Starting phenix.refine on Sat Dec 28 21:06:31 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6109584.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_6109584.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6109584.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: 2.09, per 1000 atoms: 0.62 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: 0.69 Conformation dependent library (CDL) restraints added in 290.3 milliseconds Time building geometry restraints manager: 0.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.62 - 0.88: 354 0.88 - 1.14: 1254 1.14 - 1.41: 606 1.41 - 1.67: 899 1.67 - 1.93: 40 Bond restraints: 3153 Sorted by residual: bond pdb=" NE ARG A 27 " pdb=" CZ ARG A 27 " ideal model delta sigma weight residual 1.326 1.074 0.252 1.10e-02 8.26e+03 5.25e+02 bond pdb=" C LEU A 7 " pdb=" O LEU A 7 " ideal model delta sigma weight residual 1.236 0.978 0.258 1.14e-02 7.69e+03 5.13e+02 bond pdb=" NE ARG A 48 " pdb=" CZ ARG A 48 " ideal model delta sigma weight residual 1.326 1.539 -0.213 1.10e-02 8.26e+03 3.75e+02 bond pdb=" N PHE A 162 " pdb=" CA PHE A 162 " ideal model delta sigma weight residual 1.459 1.682 -0.223 1.23e-02 6.61e+03 3.28e+02 bond pdb=" CA VAL A 20 " pdb=" CB VAL A 20 " ideal model delta sigma weight residual 1.540 1.330 0.209 1.17e-02 7.31e+03 3.19e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.50: 3134 4.50 - 9.00: 1817 9.00 - 13.51: 653 13.51 - 18.01: 154 18.01 - 22.51: 19 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA LEU A 77 " pdb=" C LEU A 77 " pdb=" O LEU A 77 " ideal model delta sigma weight residual 120.42 134.22 -13.80 1.06e+00 8.90e-01 1.70e+02 angle pdb=" CA SER A 85 " pdb=" C SER A 85 " pdb=" O SER A 85 " ideal model delta sigma weight residual 120.32 134.53 -14.21 1.10e+00 8.26e-01 1.67e+02 angle pdb=" O SER A 3 " pdb=" C SER A 3 " pdb=" N LYS A 4 " ideal model delta sigma weight residual 123.10 108.37 14.73 1.15e+00 7.56e-01 1.64e+02 angle pdb=" O SER A 121 " pdb=" C SER A 121 " pdb=" N LYS A 122 " ideal model delta sigma weight residual 122.96 137.30 -14.34 1.13e+00 7.83e-01 1.61e+02 angle pdb=" O ASP A 131 " pdb=" C ASP A 131 " pdb=" N BLYS A 132 " ideal model delta sigma weight residual 122.15 136.13 -13.98 1.14e+00 7.69e-01 1.50e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 16.80: 929 16.80 - 33.60: 124 33.60 - 50.40: 37 50.40 - 67.20: 17 67.20 - 83.99: 4 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA ASP A 49 " pdb=" C ASP A 49 " pdb=" N VAL A 50 " pdb=" CA VAL A 50 " ideal model delta harmonic sigma weight residual 180.00 151.84 28.16 0 5.00e+00 4.00e-02 3.17e+01 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 -158.26 -21.74 0 5.00e+00 4.00e-02 1.89e+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 180.00 158.76 21.24 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.007 - 0.233: 104 0.233 - 0.459: 75 0.459 - 0.685: 39 0.685 - 0.910: 21 0.910 - 1.136: 4 Chirality restraints: 243 Sorted by residual: chirality pdb=" CG LEU A 172 " pdb=" CB LEU A 172 " pdb=" CD1 LEU A 172 " pdb=" CD2 LEU A 172 " both_signs ideal model delta sigma weight residual False -2.59 -1.45 -1.14 2.00e-01 2.50e+01 3.23e+01 chirality pdb=" CB VAL A 8 " pdb=" CA VAL A 8 " pdb=" CG1 VAL A 8 " pdb=" CG2 VAL A 8 " both_signs ideal model delta sigma weight residual False -2.63 -3.72 1.10 2.00e-01 2.50e+01 3.00e+01 chirality pdb=" CA LEU A 151 " pdb=" N LEU A 151 " pdb=" C LEU A 151 " pdb=" CB LEU A 151 " both_signs ideal model delta sigma weight residual False 2.51 1.51 1.00 2.00e-01 2.50e+01 2.52e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " -0.053 2.00e-02 2.50e+03 7.11e-02 1.52e+02 pdb=" CG ATYR A 67 " 0.094 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " -0.024 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " -0.073 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " -0.102 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " -0.048 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " 0.083 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " -0.090 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " 0.015 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " 0.028 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " 0.091 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " 0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 126 " 0.051 2.00e-02 2.50e+03 7.37e-02 1.22e+02 pdb=" CG HIS A 126 " 0.012 2.00e-02 2.50e+03 pdb=" ND1 HIS A 126 " -0.145 2.00e-02 2.50e+03 pdb=" CD2 HIS A 126 " -0.079 2.00e-02 2.50e+03 pdb=" CE1 HIS A 126 " 0.063 2.00e-02 2.50e+03 pdb=" NE2 HIS A 126 " -0.025 2.00e-02 2.50e+03 pdb=" HD2 HIS A 126 " 0.074 2.00e-02 2.50e+03 pdb=" HE1 HIS A 126 " 0.085 2.00e-02 2.50e+03 pdb=" HE2 HIS A 126 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " -0.050 2.00e-02 2.50e+03 6.22e-02 1.16e+02 pdb=" CG BTYR A 67 " 0.069 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " 0.087 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " -0.006 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " -0.026 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " 0.008 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " -0.077 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " -0.067 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " -0.082 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " -0.020 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " 0.093 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " 0.070 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.36: 1294 2.36 - 2.92: 8315 2.92 - 3.48: 10443 3.48 - 4.04: 15052 4.04 - 4.60: 21546 Nonbonded interactions: 56650 Sorted by model distance: nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.794 2.450 nonbonded pdb=" O LEU A 58 " pdb=" H LYS A 62 " model vdw 1.837 2.450 nonbonded pdb=" H THR A 125 " pdb=" HH TYR A 141 " model vdw 1.844 2.100 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.845 2.100 nonbonded pdb=" HD3 ARG A 5 " pdb="HH11 ARG A 5 " model vdw 1.846 2.270 ... (remaining 56645 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_6109584_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= 0.2608 r_free= 0.1953 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.793244 | | target function (ml) not normalized (work): 232694.010027 | | target function (ml) not normalized (free): 11827.116113 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3034 0.2186 6.9972 4.9658| | 2: 3.57 - 2.84 1.00 2876 122 0.2448 0.1689 4.3571 4.3277| | 3: 2.84 - 2.48 1.00 2833 165 0.2342 0.1676 4.1365 4.1691| | 4: 2.47 - 2.25 1.00 2825 136 0.2339 0.1426 3.8389 3.8316| | 5: 2.25 - 2.09 1.00 2756 127 0.2461 0.1784 3.807 3.8595| | 6: 2.09 - 1.97 1.00 2846 113 0.2563 0.1731 3.4833 3.5834| | 7: 1.97 - 1.87 1.00 2787 165 0.2496 0.1890 3.1328 3.2336| | 8: 1.87 - 1.79 1.00 2789 144 0.2461 0.1634 3.0696 3.0945| | 9: 1.79 - 1.72 1.00 2745 138 0.2417 0.1804 2.9232 2.9387| | 10: 1.72 - 1.66 1.00 2789 158 0.2356 0.2038 2.8107 2.9152| | 11: 1.66 - 1.61 1.00 2740 147 0.2531 0.1950 2.749 2.7788| | 12: 1.61 - 1.56 1.00 2787 146 0.2563 0.1944 2.6405 2.643| | 13: 1.56 - 1.52 1.00 2745 130 0.2574 0.1950 2.5778 2.6315| | 14: 1.52 - 1.48 1.00 2803 134 0.2642 0.1674 2.5276 2.4666| | 15: 1.48 - 1.45 1.00 2738 128 0.2604 0.2104 2.4237 2.5152| | 16: 1.45 - 1.42 1.00 2756 161 0.2657 0.2250 2.3798 2.4957| | 17: 1.42 - 1.39 1.00 2785 139 0.2702 0.2010 2.3285 2.3457| | 18: 1.39 - 1.36 1.00 2741 179 0.2650 0.2213 2.2739 2.3396| | 19: 1.36 - 1.34 1.00 2807 134 0.2646 0.2405 2.2343 2.3377| | 20: 1.34 - 1.32 1.00 2696 147 0.2642 0.2082 2.1984 2.1383| | 21: 1.32 - 1.30 1.00 2785 112 0.2698 0.2332 2.1657 2.1727| | 22: 1.29 - 1.27 1.00 2704 152 0.2743 0.2623 2.1366 2.202| | 23: 1.27 - 1.26 1.00 2802 156 0.2756 0.2499 2.1222 2.1689| | 24: 1.26 - 1.24 1.00 2744 132 0.2783 0.2535 2.0913 2.1474| | 25: 1.24 - 1.22 1.00 2734 148 0.2871 0.2579 2.046 2.0794| | 26: 1.22 - 1.21 1.00 2727 135 0.2923 0.2459 2.0245 2.1115| | 27: 1.21 - 1.19 1.00 2814 148 0.2977 0.2504 1.9972 2.009| | 28: 1.19 - 1.18 1.00 2671 147 0.3005 0.2817 1.9813 1.9989| | 29: 1.18 - 1.16 1.00 2800 134 0.2990 0.2577 1.9665 1.9834| | 30: 1.16 - 1.15 1.00 2740 148 0.3041 0.2775 1.9234 1.945| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 49.25 - 3.58 2941 171 0.87 19.06 0.76 0.23 1508.99| | 2: 3.57 - 2.84 2876 122 0.80 26.35 1.27 0.23 1508.99| | 3: 2.84 - 2.48 2833 165 0.74 32.30 1.24 0.23 1252.20| | 4: 2.47 - 2.25 2825 136 0.81 25.92 1.26 0.25 585.76| | 5: 2.25 - 2.09 2756 127 0.77 29.52 1.28 0.25 585.76| | 6: 2.09 - 1.97 2846 113 0.83 23.16 1.29 0.25 321.78| | 7: 1.97 - 1.87 2787 165 0.90 17.02 1.28 0.26 96.63| | 8: 1.87 - 1.79 2789 144 0.85 21.89 1.25 0.26 96.63| | 9: 1.79 - 1.72 2745 138 0.88 18.61 1.23 0.26 56.29| | 10: 1.72 - 1.66 2789 158 0.87 19.98 1.21 0.25 48.21| | 11: 1.66 - 1.61 2740 147 0.86 21.23 1.25 0.25 46.53| | 12: 1.61 - 1.56 2787 146 0.88 18.56 1.24 0.25 29.47| | 13: 1.56 - 1.52 2745 130 0.87 20.41 1.24 0.25 29.47| | 14: 1.52 - 1.48 2803 134 0.86 20.77 1.24 0.25 26.37| | 15: 1.48 - 1.45 2738 128 0.87 20.25 1.24 0.25 20.69| | 16: 1.45 - 1.42 2756 161 0.85 21.71 1.24 0.25 20.69| | 17: 1.42 - 1.39 2785 139 0.87 20.85 1.24 0.25 17.66| | 18: 1.39 - 1.36 2741 179 0.86 21.22 1.22 0.25 15.90| | 19: 1.36 - 1.34 2807 134 0.85 22.17 1.22 0.25 15.90| | 20: 1.34 - 1.32 2696 147 0.87 20.95 1.20 0.25 13.20| | 21: 1.32 - 1.30 2785 112 0.86 22.06 1.20 0.25 13.01| | 22: 1.29 - 1.27 2704 152 0.85 22.52 1.21 0.24 12.69| | 23: 1.27 - 1.26 2802 156 0.86 22.01 1.20 0.24 11.11| | 24: 1.26 - 1.24 2744 132 0.85 22.71 1.20 0.24 11.11| | 25: 1.24 - 1.22 2734 148 0.84 23.70 1.20 0.24 10.49| | 26: 1.22 - 1.21 2727 135 0.84 23.60 1.20 0.24 9.80| | 27: 1.21 - 1.19 2814 148 0.83 24.51 1.21 0.24 9.80| | 28: 1.19 - 1.18 2671 147 0.83 24.78 1.19 0.23 8.93| | 29: 1.18 - 1.16 2800 134 0.83 25.01 1.17 0.23 8.61| | 30: 1.16 - 1.15 2740 148 0.82 26.45 1.15 0.23 8.61| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 8.61 max = 1508.99 mean = 219.38| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.99 mean = 22.65| |phase err.(test): min = 0.00 max = 89.71 mean = 22.51| |-----------------------------------------------------------------------------| ----------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 : 0.081 0.258 1557 Z= 5.426 Angle : 5.213 16.162 2118 Z= 3.693 Chirality : 0.407 1.136 243 Planarity : 0.032 0.103 284 Dihedral : 14.506 83.994 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.24 % Favored : 96.22 % Rotamer: Outliers : 1.24 % Allowed : 2.48 % Favored : 96.27 % Cbeta Deviations : 28.11 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.53), residues: 224 helix: -2.39 (0.40), residues: 102 sheet: -0.59 (0.89), residues: 30 loop : 1.29 (0.65), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.105 0.019 ARG A 28 TYR 0.101 0.031 TYR A 139 PHE 0.071 0.025 PHE A 164 HIS 0.099 0.048 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= 0.2608 r_free= 0.1953 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.793244 | | target function (ml) not normalized (work): 232694.010027 | | target function (ml) not normalized (free): 11827.116113 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2568 0.2609 0.1953 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2568 0.2609 0.1953 n_refl.: 87602 remove outliers: r(all,work,free)=0.1980 0.1983 0.1953 n_refl.: 87594 overall B=0.19 to atoms: r(all,work,free)=0.2003 0.2007 0.1965 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1645 0.1639 0.1766 n_refl.: 87594 remove outliers: r(all,work,free)=0.1645 0.1639 0.1766 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 0.3819 386.379 360.719 0.682 1.003 0.414 11.894-9.307 99.02 97 4 0.1839 613.744 595.135 0.932 1.004 0.400 9.237-7.194 100.00 213 7 0.2150 501.967 491.812 0.961 1.004 0.370 7.162-5.571 100.00 427 22 0.2184 376.698 365.384 0.931 1.004 0.302 5.546-4.326 100.00 867 58 0.1260 517.113 511.214 0.965 1.004 0.209 4.315-3.360 100.00 1859 96 0.1131 491.778 487.630 1.002 1.003 0.179 3.356-2.611 100.00 3867 181 0.1454 323.073 319.592 1.000 1.002 0.080 2.608-2.026 99.99 8198 413 0.1335 214.168 212.042 1.008 1.001 0.000 2.025-1.573 100.00 17313 902 0.1660 104.588 103.928 1.012 0.998 0.000 1.573-1.221 100.00 36679 1900 0.2080 46.379 45.077 1.006 0.994 0.000 1.221-1.150 99.97 13689 708 0.2589 29.222 26.935 0.981 0.990 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0436 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1639 r_free=0.1766 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1639 r_free=0.1766 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.971823 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2025.488684 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 0.1470 0.0258 0.007 1.0 1.3 0.5 0.0 0 12.986 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.12 14.70 2.58 3.013 19.049 2025.489 0.017 12.40 15.40 2.99 3.139 19.495 2025.489 0.016 Individual atomic B min max mean iso aniso Overall: 8.40 118.40 20.92 2.88 0 1785 Protein: 8.40 118.40 17.79 2.88 0 1519 Water: 11.02 114.68 39.11 N/A 0 258 Other: 22.77 35.80 28.97 N/A 0 8 Chain A: 8.40 118.40 20.92 N/A 0 1785 Histogram: Values Number of atoms 8.40 - 19.40 1207 19.40 - 30.40 231 30.40 - 41.40 164 41.40 - 52.40 99 52.40 - 63.40 55 63.40 - 74.40 17 74.40 - 85.40 5 85.40 - 96.40 4 96.40 - 107.40 0 107.40 - 118.40 3 =========================== Idealize ADP of riding H ========================== r_work=0.1241 r_free=0.1540 r_work=0.1245 r_free=0.1544 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1245 r_free = 0.1544 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 = 0.1245 r_free = 0.1548 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.20 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= 0.1245 r_free= 0.1548 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.015398 | | target function (ls_wunit_k1) not normalized (work): 1282.605769 | | target function (ls_wunit_k1) not normalized (free): 115.595646 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1260 0.1245 0.1548 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1690 0.1688 0.1764 n_refl.: 87593 remove outliers: r(all,work,free)=0.1690 0.1688 0.1764 n_refl.: 87593 overall B=0.18 to atoms: r(all,work,free)=0.1720 0.1719 0.1785 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1258 0.1244 0.1542 n_refl.: 87593 remove outliers: r(all,work,free)=0.1258 0.1243 0.1542 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 0.3591 299.887 279.226 0.630 1.002 0.374 11.894-9.307 99.02 97 4 0.1601 480.403 468.801 0.906 1.003 0.370 9.237-7.194 100.00 213 7 0.1833 392.911 387.758 0.948 1.003 0.340 7.162-5.571 100.00 427 22 0.1713 294.858 289.410 0.922 1.003 0.253 5.546-4.326 100.00 867 58 0.0913 404.767 402.283 0.948 1.003 0.199 4.315-3.360 100.00 1859 96 0.0776 384.936 383.940 0.992 1.002 0.179 3.356-2.611 100.00 3867 181 0.1022 252.883 252.182 0.997 1.002 0.109 2.608-2.026 99.99 8198 413 0.0974 167.638 167.067 1.008 1.001 0.000 2.025-1.573 100.00 17313 902 0.1212 81.866 82.038 1.016 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1654 36.303 35.758 1.005 0.997 0.000 1.221-1.150 99.97 13689 708 0.2360 22.873 21.368 0.970 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0418 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1243 r_free=0.1542 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=0.1245 r_free=0.1543 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1245 r_free=0.1543 | n_water=258 | time (s): 2.300 (total time: 2.300) Filter (dist) r_work=0.1254 r_free=0.1540 | n_water=252 | time (s): 25.430 (total time: 27.730) Filter (q & B) r_work=0.1257 r_free=0.1539 | n_water=249 | time (s): 3.640 (total time: 31.370) Compute maps r_work=0.1257 r_free=0.1539 | n_water=249 | time (s): 1.800 (total time: 33.170) Filter (map) r_work=0.1282 r_free=0.1553 | n_water=232 | time (s): 3.620 (total time: 36.790) Find peaks r_work=0.1282 r_free=0.1553 | n_water=232 | time (s): 0.710 (total time: 37.500) Add new water r_work=0.1429 r_free=0.1706 | n_water=448 | time (s): 3.520 (total time: 41.020) Refine new water occ: r_work=0.1333 r_free=0.1578 adp: r_work=0.1254 r_free=0.1527 occ: r_work=0.1268 r_free=0.1514 adp: r_work=0.1235 r_free=0.1501 occ: r_work=0.1239 r_free=0.1489 adp: r_work=0.1229 r_free=0.1489 ADP+occupancy (water only), MIN, final r_work=0.1229 r_free=0.1489 r_work=0.1229 r_free=0.1489 | n_water=448 | time (s): 85.830 (total time: 126.850) Filter (q & B) r_work=0.1233 r_free=0.1492 | n_water=427 | time (s): 3.970 (total time: 130.820) Filter (dist only) r_work=0.1233 r_free=0.1492 | n_water=427 | time (s): 39.520 (total time: 170.340) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.083024 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1523.799760 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 0.1229 0.1519 0.0290 0.007 0.9 2.9 0.5 0.0 0 13.042 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.29 15.19 2.90 3.778 23.032 1523.800 0.015 11.99 14.88 2.89 4.128 22.859 1523.800 0.015 Individual atomic B min max mean iso aniso Overall: 8.76 114.37 22.98 2.61 195 1759 Protein: 8.76 114.37 17.65 2.61 0 1519 Water: 10.94 73.11 41.83 N/A 195 232 Other: 23.83 35.90 29.18 N/A 0 8 Chain A: 8.76 114.37 20.33 N/A 0 1759 Chain S: 16.11 70.15 46.92 N/A 195 0 Histogram: Values Number of atoms 8.76 - 19.32 1207 19.32 - 29.88 258 29.88 - 40.44 184 40.44 - 51.00 144 51.00 - 61.56 104 61.56 - 72.13 46 72.13 - 82.69 5 82.69 - 93.25 3 93.25 - 103.81 1 103.81 - 114.37 2 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1488 r_work=0.1199 r_free=0.1487 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 r_free = 0.1487 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1200 r_free = 0.1486 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.13 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= 0.1486 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.013900 | | target function (ls_wunit_k1) not normalized (work): 1157.821144 | | target function (ls_wunit_k1) not normalized (free): 105.094520 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1214 0.1200 0.1486 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1605 0.1600 0.1732 n_refl.: 87592 remove outliers: r(all,work,free)=0.1605 0.1600 0.1732 n_refl.: 87592 overall B=0.03 to atoms: r(all,work,free)=0.1610 0.1605 0.1735 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1210 0.1196 0.1481 n_refl.: 87592 remove outliers: r(all,work,free)=0.1209 0.1195 0.1481 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 0.3457 295.812 272.816 0.632 0.940 0.370 11.894-9.307 99.02 97 4 0.1484 480.403 476.939 0.974 0.941 0.356 9.237-7.194 100.00 213 7 0.1686 392.911 394.182 1.038 0.941 0.290 7.162-5.571 100.00 427 22 0.1481 294.858 291.521 1.007 0.941 0.233 5.546-4.326 100.00 867 58 0.0824 404.767 402.175 1.020 0.941 0.200 4.315-3.360 100.00 1859 96 0.0706 384.936 383.805 1.065 0.941 0.184 3.356-2.611 100.00 3867 181 0.0956 252.883 252.308 1.074 0.942 0.150 2.608-2.026 99.99 8198 413 0.0972 167.638 167.225 1.081 0.942 0.000 2.025-1.573 100.00 17313 902 0.1178 81.866 82.054 1.089 0.944 0.000 1.573-1.221 100.00 36679 1900 0.1602 36.303 35.808 1.073 0.946 0.000 1.221-1.150 99.97 13689 708 0.2334 22.873 21.426 1.031 0.948 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0484 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1195 r_free=0.1481 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1195 r_free=0.1481 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1195 r_free=0.1481 | n_water=427 | time (s): 2.330 (total time: 2.330) Filter (dist) r_work=0.1197 r_free=0.1481 | n_water=425 | time (s): 37.670 (total time: 40.000) Filter (q & B) r_work=0.1197 r_free=0.1481 | n_water=425 | time (s): 1.390 (total time: 41.390) Compute maps r_work=0.1197 r_free=0.1481 | n_water=425 | time (s): 1.380 (total time: 42.770) Filter (map) r_work=0.1235 r_free=0.1475 | n_water=288 | time (s): 3.020 (total time: 45.790) Find peaks r_work=0.1235 r_free=0.1475 | n_water=288 | time (s): 0.490 (total time: 46.280) Add new water r_work=0.1364 r_free=0.1597 | n_water=482 | time (s): 2.650 (total time: 48.930) Refine new water occ: r_work=0.1262 r_free=0.1516 adp: r_work=0.1263 r_free=0.1516 occ: r_work=0.1241 r_free=0.1497 adp: r_work=0.1239 r_free=0.1496 occ: r_work=0.1225 r_free=0.1482 adp: r_work=0.1218 r_free=0.1478 ADP+occupancy (water only), MIN, final r_work=0.1218 r_free=0.1478 r_work=0.1218 r_free=0.1478 | n_water=482 | time (s): 225.460 (total time: 274.390) Filter (q & B) r_work=0.1223 r_free=0.1483 | n_water=446 | time (s): 3.080 (total time: 277.470) Filter (dist only) r_work=0.1223 r_free=0.1483 | n_water=446 | time (s): 36.350 (total time: 313.820) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.033136 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 38.590546 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 0.1453 0.0221 0.006 0.9 3.5 0.5 0.0 0 1.017 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.32 14.53 2.21 3.623 22.087 38.591 3.726 12.26 14.17 1.90 4.015 21.933 38.591 3.665 Individual atomic B min max mean iso aniso Overall: 9.26 110.13 21.69 2.30 216 1757 Protein: 9.26 110.13 17.30 2.31 0 1519 Water: 11.74 72.46 36.55 N/A 216 230 Other: 19.94 32.00 26.57 N/A 0 8 Chain A: 9.26 110.13 19.95 N/A 0 1757 Chain S: 16.21 64.80 35.86 N/A 216 0 Histogram: Values Number of atoms 9.26 - 19.35 1230 19.35 - 29.43 285 29.43 - 39.52 214 39.52 - 49.61 137 49.61 - 59.70 74 59.70 - 69.78 20 69.78 - 79.87 7 79.87 - 89.96 3 89.96 - 100.05 1 100.05 - 110.13 2 =========================== Idealize ADP of riding H ========================== r_work=0.1226 r_free=0.1417 r_work=0.1227 r_free=0.1417 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1227 r_free = 0.1417 target_work(ml) = 3.665 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1221 r_free = 0.1418 target_work(ml) = 3.662 | | occupancies: max = 1.00 min = 0.14 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= 0.1221 r_free= 0.1418 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.662418 | | target function (ml) not normalized (work): 305053.789871 | | target function (ml) not normalized (free): 16099.847076 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1230 0.1221 0.1418 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1552 0.1551 0.1607 n_refl.: 87589 remove outliers: r(all,work,free)=0.1552 0.1551 0.1607 n_refl.: 87589 overall B=-0.02 to atoms: r(all,work,free)=0.1550 0.1548 0.1606 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1221 0.1213 0.1383 n_refl.: 87589 remove outliers: r(all,work,free)=0.1218 0.1209 0.1383 n_refl.: 87581 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 90.62 82 5 0.3939 292.553 261.057 0.467 1.000 0.297 11.894-9.307 97.06 95 4 0.2399 473.770 460.687 0.852 1.002 0.280 9.237-7.194 98.18 209 7 0.2379 387.530 386.952 0.944 1.002 0.180 7.162-5.571 100.00 427 22 0.2014 294.858 284.497 0.915 1.002 0.160 5.546-4.326 100.00 867 58 0.1108 404.767 400.278 0.951 1.002 0.157 4.315-3.360 100.00 1859 96 0.0935 384.936 382.203 0.995 1.002 0.154 3.356-2.611 100.00 3867 181 0.1162 252.883 251.125 1.000 1.002 0.062 2.608-2.026 99.99 8198 413 0.1057 167.638 166.594 1.012 1.001 0.000 2.025-1.573 100.00 17313 902 0.1034 81.866 82.006 1.027 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1307 36.303 35.869 1.022 0.998 0.000 1.221-1.150 99.97 13689 708 0.2135 22.873 21.476 0.982 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0413 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1209 r_free=0.1383 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1209 r_free=0.1383 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1209 r_free=0.1383 | n_water=446 | time (s): 2.030 (total time: 2.030) Filter (dist) r_work=0.1209 r_free=0.1383 | n_water=445 | time (s): 35.720 (total time: 37.750) Filter (q & B) r_work=0.1209 r_free=0.1382 | n_water=444 | time (s): 2.730 (total time: 40.480) Compute maps r_work=0.1209 r_free=0.1382 | n_water=444 | time (s): 1.310 (total time: 41.790) Filter (map) r_work=0.1234 r_free=0.1377 | n_water=311 | time (s): 2.640 (total time: 44.430) Find peaks r_work=0.1234 r_free=0.1377 | n_water=311 | time (s): 0.550 (total time: 44.980) Add new water r_work=0.1296 r_free=0.1438 | n_water=476 | time (s): 2.620 (total time: 47.600) Refine new water occ: r_work=0.1222 r_free=0.1367 adp: r_work=0.1222 r_free=0.1370 occ: r_work=0.1207 r_free=0.1358 adp: r_work=0.1205 r_free=0.1358 occ: r_work=0.1197 r_free=0.1355 adp: r_work=0.1193 r_free=0.1351 ADP+occupancy (water only), MIN, final r_work=0.1193 r_free=0.1351 r_work=0.1193 r_free=0.1351 | n_water=476 | time (s): 235.400 (total time: 283.000) Filter (q & B) r_work=0.1199 r_free=0.1355 | n_water=444 | time (s): 2.970 (total time: 285.970) Filter (dist only) r_work=0.1199 r_free=0.1354 | n_water=443 | time (s): 38.350 (total time: 324.320) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.943002 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 48.444661 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 0.1205 0.1389 0.0185 0.006 0.9 3.2 0.5 0.0 0 0.972 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.05 13.89 1.85 3.437 21.578 48.445 3.649 11.84 13.79 1.94 3.912 21.429 48.445 3.631 Individual atomic B min max mean iso aniso Overall: 9.23 105.70 21.24 2.18 214 1756 Protein: 9.23 105.70 16.94 2.18 0 1519 Water: 11.54 71.22 35.95 N/A 214 229 Other: 18.44 28.51 23.58 N/A 0 8 Chain A: 9.23 105.70 19.53 N/A 0 1756 Chain S: 15.99 57.34 35.27 N/A 214 0 Histogram: Values Number of atoms 9.23 - 18.88 1229 18.88 - 28.52 286 28.52 - 38.17 208 38.17 - 47.82 134 47.82 - 57.46 77 57.46 - 67.11 22 67.11 - 76.76 9 76.76 - 86.40 2 86.40 - 96.05 1 96.05 - 105.70 2 =========================== Idealize ADP of riding H ========================== r_work=0.1184 r_free=0.1379 r_work=0.1185 r_free=0.1379 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1185 r_free = 0.1379 target_work(ml) = 3.631 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1182 r_free = 0.1374 target_work(ml) = 3.629 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87581 (all), 4.91 % free)------------| | | | r_work= 0.1182 r_free= 0.1374 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.629457 | | target function (ml) not normalized (work): 302279.308694 | | target function (ml) not normalized (free): 15973.250628 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1191 0.1182 0.1374 n_refl.: 87581 re-set all scales: r(all,work,free)=0.1507 0.1505 0.1572 n_refl.: 87581 remove outliers: r(all,work,free)=0.1507 0.1505 0.1572 n_refl.: 87581 overall B=-0.01 to atoms: r(all,work,free)=0.1505 0.1503 0.1571 n_refl.: 87581 bulk-solvent and scaling: r(all,work,free)=0.1191 0.1182 0.1376 n_refl.: 87581 remove outliers: r(all,work,free)=0.1189 0.1179 0.1376 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 88.54 80 5 0.3957 290.524 254.488 0.451 0.999 0.320 11.894-9.307 94.12 92 4 0.2313 473.404 451.911 0.830 1.001 0.232 9.237-7.194 97.73 208 7 0.2463 385.506 381.287 0.919 1.001 0.150 7.162-5.571 100.00 427 22 0.2157 294.858 284.000 0.909 1.001 0.140 5.546-4.326 100.00 867 58 0.1148 404.767 399.857 0.950 1.001 0.140 4.315-3.360 100.00 1859 96 0.0938 384.936 382.673 0.995 1.001 0.140 3.356-2.611 100.00 3867 181 0.1150 252.883 251.211 1.002 1.001 0.090 2.608-2.026 99.99 8198 413 0.1018 167.638 166.783 1.012 1.001 0.000 2.025-1.573 100.00 17313 902 0.0970 81.866 82.135 1.026 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1250 36.303 35.918 1.019 1.000 0.000 1.221-1.150 99.97 13689 708 0.2124 22.873 21.456 0.975 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0306 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1179 r_free=0.1376 After: r_work=0.1180 r_free=0.1376 ================================== NQH flips ================================== r_work=0.1180 r_free=0.1376 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=0.1180 r_free=0.1376 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1180 r_free=0.1376 | n_water=443 | time (s): 1.700 (total time: 1.700) Filter (dist) r_work=0.1180 r_free=0.1376 | n_water=443 | time (s): 37.240 (total time: 38.940) Filter (q & B) r_work=0.1180 r_free=0.1375 | n_water=441 | time (s): 3.480 (total time: 42.420) Compute maps r_work=0.1180 r_free=0.1375 | n_water=441 | time (s): 1.410 (total time: 43.830) Filter (map) r_work=0.1206 r_free=0.1385 | n_water=324 | time (s): 3.460 (total time: 47.290) Find peaks r_work=0.1206 r_free=0.1385 | n_water=324 | time (s): 0.610 (total time: 47.900) Add new water r_work=0.1254 r_free=0.1425 | n_water=476 | time (s): 3.560 (total time: 51.460) Refine new water occ: r_work=0.1190 r_free=0.1368 adp: r_work=0.1190 r_free=0.1369 occ: r_work=0.1179 r_free=0.1360 adp: r_work=0.1177 r_free=0.1360 occ: r_work=0.1171 r_free=0.1352 adp: r_work=0.1168 r_free=0.1352 ADP+occupancy (water only), MIN, final r_work=0.1168 r_free=0.1352 r_work=0.1168 r_free=0.1352 | n_water=476 | time (s): 252.450 (total time: 303.910) Filter (q & B) r_work=0.1175 r_free=0.1361 | n_water=441 | time (s): 3.060 (total time: 306.970) Filter (dist only) r_work=0.1175 r_free=0.1360 | n_water=439 | time (s): 38.040 (total time: 345.010) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.969179 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 43.274425 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 0.1202 0.1393 0.0191 0.007 1.1 6.4 0.5 0.0 0 0.985 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.02 13.93 1.91 3.302 21.072 43.274 3.638 12.03 13.91 1.88 3.383 21.039 43.274 3.632 Individual atomic B min max mean iso aniso Overall: 9.26 103.42 20.96 2.08 212 1754 Protein: 9.26 103.42 16.84 2.08 0 1519 Water: 11.53 70.92 35.15 N/A 212 227 Other: 18.39 27.28 23.41 N/A 0 8 Chain A: 9.26 103.42 19.40 N/A 0 1754 Chain S: 15.64 55.07 33.89 N/A 212 0 Histogram: Values Number of atoms 9.26 - 18.68 1227 18.68 - 28.09 291 28.09 - 37.51 202 37.51 - 46.92 139 46.92 - 56.34 66 56.34 - 65.76 25 65.76 - 75.17 12 75.17 - 84.59 1 84.59 - 94.00 1 94.00 - 103.42 2 =========================== Idealize ADP of riding H ========================== r_work=0.1203 r_free=0.1391 r_work=0.1204 r_free=0.1391 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1204 r_free = 0.1391 target_work(ml) = 3.632 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1200 r_free = 0.1390 target_work(ml) = 3.631 | | 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= 0.1200 r_free= 0.1390 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.630782 | | target function (ml) not normalized (work): 302367.879564 | | target function (ml) not normalized (free): 15989.048908 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1418 0.1445 5.6777 5.6665| | 2: 3.57 - 2.84 1.00 2888 124 0.1119 0.1479 5.2155 5.2783| | 3: 2.83 - 2.48 1.00 2820 163 0.1206 0.1316 5.0163 5.0431| | 4: 2.47 - 2.25 1.00 2825 136 0.1035 0.1184 4.7254 4.778| | 5: 2.25 - 2.09 1.00 2756 127 0.1005 0.1144 4.6684 4.7431| | 6: 2.09 - 1.97 1.00 2846 113 0.0982 0.1239 4.3722 4.5181| | 7: 1.97 - 1.87 1.00 2787 165 0.0998 0.1178 4.0891 4.1753| | 8: 1.87 - 1.79 1.00 2789 144 0.1033 0.1257 4.0077 4.0954| | 9: 1.79 - 1.72 1.00 2745 138 0.0976 0.1308 3.7366 3.9238| | 10: 1.72 - 1.66 1.00 2831 160 0.1016 0.1279 3.6472 3.7754| | 11: 1.66 - 1.61 1.00 2712 147 0.0984 0.1102 3.5867 3.6175| | 12: 1.61 - 1.56 1.00 2773 144 0.0932 0.1222 3.3621 3.5074| | 13: 1.56 - 1.52 1.00 2745 130 0.0980 0.1094 3.3471 3.4434| | 14: 1.52 - 1.48 1.00 2803 134 0.0997 0.1096 3.2704 3.3493| | 15: 1.48 - 1.45 1.00 2738 128 0.1015 0.1348 3.1758 3.3239| | 16: 1.45 - 1.42 1.00 2756 161 0.1069 0.1279 3.156 3.258| | 17: 1.42 - 1.39 1.00 2785 139 0.1119 0.1273 3.1199 3.2303| | 18: 1.39 - 1.36 1.00 2741 179 0.1165 0.1389 3.0962 3.2798| | 19: 1.36 - 1.34 1.00 2807 134 0.1224 0.1593 3.1006 3.2964| | 20: 1.34 - 1.32 1.00 2696 147 0.1314 0.1490 3.0895 3.1472| | 21: 1.32 - 1.30 1.00 2785 112 0.1421 0.1632 3.0955 3.1721| | 22: 1.29 - 1.27 1.00 2704 152 0.1475 0.1934 3.0905 3.2919| | 23: 1.27 - 1.26 1.00 2802 156 0.1575 0.1857 3.1064 3.2175| | 24: 1.26 - 1.24 1.00 2744 132 0.1630 0.1784 3.0991 3.2022| | 25: 1.24 - 1.22 1.00 2733 148 0.1798 0.2320 3.1126 3.296| | 26: 1.22 - 1.21 1.00 2727 135 0.1864 0.1778 3.1283 3.1963| | 27: 1.21 - 1.19 1.00 2814 148 0.2009 0.2087 3.1449 3.1479| | 28: 1.19 - 1.18 1.00 2671 147 0.2142 0.2334 3.1431 3.1709| | 29: 1.18 - 1.16 1.00 2800 134 0.2215 0.2379 3.13 3.2257| | 30: 1.16 - 1.15 1.00 2739 148 0.2378 0.2488 3.1195 3.1691| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 0.94 9.31 1.00 0.97 6593.50| | 2: 3.57 - 2.84 2888 124 0.92 13.69 1.01 0.97 6593.50| | 3: 2.83 - 2.48 2820 163 0.88 17.92 0.98 0.97 5527.30| | 4: 2.47 - 2.25 2825 136 0.91 14.98 1.00 0.98 2777.91| | 5: 2.25 - 2.09 2756 127 0.89 17.28 1.01 0.98 2777.91| | 6: 2.09 - 1.97 2846 113 0.91 14.00 1.02 0.98 1632.07| | 7: 1.97 - 1.87 2787 165 0.94 11.08 1.02 0.98 654.82| | 8: 1.87 - 1.79 2789 144 0.91 14.77 1.00 0.98 654.82| | 9: 1.79 - 1.72 2745 138 0.93 11.58 0.98 0.97 351.41| | 10: 1.72 - 1.66 2831 160 0.93 12.42 0.98 0.97 290.65| | 11: 1.66 - 1.61 2712 147 0.93 13.06 0.98 0.97 277.26| | 12: 1.61 - 1.56 2773 144 0.95 9.63 0.99 0.97 150.98| | 13: 1.56 - 1.52 2745 130 0.94 11.23 1.02 0.97 150.98| | 14: 1.52 - 1.48 2803 134 0.94 11.40 1.02 0.98 134.61| | 15: 1.48 - 1.45 2738 128 0.95 10.47 1.01 0.99 104.63| | 16: 1.45 - 1.42 2756 161 0.94 11.64 1.01 0.99 104.63| | 17: 1.42 - 1.39 2785 139 0.94 11.51 1.01 0.99 94.65| | 18: 1.39 - 1.36 2741 179 0.94 11.80 1.01 0.99 88.88| | 19: 1.36 - 1.34 2807 134 0.94 12.40 1.00 0.99 88.88| | 20: 1.34 - 1.32 2696 147 0.94 12.53 0.99 0.97 83.86| | 21: 1.32 - 1.30 2785 112 0.93 13.42 0.98 0.97 83.51| | 22: 1.29 - 1.27 2704 152 0.93 13.96 0.98 0.96 83.62| | 23: 1.27 - 1.26 2802 156 0.92 14.91 0.97 0.95 84.16| | 24: 1.26 - 1.24 2744 132 0.92 15.04 0.97 0.95 84.16| | 25: 1.24 - 1.22 2733 148 0.91 16.40 0.96 0.94 85.54| | 26: 1.22 - 1.21 2727 135 0.90 18.18 1.02 0.94 87.07| | 27: 1.21 - 1.19 2814 148 0.89 18.77 1.02 0.94 87.07| | 28: 1.19 - 1.18 2671 147 0.88 20.22 1.01 0.93 90.17| | 29: 1.18 - 1.16 2800 134 0.88 20.53 0.99 0.93 91.34| | 30: 1.16 - 1.15 2739 148 0.86 21.97 0.98 0.93 91.34| |alpha: min = 0.93 max = 0.99 mean = 0.97| |beta: min = 83.51 max = 6593.50 mean = 1024.96| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.96 mean = 14.19| |phase err.(test): min = 0.00 max = 87.32 mean = 14.31| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1209 0.1200 0.1390 n_refl.: 87575 re-set all scales: r(all,work,free)=0.1521 0.1520 0.1585 n_refl.: 87575 remove outliers: r(all,work,free)=0.1521 0.1520 0.1585 n_refl.: 87575 overall B=-0.01 to atoms: r(all,work,free)=0.1520 0.1518 0.1583 n_refl.: 87575 bulk-solvent and scaling: r(all,work,free)=0.1209 0.1200 0.1390 n_refl.: 87575 remove outliers: r(all,work,free)=0.1209 0.1200 0.1390 n_refl.: 87574 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.4114 290.524 254.792 0.442 1.000 0.297 11.894-9.307 93.14 91 4 0.2437 473.432 449.508 0.828 1.002 0.216 9.237-7.194 97.73 208 7 0.2584 385.506 377.907 0.903 1.002 0.155 7.162-5.571 100.00 427 22 0.2240 294.858 283.844 0.900 1.002 0.150 5.546-4.326 100.00 867 58 0.1198 404.767 400.123 0.950 1.002 0.116 4.315-3.360 100.00 1859 96 0.0983 384.936 382.609 0.995 1.002 0.107 3.356-2.611 100.00 3867 181 0.1179 252.883 251.065 1.002 1.001 0.043 2.608-2.026 99.99 8198 413 0.1042 167.638 166.718 1.013 1.000 0.000 2.025-1.573 100.00 17313 902 0.0989 81.866 82.118 1.027 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1230 36.303 35.934 1.022 0.996 0.000 1.221-1.150 99.97 13689 708 0.2116 22.873 21.497 0.980 0.993 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0252 ================= 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 : 0.2608 0.1953 0.081 5.213 8.8 119.3 19.9 258 0.000 1_bss: 0.1639 0.1766 0.081 5.213 9.0 119.5 20.1 258 0.000 1_settarget: 0.1639 0.1766 0.081 5.213 9.0 119.5 20.1 258 0.000 1_nqh: 0.1639 0.1766 0.081 5.213 9.0 119.5 20.1 258 0.000 1_weight: 0.1639 0.1766 0.081 5.213 9.0 119.5 20.1 258 0.000 1_xyzrec: 0.1212 0.1470 0.007 0.961 9.0 119.5 20.1 258 0.124 1_adp: 0.1241 0.1540 0.007 0.961 8.4 118.4 20.9 258 0.124 1_regHadp: 0.1245 0.1544 0.007 0.961 8.4 118.4 20.9 258 0.124 1_occ: 0.1245 0.1548 0.007 0.961 8.4 118.4 20.9 258 0.124 2_bss: 0.1243 0.1542 0.007 0.961 8.6 118.6 21.1 258 0.124 2_settarget: 0.1243 0.1542 0.007 0.961 8.6 118.6 21.1 258 0.124 2_updatecdl: 0.1243 0.1542 0.007 0.967 8.6 118.6 21.1 258 0.124 2_nqh: 0.1245 0.1543 0.007 0.967 8.6 118.6 21.1 258 0.127 2_sol: 0.1233 0.1492 0.007 0.967 8.6 118.6 23.3 427 n/a 2_weight: 0.1233 0.1492 0.007 0.967 8.6 118.6 23.3 427 n/a 2_xyzrec: 0.1229 0.1519 0.007 0.884 8.6 118.6 23.3 427 n/a 2_adp: 0.1199 0.1488 0.007 0.884 8.8 114.4 23.0 427 n/a 2_regHadp: 0.1199 0.1487 0.007 0.884 8.8 114.4 23.0 427 n/a 2_occ: 0.1200 0.1486 0.007 0.884 8.8 114.4 23.0 427 n/a 3_bss: 0.1195 0.1481 0.007 0.884 8.8 114.4 23.0 427 n/a 3_settarget: 0.1195 0.1481 0.007 0.884 8.8 114.4 23.0 427 n/a 3_updatecdl: 0.1195 0.1481 0.007 0.884 8.8 114.4 23.0 427 n/a 3_nqh: 0.1195 0.1481 0.007 0.884 8.8 114.4 23.0 427 n/a 3_sol: 0.1223 0.1483 0.007 0.884 8.8 114.4 22.0 446 n/a 3_weight: 0.1223 0.1483 0.007 0.884 8.8 114.4 22.0 446 n/a 3_xyzrec: 0.1232 0.1453 0.006 0.923 8.8 114.4 22.0 446 n/a 3_adp: 0.1226 0.1417 0.006 0.923 9.3 110.1 21.7 446 n/a 3_regHadp: 0.1227 0.1417 0.006 0.923 9.3 110.1 21.7 446 n/a 3_occ: 0.1221 0.1418 0.006 0.923 9.3 110.1 21.7 446 n/a 4_bss: 0.1209 0.1383 0.006 0.923 9.2 110.1 21.7 446 n/a 4_settarget: 0.1209 0.1383 0.006 0.923 9.2 110.1 21.7 446 n/a 4_updatecdl: 0.1209 0.1383 0.006 0.923 9.2 110.1 21.7 446 n/a 4_nqh: 0.1209 0.1383 0.006 0.923 9.2 110.1 21.7 446 n/a 4_sol: 0.1199 0.1354 0.006 0.923 9.2 110.1 21.5 443 n/a 4_weight: 0.1199 0.1354 0.006 0.923 9.2 110.1 21.5 443 n/a 4_xyzrec: 0.1205 0.1389 0.006 0.945 9.2 110.1 21.5 443 n/a 4_adp: 0.1184 0.1379 0.006 0.945 9.2 105.7 21.2 443 n/a 4_regHadp: 0.1185 0.1379 0.006 0.945 9.2 105.7 21.2 443 n/a 4_occ: 0.1182 0.1374 0.006 0.945 9.2 105.7 21.2 443 n/a 5_bss: 0.1179 0.1376 0.006 0.945 9.2 105.7 21.2 443 n/a 5_settarget: 0.1179 0.1376 0.006 0.945 9.2 105.7 21.2 443 n/a 5_updatecdl: 0.1179 0.1376 0.006 0.946 9.2 105.7 21.2 443 n/a 5_setrh: 0.1180 0.1376 0.006 0.946 9.2 105.7 21.2 443 n/a 5_nqh: 0.1180 0.1376 0.006 0.946 9.2 105.7 21.2 443 n/a 5_sol: 0.1175 0.1360 0.006 0.946 9.2 105.7 21.0 439 n/a 5_weight: 0.1175 0.1360 0.006 0.946 9.2 105.7 21.0 439 n/a 5_xyzrec: 0.1202 0.1393 0.007 1.057 9.2 105.7 21.0 439 n/a 5_adp: 0.1203 0.1391 0.007 1.057 9.3 103.4 21.0 439 n/a 5_regHadp: 0.1204 0.1391 0.007 1.057 9.3 103.4 21.0 439 n/a 5_occ: 0.1200 0.1390 0.007 1.057 9.3 103.4 21.0 439 n/a end: 0.1200 0.1390 0.007 1.057 9.3 103.4 20.9 439 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_6109584_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_6109584_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.8000 Refinement macro-cycles (run) : 3592.3900 Write final files (write_after_run_outputs) : 58.2300 Total : 3655.4200 Total CPU time: 61.51 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:13:11 PST -0800 (1735452791.12 s) Start R-work = 0.1639, R-free = 0.1766 Final R-work = 0.1200, R-free = 0.1390 =============================================================================== Job complete usr+sys time: 3785.54 seconds wall clock time: 68 minutes 19.29 seconds (4099.29 seconds total)