Starting phenix.refine on Wed Apr 10 15:59:19 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, 4R5R_complete.pdb Found miller_array, 4R5R.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 { model { file = "4R5R_complete.pdb" } default_model = "4R5R_complete.pdb" miller_array { file = "4R5R.mtz" } default_miller_array = "4R5R.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 { 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: 2768 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 988 Classifications: {'peptide': 68} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 61} Chain: "B" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 988 Classifications: {'peptide': 68} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 61} Chain: "A" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 417 Classifications: {'water': 139} Link IDs: {None: 138} Chain: "B" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 375 Classifications: {'water': 125} Link IDs: {None: 124} Time building chain proxies: 0.55, per 1000 atoms: 0.20 Number of scatterers: 2768 At special positions: 0 Unit cell: (18.083, 79.986, 39.497, 90, 91.3, 90) Space group: P 1 21 1 (No. 4) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 26 16.00 O1- 14 9.00 O 450 8.00 N 196 7.00 C 598 6.00 H 1484 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 4 " - pdb=" SG CYS A 19 " distance=2.04 Simple disulfide: pdb=" SG CYS A 6 " - pdb=" SG CYS A 14 " distance=2.05 Simple disulfide: pdb=" SG CYS A 13 " - pdb=" SG CYS A 36 " distance=2.02 Simple disulfide: pdb=" SG CYS A 27 " - pdb=" SG CYS A 33 " distance=2.06 Simple disulfide: pdb=" SG CYS A 32 " - pdb=" SG CYS A 57 " distance=2.04 Simple disulfide: pdb=" SG CYS A 45 " - pdb=" SG CYS A 64 " distance=2.03 Simple disulfide: pdb=" SG CYS B 4 " - pdb=" SG CYS B 19 " distance=2.04 Simple disulfide: pdb=" SG CYS B 6 " - pdb=" SG CYS B 14 " distance=2.05 Simple disulfide: pdb=" SG CYS B 13 " - pdb=" SG CYS B 36 " distance=2.03 Simple disulfide: pdb=" SG CYS B 27 " - pdb=" SG CYS B 33 " distance=2.06 Simple disulfide: pdb=" SG CYS B 32 " - pdb=" SG CYS B 57 " distance=2.05 Simple disulfide: pdb=" SG CYS B 45 " - pdb=" SG CYS B 64 " distance=2.01 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: 1.17 Conformation dependent library (CDL) restraints added in 62.8 milliseconds Time building geometry restraints manager: 1.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.85 - 1.05: 784 1.05 - 1.25: 847 1.25 - 1.45: 331 1.45 - 1.65: 530 1.65 - 1.85: 28 Bond restraints: 2520 Sorted by residual: bond pdb=" N ILE A 47 " pdb=" H ILE A 47 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.44e+01 bond pdb=" N HIS B 68 " pdb=" H HIS B 68 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.44e+01 bond pdb=" NE2 GLN A 60 " pdb="HE22 GLN A 60 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.44e+01 bond pdb=" N CYS A 19 " pdb=" H CYS A 19 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.44e+01 bond pdb=" N GLU A 3 " pdb=" H GLU A 3 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.44e+01 ... (remaining 2515 not shown) Histogram of bond angle deviations from ideal: 92.15 - 100.12: 4 100.12 - 108.09: 802 108.09 - 116.06: 2102 116.06 - 124.03: 804 124.03 - 132.00: 164 Bond angle restraints: 3876 Sorted by residual: angle pdb=" O GLY B 28 " pdb=" C GLY B 28 " pdb=" N GLU B 29 " ideal model delta sigma weight residual 122.70 112.58 10.12 1.30e+00 5.92e-01 6.06e+01 angle pdb=" CD LYS B 37 " pdb=" CE LYS B 37 " pdb=" NZ LYS B 37 " ideal model delta sigma weight residual 111.90 92.15 19.75 3.20e+00 9.77e-02 3.81e+01 angle pdb=" CD ARG A 49 " pdb=" NE ARG A 49 " pdb=" CZ ARG A 49 " ideal model delta sigma weight residual 124.40 132.00 -7.60 1.40e+00 5.10e-01 2.95e+01 angle pdb=" OE1 GLU A 3 " pdb=" CD GLU A 3 " pdb=" OE2 GLU A 3 " ideal model delta sigma weight residual 122.90 111.94 10.96 2.40e+00 1.74e-01 2.09e+01 angle pdb=" CA ALA A 17 " pdb=" C ALA A 17 " pdb=" O ALA A 17 " ideal model delta sigma weight residual 119.97 115.63 4.34 1.15e+00 7.56e-01 1.43e+01 ... (remaining 3871 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.14: 630 15.14 - 30.29: 66 30.29 - 45.43: 23 45.43 - 60.57: 10 60.57 - 75.72: 1 Dihedral angle restraints: 730 sinusoidal: 570 harmonic: 160 Sorted by residual: dihedral pdb=" CA GLU B 29 " pdb=" C GLU B 29 " pdb=" N GLY B 30 " pdb=" CA GLY B 30 " ideal model delta harmonic sigma weight residual 180.00 164.53 15.47 0 5.00e+00 4.00e-02 9.57e+00 dihedral pdb=" CB LYS B 37 " pdb=" CG LYS B 37 " pdb=" CD LYS B 37 " pdb=" CE LYS B 37 " ideal model delta sinusoidal sigma weight residual -180.00 -122.26 -57.74 3 1.50e+01 4.44e-03 9.45e+00 dihedral pdb=" CA ARG B 66 " pdb=" CB ARG B 66 " pdb=" CG ARG B 66 " pdb=" CD ARG B 66 " ideal model delta sinusoidal sigma weight residual -60.00 -117.34 57.34 3 1.50e+01 4.44e-03 9.44e+00 ... (remaining 727 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 81 0.099 - 0.199: 33 0.199 - 0.298: 18 0.298 - 0.397: 3 0.397 - 0.497: 3 Chirality restraints: 138 Sorted by residual: chirality pdb=" CA ARG A 42 " pdb=" N ARG A 42 " pdb=" C ARG A 42 " pdb=" CB ARG A 42 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.17e+00 chirality pdb=" CA ARG B 42 " pdb=" N ARG B 42 " pdb=" C ARG B 42 " pdb=" CB ARG B 42 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.83e+00 chirality pdb=" CA CYS A 19 " pdb=" N CYS A 19 " pdb=" C CYS A 19 " pdb=" CB CYS A 19 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.07e+00 ... (remaining 135 not shown) Planarity restraints: 316 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 67 " -0.063 2.00e-02 2.50e+03 5.20e-02 8.11e+01 pdb=" CG TYR B 67 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR B 67 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR B 67 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR B 67 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR B 67 " 0.028 2.00e-02 2.50e+03 pdb=" CZ TYR B 67 " -0.032 2.00e-02 2.50e+03 pdb=" OH TYR B 67 " -0.116 2.00e-02 2.50e+03 pdb=" HD1 TYR B 67 " 0.015 2.00e-02 2.50e+03 pdb=" HD2 TYR B 67 " -0.030 2.00e-02 2.50e+03 pdb=" HE1 TYR B 67 " 0.049 2.00e-02 2.50e+03 pdb=" HE2 TYR B 67 " 0.095 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 67 " 0.073 2.00e-02 2.50e+03 3.84e-02 4.42e+01 pdb=" CG TYR A 67 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR A 67 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR A 67 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR A 67 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR A 67 " -0.012 2.00e-02 2.50e+03 pdb=" CZ TYR A 67 " 0.021 2.00e-02 2.50e+03 pdb=" OH TYR A 67 " 0.074 2.00e-02 2.50e+03 pdb=" HD1 TYR A 67 " -0.040 2.00e-02 2.50e+03 pdb=" HD2 TYR A 67 " -0.037 2.00e-02 2.50e+03 pdb=" HE1 TYR A 67 " -0.031 2.00e-02 2.50e+03 pdb=" HE2 TYR A 67 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 38 " 0.069 2.00e-02 2.50e+03 3.20e-02 3.07e+01 pdb=" CG PHE A 38 " -0.002 2.00e-02 2.50e+03 pdb=" CD1 PHE A 38 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE A 38 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE A 38 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 38 " -0.011 2.00e-02 2.50e+03 pdb=" CZ PHE A 38 " 0.017 2.00e-02 2.50e+03 pdb=" HD1 PHE A 38 " -0.048 2.00e-02 2.50e+03 pdb=" HD2 PHE A 38 " -0.013 2.00e-02 2.50e+03 pdb=" HE1 PHE A 38 " -0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE A 38 " -0.035 2.00e-02 2.50e+03 pdb=" HZ PHE A 38 " 0.054 2.00e-02 2.50e+03 ... (remaining 313 not shown) Histogram of nonbonded interaction distances: 1.09 - 1.80: 37 1.80 - 2.50: 2632 2.50 - 3.20: 10058 3.20 - 3.90: 15431 3.90 - 4.60: 23755 Nonbonded interactions: 51913 Sorted by model distance: nonbonded pdb=" HZ3 LYS A 39 " pdb="HE22 GLN A 60 " model vdw sym.op. 1.094 2.100 x+1,y,z nonbonded pdb=" HG3 ARG B 49 " pdb=" HD3 ARG B 66 " model vdw sym.op. 1.196 2.440 x-1,y,z nonbonded pdb=" H GLY A 24 " pdb=" O HOH A 188 " model vdw sym.op. 1.441 1.850 x-1,y,z nonbonded pdb="HH12 ARG A 49 " pdb=" O HOH A 221 " model vdw sym.op. 1.456 1.850 -x+2,y+1/2,-z+1 nonbonded pdb=" HE2 LYS B 41 " pdb=" O HOH B 210 " model vdw 1.506 2.620 ... (remaining 51908 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: 6 Type Number sf(0) Gaussians S 26 15.96 2 O1- 14 8.97 3 O 450 7.97 2 N 196 6.98 3 C 598 5.99 3 H 1484 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 = 2768 n_use_u_iso = 1484 n_use_u_aniso = 1284 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 = 2768 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (2768 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 1484 aniso = 1284) group_adp = False (0 atoms in 0 groups) tls = False (0 atoms in 0 groups) occupancies = True (3 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 = "4R5R_complete_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1484 occupancy sum: 1484.00 (% of total atoms 53.64) Rotatable: count: 152 occupancy sum: 152.00 (% of total atoms 5.49) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 0.96 - 28.10 A, n_refl.=67502 (all), 5.06 % free)------------| | | | r_work= 0.2086 r_free= 0.2093 coordinate error (max.-lik. estimate): 0.18 A | | | | normalized target function (ml) (work): 2.492769 | | target function (ml) not normalized (work): 159754.087446 | | target function (ml) not normalized (free): 8585.813845 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 28.10 - 2.77 0.98 2689 159 0.2283 0.2180 5.8615 5.6449| | 2: 2.77 - 2.20 1.00 2691 148 0.1743 0.1779 4.8868 4.9157| | 3: 2.20 - 1.92 1.00 2721 158 0.1753 0.1861 4.2533 4.3097| | 4: 1.92 - 1.74 1.00 2683 146 0.1757 0.1822 3.8528 3.8945| | 5: 1.74 - 1.62 1.00 2698 147 0.1808 0.1836 3.4982 3.5606| | 6: 1.62 - 1.52 1.00 2720 119 0.1869 0.2096 3.2987 3.3209| | 7: 1.52 - 1.45 1.00 2720 159 0.1967 0.2059 3.1025 3.0974| | 8: 1.45 - 1.38 1.00 2649 139 0.2077 0.1988 2.9166 2.8867| | 9: 1.38 - 1.33 1.00 2712 155 0.2207 0.2400 2.7296 2.8171| | 10: 1.33 - 1.29 1.00 2650 151 0.2368 0.2563 2.573 2.5688| | 11: 1.29 - 1.25 1.00 2742 140 0.2456 0.2656 2.4736 2.4176| | 12: 1.25 - 1.21 1.00 2620 152 0.2546 0.2530 2.3448 2.3882| | 13: 1.21 - 1.18 1.00 2742 126 0.2718 0.2572 2.2468 2.1716| | 14: 1.18 - 1.15 1.00 2682 141 0.2823 0.2824 2.1305 2.1102| | 15: 1.15 - 1.12 1.00 2685 126 0.2964 0.3403 1.9991 2.1431| | 16: 1.12 - 1.10 1.00 2684 152 0.3139 0.2906 1.8701 1.8166| | 17: 1.10 - 1.08 1.00 2657 153 0.3297 0.3317 1.7109 1.7554| | 18: 1.08 - 1.06 0.99 2674 152 0.3489 0.3382 1.5521 1.5158| | 19: 1.06 - 1.04 0.99 2676 134 0.3752 0.3299 1.3913 1.3034| | 20: 1.04 - 1.02 0.99 2651 122 0.3936 0.2917 1.285 1.146| | 21: 1.02 - 1.00 0.98 2631 127 0.4039 0.3979 1.1024 1.0146| | 22: 1.00 - 0.99 0.98 2666 152 0.4317 0.3612 0.94947 0.8816| | 23: 0.99 - 0.97 0.96 2618 137 0.4261 0.4549 0.79968 0.85353| | 24: 0.97 - 0.96 0.92 2426 120 0.4248 0.3857 0.65819 0.51936| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 28.10 - 2.77 2689 159 0.83 24.05 0.97 1.39 11888.63| | 2: 2.77 - 2.20 2691 148 0.79 28.17 1.06 1.43 4693.13| | 3: 2.20 - 1.92 2721 158 0.89 17.72 1.08 1.46 822.39| | 4: 1.92 - 1.74 2683 146 0.89 18.36 1.05 1.46 371.68| | 5: 1.74 - 1.62 2698 147 0.87 19.89 1.03 1.42 188.67| | 6: 1.62 - 1.52 2720 119 0.88 19.79 1.02 1.39 121.40| | 7: 1.52 - 1.45 2720 159 0.87 20.41 1.01 1.39 79.38| | 8: 1.45 - 1.38 2649 139 0.86 21.93 0.99 1.37 55.09| | 9: 1.38 - 1.33 2712 155 0.84 23.72 0.98 1.32 39.53| | 10: 1.33 - 1.29 2650 151 0.81 26.43 0.97 1.28 29.87| | 11: 1.29 - 1.25 2742 140 0.81 26.26 0.95 1.26 23.16| | 12: 1.25 - 1.21 2620 152 0.80 27.59 0.94 1.26 18.81| | 13: 1.21 - 1.18 2742 126 0.79 28.35 0.93 1.25 15.34| | 14: 1.18 - 1.15 2682 141 0.77 30.34 0.91 1.22 12.31| | 15: 1.15 - 1.12 2685 126 0.75 31.82 0.89 1.17 9.74| | 16: 1.12 - 1.10 2684 152 0.74 32.63 0.86 1.13 7.44| | 17: 1.10 - 1.08 2657 153 0.72 34.23 0.83 1.09 5.48| | 18: 1.08 - 1.06 2674 152 0.71 35.14 0.81 1.09 3.91| | 19: 1.06 - 1.04 2676 134 0.71 35.39 0.77 1.11 2.73| | 20: 1.04 - 1.02 2651 122 0.72 34.93 0.76 1.09 1.96| | 21: 1.02 - 1.00 2631 127 0.69 37.37 0.74 1.04 1.54| | 22: 1.00 - 0.99 2666 152 0.68 38.10 0.71 0.97 1.17| | 23: 0.99 - 0.97 2618 137 0.66 39.61 0.72 0.94 0.92| | 24: 0.97 - 0.96 2426 120 0.66 39.95 0.71 0.94 0.67| |alpha: min = 0.94 max = 1.46 mean = 1.23| |beta: min = 0.67 max = 11888.63 mean = 772.43| |figures of merit: min = 0.00 max = 1.00 mean = 0.78| |phase err.(work): min = 0.00 max = 89.93 mean = 28.75| |phase err.(test): min = 0.00 max = 89.51 mean = 28.85| |-----------------------------------------------------------------------------| ----------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 : 0.026 0.229 1036 Z= 1.769 Angle : 1.917 19.753 1386 Z= 1.103 Chirality : 0.146 0.497 138 Planarity : 0.015 0.053 194 Dihedral : 13.304 75.717 422 Min Nonbonded Distance : 1.670 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.72 % Allowed : 4.31 % Favored : 93.97 % Cbeta Deviations : 3.23 % 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: -0.22 (0.67), residues: 132 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.16 (0.51), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.004 ARG B 66 TYR 0.074 0.033 TYR B 67 PHE 0.035 0.015 PHE A 38 HIS 0.017 0.010 HIS A 68 Individual atomic B min max mean iso aniso Overall: 14.27 107.98 23.02 2.28 0 1284 Protein: 14.27 51.36 20.30 2.28 0 1020 Water: 15.72 107.98 33.55 N/A 0 264 Chain A: 14.27 107.98 22.37 N/A 0 649 Chain B: 14.71 98.52 23.68 N/A 0 635 Histogram: Values Number of atoms 14.27 - 23.64 901 23.64 - 33.01 221 33.01 - 42.38 109 42.38 - 51.75 38 51.75 - 61.13 7 61.13 - 70.50 2 70.50 - 79.87 2 79.87 - 89.24 1 89.24 - 98.61 1 98.61 - 107.98 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 0.96 - 28.10 A, n_refl.=67502 (all), 5.06 % free)------------| | | | r_work= 0.2086 r_free= 0.2093 coordinate error (max.-lik. estimate): 0.18 A | | | | normalized target function (ml) (work): 2.492769 | | target function (ml) not normalized (work): 159754.087446 | | target function (ml) not normalized (free): 8585.813845 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2085 0.2086 0.2093 n_refl.: 67502 re-set all scales: r(all,work,free)=0.2085 0.2086 0.2093 n_refl.: 67502 remove outliers: r(all,work,free)=0.2041 0.2038 0.2093 n_refl.: 67499 overall B=0.24 to atoms: r(all,work,free)=0.2045 0.2042 0.2094 n_refl.: 67499 bulk-solvent and scaling: r(all,work,free)=0.1416 0.1410 0.1533 n_refl.: 67499 remove outliers: r(all,work,free)=0.1415 0.1408 0.1533 n_refl.: 67498 ======================== 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 19.997-8.097 82.91 94 3 0.2357 151.035 141.600 0.930 1.000 0.380 8.032-6.584 99.01 94 6 0.2008 162.881 158.714 0.935 1.001 0.390 6.581-5.402 99.44 164 12 0.2308 163.391 155.646 0.931 1.001 0.389 5.392-4.419 97.13 292 13 0.1673 202.991 198.985 0.970 1.002 0.389 4.418-3.621 97.21 520 38 0.1514 217.431 213.966 1.005 1.004 0.289 3.620-2.967 99.34 1005 52 0.1507 172.494 171.022 0.992 1.005 0.139 2.967-2.431 100.00 1801 115 0.1596 106.834 105.057 0.961 1.008 0.000 2.430-1.992 100.00 3268 160 0.1407 73.608 72.202 0.977 1.015 0.000 1.992-1.632 100.00 5917 343 0.1279 35.582 35.239 0.975 1.023 0.000 1.632-1.337 99.89 10815 573 0.1039 15.388 15.292 0.963 1.040 0.000 1.337-1.096 99.72 19512 1023 0.1054 5.483 5.452 0.947 1.073 0.000 1.096-0.960 97.49 20601 1077 0.1393 1.576 1.566 0.887 1.122 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.2390 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1408 r_free=0.1533 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 GLN Total number of N/Q/H flips: 1 r_work=0.1409 r_free=0.1535 ========================= Local real-space refinement ========================= Before: r_work=0.1409 r_free=0.1535 27 residues out of total 92 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 24 time to evaluate : 0.094 revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 25 average time/residue: 2.5771 time to fit residues: 64.9408 After: r_work=0.1468 r_free=0.1582 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 16.312923 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 688.927423 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 0.1638 0.1763 0.0125 0.003 0.6 2.5 0.0 0.9 0 0.125 0.1606 0.1751 0.0145 0.003 0.6 2.5 0.0 0.9 0 0.250 0.1571 0.1751 0.0180 0.003 0.6 3.0 0.0 0.9 0 0.500 0.1545 0.1782 0.0237 0.003 0.7 3.0 0.0 0.9 0 1.000 0.1517 0.1812 0.0295 0.004 0.7 3.0 0.0 0.9 0 2.000 0.1510 0.1841 0.0331 0.006 0.8 3.0 0.0 0.9 0 3.000 0.1492 0.1839 0.0347 0.006 0.8 3.0 0.0 0.9 0 4.000 0.1491 0.1858 0.0367 0.007 0.9 3.0 0.0 0.9 0 5.000 0.1479 0.1845 0.0366 0.008 0.9 3.0 0.0 0.9 0 6.000 0.1474 0.1848 0.0374 0.009 0.9 3.0 0.0 0.9 0 7.000 0.1463 0.1841 0.0377 0.010 1.0 3.5 0.0 0.9 0 8.000 0.1461 0.1844 0.0383 0.011 1.0 4.0 0.0 0.9 0 9.000 0.1452 0.1834 0.0382 0.011 1.1 3.5 0.0 1.7 0 10.000 0.1465 0.1845 0.0380 0.010 1.0 3.5 0.0 0.9 0 8.156 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1606 0.1751 0.0145 0.003 0.6 2.5 0.0 0.9 0 0.250 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.1606 r_free=0.1751 24 residues out of total 92 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 23 time to evaluate : 0.099 outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.8474 time to fit residues: 0.9454 After: r_work=0.1606 r_free=0.1752 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 16.06 17.52 1.46 1.460 24.625 688.927 0.033 16.07 17.50 1.43 1.323 24.625 20.668 0.033 17.49 20.92 3.43 2.867 25.124 86.116 0.026 16.48 21.56 5.08 7.346 26.698 344.464 0.021 16.20 21.62 5.42 8.731 27.212 688.927 0.020 16.10 21.68 5.58 9.313 27.364 1033.391 0.019 16.11 22.11 6.01 8.950 27.353 1377.855 0.018 16.04 22.22 6.18 8.656 27.277 1722.319 0.018 16.06 22.40 6.34 9.345 27.524 2066.782 0.018 16.11 22.76 6.65 9.189 27.495 2411.246 0.018 16.08 22.93 6.85 9.563 27.617 2755.710 0.018 16.20 23.07 6.87 10.164 27.834 3100.173 0.018 15.94 22.53 6.60 10.324 27.766 3444.637 0.017 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 20.668 Accepted refinement result: 16.07 17.50 1.43 1.323 24.625 20.668 0.033 Individual atomic B min max mean iso aniso Overall: 14.52 108.22 23.27 2.04 0 1284 Protein: 14.52 51.22 20.54 2.04 0 1020 Water: 15.94 108.22 33.80 N/A 0 264 Chain A: 14.52 108.22 22.62 N/A 0 649 Chain B: 15.05 98.76 23.93 N/A 0 635 Histogram: Values Number of atoms 14.52 - 23.89 900 23.89 - 33.26 226 33.26 - 42.63 105 42.63 - 52.00 38 52.00 - 61.37 7 61.37 - 70.74 2 70.74 - 80.11 2 80.11 - 89.48 1 89.48 - 98.85 1 98.85 - 108.22 2 =========================== Idealize ADP of riding H ========================== r_work=0.1607 r_free=0.1750 r_work=0.1597 r_free=0.1742 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1597 r_free = 0.1742 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1590 r_free = 0.1745 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 0.96 - 20.00 A, n_refl.=67498 (all), 5.06 % free)------------| | | | r_work= 0.1590 r_free= 0.1745 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.032050 | | target function (ls_wunit_k1) not normalized (work): 2053.872105 | | target function (ls_wunit_k1) not normalized (free): 124.375380 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1598 0.1590 0.1745 n_refl.: 67498 re-set all scales: r(all,work,free)=0.2170 0.2165 0.2267 n_refl.: 67498 remove outliers: r(all,work,free)=0.2170 0.2165 0.2267 n_refl.: 67498 overall B=0.16 to atoms: r(all,work,free)=0.2175 0.2170 0.2269 n_refl.: 67498 bulk-solvent and scaling: r(all,work,free)=0.1598 0.1589 0.1749 n_refl.: 67498 remove outliers: r(all,work,free)=0.1598 0.1589 0.1749 n_refl.: 67498 ======================== 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 19.997-8.097 82.91 94 3 0.2185 151.035 143.577 0.884 1.001 0.370 8.032-6.584 99.01 94 6 0.2031 162.881 157.923 0.895 1.002 0.380 6.581-5.402 99.44 164 12 0.2049 163.391 159.591 0.898 1.003 0.380 5.392-4.419 97.13 292 13 0.1647 202.991 199.944 0.902 1.005 0.349 4.418-3.621 97.21 520 38 0.1512 217.431 214.188 0.957 1.008 0.319 3.620-2.967 99.34 1005 52 0.1521 172.494 171.003 0.947 1.011 0.130 2.967-2.431 100.00 1801 115 0.1653 106.834 105.051 0.920 1.018 0.000 2.430-1.992 100.00 3268 160 0.1572 73.608 72.058 0.936 1.030 0.000 1.992-1.632 100.00 5917 343 0.1575 35.582 35.094 0.922 1.046 0.000 1.632-1.337 99.89 10815 573 0.1471 15.388 15.199 0.903 1.075 0.000 1.337-1.096 99.72 19512 1023 0.1558 5.483 5.410 0.882 1.127 0.000 1.096-0.960 97.49 20601 1077 0.1834 1.576 1.548 0.827 1.200 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=0.0690 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1589 r_free=0.1749 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 GLN Total number of N/Q/H flips: 1 r_work=0.1589 r_free=0.1749 ========================= Local real-space refinement ========================= Before: r_work=0.1589 r_free=0.1749 25 residues out of total 92 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.177 outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 5.0502 time to fit residues: 127.1888 After: r_work=0.1591 r_free=0.1749 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 16.654433 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 582.758060 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 0.1682 0.1832 0.0149 0.002 0.5 2.5 0.0 0.0 0 0.125 0.1628 0.1798 0.0170 0.002 0.5 2.0 0.0 0.0 0 0.250 0.1572 0.1780 0.0208 0.003 0.6 1.5 0.0 0.0 0 0.500 0.1529 0.1778 0.0250 0.003 0.6 2.0 0.0 0.0 0 1.000 0.1522 0.1847 0.0326 0.004 0.7 4.0 0.0 0.0 0 2.000 0.1499 0.1846 0.0346 0.005 0.7 5.1 0.0 0.0 0 3.000 0.1484 0.1845 0.0361 0.006 0.8 5.1 0.0 0.0 0 4.000 0.1470 0.1840 0.0370 0.006 0.9 4.6 0.0 0.0 0 5.000 0.1462 0.1837 0.0375 0.007 0.9 4.6 0.0 0.0 0 6.000 0.1459 0.1847 0.0388 0.008 1.0 5.6 0.0 0.0 0 7.000 0.1450 0.1842 0.0392 0.009 1.0 4.6 0.0 0.0 0 8.000 0.1451 0.1853 0.0402 0.010 1.0 4.6 0.0 0.0 0 9.000 0.1447 0.1854 0.0407 0.010 1.1 4.6 0.0 0.0 0 10.000 0.1448 0.1841 0.0394 0.009 1.0 4.6 0.0 0.0 0 8.327 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1529 0.1778 0.0250 0.003 0.6 2.0 0.0 0.0 0 1.000 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.1529 r_free=0.1778 27 residues out of total 92 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.266 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1688 After: r_work=0.1529 r_free=0.1778 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 15.29 17.78 2.50 4.486 27.542 582.758 0.027 15.29 17.78 2.50 4.486 27.542 17.483 0.027 16.29 20.61 4.32 4.249 28.086 72.845 0.022 15.25 20.60 5.35 4.963 29.129 291.379 0.018 14.94 20.79 5.85 5.984 29.698 582.758 0.016 14.75 21.02 6.27 5.799 29.681 874.137 0.016 14.69 21.26 6.58 5.661 29.707 1165.516 0.015 14.64 21.28 6.63 6.118 29.863 1456.895 0.015 14.68 21.69 7.01 6.147 29.918 1748.274 0.015 14.70 21.85 7.15 6.421 30.032 2039.653 0.015 14.65 21.76 7.11 6.465 30.037 2331.032 0.014 14.59 21.73 7.14 6.238 29.956 2622.411 0.014 14.52 21.63 7.11 6.116 29.890 2913.790 0.014 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 17.483 Accepted refinement result: 15.29 17.78 2.50 4.486 27.542 17.483 0.027 Individual atomic B min max mean iso aniso Overall: 14.68 108.38 23.43 2.04 0 1284 Protein: 14.68 51.38 20.70 2.04 0 1020 Water: 16.09 108.38 33.96 N/A 0 264 Chain A: 14.68 108.38 22.78 N/A 0 649 Chain B: 15.21 98.92 24.09 N/A 0 635 Histogram: Values Number of atoms 14.68 - 24.05 900 24.05 - 33.42 226 33.42 - 42.79 105 42.79 - 52.16 38 52.16 - 61.53 7 61.53 - 70.90 2 70.90 - 80.27 2 80.27 - 89.64 1 89.64 - 99.01 1 99.01 - 108.38 2 =========================== Idealize ADP of riding H ========================== r_work=0.1529 r_free=0.1778 r_work=0.1529 r_free=0.1778 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1529 r_free = 0.1778 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1529 r_free = 0.1779 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 0.96 - 20.00 A, n_refl.=67498 (all), 5.06 % free)------------| | | | r_work= 0.1529 r_free= 0.1779 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.027076 | | target function (ls_wunit_k1) not normalized (work): 1735.083262 | | target function (ls_wunit_k1) not normalized (free): 126.455886 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1542 0.1529 0.1779 n_refl.: 67498 re-set all scales: r(all,work,free)=0.2119 0.2109 0.2293 n_refl.: 67498 remove outliers: r(all,work,free)=0.2119 0.2109 0.2293 n_refl.: 67498 overall B=0.08 to atoms: r(all,work,free)=0.2121 0.2112 0.2296 n_refl.: 67498 bulk-solvent and scaling: r(all,work,free)=0.1546 0.1533 0.1771 n_refl.: 67498 remove outliers: r(all,work,free)=0.1546 0.1533 0.1771 n_refl.: 67498 ======================== 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 19.997-8.097 82.91 94 3 0.1997 131.207 126.129 0.934 0.918 0.360 8.032-6.584 99.01 94 6 0.1836 141.497 138.023 0.977 0.920 0.390 6.581-5.402 99.44 164 12 0.1791 141.941 140.841 0.978 0.921 0.390 5.392-4.419 97.13 292 13 0.1495 176.342 174.212 0.973 0.923 0.360 4.418-3.621 97.21 520 38 0.1299 188.886 187.078 1.032 0.926 0.310 3.620-2.967 99.34 1005 52 0.1334 149.848 148.806 1.023 0.928 0.130 2.967-2.431 100.00 1801 115 0.1587 92.808 91.528 0.989 0.935 0.000 2.430-1.992 100.00 3268 160 0.1519 63.944 62.741 1.015 0.944 0.000 1.992-1.632 100.00 5917 343 0.1588 30.910 30.471 1.001 0.957 0.000 1.632-1.337 99.89 10815 573 0.1526 13.368 13.154 0.986 0.975 0.000 1.337-1.096 99.72 19512 1023 0.1661 4.763 4.677 0.985 1.005 0.000 1.096-0.960 97.49 20601 1077 0.1973 1.369 1.333 0.953 1.041 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=0.1073 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1533 r_free=0.1771 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1533 r_free=0.1771 ========================= Local real-space refinement ========================= Before: r_work=0.1533 r_free=0.1771 28 residues out of total 92 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.100 outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 4.0621 time to fit residues: 114.5242 After: r_work=0.1537 r_free=0.1793 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.730917 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 10.532212 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 0.1490 0.1649 0.0159 0.003 0.7 3.5 0.0 0.0 0 0.087 0.1454 0.1610 0.0156 0.004 0.8 3.5 0.0 0.0 0 0.260 0.1443 0.1603 0.0160 0.005 0.9 2.0 0.0 0.0 0 0.519 0.1440 0.1606 0.0167 0.006 1.0 2.0 0.0 0.0 0 0.779 0.1434 0.1602 0.0168 0.007 1.0 2.5 0.0 0.0 0 1.039 0.1432 0.1602 0.0170 0.008 1.1 2.5 0.0 0.0 0 1.298 0.1429 0.1597 0.0168 0.009 1.1 2.5 0.0 0.0 0 1.558 0.1427 0.1599 0.0172 0.010 1.1 2.5 0.0 0.0 0 1.817 0.1435 0.1605 0.0170 0.007 1.0 2.0 0.0 0.0 0 0.865 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1429 0.1597 0.0168 0.009 1.1 2.5 0.0 0.0 0 1.558 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.1429 r_free=0.1597 23 residues out of total 92 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.097 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0834 After: r_work=0.1429 r_free=0.1597 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 14.29 15.97 1.68 4.508 27.642 10.532 1.418 14.29 15.97 1.68 4.507 27.642 0.316 1.418 14.32 15.97 1.65 4.498 27.641 1.317 1.413 14.43 15.99 1.56 4.509 27.629 5.266 1.398 14.41 16.00 1.60 4.543 27.604 10.532 1.385 14.39 16.01 1.62 4.551 27.603 15.798 1.377 14.35 15.99 1.64 4.553 27.604 21.064 1.372 14.34 15.97 1.63 4.561 27.601 26.331 1.368 14.32 15.97 1.65 4.559 27.605 31.597 1.366 14.30 15.97 1.67 4.556 27.610 36.863 1.364 14.28 15.97 1.68 4.554 27.613 42.129 1.363 14.27 15.96 1.69 4.552 27.616 47.395 1.362 14.26 15.96 1.70 4.549 27.618 52.661 1.361 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 47.395 Accepted refinement result: 14.27 15.96 1.69 4.552 27.616 47.395 1.362 Individual atomic B min max mean iso aniso Overall: 14.83 108.38 23.45 1.95 0 1284 Protein: 14.83 50.06 20.71 1.95 0 1020 Water: 16.23 108.38 34.07 N/A 0 264 Chain A: 14.83 108.38 22.80 N/A 0 649 Chain B: 15.34 98.94 24.11 N/A 0 635 Histogram: Values Number of atoms 14.83 - 24.19 911 24.19 - 33.54 220 33.54 - 42.90 101 42.90 - 52.25 37 52.25 - 61.61 7 61.61 - 70.96 2 70.96 - 80.32 2 80.32 - 89.67 1 89.67 - 99.02 1 99.02 - 108.38 2 =========================== Idealize ADP of riding H ========================== r_work=0.1427 r_free=0.1596 r_work=0.1427 r_free=0.1595 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1427 r_free = 0.1595 target_work(ml) = 1.362 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1427 r_free = 0.1595 target_work(ml) = 1.362 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 0.96 - 20.00 A, n_refl.=67498 (all), 5.06 % free)------------| | | | r_work= 0.1427 r_free= 0.1595 coordinate error (max.-lik. estimate): 0.06 A | | | | normalized target function (ml) (work): 1.361621 | | target function (ml) not normalized (work): 87256.729154 | | target function (ml) not normalized (free): 5122.752978 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1436 0.1427 0.1595 n_refl.: 67498 re-set all scales: r(all,work,free)=0.2095 0.2091 0.2181 n_refl.: 67498 remove outliers: r(all,work,free)=0.2095 0.2091 0.2181 n_refl.: 67498 overall B=-0.02 to atoms: r(all,work,free)=0.2094 0.2090 0.2181 n_refl.: 67498 bulk-solvent and scaling: r(all,work,free)=0.1436 0.1426 0.1609 n_refl.: 67498 remove outliers: r(all,work,free)=0.1436 0.1426 0.1609 n_refl.: 67498 ======================== 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 19.997-8.097 82.91 94 3 0.2322 131.207 123.965 0.871 1.000 0.370 8.032-6.584 99.01 94 6 0.1915 141.497 137.203 0.906 1.001 0.374 6.581-5.402 99.44 164 12 0.2090 141.941 138.660 0.905 1.001 0.373 5.392-4.419 97.13 292 13 0.1652 176.342 173.386 0.910 1.003 0.367 4.418-3.621 97.21 520 38 0.1517 188.886 185.916 0.960 1.005 0.300 3.620-2.967 99.34 1005 52 0.1485 149.848 148.197 0.948 1.006 0.064 2.967-2.431 100.00 1801 115 0.1634 92.808 91.199 0.926 1.010 0.000 2.430-1.992 100.00 3268 160 0.1436 63.944 62.672 0.950 1.018 0.000 1.992-1.632 100.00 5917 343 0.1336 30.910 30.620 0.948 1.029 0.000 1.632-1.337 99.89 10815 573 0.1095 13.368 13.287 0.937 1.049 0.000 1.337-1.096 99.72 19512 1023 0.1100 4.763 4.744 0.938 1.088 0.000 1.096-0.960 97.49 20601 1077 0.1273 1.369 1.368 0.890 1.145 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-0.0578 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1426 r_free=0.1609 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 GLN Total number of N/Q/H flips: 1 r_work=0.1427 r_free=0.1611 ========================= Local real-space refinement ========================= Before: r_work=0.1427 r_free=0.1611 24 residues out of total 92 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.102 outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 4.2258 time to fit residues: 102.1925 After: r_work=0.1432 r_free=0.1626 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.509112 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 8.037405 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 0.1476 0.1637 0.0161 0.003 0.7 3.0 0.0 0.0 0 0.075 0.1455 0.1625 0.0170 0.004 0.8 2.0 0.0 0.0 0 0.226 0.1443 0.1610 0.0167 0.006 1.0 2.5 0.0 0.0 0 0.453 0.1437 0.1607 0.0170 0.007 1.1 2.5 0.0 0.0 0 0.679 0.1435 0.1607 0.0172 0.008 1.1 3.0 0.0 0.0 0 0.905 0.1431 0.1608 0.0177 0.009 1.2 3.0 0.0 0.0 0 1.132 0.1431 0.1607 0.0176 0.010 1.2 3.0 0.0 0.0 0 1.358 0.1428 0.1608 0.0179 0.011 1.2 3.0 0.0 0.0 0 1.585 0.1436 0.1607 0.0171 0.007 1.1 3.0 0.0 0.0 0 0.755 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1435 0.1607 0.0172 0.008 1.1 3.0 0.0 0.0 0 0.905 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.1435 r_free=0.1607 25 residues out of total 92 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.187 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0891 After: r_work=0.1435 r_free=0.1607 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 14.35 16.07 1.72 4.495 27.579 8.037 1.335 14.35 16.07 1.72 4.495 27.579 0.241 1.335 14.36 16.07 1.71 4.493 27.579 1.005 1.334 14.36 16.05 1.69 4.492 27.578 4.019 1.330 14.36 16.04 1.68 4.494 27.576 8.037 1.325 14.35 16.03 1.68 4.497 27.573 12.056 1.321 14.34 16.01 1.67 4.505 27.566 16.075 1.318 14.33 16.01 1.67 4.508 27.564 20.094 1.315 14.33 15.99 1.67 4.512 27.562 24.112 1.313 14.32 15.98 1.66 4.514 27.561 28.131 1.311 14.32 15.99 1.67 4.519 27.558 32.150 1.310 14.31 15.99 1.68 4.520 27.558 36.168 1.309 14.31 15.99 1.68 4.530 27.553 40.187 1.307 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 28.131 Accepted refinement result: 14.32 15.98 1.66 4.514 27.561 28.131 1.311 Individual atomic B min max mean iso aniso Overall: 14.82 108.34 23.40 1.89 0 1284 Protein: 14.82 49.58 20.64 1.89 0 1020 Water: 16.19 108.34 34.04 N/A 0 264 Chain A: 14.82 108.34 22.74 N/A 0 649 Chain B: 15.35 98.91 24.06 N/A 0 635 Histogram: Values Number of atoms 14.82 - 24.17 913 24.17 - 33.52 219 33.52 - 42.87 100 42.87 - 52.23 37 52.23 - 61.58 7 61.58 - 70.93 2 70.93 - 80.28 2 80.28 - 89.64 1 89.64 - 98.99 1 98.99 - 108.34 2 =========================== Idealize ADP of riding H ========================== r_work=0.1432 r_free=0.1598 r_work=0.1432 r_free=0.1598 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1432 r_free = 0.1598 target_work(ml) = 1.311 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1432 r_free = 0.1598 target_work(ml) = 1.311 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 0.96 - 20.00 A, n_refl.=67498 (all), 5.06 % free)------------| | | | r_work= 0.1432 r_free= 0.1598 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 1.311317 | | target function (ml) not normalized (work): 84033.117123 | | target function (ml) not normalized (free): 5004.688272 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1441 0.1432 0.1598 n_refl.: 67498 re-set all scales: r(all,work,free)=0.2093 0.2088 0.2186 n_refl.: 67498 remove outliers: r(all,work,free)=0.2093 0.2088 0.2186 n_refl.: 67498 overall B=-0.01 to atoms: r(all,work,free)=0.2092 0.2087 0.2186 n_refl.: 67498 bulk-solvent and scaling: r(all,work,free)=0.1440 0.1432 0.1586 n_refl.: 67498 remove outliers: r(all,work,free)=0.1440 0.1432 0.1586 n_refl.: 67498 ======================== 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 19.997-8.097 82.91 94 3 0.2332 131.207 124.429 0.869 1.000 0.360 8.032-6.584 99.01 94 6 0.2003 141.497 136.249 0.906 1.001 0.380 6.581-5.402 99.44 164 12 0.2043 141.941 139.247 0.906 1.001 0.400 5.392-4.419 97.13 292 13 0.1680 176.342 173.187 0.916 1.003 0.400 4.418-3.621 97.21 520 38 0.1539 188.886 185.418 0.960 1.005 0.300 3.620-2.967 99.34 1005 52 0.1507 149.848 148.333 0.950 1.006 0.140 2.967-2.431 100.00 1801 115 0.1664 92.808 91.162 0.926 1.010 0.000 2.430-1.992 100.00 3268 160 0.1439 63.944 62.696 0.951 1.018 0.000 1.992-1.632 100.00 5917 343 0.1338 30.910 30.614 0.947 1.028 0.000 1.632-1.337 99.89 10815 573 0.1087 13.368 13.292 0.937 1.047 0.000 1.337-1.096 99.72 19512 1023 0.1064 4.763 4.746 0.938 1.085 0.000 1.096-0.960 97.49 20601 1077 0.1195 1.369 1.370 0.890 1.140 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-0.0526 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1432 r_free=0.1586 After: r_work=0.1432 r_free=0.1587 ================================== NQH flips ================================== r_work=0.1432 r_free=0.1587 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1432 r_free=0.1587 ========================= Local real-space refinement ========================= Before: r_work=0.1432 r_free=0.1587 25 residues out of total 92 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.094 outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 2.5632 time to fit residues: 64.6010 After: r_work=0.1438 r_free=0.1594 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.489932 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 7.167215 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 0.1477 0.1616 0.0138 0.005 0.8 3.5 0.0 0.0 0 0.074 0.1455 0.1600 0.0145 0.005 0.9 3.5 0.0 0.0 0 0.223 0.1447 0.1595 0.0148 0.006 1.0 3.5 0.0 0.0 0 0.447 0.1441 0.1592 0.0150 0.008 1.1 3.5 0.0 0.0 0 0.670 0.1438 0.1590 0.0152 0.009 1.1 3.5 0.0 0.0 0 0.894 0.1436 0.1591 0.0155 0.009 1.2 3.5 0.0 0.0 0 1.117 0.1435 0.1591 0.0157 0.010 1.2 3.5 0.0 0.0 0 1.341 0.1433 0.1591 0.0158 0.011 1.3 3.0 0.0 0.0 0 1.564 0.1440 0.1591 0.0151 0.008 1.1 3.5 0.0 0.0 0 0.745 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1438 0.1590 0.0152 0.009 1.1 3.5 0.0 0.0 0 0.894 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.1438 r_free=0.1590 23 residues out of total 92 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.090 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0792 After: r_work=0.1438 r_free=0.1590 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 14.38 15.90 1.52 4.477 27.519 7.167 1.313 14.38 15.90 1.52 4.477 27.519 0.215 1.313 14.38 15.90 1.52 4.477 27.519 0.896 1.313 14.39 15.90 1.52 4.477 27.519 3.584 1.312 14.39 15.91 1.52 4.476 27.519 7.167 1.313 14.39 15.91 1.52 4.477 27.519 10.751 1.312 14.38 15.91 1.53 4.477 27.518 14.334 1.312 14.39 15.91 1.53 4.478 27.517 17.918 1.312 14.39 15.91 1.52 4.482 27.515 21.502 1.311 14.39 15.90 1.51 4.486 27.512 25.085 1.310 14.44 15.93 1.49 4.523 27.490 28.669 1.309 14.44 15.94 1.50 4.531 27.488 32.252 1.307 14.43 15.93 1.51 4.531 27.490 35.836 1.306 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 0.215 Accepted refinement result: 14.38 15.90 1.52 4.477 27.519 0.215 1.313 Individual atomic B min max mean iso aniso Overall: 14.80 108.33 23.38 1.89 0 1284 Protein: 14.80 49.56 20.63 1.89 0 1020 Water: 16.18 108.33 34.02 N/A 0 264 Chain A: 14.80 108.33 22.73 N/A 0 649 Chain B: 15.33 98.90 24.05 N/A 0 635 Histogram: Values Number of atoms 14.80 - 24.15 913 24.15 - 33.51 219 33.51 - 42.86 100 42.86 - 52.21 37 52.21 - 61.56 7 61.56 - 70.92 2 70.92 - 80.27 2 80.27 - 89.62 1 89.62 - 98.97 1 98.97 - 108.33 2 =========================== Idealize ADP of riding H ========================== r_work=0.1438 r_free=0.1590 r_work=0.1438 r_free=0.1590 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1438 r_free = 0.1590 target_work(ml) = 1.313 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1438 r_free = 0.1590 target_work(ml) = 1.313 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.96 - 20.00 A, n_refl.=67498 (all), 5.06 % free)------------| | | | r_work= 0.1438 r_free= 0.1590 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 1.312653 | | target function (ml) not normalized (work): 84118.732313 | | target function (ml) not normalized (free): 4998.863754 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 20.00 - 2.77 0.98 2688 159 0.1641 0.1729 4.8501 4.869| | 2: 2.77 - 2.20 1.00 2694 148 0.1609 0.1702 4.2399 4.2644| | 3: 2.20 - 1.92 1.00 2719 159 0.1385 0.1641 3.6407 3.7488| | 4: 1.92 - 1.74 1.00 2685 146 0.1316 0.1456 3.1677 3.2185| | 5: 1.74 - 1.62 1.00 2698 146 0.1281 0.1632 2.7384 2.8963| | 6: 1.62 - 1.52 1.00 2719 120 0.1134 0.1209 2.4077 2.3691| | 7: 1.52 - 1.45 1.00 2716 159 0.1074 0.1197 2.0853 2.1594| | 8: 1.45 - 1.38 1.00 2650 138 0.1049 0.1207 1.8268 1.8706| | 9: 1.38 - 1.33 1.00 2714 156 0.1059 0.1402 1.5977 1.8133| | 10: 1.33 - 1.29 1.00 2648 150 0.1098 0.1355 1.4334 1.5689| | 11: 1.29 - 1.25 1.00 2742 141 0.1072 0.1275 1.2605 1.3128| | 12: 1.25 - 1.21 1.00 2619 151 0.1065 0.1251 1.0967 1.2735| | 13: 1.21 - 1.18 1.00 2742 126 0.1045 0.1232 0.92754 1.0308| | 14: 1.18 - 1.15 1.00 2685 141 0.1020 0.1219 0.75215 0.91488| | 15: 1.15 - 1.12 1.00 2681 126 0.1062 0.1129 0.59612 0.69993| | 16: 1.12 - 1.10 1.00 2684 152 0.1083 0.1197 0.44148 0.50642| | 17: 1.10 - 1.08 1.00 2657 153 0.1073 0.1203 0.2921 0.426| | 18: 1.08 - 1.06 0.99 2674 152 0.1090 0.1317 0.1054 0.2465| | 19: 1.06 - 1.04 0.99 2676 134 0.1116 0.1219 -0.061701 -0.0038595| | 20: 1.04 - 1.02 0.99 2651 122 0.1117 0.1356 -0.21084 -0.040885| | 21: 1.02 - 1.00 0.98 2633 127 0.1225 0.1603 -0.34632 -0.21211| | 22: 1.00 - 0.99 0.98 2664 152 0.1278 0.1493 -0.47193 -0.37923| | 23: 0.99 - 0.97 0.96 2618 137 0.1453 0.1711 -0.57076 -0.34386| | 24: 0.97 - 0.96 0.92 2426 120 0.1631 0.1901 -0.68486 -0.55109| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 20.00 - 2.77 2688 159 0.90 16.79 1.00 0.98 2328.01| | 2: 2.77 - 2.20 2694 148 0.86 20.83 0.99 0.99 1004.54| | 3: 2.20 - 1.92 2719 159 0.91 15.42 1.02 1.00 254.88| | 4: 1.92 - 1.74 2685 146 0.91 15.13 1.00 0.99 102.67| | 5: 1.74 - 1.62 2698 146 0.92 14.82 0.98 0.97 44.90| | 6: 1.62 - 1.52 2719 120 0.93 12.73 1.01 0.96 21.80| | 7: 1.52 - 1.45 2716 159 0.94 11.19 1.00 0.97 11.48| | 8: 1.45 - 1.38 2650 138 0.94 11.11 0.99 0.98 6.86| | 9: 1.38 - 1.33 2714 156 0.94 11.34 0.99 0.97 4.55| | 10: 1.33 - 1.29 2648 150 0.93 12.43 1.02 0.98 3.19| | 11: 1.29 - 1.25 2742 141 0.94 11.34 1.01 0.98 2.16| | 12: 1.25 - 1.21 2619 151 0.95 10.96 1.00 0.99 1.59| | 13: 1.21 - 1.18 2742 126 0.95 10.78 0.99 0.98 1.17| | 14: 1.18 - 1.15 2685 141 0.94 10.90 0.99 0.97 0.83| | 15: 1.15 - 1.12 2681 126 0.95 10.43 0.97 0.97 0.58| | 16: 1.12 - 1.10 2684 152 0.95 9.57 0.96 0.97 0.40| | 17: 1.10 - 1.08 2657 153 0.95 10.45 1.02 0.98 0.29| | 18: 1.08 - 1.06 2674 152 0.95 10.88 1.02 0.99 0.21| | 19: 1.06 - 1.04 2676 134 0.94 11.43 1.01 0.99 0.16| | 20: 1.04 - 1.02 2651 122 0.95 11.40 0.99 0.98 0.12| | 21: 1.02 - 1.00 2633 127 0.95 11.75 0.96 0.95 0.09| | 22: 1.00 - 0.99 2664 152 0.95 11.98 0.95 0.93 0.07| | 23: 0.99 - 0.97 2618 137 0.94 12.63 0.93 0.91 0.06| | 24: 0.97 - 0.96 2426 120 0.94 12.94 0.91 0.89 0.04| |alpha: min = 0.89 max = 1.00 mean = 0.97| |beta: min = 0.04 max = 2328.01 mean = 159.23| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.73 mean = 12.47| |phase err.(test): min = 0.00 max = 88.11 mean = 12.71| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1446 0.1438 0.1590 n_refl.: 67498 re-set all scales: r(all,work,free)=0.2096 0.2091 0.2184 n_refl.: 67498 remove outliers: r(all,work,free)=0.2096 0.2091 0.2184 n_refl.: 67498 overall B=-0.01 to atoms: r(all,work,free)=0.2095 0.2091 0.2184 n_refl.: 67498 bulk-solvent and scaling: r(all,work,free)=0.1447 0.1439 0.1597 n_refl.: 67498 remove outliers: r(all,work,free)=0.1447 0.1439 0.1597 n_refl.: 67498 ======================== 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 19.997-8.097 82.91 94 3 0.2343 131.207 124.066 0.876 1.000 0.370 8.032-6.584 99.01 94 6 0.1995 141.497 136.452 0.906 1.001 0.375 6.581-5.402 99.44 164 12 0.2114 141.941 138.937 0.908 1.001 0.376 5.392-4.419 97.13 292 13 0.1715 176.342 173.202 0.912 1.003 0.360 4.418-3.621 97.21 520 38 0.1545 188.886 185.366 0.959 1.005 0.300 3.620-2.967 99.34 1005 52 0.1514 149.848 148.366 0.950 1.006 0.130 2.967-2.431 100.00 1801 115 0.1671 92.808 91.144 0.926 1.010 0.000 2.430-1.992 100.00 3268 160 0.1439 63.944 62.708 0.951 1.018 0.000 1.992-1.632 100.00 5917 343 0.1346 30.910 30.606 0.947 1.028 0.000 1.632-1.337 99.89 10815 573 0.1092 13.368 13.294 0.936 1.047 0.000 1.337-1.096 99.72 19512 1023 0.1068 4.763 4.747 0.937 1.085 0.000 1.096-0.960 97.49 20601 1077 0.1190 1.369 1.370 0.889 1.139 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-0.0438 ================= 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 : 0.2086 0.2093 0.026 1.917 14.3 108.0 23.0 792 0.000 1_bss: 0.1408 0.1533 0.026 1.917 14.5 108.2 23.3 792 0.000 1_settarget: 0.1408 0.1533 0.026 1.917 14.5 108.2 23.3 792 0.000 1_nqh: 0.1409 0.1535 0.026 1.917 14.5 108.2 23.3 792 0.004 1_realsrl: 0.1468 0.1582 0.026 1.917 14.5 108.2 23.3 792 0.043 1_weight: 0.1468 0.1582 0.026 1.917 14.5 108.2 23.3 792 0.043 1_xyzrec: 0.1606 0.1751 0.003 0.605 14.5 108.2 23.3 792 0.114 1_realsrl2: 0.1606 0.1752 0.003 0.605 14.5 108.2 23.3 792 0.114 1_adp: 0.1607 0.1750 0.003 0.605 14.5 108.2 23.3 792 0.114 1_regHadp: 0.1597 0.1742 0.003 0.605 14.5 108.2 23.3 792 0.114 1_occ: 0.1590 0.1745 0.003 0.605 14.5 108.2 23.3 792 0.114 2_bss: 0.1589 0.1749 0.003 0.605 14.7 108.4 23.4 792 0.114 2_settarget: 0.1589 0.1749 0.003 0.605 14.7 108.4 23.4 792 0.114 2_updatecdl: 0.1589 0.1749 0.003 0.631 14.7 108.4 23.4 792 0.114 2_nqh: 0.1589 0.1749 0.003 0.631 14.7 108.4 23.4 792 0.112 2_realsrl: 0.1591 0.1749 0.003 0.631 14.7 108.4 23.4 792 0.130 2_weight: 0.1591 0.1749 0.003 0.631 14.7 108.4 23.4 792 0.130 2_xyzrec: 0.1529 0.1778 0.003 0.606 14.7 108.4 23.4 792 0.156 2_realsrl2: 0.1529 0.1778 0.003 0.606 14.7 108.4 23.4 792 0.156 2_adp: 0.1529 0.1778 0.003 0.606 14.7 108.4 23.4 792 0.156 2_regHadp: 0.1529 0.1778 0.003 0.606 14.7 108.4 23.4 792 0.156 2_occ: 0.1529 0.1779 0.003 0.606 14.7 108.4 23.4 792 0.156 3_bss: 0.1533 0.1771 0.003 0.606 14.8 108.5 23.5 792 0.156 3_settarget: 0.1533 0.1771 0.003 0.606 14.8 108.5 23.5 792 0.156 3_updatecdl: 0.1533 0.1771 0.003 0.623 14.8 108.5 23.5 792 0.156 3_nqh: 0.1533 0.1771 0.003 0.623 14.8 108.5 23.5 792 0.156 3_realsrl: 0.1537 0.1793 0.003 0.623 14.8 108.5 23.5 792 0.167 3_weight: 0.1537 0.1793 0.003 0.623 14.8 108.5 23.5 792 0.167 3_xyzrec: 0.1429 0.1597 0.009 1.111 14.8 108.5 23.5 792 0.135 3_realsrl2: 0.1429 0.1597 0.009 1.111 14.8 108.5 23.5 792 0.135 3_adp: 0.1427 0.1596 0.009 1.111 14.8 108.4 23.5 792 0.135 3_regHadp: 0.1427 0.1595 0.009 1.111 14.8 108.4 23.5 792 0.135 3_occ: 0.1427 0.1595 0.009 1.111 14.8 108.4 23.5 792 0.135 4_bss: 0.1426 0.1609 0.009 1.111 14.8 108.4 23.4 792 0.135 4_settarget: 0.1426 0.1609 0.009 1.111 14.8 108.4 23.4 792 0.135 4_updatecdl: 0.1426 0.1609 0.009 1.115 14.8 108.4 23.4 792 0.135 4_nqh: 0.1427 0.1611 0.009 1.115 14.8 108.4 23.4 792 0.132 4_realsrl: 0.1432 0.1626 0.009 1.115 14.8 108.4 23.4 792 0.136 4_weight: 0.1432 0.1626 0.009 1.115 14.8 108.4 23.4 792 0.136 4_xyzrec: 0.1435 0.1607 0.008 1.116 14.8 108.4 23.4 792 0.137 4_realsrl2: 0.1435 0.1607 0.008 1.116 14.8 108.4 23.4 792 0.137 4_adp: 0.1432 0.1598 0.008 1.116 14.8 108.3 23.4 792 0.137 4_regHadp: 0.1432 0.1598 0.008 1.116 14.8 108.3 23.4 792 0.137 4_occ: 0.1432 0.1598 0.008 1.116 14.8 108.3 23.4 792 0.137 5_bss: 0.1432 0.1586 0.008 1.116 14.8 108.3 23.4 792 0.137 5_settarget: 0.1432 0.1586 0.008 1.116 14.8 108.3 23.4 792 0.137 5_updatecdl: 0.1432 0.1586 0.008 1.115 14.8 108.3 23.4 792 0.137 5_setrh: 0.1432 0.1587 0.008 1.115 14.8 108.3 23.4 792 0.136 5_nqh: 0.1432 0.1587 0.008 1.115 14.8 108.3 23.4 792 0.136 5_realsrl: 0.1438 0.1594 0.008 1.115 14.8 108.3 23.4 792 0.141 5_weight: 0.1438 0.1594 0.008 1.115 14.8 108.3 23.4 792 0.141 5_xyzrec: 0.1438 0.1590 0.009 1.137 14.8 108.3 23.4 792 0.139 5_realsrl2: 0.1438 0.1590 0.009 1.137 14.8 108.3 23.4 792 0.139 5_adp: 0.1438 0.1590 0.009 1.137 14.8 108.3 23.4 792 0.139 5_regHadp: 0.1438 0.1590 0.009 1.137 14.8 108.3 23.4 792 0.139 5_occ: 0.1438 0.1590 0.009 1.137 14.8 108.3 23.4 792 0.139 end: 0.1439 0.1597 0.009 1.137 14.8 108.3 23.4 792 0.139 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/highres/finalised/4R5R_complete_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/highres/finalised/4R5R_complete_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 1.8900 Refinement macro-cycles (run) : 1338.8400 Write final files (write_after_run_outputs) : 45.7500 Total : 1386.4800 Total CPU time: 23.36 minutes =========================== phenix.refine: finished =========================== # Date 2024-04-10 Time 16:31:21 PDT -0700 (1712791881.21 s) Start R-work = 0.1408, R-free = 0.1533 Final R-work = 0.1439, R-free = 0.1597 =============================================================================== Job complete usr+sys time: 1477.78 seconds wall clock time: 33 minutes 19.50 seconds (1999.50 seconds total)