Starting phenix.refine on Fri Dec 27 17:58:26 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3337960.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3337960.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3337960.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } pdb_interpretation { nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.64, per 1000 atoms: 0.49 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 0.56 Conformation dependent library (CDL) restraints added in 143.1 milliseconds Time building geometry restraints manager: 0.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.64 - 0.90: 427 0.90 - 1.16: 1204 1.16 - 1.42: 637 1.42 - 1.67: 845 1.67 - 1.93: 40 Bond restraints: 3153 Sorted by residual: bond pdb=" C GLN A 95 " pdb=" O GLN A 95 " ideal model delta sigma weight residual 1.237 1.480 -0.244 1.19e-02 7.06e+03 4.19e+02 bond pdb=" CE1 HIS A 115 " pdb=" NE2 HIS A 115 " ideal model delta sigma weight residual 1.321 1.520 -0.199 1.00e-02 1.00e+04 3.95e+02 bond pdb=" CA LEU A 101 " pdb=" C LEU A 101 " ideal model delta sigma weight residual 1.523 1.289 0.234 1.23e-02 6.61e+03 3.61e+02 bond pdb=" N ALA A 183 " pdb=" CA ALA A 183 " ideal model delta sigma weight residual 1.462 1.319 0.143 7.70e-03 1.69e+04 3.43e+02 bond pdb=" C ILE A 168 " pdb=" O ILE A 168 " ideal model delta sigma weight residual 1.236 1.440 -0.204 1.11e-02 8.12e+03 3.36e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.28: 2930 4.28 - 8.55: 1862 8.55 - 12.83: 781 12.83 - 17.11: 179 17.11 - 21.39: 25 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O LYS A 89 " pdb=" C LYS A 89 " pdb=" N BGLU A 90 " ideal model delta sigma weight residual 122.09 138.18 -16.09 1.04e+00 9.25e-01 2.39e+02 angle pdb=" O LYS A 89 " pdb=" C LYS A 89 " pdb=" N AGLU A 90 " ideal model delta sigma weight residual 122.09 138.01 -15.92 1.04e+00 9.25e-01 2.34e+02 angle pdb=" C ALYS A 99 " pdb=" N GLY A 100 " pdb=" CA GLY A 100 " ideal model delta sigma weight residual 122.36 136.29 -13.93 9.70e-01 1.06e+00 2.06e+02 angle pdb=" N ILE A 21 " pdb=" CA ILE A 21 " pdb=" CB ILE A 21 " ideal model delta sigma weight residual 110.52 119.67 -9.15 6.70e-01 2.23e+00 1.86e+02 angle pdb=" O ILE A 21 " pdb=" C ILE A 21 " pdb=" N PRO A 22 " ideal model delta sigma weight residual 120.42 112.03 8.39 6.40e-01 2.44e+00 1.72e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.17: 934 17.17 - 34.33: 124 34.33 - 51.50: 38 51.50 - 68.66: 11 68.66 - 85.82: 4 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA SER A 155 " pdb=" C SER A 155 " pdb=" N ARG A 156 " pdb=" CA ARG A 156 " ideal model delta harmonic sigma weight residual -180.00 -150.29 -29.71 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" CA ALA A 56 " pdb=" C ALA A 56 " pdb=" N SER A 57 " pdb=" CA SER A 57 " ideal model delta harmonic sigma weight residual 180.00 156.24 23.76 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA VAL A 123 " pdb=" C VAL A 123 " pdb=" N THR A 124 " pdb=" CA THR A 124 " ideal model delta harmonic sigma weight residual 180.00 157.00 23.00 0 5.00e+00 4.00e-02 2.12e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.204: 87 0.204 - 0.407: 61 0.407 - 0.610: 55 0.610 - 0.813: 33 0.813 - 1.016: 7 Chirality restraints: 243 Sorted by residual: chirality pdb=" CG LEU A 172 " pdb=" CB LEU A 172 " pdb=" CD1 LEU A 172 " pdb=" CD2 LEU A 172 " both_signs ideal model delta sigma weight residual False -2.59 -1.57 -1.02 2.00e-01 2.50e+01 2.58e+01 chirality pdb=" CA LEU A 38 " pdb=" N LEU A 38 " pdb=" C LEU A 38 " pdb=" CB LEU A 38 " both_signs ideal model delta sigma weight residual False 2.51 1.57 0.94 2.00e-01 2.50e+01 2.22e+01 chirality pdb=" CA ARG A 48 " pdb=" N ARG A 48 " pdb=" C ARG A 48 " pdb=" CB ARG A 48 " both_signs ideal model delta sigma weight residual False 2.51 1.61 0.90 2.00e-01 2.50e+01 2.03e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 115 " -0.071 2.00e-02 2.50e+03 7.77e-02 1.36e+02 pdb=" CG HIS A 115 " 0.129 2.00e-02 2.50e+03 pdb=" ND1 HIS A 115 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 HIS A 115 " 0.044 2.00e-02 2.50e+03 pdb=" CE1 HIS A 115 " 0.060 2.00e-02 2.50e+03 pdb=" NE2 HIS A 115 " 0.037 2.00e-02 2.50e+03 pdb=" HD2 HIS A 115 " -0.102 2.00e-02 2.50e+03 pdb=" HE1 HIS A 115 " -0.122 2.00e-02 2.50e+03 pdb=" HE2 HIS A 115 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " -0.050 2.00e-02 2.50e+03 6.28e-02 1.18e+02 pdb=" CG TYR A 139 " 0.085 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " -0.052 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " 0.112 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " -0.030 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " 0.090 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.002 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " -0.000 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " -0.068 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.008 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " -0.093 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 126 " 0.046 2.00e-02 2.50e+03 6.45e-02 9.35e+01 pdb=" CG HIS A 126 " -0.156 2.00e-02 2.50e+03 pdb=" ND1 HIS A 126 " 0.060 2.00e-02 2.50e+03 pdb=" CD2 HIS A 126 " 0.060 2.00e-02 2.50e+03 pdb=" CE1 HIS A 126 " -0.004 2.00e-02 2.50e+03 pdb=" NE2 HIS A 126 " -0.054 2.00e-02 2.50e+03 pdb=" HD2 HIS A 126 " 0.016 2.00e-02 2.50e+03 pdb=" HE1 HIS A 126 " 0.013 2.00e-02 2.50e+03 pdb=" HE2 HIS A 126 " 0.018 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.37: 1380 2.37 - 2.92: 8342 2.92 - 3.48: 10421 3.48 - 4.04: 15124 4.04 - 4.60: 21393 Nonbonded interactions: 56660 Sorted by model distance: nonbonded pdb=" HG SER A 47 " pdb="HH11 ARG A 48 " model vdw 1.808 2.100 nonbonded pdb=" HE2 HIS A 126 " pdb=" O PRO A 184 " model vdw sym.op. 1.822 1.850 x-y,-y,-z-4/3 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.832 2.100 nonbonded pdb=" HD3 ARG A 5 " pdb="HH11 ARG A 5 " model vdw 1.832 2.270 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.837 2.100 ... (remaining 56655 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 10 15.96 2 O1- 2 8.97 3 O 551 7.97 2 N 265 6.97 2 C 957 5.97 2 H 1596 1.00 2 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 ===================== ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 3381 n_use_u_iso = 1596 n_use_u_aniso = 1785 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 = 3381 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (3381 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 1596 aniso = 1785) group_adp = False (0 atoms in 0 groups) tls = False (0 atoms in 0 groups) occupancies = True (876 atoms) group_anomalous = False ============================ Non-default parameters =========================== A complete record of all parameters was written to the .eff file above. Below are only the non-defaults. #phil __ON__ refinement { electron_density_maps { map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT" mtz_label_phases = "PH2FOFCWT" fill_missing_f_obs = True } map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT_no_fill" mtz_label_phases = "PH2FOFCWT_no_fill" } map_coefficients { map_type = "mFo-DFc" mtz_label_amplitudes = "FOFCWT" mtz_label_phases = "PHFOFCWT" } map_coefficients { map_type = "anomalous" mtz_label_amplitudes = "ANOM" mtz_label_phases = "PANOM" } map { map_type = "2mFo-DFc" fill_missing_f_obs = True } map { map_type = "2mFo-DFc" } map { map_type = "mFo-DFc" } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } hydrogens { refine = individual *riding Auto } pdb_interpretation { c_beta_restraints = False nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } output { prefix = "shake_3337960_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1596 occupancy sum: 1438.50 (% of total atoms 46.85) Rotatable: count: 507 occupancy sum: 483.00 (% of total atoms 15.73) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2603 r_free= 0.1907 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.781820 | | target function (ml) not normalized (work): 231742.301990 | | target function (ml) not normalized (free): 11750.884665 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 49.25 - 3.58 1.00 2941 171 0.3025 0.2083 7.0882 4.9446| | 2: 3.57 - 2.84 1.00 2876 122 0.2407 0.1733 4.3431 4.3333| | 3: 2.84 - 2.48 1.00 2833 165 0.2355 0.1689 4.1239 4.1409| | 4: 2.47 - 2.25 1.00 2825 136 0.2391 0.1399 3.8296 3.8111| | 5: 2.25 - 2.09 1.00 2756 127 0.2471 0.1505 3.7883 3.8132| | 6: 2.09 - 1.97 1.00 2846 113 0.2521 0.1808 3.4548 3.5161| | 7: 1.97 - 1.87 1.00 2787 165 0.2553 0.1595 3.1259 3.0929| | 8: 1.87 - 1.79 1.00 2789 144 0.2515 0.1761 3.0493 3.0873| | 9: 1.79 - 1.72 1.00 2745 138 0.2465 0.1991 2.8986 2.9478| | 10: 1.72 - 1.66 1.00 2789 158 0.2389 0.1873 2.7752 2.8283| | 11: 1.66 - 1.61 1.00 2740 147 0.2438 0.1858 2.7164 2.7469| | 12: 1.61 - 1.56 1.00 2787 146 0.2504 0.1856 2.6106 2.6009| | 13: 1.56 - 1.52 1.00 2745 130 0.2575 0.1995 2.568 2.666| | 14: 1.52 - 1.48 1.00 2803 134 0.2591 0.1899 2.507 2.5444| | 15: 1.48 - 1.45 1.00 2738 128 0.2588 0.2044 2.4144 2.4295| | 16: 1.45 - 1.42 1.00 2756 161 0.2670 0.2015 2.3776 2.3791| | 17: 1.42 - 1.39 1.00 2785 139 0.2683 0.2067 2.3216 2.3362| | 18: 1.39 - 1.36 1.00 2741 179 0.2696 0.2244 2.2721 2.3793| | 19: 1.36 - 1.34 1.00 2807 134 0.2621 0.2379 2.2072 2.3091| | 20: 1.34 - 1.32 1.00 2696 147 0.2671 0.2091 2.1861 2.1875| | 21: 1.32 - 1.30 1.00 2785 112 0.2658 0.2193 2.1326 2.1598| | 22: 1.29 - 1.27 1.00 2704 152 0.2723 0.2266 2.1326 2.1212| | 23: 1.27 - 1.26 1.00 2802 156 0.2732 0.2467 2.0969 2.1489| | 24: 1.26 - 1.24 1.00 2744 132 0.2740 0.2505 2.0679 2.1423| | 25: 1.24 - 1.22 1.00 2734 148 0.2794 0.2551 2.0335 2.1027| | 26: 1.22 - 1.21 1.00 2727 135 0.2799 0.2444 1.9989 2.1503| | 27: 1.21 - 1.19 1.00 2814 148 0.2921 0.2650 1.9991 1.9827| | 28: 1.19 - 1.18 1.00 2671 147 0.2959 0.2701 1.9822 1.9873| | 29: 1.18 - 1.16 1.00 2800 134 0.2934 0.2737 1.9676 2.0252| | 30: 1.16 - 1.15 1.00 2740 148 0.3053 0.3016 1.9273 2.0103| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 49.25 - 3.58 2941 171 0.87 18.73 0.76 0.23 1458.10| | 2: 3.57 - 2.84 2876 122 0.81 25.79 1.27 0.23 1458.10| | 3: 2.84 - 2.48 2833 165 0.74 31.75 1.24 0.23 1207.80| | 4: 2.47 - 2.25 2825 136 0.81 25.38 1.26 0.25 558.23| | 5: 2.25 - 2.09 2756 127 0.77 29.06 1.28 0.25 558.23| | 6: 2.09 - 1.97 2846 113 0.84 22.33 1.29 0.25 303.14| | 7: 1.97 - 1.87 2787 165 0.90 16.15 1.29 0.26 85.59| | 8: 1.87 - 1.79 2789 144 0.86 20.52 1.25 0.26 85.59| | 9: 1.79 - 1.72 2745 138 0.88 18.25 1.24 0.25 52.56| | 10: 1.72 - 1.66 2789 158 0.87 19.62 1.22 0.25 45.94| | 11: 1.66 - 1.61 2740 147 0.86 20.87 1.23 0.25 44.36| | 12: 1.61 - 1.56 2787 146 0.88 18.44 1.23 0.25 28.38| | 13: 1.56 - 1.52 2745 130 0.87 19.87 1.24 0.25 28.38| | 14: 1.52 - 1.48 2803 134 0.87 20.36 1.24 0.25 25.37| | 15: 1.48 - 1.45 2738 128 0.88 19.65 1.23 0.25 19.85| | 16: 1.45 - 1.42 2756 161 0.86 21.22 1.24 0.25 19.85| | 17: 1.42 - 1.39 2785 139 0.87 20.52 1.24 0.25 16.96| | 18: 1.39 - 1.36 2741 179 0.87 20.91 1.23 0.25 15.29| | 19: 1.36 - 1.34 2807 134 0.86 21.82 1.23 0.25 15.29| | 20: 1.34 - 1.32 2696 147 0.87 20.54 1.22 0.24 12.58| | 21: 1.32 - 1.30 2785 112 0.86 21.80 1.20 0.24 12.39| | 22: 1.29 - 1.27 2704 152 0.86 21.73 1.21 0.24 12.14| | 23: 1.27 - 1.26 2802 156 0.86 21.80 1.21 0.24 10.87| | 24: 1.26 - 1.24 2744 132 0.85 22.49 1.20 0.24 10.87| | 25: 1.24 - 1.22 2734 148 0.84 23.50 1.20 0.24 10.48| | 26: 1.22 - 1.21 2727 135 0.84 24.19 1.19 0.23 10.03| | 27: 1.21 - 1.19 2814 148 0.83 25.02 1.20 0.23 10.03| | 28: 1.19 - 1.18 2671 147 0.82 25.90 1.19 0.22 9.50| | 29: 1.18 - 1.16 2800 134 0.82 26.24 1.16 0.22 9.30| | 30: 1.16 - 1.15 2740 148 0.80 27.90 1.16 0.22 9.30| |alpha: min = 0.22 max = 0.26 mean = 0.24| |beta: min = 9.30 max = 1458.10 mean = 210.61| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 90.00 mean = 22.41| |phase err.(test): min = 0.00 max = 89.87 mean = 22.37| |-----------------------------------------------------------------------------| ----------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 : 0.082 0.267 1557 Z= 5.518 Angle : 5.435 18.859 2118 Z= 3.876 Chirality : 0.419 1.016 243 Planarity : 0.033 0.105 284 Dihedral : 14.574 85.823 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.24 % Favored : 96.22 % Rotamer: Outliers : 1.24 % Allowed : 3.73 % Favored : 95.03 % Cbeta Deviations : 34.05 % Peptide Plane: Cis-proline : 18.18 % 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: -2.55 (0.48), residues: 224 helix: -2.75 (0.40), residues: 103 sheet: 0.14 (1.08), residues: 28 loop : -0.72 (0.50), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.081 0.021 ARG A 27 TYR 0.063 0.022 TYR A 139 PHE 0.072 0.032 PHE A 164 HIS 0.109 0.042 HIS A 126 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2603 r_free= 0.1907 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.781820 | | target function (ml) not normalized (work): 231742.301990 | | target function (ml) not normalized (free): 11750.884665 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2560 0.2603 0.1907 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2560 0.2603 0.1907 n_refl.: 87602 remove outliers: r(all,work,free)=0.1972 0.1978 0.1907 n_refl.: 87594 overall B=0.22 to atoms: r(all,work,free)=0.2000 0.2006 0.1924 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1636 0.1631 0.1730 n_refl.: 87594 remove outliers: r(all,work,free)=0.1636 0.1631 0.1730 n_refl.: 87593 ======================== 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 32.574-12.150 98.94 88 5 0.3834 386.302 364.292 0.687 1.001 0.412 11.894-9.307 99.02 97 4 0.1853 613.623 590.929 0.924 1.002 0.385 9.237-7.194 100.00 213 7 0.2157 501.868 487.566 0.959 1.002 0.370 7.162-5.571 100.00 427 22 0.2246 376.624 363.998 0.929 1.002 0.340 5.546-4.326 100.00 867 58 0.1284 517.012 511.302 0.960 1.002 0.229 4.315-3.360 100.00 1859 96 0.1131 491.682 488.221 1.001 1.002 0.209 3.356-2.611 100.00 3867 181 0.1423 323.009 320.140 0.995 1.002 0.057 2.608-2.026 99.99 8198 413 0.1370 214.126 211.974 1.005 1.002 0.000 2.025-1.573 100.00 17313 902 0.1633 104.568 103.883 1.010 1.001 0.000 1.573-1.221 100.00 36679 1900 0.2048 46.370 45.056 1.001 1.000 0.000 1.221-1.150 99.97 13689 708 0.2562 29.216 26.834 0.963 1.000 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0509 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1631 r_free=0.1730 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 80 GLN B Total number of N/Q/H flips: 1 r_work=0.1631 r_free=0.1731 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 28.200042 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2018.128891 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 0.1209 0.1461 0.0252 0.008 1.0 2.9 0.5 0.6 0 14.100 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.09 14.61 2.52 3.013 19.081 2018.129 0.017 12.09 14.61 2.52 3.007 19.081 60.544 0.017 12.16 14.60 2.44 2.668 19.080 252.266 0.017 12.51 15.22 2.72 2.728 19.238 1009.064 0.016 12.31 15.30 2.98 3.003 19.445 2018.129 0.015 12.28 15.39 3.11 3.258 19.604 3027.193 0.015 12.17 15.34 3.18 3.302 19.625 4036.258 0.015 12.12 15.34 3.22 3.296 19.619 5045.322 0.015 12.09 15.35 3.26 3.318 19.611 6054.387 0.015 12.11 15.40 3.29 3.232 19.560 7063.451 0.015 12.05 15.38 3.33 3.429 19.664 8072.516 0.015 12.06 15.43 3.37 3.369 19.623 9081.580 0.015 12.04 15.43 3.38 3.407 19.635 10090.644 0.015 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 252.266 Accepted refinement result: 12.16 14.60 2.44 2.668 19.080 252.266 0.017 Individual atomic B min max mean iso aniso Overall: 9.08 119.46 20.11 3.31 0 1785 Protein: 9.08 115.02 17.02 3.32 0 1519 Water: 11.48 119.46 38.24 N/A 0 258 Other: 19.71 26.63 22.07 N/A 0 8 Chain A: 9.08 119.46 20.11 N/A 0 1785 Histogram: Values Number of atoms 9.08 - 20.12 1272 20.12 - 31.16 227 31.16 - 42.20 125 42.20 - 53.23 94 53.23 - 64.27 42 64.27 - 75.31 11 75.31 - 86.35 7 86.35 - 97.39 4 97.39 - 108.42 1 108.42 - 119.46 2 =========================== Idealize ADP of riding H ========================== r_work=0.1216 r_free=0.1460 r_work=0.1218 r_free=0.1463 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1218 r_free = 0.1463 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1210 r_free = 0.1456 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87593 (all), 4.90 % free)------------| | | | r_work= 0.1210 r_free= 0.1456 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.016492 | | target function (ls_wunit_k1) not normalized (work): 1373.739544 | | target function (ls_wunit_k1) not normalized (free): 110.607319 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1222 0.1210 0.1456 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1668 0.1670 0.1678 n_refl.: 87593 remove outliers: r(all,work,free)=0.1668 0.1670 0.1678 n_refl.: 87593 overall B=0.02 to atoms: r(all,work,free)=0.1673 0.1674 0.1681 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1218 0.1206 0.1442 n_refl.: 87593 remove outliers: r(all,work,free)=0.1217 0.1205 0.1442 n_refl.: 87591 ======================== 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 32.574-12.150 94.79 86 5 0.3558 296.925 280.992 0.639 1.002 0.375 11.894-9.307 99.02 97 4 0.1658 481.150 467.975 0.921 1.003 0.372 9.237-7.194 100.00 213 7 0.1875 393.521 388.090 0.966 1.003 0.350 7.162-5.571 100.00 427 22 0.1843 295.316 288.980 0.933 1.003 0.278 5.546-4.326 100.00 867 58 0.1009 405.396 402.088 0.965 1.003 0.209 4.315-3.360 100.00 1859 96 0.0861 385.534 384.316 1.008 1.002 0.180 3.356-2.611 100.00 3867 181 0.1138 253.276 252.126 1.010 1.002 0.053 2.608-2.026 99.99 8198 413 0.0989 167.899 167.193 1.020 1.001 0.000 2.025-1.573 100.00 17313 902 0.1083 81.993 82.214 1.027 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1437 36.359 35.868 1.020 0.997 0.000 1.221-1.150 99.97 13689 708 0.2246 22.909 21.396 0.984 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0355 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1205 r_free=0.1442 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 80 GLN B Total number of N/Q/H flips: 2 r_work=0.1207 r_free=0.1442 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1207 r_free=0.1442 | n_water=258 | time (s): 2.210 (total time: 2.210) Filter (dist) r_work=0.1215 r_free=0.1443 | n_water=252 | time (s): 20.940 (total time: 23.150) Filter (q & B) r_work=0.1217 r_free=0.1443 | n_water=249 | time (s): 2.490 (total time: 25.640) Compute maps r_work=0.1217 r_free=0.1443 | n_water=249 | time (s): 1.510 (total time: 27.150) Filter (map) r_work=0.1228 r_free=0.1449 | n_water=237 | time (s): 2.570 (total time: 29.720) Find peaks r_work=0.1228 r_free=0.1449 | n_water=237 | time (s): 0.570 (total time: 30.290) Add new water r_work=0.1377 r_free=0.1593 | n_water=448 | time (s): 3.170 (total time: 33.460) Refine new water occ: r_work=0.1289 r_free=0.1469 adp: r_work=0.1205 r_free=0.1411 occ: r_work=0.1219 r_free=0.1402 adp: r_work=0.1182 r_free=0.1389 occ: r_work=0.1185 r_free=0.1383 adp: r_work=0.1174 r_free=0.1381 ADP+occupancy (water only), MIN, final r_work=0.1174 r_free=0.1381 r_work=0.1174 r_free=0.1381 | n_water=448 | time (s): 57.250 (total time: 90.710) Filter (q & B) r_work=0.1179 r_free=0.1384 | n_water=432 | time (s): 2.440 (total time: 93.150) Filter (dist only) r_work=0.1179 r_free=0.1382 | n_water=431 | time (s): 34.900 (total time: 128.050) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 28.282695 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1492.424231 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 0.1579 0.1709 0.0130 0.001 0.4 6.4 0.0 0.0 0 0.125 0.1530 0.1663 0.0133 0.001 0.4 6.1 0.0 0.0 0 0.250 0.1391 0.1546 0.0155 0.001 0.4 5.8 0.0 0.0 0 0.500 0.1339 0.1504 0.0165 0.002 0.5 5.4 0.0 0.0 0 0.750 0.1296 0.1466 0.0170 0.002 0.5 4.8 0.0 0.0 0 1.000 0.1315 0.1490 0.0175 0.002 0.5 4.5 0.0 0.0 0 1.000 0.1240 0.1430 0.0190 0.002 0.6 4.8 0.5 0.0 0 2.000 0.1215 0.1423 0.0208 0.003 0.6 4.5 0.5 0.0 0 3.000 0.1206 0.1421 0.0215 0.003 0.7 4.5 0.5 0.0 0 4.000 0.1198 0.1418 0.0220 0.004 0.7 4.8 0.5 0.0 0 5.000 0.1195 0.1412 0.0217 0.004 0.7 4.8 0.5 0.0 0 6.000 0.1190 0.1409 0.0219 0.005 0.8 4.8 0.5 0.0 0 7.000 0.1187 0.1408 0.0221 0.005 0.8 4.5 0.5 0.0 0 8.000 0.1187 0.1407 0.0220 0.006 0.8 4.8 0.5 0.0 0 9.000 0.1182 0.1402 0.0220 0.006 0.8 5.1 0.5 0.0 0 10.000 0.1180 0.1406 0.0225 0.006 0.9 4.8 0.5 0.0 0 11.000 0.1177 0.1401 0.0224 0.007 0.9 5.4 0.5 0.0 0 12.000 0.1177 0.1408 0.0230 0.007 0.9 5.1 0.5 0.0 0 13.000 0.1175 0.1404 0.0229 0.008 0.9 5.4 0.5 0.6 0 14.141 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1177 0.1401 0.0224 0.007 0.9 5.4 0.5 0.0 0 12.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.77 14.01 2.24 3.777 21.954 1492.424 0.015 11.77 14.01 2.24 3.777 21.954 44.773 0.015 11.77 14.01 2.24 3.777 21.954 186.553 0.015 11.97 14.48 2.51 3.618 21.972 746.212 0.015 11.94 14.75 2.81 3.547 22.043 1492.424 0.014 11.84 14.71 2.87 3.486 22.422 2238.636 0.014 11.70 14.65 2.95 3.452 22.329 2984.848 0.014 11.61 14.59 2.98 3.471 22.313 3731.061 0.014 11.57 14.56 3.00 3.484 22.293 4477.273 0.013 11.59 14.70 3.11 3.512 22.356 5223.485 0.013 11.54 14.66 3.12 3.522 22.350 5969.697 0.013 11.57 14.77 3.20 3.550 22.391 6715.909 0.013 11.53 14.74 3.21 3.559 22.382 7462.121 0.013 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 186.553 Accepted refinement result: 11.77 14.01 2.24 3.777 21.954 186.553 0.015 Individual atomic B min max mean iso aniso Overall: 9.10 115.04 22.49 3.31 194 1764 Protein: 9.10 115.04 17.04 3.32 0 1519 Water: 11.51 79.16 41.70 N/A 194 237 Other: 19.73 26.66 22.10 N/A 0 8 Chain A: 9.10 115.04 19.68 N/A 0 1764 Chain S: 14.14 60.00 48.05 N/A 194 0 Histogram: Values Number of atoms 9.10 - 19.70 1259 19.70 - 30.29 246 30.29 - 40.88 154 40.88 - 51.48 140 51.48 - 62.07 134 62.07 - 72.66 13 72.66 - 83.26 6 83.26 - 93.85 4 93.85 - 104.45 0 104.45 - 115.04 2 =========================== Idealize ADP of riding H ========================== r_work=0.1177 r_free=0.1401 r_work=0.1177 r_free=0.1401 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1177 r_free = 0.1401 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1179 r_free = 0.1408 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87591 (all), 4.90 % free)------------| | | | r_work= 0.1179 r_free= 0.1408 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.014712 | | target function (ls_wunit_k1) not normalized (work): 1225.464943 | | target function (ls_wunit_k1) not normalized (free): 100.223367 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1190 0.1179 0.1408 n_refl.: 87591 re-set all scales: r(all,work,free)=0.1572 0.1570 0.1635 n_refl.: 87591 remove outliers: r(all,work,free)=0.1572 0.1570 0.1635 n_refl.: 87591 overall B=0.00 to atoms: r(all,work,free)=0.1572 0.1571 0.1636 n_refl.: 87591 bulk-solvent and scaling: r(all,work,free)=0.1186 0.1175 0.1405 n_refl.: 87591 remove outliers: r(all,work,free)=0.1185 0.1174 0.1405 n_refl.: 87589 ======================== 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 32.574-12.150 92.71 84 5 0.3300 296.272 270.913 0.596 1.003 0.360 11.894-9.307 99.02 97 4 0.1634 481.150 475.554 0.926 1.003 0.319 9.237-7.194 100.00 213 7 0.1629 393.521 394.437 0.991 1.003 0.290 7.162-5.571 100.00 427 22 0.1578 295.316 290.502 0.938 1.003 0.229 5.546-4.326 100.00 867 58 0.0878 405.396 402.562 0.961 1.003 0.220 4.315-3.360 100.00 1859 96 0.0762 385.534 384.727 1.003 1.003 0.190 3.356-2.611 100.00 3867 181 0.1075 253.276 252.235 1.009 1.002 0.110 2.608-2.026 99.99 8198 413 0.1003 167.899 167.348 1.021 1.001 0.000 2.025-1.573 100.00 17313 902 0.1089 81.993 82.228 1.030 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1437 36.359 35.904 1.025 0.997 0.000 1.221-1.150 99.97 13689 708 0.2253 22.909 21.429 0.989 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0066 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1174 r_free=0.1405 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1174 r_free=0.1405 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1174 r_free=0.1405 | n_water=431 | time (s): 2.050 (total time: 2.050) Filter (dist) r_work=0.1174 r_free=0.1403 | n_water=430 | time (s): 36.670 (total time: 38.720) Filter (q & B) r_work=0.1174 r_free=0.1403 | n_water=430 | time (s): 1.020 (total time: 39.740) Compute maps r_work=0.1174 r_free=0.1403 | n_water=430 | time (s): 1.470 (total time: 41.210) Filter (map) r_work=0.1212 r_free=0.1400 | n_water=294 | time (s): 3.420 (total time: 44.630) Find peaks r_work=0.1212 r_free=0.1400 | n_water=294 | time (s): 0.600 (total time: 45.230) Add new water r_work=0.1326 r_free=0.1504 | n_water=475 | time (s): 3.010 (total time: 48.240) Refine new water occ: r_work=0.1236 r_free=0.1420 adp: r_work=0.1237 r_free=0.1421 occ: r_work=0.1215 r_free=0.1403 adp: r_work=0.1213 r_free=0.1402 occ: r_work=0.1198 r_free=0.1394 adp: r_work=0.1193 r_free=0.1391 ADP+occupancy (water only), MIN, final r_work=0.1193 r_free=0.1391 r_work=0.1193 r_free=0.1391 | n_water=475 | time (s): 187.690 (total time: 235.930) Filter (q & B) r_work=0.1199 r_free=0.1394 | n_water=440 | time (s): 2.990 (total time: 238.920) Filter (dist only) r_work=0.1199 r_free=0.1392 | n_water=439 | time (s): 35.320 (total time: 274.240) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.751100 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 39.816506 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 0.1235 0.1379 0.0144 0.002 0.6 4.5 0.5 0.0 0 0.088 0.1186 0.1342 0.0156 0.003 0.7 3.8 0.5 0.0 0 0.263 0.1171 0.1330 0.0159 0.004 0.8 3.2 0.5 0.0 0 0.525 0.1162 0.1326 0.0164 0.005 0.9 2.9 0.5 0.0 0 0.788 0.1158 0.1323 0.0166 0.006 1.0 3.2 0.5 0.0 0 1.051 0.1156 0.1328 0.0172 0.007 1.0 3.5 0.5 0.0 0 1.313 0.1154 0.1326 0.0172 0.007 1.1 3.5 0.5 0.0 0 1.576 0.1152 0.1325 0.0173 0.008 1.1 3.8 0.5 0.0 0 1.839 0.1159 0.1326 0.0167 0.005 0.9 2.9 0.5 0.0 0 0.876 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1158 0.1323 0.0166 0.006 1.0 3.2 0.5 0.0 0 1.051 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.58 13.23 1.66 3.780 21.332 39.817 3.620 11.58 13.23 1.66 3.779 21.332 1.194 3.620 11.58 13.23 1.66 3.779 21.332 4.977 3.620 11.60 13.29 1.69 3.710 21.325 19.908 3.614 11.69 13.46 1.77 3.719 21.296 39.817 3.617 11.60 13.41 1.82 3.746 21.283 59.725 3.611 11.53 13.37 1.84 3.761 21.279 79.633 3.605 11.49 13.33 1.84 3.769 21.278 99.541 3.602 11.48 13.33 1.86 3.780 21.270 119.450 3.600 11.45 13.30 1.85 3.787 21.269 139.358 3.598 11.46 13.35 1.88 3.805 21.251 159.266 3.599 11.44 13.33 1.89 3.812 21.251 179.174 3.597 11.44 13.33 1.88 3.823 21.243 199.083 3.597 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.194 Accepted refinement result: 11.58 13.23 1.66 3.779 21.332 1.194 3.620 Individual atomic B min max mean iso aniso Overall: 9.11 115.04 21.35 3.31 207 1759 Protein: 9.11 115.04 17.04 3.32 0 1519 Water: 11.51 76.70 36.25 N/A 207 232 Other: 19.73 26.66 22.10 N/A 0 8 Chain A: 9.11 115.04 19.56 N/A 0 1759 Chain S: 14.15 60.00 36.57 N/A 207 0 Histogram: Values Number of atoms 9.11 - 19.70 1263 19.70 - 30.29 292 30.29 - 40.89 194 40.89 - 51.48 132 51.48 - 62.08 62 62.08 - 72.67 12 72.67 - 83.26 5 83.26 - 93.86 4 93.86 - 104.45 0 104.45 - 115.04 2 =========================== Idealize ADP of riding H ========================== r_work=0.1158 r_free=0.1323 r_work=0.1158 r_free=0.1323 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1158 r_free = 0.1323 target_work(ml) = 3.620 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1150 r_free = 0.1322 target_work(ml) = 3.614 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87589 (all), 4.90 % free)------------| | | | r_work= 0.1150 r_free= 0.1322 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.613668 | | target function (ml) not normalized (work): 300993.246171 | | target function (ml) not normalized (free): 15838.512737 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1159 0.1150 0.1322 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1495 0.1493 0.1553 n_refl.: 87589 remove outliers: r(all,work,free)=0.1495 0.1493 0.1553 n_refl.: 87589 overall B=-0.01 to atoms: r(all,work,free)=0.1494 0.1492 0.1552 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1153 0.1145 0.1316 n_refl.: 87589 remove outliers: r(all,work,free)=0.1151 0.1143 0.1316 n_refl.: 87584 ======================== 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 32.574-12.150 92.71 84 5 0.3894 296.272 269.713 0.501 1.000 0.330 11.894-9.307 98.04 96 4 0.2357 481.274 465.554 0.880 1.002 0.310 9.237-7.194 98.18 209 7 0.2228 385.025 388.300 0.959 1.002 0.214 7.162-5.571 100.00 427 22 0.2021 295.316 284.568 0.921 1.002 0.190 5.546-4.326 100.00 867 58 0.1115 405.396 400.741 0.966 1.002 0.160 4.315-3.360 100.00 1859 96 0.0920 385.534 383.213 1.004 1.002 0.150 3.356-2.611 100.00 3867 181 0.1134 253.276 251.128 1.008 1.001 0.038 2.608-2.026 99.99 8198 413 0.0930 167.899 167.189 1.024 1.001 0.000 2.025-1.573 100.00 17313 902 0.0905 81.993 82.267 1.036 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1265 36.359 35.945 1.029 0.997 0.000 1.221-1.150 99.97 13689 708 0.2171 22.909 21.449 0.991 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0208 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1143 r_free=0.1316 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1143 r_free=0.1316 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1143 r_free=0.1316 | n_water=439 | time (s): 1.940 (total time: 1.940) Filter (dist) r_work=0.1143 r_free=0.1316 | n_water=438 | time (s): 38.880 (total time: 40.820) Filter (q & B) r_work=0.1144 r_free=0.1316 | n_water=436 | time (s): 3.330 (total time: 44.150) Compute maps r_work=0.1144 r_free=0.1316 | n_water=436 | time (s): 1.390 (total time: 45.540) Filter (map) r_work=0.1162 r_free=0.1290 | n_water=337 | time (s): 3.290 (total time: 48.830) Find peaks r_work=0.1162 r_free=0.1290 | n_water=337 | time (s): 0.600 (total time: 49.430) Add new water r_work=0.1226 r_free=0.1358 | n_water=492 | time (s): 3.310 (total time: 52.740) Refine new water occ: r_work=0.1162 r_free=0.1294 adp: r_work=0.1162 r_free=0.1296 occ: r_work=0.1149 r_free=0.1286 adp: r_work=0.1147 r_free=0.1286 occ: r_work=0.1138 r_free=0.1283 adp: r_work=0.1134 r_free=0.1279 ADP+occupancy (water only), MIN, final r_work=0.1134 r_free=0.1279 r_work=0.1134 r_free=0.1279 | n_water=492 | time (s): 136.740 (total time: 189.480) Filter (q & B) r_work=0.1140 r_free=0.1284 | n_water=461 | time (s): 3.280 (total time: 192.760) Filter (dist only) r_work=0.1140 r_free=0.1283 | n_water=460 | time (s): 39.390 (total time: 232.150) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.766747 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 48.580673 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 0.1194 0.1326 0.0132 0.002 0.6 4.2 0.5 0.0 0 0.088 0.1159 0.1306 0.0146 0.003 0.7 2.9 0.5 0.0 0 0.265 0.1146 0.1301 0.0155 0.005 0.9 3.5 0.5 0.0 0 0.530 0.1139 0.1296 0.0157 0.006 0.9 3.8 0.5 0.0 0 0.795 0.1135 0.1294 0.0159 0.007 1.0 3.5 0.5 0.0 0 1.060 0.1133 0.1296 0.0164 0.007 1.0 3.8 0.5 0.0 0 1.325 0.1131 0.1294 0.0163 0.008 1.1 3.8 0.5 0.0 0 1.590 0.1129 0.1294 0.0165 0.009 1.1 3.8 0.5 0.0 0 1.855 0.1137 0.1295 0.0157 0.006 1.0 3.8 0.5 0.0 0 0.883 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1135 0.1294 0.0159 0.007 1.0 3.5 0.5 0.0 0 1.060 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.35 12.94 1.59 3.780 21.352 48.581 3.604 11.35 12.94 1.59 3.780 21.352 1.457 3.604 11.35 12.94 1.58 3.770 21.352 6.073 3.604 11.42 13.02 1.60 3.712 21.339 24.290 3.601 11.37 13.03 1.66 3.738 21.323 48.581 3.597 11.37 13.11 1.74 3.753 21.305 72.871 3.595 11.31 13.07 1.76 3.770 21.298 97.161 3.590 11.27 13.03 1.76 3.780 21.300 121.452 3.587 11.26 13.06 1.80 3.799 21.286 145.742 3.586 11.25 13.05 1.80 3.812 21.280 170.032 3.585 11.23 13.03 1.80 3.820 21.280 194.323 3.584 11.22 13.02 1.80 3.826 21.280 218.613 3.583 11.22 13.02 1.80 3.835 21.276 242.903 3.582 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.457 Accepted refinement result: 11.35 12.94 1.59 3.780 21.352 1.457 3.604 Individual atomic B min max mean iso aniso Overall: 9.10 115.04 21.39 3.31 228 1759 Protein: 9.10 115.04 17.04 3.32 0 1519 Water: 11.50 76.70 35.78 N/A 228 232 Other: 19.73 26.65 22.09 N/A 0 8 Chain A: 9.10 115.04 19.56 N/A 0 1759 Chain S: 14.14 60.00 35.58 N/A 228 0 Histogram: Values Number of atoms 9.10 - 19.69 1266 19.69 - 30.29 294 30.29 - 40.88 212 40.88 - 51.47 136 51.47 - 62.07 56 62.07 - 72.66 12 72.66 - 83.26 5 83.26 - 93.85 4 93.85 - 104.44 0 104.44 - 115.04 2 =========================== Idealize ADP of riding H ========================== r_work=0.1135 r_free=0.1294 r_work=0.1135 r_free=0.1294 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1135 r_free = 0.1294 target_work(ml) = 3.604 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1130 r_free = 0.1293 target_work(ml) = 3.602 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87584 (all), 4.91 % free)------------| | | | r_work= 0.1130 r_free= 0.1293 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.602282 | | target function (ml) not normalized (work): 300026.858689 | | target function (ml) not normalized (free): 15805.875914 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1138 0.1130 0.1293 n_refl.: 87584 re-set all scales: r(all,work,free)=0.1466 0.1463 0.1531 n_refl.: 87584 remove outliers: r(all,work,free)=0.1466 0.1463 0.1531 n_refl.: 87584 overall B=-0.01 to atoms: r(all,work,free)=0.1465 0.1462 0.1530 n_refl.: 87584 bulk-solvent and scaling: r(all,work,free)=0.1137 0.1129 0.1295 n_refl.: 87584 remove outliers: r(all,work,free)=0.1133 0.1125 0.1295 n_refl.: 87576 ======================== 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 32.574-12.150 89.58 81 5 0.3970 295.635 252.569 0.456 0.999 0.308 11.894-9.307 93.14 91 4 0.2277 475.877 460.551 0.862 1.001 0.232 9.237-7.194 98.18 209 7 0.2305 385.025 381.159 0.936 1.002 0.170 7.162-5.571 100.00 427 22 0.2101 295.316 285.097 0.915 1.002 0.160 5.546-4.326 100.00 867 58 0.1122 405.396 401.395 0.967 1.002 0.120 4.315-3.360 100.00 1859 96 0.0909 385.534 383.420 1.003 1.002 0.120 3.356-2.611 100.00 3867 181 0.1089 253.276 251.604 1.010 1.002 0.034 2.608-2.026 99.99 8198 413 0.0906 167.899 167.326 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0882 81.993 82.350 1.036 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1256 36.359 35.967 1.029 0.997 0.000 1.221-1.150 99.97 13689 708 0.2172 22.909 21.456 0.991 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0152 b_overall=-0.0158 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1125 r_free=0.1295 After: r_work=0.1126 r_free=0.1295 ================================== NQH flips ================================== r_work=0.1126 r_free=0.1295 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1126 r_free=0.1295 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1126 r_free=0.1295 | n_water=460 | time (s): 2.590 (total time: 2.590) Filter (dist) r_work=0.1126 r_free=0.1295 | n_water=460 | time (s): 44.080 (total time: 46.670) Filter (q & B) r_work=0.1126 r_free=0.1296 | n_water=459 | time (s): 4.080 (total time: 50.750) Compute maps r_work=0.1126 r_free=0.1296 | n_water=459 | time (s): 1.900 (total time: 52.650) Filter (map) r_work=0.1151 r_free=0.1293 | n_water=364 | time (s): 4.000 (total time: 56.650) Find peaks r_work=0.1151 r_free=0.1293 | n_water=364 | time (s): 0.700 (total time: 57.350) Add new water r_work=0.1194 r_free=0.1352 | n_water=500 | time (s): 3.640 (total time: 60.990) Refine new water occ: r_work=0.1142 r_free=0.1298 adp: r_work=0.1142 r_free=0.1299 occ: r_work=0.1133 r_free=0.1286 adp: r_work=0.1132 r_free=0.1287 occ: r_work=0.1125 r_free=0.1276 adp: r_work=0.1122 r_free=0.1276 ADP+occupancy (water only), MIN, final r_work=0.1122 r_free=0.1276 r_work=0.1122 r_free=0.1276 | n_water=500 | time (s): 233.430 (total time: 294.420) Filter (q & B) r_work=0.1130 r_free=0.1284 | n_water=466 | time (s): 3.910 (total time: 298.330) Filter (dist only) r_work=0.1131 r_free=0.1284 | n_water=464 | time (s): 48.480 (total time: 346.810) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.705818 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 43.522506 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 0.1216 0.1344 0.0128 0.004 0.7 6.1 0.0 0.0 0 0.085 0.1164 0.1306 0.0143 0.004 0.8 6.1 0.0 0.0 0 0.256 0.1143 0.1292 0.0149 0.005 0.9 5.8 0.5 0.0 0 0.512 0.1135 0.1286 0.0151 0.006 1.0 5.4 0.5 0.0 0 0.768 0.1131 0.1284 0.0154 0.006 1.0 5.4 0.5 0.0 0 1.023 0.1130 0.1284 0.0154 0.007 1.0 5.4 0.5 0.0 0 1.279 0.1129 0.1284 0.0155 0.007 1.0 5.4 0.5 0.0 0 1.535 0.1128 0.1283 0.0155 0.008 1.1 5.4 0.5 0.0 0 1.791 0.1132 0.1285 0.0153 0.006 1.0 5.4 0.5 0.0 0 0.853 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1128 0.1283 0.0155 0.008 1.1 5.4 0.5 0.0 0 1.791 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.28 12.83 1.55 3.779 21.325 43.523 3.599 11.28 12.83 1.55 3.779 21.325 1.306 3.599 11.28 12.83 1.55 3.779 21.325 5.440 3.599 11.30 12.86 1.56 3.711 21.320 21.761 3.594 11.37 13.00 1.64 3.728 21.291 43.523 3.596 11.30 12.98 1.69 3.752 21.281 65.284 3.591 11.24 12.94 1.71 3.767 21.278 87.045 3.586 11.21 12.93 1.72 3.776 21.276 108.806 3.584 11.18 12.89 1.72 3.782 21.277 130.568 3.581 11.18 12.94 1.76 3.800 21.265 152.329 3.581 11.17 12.93 1.76 3.813 21.256 174.090 3.580 11.16 12.94 1.78 3.822 21.257 195.851 3.580 11.16 12.94 1.78 3.830 21.256 217.613 3.579 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.306 Accepted refinement result: 11.28 12.83 1.55 3.779 21.325 1.306 3.599 Individual atomic B min max mean iso aniso Overall: 9.09 115.03 21.35 3.31 233 1758 Protein: 9.09 115.03 17.03 3.32 0 1519 Water: 11.50 76.69 35.49 N/A 233 231 Other: 19.72 26.65 22.09 N/A 0 8 Chain A: 9.09 115.03 19.53 N/A 0 1758 Chain S: 14.14 59.99 35.09 N/A 233 0 Histogram: Values Number of atoms 9.09 - 19.69 1265 19.69 - 30.28 297 30.28 - 40.88 222 40.88 - 51.47 129 51.47 - 62.06 55 62.06 - 72.66 12 72.66 - 83.25 5 83.25 - 93.84 4 93.84 - 104.44 0 104.44 - 115.03 2 =========================== Idealize ADP of riding H ========================== r_work=0.1128 r_free=0.1283 r_work=0.1128 r_free=0.1283 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1128 r_free = 0.1283 target_work(ml) = 3.599 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1124 r_free = 0.1279 target_work(ml) = 3.598 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87576 (all), 4.91 % free)------------| | | | r_work= 0.1124 r_free= 0.1279 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.597557 | | target function (ml) not normalized (work): 299604.550521 | | target function (ml) not normalized (free): 15790.932803 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2918 171 0.1321 0.1300 5.6282 5.6029| | 2: 3.57 - 2.84 1.00 2888 124 0.1050 0.1358 5.1485 5.2082| | 3: 2.83 - 2.48 1.00 2820 163 0.1091 0.1225 4.9347 4.9794| | 4: 2.47 - 2.25 1.00 2825 136 0.0888 0.0994 4.6194 4.651| | 5: 2.25 - 2.09 1.00 2756 127 0.0863 0.0966 4.566 4.621| | 6: 2.09 - 1.97 1.00 2846 113 0.0843 0.1008 4.2532 4.3481| | 7: 1.97 - 1.87 1.00 2787 165 0.0874 0.1090 3.9662 4.0713| | 8: 1.87 - 1.79 1.00 2789 144 0.0901 0.1145 3.8732 4.0034| | 9: 1.79 - 1.72 1.00 2745 138 0.0853 0.1174 3.6328 3.8087| | 10: 1.72 - 1.66 1.00 2831 160 0.0913 0.1167 3.5557 3.6995| | 11: 1.66 - 1.61 1.00 2712 147 0.0868 0.0997 3.4901 3.5527| | 12: 1.61 - 1.56 1.00 2773 144 0.0902 0.1152 3.3247 3.4698| | 13: 1.56 - 1.52 1.00 2745 130 0.0944 0.1037 3.3005 3.3949| | 14: 1.52 - 1.48 1.00 2803 134 0.0978 0.1065 3.2335 3.3248| | 15: 1.48 - 1.45 1.00 2738 128 0.1003 0.1218 3.1507 3.2588| | 16: 1.45 - 1.42 1.00 2756 161 0.1056 0.1242 3.1314 3.2402| | 17: 1.42 - 1.39 1.00 2785 139 0.1143 0.1293 3.1184 3.2255| | 18: 1.39 - 1.36 1.00 2741 179 0.1198 0.1333 3.1016 3.2352| | 19: 1.36 - 1.34 1.00 2807 134 0.1267 0.1569 3.1114 3.2675| | 20: 1.34 - 1.32 1.00 2696 147 0.1374 0.1474 3.1118 3.1586| | 21: 1.32 - 1.30 1.00 2785 112 0.1470 0.1543 3.112 3.1139| | 22: 1.29 - 1.27 1.00 2704 152 0.1568 0.1989 3.1227 3.2888| | 23: 1.27 - 1.26 1.00 2802 156 0.1652 0.1787 3.1319 3.1971| | 24: 1.26 - 1.24 1.00 2744 132 0.1707 0.1835 3.1241 3.2218| | 25: 1.24 - 1.22 1.00 2733 148 0.1878 0.2138 3.1397 3.2513| | 26: 1.22 - 1.21 1.00 2727 135 0.1911 0.1783 3.1458 3.2028| | 27: 1.21 - 1.19 1.00 2814 148 0.2077 0.2195 3.1678 3.1628| | 28: 1.19 - 1.18 1.00 2671 147 0.2204 0.2302 3.1631 3.1703| | 29: 1.18 - 1.16 1.00 2800 134 0.2266 0.2391 3.1451 3.2285| | 30: 1.16 - 1.15 1.00 2739 148 0.2449 0.2466 3.1409 3.1673| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 32.57 - 3.58 2918 171 0.95 8.37 1.00 0.96 5620.96| | 2: 3.57 - 2.84 2888 124 0.93 12.40 1.01 0.96 5620.96| | 3: 2.83 - 2.48 2820 163 0.90 16.38 0.99 0.97 4695.58| | 4: 2.47 - 2.25 2825 136 0.92 13.28 1.00 0.98 2309.35| | 5: 2.25 - 2.09 2756 127 0.90 15.54 1.01 0.98 2309.35| | 6: 2.09 - 1.97 2846 113 0.93 12.26 1.02 0.97 1333.62| | 7: 1.97 - 1.87 2787 165 0.95 9.18 1.02 0.97 501.46| | 8: 1.87 - 1.79 2789 144 0.93 12.56 1.00 0.97 501.46| | 9: 1.79 - 1.72 2745 138 0.94 9.97 0.98 0.97 285.49| | 10: 1.72 - 1.66 2831 160 0.94 11.11 0.98 0.97 242.24| | 11: 1.66 - 1.61 2712 147 0.94 11.70 0.98 0.97 232.10| | 12: 1.61 - 1.56 2773 144 0.95 8.91 0.99 0.97 136.48| | 13: 1.56 - 1.52 2745 130 0.95 10.38 1.03 0.97 136.48| | 14: 1.52 - 1.48 2803 134 0.94 10.76 1.02 0.97 122.64| | 15: 1.48 - 1.45 2738 128 0.95 9.90 1.02 0.98 97.30| | 16: 1.45 - 1.42 2756 161 0.94 11.11 1.02 0.98 97.30| | 17: 1.42 - 1.39 2785 139 0.95 10.95 1.01 0.98 88.72| | 18: 1.39 - 1.36 2741 179 0.94 11.58 1.01 0.98 83.75| | 19: 1.36 - 1.34 2807 134 0.94 11.89 1.00 0.98 83.75| | 20: 1.34 - 1.32 2696 147 0.94 12.18 0.98 0.96 80.05| | 21: 1.32 - 1.30 2785 112 0.94 13.15 0.98 0.96 79.79| | 22: 1.29 - 1.27 2704 152 0.93 13.73 0.98 0.96 80.17| | 23: 1.27 - 1.26 2802 156 0.92 14.88 0.97 0.94 82.11| | 24: 1.26 - 1.24 2744 132 0.92 14.89 0.96 0.94 82.11| | 25: 1.24 - 1.22 2733 148 0.91 16.40 0.96 0.94 84.09| | 26: 1.22 - 1.21 2727 135 0.90 18.16 1.03 0.93 86.30| | 27: 1.21 - 1.19 2814 148 0.89 18.82 1.02 0.93 86.30| | 28: 1.19 - 1.18 2671 147 0.88 20.49 1.01 0.92 90.04| | 29: 1.18 - 1.16 2800 134 0.88 20.59 0.99 0.92 91.45| | 30: 1.16 - 1.15 2739 148 0.86 22.12 0.98 0.92 91.45| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 79.79 max = 5620.96 mean = 868.93| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.96 mean = 13.44| |phase err.(test): min = 0.00 max = 88.57 mean = 13.43| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1132 0.1124 0.1279 n_refl.: 87576 re-set all scales: r(all,work,free)=0.1440 0.1438 0.1509 n_refl.: 87576 remove outliers: r(all,work,free)=0.1440 0.1438 0.1509 n_refl.: 87576 overall B=-0.00 to atoms: r(all,work,free)=0.1440 0.1437 0.1508 n_refl.: 87576 bulk-solvent and scaling: r(all,work,free)=0.1132 0.1124 0.1277 n_refl.: 87576 remove outliers: r(all,work,free)=0.1131 0.1123 0.1277 n_refl.: 87574 ======================== 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 32.574-12.150 88.54 80 5 0.3942 292.257 260.635 0.458 0.999 0.291 11.894-9.307 93.14 91 4 0.2396 475.877 461.518 0.865 1.001 0.228 9.237-7.194 97.73 208 7 0.2363 386.105 378.986 0.924 1.002 0.189 7.162-5.571 100.00 427 22 0.2122 295.316 284.788 0.914 1.002 0.136 5.546-4.326 100.00 867 58 0.1119 405.396 401.499 0.964 1.002 0.105 4.315-3.360 100.00 1859 96 0.0905 385.534 383.588 1.002 1.002 0.100 3.356-2.611 100.00 3867 181 0.1090 253.276 251.564 1.010 1.002 0.024 2.608-2.026 99.99 8198 413 0.0901 167.899 167.278 1.026 1.001 0.000 2.025-1.573 100.00 17313 902 0.0879 81.993 82.325 1.036 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1251 36.359 35.960 1.029 0.996 0.000 1.221-1.150 99.97 13689 708 0.2170 22.909 21.453 0.990 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0139 ================= 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_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2603 0.1907 0.082 5.435 8.8 119.3 19.9 258 0.000 1_bss: 0.1631 0.1730 0.082 5.435 9.1 119.5 20.1 258 0.000 1_settarget: 0.1631 0.1730 0.082 5.435 9.1 119.5 20.1 258 0.000 1_nqh: 0.1631 0.1731 0.082 5.435 9.1 119.5 20.1 258 0.003 1_weight: 0.1631 0.1731 0.082 5.435 9.1 119.5 20.1 258 0.003 1_xyzrec: 0.1209 0.1461 0.008 0.979 9.1 119.5 20.1 258 0.126 1_adp: 0.1216 0.1460 0.008 0.979 9.1 119.5 20.1 258 0.126 1_regHadp: 0.1218 0.1463 0.008 0.979 9.1 119.5 20.1 258 0.126 1_occ: 0.1210 0.1456 0.008 0.979 9.1 119.5 20.1 258 0.126 2_bss: 0.1205 0.1442 0.008 0.979 9.1 119.5 20.1 258 0.126 2_settarget: 0.1205 0.1442 0.008 0.979 9.1 119.5 20.1 258 0.126 2_updatecdl: 0.1205 0.1442 0.008 0.982 9.1 119.5 20.1 258 0.126 2_nqh: 0.1207 0.1442 0.008 0.982 9.1 119.5 20.1 258 0.126 2_sol: 0.1179 0.1382 0.008 0.982 9.1 115.0 22.5 431 n/a 2_weight: 0.1179 0.1382 0.008 0.982 9.1 115.0 22.5 431 n/a 2_xyzrec: 0.1177 0.1401 0.007 0.890 9.1 115.0 22.5 431 n/a 2_adp: 0.1177 0.1401 0.007 0.890 9.1 115.0 22.5 431 n/a 2_regHadp: 0.1177 0.1401 0.007 0.890 9.1 115.0 22.5 431 n/a 2_occ: 0.1179 0.1408 0.007 0.890 9.1 115.0 22.5 431 n/a 3_bss: 0.1174 0.1405 0.007 0.890 9.1 115.0 22.5 431 n/a 3_settarget: 0.1174 0.1405 0.007 0.890 9.1 115.0 22.5 431 n/a 3_updatecdl: 0.1174 0.1405 0.007 0.886 9.1 115.0 22.5 431 n/a 3_nqh: 0.1174 0.1405 0.007 0.886 9.1 115.0 22.5 431 n/a 3_sol: 0.1199 0.1392 0.007 0.886 9.1 115.0 21.4 439 n/a 3_weight: 0.1199 0.1392 0.007 0.886 9.1 115.0 21.4 439 n/a 3_xyzrec: 0.1158 0.1323 0.006 0.966 9.1 115.0 21.4 439 n/a 3_adp: 0.1158 0.1323 0.006 0.966 9.1 115.0 21.4 439 n/a 3_regHadp: 0.1158 0.1323 0.006 0.966 9.1 115.0 21.4 439 n/a 3_occ: 0.1150 0.1322 0.006 0.966 9.1 115.0 21.4 439 n/a 4_bss: 0.1143 0.1316 0.006 0.966 9.1 115.0 21.3 439 n/a 4_settarget: 0.1143 0.1316 0.006 0.966 9.1 115.0 21.3 439 n/a 4_updatecdl: 0.1143 0.1316 0.006 0.969 9.1 115.0 21.3 439 n/a 4_nqh: 0.1143 0.1316 0.006 0.969 9.1 115.0 21.3 439 n/a 4_sol: 0.1140 0.1283 0.006 0.969 9.1 115.0 21.4 460 n/a 4_weight: 0.1140 0.1283 0.006 0.969 9.1 115.0 21.4 460 n/a 4_xyzrec: 0.1135 0.1294 0.007 1.005 9.1 115.0 21.4 460 n/a 4_adp: 0.1135 0.1294 0.007 1.005 9.1 115.0 21.4 460 n/a 4_regHadp: 0.1135 0.1294 0.007 1.005 9.1 115.0 21.4 460 n/a 4_occ: 0.1130 0.1293 0.007 1.005 9.1 115.0 21.4 460 n/a 5_bss: 0.1125 0.1295 0.007 1.005 9.1 115.0 21.4 460 n/a 5_settarget: 0.1125 0.1295 0.007 1.005 9.1 115.0 21.4 460 n/a 5_updatecdl: 0.1125 0.1295 0.007 1.006 9.1 115.0 21.4 460 n/a 5_setrh: 0.1126 0.1295 0.007 1.006 9.1 115.0 21.4 460 n/a 5_nqh: 0.1126 0.1295 0.007 1.006 9.1 115.0 21.4 460 n/a 5_sol: 0.1131 0.1284 0.007 1.006 9.1 115.0 21.4 464 n/a 5_weight: 0.1131 0.1284 0.007 1.006 9.1 115.0 21.4 464 n/a 5_xyzrec: 0.1128 0.1283 0.008 1.080 9.1 115.0 21.4 464 n/a 5_adp: 0.1128 0.1283 0.008 1.080 9.1 115.0 21.4 464 n/a 5_regHadp: 0.1128 0.1283 0.008 1.080 9.1 115.0 21.4 464 n/a 5_occ: 0.1124 0.1279 0.008 1.080 9.1 115.0 21.4 464 n/a end: 0.1123 0.1277 0.008 1.080 9.1 115.0 21.3 464 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_3337960_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_3337960_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.8600 Refinement macro-cycles (run) : 11343.2700 Write final files (write_after_run_outputs) : 97.8600 Total : 11444.9900 Total CPU time: 3.19 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 21:26:16 PST -0800 (1735363576.19 s) Start R-work = 0.1631, R-free = 0.1730 Final R-work = 0.1123, R-free = 0.1277 =============================================================================== Job complete usr+sys time: 11632.33 seconds wall clock time: 211 minutes 5.08 seconds (12665.08 seconds total)