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_8954467.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 { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" 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" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8954467.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8954467.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { 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 =============================================================================== 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: 2.29, per 1000 atoms: 0.68 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: 0.87 Conformation dependent library (CDL) restraints added in 311.7 milliseconds Time building geometry restraints manager: 0.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.68 - 0.93: 641 0.93 - 1.18: 1015 1.18 - 1.43: 645 1.43 - 1.68: 820 1.68 - 1.93: 32 Bond restraints: 3153 Sorted by residual: bond pdb=" N GLY A 100 " pdb=" CA GLY A 100 " ideal model delta sigma weight residual 1.444 1.645 -0.201 1.06e-02 8.90e+03 3.60e+02 bond pdb=" CA ILE A 117 " pdb=" CB ILE A 117 " ideal model delta sigma weight residual 1.542 1.779 -0.237 1.26e-02 6.30e+03 3.54e+02 bond pdb=" C GLY A 40 " pdb=" O GLY A 40 " ideal model delta sigma weight residual 1.232 1.384 -0.152 8.20e-03 1.49e+04 3.42e+02 bond pdb=" CA LYS A 130 " pdb=" C LYS A 130 " ideal model delta sigma weight residual 1.524 1.749 -0.225 1.24e-02 6.50e+03 3.29e+02 bond pdb=" N VAL A 146 " pdb=" CA VAL A 146 " ideal model delta sigma weight residual 1.458 1.663 -0.205 1.18e-02 7.18e+03 3.02e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.88: 3324 4.88 - 9.75: 1797 9.75 - 14.63: 571 14.63 - 19.51: 78 19.51 - 24.39: 7 Bond angle restraints: 5777 Sorted by residual: angle pdb=" OE1 GLN A 45 " pdb=" CD GLN A 45 " pdb=" NE2 GLN A 45 " ideal model delta sigma weight residual 122.60 107.17 15.43 1.00e+00 1.00e+00 2.38e+02 angle pdb=" O GLY A 40 " pdb=" C GLY A 40 " pdb=" N BLYS A 41 " ideal model delta sigma weight residual 123.43 111.66 11.77 8.50e-01 1.38e+00 1.92e+02 angle pdb=" CA ALYS A 99 " pdb=" C ALYS A 99 " pdb=" N GLY A 100 " ideal model delta sigma weight residual 115.67 99.67 16.00 1.23e+00 6.61e-01 1.69e+02 angle pdb=" O ILE A 9 " pdb=" C ILE A 9 " pdb=" N LEU A 10 " ideal model delta sigma weight residual 122.94 138.67 -15.73 1.22e+00 6.72e-01 1.66e+02 angle pdb=" CA ALYS A 99 " pdb=" C ALYS A 99 " pdb=" O ALYS A 99 " ideal model delta sigma weight residual 121.65 136.61 -14.96 1.17e+00 7.31e-01 1.64e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.15: 939 17.15 - 34.31: 126 34.31 - 51.46: 33 51.46 - 68.61: 9 68.61 - 85.76: 4 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA SER A 155 " pdb=" C SER A 155 " pdb=" N ARG A 156 " pdb=" CA ARG A 156 " ideal model delta harmonic sigma weight residual 180.00 -155.85 -24.15 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA THR A 125 " pdb=" C THR A 125 " pdb=" N HIS A 126 " pdb=" CA HIS A 126 " ideal model delta harmonic sigma weight residual 180.00 157.37 22.63 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CD2BTYR A 67 " pdb=" CG BTYR A 67 " pdb=" CD1BTYR A 67 " pdb=" HD1BTYR A 67 " ideal model delta harmonic sigma weight residual 180.00 157.91 22.09 0 5.00e+00 4.00e-02 1.95e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.009 - 0.244: 117 0.244 - 0.480: 77 0.480 - 0.715: 34 0.715 - 0.950: 12 0.950 - 1.185: 3 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA HIS A 115 " pdb=" N HIS A 115 " pdb=" C HIS A 115 " pdb=" CB HIS A 115 " both_signs ideal model delta sigma weight residual False 2.51 1.33 1.18 2.00e-01 2.50e+01 3.51e+01 chirality pdb=" CA LEU A 187 " pdb=" N LEU A 187 " pdb=" C LEU A 187 " pdb=" CB LEU A 187 " both_signs ideal model delta sigma weight residual False 2.51 1.38 1.13 2.00e-01 2.50e+01 3.19e+01 chirality pdb=" CG LEU A 101 " pdb=" CB LEU A 101 " pdb=" CD1 LEU A 101 " pdb=" CD2 LEU A 101 " both_signs ideal model delta sigma weight residual False -2.59 -3.56 0.97 2.00e-01 2.50e+01 2.34e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " -0.051 2.00e-02 2.50e+03 5.87e-02 1.03e+02 pdb=" CG PHE A 162 " 0.082 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " -0.125 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " 0.050 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " 0.054 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " 0.026 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " 0.026 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " 0.044 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " -0.046 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " -0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.050 2.00e-02 2.50e+03 5.52e-02 9.14e+01 pdb=" CG PHE A 164 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.056 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.034 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.019 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.135 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.008 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.064 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.009 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.048 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " -0.050 2.00e-02 2.50e+03 5.51e-02 9.09e+01 pdb=" CG BTYR A 67 " 0.004 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " -0.095 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " 0.055 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " -0.043 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " -0.004 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " 0.056 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " -0.001 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " 0.121 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " 0.016 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " -0.019 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " -0.040 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.37: 1413 2.37 - 2.93: 8349 2.93 - 3.48: 10433 3.48 - 4.04: 15097 4.04 - 4.60: 21277 Nonbonded interactions: 56569 Sorted by model distance: nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.811 2.100 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.826 2.450 nonbonded pdb=" HB2BGLN A 80 " pdb="HE21BGLN A 80 " model vdw 1.840 2.270 nonbonded pdb=" HG SER A 47 " pdb="HH11 ARG A 48 " model vdw 1.860 2.100 nonbonded pdb=" HA AASN A 76 " pdb="HD22AASN A 76 " model vdw 1.873 2.270 ... (remaining 56564 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_8954467_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= 0.2607 r_free= 0.1919 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.792701 | | target function (ml) not normalized (work): 232648.778296 | | target function (ml) not normalized (free): 11775.498717 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3042 0.1985 7.1501 4.9168| | 2: 3.57 - 2.84 1.00 2876 122 0.2425 0.1835 4.339 4.3445| | 3: 2.84 - 2.48 1.00 2833 165 0.2364 0.1679 4.1156 4.1416| | 4: 2.47 - 2.25 1.00 2825 136 0.2329 0.1423 3.8296 3.8205| | 5: 2.25 - 2.09 1.00 2756 127 0.2449 0.1591 3.7867 3.8037| | 6: 2.09 - 1.97 1.00 2846 113 0.2537 0.1679 3.4585 3.5275| | 7: 1.97 - 1.87 1.00 2787 165 0.2515 0.1841 3.1176 3.2402| | 8: 1.87 - 1.79 1.00 2789 144 0.2489 0.1885 3.0676 3.095| | 9: 1.79 - 1.72 1.00 2745 138 0.2416 0.1950 2.8893 2.9538| | 10: 1.72 - 1.66 1.00 2789 158 0.2414 0.2091 2.7931 2.9327| | 11: 1.66 - 1.61 1.00 2740 147 0.2528 0.1988 2.7435 2.8094| | 12: 1.61 - 1.56 1.00 2787 146 0.2536 0.1863 2.6391 2.6084| | 13: 1.56 - 1.52 1.00 2745 130 0.2585 0.1955 2.5776 2.6317| | 14: 1.52 - 1.48 1.00 2803 134 0.2612 0.1950 2.5179 2.5465| | 15: 1.48 - 1.45 1.00 2738 128 0.2588 0.2074 2.4174 2.475| | 16: 1.45 - 1.42 1.00 2756 161 0.2651 0.2033 2.3803 2.417| | 17: 1.42 - 1.39 1.00 2785 139 0.2676 0.2102 2.3399 2.3844| | 18: 1.39 - 1.36 1.00 2741 179 0.2657 0.2202 2.2778 2.3351| | 19: 1.36 - 1.34 1.00 2807 134 0.2696 0.2293 2.2685 2.3349| | 20: 1.34 - 1.32 1.00 2696 147 0.2720 0.2274 2.2196 2.2143| | 21: 1.32 - 1.30 1.00 2785 112 0.2721 0.2050 2.1609 2.0784| | 22: 1.29 - 1.27 1.00 2704 152 0.2686 0.2484 2.1186 2.1527| | 23: 1.27 - 1.26 1.00 2802 156 0.2803 0.2288 2.1097 2.1382| | 24: 1.26 - 1.24 1.00 2744 132 0.2767 0.2417 2.0707 2.1099| | 25: 1.24 - 1.22 1.00 2734 148 0.2804 0.2409 2.0397 2.0091| | 26: 1.22 - 1.21 1.00 2727 135 0.2886 0.2472 2.0124 2.1193| | 27: 1.21 - 1.19 1.00 2814 148 0.2940 0.2556 2.0072 1.977| | 28: 1.19 - 1.18 1.00 2671 147 0.2999 0.2753 1.9926 2.003| | 29: 1.18 - 1.16 1.00 2800 134 0.2962 0.2603 1.9632 1.9876| | 30: 1.16 - 1.15 1.00 2740 148 0.3004 0.2740 1.9162 1.9528| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.55 0.76 0.23 1443.11| | 2: 3.57 - 2.84 2876 122 0.81 25.67 1.27 0.23 1443.11| | 3: 2.84 - 2.48 2833 165 0.74 31.69 1.24 0.24 1196.66| | 4: 2.47 - 2.25 2825 136 0.82 25.11 1.25 0.25 557.06| | 5: 2.25 - 2.09 2756 127 0.78 28.93 1.28 0.25 557.06| | 6: 2.09 - 1.97 2846 113 0.84 22.38 1.29 0.25 305.09| | 7: 1.97 - 1.87 2787 165 0.90 16.36 1.28 0.26 90.20| | 8: 1.87 - 1.79 2789 144 0.86 20.83 1.25 0.26 90.20| | 9: 1.79 - 1.72 2745 138 0.88 18.46 1.23 0.26 55.22| | 10: 1.72 - 1.66 2789 158 0.87 20.19 1.22 0.25 48.22| | 11: 1.66 - 1.61 2740 147 0.85 21.54 1.24 0.25 46.57| | 12: 1.61 - 1.56 2787 146 0.88 18.56 1.24 0.25 29.84| | 13: 1.56 - 1.52 2745 130 0.87 20.47 1.25 0.25 29.84| | 14: 1.52 - 1.48 2803 134 0.86 20.71 1.23 0.25 26.57| | 15: 1.48 - 1.45 2738 128 0.87 20.11 1.24 0.25 20.57| | 16: 1.45 - 1.42 2756 161 0.86 21.68 1.24 0.25 20.57| | 17: 1.42 - 1.39 2785 139 0.87 20.47 1.23 0.25 17.38| | 18: 1.39 - 1.36 2741 179 0.87 20.85 1.22 0.25 15.53| | 19: 1.36 - 1.34 2807 134 0.86 21.67 1.21 0.25 15.53| | 20: 1.34 - 1.32 2696 147 0.87 20.42 1.21 0.25 12.48| | 21: 1.32 - 1.30 2785 112 0.87 21.21 1.22 0.25 12.27| | 22: 1.29 - 1.27 2704 152 0.86 21.67 1.21 0.25 11.97| | 23: 1.27 - 1.26 2802 156 0.87 21.32 1.22 0.24 10.45| | 24: 1.26 - 1.24 2744 132 0.86 21.88 1.20 0.24 10.45| | 25: 1.24 - 1.22 2734 148 0.85 22.85 1.20 0.24 9.94| | 26: 1.22 - 1.21 2727 135 0.85 23.43 1.20 0.23 9.37| | 27: 1.21 - 1.19 2814 148 0.84 23.82 1.20 0.23 9.37| | 28: 1.19 - 1.18 2671 147 0.83 24.70 1.18 0.23 8.84| | 29: 1.18 - 1.16 2800 134 0.84 24.63 1.16 0.23 8.64| | 30: 1.16 - 1.15 2740 148 0.82 26.16 1.15 0.23 8.64| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 8.64 max = 1443.11 mean = 209.76| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.98 mean = 22.21| |phase err.(test): min = 0.00 max = 89.62 mean = 22.11| |-----------------------------------------------------------------------------| ----------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 : 0.080 0.237 1557 Z= 5.365 Angle : 5.131 15.998 2118 Z= 3.654 Chirality : 0.383 1.185 243 Planarity : 0.034 0.111 284 Dihedral : 13.667 85.762 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.24 % Favored : 96.22 % Rotamer: Outliers : 1.86 % Allowed : 2.48 % Favored : 95.65 % Cbeta Deviations : 33.51 % 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: -2.82 (0.46), residues: 224 helix: -2.43 (0.37), residues: 109 sheet: -0.72 (0.87), residues: 28 loop : -1.20 (0.58), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.116 0.021 ARG A 28 TYR 0.068 0.032 TYR A 139 PHE 0.113 0.037 PHE A 164 HIS 0.045 0.020 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= 0.2607 r_free= 0.1919 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.792701 | | target function (ml) not normalized (work): 232648.778296 | | target function (ml) not normalized (free): 11775.498717 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2566 0.2608 0.1919 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2566 0.2608 0.1919 n_refl.: 87602 remove outliers: r(all,work,free)=0.1980 0.1985 0.1919 n_refl.: 87594 overall B=0.20 to atoms: r(all,work,free)=0.2003 0.2009 0.1932 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1645 0.1639 0.1757 n_refl.: 87594 remove outliers: r(all,work,free)=0.1644 0.1638 0.1757 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 97.87 87 5 0.3825 381.971 355.067 0.672 1.002 0.403 11.894-9.307 99.02 97 4 0.1800 613.554 596.120 0.927 1.003 0.390 9.237-7.194 100.00 213 7 0.2171 501.812 489.822 0.946 1.004 0.359 7.162-5.571 100.00 427 22 0.2224 376.582 363.894 0.926 1.004 0.293 5.546-4.326 100.00 867 58 0.1295 516.954 510.768 0.966 1.004 0.224 4.315-3.360 100.00 1859 96 0.1137 491.627 487.760 1.006 1.003 0.199 3.356-2.611 100.00 3867 181 0.1447 322.973 319.538 0.996 1.003 0.129 2.608-2.026 99.99 8198 413 0.1354 214.102 211.941 1.006 1.001 0.000 2.025-1.573 100.00 17313 902 0.1633 104.556 103.880 1.012 0.999 0.000 1.573-1.221 100.00 36679 1900 0.2077 46.364 45.075 1.006 0.995 0.000 1.221-1.150 99.97 13689 708 0.2590 29.213 26.987 0.975 0.992 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0017 b_overall=0.0449 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1638 r_free=0.1757 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN Total number of N/Q/H flips: 1 r_work=0.1639 r_free=0.1759 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.135690 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2011.532648 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1209 0.1462 0.0253 0.008 1.0 1.0 0.5 0.0 0 13.568 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.09 14.62 2.53 3.013 19.054 2011.533 0.017 12.39 15.38 3.00 2.973 19.386 2011.533 0.016 Individual atomic B min max mean iso aniso Overall: 8.31 117.98 20.71 2.89 0 1785 Protein: 8.31 117.98 17.65 2.89 0 1519 Water: 10.91 114.83 38.52 N/A 0 258 Other: 22.41 34.37 27.66 N/A 0 8 Chain A: 8.31 117.98 20.71 N/A 0 1785 Histogram: Values Number of atoms 8.31 - 19.27 1209 19.27 - 30.24 241 30.24 - 41.21 158 41.21 - 52.17 98 52.17 - 63.14 49 63.14 - 74.11 19 74.11 - 85.07 4 85.07 - 96.04 3 96.04 - 107.01 1 107.01 - 117.98 3 =========================== Idealize ADP of riding H ========================== r_work=0.1239 r_free=0.1538 r_work=0.1243 r_free=0.1543 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1243 r_free = 0.1543 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 = 0.1242 r_free = 0.1546 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1242 r_free= 0.1546 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.015291 | | target function (ls_wunit_k1) not normalized (work): 1273.713468 | | target function (ls_wunit_k1) not normalized (free): 113.297925 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1257 0.1242 0.1546 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1690 0.1689 0.1767 n_refl.: 87592 remove outliers: r(all,work,free)=0.1690 0.1689 0.1767 n_refl.: 87592 overall B=0.18 to atoms: r(all,work,free)=0.1719 0.1718 0.1786 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1255 0.1240 0.1542 n_refl.: 87592 remove outliers: r(all,work,free)=0.1254 0.1239 0.1542 n_refl.: 87591 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 94.79 86 5 0.3556 296.518 276.811 0.626 1.002 0.380 11.894-9.307 99.02 97 4 0.1602 480.490 468.308 0.906 1.003 0.380 9.237-7.194 100.00 213 7 0.1849 392.982 387.494 0.945 1.003 0.340 7.162-5.571 100.00 427 22 0.1756 294.911 289.193 0.920 1.003 0.258 5.546-4.326 100.00 867 58 0.0929 404.840 402.183 0.949 1.003 0.214 4.315-3.360 100.00 1859 96 0.0778 385.006 384.121 0.995 1.003 0.199 3.356-2.611 100.00 3867 181 0.1014 252.929 252.244 0.996 1.002 0.062 2.608-2.026 99.99 8198 413 0.0960 167.669 167.168 1.007 1.001 0.000 2.025-1.573 100.00 17313 902 0.1200 81.881 82.090 1.015 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1657 36.309 35.756 1.004 0.998 0.000 1.221-1.150 99.97 13689 708 0.2366 22.877 21.381 0.969 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0410 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1239 r_free=0.1542 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=0.1239 r_free=0.1542 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1239 r_free=0.1542 | n_water=258 | time (s): 2.230 (total time: 2.230) Filter (dist) r_work=0.1249 r_free=0.1539 | n_water=252 | time (s): 25.430 (total time: 27.660) Filter (q & B) r_work=0.1252 r_free=0.1538 | n_water=249 | time (s): 3.350 (total time: 31.010) Compute maps r_work=0.1252 r_free=0.1538 | n_water=249 | time (s): 1.700 (total time: 32.710) Filter (map) r_work=0.1265 r_free=0.1551 | n_water=236 | time (s): 3.840 (total time: 36.550) Find peaks r_work=0.1265 r_free=0.1551 | n_water=236 | time (s): 0.710 (total time: 37.260) Add new water r_work=0.1422 r_free=0.1718 | n_water=453 | time (s): 3.550 (total time: 40.810) Refine new water occ: r_work=0.1329 r_free=0.1564 adp: r_work=0.1249 r_free=0.1524 occ: r_work=0.1263 r_free=0.1517 adp: r_work=0.1227 r_free=0.1506 occ: r_work=0.1231 r_free=0.1496 adp: r_work=0.1220 r_free=0.1497 ADP+occupancy (water only), MIN, final r_work=0.1220 r_free=0.1497 r_work=0.1220 r_free=0.1497 | n_water=453 | time (s): 121.140 (total time: 161.950) Filter (q & B) r_work=0.1227 r_free=0.1503 | n_water=428 | time (s): 3.950 (total time: 165.900) Filter (dist only) r_work=0.1227 r_free=0.1503 | n_water=428 | time (s): 40.590 (total time: 206.490) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.790420 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1430.691811 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 0.1509 0.0289 0.007 0.9 2.9 0.5 0.0 0 13.395 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.21 15.09 2.89 3.748 22.927 1430.692 0.015 11.98 14.80 2.83 4.034 22.775 1430.692 0.015 Individual atomic B min max mean iso aniso Overall: 8.81 113.15 22.99 2.56 192 1763 Protein: 8.81 113.15 17.57 2.56 0 1519 Water: 10.96 73.58 42.19 N/A 192 236 Other: 22.21 33.00 26.42 N/A 0 8 Chain A: 8.81 113.15 20.20 N/A 0 1763 Chain S: 16.10 70.98 48.63 N/A 192 0 Histogram: Values Number of atoms 8.81 - 19.24 1206 19.24 - 29.68 250 29.68 - 40.11 186 40.11 - 50.55 146 50.55 - 60.98 107 60.98 - 71.41 49 71.41 - 81.85 5 81.85 - 92.28 3 92.28 - 102.72 1 102.72 - 113.15 2 =========================== Idealize ADP of riding H ========================== r_work=0.1198 r_free=0.1480 r_work=0.1198 r_free=0.1481 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1198 r_free = 0.1481 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 = 0.1199 r_free = 0.1470 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87591 (all), 4.90 % free)------------| | | | r_work= 0.1199 r_free= 0.1470 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.013804 | | target function (ls_wunit_k1) not normalized (work): 1149.844550 | | target function (ls_wunit_k1) not normalized (free): 102.706494 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1212 0.1199 0.1470 n_refl.: 87591 re-set all scales: r(all,work,free)=0.1606 0.1603 0.1690 n_refl.: 87591 remove outliers: r(all,work,free)=0.1606 0.1603 0.1690 n_refl.: 87591 overall B=0.04 to atoms: r(all,work,free)=0.1612 0.1610 0.1694 n_refl.: 87591 bulk-solvent and scaling: r(all,work,free)=0.1210 0.1196 0.1469 n_refl.: 87591 remove outliers: r(all,work,free)=0.1209 0.1195 0.1469 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 0.3369 295.866 270.024 0.595 1.002 0.370 11.894-9.307 99.02 97 4 0.1492 480.490 477.335 0.917 1.003 0.360 9.237-7.194 100.00 213 7 0.1647 392.982 395.234 0.975 1.003 0.290 7.162-5.571 100.00 427 22 0.1499 294.911 291.014 0.941 1.003 0.239 5.546-4.326 100.00 867 58 0.0849 404.840 402.159 0.959 1.003 0.220 4.315-3.360 100.00 1859 96 0.0707 385.006 383.907 1.002 1.002 0.210 3.356-2.611 100.00 3867 181 0.0963 252.929 252.328 1.008 1.002 0.072 2.608-2.026 99.99 8198 413 0.0950 167.669 167.240 1.017 1.001 0.000 2.025-1.573 100.00 17313 902 0.1178 81.881 82.085 1.027 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1613 36.309 35.814 1.016 0.998 0.000 1.221-1.150 99.97 13689 708 0.2346 22.877 21.393 0.975 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0652 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1195 r_free=0.1469 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1195 r_free=0.1469 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1195 r_free=0.1469 | n_water=428 | time (s): 1.930 (total time: 1.930) Filter (dist) r_work=0.1195 r_free=0.1468 | n_water=426 | time (s): 37.950 (total time: 39.880) Filter (q & B) r_work=0.1195 r_free=0.1468 | n_water=426 | time (s): 1.020 (total time: 40.900) Compute maps r_work=0.1195 r_free=0.1468 | n_water=426 | time (s): 1.270 (total time: 42.170) Filter (map) r_work=0.1234 r_free=0.1482 | n_water=293 | time (s): 2.630 (total time: 44.800) Find peaks r_work=0.1234 r_free=0.1482 | n_water=293 | time (s): 0.670 (total time: 45.470) Add new water r_work=0.1364 r_free=0.1611 | n_water=487 | time (s): 3.070 (total time: 48.540) Refine new water occ: r_work=0.1265 r_free=0.1522 adp: r_work=0.1266 r_free=0.1524 occ: r_work=0.1242 r_free=0.1500 adp: r_work=0.1241 r_free=0.1501 occ: r_work=0.1226 r_free=0.1484 adp: r_work=0.1220 r_free=0.1482 ADP+occupancy (water only), MIN, final r_work=0.1220 r_free=0.1482 r_work=0.1220 r_free=0.1482 | n_water=487 | time (s): 155.810 (total time: 204.350) Filter (q & B) r_work=0.1225 r_free=0.1482 | n_water=448 | time (s): 3.210 (total time: 207.560) Filter (dist only) r_work=0.1225 r_free=0.1482 | n_water=448 | time (s): 36.210 (total time: 243.770) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.025540 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 42.476957 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 0.1230 0.1439 0.0209 0.006 0.9 1.9 0.5 0.0 0 1.013 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.30 14.39 2.09 3.583 21.975 42.477 3.730 12.16 13.90 1.74 4.041 21.792 42.477 3.656 Individual atomic B min max mean iso aniso Overall: 9.21 109.47 21.54 2.29 215 1760 Protein: 9.21 109.47 17.17 2.29 0 1519 Water: 11.54 72.82 36.32 N/A 215 233 Other: 19.07 28.90 24.34 N/A 0 8 Chain A: 9.21 109.47 19.76 N/A 0 1760 Chain S: 15.93 63.17 36.13 N/A 215 0 Histogram: Values Number of atoms 9.21 - 19.24 1238 19.24 - 29.26 279 29.26 - 39.29 222 39.29 - 49.31 129 49.31 - 59.34 72 59.34 - 69.37 23 69.37 - 79.39 6 79.39 - 89.42 3 89.42 - 99.44 1 99.44 - 109.47 2 =========================== Idealize ADP of riding H ========================== r_work=0.1216 r_free=0.1390 r_work=0.1217 r_free=0.1391 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1217 r_free = 0.1391 target_work(ml) = 3.656 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1210 r_free = 0.1389 target_work(ml) = 3.653 | | occupancies: max = 1.00 min = 0.17 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= 0.1210 r_free= 0.1389 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.653346 | | target function (ml) not normalized (work): 304298.182277 | | target function (ml) not normalized (free): 16054.812306 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1219 0.1210 0.1389 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1535 0.1534 0.1575 n_refl.: 87589 remove outliers: r(all,work,free)=0.1535 0.1534 0.1575 n_refl.: 87589 overall B=-0.01 to atoms: r(all,work,free)=0.1533 0.1532 0.1574 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1206 0.1198 0.1357 n_refl.: 87589 remove outliers: r(all,work,free)=0.1201 0.1193 0.1357 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 89.58 81 5 0.3872 295.230 259.379 0.465 1.000 0.314 11.894-9.307 95.10 93 4 0.2278 479.688 461.063 0.850 1.002 0.310 9.237-7.194 97.73 208 7 0.2311 385.576 386.912 0.944 1.002 0.190 7.162-5.571 100.00 427 22 0.2048 294.911 285.152 0.913 1.002 0.172 5.546-4.326 100.00 867 58 0.1109 404.840 400.212 0.954 1.002 0.163 4.315-3.360 100.00 1859 96 0.0924 385.006 382.480 0.993 1.002 0.157 3.356-2.611 100.00 3867 181 0.1148 252.929 251.046 0.999 1.002 0.062 2.608-2.026 99.99 8198 413 0.1049 167.669 166.723 1.011 1.001 0.000 2.025-1.573 100.00 17313 902 0.1006 81.881 82.053 1.026 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1289 36.309 35.890 1.019 0.998 0.000 1.221-1.150 99.97 13689 708 0.2128 22.877 21.484 0.977 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0241 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1193 r_free=0.1357 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=0.1193 r_free=0.1357 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1357 | n_water=448 | time (s): 2.170 (total time: 2.170) Filter (dist) r_work=0.1193 r_free=0.1357 | n_water=447 | time (s): 41.420 (total time: 43.590) Filter (q & B) r_work=0.1193 r_free=0.1356 | n_water=445 | time (s): 3.270 (total time: 46.860) Compute maps r_work=0.1193 r_free=0.1356 | n_water=445 | time (s): 1.430 (total time: 48.290) Filter (map) r_work=0.1215 r_free=0.1377 | n_water=312 | time (s): 3.300 (total time: 51.590) Find peaks r_work=0.1215 r_free=0.1377 | n_water=312 | time (s): 0.490 (total time: 52.080) Add new water r_work=0.1287 r_free=0.1454 | n_water=489 | time (s): 2.610 (total time: 54.690) Refine new water occ: r_work=0.1215 r_free=0.1380 adp: r_work=0.1215 r_free=0.1381 occ: r_work=0.1199 r_free=0.1367 adp: r_work=0.1198 r_free=0.1367 occ: r_work=0.1188 r_free=0.1357 adp: r_work=0.1185 r_free=0.1355 ADP+occupancy (water only), MIN, final r_work=0.1185 r_free=0.1355 r_work=0.1185 r_free=0.1355 | n_water=489 | time (s): 187.620 (total time: 242.310) Filter (q & B) r_work=0.1192 r_free=0.1356 | n_water=446 | time (s): 2.990 (total time: 245.300) Filter (dist only) r_work=0.1192 r_free=0.1355 | n_water=445 | time (s): 37.090 (total time: 282.390) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.207764 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 48.197680 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 0.1192 0.1358 0.0167 0.006 1.0 3.8 0.5 0.0 0 1.104 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.92 13.58 1.67 3.402 21.432 48.198 3.636 11.73 13.53 1.79 3.804 21.301 48.198 3.620 Individual atomic B min max mean iso aniso Overall: 9.24 104.46 21.16 2.16 213 1759 Protein: 9.24 104.46 16.87 2.16 0 1519 Water: 11.42 71.64 35.76 N/A 213 232 Other: 19.59 27.31 23.33 N/A 0 8 Chain A: 9.24 104.46 19.42 N/A 0 1759 Chain S: 16.22 63.52 35.53 N/A 213 0 Histogram: Values Number of atoms 9.24 - 18.76 1224 18.76 - 28.28 291 28.28 - 37.80 208 37.80 - 47.32 133 47.32 - 56.85 75 56.85 - 66.37 27 66.37 - 75.89 9 75.89 - 85.41 2 85.41 - 94.94 1 94.94 - 104.46 2 =========================== Idealize ADP of riding H ========================== r_work=0.1173 r_free=0.1353 r_work=0.1174 r_free=0.1353 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1174 r_free = 0.1353 target_work(ml) = 3.620 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1171 r_free = 0.1352 target_work(ml) = 3.619 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87577 (all), 4.91 % free)------------| | | | r_work= 0.1171 r_free= 0.1352 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.619409 | | target function (ml) not normalized (work): 301428.027004 | | target function (ml) not normalized (free): 15930.147366 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1180 0.1171 0.1352 n_refl.: 87577 re-set all scales: r(all,work,free)=0.1493 0.1492 0.1543 n_refl.: 87577 remove outliers: r(all,work,free)=0.1493 0.1492 0.1543 n_refl.: 87577 overall B=-0.01 to atoms: r(all,work,free)=0.1491 0.1490 0.1543 n_refl.: 87577 bulk-solvent and scaling: r(all,work,free)=0.1179 0.1170 0.1350 n_refl.: 87577 remove outliers: r(all,work,free)=0.1179 0.1170 0.1350 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 89.58 81 5 0.4146 295.230 254.348 0.452 1.001 0.319 11.894-9.307 95.10 93 4 0.2377 479.688 463.502 0.848 1.002 0.312 9.237-7.194 97.73 208 7 0.2463 385.576 379.682 0.914 1.003 0.148 7.162-5.571 100.00 427 22 0.2164 294.911 284.961 0.906 1.003 0.133 5.546-4.326 100.00 867 58 0.1152 404.840 400.054 0.954 1.003 0.130 4.315-3.360 100.00 1859 96 0.0932 385.006 382.584 0.992 1.002 0.130 3.356-2.611 100.00 3867 181 0.1147 252.929 250.977 1.000 1.002 0.100 2.608-2.026 99.99 8198 413 0.1005 167.669 166.791 1.012 1.001 0.000 2.025-1.573 100.00 17313 902 0.0950 81.881 82.165 1.026 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1235 36.309 35.945 1.020 0.997 0.000 1.221-1.150 99.97 13689 708 0.2123 22.877 21.502 0.978 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0208 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1170 r_free=0.1350 After: r_work=0.1171 r_free=0.1351 ================================== NQH flips ================================== r_work=0.1171 r_free=0.1351 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=0.1171 r_free=0.1351 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1171 r_free=0.1351 | n_water=445 | time (s): 2.020 (total time: 2.020) Filter (dist) r_work=0.1171 r_free=0.1351 | n_water=445 | time (s): 34.340 (total time: 36.360) Filter (q & B) r_work=0.1171 r_free=0.1351 | n_water=444 | time (s): 3.160 (total time: 39.520) Compute maps r_work=0.1171 r_free=0.1351 | n_water=444 | time (s): 1.280 (total time: 40.800) Filter (map) r_work=0.1197 r_free=0.1388 | n_water=323 | time (s): 2.350 (total time: 43.150) Find peaks r_work=0.1197 r_free=0.1388 | n_water=323 | time (s): 0.500 (total time: 43.650) Add new water r_work=0.1250 r_free=0.1441 | n_water=474 | time (s): 2.420 (total time: 46.070) Refine new water occ: r_work=0.1187 r_free=0.1374 adp: r_work=0.1187 r_free=0.1377 occ: r_work=0.1176 r_free=0.1360 adp: r_work=0.1175 r_free=0.1363 occ: r_work=0.1167 r_free=0.1347 adp: r_work=0.1164 r_free=0.1348 ADP+occupancy (water only), MIN, final r_work=0.1164 r_free=0.1348 r_work=0.1164 r_free=0.1348 | n_water=474 | time (s): 173.090 (total time: 219.160) Filter (q & B) r_work=0.1171 r_free=0.1352 | n_water=436 | time (s): 3.360 (total time: 222.520) Filter (dist only) r_work=0.1171 r_free=0.1351 | n_water=434 | time (s): 36.700 (total time: 259.220) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.896398 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 52.108577 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 0.1193 0.1370 0.0178 0.007 1.1 3.2 0.5 0.0 0 0.948 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.93 13.70 1.78 3.279 21.029 52.109 3.628 11.95 13.67 1.71 3.470 20.956 52.109 3.620 Individual atomic B min max mean iso aniso Overall: 9.23 100.94 20.88 2.05 203 1758 Protein: 9.23 100.94 16.70 2.05 0 1519 Water: 11.53 70.88 35.46 N/A 203 231 Other: 20.28 28.12 23.94 N/A 0 8 Chain A: 9.23 100.94 19.23 N/A 0 1758 Chain S: 14.80 63.78 35.20 N/A 203 0 Histogram: Values Number of atoms 9.23 - 18.40 1217 18.40 - 27.57 289 27.57 - 36.75 196 36.75 - 45.92 133 45.92 - 55.09 82 55.09 - 64.26 29 64.26 - 73.43 11 73.43 - 82.60 1 82.60 - 91.77 1 91.77 - 100.94 2 =========================== Idealize ADP of riding H ========================== r_work=0.1195 r_free=0.1367 r_work=0.1195 r_free=0.1367 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1195 r_free = 0.1367 target_work(ml) = 3.620 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1193 r_free = 0.1365 target_work(ml) = 3.619 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87577 (all), 4.91 % free)------------| | | | r_work= 0.1193 r_free= 0.1365 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.619070 | | target function (ml) not normalized (work): 301399.802435 | | target function (ml) not normalized (free): 15926.260391 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1430 0.1430 5.7027 5.6482| | 2: 3.57 - 2.84 1.00 2888 124 0.1134 0.1472 5.2102 5.2722| | 3: 2.83 - 2.48 1.00 2820 163 0.1212 0.1244 5.009 5.0346| | 4: 2.47 - 2.25 1.00 2825 136 0.1016 0.1126 4.7093 4.7523| | 5: 2.25 - 2.09 1.00 2756 127 0.0980 0.1157 4.6505 4.7239| | 6: 2.09 - 1.97 1.00 2846 113 0.0956 0.1162 4.3451 4.4587| | 7: 1.97 - 1.87 1.00 2787 165 0.0974 0.1173 4.0639 4.1601| | 8: 1.87 - 1.79 1.00 2789 144 0.1021 0.1222 3.9815 4.0666| | 9: 1.79 - 1.72 1.00 2745 138 0.0938 0.1281 3.7011 3.8797| | 10: 1.72 - 1.66 1.00 2831 160 0.0993 0.1235 3.6218 3.7472| | 11: 1.66 - 1.61 1.00 2712 147 0.0951 0.1074 3.5546 3.5938| | 12: 1.61 - 1.56 1.00 2773 144 0.0906 0.1180 3.3374 3.4839| | 13: 1.56 - 1.52 1.00 2745 130 0.0965 0.1077 3.3303 3.4353| | 14: 1.52 - 1.48 1.00 2803 134 0.0976 0.1101 3.254 3.3318| | 15: 1.48 - 1.45 1.00 2738 128 0.1002 0.1349 3.164 3.3252| | 16: 1.45 - 1.42 1.00 2756 161 0.1058 0.1238 3.1456 3.2341| | 17: 1.42 - 1.39 1.00 2785 139 0.1114 0.1285 3.1142 3.2203| | 18: 1.39 - 1.36 1.00 2741 179 0.1135 0.1352 3.0805 3.2648| | 19: 1.36 - 1.34 1.00 2807 134 0.1205 0.1592 3.0889 3.2709| | 20: 1.34 - 1.32 1.00 2696 147 0.1311 0.1502 3.0857 3.1504| | 21: 1.32 - 1.30 1.00 2785 112 0.1407 0.1623 3.0856 3.1618| | 22: 1.29 - 1.27 1.00 2704 152 0.1462 0.1911 3.0815 3.2818| | 23: 1.27 - 1.26 1.00 2802 156 0.1570 0.1838 3.1021 3.2056| | 24: 1.26 - 1.24 1.00 2744 132 0.1621 0.1781 3.0944 3.1942| | 25: 1.24 - 1.22 1.00 2733 148 0.1789 0.2315 3.1089 3.2916| | 26: 1.22 - 1.21 1.00 2727 135 0.1856 0.1787 3.1247 3.2028| | 27: 1.21 - 1.19 1.00 2814 148 0.2002 0.2083 3.1413 3.1483| | 28: 1.19 - 1.18 1.00 2671 147 0.2132 0.2307 3.1404 3.1644| | 29: 1.18 - 1.16 1.00 2800 134 0.2215 0.2392 3.1283 3.231| | 30: 1.16 - 1.15 1.00 2739 148 0.2373 0.2459 3.1187 3.1618| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 9.11 1.00 0.97 6370.46| | 2: 3.57 - 2.84 2888 124 0.92 13.42 1.01 0.97 6370.46| | 3: 2.83 - 2.48 2820 163 0.89 17.53 0.99 0.98 5333.68| | 4: 2.47 - 2.25 2825 136 0.91 14.60 1.00 0.98 2660.18| | 5: 2.25 - 2.09 2756 127 0.89 16.84 1.01 0.98 2660.18| | 6: 2.09 - 1.97 2846 113 0.92 13.50 1.02 0.98 1552.55| | 7: 1.97 - 1.87 2787 165 0.94 10.56 1.02 0.97 607.89| | 8: 1.87 - 1.79 2789 144 0.92 14.14 1.00 0.97 607.89| | 9: 1.79 - 1.72 2745 138 0.94 11.18 0.98 0.97 329.78| | 10: 1.72 - 1.66 2831 160 0.93 12.02 0.98 0.97 274.09| | 11: 1.66 - 1.61 2712 147 0.93 12.65 0.98 0.97 261.78| | 12: 1.61 - 1.56 2773 144 0.95 9.46 0.99 0.97 145.65| | 13: 1.56 - 1.52 2745 130 0.94 10.92 1.02 0.97 145.65| | 14: 1.52 - 1.48 2803 134 0.94 11.12 1.02 0.98 130.33| | 15: 1.48 - 1.45 2738 128 0.95 10.30 1.01 0.98 102.27| | 16: 1.45 - 1.42 2756 161 0.94 11.46 1.02 0.98 102.27| | 17: 1.42 - 1.39 2785 139 0.95 11.27 1.01 0.98 92.51| | 18: 1.39 - 1.36 2741 179 0.94 11.61 1.01 0.99 86.86| | 19: 1.36 - 1.34 2807 134 0.94 12.19 1.00 0.99 86.86| | 20: 1.34 - 1.32 2696 147 0.94 12.34 0.99 0.97 82.18| | 21: 1.32 - 1.30 2785 112 0.94 13.29 0.98 0.97 81.86| | 22: 1.29 - 1.27 2704 152 0.93 13.79 0.98 0.96 82.02| | 23: 1.27 - 1.26 2802 156 0.92 14.75 0.97 0.95 82.84| | 24: 1.26 - 1.24 2744 132 0.93 14.87 0.96 0.95 82.84| | 25: 1.24 - 1.22 2733 148 0.91 16.27 0.96 0.94 84.44| | 26: 1.22 - 1.21 2727 135 0.90 18.01 1.02 0.94 86.21| | 27: 1.21 - 1.19 2814 148 0.89 18.64 1.02 0.94 86.21| | 28: 1.19 - 1.18 2671 147 0.88 20.12 1.01 0.93 89.51| | 29: 1.18 - 1.16 2800 134 0.88 20.46 0.99 0.93 90.75| | 30: 1.16 - 1.15 2739 148 0.86 21.84 0.98 0.93 90.75| |alpha: min = 0.93 max = 0.99 mean = 0.97| |beta: min = 81.86 max = 6370.46 mean = 986.20| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 90.00 mean = 13.93| |phase err.(test): min = 0.00 max = 88.80 mean = 14.05| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1201 0.1193 0.1365 n_refl.: 87577 re-set all scales: r(all,work,free)=0.1515 0.1515 0.1548 n_refl.: 87577 remove outliers: r(all,work,free)=0.1515 0.1515 0.1548 n_refl.: 87577 overall B=-0.00 to atoms: r(all,work,free)=0.1515 0.1515 0.1547 n_refl.: 87577 bulk-solvent and scaling: r(all,work,free)=0.1202 0.1193 0.1366 n_refl.: 87577 remove outliers: r(all,work,free)=0.1200 0.1191 0.1366 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 0.4118 287.108 255.767 0.448 1.000 0.310 11.894-9.307 93.14 91 4 0.2295 473.518 459.344 0.858 1.001 0.222 9.237-7.194 97.73 208 7 0.2599 385.576 377.405 0.914 1.002 0.140 7.162-5.571 100.00 427 22 0.2287 294.911 283.473 0.909 1.002 0.140 5.546-4.326 100.00 867 58 0.1206 404.840 399.892 0.964 1.002 0.120 4.315-3.360 100.00 1859 96 0.0984 385.006 382.219 1.003 1.002 0.120 3.356-2.611 100.00 3867 181 0.1191 252.929 250.890 1.009 1.002 0.048 2.608-2.026 99.99 8198 413 0.1029 167.669 166.726 1.022 1.001 0.000 2.025-1.573 100.00 17313 902 0.0965 81.881 82.144 1.035 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1219 36.309 35.943 1.026 1.000 0.000 1.221-1.150 99.97 13689 708 0.2113 22.877 21.465 0.980 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0063 ================= 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 : 0.2607 0.1919 0.080 5.131 8.8 119.3 19.9 258 0.000 1_bss: 0.1638 0.1757 0.080 5.131 9.0 119.5 20.1 258 0.000 1_settarget: 0.1638 0.1757 0.080 5.131 9.0 119.5 20.1 258 0.000 1_nqh: 0.1639 0.1759 0.080 5.131 9.0 119.5 20.1 258 0.003 1_weight: 0.1639 0.1759 0.080 5.131 9.0 119.5 20.1 258 0.003 1_xyzrec: 0.1209 0.1462 0.008 0.979 9.0 119.5 20.1 258 0.121 1_adp: 0.1239 0.1538 0.008 0.979 8.3 118.0 20.7 258 0.121 1_regHadp: 0.1243 0.1543 0.008 0.979 8.3 118.0 20.7 258 0.121 1_occ: 0.1242 0.1546 0.008 0.979 8.3 118.0 20.7 258 0.121 2_bss: 0.1239 0.1542 0.008 0.979 8.5 118.2 20.9 258 0.121 2_settarget: 0.1239 0.1542 0.008 0.979 8.5 118.2 20.9 258 0.121 2_updatecdl: 0.1239 0.1542 0.008 0.989 8.5 118.2 20.9 258 0.121 2_nqh: 0.1239 0.1542 0.008 0.989 8.5 118.2 20.9 258 0.121 2_sol: 0.1227 0.1503 0.008 0.989 8.5 118.2 23.3 428 n/a 2_weight: 0.1227 0.1503 0.008 0.989 8.5 118.2 23.3 428 n/a 2_xyzrec: 0.1221 0.1509 0.007 0.892 8.5 118.2 23.3 428 n/a 2_adp: 0.1198 0.1480 0.007 0.892 8.8 113.2 23.0 428 n/a 2_regHadp: 0.1198 0.1481 0.007 0.892 8.8 113.2 23.0 428 n/a 2_occ: 0.1199 0.1470 0.007 0.892 8.8 113.2 23.0 428 n/a 3_bss: 0.1195 0.1469 0.007 0.892 8.8 113.2 23.0 428 n/a 3_settarget: 0.1195 0.1469 0.007 0.892 8.8 113.2 23.0 428 n/a 3_updatecdl: 0.1195 0.1469 0.007 0.890 8.8 113.2 23.0 428 n/a 3_nqh: 0.1195 0.1469 0.007 0.890 8.8 113.2 23.0 428 n/a 3_sol: 0.1225 0.1482 0.007 0.890 8.8 113.2 21.9 448 n/a 3_weight: 0.1225 0.1482 0.007 0.890 8.8 113.2 21.9 448 n/a 3_xyzrec: 0.1230 0.1439 0.006 0.919 8.8 113.2 21.9 448 n/a 3_adp: 0.1216 0.1390 0.006 0.919 9.2 109.5 21.5 448 n/a 3_regHadp: 0.1217 0.1391 0.006 0.919 9.2 109.5 21.5 448 n/a 3_occ: 0.1210 0.1389 0.006 0.919 9.2 109.5 21.5 448 n/a 4_bss: 0.1193 0.1357 0.006 0.919 9.2 109.5 21.5 448 n/a 4_settarget: 0.1193 0.1357 0.006 0.919 9.2 109.5 21.5 448 n/a 4_updatecdl: 0.1193 0.1357 0.006 0.918 9.2 109.5 21.5 448 n/a 4_nqh: 0.1193 0.1357 0.006 0.918 9.2 109.5 21.5 448 n/a 4_sol: 0.1192 0.1355 0.006 0.918 9.2 109.5 21.4 445 n/a 4_weight: 0.1192 0.1355 0.006 0.918 9.2 109.5 21.4 445 n/a 4_xyzrec: 0.1192 0.1358 0.006 0.979 9.2 109.5 21.4 445 n/a 4_adp: 0.1173 0.1353 0.006 0.979 9.2 104.5 21.2 445 n/a 4_regHadp: 0.1174 0.1353 0.006 0.979 9.2 104.5 21.2 445 n/a 4_occ: 0.1171 0.1352 0.006 0.979 9.2 104.5 21.2 445 n/a 5_bss: 0.1170 0.1350 0.006 0.979 9.2 104.5 21.2 445 n/a 5_settarget: 0.1170 0.1350 0.006 0.979 9.2 104.5 21.2 445 n/a 5_updatecdl: 0.1170 0.1350 0.006 0.980 9.2 104.5 21.2 445 n/a 5_setrh: 0.1171 0.1351 0.006 0.980 9.2 104.5 21.2 445 n/a 5_nqh: 0.1171 0.1351 0.006 0.980 9.2 104.5 21.2 445 n/a 5_sol: 0.1171 0.1351 0.006 0.980 9.2 104.5 21.0 434 n/a 5_weight: 0.1171 0.1351 0.006 0.980 9.2 104.5 21.0 434 n/a 5_xyzrec: 0.1193 0.1370 0.007 1.058 9.2 104.5 21.0 434 n/a 5_adp: 0.1195 0.1367 0.007 1.058 9.2 100.9 20.9 434 n/a 5_regHadp: 0.1195 0.1367 0.007 1.058 9.2 100.9 20.9 434 n/a 5_occ: 0.1193 0.1365 0.007 1.058 9.2 100.9 20.9 434 n/a end: 0.1191 0.1366 0.007 1.058 9.2 100.9 20.9 434 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_8954467_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_8954467_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.9500 Refinement macro-cycles (run) : 3312.6800 Write final files (write_after_run_outputs) : 79.2200 Total : 3396.8500 Total CPU time: 57.23 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:07:57 PST -0800 (1735452477.39 s) Start R-work = 0.1638, R-free = 0.1757 Final R-work = 0.1191, R-free = 0.1366 =============================================================================== Job complete usr+sys time: 3562.14 seconds wall clock time: 63 minutes 39.75 seconds (3819.75 seconds total)