) Start R-work = 0.2628, R-free = 0.3103 Final R-work = 0.2351, R-free = 0.2906 =============================================================================== Job complete usr+sys time: 514.77 seconds wall clock time: 22 minutes 17.41 seconds (1337.41 seconds total)