Starting phenix.refine on Sat Dec 28 21:06:31 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8736282.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_8736282.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8736282.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 1 residue(s): 0.01s 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: 2.33, per 1000 atoms: 0.69 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: 0.63 Conformation dependent library (CDL) restraints added in 215.5 milliseconds Time building geometry restraints manager: 0.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.61 - 0.87: 288 0.87 - 1.13: 1291 1.13 - 1.39: 588 1.39 - 1.65: 919 1.65 - 1.91: 67 Bond restraints: 3153 Sorted by residual: bond pdb=" CA PRO A 73 " pdb=" C PRO A 73 " ideal model delta sigma weight residual 1.521 1.318 0.203 1.20e-02 6.94e+03 2.87e+02 bond pdb=" C LEU A 185 " pdb=" O LEU A 185 " ideal model delta sigma weight residual 1.236 1.013 0.223 1.32e-02 5.74e+03 2.85e+02 bond pdb=" CA ATYR A 67 " pdb=" C ATYR A 67 " ideal model delta sigma weight residual 1.522 1.322 0.200 1.19e-02 7.06e+03 2.83e+02 bond pdb=" C VAL A 51 " pdb=" O VAL A 51 " ideal model delta sigma weight residual 1.237 1.417 -0.180 1.08e-02 8.57e+03 2.77e+02 bond pdb=" CA ILE A 31 " pdb=" C ILE A 31 " ideal model delta sigma weight residual 1.523 1.333 0.190 1.14e-02 7.69e+03 2.77e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.28: 3452 5.28 - 10.55: 1819 10.55 - 15.82: 448 15.82 - 21.09: 54 21.09 - 26.37: 4 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O GLY A 40 " pdb=" C GLY A 40 " pdb=" N BLYS A 41 " ideal model delta sigma weight residual 123.35 108.99 14.36 9.50e-01 1.11e+00 2.28e+02 angle pdb=" CA GLY A 174 " pdb=" C GLY A 174 " pdb=" O GLY A 174 " ideal model delta sigma weight residual 122.57 135.23 -12.66 9.20e-01 1.18e+00 1.89e+02 angle pdb=" O GLY A 136 " pdb=" C GLY A 136 " pdb=" N GLY A 137 " ideal model delta sigma weight residual 122.42 105.72 16.70 1.31e+00 5.83e-01 1.62e+02 angle pdb=" OE1 GLN A 95 " pdb=" CD GLN A 95 " pdb=" NE2 GLN A 95 " ideal model delta sigma weight residual 122.60 109.95 12.65 1.00e+00 1.00e+00 1.60e+02 angle pdb=" O VAL A 35 " pdb=" C VAL A 35 " pdb=" N ALA A 36 " ideal model delta sigma weight residual 122.62 108.76 13.86 1.17e+00 7.31e-01 1.40e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.87: 958 17.87 - 35.74: 99 35.74 - 53.61: 38 53.61 - 71.48: 15 71.48 - 89.35: 1 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: 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 180.00 154.76 25.24 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA VAL A 35 " pdb=" C VAL A 35 " pdb=" N ALA A 36 " pdb=" CA ALA A 36 " ideal model delta harmonic sigma weight residual -180.00 -156.61 -23.39 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA LYS A 182 " pdb=" C LYS A 182 " pdb=" N ALA A 183 " pdb=" CA ALA A 183 " ideal model delta harmonic sigma weight residual -180.00 -157.36 -22.64 0 5.00e+00 4.00e-02 2.05e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.004 - 0.200: 92 0.200 - 0.397: 73 0.397 - 0.593: 41 0.593 - 0.789: 29 0.789 - 0.986: 8 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA PHE A 119 " pdb=" N PHE A 119 " pdb=" C PHE A 119 " pdb=" CB PHE A 119 " both_signs ideal model delta sigma weight residual False 2.51 1.52 0.99 2.00e-01 2.50e+01 2.43e+01 chirality pdb=" CA VAL A 23 " pdb=" N VAL A 23 " pdb=" C VAL A 23 " pdb=" CB VAL A 23 " both_signs ideal model delta sigma weight residual False 2.44 3.36 -0.92 2.00e-01 2.50e+01 2.12e+01 chirality pdb=" CA ALA A 183 " pdb=" N ALA A 183 " pdb=" C ALA A 183 " pdb=" CB ALA A 183 " both_signs ideal model delta sigma weight residual False 2.48 3.39 -0.90 2.00e-01 2.50e+01 2.04e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " -0.077 2.00e-02 2.50e+03 5.81e-02 1.01e+02 pdb=" CG ATYR A 67 " 0.056 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " 0.004 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " 0.101 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " 0.073 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " 0.042 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " -0.003 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " -0.057 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " 0.008 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " -0.085 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " -0.059 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 145 " -0.061 9.50e-02 1.11e+02 6.84e-02 9.63e+01 pdb=" NE ARG A 145 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARG A 145 " -0.061 2.00e-02 2.50e+03 pdb=" NH1 ARG A 145 " 0.027 2.00e-02 2.50e+03 pdb=" NH2 ARG A 145 " 0.077 2.00e-02 2.50e+03 pdb="HH11 ARG A 145 " -0.067 2.00e-02 2.50e+03 pdb="HH12 ARG A 145 " 0.099 2.00e-02 2.50e+03 pdb="HH21 ARG A 145 " 0.023 2.00e-02 2.50e+03 pdb="HH22 ARG A 145 " -0.113 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.086 2.00e-02 2.50e+03 5.52e-02 9.13e+01 pdb=" CG PHE A 164 " 0.111 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.040 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " -0.079 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.037 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.077 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.008 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.015 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.030 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.002 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.015 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.32: 1060 2.32 - 2.89: 8105 2.89 - 3.46: 10509 3.46 - 4.03: 15335 4.03 - 4.60: 21607 Nonbonded interactions: 56616 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.754 2.100 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.778 2.450 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.813 2.100 nonbonded pdb=" H THR A 124 " pdb=" HG1 THR A 154 " model vdw 1.834 2.100 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.834 2.450 ... (remaining 56611 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_8736282_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= 0.2612 r_free= 0.1988 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.799588 | | target function (ml) not normalized (work): 233222.447168 | | target function (ml) not normalized (free): 11870.779398 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3018 0.2115 7.0143 4.9474| | 2: 3.57 - 2.84 1.00 2876 122 0.2418 0.1840 4.3513 4.3614| | 3: 2.84 - 2.48 1.00 2833 165 0.2372 0.1778 4.137 4.1642| | 4: 2.47 - 2.25 1.00 2825 136 0.2323 0.1464 3.8442 3.8312| | 5: 2.25 - 2.09 1.00 2756 127 0.2489 0.1678 3.8105 3.8507| | 6: 2.09 - 1.97 1.00 2846 113 0.2568 0.1744 3.4794 3.5643| | 7: 1.97 - 1.87 1.00 2787 165 0.2517 0.1824 3.1488 3.2053| | 8: 1.87 - 1.79 1.00 2789 144 0.2514 0.1916 3.0909 3.1685| | 9: 1.79 - 1.72 1.00 2745 138 0.2470 0.1926 2.9163 2.9206| | 10: 1.72 - 1.66 1.00 2789 158 0.2388 0.2160 2.8368 2.9399| | 11: 1.66 - 1.61 1.00 2740 147 0.2531 0.1836 2.7522 2.7698| | 12: 1.61 - 1.56 1.00 2787 146 0.2574 0.2073 2.6593 2.7021| | 13: 1.56 - 1.52 1.00 2745 130 0.2568 0.1999 2.5905 2.6694| | 14: 1.52 - 1.48 1.00 2803 134 0.2552 0.1980 2.5124 2.5743| | 15: 1.48 - 1.45 1.00 2738 128 0.2577 0.1961 2.4258 2.4594| | 16: 1.45 - 1.42 1.00 2756 161 0.2668 0.2219 2.4077 2.4884| | 17: 1.42 - 1.39 1.00 2785 139 0.2707 0.2257 2.3424 2.3854| | 18: 1.39 - 1.36 1.00 2741 179 0.2702 0.2069 2.2704 2.2648| | 19: 1.36 - 1.34 1.00 2807 134 0.2727 0.2415 2.2598 2.3313| | 20: 1.34 - 1.32 1.00 2696 147 0.2688 0.2467 2.2038 2.2454| | 21: 1.32 - 1.30 1.00 2785 112 0.2698 0.2329 2.1657 2.1808| | 22: 1.29 - 1.27 1.00 2704 152 0.2712 0.2569 2.1278 2.1948| | 23: 1.27 - 1.26 1.00 2802 156 0.2853 0.2526 2.1172 2.1711| | 24: 1.26 - 1.24 1.00 2744 132 0.2789 0.2370 2.0779 2.0959| | 25: 1.24 - 1.22 1.00 2734 148 0.2887 0.2565 2.0526 2.0817| | 26: 1.22 - 1.21 1.00 2727 135 0.2845 0.2534 2.0077 2.1243| | 27: 1.21 - 1.19 1.00 2814 148 0.2947 0.2558 2.0064 2.0303| | 28: 1.19 - 1.18 1.00 2671 147 0.3042 0.2829 2.0015 1.9986| | 29: 1.18 - 1.16 1.00 2800 134 0.3023 0.2805 1.9842 2.0476| | 30: 1.16 - 1.15 1.00 2740 148 0.3063 0.2976 1.9392 1.992| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 19.04 0.76 0.23 1516.93| | 2: 3.57 - 2.84 2876 122 0.80 26.27 1.27 0.23 1516.93| | 3: 2.84 - 2.48 2833 165 0.73 32.42 1.25 0.24 1258.58| | 4: 2.47 - 2.25 2825 136 0.81 25.84 1.25 0.25 588.12| | 5: 2.25 - 2.09 2756 127 0.77 29.66 1.28 0.25 588.12| | 6: 2.09 - 1.97 2846 113 0.83 23.22 1.30 0.25 323.40| | 7: 1.97 - 1.87 2787 165 0.90 17.08 1.28 0.26 97.63| | 8: 1.87 - 1.79 2789 144 0.85 21.79 1.25 0.26 97.63| | 9: 1.79 - 1.72 2745 138 0.87 19.40 1.24 0.26 59.61| | 10: 1.72 - 1.66 2789 158 0.86 20.93 1.21 0.25 52.00| | 11: 1.66 - 1.61 2740 147 0.84 22.44 1.25 0.25 50.15| | 12: 1.61 - 1.56 2787 146 0.88 19.03 1.24 0.25 31.41| | 13: 1.56 - 1.52 2745 130 0.86 21.06 1.24 0.25 31.41| | 14: 1.52 - 1.48 2803 134 0.86 21.37 1.23 0.25 27.93| | 15: 1.48 - 1.45 2738 128 0.87 20.35 1.24 0.25 21.55| | 16: 1.45 - 1.42 2756 161 0.85 22.05 1.23 0.25 21.55| | 17: 1.42 - 1.39 2785 139 0.86 21.25 1.24 0.25 18.14| | 18: 1.39 - 1.36 2741 179 0.86 21.39 1.24 0.25 16.16| | 19: 1.36 - 1.34 2807 134 0.85 22.43 1.22 0.25 16.16| | 20: 1.34 - 1.32 2696 147 0.86 21.32 1.21 0.24 13.45| | 21: 1.32 - 1.30 2785 112 0.85 22.36 1.20 0.24 13.26| | 22: 1.29 - 1.27 2704 152 0.85 22.77 1.21 0.24 12.94| | 23: 1.27 - 1.26 2802 156 0.85 22.63 1.22 0.24 11.32| | 24: 1.26 - 1.24 2744 132 0.85 23.06 1.20 0.24 11.32| | 25: 1.24 - 1.22 2734 148 0.84 23.95 1.21 0.24 10.80| | 26: 1.22 - 1.21 2727 135 0.84 24.31 1.20 0.23 10.21| | 27: 1.21 - 1.19 2814 148 0.83 24.96 1.20 0.23 10.21| | 28: 1.19 - 1.18 2671 147 0.82 25.63 1.18 0.23 9.57| | 29: 1.18 - 1.16 2800 134 0.82 26.05 1.16 0.23 9.32| | 30: 1.16 - 1.15 2740 148 0.80 27.48 1.15 0.23 9.32| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 9.32 max = 1516.93 mean = 221.20| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.95 mean = 23.05| |phase err.(test): min = 0.00 max = 88.86 mean = 23.05| |-----------------------------------------------------------------------------| ----------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 0.238 1557 Z= 5.499 Angle : 5.270 16.705 2118 Z= 3.642 Chirality : 0.390 0.986 243 Planarity : 0.033 0.085 284 Dihedral : 13.762 89.347 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.78 % Favored : 95.68 % Rotamer: Outliers : 1.86 % Allowed : 2.48 % Favored : 95.65 % Cbeta Deviations : 35.68 % 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: -3.01 (0.46), residues: 224 helix: -3.33 (0.31), residues: 103 sheet: -0.11 (0.89), residues: 28 loop : -0.66 (0.57), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.077 0.023 ARG A 145 TYR 0.087 0.040 TYR A 141 PHE 0.109 0.040 PHE A 164 HIS 0.107 0.036 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= 0.2612 r_free= 0.1988 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.799588 | | target function (ml) not normalized (work): 233222.447168 | | target function (ml) not normalized (free): 11870.779398 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2572 0.2613 0.1989 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2572 0.2613 0.1989 n_refl.: 87602 remove outliers: r(all,work,free)=0.1988 0.1991 0.1989 n_refl.: 87594 overall B=0.19 to atoms: r(all,work,free)=0.2011 0.2015 0.2002 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1654 0.1646 0.1811 n_refl.: 87594 remove outliers: r(all,work,free)=0.1653 0.1645 0.1811 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 0.3884 386.541 355.242 0.670 1.002 0.403 11.894-9.307 99.02 97 4 0.1803 614.002 594.547 0.928 1.003 0.390 9.237-7.194 100.00 213 7 0.2131 502.178 492.214 0.957 1.004 0.354 7.162-5.571 100.00 427 22 0.2194 376.856 363.821 0.927 1.004 0.283 5.546-4.326 100.00 867 58 0.1285 517.331 511.869 0.964 1.004 0.249 4.315-3.360 100.00 1859 96 0.1155 491.985 488.056 1.004 1.003 0.189 3.356-2.611 100.00 3867 181 0.1427 323.209 319.857 0.995 1.003 0.099 2.608-2.026 99.99 8198 413 0.1355 214.258 211.986 1.007 1.002 0.000 2.025-1.573 100.00 17313 902 0.1675 104.632 103.834 1.012 1.000 0.000 1.573-1.221 100.00 36679 1900 0.2071 46.398 45.119 1.004 0.997 0.000 1.221-1.150 99.97 13689 708 0.2621 29.234 26.954 0.975 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0442 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1645 r_free=0.1811 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 A 180 GLN Total number of N/Q/H flips: 3 r_work=0.1650 r_free=0.1814 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.941869 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2004.256912 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 0.1215 0.1458 0.0243 0.007 1.0 1.3 0.5 0.0 0 11.971 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.15 14.58 2.43 3.013 19.051 2004.257 0.017 12.35 15.28 2.92 3.030 19.438 2004.257 0.016 Individual atomic B min max mean iso aniso Overall: 8.45 118.13 20.81 2.89 0 1785 Protein: 8.45 118.13 17.73 2.89 0 1519 Water: 11.06 115.06 38.74 N/A 0 258 Other: 22.24 34.77 28.24 N/A 0 8 Chain A: 8.45 118.13 20.81 N/A 0 1785 Histogram: Values Number of atoms 8.45 - 19.42 1210 19.42 - 30.39 237 30.39 - 41.35 158 41.35 - 52.32 101 52.32 - 63.29 50 63.29 - 74.26 18 74.26 - 85.22 4 85.22 - 96.19 4 96.19 - 107.16 0 107.16 - 118.13 3 =========================== Idealize ADP of riding H ========================== r_work=0.1236 r_free=0.1528 r_work=0.1239 r_free=0.1532 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1239 r_free = 0.1532 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 = 0.1239 r_free = 0.1536 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.28 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= 0.1239 r_free= 0.1536 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.015351 | | target function (ls_wunit_k1) not normalized (work): 1278.689798 | | target function (ls_wunit_k1) not normalized (free): 113.582490 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1253 0.1239 0.1536 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1694 0.1693 0.1766 n_refl.: 87593 remove outliers: r(all,work,free)=0.1694 0.1693 0.1766 n_refl.: 87593 overall B=0.13 to atoms: r(all,work,free)=0.1715 0.1714 0.1781 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1251 0.1237 0.1531 n_refl.: 87593 remove outliers: r(all,work,free)=0.1251 0.1237 0.1531 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 0.3590 299.130 278.909 0.638 1.002 0.380 11.894-9.307 99.02 97 4 0.1625 479.190 467.509 0.910 1.003 0.380 9.237-7.194 100.00 213 7 0.1804 391.918 387.380 0.950 1.003 0.340 7.162-5.571 100.00 427 22 0.1726 294.113 288.705 0.921 1.003 0.258 5.546-4.326 100.00 867 58 0.0927 403.744 401.020 0.953 1.003 0.230 4.315-3.360 100.00 1859 96 0.0783 383.964 383.075 0.995 1.003 0.190 3.356-2.611 100.00 3867 181 0.1025 252.244 251.514 0.998 1.002 0.110 2.608-2.026 99.99 8198 413 0.0969 167.215 166.689 1.009 1.002 0.000 2.025-1.573 100.00 17313 902 0.1195 81.659 81.857 1.017 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1634 36.211 35.673 1.006 0.998 0.000 1.221-1.150 99.97 13689 708 0.2355 22.815 21.327 0.970 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0497 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1237 r_free=0.1531 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN Total number of N/Q/H flips: 1 r_work=0.1238 r_free=0.1530 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1238 r_free=0.1530 | n_water=258 | time (s): 2.260 (total time: 2.260) Filter (dist) r_work=0.1247 r_free=0.1528 | n_water=252 | time (s): 26.750 (total time: 29.010) Filter (q & B) r_work=0.1250 r_free=0.1527 | n_water=249 | time (s): 3.580 (total time: 32.590) Compute maps r_work=0.1250 r_free=0.1527 | n_water=249 | time (s): 1.760 (total time: 34.350) Filter (map) r_work=0.1264 r_free=0.1539 | n_water=236 | time (s): 3.580 (total time: 37.930) Find peaks r_work=0.1264 r_free=0.1539 | n_water=236 | time (s): 0.700 (total time: 38.630) Add new water r_work=0.1425 r_free=0.1695 | n_water=460 | time (s): 3.660 (total time: 42.290) Refine new water occ: r_work=0.1332 r_free=0.1552 adp: r_work=0.1247 r_free=0.1506 occ: r_work=0.1259 r_free=0.1500 adp: r_work=0.1224 r_free=0.1490 occ: r_work=0.1227 r_free=0.1478 adp: r_work=0.1217 r_free=0.1484 ADP+occupancy (water only), MIN, final r_work=0.1217 r_free=0.1484 r_work=0.1217 r_free=0.1484 | n_water=460 | time (s): 71.630 (total time: 113.920) Filter (q & B) r_work=0.1223 r_free=0.1491 | n_water=438 | time (s): 4.070 (total time: 117.990) Filter (dist only) r_work=0.1223 r_free=0.1491 | n_water=438 | time (s): 41.190 (total time: 159.180) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.628417 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1600.055665 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 0.1221 0.1511 0.0290 0.007 0.9 2.9 0.5 0.0 0 12.314 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.21 15.11 2.90 3.762 22.957 1600.056 0.015 11.92 14.80 2.88 4.053 22.809 1600.056 0.015 Individual atomic B min max mean iso aniso Overall: 8.76 114.14 23.01 2.60 202 1763 Protein: 8.76 114.14 17.56 2.60 0 1519 Water: 11.02 73.90 41.77 N/A 202 236 Other: 24.79 36.68 30.13 N/A 0 8 Chain A: 8.76 114.14 20.23 N/A 0 1763 Chain S: 15.35 70.78 47.29 N/A 202 0 Histogram: Values Number of atoms 8.76 - 19.30 1209 19.30 - 29.84 248 29.84 - 40.38 202 40.38 - 50.91 151 50.91 - 61.45 94 61.45 - 71.99 50 71.99 - 82.53 5 82.53 - 93.07 3 93.07 - 103.61 1 103.61 - 114.14 2 =========================== Idealize ADP of riding H ========================== r_work=0.1192 r_free=0.1480 r_work=0.1192 r_free=0.1480 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1192 r_free = 0.1480 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 = 0.1194 r_free = 0.1465 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.19 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= 0.1194 r_free= 0.1465 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.013888 | | target function (ls_wunit_k1) not normalized (work): 1156.807069 | | target function (ls_wunit_k1) not normalized (free): 102.379440 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1207 0.1194 0.1465 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1593 0.1589 0.1711 n_refl.: 87592 remove outliers: r(all,work,free)=0.1593 0.1589 0.1711 n_refl.: 87592 overall B=0.04 to atoms: r(all,work,free)=0.1599 0.1595 0.1715 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1204 0.1191 0.1462 n_refl.: 87592 remove outliers: r(all,work,free)=0.1203 0.1190 0.1462 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 0.3431 295.065 271.323 0.592 1.002 0.370 11.894-9.307 99.02 97 4 0.1500 479.190 478.469 0.915 1.003 0.370 9.237-7.194 100.00 213 7 0.1679 391.918 394.367 0.981 1.003 0.280 7.162-5.571 100.00 427 22 0.1509 294.113 290.516 0.939 1.003 0.230 5.546-4.326 100.00 867 58 0.0843 403.744 400.999 0.959 1.003 0.210 4.315-3.360 100.00 1859 96 0.0708 383.964 382.868 1.002 1.002 0.200 3.356-2.611 100.00 3867 181 0.0953 252.244 251.623 1.009 1.002 0.150 2.608-2.026 99.99 8198 413 0.0952 167.215 166.808 1.017 1.001 0.000 2.025-1.573 100.00 17313 902 0.1169 81.659 81.862 1.027 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1599 36.211 35.723 1.017 0.998 0.000 1.221-1.150 99.97 13689 708 0.2333 22.815 21.345 0.977 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0597 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1190 r_free=0.1462 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=0.1190 r_free=0.1462 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1190 r_free=0.1462 | n_water=438 | time (s): 1.880 (total time: 1.880) Filter (dist) r_work=0.1190 r_free=0.1463 | n_water=437 | time (s): 39.840 (total time: 41.720) Filter (q & B) r_work=0.1191 r_free=0.1465 | n_water=436 | time (s): 2.960 (total time: 44.680) Compute maps r_work=0.1191 r_free=0.1465 | n_water=436 | time (s): 1.510 (total time: 46.190) Filter (map) r_work=0.1226 r_free=0.1473 | n_water=296 | time (s): 3.310 (total time: 49.500) Find peaks r_work=0.1226 r_free=0.1473 | n_water=296 | time (s): 0.510 (total time: 50.010) Add new water r_work=0.1350 r_free=0.1619 | n_water=481 | time (s): 2.700 (total time: 52.710) Refine new water occ: r_work=0.1254 r_free=0.1530 adp: r_work=0.1255 r_free=0.1531 occ: r_work=0.1233 r_free=0.1506 adp: r_work=0.1232 r_free=0.1507 occ: r_work=0.1218 r_free=0.1490 adp: r_work=0.1212 r_free=0.1489 ADP+occupancy (water only), MIN, final r_work=0.1212 r_free=0.1489 r_work=0.1212 r_free=0.1489 | n_water=481 | time (s): 212.850 (total time: 265.560) Filter (q & B) r_work=0.1216 r_free=0.1485 | n_water=448 | time (s): 2.640 (total time: 268.200) Filter (dist only) r_work=0.1216 r_free=0.1485 | n_water=448 | time (s): 35.130 (total time: 303.330) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.985891 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 51.481633 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 0.1221 0.1456 0.0235 0.006 0.9 2.2 0.5 0.0 0 0.993 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.21 14.56 2.35 3.604 21.995 51.482 3.722 12.09 14.13 2.03 4.084 21.810 51.482 3.652 Individual atomic B min max mean iso aniso Overall: 9.17 109.95 21.54 2.33 214 1761 Protein: 9.17 109.95 17.15 2.34 0 1519 Water: 11.48 72.99 36.32 N/A 214 234 Other: 20.59 32.42 26.86 N/A 0 8 Chain A: 9.17 109.95 19.79 N/A 0 1761 Chain S: 16.05 64.50 35.97 N/A 214 0 Histogram: Values Number of atoms 9.17 - 19.24 1236 19.24 - 29.32 273 29.32 - 39.40 232 39.40 - 49.48 132 49.48 - 59.56 70 59.56 - 69.64 20 69.64 - 79.72 6 79.72 - 89.79 3 89.79 - 99.87 1 99.87 - 109.95 2 =========================== Idealize ADP of riding H ========================== r_work=0.1209 r_free=0.1413 r_work=0.1210 r_free=0.1413 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1210 r_free = 0.1413 target_work(ml) = 3.652 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1204 r_free = 0.1413 target_work(ml) = 3.650 | | 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= 0.1204 r_free= 0.1413 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.649702 | | target function (ml) not normalized (work): 303994.643949 | | target function (ml) not normalized (free): 16059.214611 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1215 0.1204 0.1413 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1528 0.1527 0.1587 n_refl.: 87589 remove outliers: r(all,work,free)=0.1528 0.1527 0.1587 n_refl.: 87589 overall B=-0.01 to atoms: r(all,work,free)=0.1527 0.1525 0.1586 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1203 0.1194 0.1378 n_refl.: 87589 remove outliers: r(all,work,free)=0.1200 0.1191 0.1378 n_refl.: 87581 ======================== 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 90.62 82 5 0.3953 291.814 261.359 0.467 1.000 0.290 11.894-9.307 97.06 95 4 0.2488 472.574 458.836 0.860 1.001 0.277 9.237-7.194 98.18 209 7 0.2347 383.457 385.894 0.952 1.002 0.190 7.162-5.571 100.00 427 22 0.2054 294.113 284.176 0.922 1.002 0.170 5.546-4.326 100.00 867 58 0.1104 403.744 399.143 0.961 1.002 0.155 4.315-3.360 100.00 1859 96 0.0922 383.964 381.430 1.003 1.002 0.150 3.356-2.611 100.00 3867 181 0.1151 252.244 250.373 1.010 1.002 0.067 2.608-2.026 99.99 8198 413 0.1042 167.215 166.218 1.021 1.001 0.000 2.025-1.573 100.00 17313 902 0.1000 81.659 81.779 1.036 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1280 36.211 35.785 1.029 0.998 0.000 1.221-1.150 99.97 13689 708 0.2124 22.815 21.425 0.986 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0188 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1191 r_free=0.1378 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=0.1191 r_free=0.1378 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1191 r_free=0.1378 | n_water=448 | time (s): 2.060 (total time: 2.060) Filter (dist) r_work=0.1191 r_free=0.1378 | n_water=447 | time (s): 41.620 (total time: 43.680) Filter (q & B) r_work=0.1191 r_free=0.1378 | n_water=445 | time (s): 3.280 (total time: 46.960) Compute maps r_work=0.1191 r_free=0.1378 | n_water=445 | time (s): 1.590 (total time: 48.550) Filter (map) r_work=0.1217 r_free=0.1386 | n_water=314 | time (s): 3.530 (total time: 52.080) Find peaks r_work=0.1217 r_free=0.1386 | n_water=314 | time (s): 0.470 (total time: 52.550) Add new water r_work=0.1284 r_free=0.1461 | n_water=483 | time (s): 2.560 (total time: 55.110) Refine new water occ: r_work=0.1210 r_free=0.1380 adp: r_work=0.1211 r_free=0.1384 occ: r_work=0.1195 r_free=0.1364 adp: r_work=0.1194 r_free=0.1366 occ: r_work=0.1185 r_free=0.1354 adp: r_work=0.1181 r_free=0.1354 ADP+occupancy (water only), MIN, final r_work=0.1181 r_free=0.1354 r_work=0.1181 r_free=0.1354 | n_water=483 | time (s): 180.040 (total time: 235.150) Filter (q & B) r_work=0.1190 r_free=0.1354 | n_water=441 | time (s): 2.920 (total time: 238.070) Filter (dist only) r_work=0.1190 r_free=0.1353 | n_water=440 | time (s): 36.420 (total time: 274.490) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.943251 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 35.789520 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 0.1191 0.1371 0.0180 0.006 1.0 1.9 0.5 0.0 0 0.972 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.91 13.71 1.80 3.419 21.392 35.790 3.634 11.92 13.67 1.75 3.488 21.359 35.790 3.630 Individual atomic B min max mean iso aniso Overall: 9.25 108.08 21.26 2.22 208 1759 Protein: 9.25 108.08 17.08 2.22 0 1519 Water: 11.43 72.79 35.61 N/A 208 232 Other: 20.70 31.35 26.55 N/A 0 8 Chain A: 9.25 108.08 19.66 N/A 0 1759 Chain S: 16.00 60.01 34.76 N/A 208 0 Histogram: Values Number of atoms 9.25 - 19.13 1238 19.13 - 29.01 277 29.01 - 38.90 222 38.90 - 48.78 132 48.78 - 58.67 66 58.67 - 68.55 20 68.55 - 78.43 8 78.43 - 88.32 1 88.32 - 98.20 1 98.20 - 108.08 2 =========================== Idealize ADP of riding H ========================== r_work=0.1192 r_free=0.1367 r_work=0.1192 r_free=0.1367 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1192 r_free = 0.1367 target_work(ml) = 3.630 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1188 r_free = 0.1365 target_work(ml) = 3.629 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87581 (all), 4.91 % free)------------| | | | r_work= 0.1188 r_free= 0.1365 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.629196 | | target function (ml) not normalized (work): 302257.627179 | | target function (ml) not normalized (free): 15972.439923 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1196 0.1188 0.1365 n_refl.: 87581 re-set all scales: r(all,work,free)=0.1500 0.1498 0.1576 n_refl.: 87581 remove outliers: r(all,work,free)=0.1500 0.1498 0.1576 n_refl.: 87581 overall B=-0.00 to atoms: r(all,work,free)=0.1500 0.1497 0.1576 n_refl.: 87581 bulk-solvent and scaling: r(all,work,free)=0.1196 0.1187 0.1370 n_refl.: 87581 remove outliers: r(all,work,free)=0.1195 0.1185 0.1370 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 88.54 80 5 0.4193 289.790 250.967 0.447 0.998 0.308 11.894-9.307 96.08 94 4 0.2547 476.413 454.362 0.832 1.000 0.223 9.237-7.194 97.73 208 7 0.2409 384.532 378.828 0.927 1.001 0.150 7.162-5.571 100.00 427 22 0.2137 294.113 284.560 0.915 1.001 0.150 5.546-4.326 100.00 867 58 0.1137 403.744 399.039 0.962 1.001 0.138 4.315-3.360 100.00 1859 96 0.0943 383.964 381.447 1.004 1.001 0.133 3.356-2.611 100.00 3867 181 0.1154 252.244 250.565 1.011 1.001 0.057 2.608-2.026 99.99 8198 413 0.1026 167.215 166.399 1.022 1.001 0.000 2.025-1.573 100.00 17313 902 0.0983 81.659 81.930 1.035 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1249 36.211 35.813 1.026 1.000 0.000 1.221-1.150 99.97 13689 708 0.2124 22.815 21.362 0.981 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0109 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1185 r_free=0.1370 After: r_work=0.1186 r_free=0.1370 ================================== NQH flips ================================== r_work=0.1186 r_free=0.1370 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=0.1186 r_free=0.1370 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1186 r_free=0.1370 | n_water=440 | time (s): 1.750 (total time: 1.750) Filter (dist) r_work=0.1186 r_free=0.1370 | n_water=440 | time (s): 35.340 (total time: 37.090) Filter (q & B) r_work=0.1187 r_free=0.1371 | n_water=435 | time (s): 2.650 (total time: 39.740) Compute maps r_work=0.1187 r_free=0.1371 | n_water=435 | time (s): 1.330 (total time: 41.070) Filter (map) r_work=0.1209 r_free=0.1393 | n_water=324 | time (s): 3.260 (total time: 44.330) Find peaks r_work=0.1209 r_free=0.1393 | n_water=324 | time (s): 0.540 (total time: 44.870) Add new water r_work=0.1259 r_free=0.1455 | n_water=474 | time (s): 2.500 (total time: 47.370) Refine new water occ: r_work=0.1195 r_free=0.1383 adp: r_work=0.1196 r_free=0.1384 occ: r_work=0.1184 r_free=0.1372 adp: r_work=0.1184 r_free=0.1373 occ: r_work=0.1176 r_free=0.1364 adp: r_work=0.1174 r_free=0.1363 ADP+occupancy (water only), MIN, final r_work=0.1174 r_free=0.1363 r_work=0.1174 r_free=0.1363 | n_water=474 | time (s): 246.650 (total time: 294.020) Filter (q & B) r_work=0.1181 r_free=0.1368 | n_water=438 | time (s): 2.420 (total time: 296.440) Filter (dist only) r_work=0.1181 r_free=0.1367 | n_water=437 | time (s): 37.240 (total time: 333.680) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.267515 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 41.577762 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 0.1203 0.1384 0.0181 0.007 1.1 5.1 0.5 0.0 0 1.134 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.03 13.84 1.81 3.359 21.210 41.578 3.638 12.00 13.95 1.95 3.774 21.086 41.578 3.630 Individual atomic B min max mean iso aniso Overall: 9.27 103.08 20.84 2.06 207 1757 Protein: 9.27 103.08 16.78 2.06 0 1519 Water: 11.37 71.69 34.88 N/A 207 230 Other: 20.36 28.85 25.31 N/A 0 8 Chain A: 9.27 103.08 19.31 N/A 0 1757 Chain S: 14.47 57.96 33.84 N/A 207 0 Histogram: Values Number of atoms 9.27 - 18.65 1231 18.65 - 28.03 279 28.03 - 37.41 221 37.41 - 46.79 129 46.79 - 56.17 66 56.17 - 65.55 23 65.55 - 74.94 11 74.94 - 84.32 1 84.32 - 93.70 1 93.70 - 103.08 2 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1395 r_work=0.1200 r_free=0.1395 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1395 target_work(ml) = 3.630 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1196 r_free = 0.1391 target_work(ml) = 3.629 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87577 (all), 4.91 % free)------------| | | | r_work= 0.1196 r_free= 0.1391 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.628791 | | target function (ml) not normalized (work): 302209.330116 | | target function (ml) not normalized (free): 15990.699430 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1411 0.1495 5.6693 5.693| | 2: 3.57 - 2.84 1.00 2888 124 0.1135 0.1443 5.2224 5.2767| | 3: 2.83 - 2.48 1.00 2820 163 0.1219 0.1221 5.0249 5.0328| | 4: 2.47 - 2.25 1.00 2825 136 0.1015 0.1172 4.724 4.7753| | 5: 2.25 - 2.09 1.00 2756 127 0.0985 0.1128 4.669 4.7356| | 6: 2.09 - 1.97 1.00 2846 113 0.0975 0.1166 4.362 4.4859| | 7: 1.97 - 1.87 1.00 2787 165 0.0978 0.1293 4.0758 4.2204| | 8: 1.87 - 1.79 1.00 2789 144 0.1022 0.1258 3.9966 4.09| | 9: 1.79 - 1.72 1.00 2745 138 0.0949 0.1302 3.7221 3.9046| | 10: 1.72 - 1.66 1.00 2831 160 0.0997 0.1297 3.64 3.7922| | 11: 1.66 - 1.61 1.00 2712 147 0.0961 0.1138 3.5767 3.6367| | 12: 1.61 - 1.56 1.00 2773 144 0.0922 0.1243 3.3615 3.5177| | 13: 1.56 - 1.52 1.00 2745 130 0.0986 0.1068 3.3495 3.4474| | 14: 1.52 - 1.48 1.00 2803 134 0.0997 0.1163 3.272 3.3677| | 15: 1.48 - 1.45 1.00 2738 128 0.1029 0.1339 3.1818 3.3154| | 16: 1.45 - 1.42 1.00 2756 161 0.1087 0.1263 3.1645 3.2486| | 17: 1.42 - 1.39 1.00 2785 139 0.1129 0.1333 3.1232 3.2488| | 18: 1.39 - 1.36 1.00 2741 179 0.1163 0.1403 3.0938 3.2667| | 19: 1.36 - 1.34 1.00 2807 134 0.1216 0.1657 3.0963 3.2973| | 20: 1.34 - 1.32 1.00 2696 147 0.1321 0.1451 3.0914 3.122| | 21: 1.32 - 1.30 1.00 2785 112 0.1424 0.1655 3.0928 3.1785| | 22: 1.29 - 1.27 1.00 2704 152 0.1468 0.1918 3.0865 3.2805| | 23: 1.27 - 1.26 1.00 2802 156 0.1571 0.1858 3.106 3.2044| | 24: 1.26 - 1.24 1.00 2744 132 0.1615 0.1739 3.0973 3.1849| | 25: 1.24 - 1.22 1.00 2733 148 0.1789 0.2340 3.1124 3.3023| | 26: 1.22 - 1.21 1.00 2727 135 0.1866 0.1778 3.126 3.1985| | 27: 1.21 - 1.19 1.00 2814 148 0.2019 0.2118 3.1415 3.1571| | 28: 1.19 - 1.18 1.00 2671 147 0.2154 0.2272 3.1426 3.1566| | 29: 1.18 - 1.16 1.00 2800 134 0.2220 0.2386 3.1294 3.2329| | 30: 1.16 - 1.15 1.00 2739 148 0.2372 0.2502 3.1179 3.1677| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 0.94 9.52 1.00 0.96 6750.53| | 2: 3.57 - 2.84 2888 124 0.92 14.02 1.01 0.96 6750.53| | 3: 2.83 - 2.48 2820 163 0.88 18.17 0.99 0.96 5649.98| | 4: 2.47 - 2.25 2825 136 0.91 15.07 1.00 0.97 2812.02| | 5: 2.25 - 2.09 2756 127 0.89 17.38 1.01 0.97 2812.02| | 6: 2.09 - 1.97 2846 113 0.91 14.00 1.02 0.97 1638.66| | 7: 1.97 - 1.87 2787 165 0.94 10.93 1.02 0.97 637.93| | 8: 1.87 - 1.79 2789 144 0.91 14.55 1.00 0.97 637.93| | 9: 1.79 - 1.72 2745 138 0.93 11.54 0.98 0.96 347.52| | 10: 1.72 - 1.66 2831 160 0.93 12.42 0.98 0.96 289.37| | 11: 1.66 - 1.61 2712 147 0.93 13.08 0.98 0.96 276.36| | 12: 1.61 - 1.56 2773 144 0.95 9.80 0.99 0.96 153.67| | 13: 1.56 - 1.52 2745 130 0.94 11.45 1.02 0.96 153.67| | 14: 1.52 - 1.48 2803 134 0.94 11.54 1.02 0.97 136.76| | 15: 1.48 - 1.45 2738 128 0.95 10.62 1.02 0.97 105.80| | 16: 1.45 - 1.42 2756 161 0.94 11.80 1.02 0.97 105.80| | 17: 1.42 - 1.39 2785 139 0.94 11.52 1.01 0.98 95.03| | 18: 1.39 - 1.36 2741 179 0.94 11.91 1.01 0.98 88.80| | 19: 1.36 - 1.34 2807 134 0.94 12.44 1.00 0.98 88.80| | 20: 1.34 - 1.32 2696 147 0.94 12.46 0.99 0.96 83.09| | 21: 1.32 - 1.30 2785 112 0.93 13.41 0.99 0.96 82.69| | 22: 1.29 - 1.27 2704 152 0.93 13.85 0.99 0.96 82.81| | 23: 1.27 - 1.26 2802 156 0.93 14.77 0.98 0.94 83.40| | 24: 1.26 - 1.24 2744 132 0.92 14.94 0.97 0.94 83.40| | 25: 1.24 - 1.22 2733 148 0.91 16.37 0.96 0.94 84.85| | 26: 1.22 - 1.21 2727 135 0.90 18.12 1.03 0.93 86.47| | 27: 1.21 - 1.19 2814 148 0.89 18.80 1.03 0.93 86.47| | 28: 1.19 - 1.18 2671 147 0.88 20.26 1.01 0.93 89.59| | 29: 1.18 - 1.16 2800 134 0.88 20.54 1.00 0.92 90.77| | 30: 1.16 - 1.15 2739 148 0.86 21.89 0.99 0.92 90.77| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 82.69 max = 6750.53 mean = 1041.47| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.97 mean = 14.23| |phase err.(test): min = 0.00 max = 88.89 mean = 14.38| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1206 0.1196 0.1391 n_refl.: 87577 re-set all scales: r(all,work,free)=0.1514 0.1512 0.1575 n_refl.: 87577 remove outliers: r(all,work,free)=0.1514 0.1512 0.1575 n_refl.: 87577 overall B=-0.01 to atoms: r(all,work,free)=0.1512 0.1510 0.1573 n_refl.: 87577 bulk-solvent and scaling: r(all,work,free)=0.1205 0.1196 0.1389 n_refl.: 87577 remove outliers: r(all,work,free)=0.1205 0.1195 0.1389 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 87.50 79 5 0.4008 286.331 252.502 0.444 1.001 0.303 11.894-9.307 96.08 94 4 0.2333 476.413 464.107 0.842 1.002 0.244 9.237-7.194 97.73 208 7 0.2553 384.532 376.009 0.900 1.002 0.171 7.162-5.571 100.00 427 22 0.2222 294.113 283.074 0.896 1.003 0.151 5.546-4.326 100.00 867 58 0.1205 403.744 398.761 0.953 1.003 0.123 4.315-3.360 100.00 1859 96 0.0986 383.964 381.209 0.994 1.002 0.120 3.356-2.611 100.00 3867 181 0.1196 252.244 250.084 1.001 1.002 0.057 2.608-2.026 99.99 8198 413 0.1032 167.215 166.269 1.014 1.001 0.000 2.025-1.573 100.00 17313 902 0.0970 81.659 81.898 1.027 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1231 36.211 35.847 1.023 0.996 0.000 1.221-1.150 99.97 13689 708 0.2119 22.815 21.444 0.982 0.993 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0333 ================= 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 : 0.2612 0.1988 0.082 5.270 8.8 119.3 19.9 258 0.000 1_bss: 0.1645 0.1811 0.082 5.270 9.0 119.5 20.1 258 0.000 1_settarget: 0.1645 0.1811 0.082 5.270 9.0 119.5 20.1 258 0.000 1_nqh: 0.1650 0.1814 0.082 5.270 9.0 119.5 20.1 258 0.009 1_weight: 0.1650 0.1814 0.082 5.270 9.0 119.5 20.1 258 0.009 1_xyzrec: 0.1215 0.1458 0.007 0.951 9.0 119.5 20.1 258 0.134 1_adp: 0.1236 0.1528 0.007 0.951 8.5 118.1 20.8 258 0.134 1_regHadp: 0.1239 0.1532 0.007 0.951 8.5 118.1 20.8 258 0.134 1_occ: 0.1239 0.1536 0.007 0.951 8.5 118.1 20.8 258 0.134 2_bss: 0.1237 0.1531 0.007 0.951 8.6 118.3 20.9 258 0.134 2_settarget: 0.1237 0.1531 0.007 0.951 8.6 118.3 20.9 258 0.134 2_updatecdl: 0.1237 0.1531 0.007 0.944 8.6 118.3 20.9 258 0.134 2_nqh: 0.1238 0.1530 0.007 0.944 8.6 118.3 20.9 258 0.131 2_sol: 0.1223 0.1491 0.007 0.944 8.6 118.3 23.3 438 n/a 2_weight: 0.1223 0.1491 0.007 0.944 8.6 118.3 23.3 438 n/a 2_xyzrec: 0.1221 0.1511 0.007 0.869 8.6 118.3 23.3 438 n/a 2_adp: 0.1192 0.1480 0.007 0.869 8.8 114.1 23.0 438 n/a 2_regHadp: 0.1192 0.1480 0.007 0.869 8.8 114.1 23.0 438 n/a 2_occ: 0.1194 0.1465 0.007 0.869 8.8 114.1 23.0 438 n/a 3_bss: 0.1190 0.1462 0.007 0.869 8.8 114.2 23.0 438 n/a 3_settarget: 0.1190 0.1462 0.007 0.869 8.8 114.2 23.0 438 n/a 3_updatecdl: 0.1190 0.1462 0.007 0.872 8.8 114.2 23.0 438 n/a 3_nqh: 0.1190 0.1462 0.007 0.872 8.8 114.2 23.0 438 n/a 3_sol: 0.1216 0.1485 0.007 0.872 8.8 114.2 21.9 448 n/a 3_weight: 0.1216 0.1485 0.007 0.872 8.8 114.2 21.9 448 n/a 3_xyzrec: 0.1221 0.1456 0.006 0.916 8.8 114.2 21.9 448 n/a 3_adp: 0.1209 0.1413 0.006 0.916 9.2 110.0 21.5 448 n/a 3_regHadp: 0.1210 0.1413 0.006 0.916 9.2 110.0 21.5 448 n/a 3_occ: 0.1204 0.1413 0.006 0.916 9.2 110.0 21.5 448 n/a 4_bss: 0.1191 0.1378 0.006 0.916 9.2 109.9 21.5 448 n/a 4_settarget: 0.1191 0.1378 0.006 0.916 9.2 109.9 21.5 448 n/a 4_updatecdl: 0.1191 0.1378 0.006 0.916 9.2 109.9 21.5 448 n/a 4_nqh: 0.1191 0.1378 0.006 0.916 9.2 109.9 21.5 448 n/a 4_sol: 0.1190 0.1353 0.006 0.916 9.2 109.9 21.3 440 n/a 4_weight: 0.1190 0.1353 0.006 0.916 9.2 109.9 21.3 440 n/a 4_xyzrec: 0.1191 0.1371 0.006 0.955 9.2 109.9 21.3 440 n/a 4_adp: 0.1192 0.1367 0.006 0.955 9.2 108.1 21.3 440 n/a 4_regHadp: 0.1192 0.1367 0.006 0.955 9.2 108.1 21.3 440 n/a 4_occ: 0.1188 0.1365 0.006 0.955 9.2 108.1 21.3 440 n/a 5_bss: 0.1185 0.1370 0.006 0.955 9.2 108.1 21.3 440 n/a 5_settarget: 0.1185 0.1370 0.006 0.955 9.2 108.1 21.3 440 n/a 5_updatecdl: 0.1185 0.1370 0.006 0.957 9.2 108.1 21.3 440 n/a 5_setrh: 0.1186 0.1370 0.006 0.957 9.2 108.1 21.3 440 n/a 5_nqh: 0.1186 0.1370 0.006 0.957 9.2 108.1 21.3 440 n/a 5_sol: 0.1181 0.1367 0.006 0.957 9.2 108.1 21.1 437 n/a 5_weight: 0.1181 0.1367 0.006 0.957 9.2 108.1 21.1 437 n/a 5_xyzrec: 0.1203 0.1384 0.007 1.078 9.2 108.1 21.1 437 n/a 5_adp: 0.1200 0.1395 0.007 1.078 9.3 103.1 20.8 437 n/a 5_regHadp: 0.1200 0.1395 0.007 1.078 9.3 103.1 20.8 437 n/a 5_occ: 0.1196 0.1391 0.007 1.078 9.3 103.1 20.8 437 n/a end: 0.1195 0.1389 0.007 1.078 9.3 103.1 20.8 437 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_8736282_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_8736282_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.8900 Refinement macro-cycles (run) : 3528.3100 Write final files (write_after_run_outputs) : 62.9700 Total : 3596.1700 Total CPU time: 60.53 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:12:11 PST -0800 (1735452731.64 s) Start R-work = 0.1645, R-free = 0.1811 Final R-work = 0.1195, R-free = 0.1389 =============================================================================== Job complete usr+sys time: 3728.29 seconds wall clock time: 67 minutes 21.33 seconds (4041.33 seconds total)