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_2359181.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2359181.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2359181.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 2.24, per 1000 atoms: 0.66 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.86 Conformation dependent library (CDL) restraints added in 309.4 milliseconds Time building geometry restraints manager: 0.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.65 - 0.90: 484 0.90 - 1.15: 1140 1.15 - 1.41: 607 1.41 - 1.66: 864 1.66 - 1.91: 58 Bond restraints: 3153 Sorted by residual: bond pdb=" C GLN A 95 " pdb=" O GLN A 95 " ideal model delta sigma weight residual 1.236 0.915 0.321 1.15e-02 7.56e+03 7.78e+02 bond pdb=" C ALA A 6 " pdb=" O ALA A 6 " ideal model delta sigma weight residual 1.235 1.487 -0.252 1.28e-02 6.10e+03 3.87e+02 bond pdb=" N MET A 134 " pdb=" CA MET A 134 " ideal model delta sigma weight residual 1.457 1.677 -0.220 1.32e-02 5.74e+03 2.77e+02 bond pdb=" N BGLU A 90 " pdb=" CA BGLU A 90 " ideal model delta sigma weight residual 1.459 1.651 -0.192 1.17e-02 7.31e+03 2.68e+02 bond pdb=" NE ARG A 156 " pdb=" CZ ARG A 156 " ideal model delta sigma weight residual 1.326 1.503 -0.177 1.10e-02 8.26e+03 2.60e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.32: 3461 5.32 - 10.64: 1796 10.64 - 15.96: 477 15.96 - 21.28: 40 21.28 - 26.60: 3 Bond angle restraints: 5777 Sorted by residual: angle pdb=" N ILE A 21 " pdb=" CA ILE A 21 " pdb=" CB ILE A 21 " ideal model delta sigma weight residual 110.50 123.40 -12.90 6.30e-01 2.52e+00 4.19e+02 angle pdb=" O VAL A 123 " pdb=" C VAL A 123 " pdb=" N THR A 124 " ideal model delta sigma weight residual 123.00 140.57 -17.57 1.14e+00 7.69e-01 2.37e+02 angle pdb=" N VAL A 20 " pdb=" CA VAL A 20 " pdb=" C VAL A 20 " ideal model delta sigma weight residual 110.62 123.94 -13.32 1.02e+00 9.61e-01 1.70e+02 angle pdb=" CA GLY A 174 " pdb=" C GLY A 174 " pdb=" O GLY A 174 " ideal model delta sigma weight residual 122.23 113.29 8.94 6.90e-01 2.10e+00 1.68e+02 angle pdb=" OD1BASN A 97 " pdb=" CG BASN A 97 " pdb=" ND2BASN A 97 " ideal model delta sigma weight residual 122.60 135.43 -12.83 1.00e+00 1.00e+00 1.65e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 944 17.56 - 35.12: 119 35.12 - 52.68: 33 52.68 - 70.23: 13 70.23 - 87.79: 2 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA THR A 125 " pdb=" C THR A 125 " pdb=" N HIS A 126 " pdb=" CA HIS A 126 " ideal model delta harmonic sigma weight residual 180.00 153.94 26.06 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA VAL A 123 " pdb=" C VAL A 123 " pdb=" N THR A 124 " pdb=" CA THR A 124 " ideal model delta harmonic sigma weight residual 180.00 160.87 19.13 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA BLYS A 99 " pdb=" C BLYS A 99 " pdb=" N GLY A 100 " pdb=" CA GLY A 100 " ideal model delta harmonic sigma weight residual 180.00 161.32 18.68 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.210: 102 0.210 - 0.420: 67 0.420 - 0.630: 48 0.630 - 0.840: 18 0.840 - 1.050: 8 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA ASP A 49 " pdb=" N ASP A 49 " pdb=" C ASP A 49 " pdb=" CB ASP A 49 " both_signs ideal model delta sigma weight residual False 2.51 1.46 1.05 2.00e-01 2.50e+01 2.75e+01 chirality pdb=" CB VAL A 70 " pdb=" CA VAL A 70 " pdb=" CG1 VAL A 70 " pdb=" CG2 VAL A 70 " both_signs ideal model delta sigma weight residual False -2.63 -3.62 0.99 2.00e-01 2.50e+01 2.45e+01 chirality pdb=" CA BASN A 76 " pdb=" N BASN A 76 " pdb=" C BASN A 76 " pdb=" CB BASN A 76 " both_signs ideal model delta sigma weight residual False 2.51 1.54 0.97 2.00e-01 2.50e+01 2.35e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.050 2.00e-02 2.50e+03 6.43e-02 1.24e+02 pdb=" CG PHE A 164 " 0.068 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " -0.083 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.028 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.031 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.120 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.041 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.096 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.092 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " 0.033 2.00e-02 2.50e+03 5.07e-02 7.72e+01 pdb=" CG TYR A 139 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " 0.071 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.035 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " -0.093 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.019 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " 0.015 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " -0.066 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.045 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " 0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 98 " -0.068 9.50e-02 1.11e+02 6.18e-02 7.51e+01 pdb=" NE ARG A 98 " -0.069 2.00e-02 2.50e+03 pdb=" CZ ARG A 98 " 0.112 2.00e-02 2.50e+03 pdb=" NH1 ARG A 98 " 0.071 2.00e-02 2.50e+03 pdb=" NH2 ARG A 98 " -0.047 2.00e-02 2.50e+03 pdb="HH11 ARG A 98 " -0.036 2.00e-02 2.50e+03 pdb="HH12 ARG A 98 " -0.038 2.00e-02 2.50e+03 pdb="HH21 ARG A 98 " 0.040 2.00e-02 2.50e+03 pdb="HH22 ARG A 98 " -0.030 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.21: 476 2.21 - 2.81: 7244 2.81 - 3.41: 10799 3.41 - 4.00: 15502 4.00 - 4.60: 22527 Nonbonded interactions: 56548 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.618 2.100 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.721 2.100 nonbonded pdb=" HD3 ARG A 5 " pdb="HH11 ARG A 5 " model vdw 1.761 2.270 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.803 2.450 nonbonded pdb=" O GLY A 75 " pdb=" H ALA A 79 " model vdw 1.831 2.450 ... (remaining 56543 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_2359181_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= 0.2611 r_free= 0.1970 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.797071 | | target function (ml) not normalized (work): 233012.775185 | | target function (ml) not normalized (free): 11890.683060 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3023 0.2056 7.0457 4.944| | 2: 3.57 - 2.84 1.00 2876 122 0.2446 0.1720 4.3482 4.3455| | 3: 2.84 - 2.48 1.00 2833 165 0.2371 0.1698 4.1352 4.1587| | 4: 2.47 - 2.25 1.00 2825 136 0.2335 0.1410 3.8405 3.838| | 5: 2.25 - 2.09 1.00 2756 127 0.2501 0.1675 3.7991 3.8447| | 6: 2.09 - 1.97 1.00 2846 113 0.2559 0.1835 3.4781 3.6046| | 7: 1.97 - 1.87 1.00 2787 165 0.2537 0.2042 3.1582 3.2241| | 8: 1.87 - 1.79 1.00 2789 144 0.2474 0.2066 3.0859 3.1617| | 9: 1.79 - 1.72 1.00 2745 138 0.2452 0.2122 2.9052 3.0184| | 10: 1.72 - 1.66 1.00 2789 158 0.2361 0.2123 2.8041 2.9569| | 11: 1.66 - 1.61 1.00 2740 147 0.2499 0.1818 2.7633 2.7869| | 12: 1.61 - 1.56 1.00 2787 146 0.2566 0.1877 2.637 2.6006| | 13: 1.56 - 1.52 1.00 2745 130 0.2536 0.1881 2.5698 2.6161| | 14: 1.52 - 1.48 1.00 2803 134 0.2534 0.2063 2.505 2.6034| | 15: 1.48 - 1.45 1.00 2738 128 0.2571 0.2047 2.4305 2.4417| | 16: 1.45 - 1.42 1.00 2756 161 0.2650 0.2215 2.3888 2.4653| | 17: 1.42 - 1.39 1.00 2785 139 0.2713 0.2257 2.3419 2.4338| | 18: 1.39 - 1.36 1.00 2741 179 0.2706 0.2077 2.2887 2.3029| | 19: 1.36 - 1.34 1.00 2807 134 0.2675 0.2567 2.2534 2.3619| | 20: 1.34 - 1.32 1.00 2696 147 0.2677 0.2229 2.2103 2.2163| | 21: 1.32 - 1.30 1.00 2785 112 0.2692 0.2333 2.1743 2.2202| | 22: 1.29 - 1.27 1.00 2704 152 0.2800 0.2692 2.151 2.2953| | 23: 1.27 - 1.26 1.00 2802 156 0.2704 0.2099 2.0962 2.0779| | 24: 1.26 - 1.24 1.00 2744 132 0.2804 0.2482 2.0768 2.1215| | 25: 1.24 - 1.22 1.00 2734 148 0.2855 0.2691 2.0501 2.094| | 26: 1.22 - 1.21 1.00 2727 135 0.2845 0.2375 2.0135 2.086| | 27: 1.21 - 1.19 1.00 2814 148 0.2946 0.2595 2.0162 2.0274| | 28: 1.19 - 1.18 1.00 2671 147 0.3016 0.2695 1.9931 1.9628| | 29: 1.18 - 1.16 1.00 2800 134 0.2984 0.3014 1.9695 2.109| | 30: 1.16 - 1.15 1.00 2740 148 0.3064 0.2912 1.9282 1.9954| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.93 0.76 0.23 1483.00| | 2: 3.57 - 2.84 2876 122 0.80 26.26 1.28 0.23 1483.00| | 3: 2.84 - 2.48 2833 165 0.74 31.96 1.24 0.23 1231.47| | 4: 2.47 - 2.25 2825 136 0.81 25.68 1.26 0.25 578.71| | 5: 2.25 - 2.09 2756 127 0.77 29.60 1.28 0.25 578.71| | 6: 2.09 - 1.97 2846 113 0.83 23.06 1.29 0.25 319.77| | 7: 1.97 - 1.87 2787 165 0.89 17.31 1.28 0.26 98.94| | 8: 1.87 - 1.79 2789 144 0.85 21.98 1.25 0.26 98.94| | 9: 1.79 - 1.72 2745 138 0.87 19.33 1.24 0.25 60.27| | 10: 1.72 - 1.66 2789 158 0.86 20.99 1.22 0.25 52.53| | 11: 1.66 - 1.61 2740 147 0.85 22.17 1.24 0.25 50.53| | 12: 1.61 - 1.56 2787 146 0.88 18.91 1.24 0.25 30.26| | 13: 1.56 - 1.52 2745 130 0.86 20.78 1.24 0.25 30.26| | 14: 1.52 - 1.48 2803 134 0.86 20.99 1.22 0.25 27.01| | 15: 1.48 - 1.45 2738 128 0.87 20.32 1.23 0.25 21.05| | 16: 1.45 - 1.42 2756 161 0.85 21.93 1.23 0.25 21.05| | 17: 1.42 - 1.39 2785 139 0.86 21.18 1.23 0.25 17.97| | 18: 1.39 - 1.36 2741 179 0.86 21.44 1.23 0.25 16.18| | 19: 1.36 - 1.34 2807 134 0.85 22.32 1.22 0.25 16.18| | 20: 1.34 - 1.32 2696 147 0.86 21.51 1.20 0.25 13.68| | 21: 1.32 - 1.30 2785 112 0.85 22.39 1.20 0.25 13.50| | 22: 1.29 - 1.27 2704 152 0.84 23.35 1.21 0.24 13.18| | 23: 1.27 - 1.26 2802 156 0.85 22.53 1.20 0.24 11.54| | 24: 1.26 - 1.24 2744 132 0.84 23.44 1.20 0.24 11.54| | 25: 1.24 - 1.22 2734 148 0.83 24.45 1.20 0.24 11.00| | 26: 1.22 - 1.21 2727 135 0.84 24.42 1.20 0.23 10.40| | 27: 1.21 - 1.19 2814 148 0.83 25.36 1.19 0.23 10.40| | 28: 1.19 - 1.18 2671 147 0.82 25.96 1.18 0.23 9.83| | 29: 1.18 - 1.16 2800 134 0.82 26.40 1.17 0.23 9.62| | 30: 1.16 - 1.15 2740 148 0.80 28.23 1.16 0.23 9.62| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 9.62 max = 1483.00 mean = 217.24| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.97 mean = 23.11| |phase err.(test): min = 0.00 max = 89.91 mean = 23.03| |-----------------------------------------------------------------------------| ----------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 0.321 1557 Z= 5.432 Angle : 5.425 18.199 2118 Z= 3.832 Chirality : 0.393 1.050 243 Planarity : 0.033 0.107 284 Dihedral : 13.757 87.793 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 1.08 % Allowed : 2.70 % Favored : 96.22 % Rotamer: Outliers : 1.24 % Allowed : 4.35 % Favored : 94.41 % Cbeta Deviations : 44.86 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.28 (0.45), residues: 224 helix: -3.02 (0.38), residues: 109 sheet: -1.50 (0.82), residues: 28 loop : -0.87 (0.53), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.093 0.023 ARG A 98 TYR 0.077 0.038 TYR A 141 PHE 0.090 0.034 PHE A 119 HIS 0.071 0.024 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= 0.2611 r_free= 0.1970 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.797071 | | target function (ml) not normalized (work): 233012.775185 | | target function (ml) not normalized (free): 11890.683060 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2571 0.2612 0.1970 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2571 0.2612 0.1970 n_refl.: 87602 remove outliers: r(all,work,free)=0.1989 0.1992 0.1970 n_refl.: 87594 overall B=0.22 to atoms: r(all,work,free)=0.2016 0.2019 0.1986 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1650 0.1642 0.1788 n_refl.: 87594 remove outliers: r(all,work,free)=0.1648 0.1641 0.1788 n_refl.: 87591 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 97.87 87 5 0.3852 382.080 355.337 0.675 1.003 0.408 11.894-9.307 98.04 96 4 0.1669 616.220 587.718 0.935 1.003 0.400 9.237-7.194 100.00 213 7 0.2131 501.955 493.145 0.959 1.003 0.344 7.162-5.571 100.00 427 22 0.2210 376.689 364.778 0.935 1.003 0.320 5.546-4.326 100.00 867 58 0.1289 517.101 510.369 0.960 1.003 0.229 4.315-3.360 100.00 1859 96 0.1132 491.767 487.639 1.002 1.003 0.209 3.356-2.611 100.00 3867 181 0.1458 323.065 320.043 0.999 1.002 0.043 2.608-2.026 99.99 8198 413 0.1358 214.163 212.152 1.008 1.001 0.000 2.025-1.573 100.00 17313 902 0.1645 104.586 103.888 1.012 0.999 0.000 1.573-1.221 100.00 36679 1900 0.2075 46.378 45.016 1.002 0.996 0.000 1.221-1.150 99.97 13689 708 0.2590 29.221 26.951 0.976 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0017 b_overall=0.0503 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1641 r_free=0.1788 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=0.1641 r_free=0.1788 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.393332 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2020.734996 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 0.1212 0.1466 0.0254 0.007 1.0 1.6 0.5 0.0 0 12.697 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.12 14.66 2.54 3.012 19.077 2020.735 0.017 12.45 15.49 3.04 2.958 19.396 2020.735 0.015 Individual atomic B min max mean iso aniso Overall: 8.43 118.00 20.71 2.89 0 1785 Protein: 8.43 118.00 17.64 2.90 0 1519 Water: 11.03 115.63 38.55 N/A 0 258 Other: 22.30 34.22 27.46 N/A 0 8 Chain A: 8.43 118.00 20.71 N/A 0 1785 Histogram: Values Number of atoms 8.43 - 19.39 1206 19.39 - 30.34 248 30.34 - 41.30 153 41.30 - 52.26 103 52.26 - 63.22 45 63.22 - 74.17 19 74.17 - 85.13 4 85.13 - 96.09 3 96.09 - 107.05 1 107.05 - 118.00 3 =========================== Idealize ADP of riding H ========================== r_work=0.1246 r_free=0.1550 r_work=0.1250 r_free=0.1553 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1250 r_free = 0.1553 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 = 0.1249 r_free = 0.1558 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87591 (all), 4.90 % free)------------| | | | r_work= 0.1249 r_free= 0.1558 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.015246 | | target function (ls_wunit_k1) not normalized (work): 1269.907070 | | target function (ls_wunit_k1) not normalized (free): 115.377595 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1264 0.1249 0.1558 n_refl.: 87591 re-set all scales: r(all,work,free)=0.1699 0.1697 0.1776 n_refl.: 87591 remove outliers: r(all,work,free)=0.1699 0.1697 0.1776 n_refl.: 87591 overall B=0.15 to atoms: r(all,work,free)=0.1723 0.1722 0.1792 n_refl.: 87591 bulk-solvent and scaling: r(all,work,free)=0.1261 0.1246 0.1550 n_refl.: 87591 remove outliers: r(all,work,free)=0.1261 0.1246 0.1550 n_refl.: 87590 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 94.79 86 5 0.3563 296.157 276.188 0.631 1.003 0.380 11.894-9.307 98.04 96 4 0.1525 481.853 470.680 0.920 1.003 0.380 9.237-7.194 100.00 213 7 0.1805 392.503 387.885 0.951 1.003 0.319 7.162-5.571 100.00 427 22 0.1727 294.552 289.166 0.922 1.003 0.263 5.546-4.326 100.00 867 58 0.0939 404.347 401.487 0.950 1.003 0.214 4.315-3.360 100.00 1859 96 0.0781 384.537 383.575 0.994 1.003 0.199 3.356-2.611 100.00 3867 181 0.1015 252.621 251.938 1.000 1.002 0.052 2.608-2.026 99.99 8198 413 0.0966 167.464 166.978 1.010 1.001 0.000 2.025-1.573 100.00 17313 902 0.1210 81.781 81.967 1.017 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1674 36.265 35.708 1.004 0.999 0.000 1.221-1.150 99.97 13689 708 0.2380 22.849 21.353 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=0.0584 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1246 r_free=0.1550 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=0.1246 r_free=0.1550 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1246 r_free=0.1550 | n_water=258 | time (s): 2.260 (total time: 2.260) Filter (dist) r_work=0.1255 r_free=0.1548 | n_water=252 | time (s): 27.790 (total time: 30.050) Filter (q & B) r_work=0.1258 r_free=0.1547 | n_water=249 | time (s): 3.610 (total time: 33.660) Compute maps r_work=0.1258 r_free=0.1547 | n_water=249 | time (s): 1.780 (total time: 35.440) Filter (map) r_work=0.1268 r_free=0.1554 | n_water=238 | time (s): 3.730 (total time: 39.170) Find peaks r_work=0.1268 r_free=0.1554 | n_water=238 | time (s): 0.710 (total time: 39.880) Add new water r_work=0.1430 r_free=0.1712 | n_water=460 | time (s): 3.740 (total time: 43.620) Refine new water occ: r_work=0.1337 r_free=0.1578 adp: r_work=0.1253 r_free=0.1528 occ: r_work=0.1266 r_free=0.1518 adp: r_work=0.1229 r_free=0.1504 occ: r_work=0.1231 r_free=0.1494 adp: r_work=0.1221 r_free=0.1497 ADP+occupancy (water only), MIN, final r_work=0.1221 r_free=0.1497 r_work=0.1221 r_free=0.1497 | n_water=460 | time (s): 106.270 (total time: 149.890) Filter (q & B) r_work=0.1227 r_free=0.1501 | n_water=437 | time (s): 3.860 (total time: 153.750) Filter (dist only) r_work=0.1227 r_free=0.1500 | n_water=436 | time (s): 44.810 (total time: 198.560) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.952606 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1451.125750 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 0.1225 0.1520 0.0295 0.007 0.9 2.6 0.5 0.0 0 12.976 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.25 15.20 2.95 3.746 22.975 1451.126 0.015 11.91 14.82 2.91 4.021 22.868 1451.126 0.014 Individual atomic B min max mean iso aniso Overall: 8.69 113.15 23.20 2.55 198 1765 Protein: 8.69 113.15 17.56 2.55 0 1519 Water: 11.10 73.40 42.73 N/A 198 238 Other: 24.82 35.99 30.41 N/A 0 8 Chain A: 8.69 113.15 20.27 N/A 0 1765 Chain S: 16.07 73.40 49.36 N/A 198 0 Histogram: Values Number of atoms 8.69 - 19.13 1205 19.13 - 29.58 249 29.58 - 40.03 190 40.03 - 50.47 135 50.47 - 60.92 119 60.92 - 71.37 50 71.37 - 81.81 9 81.81 - 92.26 3 92.26 - 102.71 1 102.71 - 113.15 2 =========================== Idealize ADP of riding H ========================== r_work=0.1191 r_free=0.1483 r_work=0.1192 r_free=0.1483 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1192 r_free = 0.1483 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1192 r_free = 0.1475 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.=87590 (all), 4.90 % free)------------| | | | r_work= 0.1192 r_free= 0.1475 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.013676 | | target function (ls_wunit_k1) not normalized (work): 1139.142118 | | target function (ls_wunit_k1) not normalized (free): 103.268115 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1205 0.1192 0.1475 n_refl.: 87590 re-set all scales: r(all,work,free)=0.1605 0.1600 0.1726 n_refl.: 87590 remove outliers: r(all,work,free)=0.1605 0.1600 0.1726 n_refl.: 87590 overall B=0.03 to atoms: r(all,work,free)=0.1610 0.1605 0.1729 n_refl.: 87590 bulk-solvent and scaling: r(all,work,free)=0.1202 0.1188 0.1473 n_refl.: 87590 remove outliers: r(all,work,free)=0.1202 0.1188 0.1473 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 93.75 85 5 0.3504 298.134 265.697 0.644 0.936 0.380 11.894-9.307 98.04 96 4 0.1444 481.853 478.242 0.991 0.937 0.360 9.237-7.194 100.00 213 7 0.1604 392.503 394.688 1.046 0.937 0.280 7.162-5.571 100.00 427 22 0.1478 294.552 290.855 1.004 0.937 0.229 5.546-4.326 100.00 867 58 0.0848 404.347 401.041 1.024 0.938 0.218 4.315-3.360 100.00 1859 96 0.0710 384.537 383.575 1.070 0.938 0.216 3.356-2.611 100.00 3867 181 0.0965 252.621 251.836 1.077 0.939 0.067 2.608-2.026 99.99 8198 413 0.0947 167.464 167.039 1.084 0.940 0.000 2.025-1.573 100.00 17313 902 0.1162 81.781 81.984 1.091 0.942 0.000 1.573-1.221 100.00 36679 1900 0.1597 36.265 35.775 1.076 0.945 0.000 1.221-1.150 99.97 13689 708 0.2332 22.849 21.393 1.031 0.947 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0465 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1188 r_free=0.1473 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 r_work=0.1189 r_free=0.1476 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1189 r_free=0.1476 | n_water=436 | time (s): 2.170 (total time: 2.170) Filter (dist) r_work=0.1189 r_free=0.1476 | n_water=435 | time (s): 40.560 (total time: 42.730) Filter (q & B) r_work=0.1189 r_free=0.1476 | n_water=435 | time (s): 1.050 (total time: 43.780) Compute maps r_work=0.1189 r_free=0.1476 | n_water=435 | time (s): 1.620 (total time: 45.400) Filter (map) r_work=0.1228 r_free=0.1471 | n_water=302 | time (s): 3.030 (total time: 48.430) Find peaks r_work=0.1228 r_free=0.1471 | n_water=302 | time (s): 0.480 (total time: 48.910) Add new water r_work=0.1354 r_free=0.1597 | n_water=494 | time (s): 2.620 (total time: 51.530) Refine new water occ: r_work=0.1256 r_free=0.1520 adp: r_work=0.1258 r_free=0.1520 occ: r_work=0.1231 r_free=0.1502 adp: r_work=0.1230 r_free=0.1501 occ: r_work=0.1214 r_free=0.1488 adp: r_work=0.1207 r_free=0.1485 ADP+occupancy (water only), MIN, final r_work=0.1207 r_free=0.1485 r_work=0.1207 r_free=0.1485 | n_water=494 | time (s): 222.840 (total time: 274.370) Filter (q & B) r_work=0.1211 r_free=0.1488 | n_water=456 | time (s): 2.690 (total time: 277.060) Filter (dist only) r_work=0.1211 r_free=0.1488 | n_water=456 | time (s): 37.440 (total time: 314.500) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.037820 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 48.257724 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 0.1217 0.1448 0.0231 0.006 0.9 1.9 0.5 0.0 0 1.019 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.17 14.48 2.31 3.579 22.118 48.258 3.723 12.01 13.99 1.98 4.096 21.930 48.258 3.651 Individual atomic B min max mean iso aniso Overall: 9.19 108.63 21.81 2.28 220 1763 Protein: 9.19 108.63 17.13 2.28 0 1519 Water: 11.58 71.44 37.31 N/A 220 236 Other: 20.62 32.14 26.72 N/A 0 8 Chain A: 9.19 108.63 19.80 N/A 0 1763 Chain S: 14.85 67.53 37.91 N/A 220 0 Histogram: Values Number of atoms 9.19 - 19.13 1231 19.13 - 29.07 273 29.07 - 39.02 217 39.02 - 48.96 138 48.96 - 58.91 85 58.91 - 68.85 27 68.85 - 78.80 6 78.80 - 88.74 3 88.74 - 98.69 1 98.69 - 108.63 2 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1399 r_work=0.1202 r_free=0.1399 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1202 r_free = 0.1399 target_work(ml) = 3.651 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1196 r_free = 0.1395 target_work(ml) = 3.649 | | occupancies: max = 1.00 min = 0.16 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= 0.1196 r_free= 0.1395 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.648613 | | target function (ml) not normalized (work): 303903.951059 | | target function (ml) not normalized (free): 16049.920641 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1206 0.1196 0.1395 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1528 0.1528 0.1567 n_refl.: 87589 remove outliers: r(all,work,free)=0.1528 0.1528 0.1567 n_refl.: 87589 overall B=-0.01 to atoms: r(all,work,free)=0.1526 0.1525 0.1565 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1196 0.1188 0.1359 n_refl.: 87589 remove outliers: r(all,work,free)=0.1193 0.1184 0.1359 n_refl.: 87580 ======================== 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 0.3829 292.249 264.141 0.486 1.001 0.320 11.894-9.307 96.08 94 4 0.2300 482.117 465.005 0.866 1.002 0.280 9.237-7.194 98.18 209 7 0.2303 384.029 386.815 0.944 1.002 0.189 7.162-5.571 100.00 427 22 0.2060 294.552 283.969 0.907 1.002 0.171 5.546-4.326 100.00 867 58 0.1077 404.347 400.347 0.953 1.002 0.170 4.315-3.360 100.00 1859 96 0.0917 384.537 381.805 0.992 1.002 0.160 3.356-2.611 100.00 3867 181 0.1142 252.621 250.881 0.999 1.002 0.062 2.608-2.026 99.99 8198 413 0.1031 167.464 166.467 1.012 1.001 0.000 2.025-1.573 100.00 17313 902 0.0997 81.781 81.974 1.027 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1286 36.265 35.850 1.021 0.999 0.000 1.221-1.150 99.97 13689 708 0.2126 22.849 21.470 0.980 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0385 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1184 r_free=0.1359 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 r_work=0.1185 r_free=0.1361 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1185 r_free=0.1361 | n_water=456 | time (s): 1.840 (total time: 1.840) Filter (dist) r_work=0.1185 r_free=0.1361 | n_water=456 | time (s): 35.190 (total time: 37.030) Filter (q & B) r_work=0.1185 r_free=0.1361 | n_water=454 | time (s): 3.070 (total time: 40.100) Compute maps r_work=0.1185 r_free=0.1361 | n_water=454 | time (s): 1.660 (total time: 41.760) Filter (map) r_work=0.1214 r_free=0.1387 | n_water=313 | time (s): 3.340 (total time: 45.100) Find peaks r_work=0.1214 r_free=0.1387 | n_water=313 | time (s): 0.610 (total time: 45.710) Add new water r_work=0.1282 r_free=0.1460 | n_water=491 | time (s): 2.930 (total time: 48.640) Refine new water occ: r_work=0.1208 r_free=0.1382 adp: r_work=0.1208 r_free=0.1385 occ: r_work=0.1192 r_free=0.1368 adp: r_work=0.1191 r_free=0.1368 occ: r_work=0.1180 r_free=0.1357 adp: r_work=0.1176 r_free=0.1355 ADP+occupancy (water only), MIN, final r_work=0.1176 r_free=0.1355 r_work=0.1176 r_free=0.1355 | n_water=491 | time (s): 160.610 (total time: 209.250) Filter (q & B) r_work=0.1185 r_free=0.1353 | n_water=450 | time (s): 2.730 (total time: 211.980) Filter (dist only) r_work=0.1192 r_free=0.1353 | n_water=448 | time (s): 36.790 (total time: 248.770) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.895171 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 39.647969 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1201 0.1357 0.0156 0.006 0.9 1.9 0.5 0.0 0 0.948 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.01 13.57 1.56 3.386 21.378 39.648 3.639 11.99 13.58 1.58 3.645 21.297 39.648 3.629 Individual atomic B min max mean iso aniso Overall: 9.24 104.19 21.21 2.11 216 1759 Protein: 9.24 104.19 16.93 2.11 0 1519 Water: 11.50 70.65 35.62 N/A 216 232 Other: 20.57 29.50 25.61 N/A 0 8 Chain A: 9.24 104.19 19.52 N/A 0 1759 Chain S: 15.72 59.61 34.97 N/A 216 0 Histogram: Values Number of atoms 9.24 - 18.73 1226 18.73 - 28.23 282 28.23 - 37.73 222 37.73 - 47.22 128 47.22 - 56.72 78 56.72 - 66.21 26 66.21 - 75.71 8 75.71 - 85.20 2 85.20 - 94.70 1 94.70 - 104.19 2 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1358 r_work=0.1200 r_free=0.1358 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1358 target_work(ml) = 3.629 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1194 r_free = 0.1355 target_work(ml) = 3.628 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87580 (all), 4.91 % free)------------| | | | r_work= 0.1194 r_free= 0.1355 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.627558 | | target function (ml) not normalized (work): 302117.574176 | | target function (ml) not normalized (free): 15956.682333 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1202 0.1194 0.1355 n_refl.: 87580 re-set all scales: r(all,work,free)=0.1508 0.1506 0.1569 n_refl.: 87580 remove outliers: r(all,work,free)=0.1508 0.1506 0.1569 n_refl.: 87580 overall B=-0.02 to atoms: r(all,work,free)=0.1505 0.1503 0.1567 n_refl.: 87580 bulk-solvent and scaling: r(all,work,free)=0.1200 0.1192 0.1356 n_refl.: 87580 remove outliers: r(all,work,free)=0.1197 0.1189 0.1356 n_refl.: 87573 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 89.58 81 5 0.4003 287.625 256.677 0.445 0.999 0.285 11.894-9.307 92.16 90 4 0.2404 469.091 459.613 0.865 1.001 0.217 9.237-7.194 97.27 207 7 0.2447 384.632 377.244 0.911 1.001 0.162 7.162-5.571 100.00 427 22 0.2183 294.552 283.881 0.905 1.001 0.148 5.546-4.326 100.00 867 58 0.1150 404.347 400.017 0.955 1.002 0.126 4.315-3.360 100.00 1859 96 0.0961 384.537 381.745 0.994 1.002 0.123 3.356-2.611 100.00 3867 181 0.1169 252.621 250.664 1.001 1.001 0.057 2.608-2.026 99.99 8198 413 0.1039 167.464 166.500 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0974 81.781 82.015 1.028 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1245 36.265 35.884 1.022 0.999 0.000 1.221-1.150 99.97 13689 708 0.2120 22.849 21.472 0.980 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0444 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1189 r_free=0.1356 After: r_work=0.1189 r_free=0.1355 ================================== NQH flips ================================== r_work=0.1189 r_free=0.1355 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1189 r_free=0.1355 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1189 r_free=0.1355 | n_water=448 | time (s): 1.950 (total time: 1.950) Filter (dist) r_work=0.1189 r_free=0.1355 | n_water=448 | time (s): 34.540 (total time: 36.490) Filter (q & B) r_work=0.1190 r_free=0.1356 | n_water=445 | time (s): 3.240 (total time: 39.730) Compute maps r_work=0.1190 r_free=0.1356 | n_water=445 | time (s): 1.660 (total time: 41.390) Filter (map) r_work=0.1209 r_free=0.1368 | n_water=332 | time (s): 2.830 (total time: 44.220) Find peaks r_work=0.1209 r_free=0.1368 | n_water=332 | time (s): 0.460 (total time: 44.680) Add new water r_work=0.1263 r_free=0.1411 | n_water=501 | time (s): 3.250 (total time: 47.930) Refine new water occ: r_work=0.1199 r_free=0.1361 adp: r_work=0.1199 r_free=0.1362 occ: r_work=0.1185 r_free=0.1347 adp: r_work=0.1184 r_free=0.1348 occ: r_work=0.1176 r_free=0.1339 adp: r_work=0.1172 r_free=0.1338 ADP+occupancy (water only), MIN, final r_work=0.1172 r_free=0.1338 r_work=0.1172 r_free=0.1338 | n_water=501 | time (s): 169.070 (total time: 217.000) Filter (q & B) r_work=0.1182 r_free=0.1342 | n_water=453 | time (s): 3.350 (total time: 220.350) Filter (dist only) r_work=0.1182 r_free=0.1339 | n_water=451 | time (s): 41.150 (total time: 261.500) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.973745 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 43.565294 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 0.1375 0.0166 0.007 1.0 2.9 0.5 0.0 0 0.987 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.10 13.75 1.66 3.274 21.150 43.565 3.634 12.10 13.72 1.62 3.691 21.035 43.565 3.624 Individual atomic B min max mean iso aniso Overall: 9.28 99.18 20.97 1.97 220 1758 Protein: 9.28 99.18 16.61 1.97 0 1519 Water: 11.54 69.01 35.57 N/A 220 231 Other: 20.82 28.46 24.86 N/A 0 8 Chain A: 9.28 99.18 19.16 N/A 0 1758 Chain S: 14.51 60.17 35.38 N/A 220 0 Histogram: Values Number of atoms 9.28 - 18.27 1216 18.27 - 27.26 274 27.26 - 36.25 227 36.25 - 45.24 128 45.24 - 54.23 88 54.23 - 63.22 29 63.22 - 72.21 12 72.21 - 81.20 1 81.20 - 90.19 1 90.19 - 99.18 2 =========================== Idealize ADP of riding H ========================== r_work=0.1210 r_free=0.1372 r_work=0.1210 r_free=0.1372 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1210 r_free = 0.1372 target_work(ml) = 3.624 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1207 r_free = 0.1369 target_work(ml) = 3.623 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87573 (all), 4.91 % free)------------| | | | r_work= 0.1207 r_free= 0.1369 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.623127 | | target function (ml) not normalized (work): 301723.158444 | | target function (ml) not normalized (free): 15932.912165 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2915 171 0.1448 0.1442 5.708 5.6463| | 2: 3.57 - 2.84 1.00 2888 124 0.1152 0.1426 5.2127 5.2672| | 3: 2.83 - 2.48 1.00 2820 163 0.1232 0.1317 5.0108 5.0281| | 4: 2.47 - 2.25 1.00 2825 136 0.1041 0.1160 4.7084 4.7675| | 5: 2.25 - 2.09 1.00 2756 127 0.0989 0.1079 4.6458 4.7097| | 6: 2.09 - 1.97 1.00 2846 113 0.0986 0.1140 4.3529 4.4268| | 7: 1.97 - 1.87 1.00 2787 165 0.0996 0.1222 4.0749 4.1817| | 8: 1.87 - 1.79 1.00 2789 144 0.1017 0.1222 3.9859 4.0699| | 9: 1.79 - 1.72 1.00 2745 138 0.0943 0.1281 3.7102 3.9112| | 10: 1.72 - 1.66 1.00 2831 160 0.0996 0.1263 3.6307 3.7705| | 11: 1.66 - 1.61 1.00 2712 147 0.0968 0.1072 3.5657 3.5935| | 12: 1.61 - 1.56 1.00 2773 144 0.0919 0.1165 3.3473 3.485| | 13: 1.56 - 1.52 1.00 2745 130 0.0979 0.1087 3.3383 3.4487| | 14: 1.52 - 1.48 1.00 2803 134 0.0984 0.1086 3.2591 3.3292| | 15: 1.48 - 1.45 1.00 2738 128 0.1014 0.1312 3.1693 3.3197| | 16: 1.45 - 1.42 1.00 2756 161 0.1065 0.1240 3.1482 3.2395| | 17: 1.42 - 1.39 1.00 2785 139 0.1125 0.1300 3.1178 3.2323| | 18: 1.39 - 1.36 1.00 2741 179 0.1154 0.1386 3.0863 3.2582| | 19: 1.36 - 1.34 1.00 2807 134 0.1210 0.1609 3.0923 3.2798| | 20: 1.34 - 1.32 1.00 2696 147 0.1321 0.1469 3.0878 3.1245| | 21: 1.32 - 1.30 1.00 2785 112 0.1422 0.1615 3.0889 3.1608| | 22: 1.29 - 1.27 1.00 2704 152 0.1476 0.1920 3.0867 3.2833| | 23: 1.27 - 1.26 1.00 2802 156 0.1579 0.1826 3.1052 3.209| | 24: 1.26 - 1.24 1.00 2744 132 0.1626 0.1744 3.0978 3.1848| | 25: 1.24 - 1.22 1.00 2733 148 0.1787 0.2271 3.1092 3.2866| | 26: 1.22 - 1.21 1.00 2727 135 0.1859 0.1796 3.125 3.1997| | 27: 1.21 - 1.19 1.00 2814 148 0.2014 0.2113 3.1443 3.1569| | 28: 1.19 - 1.18 1.00 2671 147 0.2148 0.2326 3.1443 3.1741| | 29: 1.18 - 1.16 1.00 2800 134 0.2214 0.2379 3.1287 3.2234| | 30: 1.16 - 1.15 1.00 2739 148 0.2373 0.2471 3.1183 3.1647| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2915 171 0.95 9.04 0.99 0.97 6256.57| | 2: 3.57 - 2.84 2888 124 0.92 13.29 1.01 0.97 6256.57| | 3: 2.83 - 2.48 2820 163 0.89 17.41 0.99 0.97 5241.77| | 4: 2.47 - 2.25 2825 136 0.91 14.58 1.00 0.98 2624.92| | 5: 2.25 - 2.09 2756 127 0.90 16.72 1.01 0.98 2624.92| | 6: 2.09 - 1.97 2846 113 0.92 13.53 1.02 0.98 1538.08| | 7: 1.97 - 1.87 2787 165 0.94 10.61 1.02 0.97 611.15| | 8: 1.87 - 1.79 2789 144 0.92 14.11 1.00 0.97 611.15| | 9: 1.79 - 1.72 2745 138 0.93 11.33 0.99 0.97 334.26| | 10: 1.72 - 1.66 2831 160 0.93 12.14 0.98 0.97 278.81| | 11: 1.66 - 1.61 2712 147 0.93 12.86 0.98 0.97 266.13| | 12: 1.61 - 1.56 2773 144 0.95 9.43 0.99 0.97 146.50| | 13: 1.56 - 1.52 2745 130 0.94 10.99 1.02 0.97 146.50| | 14: 1.52 - 1.48 2803 134 0.94 11.16 1.02 0.98 130.96| | 15: 1.48 - 1.45 2738 128 0.95 10.31 1.02 0.98 102.48| | 16: 1.45 - 1.42 2756 161 0.94 11.51 1.02 0.98 102.48| | 17: 1.42 - 1.39 2785 139 0.94 11.39 1.01 0.98 92.54| | 18: 1.39 - 1.36 2741 179 0.94 11.64 1.01 0.98 86.79| | 19: 1.36 - 1.34 2807 134 0.94 12.17 1.00 0.98 86.79| | 20: 1.34 - 1.32 2696 147 0.94 12.36 0.99 0.97 81.81| | 21: 1.32 - 1.30 2785 112 0.94 13.31 0.99 0.96 81.46| | 22: 1.29 - 1.27 2704 152 0.93 13.85 0.98 0.96 81.62| | 23: 1.27 - 1.26 2802 156 0.92 14.78 0.98 0.95 82.44| | 24: 1.26 - 1.24 2744 132 0.93 14.85 0.97 0.95 82.44| | 25: 1.24 - 1.22 2733 148 0.91 16.30 0.96 0.94 84.20| | 26: 1.22 - 1.21 2727 135 0.90 18.07 1.02 0.93 86.16| | 27: 1.21 - 1.19 2814 148 0.89 18.71 1.02 0.93 86.16| | 28: 1.19 - 1.18 2671 147 0.88 20.23 1.01 0.93 90.02| | 29: 1.18 - 1.16 2800 134 0.88 20.60 0.99 0.92 91.47| | 30: 1.16 - 1.15 2739 148 0.86 22.05 0.98 0.92 91.47| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 81.46 max = 6256.57 mean = 972.78| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.92 mean = 13.96| |phase err.(test): min = 0.00 max = 88.92 mean = 14.02| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1215 0.1207 0.1369 n_refl.: 87573 re-set all scales: r(all,work,free)=0.1518 0.1518 0.1552 n_refl.: 87573 remove outliers: r(all,work,free)=0.1518 0.1518 0.1552 n_refl.: 87573 overall B=-0.01 to atoms: r(all,work,free)=0.1516 0.1516 0.1551 n_refl.: 87573 bulk-solvent and scaling: r(all,work,free)=0.1215 0.1207 0.1367 n_refl.: 87573 remove outliers: r(all,work,free)=0.1215 0.1207 0.1367 n_refl.: 87572 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 89.58 81 5 0.4232 287.625 254.416 0.429 0.999 0.305 11.894-9.307 91.18 89 4 0.2356 471.661 445.497 0.835 1.000 0.219 9.237-7.194 97.27 207 7 0.2565 384.632 376.437 0.905 1.001 0.135 7.162-5.571 100.00 427 22 0.2315 294.552 282.570 0.892 1.001 0.110 5.546-4.326 100.00 867 58 0.1206 404.347 399.569 0.953 1.001 0.107 4.315-3.360 100.00 1859 96 0.1016 384.537 381.888 0.995 1.001 0.103 3.356-2.611 100.00 3867 181 0.1206 252.621 250.766 1.001 1.001 0.034 2.608-2.026 99.99 8198 413 0.1050 167.464 166.467 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0977 81.781 82.064 1.027 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1228 36.265 35.912 1.020 1.000 0.000 1.221-1.150 99.97 13689 708 0.2118 22.849 21.448 0.974 1.000 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0362 ================= 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 : 0.2611 0.1970 0.082 5.425 8.8 119.3 19.9 258 0.000 1_bss: 0.1641 0.1788 0.082 5.425 9.1 119.5 20.1 258 0.000 1_settarget: 0.1641 0.1788 0.082 5.425 9.1 119.5 20.1 258 0.000 1_nqh: 0.1641 0.1788 0.082 5.425 9.1 119.5 20.1 258 0.000 1_weight: 0.1641 0.1788 0.082 5.425 9.1 119.5 20.1 258 0.000 1_xyzrec: 0.1212 0.1466 0.007 0.961 9.1 119.5 20.1 258 0.125 1_adp: 0.1246 0.1550 0.007 0.961 8.4 118.0 20.7 258 0.125 1_regHadp: 0.1250 0.1553 0.007 0.961 8.4 118.0 20.7 258 0.125 1_occ: 0.1249 0.1558 0.007 0.961 8.4 118.0 20.7 258 0.125 2_bss: 0.1246 0.1550 0.007 0.961 8.6 118.2 20.9 258 0.125 2_settarget: 0.1246 0.1550 0.007 0.961 8.6 118.2 20.9 258 0.125 2_updatecdl: 0.1246 0.1550 0.007 0.964 8.6 118.2 20.9 258 0.125 2_nqh: 0.1246 0.1550 0.007 0.964 8.6 118.2 20.9 258 0.125 2_sol: 0.1227 0.1500 0.007 0.964 8.6 118.2 23.4 436 n/a 2_weight: 0.1227 0.1500 0.007 0.964 8.6 118.2 23.4 436 n/a 2_xyzrec: 0.1225 0.1520 0.007 0.885 8.6 118.2 23.4 436 n/a 2_adp: 0.1191 0.1483 0.007 0.885 8.7 113.2 23.2 436 n/a 2_regHadp: 0.1192 0.1483 0.007 0.885 8.7 113.2 23.2 436 n/a 2_occ: 0.1192 0.1475 0.007 0.885 8.7 113.2 23.2 436 n/a 3_bss: 0.1188 0.1473 0.007 0.885 8.7 113.2 23.2 436 n/a 3_settarget: 0.1188 0.1473 0.007 0.885 8.7 113.2 23.2 436 n/a 3_updatecdl: 0.1188 0.1473 0.007 0.886 8.7 113.2 23.2 436 n/a 3_nqh: 0.1189 0.1476 0.007 0.886 8.7 113.2 23.2 436 n/a 3_sol: 0.1211 0.1488 0.007 0.886 8.7 113.2 22.1 456 n/a 3_weight: 0.1211 0.1488 0.007 0.886 8.7 113.2 22.1 456 n/a 3_xyzrec: 0.1217 0.1448 0.006 0.925 8.7 113.2 22.1 456 n/a 3_adp: 0.1201 0.1399 0.006 0.925 9.2 108.6 21.8 456 n/a 3_regHadp: 0.1202 0.1399 0.006 0.925 9.2 108.6 21.8 456 n/a 3_occ: 0.1196 0.1395 0.006 0.925 9.2 108.6 21.8 456 n/a 4_bss: 0.1184 0.1359 0.006 0.925 9.2 108.6 21.8 456 n/a 4_settarget: 0.1184 0.1359 0.006 0.925 9.2 108.6 21.8 456 n/a 4_updatecdl: 0.1184 0.1359 0.006 0.923 9.2 108.6 21.8 456 n/a 4_nqh: 0.1185 0.1361 0.006 0.923 9.2 108.6 21.8 456 n/a 4_sol: 0.1192 0.1353 0.006 0.923 9.2 108.6 21.4 448 n/a 4_weight: 0.1192 0.1353 0.006 0.923 9.2 108.6 21.4 448 n/a 4_xyzrec: 0.1201 0.1357 0.006 0.949 9.2 108.6 21.4 448 n/a 4_adp: 0.1199 0.1358 0.006 0.949 9.2 104.2 21.2 448 n/a 4_regHadp: 0.1200 0.1358 0.006 0.949 9.2 104.2 21.2 448 n/a 4_occ: 0.1194 0.1355 0.006 0.949 9.2 104.2 21.2 448 n/a 5_bss: 0.1189 0.1356 0.006 0.949 9.2 104.2 21.2 448 n/a 5_settarget: 0.1189 0.1356 0.006 0.949 9.2 104.2 21.2 448 n/a 5_updatecdl: 0.1189 0.1356 0.006 0.950 9.2 104.2 21.2 448 n/a 5_setrh: 0.1189 0.1355 0.006 0.950 9.2 104.2 21.2 448 n/a 5_nqh: 0.1189 0.1355 0.006 0.950 9.2 104.2 21.2 448 n/a 5_sol: 0.1182 0.1339 0.006 0.950 9.2 104.2 21.2 451 n/a 5_weight: 0.1182 0.1339 0.006 0.950 9.2 104.2 21.2 451 n/a 5_xyzrec: 0.1210 0.1375 0.007 1.037 9.2 104.2 21.2 451 n/a 5_adp: 0.1210 0.1372 0.007 1.037 9.3 99.2 21.0 451 n/a 5_regHadp: 0.1210 0.1372 0.007 1.037 9.3 99.2 21.0 451 n/a 5_occ: 0.1207 0.1369 0.007 1.037 9.3 99.2 21.0 451 n/a end: 0.1207 0.1367 0.007 1.037 9.3 99.2 21.0 451 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_2359181_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_2359181_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.7100 Refinement macro-cycles (run) : 3375.9100 Write final files (write_after_run_outputs) : 72.0900 Total : 3452.7100 Total CPU time: 58.16 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:09:07 PST -0800 (1735452547.76 s) Start R-work = 0.1641, R-free = 0.1788 Final R-work = 0.1207, R-free = 0.1367 =============================================================================== Job complete usr+sys time: 3606.99 seconds wall clock time: 64 minutes 37.35 seconds (3877.35 seconds total)