Starting phenix.refine on Sat Dec 28 21:06:33 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7326401.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7326401.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7326401.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den 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 } 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 } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 2 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: 2.23, per 1000 atoms: 0.66 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: 0.52 Conformation dependent library (CDL) restraints added in 204.5 milliseconds Time building geometry restraints manager: 0.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.65 - 0.90: 467 0.90 - 1.15: 1156 1.15 - 1.40: 583 1.40 - 1.65: 876 1.65 - 1.90: 71 Bond restraints: 3153 Sorted by residual: bond pdb=" CA ALEU A 153 " pdb=" C ALEU A 153 " ideal model delta sigma weight residual 1.521 1.296 0.226 1.17e-02 7.31e+03 3.72e+02 bond pdb=" CG HIS A 138 " pdb=" ND1 HIS A 138 " ideal model delta sigma weight residual 1.378 1.176 0.202 1.10e-02 8.26e+03 3.37e+02 bond pdb=" N LEU A 151 " pdb=" CA LEU A 151 " ideal model delta sigma weight residual 1.456 1.215 0.241 1.32e-02 5.74e+03 3.33e+02 bond pdb=" CA VAL A 186 " pdb=" C VAL A 186 " ideal model delta sigma weight residual 1.523 1.739 -0.216 1.27e-02 6.20e+03 2.90e+02 bond pdb=" C VAL A 71 " pdb=" O VAL A 71 " ideal model delta sigma weight residual 1.238 1.434 -0.197 1.17e-02 7.31e+03 2.83e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.73: 3246 4.73 - 9.45: 1828 9.45 - 14.18: 583 14.18 - 18.90: 113 18.90 - 23.63: 7 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA ILE A 52 " pdb=" C ILE A 52 " pdb=" O ILE A 52 " ideal model delta sigma weight residual 120.39 136.33 -15.94 1.05e+00 9.07e-01 2.31e+02 angle pdb=" CA PHE A 164 " pdb=" CB PHE A 164 " pdb=" CG PHE A 164 " ideal model delta sigma weight residual 113.80 128.63 -14.83 1.00e+00 1.00e+00 2.20e+02 angle pdb=" O ILE A 168 " pdb=" C ILE A 168 " pdb=" N VAL A 169 " ideal model delta sigma weight residual 121.91 136.04 -14.13 9.80e-01 1.04e+00 2.08e+02 angle pdb=" O ARG A 27 " pdb=" C ARG A 27 " pdb=" N ARG A 28 " ideal model delta sigma weight residual 122.12 136.84 -14.72 1.06e+00 8.90e-01 1.93e+02 angle pdb=" NE ARG A 5 " pdb=" CZ ARG A 5 " pdb=" NH1 ARG A 5 " ideal model delta sigma weight residual 121.50 134.80 -13.30 1.00e+00 1.00e+00 1.77e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.83: 979 19.83 - 39.66: 93 39.66 - 59.49: 34 59.49 - 79.32: 4 79.32 - 99.15: 1 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA ILE A 105 " pdb=" C ILE A 105 " pdb=" N CYS A 106 " pdb=" CA CYS A 106 " ideal model delta harmonic sigma weight residual 180.00 154.04 25.96 0 5.00e+00 4.00e-02 2.70e+01 dihedral pdb=" CA GLY A 74 " pdb=" C GLY A 74 " pdb=" N GLY A 75 " pdb=" CA GLY A 75 " ideal model delta harmonic sigma weight residual -180.00 -155.17 -24.83 0 5.00e+00 4.00e-02 2.47e+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 180.00 159.66 20.34 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.003 - 0.223: 95 0.223 - 0.442: 86 0.442 - 0.662: 42 0.662 - 0.881: 16 0.881 - 1.101: 4 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA PRO A 109 " pdb=" N PRO A 109 " pdb=" C PRO A 109 " pdb=" CB PRO A 109 " both_signs ideal model delta sigma weight residual False 2.72 1.62 1.10 2.00e-01 2.50e+01 3.03e+01 chirality pdb=" CA VAL A 50 " pdb=" N VAL A 50 " pdb=" C VAL A 50 " pdb=" CB VAL A 50 " both_signs ideal model delta sigma weight residual False 2.44 3.52 -1.08 2.00e-01 2.50e+01 2.89e+01 chirality pdb=" CB VAL A 20 " pdb=" CA VAL A 20 " pdb=" CG1 VAL A 20 " pdb=" CG2 VAL A 20 " both_signs ideal model delta sigma weight residual False -2.63 -1.61 -1.02 2.00e-01 2.50e+01 2.59e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " 0.042 2.00e-02 2.50e+03 6.79e-02 1.38e+02 pdb=" CG TYR A 141 " 0.099 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " -0.092 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " -0.051 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " -0.101 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " 0.126 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " 0.050 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " -0.036 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " -0.040 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " 0.053 2.00e-02 2.50e+03 6.77e-02 1.38e+02 pdb=" CG TYR A 139 " -0.076 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " 0.058 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " -0.143 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " -0.013 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.040 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " -0.053 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " 0.044 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.115 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " -0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.124 2.00e-02 2.50e+03 6.76e-02 1.37e+02 pdb=" CG PHE A 119 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.040 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.045 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.073 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.091 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.139 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " -0.011 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.018 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " 0.034 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.28: 802 2.28 - 2.86: 7824 2.86 - 3.44: 10634 3.44 - 4.02: 15246 4.02 - 4.60: 22030 Nonbonded interactions: 56536 Sorted by model distance: nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.700 2.450 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.772 2.450 x-y,-y,-z-4/3 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.800 2.450 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.809 2.100 nonbonded pdb=" O GLU A 147 " pdb=" H BTHR A 154 " model vdw 1.822 2.450 ... (remaining 56531 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 } 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 } } output { prefix = "shake_7326401_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= 0.2614 r_free= 0.1970 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.792926 | | target function (ml) not normalized (work): 232667.511929 | | target function (ml) not normalized (free): 11841.761022 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3027 0.2111 7.0218 4.9387| | 2: 3.57 - 2.84 1.00 2876 122 0.2424 0.1838 4.356 4.3531| | 3: 2.84 - 2.48 1.00 2833 165 0.2342 0.1695 4.1294 4.1866| | 4: 2.47 - 2.25 1.00 2825 136 0.2366 0.1405 3.8452 3.8257| | 5: 2.25 - 2.09 1.00 2756 127 0.2474 0.1779 3.8069 3.8307| | 6: 2.09 - 1.97 1.00 2846 113 0.2580 0.1761 3.4899 3.5475| | 7: 1.97 - 1.87 1.00 2787 165 0.2509 0.1896 3.1428 3.2383| | 8: 1.87 - 1.79 1.00 2789 144 0.2483 0.1853 3.0732 3.1339| | 9: 1.79 - 1.72 1.00 2745 138 0.2421 0.2039 2.9176 3.0314| | 10: 1.72 - 1.66 1.00 2789 158 0.2451 0.2053 2.8294 2.8732| | 11: 1.66 - 1.61 1.00 2740 147 0.2530 0.1885 2.746 2.7529| | 12: 1.61 - 1.56 1.00 2787 146 0.2555 0.1879 2.6252 2.5864| | 13: 1.56 - 1.52 1.00 2745 130 0.2625 0.1944 2.5811 2.588| | 14: 1.52 - 1.48 1.00 2803 134 0.2591 0.2038 2.4972 2.578| | 15: 1.48 - 1.45 1.00 2738 128 0.2610 0.2014 2.4118 2.4785| | 16: 1.45 - 1.42 1.00 2756 161 0.2614 0.2133 2.3797 2.4205| | 17: 1.42 - 1.39 1.00 2785 139 0.2657 0.2176 2.3316 2.3984| | 18: 1.39 - 1.36 1.00 2741 179 0.2675 0.2217 2.2752 2.3521| | 19: 1.36 - 1.34 1.00 2807 134 0.2696 0.2246 2.2481 2.2881| | 20: 1.34 - 1.32 1.00 2696 147 0.2675 0.1986 2.187 2.1392| | 21: 1.32 - 1.30 1.00 2785 112 0.2747 0.2313 2.1713 2.2311| | 22: 1.29 - 1.27 1.00 2704 152 0.2781 0.2788 2.1317 2.2787| | 23: 1.27 - 1.26 1.00 2802 156 0.2842 0.2344 2.1059 2.1607| | 24: 1.26 - 1.24 1.00 2744 132 0.2807 0.2334 2.0768 2.0688| | 25: 1.24 - 1.22 1.00 2734 148 0.2828 0.2534 2.0362 2.086| | 26: 1.22 - 1.21 1.00 2727 135 0.2910 0.2457 2.0364 2.1356| | 27: 1.21 - 1.19 1.00 2814 148 0.3001 0.2655 2.0182 2.0119| | 28: 1.19 - 1.18 1.00 2671 147 0.2988 0.2727 1.9839 2.0134| | 29: 1.18 - 1.16 1.00 2800 134 0.2935 0.2726 1.9481 2.0653| | 30: 1.16 - 1.15 1.00 2740 148 0.3046 0.2924 1.9292 1.955| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.91 0.76 0.23 1488.69| | 2: 3.57 - 2.84 2876 122 0.80 26.18 1.27 0.23 1488.69| | 3: 2.84 - 2.48 2833 165 0.74 32.16 1.24 0.23 1236.13| | 4: 2.47 - 2.25 2825 136 0.81 25.75 1.26 0.25 580.71| | 5: 2.25 - 2.09 2756 127 0.77 29.39 1.28 0.25 580.71| | 6: 2.09 - 1.97 2846 113 0.83 23.13 1.29 0.25 320.14| | 7: 1.97 - 1.87 2787 165 0.89 17.28 1.28 0.25 97.91| | 8: 1.87 - 1.79 2789 144 0.85 22.08 1.25 0.25 97.91| | 9: 1.79 - 1.72 2745 138 0.88 18.76 1.23 0.25 57.97| | 10: 1.72 - 1.66 2789 158 0.86 20.54 1.23 0.25 49.98| | 11: 1.66 - 1.61 2740 147 0.85 21.86 1.25 0.25 48.08| | 12: 1.61 - 1.56 2787 146 0.88 18.49 1.24 0.25 28.86| | 13: 1.56 - 1.52 2745 130 0.87 20.35 1.25 0.25 28.86| | 14: 1.52 - 1.48 2803 134 0.86 20.72 1.23 0.25 25.89| | 15: 1.48 - 1.45 2738 128 0.87 19.95 1.24 0.25 20.45| | 16: 1.45 - 1.42 2756 161 0.86 21.30 1.23 0.25 20.45| | 17: 1.42 - 1.39 2785 139 0.87 20.52 1.23 0.25 17.38| | 18: 1.39 - 1.36 2741 179 0.86 21.38 1.22 0.25 15.61| | 19: 1.36 - 1.34 2807 134 0.86 21.76 1.22 0.25 15.61| | 20: 1.34 - 1.32 2696 147 0.87 20.78 1.22 0.24 13.07| | 21: 1.32 - 1.30 2785 112 0.86 22.21 1.21 0.24 12.89| | 22: 1.29 - 1.27 2704 152 0.85 22.60 1.22 0.24 12.62| | 23: 1.27 - 1.26 2802 156 0.85 22.40 1.22 0.24 11.24| | 24: 1.26 - 1.24 2744 132 0.85 23.11 1.21 0.24 11.24| | 25: 1.24 - 1.22 2734 148 0.84 23.89 1.21 0.24 10.77| | 26: 1.22 - 1.21 2727 135 0.84 24.21 1.20 0.23 10.25| | 27: 1.21 - 1.19 2814 148 0.83 25.31 1.22 0.23 10.25| | 28: 1.19 - 1.18 2671 147 0.82 25.90 1.18 0.23 9.68| | 29: 1.18 - 1.16 2800 134 0.82 26.35 1.17 0.23 9.46| | 30: 1.16 - 1.15 2740 148 0.80 27.64 1.16 0.23 9.46| |alpha: min = 0.23 max = 0.25 mean = 0.24| |beta: min = 9.46 max = 1488.69 mean = 217.29| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.98 mean = 22.83| |phase err.(test): min = 0.00 max = 89.74 mean = 22.78| |-----------------------------------------------------------------------------| ----------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 : 0.084 0.261 1557 Z= 5.552 Angle : 5.318 21.366 2118 Z= 3.709 Chirality : 0.386 1.101 243 Planarity : 0.031 0.103 284 Dihedral : 13.847 99.154 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.54 % Allowed : 4.32 % Favored : 95.14 % Rotamer: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Cbeta Deviations : 27.03 % 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: -2.10 (0.47), residues: 224 helix: -2.20 (0.38), residues: 102 sheet: -1.12 (0.86), residues: 28 loop : -0.19 (0.58), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.150 0.035 ARG A 28 TYR 0.123 0.059 TYR A 141 PHE 0.085 0.028 PHE A 119 HIS 0.068 0.023 HIS A 115 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= 0.2614 r_free= 0.1970 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.792926 | | target function (ml) not normalized (work): 232667.511929 | | target function (ml) not normalized (free): 11841.761022 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2573 0.2614 0.1969 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2573 0.2614 0.1969 n_refl.: 87602 remove outliers: r(all,work,free)=0.1987 0.1990 0.1969 n_refl.: 87594 overall B=0.18 to atoms: r(all,work,free)=0.2009 0.2012 0.1982 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1654 0.1646 0.1793 n_refl.: 87594 remove outliers: r(all,work,free)=0.1653 0.1646 0.1793 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 0.3819 386.663 370.025 0.694 0.999 0.407 11.894-9.307 99.02 97 4 0.1881 614.196 593.297 0.932 1.001 0.380 9.237-7.194 100.00 213 7 0.2086 502.337 490.972 0.964 1.001 0.370 7.162-5.571 100.00 427 22 0.2299 376.976 365.281 0.937 1.001 0.288 5.546-4.326 100.00 867 58 0.1291 517.495 511.688 0.963 1.001 0.224 4.315-3.360 100.00 1859 96 0.1147 492.141 488.416 1.005 1.002 0.199 3.356-2.611 100.00 3867 181 0.1451 323.311 319.699 0.997 1.002 0.052 2.608-2.026 99.99 8198 413 0.1360 214.326 212.187 1.006 1.002 0.000 2.025-1.573 100.00 17313 902 0.1660 104.666 103.972 1.009 1.002 0.000 1.573-1.221 100.00 36679 1900 0.2066 46.413 45.096 1.000 1.002 0.000 1.221-1.150 99.97 13689 708 0.2600 29.243 26.939 0.965 1.002 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0405 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1646 r_free=0.1793 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN B Total number of N/Q/H flips: 1 r_work=0.1646 r_free=0.1793 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.245493 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1981.558983 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 0.1213 0.1461 0.0249 0.007 0.9 1.3 0.5 0.0 0 12.123 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.13 14.61 2.49 3.013 19.036 1981.559 0.017 12.31 15.21 2.90 2.968 19.391 1981.559 0.016 Individual atomic B min max mean iso aniso Overall: 8.57 117.95 20.74 2.88 0 1785 Protein: 8.57 117.95 17.66 2.88 0 1519 Water: 11.03 115.36 38.62 N/A 0 258 Other: 21.93 34.10 27.48 N/A 0 8 Chain A: 8.57 117.95 20.74 N/A 0 1785 Histogram: Values Number of atoms 8.57 - 19.51 1215 19.51 - 30.45 235 30.45 - 41.39 158 41.39 - 52.32 100 52.32 - 63.26 48 63.26 - 74.20 18 74.20 - 85.14 4 85.14 - 96.08 4 96.08 - 107.01 0 107.01 - 117.95 3 =========================== Idealize ADP of riding H ========================== r_work=0.1231 r_free=0.1521 r_work=0.1235 r_free=0.1525 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1235 r_free = 0.1525 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1234 r_free = 0.1527 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.24 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= 0.1234 r_free= 0.1527 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.015404 | | target function (ls_wunit_k1) not normalized (work): 1283.136670 | | target function (ls_wunit_k1) not normalized (free): 112.208798 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1248 0.1234 0.1527 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1689 0.1687 0.1759 n_refl.: 87593 remove outliers: r(all,work,free)=0.1689 0.1687 0.1759 n_refl.: 87593 overall B=0.12 to atoms: r(all,work,free)=0.1708 0.1707 0.1774 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1246 0.1232 0.1520 n_refl.: 87593 remove outliers: r(all,work,free)=0.1245 0.1231 0.1520 n_refl.: 87592 ======================== 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 95.83 87 5 0.3595 299.555 278.129 0.638 1.002 0.380 11.894-9.307 99.02 97 4 0.1612 479.871 468.290 0.911 1.003 0.380 9.237-7.194 100.00 213 7 0.1839 392.476 386.955 0.951 1.003 0.340 7.162-5.571 100.00 427 22 0.1728 294.531 288.887 0.927 1.003 0.280 5.546-4.326 100.00 867 58 0.0928 404.319 401.732 0.951 1.003 0.214 4.315-3.360 100.00 1859 96 0.0787 384.510 383.461 0.995 1.003 0.200 3.356-2.611 100.00 3867 181 0.1030 252.603 251.900 0.998 1.002 0.110 2.608-2.026 99.99 8198 413 0.0970 167.453 166.919 1.010 1.001 0.000 2.025-1.573 100.00 17313 902 0.1182 81.775 81.986 1.018 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1614 36.262 35.733 1.007 0.998 0.000 1.221-1.150 99.97 13689 708 0.2345 22.848 21.359 0.971 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0453 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1231 r_free=0.1520 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** Total number of N/Q/H flips: 1 r_work=0.1233 r_free=0.1522 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1233 r_free=0.1522 | n_water=258 | time (s): 2.260 (total time: 2.260) Filter (dist) r_work=0.1242 r_free=0.1520 | n_water=252 | time (s): 25.650 (total time: 27.910) Filter (q & B) r_work=0.1245 r_free=0.1519 | n_water=249 | time (s): 3.740 (total time: 31.650) Compute maps r_work=0.1245 r_free=0.1519 | n_water=249 | time (s): 1.780 (total time: 33.430) Filter (map) r_work=0.1262 r_free=0.1532 | n_water=235 | time (s): 3.750 (total time: 37.180) Find peaks r_work=0.1262 r_free=0.1532 | n_water=235 | time (s): 0.720 (total time: 37.900) Add new water r_work=0.1419 r_free=0.1674 | n_water=449 | time (s): 3.620 (total time: 41.520) Refine new water occ: r_work=0.1326 r_free=0.1563 adp: r_work=0.1245 r_free=0.1508 occ: r_work=0.1258 r_free=0.1508 adp: r_work=0.1222 r_free=0.1491 occ: r_work=0.1225 r_free=0.1480 adp: r_work=0.1215 r_free=0.1481 ADP+occupancy (water only), MIN, final r_work=0.1215 r_free=0.1481 r_work=0.1215 r_free=0.1481 | n_water=449 | time (s): 79.050 (total time: 120.570) Filter (q & B) r_work=0.1221 r_free=0.1488 | n_water=428 | time (s): 3.960 (total time: 124.530) Filter (dist only) r_work=0.1221 r_free=0.1488 | n_water=428 | time (s): 40.260 (total time: 164.790) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.436628 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1501.988965 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 0.1218 0.1505 0.0287 0.007 0.9 2.9 0.5 0.0 0 12.718 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.18 15.05 2.87 3.744 22.825 1501.989 0.015 12.04 14.94 2.89 4.004 22.726 1501.989 0.015 Individual atomic B min max mean iso aniso Overall: 8.85 113.07 22.95 2.57 193 1762 Protein: 8.85 113.07 17.57 2.57 0 1519 Water: 11.04 73.05 41.88 N/A 193 235 Other: 25.63 37.68 30.64 N/A 0 8 Chain A: 8.85 113.07 20.22 N/A 0 1762 Chain S: 19.19 69.56 47.83 N/A 193 0 Histogram: Values Number of atoms 8.85 - 19.27 1205 19.27 - 29.69 251 29.69 - 40.11 197 40.11 - 50.53 143 50.53 - 60.96 95 60.96 - 71.38 53 71.38 - 81.80 5 81.80 - 92.22 3 92.22 - 102.65 1 102.65 - 113.07 2 =========================== Idealize ADP of riding H ========================== r_work=0.1205 r_free=0.1494 r_work=0.1205 r_free=0.1494 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1205 r_free = 0.1494 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1206 r_free = 0.1482 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1206 r_free= 0.1482 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.014228 | | target function (ls_wunit_k1) not normalized (work): 1185.166223 | | target function (ls_wunit_k1) not normalized (free): 101.077262 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1219 0.1206 0.1482 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1611 0.1608 0.1708 n_refl.: 87592 remove outliers: r(all,work,free)=0.1611 0.1608 0.1708 n_refl.: 87592 overall B=0.03 to atoms: r(all,work,free)=0.1616 0.1613 0.1711 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1216 0.1203 0.1482 n_refl.: 87592 remove outliers: r(all,work,free)=0.1215 0.1201 0.1482 n_refl.: 87588 ======================== 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 91.67 83 5 0.3328 292.238 270.774 0.592 1.002 0.370 11.894-9.307 99.02 97 4 0.1521 479.871 480.548 0.919 1.003 0.370 9.237-7.194 100.00 213 7 0.1689 392.476 393.809 0.979 1.003 0.290 7.162-5.571 100.00 427 22 0.1494 294.531 290.617 0.945 1.003 0.229 5.546-4.326 100.00 867 58 0.0855 404.319 401.785 0.957 1.003 0.215 4.315-3.360 100.00 1859 96 0.0724 384.510 383.468 1.001 1.002 0.210 3.356-2.611 100.00 3867 181 0.0977 252.603 252.004 1.009 1.002 0.150 2.608-2.026 99.99 8198 413 0.0953 167.453 167.032 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1177 81.775 81.970 1.028 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1617 36.262 35.752 1.019 0.998 0.000 1.221-1.150 99.97 13689 708 0.2343 22.848 21.359 0.979 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0465 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1201 r_free=0.1482 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1201 r_free=0.1482 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1201 r_free=0.1482 | n_water=428 | time (s): 2.230 (total time: 2.230) Filter (dist) r_work=0.1201 r_free=0.1478 | n_water=425 | time (s): 37.130 (total time: 39.360) Filter (q & B) r_work=0.1201 r_free=0.1478 | n_water=425 | time (s): 1.340 (total time: 40.700) Compute maps r_work=0.1201 r_free=0.1478 | n_water=425 | time (s): 1.690 (total time: 42.390) Filter (map) r_work=0.1240 r_free=0.1482 | n_water=294 | time (s): 3.090 (total time: 45.480) Find peaks r_work=0.1240 r_free=0.1482 | n_water=294 | time (s): 0.730 (total time: 46.210) Add new water r_work=0.1372 r_free=0.1603 | n_water=482 | time (s): 2.740 (total time: 48.950) Refine new water occ: r_work=0.1269 r_free=0.1518 adp: r_work=0.1270 r_free=0.1520 occ: r_work=0.1246 r_free=0.1497 adp: r_work=0.1244 r_free=0.1498 occ: r_work=0.1230 r_free=0.1485 adp: r_work=0.1223 r_free=0.1481 ADP+occupancy (water only), MIN, final r_work=0.1223 r_free=0.1481 r_work=0.1223 r_free=0.1481 | n_water=482 | time (s): 147.830 (total time: 196.780) Filter (q & B) r_work=0.1226 r_free=0.1477 | n_water=451 | time (s): 3.410 (total time: 200.190) Filter (dist only) r_work=0.1226 r_free=0.1477 | n_water=451 | time (s): 35.730 (total time: 235.920) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.171479 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 48.911499 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 0.1232 0.1443 0.0211 0.006 0.9 3.8 0.5 0.0 0 1.086 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.32 14.43 2.11 3.587 22.022 48.911 3.725 12.16 13.93 1.77 4.139 21.826 48.911 3.651 Individual atomic B min max mean iso aniso Overall: 9.28 109.10 21.59 2.30 218 1760 Protein: 9.28 109.10 17.10 2.30 0 1519 Water: 11.45 71.80 36.62 N/A 218 233 Other: 21.63 33.14 27.25 N/A 0 8 Chain A: 9.28 109.10 19.72 N/A 0 1760 Chain S: 15.99 65.37 36.69 N/A 218 0 Histogram: Values Number of atoms 9.28 - 19.26 1238 19.26 - 29.24 272 29.24 - 39.23 222 39.23 - 49.21 140 49.21 - 59.19 73 59.19 - 69.17 22 69.17 - 79.15 5 79.15 - 89.13 3 89.13 - 99.11 1 99.11 - 109.10 2 =========================== Idealize ADP of riding H ========================== r_work=0.1216 r_free=0.1393 r_work=0.1217 r_free=0.1394 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1217 r_free = 0.1394 target_work(ml) = 3.651 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1209 r_free = 0.1389 target_work(ml) = 3.647 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87588 (all), 4.90 % free)------------| | | | r_work= 0.1209 r_free= 0.1389 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.647375 | | target function (ml) not normalized (work): 303797.161530 | | target function (ml) not normalized (free): 16031.113860 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1218 0.1209 0.1389 n_refl.: 87588 re-set all scales: r(all,work,free)=0.1537 0.1537 0.1580 n_refl.: 87588 remove outliers: r(all,work,free)=0.1537 0.1537 0.1580 n_refl.: 87588 overall B=-0.01 to atoms: r(all,work,free)=0.1535 0.1535 0.1578 n_refl.: 87588 bulk-solvent and scaling: r(all,work,free)=0.1207 0.1199 0.1368 n_refl.: 87588 remove outliers: r(all,work,free)=0.1203 0.1195 0.1368 n_refl.: 87579 ======================== 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 0.3714 291.480 255.903 0.477 0.999 0.330 11.894-9.307 97.06 95 4 0.2316 481.964 462.203 0.848 1.000 0.330 9.237-7.194 98.18 209 7 0.2337 387.101 385.648 0.947 1.001 0.170 7.162-5.571 100.00 427 22 0.2077 294.531 283.941 0.913 1.001 0.170 5.546-4.326 100.00 867 58 0.1093 404.319 400.122 0.950 1.001 0.163 4.315-3.360 100.00 1859 96 0.0935 384.510 382.125 0.992 1.002 0.157 3.356-2.611 100.00 3867 181 0.1160 252.603 251.037 0.998 1.002 0.062 2.608-2.026 99.99 8198 413 0.1049 167.453 166.649 1.010 1.002 0.000 2.025-1.573 100.00 17313 902 0.1001 81.775 81.995 1.025 1.002 0.000 1.573-1.221 100.00 36679 1900 0.1288 36.262 35.845 1.018 1.002 0.000 1.221-1.150 99.97 13689 708 0.2130 22.848 21.382 0.971 1.002 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0309 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1195 r_free=0.1368 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1195 r_free=0.1368 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1195 r_free=0.1368 | n_water=451 | time (s): 1.630 (total time: 1.630) Filter (dist) r_work=0.1195 r_free=0.1368 | n_water=450 | time (s): 35.440 (total time: 37.070) Filter (q & B) r_work=0.1195 r_free=0.1367 | n_water=449 | time (s): 3.260 (total time: 40.330) Compute maps r_work=0.1195 r_free=0.1367 | n_water=449 | time (s): 1.670 (total time: 42.000) Filter (map) r_work=0.1218 r_free=0.1355 | n_water=313 | time (s): 2.810 (total time: 44.810) Find peaks r_work=0.1218 r_free=0.1355 | n_water=313 | time (s): 0.420 (total time: 45.230) Add new water r_work=0.1284 r_free=0.1421 | n_water=482 | time (s): 2.210 (total time: 47.440) Refine new water occ: r_work=0.1213 r_free=0.1362 adp: r_work=0.1214 r_free=0.1363 occ: r_work=0.1198 r_free=0.1352 adp: r_work=0.1196 r_free=0.1351 occ: r_work=0.1187 r_free=0.1344 adp: r_work=0.1183 r_free=0.1341 ADP+occupancy (water only), MIN, final r_work=0.1183 r_free=0.1341 r_work=0.1183 r_free=0.1341 | n_water=482 | time (s): 156.240 (total time: 203.680) Filter (q & B) r_work=0.1190 r_free=0.1347 | n_water=442 | time (s): 3.810 (total time: 207.490) Filter (dist only) r_work=0.1197 r_free=0.1343 | n_water=441 | time (s): 35.640 (total time: 243.130) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.271713 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 44.990793 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 0.1200 0.1363 0.0164 0.007 1.0 5.1 0.5 0.0 0 1.136 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.00 13.63 1.64 3.388 21.324 44.991 3.637 11.88 13.63 1.75 3.642 21.245 44.991 3.624 Individual atomic B min max mean iso aniso Overall: 9.32 104.52 21.13 2.14 211 1757 Protein: 9.32 104.52 16.92 2.14 0 1519 Water: 11.43 70.98 35.53 N/A 211 230 Other: 20.85 30.53 25.92 N/A 0 8 Chain A: 9.32 104.52 19.47 N/A 0 1757 Chain S: 15.90 59.68 34.93 N/A 211 0 Histogram: Values Number of atoms 9.32 - 18.84 1226 18.84 - 28.36 278 28.36 - 37.88 223 37.88 - 47.40 128 47.40 - 56.92 77 56.92 - 66.44 22 66.44 - 75.96 9 75.96 - 85.48 2 85.48 - 95.00 1 95.00 - 104.52 2 =========================== Idealize ADP of riding H ========================== r_work=0.1189 r_free=0.1363 r_work=0.1189 r_free=0.1363 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1189 r_free = 0.1363 target_work(ml) = 3.625 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1184 r_free = 0.1366 target_work(ml) = 3.624 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87579 (all), 4.91 % free)------------| | | | r_work= 0.1184 r_free= 0.1366 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.623957 | | target function (ml) not normalized (work): 301813.998429 | | target function (ml) not normalized (free): 15958.281790 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1193 0.1184 0.1366 n_refl.: 87579 re-set all scales: r(all,work,free)=0.1505 0.1504 0.1554 n_refl.: 87579 remove outliers: r(all,work,free)=0.1505 0.1504 0.1554 n_refl.: 87579 overall B=-0.02 to atoms: r(all,work,free)=0.1503 0.1501 0.1552 n_refl.: 87579 bulk-solvent and scaling: r(all,work,free)=0.1193 0.1184 0.1364 n_refl.: 87579 remove outliers: r(all,work,free)=0.1192 0.1183 0.1364 n_refl.: 87577 ======================== 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 87.50 79 5 0.3828 286.738 260.575 0.452 1.000 0.287 11.894-9.307 96.08 94 4 0.2443 485.898 467.512 0.853 1.001 0.263 9.237-7.194 98.18 209 7 0.2404 387.101 380.394 0.925 1.002 0.140 7.162-5.571 100.00 427 22 0.2135 294.531 284.057 0.905 1.002 0.130 5.546-4.326 100.00 867 58 0.1132 404.319 400.041 0.951 1.002 0.128 4.315-3.360 100.00 1859 96 0.0941 384.510 382.048 0.994 1.002 0.127 3.356-2.611 100.00 3867 181 0.1177 252.603 250.762 1.001 1.001 0.100 2.608-2.026 99.99 8198 413 0.1040 167.453 166.520 1.012 1.001 0.000 2.025-1.573 100.00 17313 902 0.0967 81.775 82.034 1.028 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1237 36.262 35.888 1.022 0.998 0.000 1.221-1.150 99.97 13689 708 0.2121 22.848 21.473 0.980 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0421 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1183 r_free=0.1364 After: r_work=0.1184 r_free=0.1364 ================================== NQH flips ================================== r_work=0.1184 r_free=0.1364 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=0.1184 r_free=0.1364 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1184 r_free=0.1364 | n_water=441 | time (s): 2.020 (total time: 2.020) Filter (dist) r_work=0.1184 r_free=0.1364 | n_water=441 | time (s): 36.030 (total time: 38.050) Filter (q & B) r_work=0.1184 r_free=0.1362 | n_water=438 | time (s): 2.710 (total time: 40.760) Compute maps r_work=0.1184 r_free=0.1362 | n_water=438 | time (s): 1.100 (total time: 41.860) Filter (map) r_work=0.1202 r_free=0.1354 | n_water=341 | time (s): 2.810 (total time: 44.670) Find peaks r_work=0.1202 r_free=0.1354 | n_water=341 | time (s): 0.430 (total time: 45.100) Add new water r_work=0.1252 r_free=0.1397 | n_water=496 | time (s): 2.260 (total time: 47.360) Refine new water occ: r_work=0.1196 r_free=0.1340 adp: r_work=0.1196 r_free=0.1342 occ: r_work=0.1184 r_free=0.1330 adp: r_work=0.1182 r_free=0.1332 occ: r_work=0.1175 r_free=0.1325 adp: r_work=0.1171 r_free=0.1325 ADP+occupancy (water only), MIN, final r_work=0.1171 r_free=0.1325 r_work=0.1171 r_free=0.1325 | n_water=496 | time (s): 202.940 (total time: 250.300) Filter (q & B) r_work=0.1178 r_free=0.1333 | n_water=464 | time (s): 3.690 (total time: 253.990) Filter (dist only) r_work=0.1177 r_free=0.1330 | n_water=462 | time (s): 38.870 (total time: 292.860) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.915168 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 39.103585 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 0.1201 0.1348 0.0148 0.008 1.1 5.1 0.5 0.0 0 0.958 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.01 13.48 1.48 3.280 21.173 39.104 3.627 12.05 13.52 1.47 3.484 21.105 39.104 3.623 Individual atomic B min max mean iso aniso Overall: 9.30 100.86 21.09 2.00 233 1756 Protein: 9.30 100.86 16.75 2.00 0 1519 Water: 11.29 70.34 35.30 N/A 233 229 Other: 20.55 29.03 25.29 N/A 0 8 Chain A: 9.30 100.86 19.26 N/A 0 1756 Chain S: 14.70 59.47 34.92 N/A 233 0 Histogram: Values Number of atoms 9.30 - 18.45 1219 18.45 - 27.61 286 27.61 - 36.77 216 36.77 - 45.92 147 45.92 - 55.08 78 55.08 - 64.24 29 64.24 - 73.39 10 73.39 - 82.55 1 82.55 - 91.71 1 91.71 - 100.86 2 =========================== Idealize ADP of riding H ========================== r_work=0.1205 r_free=0.1352 r_work=0.1205 r_free=0.1352 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1205 r_free = 0.1352 target_work(ml) = 3.623 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1201 r_free = 0.1350 target_work(ml) = 3.622 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87577 (all), 4.91 % free)------------| | | | r_work= 0.1201 r_free= 0.1350 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.621709 | | target function (ml) not normalized (work): 301619.567779 | | target function (ml) not normalized (free): 15920.230921 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2919 171 0.1418 0.1364 5.7179 5.5974| | 2: 3.57 - 2.84 1.00 2888 124 0.1126 0.1440 5.1881 5.2612| | 3: 2.83 - 2.48 1.00 2820 163 0.1237 0.1297 4.9938 5.0138| | 4: 2.47 - 2.25 1.00 2825 136 0.1046 0.1134 4.6981 4.7406| | 5: 2.25 - 2.09 1.00 2756 127 0.1005 0.1076 4.634 4.7046| | 6: 2.09 - 1.97 1.00 2846 113 0.0967 0.1158 4.3408 4.4625| | 7: 1.97 - 1.87 1.00 2787 165 0.0994 0.1183 4.0737 4.1559| | 8: 1.87 - 1.79 1.00 2789 144 0.1021 0.1190 3.9844 4.0477| | 9: 1.79 - 1.72 1.00 2745 138 0.0937 0.1305 3.7075 3.9271| | 10: 1.72 - 1.66 1.00 2831 160 0.0999 0.1256 3.6318 3.7725| | 11: 1.66 - 1.61 1.00 2712 147 0.0972 0.1093 3.5688 3.5974| | 12: 1.61 - 1.56 1.00 2773 144 0.0910 0.1133 3.3426 3.4674| | 13: 1.56 - 1.52 1.00 2745 130 0.0975 0.1040 3.333 3.4251| | 14: 1.52 - 1.48 1.00 2803 134 0.0993 0.1087 3.2607 3.3275| | 15: 1.48 - 1.45 1.00 2738 128 0.1011 0.1364 3.1676 3.3354| | 16: 1.45 - 1.42 1.00 2756 161 0.1063 0.1275 3.1488 3.2493| | 17: 1.42 - 1.39 1.00 2785 139 0.1123 0.1301 3.1155 3.2454| | 18: 1.39 - 1.36 1.00 2741 179 0.1162 0.1393 3.092 3.278| | 19: 1.36 - 1.34 1.00 2807 134 0.1222 0.1574 3.0998 3.2575| | 20: 1.34 - 1.32 1.00 2696 147 0.1322 0.1498 3.0915 3.1382| | 21: 1.32 - 1.30 1.00 2785 112 0.1419 0.1588 3.0901 3.1524| | 22: 1.29 - 1.27 1.00 2704 152 0.1488 0.1908 3.0921 3.2807| | 23: 1.27 - 1.26 1.00 2802 156 0.1582 0.1853 3.1085 3.2128| | 24: 1.26 - 1.24 1.00 2744 132 0.1629 0.1772 3.099 3.2036| | 25: 1.24 - 1.22 1.00 2733 148 0.1800 0.2321 3.1155 3.2966| | 26: 1.22 - 1.21 1.00 2727 135 0.1870 0.1778 3.1277 3.1995| | 27: 1.21 - 1.19 1.00 2814 148 0.2016 0.2073 3.144 3.1452| | 28: 1.19 - 1.18 1.00 2671 147 0.2149 0.2361 3.143 3.1748| | 29: 1.18 - 1.16 1.00 2800 134 0.2215 0.2339 3.1294 3.2188| | 30: 1.16 - 1.15 1.00 2739 148 0.2372 0.2482 3.1174 3.1666| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2919 171 0.95 8.65 1.00 0.97 5887.72| | 2: 3.57 - 2.84 2888 124 0.92 12.78 1.01 0.97 5887.72| | 3: 2.83 - 2.48 2820 163 0.89 16.92 0.99 0.98 4941.61| | 4: 2.47 - 2.25 2825 136 0.91 14.14 1.00 0.98 2501.91| | 5: 2.25 - 2.09 2756 127 0.90 16.30 1.01 0.98 2501.91| | 6: 2.09 - 1.97 2846 113 0.92 13.29 1.02 0.98 1481.15| | 7: 1.97 - 1.87 2787 165 0.94 10.58 1.02 0.98 610.59| | 8: 1.87 - 1.79 2789 144 0.92 14.11 1.00 0.98 610.59| | 9: 1.79 - 1.72 2745 138 0.93 11.28 0.98 0.98 333.49| | 10: 1.72 - 1.66 2831 160 0.93 12.15 0.98 0.98 278.00| | 11: 1.66 - 1.61 2712 147 0.93 12.80 0.98 0.98 265.40| | 12: 1.61 - 1.56 2773 144 0.95 9.48 0.99 0.98 146.51| | 13: 1.56 - 1.52 2745 130 0.94 10.99 1.02 0.98 146.51| | 14: 1.52 - 1.48 2803 134 0.94 11.16 1.02 0.98 131.22| | 15: 1.48 - 1.45 2738 128 0.95 10.31 1.02 0.99 103.21| | 16: 1.45 - 1.42 2756 161 0.94 11.48 1.02 0.99 103.21| | 17: 1.42 - 1.39 2785 139 0.94 11.46 1.01 0.99 93.35| | 18: 1.39 - 1.36 2741 179 0.94 11.67 1.01 0.99 87.65| | 19: 1.36 - 1.34 2807 134 0.94 12.23 1.00 0.99 87.65| | 20: 1.34 - 1.32 2696 147 0.94 12.37 0.99 0.97 82.40| | 21: 1.32 - 1.30 2785 112 0.93 13.36 0.99 0.97 82.03| | 22: 1.29 - 1.27 2704 152 0.93 13.89 0.98 0.97 82.19| | 23: 1.27 - 1.26 2802 156 0.92 14.84 0.98 0.95 82.99| | 24: 1.26 - 1.24 2744 132 0.92 14.92 0.97 0.95 82.99| | 25: 1.24 - 1.22 2733 148 0.91 16.31 0.96 0.94 84.53| | 26: 1.22 - 1.21 2727 135 0.90 18.06 1.03 0.94 86.24| | 27: 1.21 - 1.19 2814 148 0.89 18.68 1.02 0.94 86.24| | 28: 1.19 - 1.18 2671 147 0.88 20.18 1.01 0.93 89.66| | 29: 1.18 - 1.16 2800 134 0.88 20.51 0.99 0.93 90.94| | 30: 1.16 - 1.15 2739 148 0.86 21.93 0.98 0.93 90.94| |alpha: min = 0.93 max = 0.99 mean = 0.97| |beta: min = 82.03 max = 5887.72 mean = 927.05| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 90.00 mean = 13.88| |phase err.(test): min = 0.00 max = 89.13 mean = 14.00| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1208 0.1201 0.1350 n_refl.: 87577 re-set all scales: r(all,work,free)=0.1512 0.1512 0.1541 n_refl.: 87577 remove outliers: r(all,work,free)=0.1512 0.1512 0.1541 n_refl.: 87577 overall B=-0.01 to atoms: r(all,work,free)=0.1510 0.1510 0.1539 n_refl.: 87577 bulk-solvent and scaling: r(all,work,free)=0.1208 0.1200 0.1353 n_refl.: 87577 remove outliers: r(all,work,free)=0.1206 0.1199 0.1353 n_refl.: 87573 ======================== 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 87.50 79 5 0.4082 286.738 250.835 0.427 1.001 0.307 11.894-9.307 93.14 91 4 0.2477 472.908 457.816 0.847 1.003 0.205 9.237-7.194 97.73 208 7 0.2511 386.638 380.118 0.913 1.003 0.111 7.162-5.571 100.00 427 22 0.2204 294.531 283.539 0.895 1.003 0.110 5.546-4.326 100.00 867 58 0.1187 404.319 399.823 0.950 1.003 0.110 4.315-3.360 100.00 1859 96 0.0981 384.510 381.704 0.993 1.003 0.110 3.356-2.611 100.00 3867 181 0.1200 252.603 250.758 1.001 1.002 0.053 2.608-2.026 99.99 8198 413 0.1051 167.453 166.419 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0973 81.775 82.003 1.029 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1230 36.262 35.874 1.024 0.995 0.000 1.221-1.150 99.97 13689 708 0.2119 22.848 21.458 0.984 0.993 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0396 ================= 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 : 0.2614 0.1970 0.084 5.318 8.8 119.3 19.9 258 0.000 1_bss: 0.1646 0.1793 0.084 5.318 9.0 119.5 20.1 258 0.000 1_settarget: 0.1646 0.1793 0.084 5.318 9.0 119.5 20.1 258 0.000 1_nqh: 0.1646 0.1793 0.084 5.318 9.0 119.5 20.1 258 0.003 1_weight: 0.1646 0.1793 0.084 5.318 9.0 119.5 20.1 258 0.003 1_xyzrec: 0.1213 0.1461 0.007 0.949 9.0 119.5 20.1 258 0.128 1_adp: 0.1231 0.1521 0.007 0.949 8.6 118.0 20.7 258 0.128 1_regHadp: 0.1235 0.1525 0.007 0.949 8.6 118.0 20.7 258 0.128 1_occ: 0.1234 0.1527 0.007 0.949 8.6 118.0 20.7 258 0.128 2_bss: 0.1231 0.1520 0.007 0.949 8.7 118.1 20.9 258 0.128 2_settarget: 0.1231 0.1520 0.007 0.949 8.7 118.1 20.9 258 0.128 2_updatecdl: 0.1231 0.1520 0.007 0.956 8.7 118.1 20.9 258 0.128 2_nqh: 0.1233 0.1522 0.007 0.956 8.7 118.1 20.9 258 0.131 2_sol: 0.1221 0.1488 0.007 0.956 8.7 118.1 23.1 428 n/a 2_weight: 0.1221 0.1488 0.007 0.956 8.7 118.1 23.1 428 n/a 2_xyzrec: 0.1218 0.1505 0.007 0.894 8.7 118.1 23.1 428 n/a 2_adp: 0.1205 0.1494 0.007 0.894 8.8 113.1 22.9 428 n/a 2_regHadp: 0.1205 0.1494 0.007 0.894 8.8 113.1 22.9 428 n/a 2_occ: 0.1206 0.1482 0.007 0.894 8.8 113.1 22.9 428 n/a 3_bss: 0.1201 0.1482 0.007 0.894 8.9 113.1 23.0 428 n/a 3_settarget: 0.1201 0.1482 0.007 0.894 8.9 113.1 23.0 428 n/a 3_updatecdl: 0.1201 0.1482 0.007 0.894 8.9 113.1 23.0 428 n/a 3_nqh: 0.1201 0.1482 0.007 0.894 8.9 113.1 23.0 428 n/a 3_sol: 0.1226 0.1477 0.007 0.894 8.9 113.1 21.9 451 n/a 3_weight: 0.1226 0.1477 0.007 0.894 8.9 113.1 21.9 451 n/a 3_xyzrec: 0.1232 0.1443 0.006 0.937 8.9 113.1 21.9 451 n/a 3_adp: 0.1216 0.1393 0.006 0.937 9.3 109.1 21.6 451 n/a 3_regHadp: 0.1217 0.1394 0.006 0.937 9.3 109.1 21.6 451 n/a 3_occ: 0.1209 0.1389 0.006 0.937 9.3 109.1 21.6 451 n/a 4_bss: 0.1195 0.1368 0.006 0.937 9.3 109.1 21.6 451 n/a 4_settarget: 0.1195 0.1368 0.006 0.937 9.3 109.1 21.6 451 n/a 4_updatecdl: 0.1195 0.1368 0.006 0.936 9.3 109.1 21.6 451 n/a 4_nqh: 0.1195 0.1368 0.006 0.936 9.3 109.1 21.6 451 n/a 4_sol: 0.1197 0.1343 0.006 0.936 9.3 109.1 21.3 441 n/a 4_weight: 0.1197 0.1343 0.006 0.936 9.3 109.1 21.3 441 n/a 4_xyzrec: 0.1200 0.1363 0.007 0.986 9.3 109.1 21.3 441 n/a 4_adp: 0.1189 0.1363 0.007 0.986 9.3 104.5 21.1 441 n/a 4_regHadp: 0.1189 0.1363 0.007 0.986 9.3 104.5 21.1 441 n/a 4_occ: 0.1184 0.1366 0.007 0.986 9.3 104.5 21.1 441 n/a 5_bss: 0.1183 0.1364 0.007 0.986 9.3 104.5 21.1 441 n/a 5_settarget: 0.1183 0.1364 0.007 0.986 9.3 104.5 21.1 441 n/a 5_updatecdl: 0.1183 0.1364 0.007 0.987 9.3 104.5 21.1 441 n/a 5_setrh: 0.1184 0.1364 0.007 0.987 9.3 104.5 21.1 441 n/a 5_nqh: 0.1184 0.1364 0.007 0.987 9.3 104.5 21.1 441 n/a 5_sol: 0.1177 0.1330 0.007 0.987 9.3 104.5 21.2 462 n/a 5_weight: 0.1177 0.1330 0.007 0.987 9.3 104.5 21.2 462 n/a 5_xyzrec: 0.1201 0.1348 0.008 1.058 9.3 104.5 21.2 462 n/a 5_adp: 0.1205 0.1352 0.008 1.058 9.3 100.9 21.1 462 n/a 5_regHadp: 0.1205 0.1352 0.008 1.058 9.3 100.9 21.1 462 n/a 5_occ: 0.1201 0.1350 0.008 1.058 9.3 100.9 21.1 462 n/a end: 0.1199 0.1353 0.008 1.058 9.3 100.8 21.1 462 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_7326401_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_7326401_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.8200 Refinement macro-cycles (run) : 3341.5000 Write final files (write_after_run_outputs) : 67.3700 Total : 3413.6900 Total CPU time: 57.50 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:09:13 PST -0800 (1735452553.65 s) Start R-work = 0.1646, R-free = 0.1793 Final R-work = 0.1199, R-free = 0.1353 =============================================================================== Job complete usr+sys time: 3556.07 seconds wall clock time: 64 minutes 31.69 seconds (3871.69 seconds total)