Starting phenix.refine on Sat Dec 28 21:06:33 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2655235.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_2655235.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2655235.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: 2.18, per 1000 atoms: 0.64 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: 0.79 Conformation dependent library (CDL) restraints added in 288.2 milliseconds Time building geometry restraints manager: 0.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.90: 478 0.90 - 1.15: 1138 1.15 - 1.40: 568 1.40 - 1.64: 894 1.64 - 1.89: 75 Bond restraints: 3153 Sorted by residual: bond pdb=" CA ILE A 91 " pdb=" CB ILE A 91 " ideal model delta sigma weight residual 1.540 1.301 0.239 1.11e-02 8.12e+03 4.63e+02 bond pdb=" NE ARG A 27 " pdb=" CZ ARG A 27 " ideal model delta sigma weight residual 1.326 1.093 0.233 1.10e-02 8.26e+03 4.47e+02 bond pdb=" ND1 HIS A 126 " pdb=" CE1 HIS A 126 " ideal model delta sigma weight residual 1.321 1.111 0.210 1.00e-02 1.00e+04 4.40e+02 bond pdb=" CA ALA A 167 " pdb=" C ALA A 167 " ideal model delta sigma weight residual 1.523 1.260 0.263 1.30e-02 5.92e+03 4.11e+02 bond pdb=" C ILE A 52 " pdb=" O ILE A 52 " ideal model delta sigma weight residual 1.237 1.422 -0.186 1.07e-02 8.73e+03 3.01e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.17: 2865 4.17 - 8.34: 1869 8.34 - 12.51: 804 12.51 - 16.68: 215 16.68 - 20.85: 24 Bond angle restraints: 5777 Sorted by residual: angle pdb=" OE1AGLN A 80 " pdb=" CD AGLN A 80 " pdb=" NE2AGLN A 80 " ideal model delta sigma weight residual 122.60 139.16 -16.56 1.00e+00 1.00e+00 2.74e+02 angle pdb=" O GLY A 40 " pdb=" C GLY A 40 " pdb=" N BLYS A 41 " ideal model delta sigma weight residual 123.06 109.64 13.42 9.50e-01 1.11e+00 1.99e+02 angle pdb=" O LYS A 182 " pdb=" C LYS A 182 " pdb=" N ALA A 183 " ideal model delta sigma weight residual 122.15 106.60 15.55 1.14e+00 7.69e-01 1.86e+02 angle pdb=" O VAL A 35 " pdb=" C VAL A 35 " pdb=" N ALA A 36 " ideal model delta sigma weight residual 122.62 107.57 15.05 1.17e+00 7.31e-01 1.66e+02 angle pdb=" O SER A 142 " pdb=" C SER A 142 " pdb=" N GLU A 143 " ideal model delta sigma weight residual 123.27 138.96 -15.69 1.22e+00 6.72e-01 1.65e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.02 - 17.91: 955 17.91 - 35.80: 106 35.80 - 53.69: 34 53.69 - 71.58: 14 71.58 - 89.48: 2 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA GLY A 74 " pdb=" C GLY A 74 " pdb=" N GLY A 75 " pdb=" CA GLY A 75 " ideal model delta harmonic sigma weight residual 180.00 -149.73 -30.27 0 5.00e+00 4.00e-02 3.67e+01 dihedral pdb=" CA ALA A 56 " pdb=" C ALA A 56 " pdb=" N SER A 57 " pdb=" CA SER A 57 " ideal model delta harmonic sigma weight residual 180.00 152.12 27.88 0 5.00e+00 4.00e-02 3.11e+01 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 -157.12 -22.88 0 5.00e+00 4.00e-02 2.09e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.004 - 0.188: 91 0.188 - 0.373: 75 0.373 - 0.558: 47 0.558 - 0.742: 20 0.742 - 0.927: 10 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA BLYS A 99 " pdb=" N BLYS A 99 " pdb=" C BLYS A 99 " pdb=" CB BLYS A 99 " both_signs ideal model delta sigma weight residual False 2.51 1.58 0.93 2.00e-01 2.50e+01 2.15e+01 chirality pdb=" CA THR A 140 " pdb=" N THR A 140 " pdb=" C THR A 140 " pdb=" CB THR A 140 " both_signs ideal model delta sigma weight residual False 2.53 1.62 0.91 2.00e-01 2.50e+01 2.05e+01 chirality pdb=" CA LYS A 62 " pdb=" N LYS A 62 " pdb=" C LYS A 62 " pdb=" CB LYS A 62 " both_signs ideal model delta sigma weight residual False 2.51 1.61 0.90 2.00e-01 2.50e+01 2.04e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.093 2.00e-02 2.50e+03 6.35e-02 1.21e+02 pdb=" CG PHE A 164 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.091 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.019 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.084 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.002 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.047 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.069 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.010 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.018 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.122 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " 0.019 2.00e-02 2.50e+03 5.90e-02 1.04e+02 pdb=" CG BTYR A 67 " 0.013 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " 0.026 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " -0.071 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " 0.096 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " -0.062 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " -0.092 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " -0.010 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " -0.052 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " 0.017 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " 0.014 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " 0.103 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BASN A 97 " -0.003 2.00e-02 2.50e+03 8.06e-02 9.74e+01 pdb=" CG BASN A 97 " 0.098 2.00e-02 2.50e+03 pdb=" OD1BASN A 97 " -0.037 2.00e-02 2.50e+03 pdb=" ND2BASN A 97 " -0.151 2.00e-02 2.50e+03 pdb="HD21BASN A 97 " 0.066 2.00e-02 2.50e+03 pdb="HD22BASN A 97 " 0.028 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.37: 1400 2.37 - 2.93: 8341 2.93 - 3.48: 10427 3.48 - 4.04: 15040 4.04 - 4.60: 21376 Nonbonded interactions: 56584 Sorted by model distance: nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.810 2.450 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.823 2.450 nonbonded pdb=" HE2 HIS A 126 " pdb=" O PRO A 184 " model vdw sym.op. 1.847 2.450 x-y,-y,-z-4/3 nonbonded pdb=" O PHE A 162 " pdb=" H LEU A 166 " model vdw 1.848 2.450 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.856 2.100 ... (remaining 56579 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_2655235_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= 0.1952 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.791181 | | target function (ml) not normalized (work): 232522.092267 | | target function (ml) not normalized (free): 11809.165722 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3051 0.2107 7.0682 4.947| | 2: 3.57 - 2.84 1.00 2876 122 0.2418 0.1822 4.3427 4.339| | 3: 2.84 - 2.48 1.00 2833 165 0.2348 0.1778 4.1301 4.1605| | 4: 2.47 - 2.25 1.00 2825 136 0.2320 0.1392 3.8288 3.8208| | 5: 2.25 - 2.09 1.00 2756 127 0.2444 0.1524 3.7959 3.8089| | 6: 2.09 - 1.97 1.00 2846 113 0.2551 0.1838 3.4625 3.568| | 7: 1.97 - 1.87 1.00 2787 165 0.2540 0.1831 3.1451 3.1497| | 8: 1.87 - 1.79 1.00 2789 144 0.2483 0.2116 3.0643 3.1736| | 9: 1.79 - 1.72 1.00 2745 138 0.2452 0.1810 2.9085 2.9412| | 10: 1.72 - 1.66 1.00 2789 158 0.2435 0.1951 2.7941 2.9394| | 11: 1.66 - 1.61 1.00 2740 147 0.2519 0.2037 2.7692 2.8466| | 12: 1.61 - 1.56 1.00 2787 146 0.2509 0.1837 2.6247 2.6108| | 13: 1.56 - 1.52 1.00 2745 130 0.2585 0.1713 2.5855 2.5411| | 14: 1.52 - 1.48 1.00 2803 134 0.2574 0.2032 2.5301 2.5733| | 15: 1.48 - 1.45 1.00 2738 128 0.2616 0.2089 2.4207 2.4657| | 16: 1.45 - 1.42 1.00 2756 161 0.2621 0.2063 2.3862 2.4212| | 17: 1.42 - 1.39 1.00 2785 139 0.2613 0.1964 2.3325 2.3348| | 18: 1.39 - 1.36 1.00 2741 179 0.2658 0.2249 2.2566 2.3177| | 19: 1.36 - 1.34 1.00 2807 134 0.2637 0.2136 2.2295 2.2712| | 20: 1.34 - 1.32 1.00 2696 147 0.2704 0.2119 2.2148 2.1851| | 21: 1.32 - 1.30 1.00 2785 112 0.2674 0.2282 2.1515 2.1882| | 22: 1.29 - 1.27 1.00 2704 152 0.2712 0.2468 2.124 2.156| | 23: 1.27 - 1.26 1.00 2802 156 0.2799 0.2626 2.1048 2.2252| | 24: 1.26 - 1.24 1.00 2744 132 0.2755 0.2527 2.0635 2.1776| | 25: 1.24 - 1.22 1.00 2734 148 0.2866 0.2533 2.0474 2.1046| | 26: 1.22 - 1.21 1.00 2727 135 0.2822 0.2197 2.0165 2.056| | 27: 1.21 - 1.19 1.00 2814 148 0.2959 0.2694 2.0122 2.0249| | 28: 1.19 - 1.18 1.00 2671 147 0.2930 0.2630 1.9799 1.9678| | 29: 1.18 - 1.16 1.00 2800 134 0.2935 0.2929 1.9523 2.0599| | 30: 1.16 - 1.15 1.00 2740 148 0.3069 0.2720 1.9375 1.9411| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.85 0.76 0.23 1473.86| | 2: 3.57 - 2.84 2876 122 0.80 26.07 1.27 0.23 1473.86| | 3: 2.84 - 2.48 2833 165 0.74 31.83 1.24 0.24 1222.52| | 4: 2.47 - 2.25 2825 136 0.81 25.50 1.25 0.25 570.24| | 5: 2.25 - 2.09 2756 127 0.77 29.20 1.28 0.25 570.24| | 6: 2.09 - 1.97 2846 113 0.83 22.69 1.29 0.25 312.92| | 7: 1.97 - 1.87 2787 165 0.90 16.81 1.28 0.26 93.46| | 8: 1.87 - 1.79 2789 144 0.86 21.25 1.25 0.26 93.46| | 9: 1.79 - 1.72 2745 138 0.88 18.87 1.24 0.26 57.50| | 10: 1.72 - 1.66 2789 158 0.86 20.62 1.23 0.25 50.30| | 11: 1.66 - 1.61 2740 147 0.85 21.87 1.24 0.25 48.49| | 12: 1.61 - 1.56 2787 146 0.88 18.91 1.24 0.25 30.15| | 13: 1.56 - 1.52 2745 130 0.86 20.87 1.24 0.25 30.15| | 14: 1.52 - 1.48 2803 134 0.87 20.68 1.23 0.25 26.77| | 15: 1.48 - 1.45 2738 128 0.87 20.34 1.24 0.25 20.59| | 16: 1.45 - 1.42 2756 161 0.85 21.74 1.23 0.25 20.59| | 17: 1.42 - 1.39 2785 139 0.87 20.60 1.22 0.25 17.35| | 18: 1.39 - 1.36 2741 179 0.86 21.08 1.23 0.25 15.47| | 19: 1.36 - 1.34 2807 134 0.86 21.93 1.22 0.25 15.47| | 20: 1.34 - 1.32 2696 147 0.87 20.93 1.21 0.24 13.04| | 21: 1.32 - 1.30 2785 112 0.86 22.03 1.20 0.24 12.87| | 22: 1.29 - 1.27 2704 152 0.85 22.65 1.21 0.24 12.61| | 23: 1.27 - 1.26 2802 156 0.85 22.53 1.22 0.24 11.26| | 24: 1.26 - 1.24 2744 132 0.85 23.05 1.20 0.24 11.26| | 25: 1.24 - 1.22 2734 148 0.84 24.04 1.20 0.24 10.75| | 26: 1.22 - 1.21 2727 135 0.84 24.16 1.20 0.23 10.18| | 27: 1.21 - 1.19 2814 148 0.83 25.22 1.20 0.23 10.18| | 28: 1.19 - 1.18 2671 147 0.83 25.44 1.17 0.23 9.53| | 29: 1.18 - 1.16 2800 134 0.82 26.07 1.16 0.22 9.29| | 30: 1.16 - 1.15 2740 148 0.81 27.43 1.15 0.22 9.29| |alpha: min = 0.22 max = 0.26 mean = 0.24| |beta: min = 9.29 max = 1473.86 mean = 214.65| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.98 mean = 22.78| |phase err.(test): min = 0.00 max = 89.90 mean = 22.67| |-----------------------------------------------------------------------------| ----------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 : 0.083 0.263 1557 Z= 5.670 Angle : 5.286 17.753 2118 Z= 3.726 Chirality : 0.365 0.927 243 Planarity : 0.033 0.083 284 Dihedral : 14.241 89.475 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.16 % Favored : 97.30 % Rotamer: Outliers : 1.24 % Allowed : 3.11 % Favored : 95.65 % Cbeta Deviations : 32.97 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.49 % 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: -2.84 (0.47), residues: 224 helix: -2.55 (0.37), residues: 107 sheet: -0.26 (0.83), residues: 38 loop : -1.38 (0.58), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.085 0.022 ARG A 5 TYR 0.058 0.025 TYR A 139 PHE 0.058 0.025 PHE A 164 HIS 0.053 0.025 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= 0.2605 r_free= 0.1952 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.791181 | | target function (ml) not normalized (work): 232522.092267 | | target function (ml) not normalized (free): 11809.165722 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2563 0.2605 0.1953 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2563 0.2605 0.1953 n_refl.: 87602 remove outliers: r(all,work,free)=0.1978 0.1981 0.1953 n_refl.: 87594 overall B=0.21 to atoms: r(all,work,free)=0.2003 0.2007 0.1967 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1639 0.1632 0.1768 n_refl.: 87594 remove outliers: r(all,work,free)=0.1638 0.1631 0.1768 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 0.3889 386.398 355.070 0.670 1.002 0.408 11.894-9.307 99.02 97 4 0.1855 613.774 595.879 0.929 1.003 0.390 9.237-7.194 100.00 213 7 0.2148 501.992 490.684 0.964 1.003 0.370 7.162-5.571 100.00 427 22 0.2207 376.717 364.066 0.928 1.003 0.297 5.546-4.326 100.00 867 58 0.1264 517.139 511.300 0.960 1.003 0.229 4.315-3.360 100.00 1859 96 0.1147 491.803 487.388 1.008 1.003 0.209 3.356-2.611 100.00 3867 181 0.1407 323.089 319.899 0.996 1.002 0.099 2.608-2.026 99.99 8198 413 0.1353 214.179 211.996 1.004 1.001 0.000 2.025-1.573 100.00 17313 902 0.1646 104.594 103.852 1.014 1.000 0.000 1.573-1.221 100.00 36679 1900 0.2062 46.381 45.105 1.003 0.997 0.000 1.221-1.150 99.97 13689 708 0.2581 29.223 27.000 0.973 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0478 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1631 r_free=0.1768 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1631 r_free=0.1768 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.798042 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1996.225757 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 0.1211 0.1465 0.0254 0.007 0.9 1.0 0.5 0.0 0 12.399 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.11 14.65 2.54 3.013 19.068 1996.226 0.017 12.44 15.39 2.95 3.229 19.562 1996.226 0.016 Individual atomic B min max mean iso aniso Overall: 8.47 118.54 21.03 2.88 0 1785 Protein: 8.47 118.54 17.90 2.88 0 1519 Water: 11.02 114.51 39.19 N/A 0 258 Other: 22.94 36.49 29.23 N/A 0 8 Chain A: 8.47 118.54 21.03 N/A 0 1785 Histogram: Values Number of atoms 8.47 - 19.48 1203 19.48 - 30.49 236 30.49 - 41.49 161 41.49 - 52.50 100 52.50 - 63.50 55 63.50 - 74.51 17 74.51 - 85.52 6 85.52 - 96.52 4 96.52 - 107.53 0 107.53 - 118.54 3 =========================== Idealize ADP of riding H ========================== r_work=0.1244 r_free=0.1539 r_work=0.1249 r_free=0.1545 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1249 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 = 0.1248 r_free = 0.1548 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.26 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= 0.1248 r_free= 0.1548 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.015405 | | target function (ls_wunit_k1) not normalized (work): 1283.231868 | | target function (ls_wunit_k1) not normalized (free): 115.623092 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1263 0.1248 0.1548 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1703 0.1702 0.1765 n_refl.: 87593 remove outliers: r(all,work,free)=0.1703 0.1702 0.1765 n_refl.: 87593 overall B=0.14 to atoms: r(all,work,free)=0.1726 0.1726 0.1781 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1260 0.1245 0.1539 n_refl.: 87593 remove outliers: r(all,work,free)=0.1259 0.1245 0.1539 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 0.3603 298.600 279.269 0.688 0.922 0.380 11.894-9.307 99.02 97 4 0.1642 478.341 465.873 0.982 0.923 0.369 9.237-7.194 100.00 213 7 0.1826 391.224 385.997 1.033 0.923 0.340 7.162-5.571 100.00 427 22 0.1727 293.592 288.185 1.000 0.924 0.253 5.546-4.326 100.00 867 58 0.0918 403.029 400.182 1.028 0.925 0.204 4.315-3.360 100.00 1859 96 0.0770 383.283 382.366 1.079 0.926 0.190 3.356-2.611 100.00 3867 181 0.1019 251.797 251.062 1.078 0.928 0.052 2.608-2.026 99.99 8198 413 0.0978 166.919 166.316 1.085 0.931 0.000 2.025-1.573 100.00 17313 902 0.1214 81.514 81.685 1.086 0.937 0.000 1.573-1.221 100.00 36679 1900 0.1655 36.147 35.610 1.060 0.947 0.000 1.221-1.150 99.97 13689 708 0.2366 22.775 21.304 1.014 0.954 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0547 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1245 r_free=0.1539 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=0.1247 r_free=0.1540 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1247 r_free=0.1540 | n_water=258 | time (s): 2.510 (total time: 2.510) Filter (dist) r_work=0.1256 r_free=0.1539 | n_water=252 | time (s): 25.830 (total time: 28.340) Filter (q & B) r_work=0.1259 r_free=0.1537 | n_water=249 | time (s): 3.830 (total time: 32.170) Compute maps r_work=0.1259 r_free=0.1537 | n_water=249 | time (s): 1.840 (total time: 34.010) Filter (map) r_work=0.1278 r_free=0.1541 | n_water=235 | time (s): 3.970 (total time: 37.980) Find peaks r_work=0.1278 r_free=0.1541 | n_water=235 | time (s): 0.720 (total time: 38.700) Add new water r_work=0.1425 r_free=0.1696 | n_water=447 | time (s): 3.820 (total time: 42.520) Refine new water occ: r_work=0.1334 r_free=0.1573 adp: r_work=0.1256 r_free=0.1520 occ: r_work=0.1270 r_free=0.1509 adp: r_work=0.1235 r_free=0.1494 occ: r_work=0.1238 r_free=0.1487 adp: r_work=0.1229 r_free=0.1484 ADP+occupancy (water only), MIN, final r_work=0.1229 r_free=0.1484 r_work=0.1229 r_free=0.1484 | n_water=447 | time (s): 107.270 (total time: 149.790) Filter (q & B) r_work=0.1234 r_free=0.1486 | n_water=426 | time (s): 3.850 (total time: 153.640) Filter (dist only) r_work=0.1234 r_free=0.1486 | n_water=426 | time (s): 40.430 (total time: 194.070) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.167656 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1521.467119 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1232 0.1510 0.0278 0.007 0.9 2.6 0.5 0.0 0 12.084 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.32 15.10 2.78 3.797 23.209 1521.467 0.015 12.01 14.89 2.88 4.192 23.013 1521.467 0.015 Individual atomic B min max mean iso aniso Overall: 8.69 114.44 23.17 2.62 191 1762 Protein: 8.69 114.44 17.72 2.62 0 1519 Water: 11.00 71.85 42.56 N/A 191 235 Other: 22.01 33.32 26.77 N/A 0 8 Chain A: 8.69 114.44 20.41 N/A 0 1762 Chain S: 13.65 69.59 48.68 N/A 191 0 Histogram: Values Number of atoms 8.69 - 19.27 1207 19.27 - 29.84 249 29.84 - 40.41 190 40.41 - 50.99 130 50.99 - 61.56 115 61.56 - 72.14 51 72.14 - 82.71 5 82.71 - 93.29 3 93.29 - 103.86 1 103.86 - 114.44 2 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1489 r_work=0.1201 r_free=0.1489 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1201 r_free = 0.1489 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 = 0.1200 r_free = 0.1483 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1200 r_free= 0.1483 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.013946 | | target function (ls_wunit_k1) not normalized (work): 1161.665906 | | target function (ls_wunit_k1) not normalized (free): 103.476708 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1214 0.1200 0.1483 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1613 0.1609 0.1711 n_refl.: 87592 remove outliers: r(all,work,free)=0.1613 0.1609 0.1711 n_refl.: 87592 overall B=0.03 to atoms: r(all,work,free)=0.1618 0.1615 0.1714 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1211 0.1197 0.1480 n_refl.: 87592 remove outliers: r(all,work,free)=0.1210 0.1196 0.1480 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 0.3375 294.542 272.905 0.617 0.938 0.350 11.894-9.307 99.02 97 4 0.1488 478.341 475.184 0.972 0.939 0.350 9.237-7.194 100.00 213 7 0.1671 391.224 390.941 1.046 0.939 0.300 7.162-5.571 100.00 427 22 0.1532 293.592 290.295 1.003 0.939 0.240 5.546-4.326 100.00 867 58 0.0824 403.029 400.289 1.021 0.940 0.212 4.315-3.360 100.00 1859 96 0.0712 383.283 382.349 1.069 0.940 0.204 3.356-2.611 100.00 3867 181 0.0953 251.797 251.106 1.075 0.941 0.067 2.608-2.026 99.99 8198 413 0.0955 166.919 166.479 1.082 0.942 0.000 2.025-1.573 100.00 17313 902 0.1180 81.514 81.711 1.089 0.944 0.000 1.573-1.221 100.00 36679 1900 0.1616 36.147 35.649 1.073 0.947 0.000 1.221-1.150 99.97 13689 708 0.2341 22.775 21.328 1.029 0.949 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0507 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1196 r_free=0.1480 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1196 r_free=0.1480 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1480 | n_water=426 | time (s): 1.890 (total time: 1.890) Filter (dist) r_work=0.1196 r_free=0.1479 | n_water=424 | time (s): 37.930 (total time: 39.820) Filter (q & B) r_work=0.1196 r_free=0.1479 | n_water=424 | time (s): 0.780 (total time: 40.600) Compute maps r_work=0.1196 r_free=0.1479 | n_water=424 | time (s): 1.490 (total time: 42.090) Filter (map) r_work=0.1236 r_free=0.1481 | n_water=292 | time (s): 2.650 (total time: 44.740) Find peaks r_work=0.1236 r_free=0.1481 | n_water=292 | time (s): 0.550 (total time: 45.290) Add new water r_work=0.1355 r_free=0.1572 | n_water=473 | time (s): 2.800 (total time: 48.090) Refine new water occ: r_work=0.1258 r_free=0.1509 adp: r_work=0.1259 r_free=0.1507 occ: r_work=0.1238 r_free=0.1500 adp: r_work=0.1235 r_free=0.1495 occ: r_work=0.1224 r_free=0.1494 adp: r_work=0.1217 r_free=0.1486 ADP+occupancy (water only), MIN, final r_work=0.1217 r_free=0.1486 r_work=0.1217 r_free=0.1486 | n_water=473 | time (s): 230.280 (total time: 278.370) Filter (q & B) r_work=0.1221 r_free=0.1488 | n_water=438 | time (s): 2.600 (total time: 280.970) Filter (dist only) r_work=0.1221 r_free=0.1489 | n_water=437 | time (s): 40.240 (total time: 321.210) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.047694 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 49.106431 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 0.1228 0.1460 0.0232 0.006 0.9 1.9 0.5 0.0 0 1.024 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.28 14.60 2.32 3.634 22.161 49.106 3.725 12.11 14.13 2.02 4.170 21.957 49.106 3.651 Individual atomic B min max mean iso aniso Overall: 9.26 109.47 21.68 2.33 203 1761 Protein: 9.26 109.47 17.24 2.34 0 1519 Water: 11.55 70.64 37.06 N/A 203 234 Other: 18.25 29.12 23.92 N/A 0 8 Chain A: 9.26 109.47 19.93 N/A 0 1761 Chain S: 16.03 61.08 36.87 N/A 203 0 Histogram: Values Number of atoms 9.26 - 19.28 1234 19.28 - 29.30 270 29.30 - 39.32 212 39.32 - 49.35 133 49.35 - 59.37 79 59.37 - 69.39 22 69.39 - 79.41 8 79.41 - 89.43 3 89.43 - 99.45 1 99.45 - 109.47 2 =========================== Idealize ADP of riding H ========================== r_work=0.1211 r_free=0.1413 r_work=0.1212 r_free=0.1414 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1212 r_free = 0.1414 target_work(ml) = 3.651 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1208 r_free = 0.1411 target_work(ml) = 3.650 | | occupancies: max = 1.00 min = 0.21 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= 0.1208 r_free= 0.1411 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.649567 | | target function (ml) not normalized (work): 303983.348046 | | target function (ml) not normalized (free): 16054.063224 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1218 0.1208 0.1411 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1549 0.1547 0.1601 n_refl.: 87589 remove outliers: r(all,work,free)=0.1549 0.1547 0.1601 n_refl.: 87589 overall B=-0.01 to atoms: r(all,work,free)=0.1546 0.1545 0.1599 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1210 0.1202 0.1381 n_refl.: 87589 remove outliers: r(all,work,free)=0.1206 0.1197 0.1381 n_refl.: 87578 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 90.62 82 5 0.3982 291.297 259.728 0.469 1.000 0.299 11.894-9.307 95.10 93 4 0.2318 476.754 459.399 0.857 1.001 0.283 9.237-7.194 97.73 208 7 0.2315 383.851 385.435 0.942 1.002 0.200 7.162-5.571 100.00 427 22 0.2051 293.592 283.578 0.914 1.002 0.180 5.546-4.326 100.00 867 58 0.1090 403.029 398.419 0.951 1.002 0.161 4.315-3.360 100.00 1859 96 0.0941 383.283 380.573 0.994 1.002 0.153 3.356-2.611 100.00 3867 181 0.1160 251.797 249.844 1.000 1.002 0.062 2.608-2.026 99.99 8198 413 0.1043 166.919 165.927 1.011 1.001 0.000 2.025-1.573 100.00 17313 902 0.1014 81.514 81.680 1.027 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1290 36.147 35.733 1.020 0.999 0.000 1.221-1.150 99.97 13689 708 0.2129 22.775 21.392 0.979 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0379 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1197 r_free=0.1381 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1197 r_free=0.1381 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1197 r_free=0.1381 | n_water=437 | time (s): 2.050 (total time: 2.050) Filter (dist) r_work=0.1197 r_free=0.1379 | n_water=435 | time (s): 40.690 (total time: 42.740) Filter (q & B) r_work=0.1197 r_free=0.1379 | n_water=435 | time (s): 1.080 (total time: 43.820) Compute maps r_work=0.1197 r_free=0.1379 | n_water=435 | time (s): 1.290 (total time: 45.110) Filter (map) r_work=0.1223 r_free=0.1400 | n_water=308 | time (s): 3.090 (total time: 48.200) Find peaks r_work=0.1223 r_free=0.1400 | n_water=308 | time (s): 0.490 (total time: 48.690) Add new water r_work=0.1289 r_free=0.1469 | n_water=466 | time (s): 2.700 (total time: 51.390) Refine new water occ: r_work=0.1214 r_free=0.1396 adp: r_work=0.1214 r_free=0.1398 occ: r_work=0.1200 r_free=0.1383 adp: r_work=0.1198 r_free=0.1385 occ: r_work=0.1189 r_free=0.1373 adp: r_work=0.1186 r_free=0.1372 ADP+occupancy (water only), MIN, final r_work=0.1186 r_free=0.1372 r_work=0.1186 r_free=0.1372 | n_water=466 | time (s): 197.320 (total time: 248.710) Filter (q & B) r_work=0.1192 r_free=0.1382 | n_water=435 | time (s): 3.540 (total time: 252.250) Filter (dist only) r_work=0.1192 r_free=0.1380 | n_water=434 | time (s): 37.980 (total time: 290.230) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.969971 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 31.093565 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 0.1196 0.1384 0.0188 0.006 0.9 2.2 0.5 0.0 0 0.985 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.96 13.84 1.88 3.433 21.452 31.094 3.636 11.98 13.80 1.83 3.486 21.427 31.094 3.632 Individual atomic B min max mean iso aniso Overall: 9.34 107.80 21.32 2.22 203 1758 Protein: 9.34 107.80 17.17 2.22 0 1519 Water: 11.53 70.46 35.77 N/A 203 231 Other: 18.24 28.06 23.61 N/A 0 8 Chain A: 9.34 107.80 19.79 N/A 0 1758 Chain S: 16.24 59.83 34.50 N/A 203 0 Histogram: Values Number of atoms 9.34 - 19.19 1238 19.19 - 29.04 282 29.04 - 38.88 206 38.88 - 48.73 135 48.73 - 58.57 66 58.57 - 68.42 20 68.42 - 78.27 9 78.27 - 88.11 2 88.11 - 97.96 1 97.96 - 107.80 2 =========================== Idealize ADP of riding H ========================== r_work=0.1198 r_free=0.1380 r_work=0.1198 r_free=0.1380 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1198 r_free = 0.1380 target_work(ml) = 3.632 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1193 r_free = 0.1376 target_work(ml) = 3.631 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87578 (all), 4.91 % free)------------| | | | r_work= 0.1193 r_free= 0.1376 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.630610 | | target function (ml) not normalized (work): 302364.452917 | | target function (ml) not normalized (free): 15967.871026 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1202 0.1193 0.1376 n_refl.: 87578 re-set all scales: r(all,work,free)=0.1520 0.1519 0.1566 n_refl.: 87578 remove outliers: r(all,work,free)=0.1520 0.1519 0.1566 n_refl.: 87578 overall B=-0.02 to atoms: r(all,work,free)=0.1517 0.1516 0.1564 n_refl.: 87578 bulk-solvent and scaling: r(all,work,free)=0.1201 0.1192 0.1377 n_refl.: 87578 remove outliers: r(all,work,free)=0.1200 0.1191 0.1377 n_refl.: 87575 ======================== 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 0.3877 285.823 255.181 0.456 1.000 0.312 11.894-9.307 95.10 93 4 0.2322 476.754 456.951 0.843 1.002 0.245 9.237-7.194 97.73 208 7 0.2462 383.851 377.357 0.913 1.002 0.168 7.162-5.571 100.00 427 22 0.2154 293.592 283.172 0.907 1.002 0.143 5.546-4.326 100.00 867 58 0.1146 403.029 398.232 0.952 1.002 0.143 4.315-3.360 100.00 1859 96 0.0946 383.283 380.872 0.996 1.002 0.140 3.356-2.611 100.00 3867 181 0.1157 251.797 249.998 1.003 1.002 0.090 2.608-2.026 99.99 8198 413 0.1038 166.919 165.985 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0993 81.514 81.789 1.028 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1257 36.147 35.753 1.022 0.997 0.000 1.221-1.150 99.97 13689 708 0.2127 22.775 21.396 0.984 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0455 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1191 r_free=0.1377 After: r_work=0.1192 r_free=0.1377 ================================== NQH flips ================================== r_work=0.1192 r_free=0.1377 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1192 r_free=0.1377 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1192 r_free=0.1377 | n_water=434 | time (s): 1.630 (total time: 1.630) Filter (dist) r_work=0.1192 r_free=0.1377 | n_water=434 | time (s): 35.790 (total time: 37.420) Filter (q & B) r_work=0.1192 r_free=0.1377 | n_water=431 | time (s): 3.230 (total time: 40.650) Compute maps r_work=0.1192 r_free=0.1377 | n_water=431 | time (s): 1.220 (total time: 41.870) Filter (map) r_work=0.1219 r_free=0.1386 | n_water=319 | time (s): 2.910 (total time: 44.780) Find peaks r_work=0.1219 r_free=0.1386 | n_water=319 | time (s): 0.690 (total time: 45.470) Add new water r_work=0.1276 r_free=0.1442 | n_water=476 | time (s): 3.300 (total time: 48.770) Refine new water occ: r_work=0.1207 r_free=0.1378 adp: r_work=0.1208 r_free=0.1380 occ: r_work=0.1194 r_free=0.1370 adp: r_work=0.1193 r_free=0.1370 occ: r_work=0.1184 r_free=0.1365 adp: r_work=0.1181 r_free=0.1363 ADP+occupancy (water only), MIN, final r_work=0.1181 r_free=0.1363 r_work=0.1181 r_free=0.1363 | n_water=476 | time (s): 163.740 (total time: 212.510) Filter (q & B) r_work=0.1187 r_free=0.1365 | n_water=440 | time (s): 2.480 (total time: 214.990) Filter (dist only) r_work=0.1188 r_free=0.1364 | n_water=439 | time (s): 37.260 (total time: 252.250) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.198996 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 46.855445 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 0.1210 0.1382 0.0172 0.007 1.1 6.7 0.5 0.0 0 1.099 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.10 13.82 1.72 3.375 21.358 46.855 3.638 11.97 13.82 1.85 3.788 21.227 46.855 3.623 Individual atomic B min max mean iso aniso Overall: 9.24 103.71 21.04 2.11 208 1758 Protein: 9.24 103.71 16.87 2.11 0 1519 Water: 11.59 69.18 35.43 N/A 208 231 Other: 18.06 25.49 22.08 N/A 0 8 Chain A: 9.24 103.71 19.46 N/A 0 1758 Chain S: 15.13 60.07 34.34 N/A 208 0 Histogram: Values Number of atoms 9.24 - 18.69 1225 18.69 - 28.14 284 28.14 - 37.58 204 37.58 - 47.03 144 47.03 - 56.48 67 56.48 - 65.93 26 65.93 - 75.37 11 75.37 - 84.82 2 84.82 - 94.27 1 94.27 - 103.71 2 =========================== Idealize ADP of riding H ========================== r_work=0.1197 r_free=0.1382 r_work=0.1198 r_free=0.1382 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1198 r_free = 0.1382 target_work(ml) = 3.623 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1192 r_free = 0.1371 target_work(ml) = 3.621 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87575 (all), 4.91 % free)------------| | | | r_work= 0.1192 r_free= 0.1371 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 3.621294 | | target function (ml) not normalized (work): 301577.750169 | | target function (ml) not normalized (free): 15943.384187 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2917 171 0.1385 0.1426 5.63 5.6531| | 2: 3.57 - 2.84 1.00 2888 124 0.1122 0.1423 5.204 5.2506| | 3: 2.83 - 2.48 1.00 2820 163 0.1222 0.1307 5.0104 5.0201| | 4: 2.47 - 2.25 1.00 2825 136 0.1027 0.1166 4.7137 4.7705| | 5: 2.25 - 2.09 1.00 2756 127 0.1001 0.1106 4.6556 4.7191| | 6: 2.09 - 1.97 1.00 2846 113 0.0971 0.1245 4.3564 4.5157| | 7: 1.97 - 1.87 1.00 2787 165 0.0987 0.1214 4.0732 4.1738| | 8: 1.87 - 1.79 1.00 2789 144 0.1017 0.1200 3.9888 4.0717| | 9: 1.79 - 1.72 1.00 2745 138 0.0952 0.1257 3.7148 3.879| | 10: 1.72 - 1.66 1.00 2831 160 0.0999 0.1215 3.6321 3.7571| | 11: 1.66 - 1.61 1.00 2712 147 0.0961 0.1113 3.5652 3.6114| | 12: 1.61 - 1.56 1.00 2773 144 0.0921 0.1216 3.3494 3.5153| | 13: 1.56 - 1.52 1.00 2745 130 0.0979 0.1061 3.3427 3.4313| | 14: 1.52 - 1.48 1.00 2803 134 0.0995 0.1102 3.2637 3.3405| | 15: 1.48 - 1.45 1.00 2738 128 0.1022 0.1306 3.1715 3.3093| | 16: 1.45 - 1.42 1.00 2756 161 0.1071 0.1278 3.1545 3.2515| | 17: 1.42 - 1.39 1.00 2785 139 0.1126 0.1290 3.1182 3.232| | 18: 1.39 - 1.36 1.00 2741 179 0.1159 0.1407 3.0883 3.2595| | 19: 1.36 - 1.34 1.00 2807 134 0.1203 0.1611 3.0872 3.2817| | 20: 1.34 - 1.32 1.00 2696 147 0.1328 0.1451 3.0917 3.1352| | 21: 1.32 - 1.30 1.00 2785 112 0.1419 0.1593 3.088 3.1678| | 22: 1.29 - 1.27 1.00 2704 152 0.1486 0.1935 3.0875 3.2926| | 23: 1.27 - 1.26 1.00 2802 156 0.1578 0.1839 3.1054 3.2052| | 24: 1.26 - 1.24 1.00 2744 132 0.1632 0.1764 3.0962 3.1842| | 25: 1.24 - 1.22 1.00 2733 148 0.1804 0.2333 3.112 3.2927| | 26: 1.22 - 1.21 1.00 2727 135 0.1866 0.1790 3.1234 3.2041| | 27: 1.21 - 1.19 1.00 2814 148 0.2008 0.2104 3.1386 3.1431| | 28: 1.19 - 1.18 1.00 2671 147 0.2146 0.2307 3.141 3.1579| | 29: 1.18 - 1.16 1.00 2800 134 0.2227 0.2420 3.128 3.2298| | 30: 1.16 - 1.15 1.00 2739 148 0.2377 0.2513 3.1174 3.1669| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2917 171 0.95 9.14 1.00 0.97 6388.96| | 2: 3.57 - 2.84 2888 124 0.92 13.63 1.01 0.97 6388.96| | 3: 2.83 - 2.48 2820 163 0.88 17.74 0.98 0.97 5354.66| | 4: 2.47 - 2.25 2825 136 0.91 14.73 1.00 0.98 2687.51| | 5: 2.25 - 2.09 2756 127 0.89 17.03 1.01 0.98 2687.51| | 6: 2.09 - 1.97 2846 113 0.92 13.76 1.02 0.98 1577.73| | 7: 1.97 - 1.87 2787 165 0.94 10.86 1.02 0.97 631.24| | 8: 1.87 - 1.79 2789 144 0.91 14.51 1.00 0.97 631.24| | 9: 1.79 - 1.72 2745 138 0.93 11.40 0.98 0.97 338.29| | 10: 1.72 - 1.66 2831 160 0.93 12.19 0.98 0.97 279.62| | 11: 1.66 - 1.61 2712 147 0.93 12.82 0.98 0.97 267.09| | 12: 1.61 - 1.56 2773 144 0.95 9.57 0.99 0.97 148.90| | 13: 1.56 - 1.52 2745 130 0.94 11.18 1.02 0.97 148.90| | 14: 1.52 - 1.48 2803 134 0.94 11.40 1.02 0.97 132.83| | 15: 1.48 - 1.45 2738 128 0.95 10.53 1.01 0.98 103.39| | 16: 1.45 - 1.42 2756 161 0.94 11.61 1.02 0.98 103.39| | 17: 1.42 - 1.39 2785 139 0.94 11.44 1.01 0.98 93.27| | 18: 1.39 - 1.36 2741 179 0.94 11.78 1.01 0.98 87.41| | 19: 1.36 - 1.34 2807 134 0.94 12.33 1.00 0.98 87.41| | 20: 1.34 - 1.32 2696 147 0.94 12.43 0.99 0.97 82.32| | 21: 1.32 - 1.30 2785 112 0.94 13.34 0.98 0.97 81.96| | 22: 1.29 - 1.27 2704 152 0.93 13.89 0.98 0.96 82.13| | 23: 1.27 - 1.26 2802 156 0.92 14.84 0.98 0.95 82.98| | 24: 1.26 - 1.24 2744 132 0.92 14.99 0.97 0.95 82.98| | 25: 1.24 - 1.22 2733 148 0.91 16.40 0.96 0.94 84.62| | 26: 1.22 - 1.21 2727 135 0.90 18.16 1.02 0.93 86.44| | 27: 1.21 - 1.19 2814 148 0.89 18.78 1.02 0.93 86.44| | 28: 1.19 - 1.18 2671 147 0.88 20.31 1.01 0.93 89.90| | 29: 1.18 - 1.16 2800 134 0.88 20.68 0.99 0.92 91.20| | 30: 1.16 - 1.15 2739 148 0.86 22.07 0.98 0.92 91.20| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 81.96 max = 6388.96 mean = 993.48| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.98 mean = 14.10| |phase err.(test): min = 0.00 max = 89.98 mean = 14.23| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1201 0.1192 0.1371 n_refl.: 87575 re-set all scales: r(all,work,free)=0.1515 0.1513 0.1586 n_refl.: 87575 remove outliers: r(all,work,free)=0.1515 0.1513 0.1586 n_refl.: 87575 overall B=-0.01 to atoms: r(all,work,free)=0.1513 0.1511 0.1585 n_refl.: 87575 bulk-solvent and scaling: r(all,work,free)=0.1202 0.1193 0.1373 n_refl.: 87575 remove outliers: r(all,work,free)=0.1202 0.1193 0.1373 n_refl.: 87575 ======================== 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 0.3904 285.823 256.560 0.453 0.999 0.308 11.894-9.307 95.10 93 4 0.2303 476.754 461.456 0.847 1.001 0.222 9.237-7.194 97.73 208 7 0.2484 383.851 377.896 0.906 1.001 0.150 7.162-5.571 100.00 427 22 0.2127 293.592 284.701 0.907 1.001 0.150 5.546-4.326 100.00 867 58 0.1173 403.029 397.896 0.952 1.001 0.140 4.315-3.360 100.00 1859 96 0.0994 383.283 380.543 0.996 1.001 0.140 3.356-2.611 100.00 3867 181 0.1183 251.797 249.655 1.001 1.001 0.120 2.608-2.026 99.99 8198 413 0.1043 166.919 165.951 1.011 1.001 0.000 2.025-1.573 100.00 17313 902 0.0975 81.514 81.780 1.025 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1233 36.147 35.789 1.018 1.000 0.000 1.221-1.150 99.97 13689 708 0.2121 22.775 21.362 0.973 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0242 ================= 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 0.1952 0.083 5.286 8.8 119.3 19.9 258 0.000 1_bss: 0.1631 0.1768 0.083 5.286 9.1 119.5 20.1 258 0.000 1_settarget: 0.1631 0.1768 0.083 5.286 9.1 119.5 20.1 258 0.000 1_nqh: 0.1631 0.1768 0.083 5.286 9.1 119.5 20.1 258 0.000 1_weight: 0.1631 0.1768 0.083 5.286 9.1 119.5 20.1 258 0.000 1_xyzrec: 0.1211 0.1465 0.007 0.937 9.1 119.5 20.1 258 0.123 1_adp: 0.1244 0.1539 0.007 0.937 8.5 118.5 21.0 258 0.123 1_regHadp: 0.1249 0.1545 0.007 0.937 8.5 118.5 21.0 258 0.123 1_occ: 0.1248 0.1548 0.007 0.937 8.5 118.5 21.0 258 0.123 2_bss: 0.1245 0.1539 0.007 0.937 8.6 118.7 21.2 258 0.123 2_settarget: 0.1245 0.1539 0.007 0.937 8.6 118.7 21.2 258 0.123 2_updatecdl: 0.1245 0.1539 0.007 0.950 8.6 118.7 21.2 258 0.123 2_nqh: 0.1247 0.1540 0.007 0.950 8.6 118.7 21.2 258 0.126 2_sol: 0.1234 0.1486 0.007 0.950 8.6 118.7 23.5 426 n/a 2_weight: 0.1234 0.1486 0.007 0.950 8.6 118.7 23.5 426 n/a 2_xyzrec: 0.1232 0.1510 0.007 0.870 8.6 118.7 23.5 426 n/a 2_adp: 0.1201 0.1489 0.007 0.870 8.7 114.4 23.2 426 n/a 2_regHadp: 0.1201 0.1489 0.007 0.870 8.7 114.4 23.2 426 n/a 2_occ: 0.1200 0.1483 0.007 0.870 8.7 114.4 23.2 426 n/a 3_bss: 0.1196 0.1480 0.007 0.870 8.7 114.5 23.2 426 n/a 3_settarget: 0.1196 0.1480 0.007 0.870 8.7 114.5 23.2 426 n/a 3_updatecdl: 0.1196 0.1480 0.007 0.871 8.7 114.5 23.2 426 n/a 3_nqh: 0.1196 0.1480 0.007 0.871 8.7 114.5 23.2 426 n/a 3_sol: 0.1221 0.1489 0.007 0.871 8.7 114.5 22.0 437 n/a 3_weight: 0.1221 0.1489 0.007 0.871 8.7 114.5 22.0 437 n/a 3_xyzrec: 0.1228 0.1460 0.006 0.919 8.7 114.5 22.0 437 n/a 3_adp: 0.1211 0.1413 0.006 0.919 9.3 109.5 21.7 437 n/a 3_regHadp: 0.1212 0.1414 0.006 0.919 9.3 109.5 21.7 437 n/a 3_occ: 0.1208 0.1411 0.006 0.919 9.3 109.5 21.7 437 n/a 4_bss: 0.1197 0.1381 0.006 0.919 9.2 109.5 21.7 437 n/a 4_settarget: 0.1197 0.1381 0.006 0.919 9.2 109.5 21.7 437 n/a 4_updatecdl: 0.1197 0.1381 0.006 0.916 9.2 109.5 21.7 437 n/a 4_nqh: 0.1197 0.1381 0.006 0.916 9.2 109.5 21.7 437 n/a 4_sol: 0.1192 0.1380 0.006 0.916 9.2 109.5 21.4 434 n/a 4_weight: 0.1192 0.1380 0.006 0.916 9.2 109.5 21.4 434 n/a 4_xyzrec: 0.1196 0.1384 0.006 0.949 9.2 109.5 21.4 434 n/a 4_adp: 0.1198 0.1380 0.006 0.949 9.3 107.8 21.3 434 n/a 4_regHadp: 0.1198 0.1380 0.006 0.949 9.3 107.8 21.3 434 n/a 4_occ: 0.1193 0.1376 0.006 0.949 9.3 107.8 21.3 434 n/a 5_bss: 0.1191 0.1377 0.006 0.949 9.3 107.8 21.3 434 n/a 5_settarget: 0.1191 0.1377 0.006 0.949 9.3 107.8 21.3 434 n/a 5_updatecdl: 0.1191 0.1377 0.006 0.950 9.3 107.8 21.3 434 n/a 5_setrh: 0.1192 0.1377 0.006 0.950 9.3 107.8 21.3 434 n/a 5_nqh: 0.1192 0.1377 0.006 0.950 9.3 107.8 21.3 434 n/a 5_sol: 0.1188 0.1364 0.006 0.950 9.3 107.8 21.3 439 n/a 5_weight: 0.1188 0.1364 0.006 0.950 9.3 107.8 21.3 439 n/a 5_xyzrec: 0.1210 0.1382 0.007 1.088 9.3 107.8 21.3 439 n/a 5_adp: 0.1197 0.1382 0.007 1.088 9.2 103.7 21.0 439 n/a 5_regHadp: 0.1198 0.1382 0.007 1.088 9.2 103.7 21.0 439 n/a 5_occ: 0.1192 0.1371 0.007 1.088 9.2 103.7 21.0 439 n/a end: 0.1193 0.1373 0.007 1.088 9.2 103.7 21.0 439 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_2655235_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_2655235_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.8700 Refinement macro-cycles (run) : 3509.4600 Write final files (write_after_run_outputs) : 69.8400 Total : 3584.1700 Total CPU time: 60.36 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:11:43 PST -0800 (1735452703.32 s) Start R-work = 0.1631, R-free = 0.1768 Final R-work = 0.1193, R-free = 0.1373 =============================================================================== Job complete usr+sys time: 3716.06 seconds wall clock time: 66 minutes 50.49 seconds (4010.49 seconds total)