Starting phenix.refine on Wed Apr 10 15:59:19 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, 4JP6_complete.pdb Found miller_array, 4JP6.mtz Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- optimize_adp=true optimize_xyz=true hydrogens.refine=riding nproc=20 main.max_number_of_iterations=50 main.number_of_m=5 refine.adp.individual.aniso=not element H refine.adp.individual.iso=element H Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "4JP6.mtz" } default_miller_array = "4JP6.mtz" model { file = "4JP6_complete.pdb" } default_model = "4JP6_complete.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 { adp { individual { isotropic = element H anisotropic = not element H } } } main { number_of_macro_cycles = 5 max_number_of_iterations = 50 nproc = 20 } hydrogens { refine = individual *riding Auto } 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: 2330 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1865 Classifications: {'peptide': 122} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PCA%NH3:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 465 Classifications: {'water': 155} Link IDs: {None: 154} Time building chain proxies: 0.60, per 1000 atoms: 0.26 Number of scatterers: 2330 At special positions: 0 Unit cell: (27.688, 54.971, 73.509, 90, 90, 90) Space group: P 21 21 21 (No. 19) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 6 16.00 O 333 8.00 N 176 7.00 C 602 6.00 H 1213 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 29 " - pdb=" SG CYS A 61 " distance=2.07 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 84 " distance=2.09 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 120 " distance=2.07 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 56.6 milliseconds Time building geometry restraints manager: 0.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.85 - 1.04: 547 1.04 - 1.24: 759 1.24 - 1.43: 374 1.43 - 1.63: 516 1.63 - 1.82: 6 Bond restraints: 2202 Sorted by residual: bond pdb=" N CYS A 50 " pdb=" H CYS A 50 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" ND2 ASN A 5 " pdb="HD22 ASN A 5 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N ARG A 66 " pdb=" H ARG A 66 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N GLN A 17 " pdb=" H GLN A 17 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" NH2 ARG A 66 " pdb="HH21 ARG A 66 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.44e+01 ... (remaining 2197 not shown) Histogram of bond angle deviations from ideal: 98.56 - 105.89: 240 105.89 - 113.22: 1949 113.22 - 120.56: 752 120.56 - 127.89: 571 127.89 - 135.22: 20 Bond angle restraints: 3532 Sorted by residual: angle pdb=" OE1 GLN A 83 " pdb=" CD GLN A 83 " pdb=" NE2 GLN A 83 " ideal model delta sigma weight residual 122.60 129.04 -6.44 1.00e+00 1.00e+00 4.15e+01 angle pdb=" C ASN A 114 " pdb=" CA ASN A 114 " pdb=" CB ASN A 114 " ideal model delta sigma weight residual 109.37 119.87 -10.50 1.83e+00 2.99e-01 3.29e+01 angle pdb=" CA GLU A 75 " pdb=" CB GLU A 75 " pdb=" CG GLU A 75 " ideal model delta sigma weight residual 114.10 124.47 -10.37 2.00e+00 2.50e-01 2.69e+01 angle pdb=" N PCA A 1 " pdb=" CA PCA A 1 " pdb=" CB PCA A 1 " ideal model delta sigma weight residual 110.50 101.80 8.70 1.70e+00 3.46e-01 2.62e+01 angle pdb=" O VAL A 67 " pdb=" C VAL A 67 " pdb=" N THR A 68 " ideal model delta sigma weight residual 123.26 127.22 -3.96 1.08e+00 8.57e-01 1.35e+01 ... (remaining 3527 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.89: 585 11.89 - 23.77: 69 23.77 - 35.66: 12 35.66 - 47.54: 14 47.54 - 59.43: 7 Dihedral angle restraints: 687 sinusoidal: 472 harmonic: 215 Sorted by residual: dihedral pdb=" CA THR A 47 " pdb=" C THR A 47 " pdb=" N ALA A 48 " pdb=" CA ALA A 48 " ideal model delta harmonic sigma weight residual 180.00 156.56 23.44 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA LEU A 65 " pdb=" C LEU A 65 " pdb=" N ARG A 66 " pdb=" CA ARG A 66 " ideal model delta harmonic sigma weight residual 180.00 159.96 20.04 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA VAL A 113 " pdb=" C VAL A 113 " pdb=" N ASN A 114 " pdb=" CA ASN A 114 " ideal model delta harmonic sigma weight residual 180.00 162.39 17.61 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 684 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.099: 84 0.099 - 0.198: 35 0.198 - 0.297: 11 0.297 - 0.396: 5 0.396 - 0.494: 2 Chirality restraints: 137 Sorted by residual: chirality pdb=" CA ASP A 35 " pdb=" N ASP A 35 " pdb=" C ASP A 35 " pdb=" CB ASP A 35 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.11e+00 chirality pdb=" CA GLN A 116 " pdb=" N GLN A 116 " pdb=" C GLN A 116 " pdb=" CB GLN A 116 " both_signs ideal model delta sigma weight residual False 2.51 2.91 -0.40 2.00e-01 2.50e+01 3.95e+00 chirality pdb=" CB THR A 76 " pdb=" CA THR A 76 " pdb=" OG1 THR A 76 " pdb=" CG2 THR A 76 " both_signs ideal model delta sigma weight residual False 2.55 2.19 0.36 2.00e-01 2.50e+01 3.22e+00 ... (remaining 134 not shown) Planarity restraints: 292 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 12 " -0.050 2.00e-02 2.50e+03 8.17e-02 2.00e+02 pdb=" CG PHE A 12 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE A 12 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A 12 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE A 12 " 0.041 2.00e-02 2.50e+03 pdb=" CE2 PHE A 12 " 0.028 2.00e-02 2.50e+03 pdb=" CZ PHE A 12 " -0.053 2.00e-02 2.50e+03 pdb=" HD1 PHE A 12 " -0.050 2.00e-02 2.50e+03 pdb=" HD2 PHE A 12 " -0.007 2.00e-02 2.50e+03 pdb=" HE1 PHE A 12 " 0.149 2.00e-02 2.50e+03 pdb=" HE2 PHE A 12 " 0.103 2.00e-02 2.50e+03 pdb=" HZ PHE A 12 " -0.191 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 32 " 0.060 2.00e-02 2.50e+03 4.58e-02 8.41e+01 pdb=" CG TRP A 32 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 TRP A 32 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TRP A 32 " 0.008 2.00e-02 2.50e+03 pdb=" NE1 TRP A 32 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP A 32 " 0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP A 32 " -0.027 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 32 " -0.025 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 32 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 32 " 0.036 2.00e-02 2.50e+03 pdb=" HD1 TRP A 32 " 0.011 2.00e-02 2.50e+03 pdb=" HE1 TRP A 32 " 0.004 2.00e-02 2.50e+03 pdb=" HE3 TRP A 32 " -0.071 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 32 " -0.097 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 32 " -0.012 2.00e-02 2.50e+03 pdb=" HH2 TRP A 32 " 0.112 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 28 " 0.068 2.00e-02 2.50e+03 5.15e-02 7.96e+01 pdb=" CG TYR A 28 " 0.011 2.00e-02 2.50e+03 pdb=" CD1 TYR A 28 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 TYR A 28 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR A 28 " 0.024 2.00e-02 2.50e+03 pdb=" CE2 TYR A 28 " -0.017 2.00e-02 2.50e+03 pdb=" CZ TYR A 28 " 0.018 2.00e-02 2.50e+03 pdb=" OH TYR A 28 " 0.012 2.00e-02 2.50e+03 pdb=" HD1 TYR A 28 " -0.120 2.00e-02 2.50e+03 pdb=" HD2 TYR A 28 " 0.019 2.00e-02 2.50e+03 pdb=" HE1 TYR A 28 " 0.076 2.00e-02 2.50e+03 pdb=" HE2 TYR A 28 " -0.062 2.00e-02 2.50e+03 ... (remaining 289 not shown) Histogram of nonbonded interaction distances: 1.08 - 1.78: 17 1.78 - 2.49: 1874 2.49 - 3.19: 8006 3.19 - 3.90: 12610 3.90 - 4.60: 18705 Nonbonded interactions: 41212 Sorted by model distance: nonbonded pdb=" HG1 THR A 76 " pdb=" HZ3 LYS A 98 " model vdw 1.077 2.100 nonbonded pdb="HE22 GLN A 116 " pdb=" O HOH A 316 " model vdw 1.419 1.850 nonbonded pdb="HE21 GLN A 116 " pdb=" O HOH A 251 " model vdw 1.554 1.850 nonbonded pdb=" HZ1 LYS A 98 " pdb=" O HOH A 354 " model vdw 1.559 1.850 nonbonded pdb=" HG3 PRO A 55 " pdb=" HZ3 LYS A 63 " model vdw 1.597 2.270 ... (remaining 41207 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 6 15.96 2 O 333 7.97 2 N 176 6.97 2 C 602 5.97 2 H 1213 1.00 3 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 ===================== n_use = 2330 n_use_u_iso = 1213 n_use_u_aniso = 1117 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 = 2330 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (2330 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 1213 aniso = 1117) group_adp = False (0 atoms in 0 groups) tls = False (0 atoms in 0 groups) occupancies = True (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 { adp { individual { isotropic = element H anisotropic = not element H } } } main { number_of_macro_cycles = 5 max_number_of_iterations = 50 nproc = 20 } hydrogens { refine = individual *riding Auto } pdb_interpretation { c_beta_restraints = False } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } output { prefix = "4JP6_complete_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1213 occupancy sum: 1213.00 (% of total atoms 52.06) Rotatable: count: 210 occupancy sum: 210.00 (% of total atoms 9.01) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 1.00 - 36.75 A, n_refl.=61516 (all), 5.00 % free)------------| | | | r_work= 0.2209 r_free= 0.2041 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 3.866013 | | target function (ml) not normalized (work): 225929.779634 | | target function (ml) not normalized (free): 12181.011600 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 36.75 - 2.80 1.00 2864 151 0.2813 0.2913 6.2634 5.8034| | 2: 2.80 - 2.22 1.00 2753 145 0.2052 0.2060 5.1594 5.236| | 3: 2.22 - 1.94 1.00 2707 143 0.2074 0.1840 4.7506 4.811| | 4: 1.94 - 1.77 1.00 2674 140 0.2123 0.1787 4.4784 4.6213| | 5: 1.77 - 1.64 1.00 2683 142 0.2042 0.1734 4.1841 4.2248| | 6: 1.64 - 1.54 1.00 2655 139 0.2015 0.1615 3.978 4.066| | 7: 1.54 - 1.46 1.00 2659 140 0.2002 0.1985 3.8572 4.0293| | 8: 1.46 - 1.40 1.00 2656 140 0.2013 0.1721 3.7907 3.8712| | 9: 1.40 - 1.35 1.00 2648 139 0.2015 0.1939 3.6955 3.8888| | 10: 1.35 - 1.30 1.00 2646 140 0.2005 0.1765 3.6527 3.6975| | 11: 1.30 - 1.26 1.00 2601 136 0.2085 0.1785 3.6453 3.8636| | 12: 1.26 - 1.22 1.00 2669 141 0.2028 0.1896 3.6183 3.8174| | 13: 1.22 - 1.19 1.00 2621 138 0.2083 0.1888 3.5742 3.7703| | 14: 1.19 - 1.16 1.00 2636 139 0.2079 0.1664 3.5089 3.5181| | 15: 1.16 - 1.14 1.00 2638 138 0.2107 0.1834 3.4956 3.6483| | 16: 1.14 - 1.11 1.00 2615 138 0.2205 0.2049 3.4789 3.6457| | 17: 1.11 - 1.09 1.00 2634 139 0.1974 0.1686 3.3552 3.5268| | 18: 1.09 - 1.07 1.00 2603 137 0.2306 0.1810 3.4959 3.5105| | 19: 1.07 - 1.05 1.00 2633 138 0.2016 0.1702 3.273 3.4068| | 20: 1.05 - 1.03 1.00 2603 137 0.2101 0.1937 3.189 3.4037| | 21: 1.03 - 1.02 1.00 2631 139 0.2163 0.1813 3.1519 3.1789| | 22: 1.02 - 1.00 1.00 2611 137 0.2221 0.2163 3.1275 3.3002| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 36.75 - 2.80 2864 151 0.82 23.26 0.86 0.91 15908.25| | 2: 2.80 - 2.22 2753 145 0.83 23.92 1.11 0.96 7263.49| | 3: 2.22 - 1.94 2707 143 0.90 16.34 1.17 1.01 2349.09| | 4: 1.94 - 1.77 2674 140 0.90 16.27 1.18 1.03 1354.01| | 5: 1.77 - 1.64 2683 142 0.91 15.79 1.17 1.01 763.98| | 6: 1.64 - 1.54 2655 139 0.92 14.62 1.18 1.02 511.89| | 7: 1.54 - 1.46 2659 140 0.91 15.19 1.18 1.03 408.08| | 8: 1.46 - 1.40 2656 140 0.91 15.57 1.19 1.05 348.91| | 9: 1.40 - 1.35 2648 139 0.90 16.83 1.18 1.04 302.81| | 10: 1.35 - 1.30 2646 140 0.88 18.00 1.18 1.05 278.46| | 11: 1.30 - 1.26 2601 136 0.88 18.68 1.19 1.04 270.10| | 12: 1.26 - 1.22 2669 141 0.88 18.60 1.18 1.03 257.68| | 13: 1.22 - 1.19 2621 138 0.87 19.44 1.19 1.03 233.35| | 14: 1.19 - 1.16 2636 139 0.88 18.67 1.20 1.05 209.69| | 15: 1.16 - 1.14 2638 138 0.88 18.19 1.21 1.06 188.57| | 16: 1.14 - 1.11 2615 138 0.87 19.16 1.21 1.05 169.26| | 17: 1.11 - 1.09 2634 139 0.86 19.76 1.19 1.05 148.64| | 18: 1.09 - 1.07 2603 137 0.85 20.36 1.23 1.02 131.98| | 19: 1.07 - 1.05 2633 138 0.82 23.34 1.17 1.04 116.81| | 20: 1.05 - 1.03 2603 137 0.83 22.85 1.20 1.03 104.56| | 21: 1.03 - 1.02 2631 139 0.80 25.01 1.21 1.04 97.42| | 22: 1.02 - 1.00 2611 137 0.79 26.83 1.21 1.01 98.50| |alpha: min = 0.91 max = 1.06 mean = 1.02| |beta: min = 97.42 max = 15908.25 mean = 1502.73| |figures of merit: min = 0.00 max = 1.00 mean = 0.87| |phase err.(work): min = 0.00 max = 89.96 mean = 19.40| |phase err.(test): min = 0.00 max = 89.83 mean = 19.40| |-----------------------------------------------------------------------------| ----------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 : 0.022 0.140 989 Z= 1.369 Angle : 1.730 10.501 1344 Z= 1.097 Chirality : 0.137 0.494 137 Planarity : 0.015 0.094 174 Dihedral : 10.997 56.887 343 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.01 % Allowed : 0.00 % Favored : 98.99 % Cbeta Deviations : 2.73 % 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: -1.08 (0.67), residues: 119 helix: -2.12 (0.68), residues: 34 sheet: 0.44 (1.12), residues: 21 loop : -0.17 (0.68), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.006 ARG A 41 TYR 0.050 0.013 TYR A 28 PHE 0.064 0.018 PHE A 12 TRP 0.042 0.015 TRP A 32 HIS 0.023 0.009 HIS A 11 Individual atomic B min max mean iso aniso Overall: 4.37 144.35 12.47 5.67 0 1117 Protein: 4.37 129.96 10.32 5.67 0 962 Water: 6.77 144.35 25.80 N/A 0 155 Chain A: 4.37 144.35 12.47 N/A 0 1117 Histogram: Values Number of atoms 4.37 - 18.36 975 18.36 - 32.36 88 32.36 - 46.36 22 46.36 - 60.36 11 60.36 - 74.36 7 74.36 - 88.36 7 88.36 - 102.36 3 102.36 - 116.35 2 116.35 - 130.35 1 130.35 - 144.35 1 |-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 5 ************************* |--(resolution: 1.00 - 36.75 A, n_refl.=61516 (all), 5.00 % free)------------| | | | r_work= 0.2209 r_free= 0.2041 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 3.866013 | | target function (ml) not normalized (work): 225929.779634 | | target function (ml) not normalized (free): 12181.011600 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2200 0.2215 0.2046 n_refl.: 61516 re-set all scales: r(all,work,free)=0.2200 0.2215 0.2046 n_refl.: 61516 remove outliers: r(all,work,free)=0.2200 0.2215 0.2048 n_refl.: 61506 overall B=-0.01 to atoms: r(all,work,free)=0.2195 0.2210 0.2046 n_refl.: 61506 bulk-solvent and scaling: r(all,work,free)=0.1593 0.1581 0.1821 n_refl.: 61506 remove outliers: r(all,work,free)=0.1593 0.1581 0.1821 n_refl.: 61506 ======================== 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 36.755-9.175 99.01 95 5 0.2908 263.536 244.482 0.792 1.010 0.400 9.162-7.294 100.00 96 5 0.2321 280.454 266.972 0.972 1.010 0.416 7.286-5.810 100.00 171 9 0.2306 244.289 235.507 0.927 1.009 0.420 5.802-4.623 100.00 314 17 0.1783 307.724 295.563 0.954 1.010 0.420 4.620-3.682 100.00 633 33 0.1629 363.002 348.059 0.998 1.008 0.420 3.680-2.930 100.00 1220 65 0.1851 293.773 281.909 1.018 1.006 0.082 2.930-2.333 99.96 2355 124 0.1793 202.863 194.214 0.968 1.002 0.000 2.333-1.857 99.98 4602 242 0.1670 155.842 148.134 1.034 0.995 0.000 1.857-1.478 99.98 9002 473 0.1466 88.040 84.178 1.036 0.985 0.000 1.478-1.177 99.97 17663 930 0.1412 55.501 53.086 1.050 0.968 0.000 1.177-1.000 99.96 22280 1172 0.1438 37.102 35.705 1.066 0.947 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0369 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1582 r_free=0.1821 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1582 r_free=0.1821 ========================= Local real-space refinement ========================= Before: r_work=0.1582 r_free=0.1821 20 residues out of total 93 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 19 time to evaluate : 0.089 outliers start: 1 outliers final: 0 residues processed: 19 average time/residue: 2.0461 time to fit residues: 39.2866 After: r_work=0.1606 r_free=0.1849 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 17.410817 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 809.326674 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1857 0.2008 0.0151 0.002 0.5 3.8 0.0 0.0 0 0.125 0.1812 0.1981 0.0168 0.002 0.6 3.8 0.0 0.0 0 0.250 0.1760 0.1956 0.0196 0.002 0.6 3.8 0.0 0.0 0 0.500 0.1728 0.1951 0.0223 0.003 0.6 3.8 0.0 0.0 0 1.000 0.1691 0.1933 0.0243 0.003 0.7 3.2 0.0 0.0 0 2.000 0.1671 0.1927 0.0257 0.004 0.7 2.7 0.0 0.0 0 3.000 0.1657 0.1922 0.0265 0.005 0.8 2.1 0.0 0.0 0 4.000 0.1650 0.1925 0.0275 0.006 0.8 3.2 0.0 0.0 0 5.000 0.1643 0.1926 0.0282 0.006 0.9 3.2 0.0 0.0 0 6.000 0.1640 0.1929 0.0289 0.007 0.9 2.7 0.0 0.0 0 7.000 0.1633 0.1924 0.0291 0.008 0.9 3.2 0.0 0.0 0 8.000 0.1632 0.1929 0.0297 0.008 1.0 2.7 0.0 0.0 0 9.000 0.1628 0.1928 0.0300 0.009 1.0 2.7 0.0 0.0 0 10.000 0.1630 0.1922 0.0292 0.008 0.9 3.2 0.0 0.0 0 8.705 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1630 0.1922 0.0292 0.008 0.9 3.2 0.0 0.0 0 8.705 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.1630 r_free=0.1922 24 residues out of total 93 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.086 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0761 After: r_work=0.1630 r_free=0.1922 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 16.30 19.22 2.92 3.797 13.683 809.327 0.034 16.46 19.26 2.80 2.997 13.758 24.280 0.034 16.62 19.54 2.92 2.977 13.811 101.166 0.033 16.79 20.00 3.20 5.688 14.851 404.663 0.031 16.91 20.28 3.37 5.735 14.912 809.327 0.031 16.73 20.34 3.61 5.734 14.904 1213.990 0.031 16.48 20.06 3.58 4.976 14.690 1618.653 0.030 16.39 20.11 3.72 4.771 14.636 2023.317 0.030 16.31 20.06 3.76 4.774 14.614 2427.980 0.029 16.40 20.28 3.87 4.918 14.669 2832.643 0.029 16.39 20.36 3.97 4.964 14.669 3237.307 0.029 16.27 20.21 3.95 4.766 14.603 3641.970 0.029 16.19 20.10 3.91 4.673 14.564 4046.633 0.029 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 24.280 Accepted refinement result: 16.46 19.26 2.80 2.997 13.758 24.280 0.034 Individual atomic B min max mean iso aniso Overall: 4.25 144.30 12.61 4.29 0 1117 Protein: 4.25 124.94 10.47 4.29 0 962 Water: 6.78 144.30 25.86 N/A 0 155 Chain A: 4.25 144.30 12.61 N/A 0 1117 Histogram: Values Number of atoms 4.25 - 18.26 968 18.26 - 32.26 89 32.26 - 46.27 26 46.27 - 60.27 12 60.27 - 74.28 8 74.28 - 88.28 8 88.28 - 102.29 2 102.29 - 116.29 2 116.29 - 130.30 1 130.30 - 144.30 1 =========================== Idealize ADP of riding H ========================== r_work=0.1646 r_free=0.1926 r_work=0.1644 r_free=0.1922 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.00 - 36.75 A, n_refl.=61506 (all), 5.00 % free)------------| | | | r_work= 0.1644 r_free= 0.1922 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ls_wunit_k1) (work): 0.034083 | | target function (ls_wunit_k1) not normalized (work): 1991.478170 | | target function (ls_wunit_k1) not normalized (free): 161.249174 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1658 0.1644 0.1922 n_refl.: 61506 re-set all scales: r(all,work,free)=0.2244 0.2255 0.2155 n_refl.: 61506 remove outliers: r(all,work,free)=0.2244 0.2255 0.2155 n_refl.: 61506 overall B=-0.04 to atoms: r(all,work,free)=0.2231 0.2242 0.2150 n_refl.: 61506 bulk-solvent and scaling: r(all,work,free)=0.1657 0.1643 0.1926 n_refl.: 61506 remove outliers: r(all,work,free)=0.1657 0.1643 0.1925 n_refl.: 61505 ======================== 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 36.755-9.175 99.01 95 5 0.2648 233.783 218.945 0.777 1.008 0.400 9.162-7.294 100.00 96 5 0.2070 248.790 242.725 0.957 1.008 0.414 7.286-5.810 100.00 171 9 0.2176 216.709 211.794 0.908 1.008 0.411 5.802-4.623 100.00 314 17 0.1620 272.982 265.506 0.922 1.008 0.400 4.620-3.682 100.00 633 33 0.1356 322.019 312.174 0.960 1.006 0.400 3.680-2.930 100.00 1220 65 0.1618 260.606 253.196 0.996 1.004 0.092 2.930-2.333 99.96 2355 124 0.1665 179.960 173.763 0.944 1.001 0.000 2.333-1.857 99.98 4602 242 0.1635 138.247 131.510 1.003 0.994 0.000 1.857-1.478 99.98 9002 473 0.1610 78.100 74.256 0.995 0.985 0.000 1.478-1.177 99.97 17663 930 0.1625 49.235 46.764 1.017 0.970 0.000 1.177-1.000 99.95 22280 1171 0.1711 32.910 31.576 1.047 0.950 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1395 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1644 r_free=0.1925 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 83 GLN A 116 GLN Total number of N/Q/H flips: 3 r_work=0.1645 r_free=0.1929 ========================= Local real-space refinement ========================= Before: r_work=0.1645 r_free=0.1929 32 residues out of total 93 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.083 outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 1.3122 time to fit residues: 42.6743 After: r_work=0.1659 r_free=0.1918 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 17.831061 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 529.709888 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1966 0.2160 0.0194 0.002 0.5 2.7 0.0 0.0 0 0.125 0.1892 0.2105 0.0213 0.002 0.5 2.7 0.0 0.0 0 0.250 0.1834 0.2067 0.0233 0.002 0.5 2.1 0.0 0.0 0 0.500 0.1757 0.2005 0.0247 0.002 0.6 2.7 0.0 0.0 0 1.000 0.1709 0.1962 0.0254 0.003 0.6 2.7 0.0 0.0 0 2.000 0.1685 0.1945 0.0260 0.004 0.7 2.7 0.0 0.0 0 3.000 0.1669 0.1931 0.0262 0.005 0.7 2.7 0.0 0.0 0 4.000 0.1659 0.1926 0.0266 0.005 0.8 2.7 0.0 0.0 0 5.000 0.1652 0.1922 0.0270 0.006 0.8 2.7 0.0 0.0 0 6.000 0.1645 0.1919 0.0273 0.007 0.9 2.7 0.0 0.0 0 7.000 0.1642 0.1918 0.0276 0.007 0.9 2.7 0.0 0.0 0 8.000 0.1638 0.1917 0.0279 0.008 0.9 2.7 0.0 0.0 0 9.000 0.1634 0.1915 0.0281 0.008 1.0 2.7 0.0 0.0 0 10.000 0.1638 0.1916 0.0278 0.008 0.9 2.1 0.0 0.0 0 8.916 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1634 0.1915 0.0281 0.008 1.0 2.7 0.0 0.0 0 10.000 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.1634 r_free=0.1915 28 residues out of total 93 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.118 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1437 After: r_work=0.1634 r_free=0.1915 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 16.34 19.15 2.81 4.244 15.313 529.710 0.033 16.34 19.15 2.81 4.244 15.313 15.891 0.033 16.43 19.31 2.87 3.959 15.404 66.214 0.033 16.45 19.64 3.19 4.090 15.350 264.855 0.032 17.06 20.74 3.69 5.430 16.556 529.710 0.031 17.11 21.11 3.99 5.242 16.510 794.565 0.031 16.81 20.99 4.18 4.462 16.085 1059.420 0.030 16.64 20.89 4.25 4.399 15.963 1324.275 0.030 16.72 20.92 4.20 4.681 16.163 1589.130 0.030 16.51 20.59 4.08 4.761 16.230 1853.985 0.029 16.53 20.58 4.05 5.065 16.386 2118.840 0.029 16.46 20.50 4.05 4.964 16.330 2383.694 0.029 16.32 20.32 4.00 4.855 16.265 2648.549 0.029 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 15.891 Accepted refinement result: 16.34 19.15 2.81 4.244 15.313 15.891 0.033 Individual atomic B min max mean iso aniso Overall: 4.21 144.26 12.57 4.29 0 1117 Protein: 4.21 124.87 10.44 4.29 0 962 Water: 6.74 144.26 25.82 N/A 0 155 Chain A: 4.21 144.26 12.57 N/A 0 1117 Histogram: Values Number of atoms 4.21 - 18.22 968 18.22 - 32.22 89 32.22 - 46.23 26 46.23 - 60.23 12 60.23 - 74.24 8 74.24 - 88.24 8 88.24 - 102.25 2 102.25 - 116.25 2 116.25 - 130.26 1 130.26 - 144.26 1 =========================== Idealize ADP of riding H ========================== r_work=0.1634 r_free=0.1915 r_work=0.1634 r_free=0.1915 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.00 - 36.75 A, n_refl.=61505 (all), 5.00 % free)------------| | | | r_work= 0.1634 r_free= 0.1915 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.033392 | | target function (ls_wunit_k1) not normalized (work): 1951.150318 | | target function (ls_wunit_k1) not normalized (free): 160.034129 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1648 0.1634 0.1915 n_refl.: 61505 re-set all scales: r(all,work,free)=0.2226 0.2238 0.2137 n_refl.: 61505 remove outliers: r(all,work,free)=0.2226 0.2238 0.2137 n_refl.: 61505 overall B=-0.03 to atoms: r(all,work,free)=0.2216 0.2227 0.2133 n_refl.: 61505 bulk-solvent and scaling: r(all,work,free)=0.1649 0.1635 0.1918 n_refl.: 61505 remove outliers: r(all,work,free)=0.1649 0.1634 0.1918 n_refl.: 61504 ======================== 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 36.755-9.175 99.01 95 5 0.2662 233.783 218.922 0.779 1.009 0.400 9.162-7.294 100.00 96 5 0.1975 248.790 244.080 0.954 1.009 0.410 7.286-5.810 100.00 171 9 0.2173 216.709 211.453 0.912 1.008 0.410 5.802-4.623 100.00 314 17 0.1548 272.982 266.393 0.924 1.008 0.410 4.620-3.682 100.00 633 33 0.1332 322.019 312.542 0.956 1.006 0.380 3.680-2.930 100.00 1220 65 0.1606 260.606 253.333 0.997 1.004 0.082 2.930-2.333 99.96 2355 124 0.1652 179.960 173.950 0.943 1.001 0.000 2.333-1.857 99.98 4602 242 0.1624 138.247 131.509 1.002 0.994 0.000 1.857-1.478 99.98 9002 473 0.1602 78.100 74.289 0.992 0.985 0.000 1.478-1.177 99.97 17663 930 0.1622 49.235 46.779 1.014 0.969 0.000 1.177-1.000 99.95 22279 1171 0.1715 32.907 31.567 1.041 0.949 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1078 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1635 r_free=0.1918 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 GLN Total number of N/Q/H flips: 1 r_work=0.1635 r_free=0.1920 ========================= Local real-space refinement ========================= Before: r_work=0.1635 r_free=0.1920 29 residues out of total 93 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.149 outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 2.3860 time to fit residues: 70.1090 After: r_work=0.1646 r_free=0.1905 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.570935 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 17.734063 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1703 0.1926 0.0224 0.002 0.6 2.1 0.0 0.0 0 0.079 0.1652 0.1867 0.0214 0.003 0.7 2.7 0.0 0.0 0 0.236 0.1635 0.1854 0.0219 0.004 0.8 3.2 0.0 0.0 0 0.471 0.1625 0.1848 0.0223 0.005 0.8 3.2 0.0 0.0 0 0.707 0.1621 0.1846 0.0225 0.006 0.9 3.2 0.0 0.0 0 0.943 0.1618 0.1845 0.0227 0.006 0.9 3.2 0.0 0.0 0 1.178 0.1615 0.1844 0.0229 0.007 1.0 3.2 0.0 0.0 0 1.414 0.1615 0.1844 0.0229 0.008 1.0 3.2 0.0 0.0 0 1.649 0.1625 0.1846 0.0222 0.005 0.9 3.2 0.0 0.0 0 0.785 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1615 0.1844 0.0229 0.008 1.0 3.2 0.0 0.0 0 1.649 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.1615 r_free=0.1844 27 residues out of total 93 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.090 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1051 After: r_work=0.1615 r_free=0.1844 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 16.15 18.44 2.29 4.240 15.278 17.734 3.789 16.16 18.44 2.29 4.218 15.278 0.532 3.790 16.15 18.44 2.29 4.161 15.280 2.217 3.788 16.00 18.33 2.33 4.116 15.305 8.867 3.765 16.00 18.39 2.39 4.138 15.326 17.734 3.761 16.07 18.52 2.45 4.137 15.369 26.601 3.758 16.00 18.49 2.48 4.150 15.371 35.468 3.754 16.03 18.53 2.50 4.132 15.414 44.335 3.757 15.94 18.47 2.53 4.143 15.399 53.202 3.759 15.91 18.46 2.55 4.146 15.403 62.069 3.759 15.92 18.47 2.55 4.145 15.415 70.936 3.759 15.92 18.49 2.57 4.147 15.427 79.803 3.759 15.90 18.47 2.57 4.152 15.427 88.670 3.758 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 8.867 Accepted refinement result: 16.00 18.33 2.33 4.116 15.305 8.867 3.765 Individual atomic B min max mean iso aniso Overall: 3.95 144.22 12.60 3.89 0 1117 Protein: 3.95 120.82 10.47 3.89 0 962 Water: 6.78 144.22 25.78 N/A 0 155 Chain A: 3.95 144.22 12.60 N/A 0 1117 Histogram: Values Number of atoms 3.95 - 17.97 962 17.97 - 32.00 93 32.00 - 46.03 28 46.03 - 60.06 12 60.06 - 74.09 8 74.09 - 88.11 8 88.11 - 102.14 3 102.14 - 116.17 1 116.17 - 130.20 1 130.20 - 144.22 1 =========================== Idealize ADP of riding H ========================== r_work=0.1600 r_free=0.1833 r_work=0.1600 r_free=0.1833 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.00 - 36.75 A, n_refl.=61504 (all), 5.00 % free)------------| | | | r_work= 0.1600 r_free= 0.1833 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 3.765181 | | target function (ml) not normalized (work): 219999.498672 | | target function (ml) not normalized (free): 11907.361300 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1612 0.1600 0.1833 n_refl.: 61504 re-set all scales: r(all,work,free)=0.2277 0.2293 0.2097 n_refl.: 61504 remove outliers: r(all,work,free)=0.2277 0.2293 0.2097 n_refl.: 61504 overall B=-0.03 to atoms: r(all,work,free)=0.2266 0.2282 0.2092 n_refl.: 61504 bulk-solvent and scaling: r(all,work,free)=0.1604 0.1592 0.1828 n_refl.: 61504 remove outliers: r(all,work,free)=0.1604 0.1592 0.1828 n_refl.: 61503 ======================== 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 36.755-9.175 99.01 95 5 0.2910 233.783 215.652 0.739 1.010 0.390 9.162-7.294 100.00 96 5 0.2274 248.790 239.089 0.935 1.010 0.427 7.286-5.810 100.00 171 9 0.2365 216.709 207.629 0.894 1.010 0.440 5.802-4.623 100.00 314 17 0.1763 272.982 262.097 0.911 1.011 0.440 4.620-3.682 100.00 633 33 0.1554 322.019 309.513 0.944 1.008 0.423 3.680-2.930 100.00 1220 65 0.1851 260.606 250.072 0.978 1.006 0.073 2.930-2.333 99.96 2355 124 0.1808 179.960 172.347 0.932 1.001 0.000 2.333-1.857 99.98 4602 242 0.1697 138.247 131.286 1.000 0.993 0.000 1.857-1.478 99.98 9002 473 0.1502 78.100 74.628 1.001 0.981 0.000 1.478-1.177 99.97 17663 930 0.1436 49.235 47.050 1.028 0.961 0.000 1.177-1.000 99.94 22278 1171 0.1425 32.905 31.629 1.053 0.937 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1017 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1593 r_free=0.1829 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 GLN Total number of N/Q/H flips: 1 r_work=0.1592 r_free=0.1830 ========================= Local real-space refinement ========================= Before: r_work=0.1592 r_free=0.1830 29 residues out of total 93 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.086 outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 1.9798 time to fit residues: 58.2035 After: r_work=0.1601 r_free=0.1844 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.468448 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 17.649712 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1671 0.1883 0.0211 0.002 0.6 2.1 0.0 0.0 0 0.073 0.1628 0.1844 0.0216 0.003 0.7 2.1 0.0 0.0 0 0.220 0.1612 0.1836 0.0224 0.004 0.8 2.1 0.0 0.0 0 0.441 0.1603 0.1831 0.0228 0.005 0.9 2.1 0.0 0.0 0 0.661 0.1598 0.1830 0.0232 0.006 0.9 2.7 0.0 0.0 0 0.881 0.1595 0.1828 0.0234 0.007 0.9 3.2 0.0 0.0 0 1.101 0.1592 0.1828 0.0236 0.007 1.0 3.8 0.0 0.0 0 1.322 0.1590 0.1828 0.0238 0.008 1.0 3.8 0.0 0.0 0 1.542 0.1602 0.1831 0.0229 0.005 0.9 2.1 0.0 0.0 0 0.734 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1592 0.1828 0.0236 0.007 1.0 3.8 0.0 0.0 0 1.322 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.1592 r_free=0.1828 31 residues out of total 93 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.161 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1152 After: r_work=0.1592 r_free=0.1828 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 15.92 18.28 2.36 4.055 15.290 17.650 3.758 15.92 18.28 2.36 4.055 15.290 0.529 3.758 15.96 18.32 2.36 4.002 15.289 2.206 3.761 15.91 18.32 2.42 3.975 15.299 8.825 3.758 15.80 18.28 2.48 3.968 15.334 17.650 3.749 15.89 18.40 2.51 3.945 15.416 26.475 3.745 15.88 18.38 2.50 3.964 15.418 35.299 3.743 15.86 18.35 2.49 3.961 15.436 44.124 3.747 15.82 18.32 2.50 3.967 15.435 52.949 3.748 15.77 18.30 2.53 3.964 15.434 61.774 3.751 15.73 18.29 2.56 3.972 15.429 70.599 3.749 15.74 18.31 2.57 3.979 15.444 79.424 3.749 15.68 18.27 2.59 3.984 15.436 88.249 3.745 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 88.249 Accepted refinement result: 15.68 18.27 2.59 3.984 15.436 88.249 3.745 Individual atomic B min max mean iso aniso Overall: 4.45 144.09 12.87 3.67 0 1117 Protein: 4.45 116.71 10.77 3.67 0 962 Water: 7.24 144.09 25.93 N/A 0 155 Chain A: 4.45 144.09 12.87 N/A 0 1117 Histogram: Values Number of atoms 4.45 - 18.41 973 18.41 - 32.38 85 32.38 - 46.34 25 46.34 - 60.30 14 60.30 - 74.27 8 74.27 - 88.23 6 88.23 - 102.20 3 102.20 - 116.16 1 116.16 - 130.12 1 130.12 - 144.09 1 =========================== Idealize ADP of riding H ========================== r_work=0.1569 r_free=0.1827 r_work=0.1568 r_free=0.1826 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.00 - 36.75 A, n_refl.=61503 (all), 5.00 % free)------------| | | | r_work= 0.1568 r_free= 0.1826 coordinate error (max.-lik. estimate): 0.04 A | | | | normalized target function (ml) (work): 3.746013 | | target function (ml) not normalized (work): 218875.819755 | | target function (ml) not normalized (free): 11920.175286 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1581 0.1568 0.1826 n_refl.: 61503 re-set all scales: r(all,work,free)=0.2352 0.2369 0.2147 n_refl.: 61503 remove outliers: r(all,work,free)=0.2352 0.2369 0.2147 n_refl.: 61503 overall B=-0.12 to atoms: r(all,work,free)=0.2304 0.2320 0.2121 n_refl.: 61503 bulk-solvent and scaling: r(all,work,free)=0.1579 0.1566 0.1830 n_refl.: 61503 remove outliers: r(all,work,free)=0.1579 0.1566 0.1830 n_refl.: 61503 ======================== 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 36.755-9.175 99.01 95 5 0.2885 233.783 216.615 0.755 1.012 0.400 9.162-7.294 100.00 96 5 0.2327 248.790 238.870 0.934 1.012 0.427 7.286-5.810 100.00 171 9 0.2377 216.709 208.200 0.884 1.012 0.429 5.802-4.623 100.00 314 17 0.1790 272.982 262.268 0.908 1.012 0.423 4.620-3.682 100.00 633 33 0.1556 322.019 310.030 0.940 1.009 0.411 3.680-2.930 100.00 1220 65 0.1836 260.606 250.509 0.978 1.007 0.078 2.930-2.333 99.96 2355 124 0.1800 179.960 172.577 0.934 1.001 0.000 2.333-1.857 99.98 4602 242 0.1656 138.247 131.555 1.010 0.993 0.000 1.857-1.478 99.98 9002 473 0.1455 78.100 74.792 1.017 0.979 0.000 1.478-1.177 99.97 17663 930 0.1394 49.235 47.102 1.054 0.957 0.000 1.177-1.000 99.94 22278 1171 0.1417 32.905 31.627 1.091 0.929 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.2722 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1568 r_free=0.1830 After: r_work=0.1569 r_free=0.1829 ================================== NQH flips ================================== r_work=0.1569 r_free=0.1829 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 GLN Total number of N/Q/H flips: 1 r_work=0.1568 r_free=0.1832 ========================= Local real-space refinement ========================= Before: r_work=0.1568 r_free=0.1832 23 residues out of total 93 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.162 outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 2.7473 time to fit residues: 63.9417 After: r_work=0.1572 r_free=0.1836 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.572248 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.210874 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1631 0.1878 0.0248 0.003 0.7 3.8 0.0 0.0 0 0.079 0.1601 0.1853 0.0252 0.004 0.8 4.3 0.0 0.0 0 0.236 0.1591 0.1847 0.0256 0.004 0.8 3.8 0.0 0.0 0 0.472 0.1582 0.1842 0.0260 0.005 0.9 3.8 0.0 0.0 0 0.708 0.1578 0.1842 0.0263 0.007 0.9 3.8 0.0 0.0 0 0.943 0.1573 0.1837 0.0264 0.008 1.0 3.8 0.0 0.0 0 1.179 0.1568 0.1835 0.0266 0.008 1.0 3.8 0.0 0.0 0 1.415 0.1566 0.1834 0.0268 0.009 1.0 3.8 0.0 0.0 0 1.651 0.1581 0.1842 0.0261 0.006 0.9 3.8 0.0 0.0 0 0.786 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1566 0.1834 0.0268 0.009 1.0 3.8 0.0 0.0 0 1.651 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.1566 r_free=0.1834 23 residues out of total 93 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.163 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1395 After: r_work=0.1566 r_free=0.1834 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 15.67 18.35 2.68 3.965 15.508 14.211 3.752 15.67 18.33 2.66 3.941 15.507 0.426 3.752 15.69 18.28 2.59 3.899 15.507 1.776 3.750 15.67 18.27 2.61 3.910 15.495 7.105 3.746 15.59 18.22 2.63 3.914 15.506 14.211 3.738 15.60 18.22 2.62 3.909 15.522 21.316 3.735 15.58 18.21 2.63 3.917 15.529 28.422 3.732 15.57 18.22 2.65 3.919 15.533 35.527 3.732 15.57 18.22 2.65 3.919 15.537 42.633 3.731 15.60 18.24 2.64 3.910 15.552 49.738 3.731 15.59 18.23 2.65 3.912 15.553 56.843 3.731 15.59 18.24 2.65 3.912 15.557 63.949 3.731 15.60 18.24 2.64 3.906 15.565 71.054 3.732 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 28.422 Accepted refinement result: 15.58 18.21 2.63 3.917 15.529 28.422 3.732 Individual atomic B min max mean iso aniso Overall: 4.48 143.96 12.80 3.50 0 1117 Protein: 4.48 113.22 10.70 3.50 0 962 Water: 7.21 143.96 25.82 N/A 0 155 Chain A: 4.48 143.96 12.80 N/A 0 1117 Histogram: Values Number of atoms 4.48 - 18.43 974 18.43 - 32.38 84 32.38 - 46.33 25 46.33 - 60.27 14 60.27 - 74.22 7 74.22 - 88.17 7 88.17 - 102.12 3 102.12 - 116.06 2 116.06 - 130.01 0 130.01 - 143.96 1 =========================== Idealize ADP of riding H ========================== r_work=0.1558 r_free=0.1821 r_work=0.1558 r_free=0.1821 ----------X-ray data---------- |--(resolution: 1.00 - 36.75 A, n_refl.=61503 (all), 5.00 % free)------------| | | | r_work= 0.1558 r_free= 0.1821 coordinate error (max.-lik. estimate): 0.06 A | | | | normalized target function (ml) (work): 3.732467 | | target function (ml) not normalized (work): 218084.297816 | | target function (ml) not normalized (free): 11893.405053 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 36.75 - 2.80 1.00 2864 151 0.1828 0.2165 5.4678 5.5287| | 2: 2.80 - 2.22 1.00 2753 145 0.1818 0.2071 5.0461 5.1554| | 3: 2.22 - 1.94 1.00 2707 143 0.1594 0.1733 4.7285 4.7877| | 4: 1.94 - 1.77 1.00 2674 140 0.1584 0.1818 4.4575 4.5982| | 5: 1.77 - 1.64 1.00 2683 142 0.1546 0.1746 4.1717 4.201| | 6: 1.64 - 1.54 1.00 2655 139 0.1404 0.1596 3.9475 4.0499| | 7: 1.54 - 1.46 1.00 2659 140 0.1371 0.1668 3.8144 3.9174| | 8: 1.46 - 1.40 1.00 2656 140 0.1367 0.1611 3.7152 3.8474| | 9: 1.40 - 1.35 1.00 2648 139 0.1405 0.1711 3.6428 3.8078| | 10: 1.35 - 1.30 1.00 2646 140 0.1381 0.1569 3.5728 3.639| | 11: 1.30 - 1.26 1.00 2600 136 0.1381 0.1672 3.5499 3.8078| | 12: 1.26 - 1.22 1.00 2667 141 0.1370 0.1738 3.4945 3.6792| | 13: 1.22 - 1.19 1.00 2621 138 0.1354 0.1687 3.4512 3.6022| | 14: 1.19 - 1.16 1.00 2636 139 0.1375 0.1561 3.4132 3.4479| | 15: 1.16 - 1.14 1.00 2638 138 0.1375 0.1544 3.3711 3.4543| | 16: 1.14 - 1.11 1.00 2615 138 0.1440 0.1992 3.3329 3.6323| | 17: 1.11 - 1.09 1.00 2632 139 0.1257 0.1514 3.2217 3.3908| | 18: 1.09 - 1.07 1.00 2603 137 0.1510 0.1510 3.3514 3.4042| | 19: 1.07 - 1.05 1.00 2633 137 0.1334 0.1662 3.0863 3.3051| | 20: 1.05 - 1.03 1.00 2602 136 0.1303 0.1690 3.0325 3.2518| | 21: 1.03 - 1.02 1.00 2629 139 0.1333 0.1677 2.9828 3.1208| | 22: 1.02 - 1.00 1.00 2608 137 0.1435 0.1887 2.9785 3.211| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 36.75 - 2.80 2864 151 0.90 15.23 0.99 1.04 7491.19| | 2: 2.80 - 2.22 2753 145 0.89 17.99 0.99 1.02 4330.19| | 3: 2.22 - 1.94 2707 143 0.91 15.76 1.00 1.03 2210.43| | 4: 1.94 - 1.77 2674 140 0.90 16.23 1.01 1.05 1314.66| | 5: 1.77 - 1.64 2683 142 0.91 15.81 1.01 1.03 738.36| | 6: 1.64 - 1.54 2655 139 0.92 14.34 1.00 1.03 480.83| | 7: 1.54 - 1.46 2659 140 0.92 14.32 1.00 1.05 364.50| | 8: 1.46 - 1.40 2656 140 0.91 15.21 1.05 1.08 312.86| | 9: 1.40 - 1.35 2648 139 0.90 16.17 1.03 1.08 273.83| | 10: 1.35 - 1.30 2646 140 0.89 17.23 1.02 1.06 244.16| | 11: 1.30 - 1.26 2600 136 0.89 17.60 1.01 1.04 226.88| | 12: 1.26 - 1.22 2667 141 0.89 17.18 0.99 1.03 208.32| | 13: 1.22 - 1.19 2621 138 0.88 17.62 0.99 1.02 184.46| | 14: 1.19 - 1.16 2636 139 0.89 17.24 1.03 1.06 169.39| | 15: 1.16 - 1.14 2638 138 0.89 17.16 1.06 1.09 155.23| | 16: 1.14 - 1.11 2615 138 0.88 18.39 1.06 1.08 144.41| | 17: 1.11 - 1.09 2632 139 0.86 19.11 1.03 1.07 127.55| | 18: 1.09 - 1.07 2603 137 0.86 19.70 1.05 1.03 112.38| | 19: 1.07 - 1.05 2633 137 0.83 22.61 0.99 1.03 99.20| | 20: 1.05 - 1.03 2602 136 0.83 22.42 0.99 1.01 88.94| | 21: 1.03 - 1.02 2629 139 0.80 24.71 0.99 1.00 84.29| | 22: 1.02 - 1.00 2608 137 0.79 26.29 0.98 0.98 84.62| |alpha: min = 0.98 max = 1.09 mean = 1.04| |beta: min = 84.29 max = 7491.19 mean = 919.57| |figures of merit: min = 0.00 max = 1.00 mean = 0.88| |phase err.(work): min = 0.00 max = 89.97 mean = 18.08| |phase err.(test): min = 0.00 max = 89.80 mean = 18.12| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1571 0.1558 0.1821 n_refl.: 61503 re-set all scales: r(all,work,free)=0.2369 0.2386 0.2166 n_refl.: 61503 remove outliers: r(all,work,free)=0.2369 0.2386 0.2166 n_refl.: 61503 overall B=-0.10 to atoms: r(all,work,free)=0.2327 0.2343 0.2142 n_refl.: 61503 bulk-solvent and scaling: r(all,work,free)=0.1568 0.1555 0.1823 n_refl.: 61503 remove outliers: r(all,work,free)=0.1568 0.1555 0.1823 n_refl.: 61503 ======================== 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 36.755-9.175 99.01 95 5 0.2970 233.783 214.293 0.748 1.009 0.400 9.162-7.294 100.00 96 5 0.2312 248.790 240.977 0.944 1.010 0.430 7.286-5.810 100.00 171 9 0.2408 216.709 209.430 0.896 1.009 0.430 5.802-4.623 100.00 314 17 0.1812 272.982 263.328 0.917 1.010 0.430 4.620-3.682 100.00 633 33 0.1540 322.019 310.562 0.945 1.007 0.421 3.680-2.930 100.00 1220 65 0.1830 260.606 251.166 0.986 1.005 0.082 2.930-2.333 99.96 2355 124 0.1802 179.960 172.353 0.938 1.000 0.000 2.333-1.857 99.98 4602 242 0.1659 138.247 131.160 1.012 0.992 0.000 1.857-1.478 99.98 9002 473 0.1462 78.100 74.469 1.019 0.980 0.000 1.478-1.177 99.97 17663 930 0.1374 49.235 47.105 1.062 0.959 0.000 1.177-1.000 99.94 22278 1171 0.1368 32.905 31.854 1.107 0.934 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-0.3697 ================= 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) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2209 0.2041 0.022 1.730 4.4 144.4 12.5 465 0.000 1_bss: 0.1582 0.1821 0.022 1.730 4.4 144.3 12.5 465 0.000 1_settarget: 0.1582 0.1821 0.022 1.730 4.4 144.3 12.5 465 0.000 1_nqh: 0.1582 0.1821 0.022 1.730 4.4 144.3 12.5 465 0.000 1_realsrl: 0.1606 0.1849 0.022 1.730 4.4 144.3 12.5 465 0.077 1_weight: 0.1606 0.1849 0.022 1.730 4.4 144.3 12.5 465 0.077 1_xyzrec: 0.1630 0.1922 0.008 0.948 4.4 144.3 12.5 465 0.176 1_realsrl2: 0.1630 0.1922 0.008 0.948 4.4 144.3 12.5 465 0.176 1_adp: 0.1646 0.1926 0.008 0.948 4.3 144.3 12.6 465 0.176 1_regHadp: 0.1644 0.1922 0.008 0.948 4.3 144.3 12.6 465 0.176 2_bss: 0.1644 0.1925 0.008 0.948 4.2 144.3 12.6 465 0.176 2_settarget: 0.1644 0.1925 0.008 0.948 4.2 144.3 12.6 465 0.176 2_updatecdl: 0.1644 0.1925 0.008 0.955 4.2 144.3 12.6 465 0.176 2_nqh: 0.1645 0.1929 0.008 0.955 4.2 144.3 12.6 465 0.184 2_realsrl: 0.1659 0.1918 0.008 0.955 4.2 144.3 12.6 465 0.199 2_weight: 0.1659 0.1918 0.008 0.955 4.2 144.3 12.6 465 0.199 2_xyzrec: 0.1634 0.1915 0.008 0.967 4.2 144.3 12.6 465 0.203 2_realsrl2: 0.1634 0.1915 0.008 0.967 4.2 144.3 12.6 465 0.203 2_adp: 0.1634 0.1915 0.008 0.967 4.2 144.3 12.6 465 0.203 2_regHadp: 0.1634 0.1915 0.008 0.967 4.2 144.3 12.6 465 0.203 3_bss: 0.1635 0.1918 0.008 0.967 4.2 144.2 12.5 465 0.203 3_settarget: 0.1635 0.1918 0.008 0.967 4.2 144.2 12.5 465 0.203 3_updatecdl: 0.1635 0.1918 0.008 0.969 4.2 144.2 12.5 465 0.203 3_nqh: 0.1635 0.1920 0.008 0.969 4.2 144.2 12.5 465 0.208 3_realsrl: 0.1646 0.1905 0.008 0.969 4.2 144.2 12.5 465 0.209 3_weight: 0.1646 0.1905 0.008 0.969 4.2 144.2 12.5 465 0.209 3_xyzrec: 0.1615 0.1844 0.008 1.006 4.2 144.2 12.5 465 0.181 3_realsrl2: 0.1615 0.1844 0.008 1.006 4.2 144.2 12.5 465 0.181 3_adp: 0.1600 0.1833 0.008 1.006 3.9 144.2 12.6 465 0.181 3_regHadp: 0.1600 0.1833 0.008 1.006 3.9 144.2 12.6 465 0.181 4_bss: 0.1593 0.1829 0.008 1.006 3.9 144.2 12.6 465 0.181 4_settarget: 0.1593 0.1829 0.008 1.006 3.9 144.2 12.6 465 0.181 4_updatecdl: 0.1593 0.1829 0.008 1.009 3.9 144.2 12.6 465 0.181 4_nqh: 0.1592 0.1830 0.008 1.009 3.9 144.2 12.6 465 0.179 4_realsrl: 0.1601 0.1844 0.008 1.009 3.9 144.2 12.6 465 0.192 4_weight: 0.1601 0.1844 0.008 1.009 3.9 144.2 12.6 465 0.192 4_xyzrec: 0.1592 0.1828 0.007 0.982 3.9 144.2 12.6 465 0.186 4_realsrl2: 0.1592 0.1828 0.007 0.982 3.9 144.2 12.6 465 0.186 4_adp: 0.1569 0.1827 0.007 0.982 4.4 144.1 12.9 465 0.186 4_regHadp: 0.1568 0.1826 0.007 0.982 4.4 144.1 12.9 465 0.186 5_bss: 0.1568 0.1830 0.007 0.982 4.3 144.0 12.8 465 0.186 5_settarget: 0.1568 0.1830 0.007 0.982 4.3 144.0 12.8 465 0.186 5_updatecdl: 0.1568 0.1830 0.007 0.981 4.3 144.0 12.8 465 0.186 5_setrh: 0.1569 0.1829 0.007 0.981 4.3 144.0 12.8 465 0.185 5_nqh: 0.1568 0.1832 0.007 0.981 4.3 144.0 12.8 465 0.180 5_realsrl: 0.1572 0.1836 0.007 0.981 4.3 144.0 12.8 465 0.189 5_weight: 0.1572 0.1836 0.007 0.981 4.3 144.0 12.8 465 0.189 5_xyzrec: 0.1566 0.1834 0.009 1.043 4.3 144.0 12.8 465 0.188 5_realsrl2: 0.1566 0.1834 0.009 1.043 4.3 144.0 12.8 465 0.188 5_adp: 0.1558 0.1821 0.009 1.043 4.5 144.0 12.8 465 0.188 5_regHadp: 0.1558 0.1821 0.009 1.043 4.5 144.0 12.8 465 0.188 end: 0.1556 0.1823 0.009 1.043 4.4 143.9 12.7 465 0.188 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/highres/finalised/4JP6_complete_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/highres/finalised/4JP6_complete_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 1.4700 Refinement macro-cycles (run) : 1071.0200 Write final files (write_after_run_outputs) : 36.2700 Total : 1108.7600 Total CPU time: 18.71 minutes =========================== phenix.refine: finished =========================== # Date 2024-04-10 Time 16:26:08 PDT -0700 (1712791568.95 s) Start R-work = 0.1582, R-free = 0.1821 Final R-work = 0.1556, R-free = 0.1823 =============================================================================== Job complete usr+sys time: 1182.47 seconds wall clock time: 27 minutes 51.09 seconds (1671.09 seconds total)