Starting phenix.refine on Sat Dec 28 21:06:34 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_1617309.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 { 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_1617309.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_1617309.pdb" 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): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 2.14, per 1000 atoms: 0.63 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: 0.61 Conformation dependent library (CDL) restraints added in 437.8 milliseconds Time building geometry restraints manager: 0.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.91: 550 0.91 - 1.17: 1095 1.17 - 1.42: 641 1.42 - 1.67: 828 1.67 - 1.93: 39 Bond restraints: 3153 Sorted by residual: bond pdb=" CA ILE A 21 " pdb=" CB ILE A 21 " ideal model delta sigma weight residual 1.537 1.400 0.137 5.00e-03 4.00e+04 7.49e+02 bond pdb=" CA TYR A 141 " pdb=" C TYR A 141 " ideal model delta sigma weight residual 1.524 1.275 0.249 1.31e-02 5.83e+03 3.61e+02 bond pdb=" C BGLN A 80 " pdb=" O BGLN A 80 " ideal model delta sigma weight residual 1.236 1.020 0.216 1.15e-02 7.56e+03 3.53e+02 bond pdb=" C GLN A 180 " pdb=" N VAL A 181 " ideal model delta sigma weight residual 1.334 1.563 -0.229 1.25e-02 6.40e+03 3.35e+02 bond pdb=" N ILE A 31 " pdb=" CA ILE A 31 " ideal model delta sigma weight residual 1.458 1.671 -0.213 1.17e-02 7.31e+03 3.32e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.34: 3470 5.34 - 10.68: 1850 10.68 - 16.02: 409 16.02 - 21.36: 45 21.36 - 26.71: 3 Bond angle restraints: 5777 Sorted by residual: angle pdb=" NE ARG A 27 " pdb=" CZ ARG A 27 " pdb=" NH2 ARG A 27 " ideal model delta sigma weight residual 119.20 104.35 14.85 9.00e-01 1.23e+00 2.72e+02 angle pdb=" O ILE A 52 " pdb=" C ILE A 52 " pdb=" N ACYS A 53 " ideal model delta sigma weight residual 123.18 138.56 -15.38 1.05e+00 9.07e-01 2.15e+02 angle pdb=" CA GLU A 170 " pdb=" C GLU A 170 " pdb=" O GLU A 170 " ideal model delta sigma weight residual 120.63 134.55 -13.92 1.08e+00 8.57e-01 1.66e+02 angle pdb=" OE1AGLN A 80 " pdb=" CD AGLN A 80 " pdb=" NE2AGLN A 80 " ideal model delta sigma weight residual 122.60 109.84 12.76 1.00e+00 1.00e+00 1.63e+02 angle pdb=" O ILE A 21 " pdb=" C ILE A 21 " pdb=" N PRO A 22 " ideal model delta sigma weight residual 120.42 128.37 -7.95 6.40e-01 2.44e+00 1.54e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.45: 938 17.45 - 34.89: 117 34.89 - 52.33: 39 52.33 - 69.78: 15 69.78 - 87.22: 2 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA SER A 121 " pdb=" C SER A 121 " pdb=" N LYS A 122 " pdb=" CA LYS A 122 " ideal model delta harmonic sigma weight residual 180.00 158.30 21.70 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA ALYS A 41 " pdb=" C ALYS A 41 " pdb=" N ASP A 42 " pdb=" CA ASP A 42 " ideal model delta harmonic sigma weight residual -180.00 -159.11 -20.89 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA ARG A 27 " pdb=" C ARG A 27 " pdb=" N ARG A 28 " pdb=" CA ARG A 28 " ideal model delta harmonic sigma weight residual 180.00 159.90 20.10 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.211: 98 0.211 - 0.419: 75 0.419 - 0.628: 53 0.628 - 0.837: 12 0.837 - 1.046: 5 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA ARG A 48 " pdb=" N ARG A 48 " pdb=" C ARG A 48 " pdb=" CB ARG A 48 " both_signs ideal model delta sigma weight residual False 2.51 1.46 1.05 2.00e-01 2.50e+01 2.73e+01 chirality pdb=" CA ALYS A 99 " pdb=" N ALYS A 99 " pdb=" C ALYS A 99 " pdb=" CB ALYS A 99 " both_signs ideal model delta sigma weight residual False 2.51 1.48 1.03 2.00e-01 2.50e+01 2.65e+01 chirality pdb=" CA BTYR A 67 " pdb=" N BTYR A 67 " pdb=" C BTYR A 67 " pdb=" CB BTYR A 67 " both_signs ideal model delta sigma weight residual False 2.51 3.44 -0.93 2.00e-01 2.50e+01 2.15e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.102 2.00e-02 2.50e+03 7.42e-02 1.65e+02 pdb=" CG PHE A 164 " 0.119 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " -0.040 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.092 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.101 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.094 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.040 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.087 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.023 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.006 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " 0.048 2.00e-02 2.50e+03 6.66e-02 1.33e+02 pdb=" CG PHE A 162 " -0.103 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " -0.086 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " 0.091 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " -0.057 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " 0.080 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " -0.064 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " 0.069 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " -0.032 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " 0.047 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " -0.034 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " 0.070 2.00e-02 2.50e+03 6.43e-02 1.24e+02 pdb=" CG BTYR A 67 " -0.051 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " -0.073 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " -0.048 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " 0.090 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " -0.059 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " -0.016 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " 0.044 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " -0.059 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " 0.109 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " 0.048 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " -0.055 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.34: 1240 2.34 - 2.91: 8270 2.91 - 3.47: 10441 3.47 - 4.04: 15154 4.04 - 4.60: 21532 Nonbonded interactions: 56637 Sorted by model distance: nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.781 2.450 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.810 2.450 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.811 2.450 nonbonded pdb=" O GLN A 95 " pdb=" H BGLY A 100 " model vdw 1.826 2.450 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.840 2.450 ... (remaining 56632 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_1617309_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= 0.2605 r_free= 0.1927 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.792367 | | target function (ml) not normalized (work): 232620.918292 | | target function (ml) not normalized (free): 11806.674244 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 49.25 - 3.58 1.00 2941 171 0.3027 0.2013 7.1352 4.9365| | 2: 3.57 - 2.84 1.00 2876 122 0.2455 0.1858 4.3436 4.336| | 3: 2.84 - 2.48 1.00 2833 165 0.2346 0.1740 4.1212 4.1811| | 4: 2.47 - 2.25 1.00 2825 136 0.2344 0.1474 3.8277 3.8186| | 5: 2.25 - 2.09 1.00 2756 127 0.2445 0.1486 3.7945 3.8267| | 6: 2.09 - 1.97 1.00 2846 113 0.2544 0.1592 3.4756 3.5415| | 7: 1.97 - 1.87 1.00 2787 165 0.2523 0.1879 3.1388 3.227| | 8: 1.87 - 1.79 1.00 2789 144 0.2555 0.1923 3.0781 3.1416| | 9: 1.79 - 1.72 1.00 2745 138 0.2376 0.1861 2.8947 2.9812| | 10: 1.72 - 1.66 1.00 2789 158 0.2384 0.1793 2.7997 2.8347| | 11: 1.66 - 1.61 1.00 2740 147 0.2486 0.1794 2.7347 2.7418| | 12: 1.61 - 1.56 1.00 2787 146 0.2482 0.1874 2.6183 2.6396| | 13: 1.56 - 1.52 1.00 2745 130 0.2551 0.2135 2.5562 2.6942| | 14: 1.52 - 1.48 1.00 2803 134 0.2585 0.1815 2.4936 2.4652| | 15: 1.48 - 1.45 1.00 2738 128 0.2609 0.2121 2.4232 2.446| | 16: 1.45 - 1.42 1.00 2756 161 0.2716 0.2166 2.3867 2.4417| | 17: 1.42 - 1.39 1.00 2785 139 0.2642 0.2241 2.3389 2.3784| | 18: 1.39 - 1.36 1.00 2741 179 0.2624 0.2086 2.2785 2.2884| | 19: 1.36 - 1.34 1.00 2807 134 0.2642 0.2377 2.2392 2.3286| | 20: 1.34 - 1.32 1.00 2696 147 0.2609 0.2222 2.198 2.1968| | 21: 1.32 - 1.30 1.00 2785 112 0.2730 0.2221 2.1532 2.1643| | 22: 1.29 - 1.27 1.00 2704 152 0.2746 0.2464 2.1482 2.1649| | 23: 1.27 - 1.26 1.00 2802 156 0.2740 0.2395 2.1036 2.1491| | 24: 1.26 - 1.24 1.00 2744 132 0.2777 0.2597 2.0729 2.1921| | 25: 1.24 - 1.22 1.00 2734 148 0.2852 0.2562 2.0482 2.0973| | 26: 1.22 - 1.21 1.00 2727 135 0.2897 0.2089 2.0116 2.0136| | 27: 1.21 - 1.19 1.00 2814 148 0.2983 0.2840 2.0139 2.059| | 28: 1.19 - 1.18 1.00 2671 147 0.2978 0.2828 1.9868 1.9973| | 29: 1.18 - 1.16 1.00 2800 134 0.2951 0.2844 1.9569 2.0322| | 30: 1.16 - 1.15 1.00 2740 148 0.3079 0.2930 1.9395 1.9908| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.63 0.76 0.23 1453.18| | 2: 3.57 - 2.84 2876 122 0.81 25.83 1.27 0.23 1453.18| | 3: 2.84 - 2.48 2833 165 0.74 31.63 1.25 0.24 1206.28| | 4: 2.47 - 2.25 2825 136 0.81 25.58 1.26 0.25 565.54| | 5: 2.25 - 2.09 2756 127 0.77 29.15 1.28 0.25 565.54| | 6: 2.09 - 1.97 2846 113 0.83 22.84 1.29 0.25 311.64| | 7: 1.97 - 1.87 2787 165 0.89 17.21 1.27 0.25 95.09| | 8: 1.87 - 1.79 2789 144 0.85 21.60 1.26 0.25 95.09| | 9: 1.79 - 1.72 2745 138 0.88 18.79 1.23 0.25 56.69| | 10: 1.72 - 1.66 2789 158 0.86 20.26 1.22 0.25 49.00| | 11: 1.66 - 1.61 2740 147 0.85 21.75 1.24 0.25 47.21| | 12: 1.61 - 1.56 2787 146 0.89 18.20 1.24 0.25 29.03| | 13: 1.56 - 1.52 2745 130 0.87 20.25 1.24 0.25 29.03| | 14: 1.52 - 1.48 2803 134 0.87 20.56 1.24 0.25 25.82| | 15: 1.48 - 1.45 2738 128 0.87 19.96 1.24 0.25 19.94| | 16: 1.45 - 1.42 2756 161 0.86 21.23 1.25 0.25 19.94| | 17: 1.42 - 1.39 2785 139 0.87 20.27 1.22 0.25 17.14| | 18: 1.39 - 1.36 2741 179 0.87 20.83 1.22 0.25 15.52| | 19: 1.36 - 1.34 2807 134 0.86 21.74 1.22 0.25 15.52| | 20: 1.34 - 1.32 2696 147 0.87 20.81 1.19 0.25 12.91| | 21: 1.32 - 1.30 2785 112 0.86 21.98 1.22 0.25 12.73| | 22: 1.29 - 1.27 2704 152 0.86 22.17 1.20 0.25 12.48| | 23: 1.27 - 1.26 2802 156 0.86 22.23 1.21 0.24 11.22| | 24: 1.26 - 1.24 2744 132 0.84 23.24 1.20 0.24 11.22| | 25: 1.24 - 1.22 2734 148 0.84 24.11 1.20 0.23 10.74| | 26: 1.22 - 1.21 2727 135 0.83 24.67 1.20 0.23 10.21| | 27: 1.21 - 1.19 2814 148 0.83 25.39 1.20 0.23 10.21| | 28: 1.19 - 1.18 2671 147 0.82 26.34 1.18 0.22 9.87| | 29: 1.18 - 1.16 2800 134 0.81 26.90 1.16 0.22 9.74| | 30: 1.16 - 1.15 2740 148 0.79 28.64 1.14 0.22 9.74| |alpha: min = 0.22 max = 0.25 mean = 0.24| |beta: min = 9.74 max = 1453.18 mean = 212.16| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.98 mean = 22.76| |phase err.(test): min = 0.00 max = 89.83 mean = 22.71| |-----------------------------------------------------------------------------| ----------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 0.249 1557 Z= 5.572 Angle : 5.349 20.777 2118 Z= 3.757 Chirality : 0.370 1.046 243 Planarity : 0.033 0.089 284 Dihedral : 13.847 87.219 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.86 % Allowed : 2.48 % Favored : 95.65 % Cbeta Deviations : 31.89 % 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: -1.93 (0.51), residues: 224 helix: -2.69 (0.40), residues: 101 sheet: 0.90 (0.96), residues: 28 loop : -0.02 (0.61), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.065 0.021 ARG A 27 TYR 0.102 0.046 TYR A 139 PHE 0.115 0.051 PHE A 164 HIS 0.086 0.045 HIS A 115 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2605 r_free= 0.1927 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.792367 | | target function (ml) not normalized (work): 232620.918292 | | target function (ml) not normalized (free): 11806.674244 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2563 0.2606 0.1928 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2563 0.2606 0.1928 n_refl.: 87602 remove outliers: r(all,work,free)=0.1977 0.1982 0.1928 n_refl.: 87594 overall B=0.21 to atoms: r(all,work,free)=0.2002 0.2007 0.1941 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1646 0.1640 0.1763 n_refl.: 87594 remove outliers: r(all,work,free)=0.1645 0.1639 0.1763 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 0.3835 386.113 358.559 0.673 1.004 0.411 11.894-9.307 99.02 97 4 0.1841 613.322 593.360 0.925 1.004 0.380 9.237-7.194 100.00 213 7 0.2104 501.622 490.673 0.959 1.004 0.363 7.162-5.571 100.00 427 22 0.2158 376.439 364.326 0.933 1.004 0.293 5.546-4.326 100.00 867 58 0.1280 516.758 511.565 0.961 1.003 0.228 4.315-3.360 100.00 1859 96 0.1153 491.441 486.660 1.007 1.003 0.199 3.356-2.611 100.00 3867 181 0.1449 322.851 319.483 0.997 1.002 0.119 2.608-2.026 99.99 8198 413 0.1357 214.021 211.939 1.007 1.001 0.000 2.025-1.573 100.00 17313 902 0.1646 104.517 103.900 1.012 0.999 0.000 1.573-1.221 100.00 36679 1900 0.2066 46.347 45.014 1.005 0.995 0.000 1.221-1.150 99.97 13689 708 0.2595 29.202 26.880 0.975 0.993 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0471 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1639 r_free=0.1763 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN A Total number of N/Q/H flips: 2 r_work=0.1646 r_free=0.1772 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.374876 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1990.950718 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 0.1459 0.0250 0.008 1.0 1.6 0.5 0.0 0 13.187 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.09 14.59 2.50 3.013 19.064 1990.951 0.017 12.41 15.41 3.00 3.206 19.544 1990.951 0.016 Individual atomic B min max mean iso aniso Overall: 8.54 118.69 21.00 2.87 0 1785 Protein: 8.54 118.69 17.88 2.87 0 1519 Water: 11.08 114.50 39.11 N/A 0 258 Other: 23.18 36.40 29.16 N/A 0 8 Chain A: 8.54 118.69 21.00 N/A 0 1785 Histogram: Values Number of atoms 8.54 - 19.56 1208 19.56 - 30.57 228 30.57 - 41.59 164 41.59 - 52.60 102 52.60 - 63.62 54 63.62 - 74.63 16 74.63 - 85.65 6 85.65 - 96.66 3 96.66 - 107.67 1 107.67 - 118.69 3 =========================== Idealize ADP of riding H ========================== r_work=0.1242 r_free=0.1541 r_work=0.1246 r_free=0.1545 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1246 r_free = 0.1545 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 = 0.1246 r_free = 0.1549 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.21 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= 0.1246 r_free= 0.1549 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.015388 | | target function (ls_wunit_k1) not normalized (work): 1281.764436 | | target function (ls_wunit_k1) not normalized (free): 114.372526 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1261 0.1246 0.1549 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1700 0.1699 0.1771 n_refl.: 87593 remove outliers: r(all,work,free)=0.1700 0.1699 0.1771 n_refl.: 87593 overall B=0.14 to atoms: r(all,work,free)=0.1723 0.1722 0.1787 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1259 0.1245 0.1543 n_refl.: 87593 remove outliers: r(all,work,free)=0.1259 0.1244 0.1543 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 0.3580 299.099 278.961 0.628 1.002 0.374 11.894-9.307 99.02 97 4 0.1603 479.140 467.865 0.907 1.003 0.369 9.237-7.194 100.00 213 7 0.1831 391.877 386.890 0.948 1.003 0.340 7.162-5.571 100.00 427 22 0.1712 294.082 288.754 0.926 1.003 0.258 5.546-4.326 100.00 867 58 0.0904 403.702 401.261 0.949 1.002 0.209 4.315-3.360 100.00 1859 96 0.0772 383.924 383.016 0.997 1.002 0.190 3.356-2.611 100.00 3867 181 0.1017 252.218 251.486 0.999 1.002 0.119 2.608-2.026 99.99 8198 413 0.0978 167.197 166.596 1.010 1.001 0.000 2.025-1.573 100.00 17313 902 0.1215 81.651 81.821 1.018 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1658 36.207 35.664 1.006 0.998 0.000 1.221-1.150 99.97 13689 708 0.2362 22.813 21.318 0.969 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0545 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1244 r_free=0.1543 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=0.1244 r_free=0.1543 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1244 r_free=0.1543 | n_water=258 | time (s): 2.430 (total time: 2.430) Filter (dist) r_work=0.1254 r_free=0.1539 | n_water=252 | time (s): 25.890 (total time: 28.320) Filter (q & B) r_work=0.1257 r_free=0.1538 | n_water=249 | time (s): 3.430 (total time: 31.750) Compute maps r_work=0.1257 r_free=0.1538 | n_water=249 | time (s): 1.830 (total time: 33.580) Filter (map) r_work=0.1281 r_free=0.1550 | n_water=233 | time (s): 3.740 (total time: 37.320) Find peaks r_work=0.1281 r_free=0.1550 | n_water=233 | time (s): 0.710 (total time: 38.030) Add new water r_work=0.1431 r_free=0.1698 | n_water=448 | time (s): 3.740 (total time: 41.770) Refine new water occ: r_work=0.1330 r_free=0.1545 adp: r_work=0.1253 r_free=0.1503 occ: r_work=0.1266 r_free=0.1491 adp: r_work=0.1233 r_free=0.1482 occ: r_work=0.1237 r_free=0.1480 adp: r_work=0.1226 r_free=0.1477 ADP+occupancy (water only), MIN, final r_work=0.1226 r_free=0.1477 r_work=0.1226 r_free=0.1477 | n_water=448 | time (s): 90.720 (total time: 132.490) Filter (q & B) r_work=0.1231 r_free=0.1484 | n_water=429 | time (s): 4.040 (total time: 136.530) Filter (dist only) r_work=0.1231 r_free=0.1484 | n_water=429 | time (s): 40.900 (total time: 177.430) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.116345 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1510.442078 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 0.1519 0.0289 0.007 0.9 1.9 0.5 0.0 0 12.558 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.30 15.19 2.89 3.789 23.133 1510.442 0.015 11.99 14.79 2.80 4.272 22.941 1510.442 0.015 Individual atomic B min max mean iso aniso Overall: 8.59 113.83 23.07 2.62 196 1760 Protein: 8.59 113.83 17.65 2.62 0 1519 Water: 11.38 74.02 42.16 N/A 196 233 Other: 23.61 34.74 28.55 N/A 0 8 Chain A: 8.59 113.83 20.37 N/A 0 1760 Chain S: 15.63 74.02 47.34 N/A 196 0 Histogram: Values Number of atoms 8.59 - 19.11 1200 19.11 - 29.63 254 29.63 - 40.16 189 40.16 - 50.68 145 50.68 - 61.21 103 61.21 - 71.73 50 71.73 - 82.26 9 82.26 - 92.78 3 92.78 - 103.31 1 103.31 - 113.83 2 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1479 r_work=0.1199 r_free=0.1478 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 r_free = 0.1478 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 = 0.1202 r_free = 0.1473 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.22 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= 0.1202 r_free= 0.1473 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.014077 | | target function (ls_wunit_k1) not normalized (work): 1172.557213 | | target function (ls_wunit_k1) not normalized (free): 101.522800 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1215 0.1202 0.1473 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1615 0.1611 0.1709 n_refl.: 87592 remove outliers: r(all,work,free)=0.1615 0.1611 0.1709 n_refl.: 87592 overall B=0.03 to atoms: r(all,work,free)=0.1619 0.1616 0.1713 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1212 0.1199 0.1471 n_refl.: 87592 remove outliers: r(all,work,free)=0.1211 0.1198 0.1471 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 0.3467 295.034 271.676 0.588 1.002 0.364 11.894-9.307 99.02 97 4 0.1504 479.140 477.417 0.917 1.003 0.360 9.237-7.194 100.00 213 7 0.1711 391.877 393.308 0.975 1.003 0.290 7.162-5.571 100.00 427 22 0.1525 294.082 290.213 0.942 1.003 0.234 5.546-4.326 100.00 867 58 0.0823 403.702 400.786 0.956 1.003 0.215 4.315-3.360 100.00 1859 96 0.0720 383.924 383.026 1.003 1.002 0.210 3.356-2.611 100.00 3867 181 0.0965 252.218 251.733 1.010 1.002 0.072 2.608-2.026 99.99 8198 413 0.0964 167.197 166.719 1.019 1.001 0.000 2.025-1.573 100.00 17313 902 0.1177 81.651 81.850 1.028 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1605 36.207 35.710 1.019 0.997 0.000 1.221-1.150 99.97 13689 708 0.2335 22.813 21.358 0.980 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0465 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1198 r_free=0.1471 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=0.1198 r_free=0.1471 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1198 r_free=0.1471 | n_water=429 | time (s): 2.000 (total time: 2.000) Filter (dist) r_work=0.1199 r_free=0.1470 | n_water=426 | time (s): 38.940 (total time: 40.940) Filter (q & B) r_work=0.1199 r_free=0.1470 | n_water=426 | time (s): 1.040 (total time: 41.980) Compute maps r_work=0.1199 r_free=0.1470 | n_water=426 | time (s): 1.720 (total time: 43.700) Filter (map) r_work=0.1239 r_free=0.1473 | n_water=296 | time (s): 3.470 (total time: 47.170) Find peaks r_work=0.1239 r_free=0.1473 | n_water=296 | time (s): 0.740 (total time: 47.910) Add new water r_work=0.1369 r_free=0.1607 | n_water=477 | time (s): 2.940 (total time: 50.850) Refine new water occ: r_work=0.1268 r_free=0.1528 adp: r_work=0.1270 r_free=0.1530 occ: r_work=0.1246 r_free=0.1505 adp: r_work=0.1244 r_free=0.1506 occ: r_work=0.1230 r_free=0.1488 adp: r_work=0.1224 r_free=0.1486 ADP+occupancy (water only), MIN, final r_work=0.1224 r_free=0.1486 r_work=0.1224 r_free=0.1486 | n_water=477 | time (s): 179.950 (total time: 230.800) Filter (q & B) r_work=0.1227 r_free=0.1488 | n_water=444 | time (s): 2.550 (total time: 233.350) Filter (dist only) r_work=0.1227 r_free=0.1488 | n_water=444 | time (s): 34.830 (total time: 268.180) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.191901 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 47.557159 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 0.1458 0.0229 0.006 0.9 2.2 0.5 0.0 0 1.096 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.30 14.58 2.29 3.616 22.071 47.557 3.723 12.23 14.22 1.99 4.036 21.897 47.557 3.657 Individual atomic B min max mean iso aniso Overall: 9.21 109.88 21.67 2.32 214 1757 Protein: 9.21 109.88 17.26 2.32 0 1519 Water: 11.37 71.44 36.71 N/A 214 230 Other: 19.31 30.61 25.46 N/A 0 8 Chain A: 9.21 109.88 19.92 N/A 0 1757 Chain S: 15.86 67.40 36.08 N/A 214 0 Histogram: Values Number of atoms 9.21 - 19.28 1230 19.28 - 29.35 280 29.35 - 39.41 221 39.41 - 49.48 133 49.48 - 59.55 75 59.55 - 69.61 18 69.61 - 79.68 8 79.68 - 89.75 3 89.75 - 99.81 1 99.81 - 109.88 2 =========================== Idealize ADP of riding H ========================== r_work=0.1223 r_free=0.1422 r_work=0.1224 r_free=0.1422 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1224 r_free = 0.1422 target_work(ml) = 3.657 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1216 r_free = 0.1420 target_work(ml) = 3.654 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87589 (all), 4.90 % free)------------| | | | r_work= 0.1216 r_free= 0.1420 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.654333 | | target function (ml) not normalized (work): 304380.333621 | | target function (ml) not normalized (free): 16082.845132 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1226 0.1216 0.1420 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1548 0.1547 0.1594 n_refl.: 87589 remove outliers: r(all,work,free)=0.1548 0.1547 0.1594 n_refl.: 87589 overall B=-0.01 to atoms: r(all,work,free)=0.1545 0.1544 0.1593 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1216 0.1207 0.1393 n_refl.: 87589 remove outliers: r(all,work,free)=0.1215 0.1206 0.1393 n_refl.: 87585 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 91.67 83 5 0.4141 289.626 266.934 0.490 1.000 0.350 11.894-9.307 98.04 96 4 0.2386 482.968 466.885 0.849 1.002 0.350 9.237-7.194 99.09 211 7 0.2416 386.416 385.627 0.944 1.002 0.190 7.162-5.571 100.00 427 22 0.2039 294.082 282.529 0.916 1.002 0.180 5.546-4.326 100.00 867 58 0.1097 403.702 399.076 0.950 1.002 0.160 4.315-3.360 100.00 1859 96 0.0952 383.924 381.161 0.992 1.002 0.150 3.356-2.611 100.00 3867 181 0.1168 252.218 250.267 0.999 1.002 0.130 2.608-2.026 99.99 8198 413 0.1059 167.197 166.129 1.011 1.001 0.000 2.025-1.573 100.00 17313 902 0.1014 81.651 81.799 1.027 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1290 36.207 35.783 1.021 0.998 0.000 1.221-1.150 99.97 13689 708 0.2130 22.813 21.428 0.979 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0365 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1206 r_free=0.1393 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1206 r_free=0.1393 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1206 r_free=0.1393 | n_water=444 | time (s): 1.780 (total time: 1.780) Filter (dist) r_work=0.1206 r_free=0.1393 | n_water=444 | time (s): 36.790 (total time: 38.570) Filter (q & B) r_work=0.1206 r_free=0.1393 | n_water=444 | time (s): 1.250 (total time: 39.820) Compute maps r_work=0.1206 r_free=0.1393 | n_water=444 | time (s): 1.500 (total time: 41.320) Filter (map) r_work=0.1233 r_free=0.1374 | n_water=309 | time (s): 2.930 (total time: 44.250) Find peaks r_work=0.1233 r_free=0.1374 | n_water=309 | time (s): 0.580 (total time: 44.830) Add new water r_work=0.1305 r_free=0.1447 | n_water=476 | time (s): 3.000 (total time: 47.830) Refine new water occ: r_work=0.1227 r_free=0.1383 adp: r_work=0.1228 r_free=0.1385 occ: r_work=0.1210 r_free=0.1364 adp: r_work=0.1208 r_free=0.1366 occ: r_work=0.1197 r_free=0.1352 adp: r_work=0.1193 r_free=0.1352 ADP+occupancy (water only), MIN, final r_work=0.1193 r_free=0.1352 r_work=0.1193 r_free=0.1352 | n_water=476 | time (s): 214.260 (total time: 262.090) Filter (q & B) r_work=0.1199 r_free=0.1356 | n_water=448 | time (s): 3.040 (total time: 265.130) Filter (dist only) r_work=0.1199 r_free=0.1355 | n_water=447 | time (s): 36.710 (total time: 301.840) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.022193 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 43.529448 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 0.1204 0.1379 0.0174 0.006 1.0 1.9 0.5 0.0 0 1.011 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.04 13.79 1.74 3.430 21.541 43.529 3.641 11.91 13.71 1.80 3.749 21.438 43.529 3.630 Individual atomic B min max mean iso aniso Overall: 9.29 106.05 21.32 2.16 220 1754 Protein: 9.29 106.05 17.01 2.16 0 1519 Water: 11.34 70.49 35.92 N/A 220 227 Other: 19.34 28.58 24.10 N/A 0 8 Chain A: 9.29 106.05 19.57 N/A 0 1754 Chain S: 15.71 60.08 35.24 N/A 220 0 Histogram: Values Number of atoms 9.29 - 18.96 1231 18.96 - 28.64 293 28.64 - 38.32 203 38.32 - 47.99 134 47.99 - 57.67 74 57.67 - 67.35 25 67.35 - 77.02 9 77.02 - 86.70 2 86.70 - 96.38 1 96.38 - 106.05 2 =========================== Idealize ADP of riding H ========================== r_work=0.1191 r_free=0.1371 r_work=0.1191 r_free=0.1371 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1191 r_free = 0.1371 target_work(ml) = 3.630 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1186 r_free = 0.1369 target_work(ml) = 3.629 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87585 (all), 4.90 % free)------------| | | | r_work= 0.1186 r_free= 0.1369 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.628615 | | target function (ml) not normalized (work): 302223.743488 | | target function (ml) not normalized (free): 15962.816776 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1195 0.1186 0.1369 n_refl.: 87585 re-set all scales: r(all,work,free)=0.1526 0.1526 0.1560 n_refl.: 87585 remove outliers: r(all,work,free)=0.1526 0.1526 0.1560 n_refl.: 87585 overall B=-0.02 to atoms: r(all,work,free)=0.1522 0.1522 0.1558 n_refl.: 87585 bulk-solvent and scaling: r(all,work,free)=0.1194 0.1185 0.1367 n_refl.: 87585 remove outliers: r(all,work,free)=0.1191 0.1182 0.1367 n_refl.: 87579 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.3938 289.760 245.490 0.445 1.000 0.320 11.894-9.307 97.06 95 4 0.2394 484.971 461.442 0.846 1.002 0.320 9.237-7.194 98.18 209 7 0.2474 383.417 380.384 0.918 1.002 0.160 7.162-5.571 100.00 427 22 0.2171 294.082 282.729 0.907 1.002 0.140 5.546-4.326 100.00 867 58 0.1160 403.702 399.034 0.950 1.002 0.130 4.315-3.360 100.00 1859 96 0.0933 383.924 381.813 0.996 1.002 0.120 3.356-2.611 100.00 3867 181 0.1145 252.218 250.451 1.002 1.002 0.090 2.608-2.026 99.99 8198 413 0.1028 167.197 166.284 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0974 81.651 81.943 1.029 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1248 36.207 35.842 1.024 0.997 0.000 1.221-1.150 99.97 13689 708 0.2123 22.813 21.458 0.983 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0509 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1182 r_free=0.1367 After: r_work=0.1183 r_free=0.1367 ================================== NQH flips ================================== r_work=0.1183 r_free=0.1367 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1183 r_free=0.1367 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1183 r_free=0.1367 | n_water=447 | time (s): 1.840 (total time: 1.840) Filter (dist) r_work=0.1183 r_free=0.1367 | n_water=447 | time (s): 34.540 (total time: 36.380) Filter (q & B) r_work=0.1183 r_free=0.1367 | n_water=446 | time (s): 3.190 (total time: 39.570) Compute maps r_work=0.1183 r_free=0.1367 | n_water=446 | time (s): 1.560 (total time: 41.130) Filter (map) r_work=0.1211 r_free=0.1374 | n_water=323 | time (s): 3.530 (total time: 44.660) Find peaks r_work=0.1211 r_free=0.1374 | n_water=323 | time (s): 0.510 (total time: 45.170) Add new water r_work=0.1264 r_free=0.1409 | n_water=486 | time (s): 3.120 (total time: 48.290) Refine new water occ: r_work=0.1194 r_free=0.1356 adp: r_work=0.1194 r_free=0.1357 occ: r_work=0.1182 r_free=0.1351 adp: r_work=0.1180 r_free=0.1350 occ: r_work=0.1173 r_free=0.1352 adp: r_work=0.1169 r_free=0.1350 ADP+occupancy (water only), MIN, final r_work=0.1169 r_free=0.1350 r_work=0.1169 r_free=0.1350 | n_water=486 | time (s): 250.720 (total time: 299.010) Filter (q & B) r_work=0.1177 r_free=0.1353 | n_water=446 | time (s): 2.840 (total time: 301.850) Filter (dist only) r_work=0.1177 r_free=0.1353 | n_water=445 | time (s): 36.930 (total time: 338.780) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.962160 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 40.877864 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 0.1374 0.0171 0.007 1.1 3.5 0.5 0.0 0 0.981 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.03 13.74 1.71 3.311 21.189 40.878 3.635 12.09 13.81 1.72 3.576 21.112 40.878 3.629 Individual atomic B min max mean iso aniso Overall: 9.28 102.06 21.02 2.02 220 1752 Protein: 9.28 102.06 16.79 2.02 0 1519 Water: 11.48 69.64 35.42 N/A 220 225 Other: 19.23 27.13 23.35 N/A 0 8 Chain A: 9.28 102.06 19.31 N/A 0 1752 Chain S: 14.94 57.47 34.66 N/A 220 0 Histogram: Values Number of atoms 9.28 - 18.56 1220 18.56 - 27.84 288 27.84 - 37.12 209 37.12 - 46.40 146 46.40 - 55.67 71 55.67 - 64.95 22 64.95 - 74.23 11 74.23 - 83.51 2 83.51 - 92.78 1 92.78 - 102.06 2 =========================== Idealize ADP of riding H ========================== r_work=0.1209 r_free=0.1381 r_work=0.1209 r_free=0.1380 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1209 r_free = 0.1380 target_work(ml) = 3.629 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1206 r_free = 0.1379 target_work(ml) = 3.628 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87579 (all), 4.91 % free)------------| | | | r_work= 0.1206 r_free= 0.1379 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.627888 | | target function (ml) not normalized (work): 302141.434917 | | target function (ml) not normalized (free): 15957.858262 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2921 171 0.1432 0.1431 5.7023 5.6467| | 2: 3.57 - 2.84 1.00 2888 124 0.1119 0.1443 5.2001 5.2543| | 3: 2.83 - 2.48 1.00 2820 163 0.1239 0.1281 5.0085 5.0255| | 4: 2.47 - 2.25 1.00 2825 136 0.1038 0.1142 4.7111 4.7491| | 5: 2.25 - 2.09 1.00 2756 127 0.1006 0.1161 4.6521 4.725| | 6: 2.09 - 1.97 1.00 2846 113 0.0976 0.1198 4.3561 4.4743| | 7: 1.97 - 1.87 1.00 2787 165 0.1002 0.1190 4.0815 4.1766| | 8: 1.87 - 1.79 1.00 2789 144 0.1035 0.1303 3.9982 4.0983| | 9: 1.79 - 1.72 1.00 2745 138 0.0967 0.1311 3.7267 3.8886| | 10: 1.72 - 1.66 1.00 2831 160 0.1013 0.1303 3.6415 3.7785| | 11: 1.66 - 1.61 1.00 2712 147 0.0970 0.1095 3.5749 3.6189| | 12: 1.61 - 1.56 1.00 2773 144 0.0925 0.1201 3.3556 3.5025| | 13: 1.56 - 1.52 1.00 2745 130 0.0992 0.1064 3.3508 3.4264| | 14: 1.52 - 1.48 1.00 2803 134 0.0999 0.1125 3.2724 3.3476| | 15: 1.48 - 1.45 1.00 2738 128 0.1026 0.1357 3.1791 3.3361| | 16: 1.45 - 1.42 1.00 2756 161 0.1084 0.1283 3.1621 3.2646| | 17: 1.42 - 1.39 1.00 2785 139 0.1132 0.1283 3.1234 3.2252| | 18: 1.39 - 1.36 1.00 2741 179 0.1164 0.1374 3.0943 3.2798| | 19: 1.36 - 1.34 1.00 2807 134 0.1226 0.1639 3.1013 3.2856| | 20: 1.34 - 1.32 1.00 2696 147 0.1325 0.1495 3.0949 3.1477| | 21: 1.32 - 1.30 1.00 2785 112 0.1426 0.1630 3.0941 3.1623| | 22: 1.29 - 1.27 1.00 2704 152 0.1483 0.1931 3.0912 3.2922| | 23: 1.27 - 1.26 1.00 2802 156 0.1576 0.1890 3.1064 3.2211| | 24: 1.26 - 1.24 1.00 2744 132 0.1631 0.1758 3.0976 3.1955| | 25: 1.24 - 1.22 1.00 2733 148 0.1798 0.2301 3.1119 3.2851| | 26: 1.22 - 1.21 1.00 2727 135 0.1858 0.1790 3.1237 3.204| | 27: 1.21 - 1.19 1.00 2814 148 0.2011 0.2084 3.1413 3.1484| | 28: 1.19 - 1.18 1.00 2671 147 0.2146 0.2327 3.1404 3.1644| | 29: 1.18 - 1.16 1.00 2800 134 0.2223 0.2347 3.1292 3.219| | 30: 1.16 - 1.15 1.00 2739 148 0.2380 0.2487 3.1176 3.1628| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2921 171 0.95 9.02 1.00 0.97 6251.23| | 2: 3.57 - 2.84 2888 124 0.92 13.23 1.01 0.97 6251.23| | 3: 2.83 - 2.48 2820 163 0.89 17.47 0.99 0.98 5243.49| | 4: 2.47 - 2.25 2825 136 0.91 14.60 1.00 0.98 2644.83| | 5: 2.25 - 2.09 2756 127 0.89 16.84 1.01 0.98 2644.83| | 6: 2.09 - 1.97 2846 113 0.92 13.70 1.02 0.98 1560.09| | 7: 1.97 - 1.87 2787 165 0.94 10.88 1.02 0.97 634.94| | 8: 1.87 - 1.79 2789 144 0.91 14.48 1.00 0.97 634.94| | 9: 1.79 - 1.72 2745 138 0.93 11.51 0.98 0.97 344.09| | 10: 1.72 - 1.66 2831 160 0.93 12.35 0.98 0.97 285.84| | 11: 1.66 - 1.61 2712 147 0.93 13.00 0.98 0.97 272.86| | 12: 1.61 - 1.56 2773 144 0.95 9.64 0.99 0.97 150.47| | 13: 1.56 - 1.52 2745 130 0.94 11.26 1.02 0.97 150.47| | 14: 1.52 - 1.48 2803 134 0.94 11.43 1.02 0.97 134.46| | 15: 1.48 - 1.45 2738 128 0.95 10.58 1.01 0.98 105.15| | 16: 1.45 - 1.42 2756 161 0.94 11.76 1.01 0.98 105.15| | 17: 1.42 - 1.39 2785 139 0.94 11.62 1.01 0.98 95.08| | 18: 1.39 - 1.36 2741 179 0.94 11.96 1.01 0.98 89.25| | 19: 1.36 - 1.34 2807 134 0.94 12.49 1.00 0.98 89.25| | 20: 1.34 - 1.32 2696 147 0.94 12.61 0.99 0.97 84.08| | 21: 1.32 - 1.30 2785 112 0.93 13.54 0.98 0.96 83.72| | 22: 1.29 - 1.27 2704 152 0.93 14.09 0.98 0.96 83.79| | 23: 1.27 - 1.26 2802 156 0.92 14.93 0.98 0.95 84.16| | 24: 1.26 - 1.24 2744 132 0.92 15.09 0.97 0.95 84.16| | 25: 1.24 - 1.22 2733 148 0.91 16.47 0.96 0.94 85.42| | 26: 1.22 - 1.21 2727 135 0.90 18.14 1.02 0.93 86.81| | 27: 1.21 - 1.19 2814 148 0.89 18.78 1.02 0.93 86.81| | 28: 1.19 - 1.18 2671 147 0.88 20.24 1.01 0.93 89.64| | 29: 1.18 - 1.16 2800 134 0.88 20.55 0.99 0.92 90.71| | 30: 1.16 - 1.15 2739 148 0.86 21.96 0.98 0.92 90.71| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 83.72 max = 6251.23 mean = 978.46| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.97 mean = 14.12| |phase err.(test): min = 0.00 max = 87.95 mean = 14.26| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1215 0.1206 0.1379 n_refl.: 87579 re-set all scales: r(all,work,free)=0.1526 0.1526 0.1571 n_refl.: 87579 remove outliers: r(all,work,free)=0.1526 0.1526 0.1571 n_refl.: 87579 overall B=-0.01 to atoms: r(all,work,free)=0.1524 0.1523 0.1569 n_refl.: 87579 bulk-solvent and scaling: r(all,work,free)=0.1214 0.1206 0.1380 n_refl.: 87579 remove outliers: r(all,work,free)=0.1214 0.1205 0.1380 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 0.4069 289.760 250.657 0.454 1.001 0.316 11.894-9.307 95.10 93 4 0.2365 485.318 460.326 0.859 1.002 0.254 9.237-7.194 98.18 209 7 0.2616 383.417 375.540 0.900 1.002 0.178 7.162-5.571 100.00 427 22 0.2289 294.082 281.955 0.902 1.002 0.157 5.546-4.326 100.00 867 58 0.1206 403.702 398.959 0.951 1.002 0.125 4.315-3.360 100.00 1859 96 0.0981 383.924 381.561 0.996 1.002 0.120 3.356-2.611 100.00 3867 181 0.1192 252.218 250.301 1.000 1.002 0.110 2.608-2.026 99.99 8198 413 0.1051 167.197 166.249 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0987 81.651 81.929 1.028 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1236 36.207 35.857 1.023 0.997 0.000 1.221-1.150 99.97 13689 708 0.2116 22.813 21.459 0.982 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0406 ================= 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 : 0.2605 0.1927 0.082 5.349 8.8 119.3 19.9 258 0.000 1_bss: 0.1639 0.1763 0.082 5.349 9.1 119.5 20.1 258 0.000 1_settarget: 0.1639 0.1763 0.082 5.349 9.1 119.5 20.1 258 0.000 1_nqh: 0.1646 0.1772 0.082 5.349 9.1 119.5 20.1 258 0.006 1_weight: 0.1646 0.1772 0.082 5.349 9.1 119.5 20.1 258 0.006 1_xyzrec: 0.1209 0.1459 0.008 0.967 9.1 119.5 20.1 258 0.125 1_adp: 0.1242 0.1541 0.008 0.967 8.5 118.7 21.0 258 0.125 1_regHadp: 0.1246 0.1545 0.008 0.967 8.5 118.7 21.0 258 0.125 1_occ: 0.1246 0.1549 0.008 0.967 8.5 118.7 21.0 258 0.125 2_bss: 0.1244 0.1543 0.008 0.967 8.7 118.8 21.1 258 0.125 2_settarget: 0.1244 0.1543 0.008 0.967 8.7 118.8 21.1 258 0.125 2_updatecdl: 0.1244 0.1543 0.008 0.973 8.7 118.8 21.1 258 0.125 2_nqh: 0.1244 0.1543 0.008 0.973 8.7 118.8 21.1 258 0.125 2_sol: 0.1231 0.1484 0.008 0.973 8.7 118.8 23.4 429 n/a 2_weight: 0.1231 0.1484 0.008 0.973 8.7 118.8 23.4 429 n/a 2_xyzrec: 0.1230 0.1519 0.007 0.883 8.7 118.8 23.4 429 n/a 2_adp: 0.1199 0.1479 0.007 0.883 8.6 113.8 23.1 429 n/a 2_regHadp: 0.1199 0.1478 0.007 0.883 8.6 113.8 23.1 429 n/a 2_occ: 0.1202 0.1473 0.007 0.883 8.6 113.8 23.1 429 n/a 3_bss: 0.1198 0.1471 0.007 0.883 8.6 113.9 23.1 429 n/a 3_settarget: 0.1198 0.1471 0.007 0.883 8.6 113.9 23.1 429 n/a 3_updatecdl: 0.1198 0.1471 0.007 0.883 8.6 113.9 23.1 429 n/a 3_nqh: 0.1198 0.1471 0.007 0.883 8.6 113.9 23.1 429 n/a 3_sol: 0.1227 0.1488 0.007 0.883 8.6 113.9 22.0 444 n/a 3_weight: 0.1227 0.1488 0.007 0.883 8.6 113.9 22.0 444 n/a 3_xyzrec: 0.1230 0.1458 0.006 0.933 8.6 113.9 22.0 444 n/a 3_adp: 0.1223 0.1422 0.006 0.933 9.2 109.9 21.7 444 n/a 3_regHadp: 0.1224 0.1422 0.006 0.933 9.2 109.9 21.7 444 n/a 3_occ: 0.1216 0.1420 0.006 0.933 9.2 109.9 21.7 444 n/a 4_bss: 0.1206 0.1393 0.006 0.933 9.2 109.9 21.7 444 n/a 4_settarget: 0.1206 0.1393 0.006 0.933 9.2 109.9 21.7 444 n/a 4_updatecdl: 0.1206 0.1393 0.006 0.930 9.2 109.9 21.7 444 n/a 4_nqh: 0.1206 0.1393 0.006 0.930 9.2 109.9 21.7 444 n/a 4_sol: 0.1199 0.1355 0.006 0.930 9.2 109.9 21.5 447 n/a 4_weight: 0.1199 0.1355 0.006 0.930 9.2 109.9 21.5 447 n/a 4_xyzrec: 0.1204 0.1379 0.006 0.958 9.2 109.9 21.5 447 n/a 4_adp: 0.1191 0.1371 0.006 0.958 9.3 106.1 21.3 447 n/a 4_regHadp: 0.1191 0.1371 0.006 0.958 9.3 106.1 21.3 447 n/a 4_occ: 0.1186 0.1369 0.006 0.958 9.3 106.1 21.3 447 n/a 5_bss: 0.1182 0.1367 0.006 0.958 9.3 106.0 21.3 447 n/a 5_settarget: 0.1182 0.1367 0.006 0.958 9.3 106.0 21.3 447 n/a 5_updatecdl: 0.1182 0.1367 0.006 0.961 9.3 106.0 21.3 447 n/a 5_setrh: 0.1183 0.1367 0.006 0.961 9.3 106.0 21.3 447 n/a 5_nqh: 0.1183 0.1367 0.006 0.961 9.3 106.0 21.3 447 n/a 5_sol: 0.1177 0.1353 0.006 0.961 9.3 106.0 21.2 445 n/a 5_weight: 0.1177 0.1353 0.006 0.961 9.3 106.0 21.2 445 n/a 5_xyzrec: 0.1203 0.1374 0.007 1.057 9.3 106.0 21.2 445 n/a 5_adp: 0.1209 0.1381 0.007 1.057 9.3 102.1 21.0 445 n/a 5_regHadp: 0.1209 0.1380 0.007 1.057 9.3 102.1 21.0 445 n/a 5_occ: 0.1206 0.1379 0.007 1.057 9.3 102.1 21.0 445 n/a end: 0.1205 0.1380 0.007 1.057 9.3 102.0 21.0 445 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_1617309_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_1617309_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.6200 Refinement macro-cycles (run) : 3517.9100 Write final files (write_after_run_outputs) : 68.4700 Total : 3591.0000 Total CPU time: 60.46 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:11:15 PST -0800 (1735452675.71 s) Start R-work = 0.1639, R-free = 0.1763 Final R-work = 0.1205, R-free = 0.1380 =============================================================================== Job complete usr+sys time: 3729.57 seconds wall clock time: 66 minutes 28.91 seconds (3988.91 seconds total)