Starting phenix.refine on Fri Dec 27 17:58:26 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.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.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" 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" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" } 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 } pdb_interpretation { nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } 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 } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } 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: 1.76, per 1000 atoms: 0.52 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: 0.57 Conformation dependent library (CDL) restraints added in 214.3 milliseconds Time building geometry restraints manager: 0.78 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 1.850 nonbonded pdb=" O LEU A 58 " pdb=" H LYS A 62 " model vdw 1.837 1.850 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 nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } 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 } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } 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 = 27.605573 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 0.1606 0.1737 0.0130 0.002 0.5 4.2 0.0 0.0 0 0.125 0.1551 0.1693 0.0142 0.002 0.5 4.2 0.0 0.0 0 0.250 0.1438 0.1601 0.0163 0.002 0.5 3.8 0.0 0.0 0 0.500 0.1366 0.1549 0.0183 0.002 0.5 3.5 0.0 0.0 0 0.750 0.1354 0.1544 0.0190 0.002 0.5 3.5 0.0 0.0 0 1.000 0.1347 0.1543 0.0196 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1295 0.1511 0.0216 0.002 0.6 3.5 0.5 0.0 0 2.000 0.1272 0.1500 0.0228 0.003 0.6 3.2 0.5 0.0 0 3.000 0.1255 0.1488 0.0233 0.003 0.7 3.2 0.5 0.0 0 4.000 0.1246 0.1484 0.0238 0.004 0.7 3.2 0.5 0.0 0 5.000 0.1239 0.1477 0.0238 0.004 0.8 3.2 0.5 0.0 0 6.000 0.1234 0.1477 0.0243 0.005 0.8 3.5 0.5 0.0 0 7.000 0.1231 0.1472 0.0241 0.005 0.8 3.5 0.5 0.0 0 8.000 0.1228 0.1474 0.0246 0.006 0.9 3.8 0.5 0.0 0 9.000 0.1229 0.1474 0.0246 0.006 0.9 3.8 0.5 0.0 0 10.000 0.1224 0.1473 0.0249 0.007 0.9 3.8 0.5 0.0 0 11.000 0.1226 0.1476 0.0250 0.007 0.9 3.5 0.5 0.6 0 12.000 0.1221 0.1470 0.0250 0.008 1.0 3.5 0.5 0.6 0 13.803 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1221 0.1470 0.0250 0.008 1.0 3.5 0.5 0.6 0 13.803 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.21 14.70 2.50 3.013 19.049 2025.489 0.017 12.21 14.70 2.49 2.995 19.049 60.765 0.017 12.28 14.67 2.39 2.668 19.047 253.186 0.017 12.62 15.23 2.61 2.740 19.203 1012.744 0.016 12.47 15.44 2.97 3.280 19.593 2025.489 0.016 12.33 15.41 3.07 3.293 19.609 3038.233 0.015 12.24 15.38 3.14 3.287 19.598 4050.977 0.015 12.24 15.38 3.15 3.288 19.577 5063.722 0.015 12.16 15.39 3.23 3.427 19.662 6076.466 0.015 12.14 15.39 3.25 3.292 19.574 7089.210 0.015 12.16 15.46 3.30 3.331 19.581 8101.955 0.015 12.12 15.44 3.32 3.399 19.614 9114.699 0.015 12.13 15.52 3.39 3.583 19.704 10127.443 0.015 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 253.186 Accepted refinement result: 12.28 14.67 2.39 2.668 19.047 253.186 0.017 Individual atomic B min max mean iso aniso Overall: 9.04 119.43 20.07 3.31 0 1785 Protein: 9.04 114.98 16.98 3.32 0 1519 Water: 11.45 119.43 38.22 N/A 0 258 Other: 19.69 26.58 22.04 N/A 0 8 Chain A: 9.04 119.43 20.07 N/A 0 1785 Histogram: Values Number of atoms 9.04 - 20.08 1272 20.08 - 31.12 227 31.12 - 42.16 125 42.16 - 53.20 94 53.20 - 64.23 42 64.23 - 75.27 11 75.27 - 86.31 7 86.31 - 97.35 4 97.35 - 108.39 1 108.39 - 119.43 2 =========================== Idealize ADP of riding H ========================== r_work=0.1228 r_free=0.1467 r_work=0.1230 r_free=0.1471 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1230 r_free = 0.1471 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1224 r_free = 0.1461 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87593 (all), 4.90 % free)------------| | | | r_work= 0.1224 r_free= 0.1461 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.016716 | | target function (ls_wunit_k1) not normalized (work): 1392.425515 | | target function (ls_wunit_k1) not normalized (free): 109.475379 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1235 0.1224 0.1461 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1665 0.1666 0.1690 n_refl.: 87593 remove outliers: r(all,work,free)=0.1665 0.1666 0.1690 n_refl.: 87593 overall B=0.04 to atoms: r(all,work,free)=0.1672 0.1673 0.1695 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1233 0.1221 0.1452 n_refl.: 87593 remove outliers: r(all,work,free)=0.1232 0.1221 0.1452 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 0.3512 302.068 281.890 0.648 1.003 0.375 11.894-9.307 99.02 97 4 0.1610 483.896 472.267 0.923 1.003 0.371 9.237-7.194 100.00 213 7 0.1905 395.768 389.254 0.963 1.003 0.350 7.162-5.571 100.00 427 22 0.1825 297.002 291.322 0.935 1.003 0.262 5.546-4.326 100.00 867 58 0.0991 407.710 405.016 0.964 1.003 0.207 4.315-3.360 100.00 1859 96 0.0867 387.735 386.677 1.007 1.003 0.180 3.356-2.611 100.00 3867 181 0.1171 254.722 253.630 1.009 1.002 0.048 2.608-2.026 99.99 8198 413 0.1014 168.857 168.138 1.019 1.001 0.000 2.025-1.573 100.00 17313 902 0.1104 82.461 82.662 1.026 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1447 36.567 36.074 1.019 0.996 0.000 1.221-1.150 99.97 13689 708 0.2246 23.040 21.521 0.981 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0562 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1221 r_free=0.1452 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=0.1223 r_free=0.1453 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1223 r_free=0.1453 | n_water=258 | time (s): 1.530 (total time: 1.530) Filter (dist) r_work=0.1231 r_free=0.1451 | n_water=250 | time (s): 20.440 (total time: 21.970) Filter (q & B) r_work=0.1233 r_free=0.1453 | n_water=247 | time (s): 2.670 (total time: 24.640) Compute maps r_work=0.1233 r_free=0.1453 | n_water=247 | time (s): 1.200 (total time: 25.840) Filter (map) r_work=0.1255 r_free=0.1455 | n_water=224 | time (s): 2.680 (total time: 28.520) Find peaks r_work=0.1255 r_free=0.1455 | n_water=224 | time (s): 0.470 (total time: 28.990) Add new water r_work=0.1397 r_free=0.1619 | n_water=430 | time (s): 2.770 (total time: 31.760) Refine new water occ: r_work=0.1302 r_free=0.1491 adp: r_work=0.1220 r_free=0.1437 occ: r_work=0.1234 r_free=0.1426 adp: r_work=0.1200 r_free=0.1410 occ: r_work=0.1202 r_free=0.1407 adp: r_work=0.1193 r_free=0.1400 ADP+occupancy (water only), MIN, final r_work=0.1193 r_free=0.1400 r_work=0.1193 r_free=0.1400 | n_water=430 | time (s): 52.950 (total time: 84.710) Filter (q & B) r_work=0.1196 r_free=0.1402 | n_water=414 | time (s): 2.500 (total time: 87.210) Filter (dist only) r_work=0.1196 r_free=0.1401 | n_water=413 | time (s): 34.510 (total time: 121.720) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 28.730954 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1479.450848 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 0.1657 0.1766 0.0109 0.001 0.4 7.4 0.0 0.0 0 0.125 0.1549 0.1669 0.0121 0.001 0.4 6.4 0.0 0.0 0 0.250 0.1416 0.1562 0.0146 0.001 0.4 5.8 0.0 0.0 0 0.500 0.1357 0.1516 0.0159 0.001 0.5 4.8 0.0 0.0 0 0.750 0.1316 0.1486 0.0169 0.002 0.5 5.1 0.0 0.0 0 1.000 0.1311 0.1482 0.0171 0.002 0.5 4.8 0.0 0.0 0 1.000 0.1254 0.1445 0.0191 0.002 0.6 4.5 0.5 0.0 0 2.000 0.1232 0.1435 0.0203 0.003 0.6 4.5 0.5 0.0 0 3.000 0.1220 0.1431 0.0212 0.003 0.7 4.5 0.5 0.0 0 4.000 0.1211 0.1424 0.0212 0.004 0.7 4.5 0.5 0.0 0 5.000 0.1209 0.1426 0.0216 0.004 0.7 4.2 0.5 0.0 0 6.000 0.1202 0.1415 0.0214 0.005 0.8 4.8 0.5 0.0 0 7.000 0.1197 0.1411 0.0214 0.005 0.8 5.4 0.5 0.0 0 8.000 0.1194 0.1408 0.0215 0.006 0.8 4.8 0.5 0.0 0 9.000 0.1192 0.1410 0.0218 0.006 0.9 4.8 0.5 0.0 0 10.000 0.1190 0.1406 0.0216 0.007 0.9 5.1 0.5 0.6 0 11.000 0.1188 0.1406 0.0218 0.007 0.9 5.4 0.5 0.6 0 12.000 0.1187 0.1408 0.0220 0.008 0.9 5.4 0.5 0.6 0 13.000 0.1185 0.1407 0.0222 0.008 1.0 4.8 0.5 0.6 0 14.365 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1190 0.1406 0.0216 0.007 0.9 5.1 0.5 0.6 0 11.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.90 14.06 2.16 3.775 21.738 1479.451 0.016 11.90 14.06 2.16 3.775 21.738 44.384 0.016 11.90 14.06 2.16 3.774 21.738 184.931 0.016 12.09 14.48 2.39 3.617 21.752 739.725 0.015 12.06 14.84 2.78 3.446 22.018 1479.451 0.015 11.96 14.86 2.90 3.495 21.901 2219.176 0.014 11.80 14.75 2.94 3.512 21.889 2958.902 0.014 11.72 14.70 2.99 3.516 21.902 3698.627 0.014 11.73 14.76 3.03 3.488 22.085 4438.353 0.014 11.69 14.72 3.03 3.508 22.048 5178.078 0.014 11.66 14.73 3.07 3.518 22.033 5917.803 0.014 11.64 14.74 3.10 3.528 22.041 6657.529 0.014 11.65 14.82 3.16 3.551 22.108 7397.254 0.014 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 184.931 Accepted refinement result: 11.90 14.06 2.16 3.774 21.738 184.931 0.016 Individual atomic B min max mean iso aniso Overall: 9.08 115.02 22.12 3.31 189 1751 Protein: 9.08 115.02 17.02 3.32 0 1519 Water: 11.49 76.69 40.90 N/A 189 224 Other: 19.73 26.62 22.08 N/A 0 8 Chain A: 9.08 115.02 19.42 N/A 0 1751 Chain S: 14.36 60.00 47.17 N/A 189 0 Histogram: Values Number of atoms 9.08 - 19.67 1259 19.67 - 30.27 241 30.27 - 40.86 165 40.86 - 51.45 134 51.45 - 62.05 119 62.05 - 72.64 11 72.64 - 83.24 5 83.24 - 93.83 4 93.83 - 104.42 0 104.42 - 115.02 2 =========================== Idealize ADP of riding H ========================== r_work=0.1190 r_free=0.1406 r_work=0.1190 r_free=0.1406 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1190 r_free = 0.1406 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1189 r_free = 0.1406 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1189 r_free= 0.1406 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.015074 | | target function (ls_wunit_k1) not normalized (work): 1255.632714 | | target function (ls_wunit_k1) not normalized (free): 104.068897 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1199 0.1189 0.1406 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1580 0.1579 0.1631 n_refl.: 87592 remove outliers: r(all,work,free)=0.1580 0.1579 0.1631 n_refl.: 87592 overall B=0.01 to atoms: r(all,work,free)=0.1583 0.1582 0.1633 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1197 0.1187 0.1398 n_refl.: 87592 remove outliers: r(all,work,free)=0.1196 0.1186 0.1398 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 93.75 85 5 0.3346 300.613 276.253 0.590 1.002 0.350 11.894-9.307 99.02 97 4 0.1623 483.896 477.053 0.920 1.003 0.337 9.237-7.194 100.00 213 7 0.1786 395.768 394.336 0.982 1.003 0.274 7.162-5.571 100.00 427 22 0.1561 297.002 292.666 0.937 1.003 0.229 5.546-4.326 100.00 867 58 0.0890 407.710 404.448 0.961 1.003 0.194 4.315-3.360 100.00 1859 96 0.0791 387.735 386.776 1.005 1.002 0.180 3.356-2.611 100.00 3867 181 0.1093 254.722 253.802 1.010 1.002 0.110 2.608-2.026 99.99 8198 413 0.1012 168.857 168.268 1.021 1.001 0.000 2.025-1.573 100.00 17313 902 0.1093 82.461 82.665 1.030 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1441 36.567 36.102 1.023 0.997 0.000 1.221-1.150 99.97 13689 708 0.2253 23.040 21.547 0.986 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0204 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1186 r_free=0.1398 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=0.1186 r_free=0.1398 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1186 r_free=0.1398 | n_water=413 | time (s): 2.100 (total time: 2.100) Filter (dist) r_work=0.1185 r_free=0.1401 | n_water=411 | time (s): 34.950 (total time: 37.050) Filter (q & B) r_work=0.1185 r_free=0.1401 | n_water=411 | time (s): 1.040 (total time: 38.090) Compute maps r_work=0.1185 r_free=0.1401 | n_water=411 | time (s): 1.770 (total time: 39.860) Filter (map) r_work=0.1220 r_free=0.1397 | n_water=289 | time (s): 3.310 (total time: 43.170) Find peaks r_work=0.1220 r_free=0.1397 | n_water=289 | time (s): 0.720 (total time: 43.890) Add new water r_work=0.1329 r_free=0.1514 | n_water=462 | time (s): 2.980 (total time: 46.870) Refine new water occ: r_work=0.1243 r_free=0.1425 adp: r_work=0.1244 r_free=0.1425 occ: r_work=0.1221 r_free=0.1405 adp: r_work=0.1220 r_free=0.1405 occ: r_work=0.1204 r_free=0.1386 adp: r_work=0.1198 r_free=0.1385 ADP+occupancy (water only), MIN, final r_work=0.1198 r_free=0.1385 r_work=0.1198 r_free=0.1385 | n_water=462 | time (s): 162.880 (total time: 209.750) Filter (q & B) r_work=0.1203 r_free=0.1387 | n_water=432 | time (s): 3.320 (total time: 213.070) Filter (dist only) r_work=0.1204 r_free=0.1386 | n_water=430 | time (s): 37.010 (total time: 250.080) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.787584 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 48.188523 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 0.1234 0.1351 0.0117 0.002 0.6 4.5 0.5 0.0 0 0.089 0.1188 0.1321 0.0133 0.003 0.7 3.5 0.5 0.0 0 0.268 0.1170 0.1313 0.0142 0.004 0.8 3.5 0.5 0.0 0 0.536 0.1162 0.1310 0.0148 0.005 0.9 3.2 0.5 0.0 0 0.804 0.1159 0.1310 0.0151 0.006 1.0 3.5 0.5 0.0 0 1.073 0.1156 0.1307 0.0151 0.007 1.0 3.5 0.5 0.6 0 1.341 0.1155 0.1311 0.0157 0.007 1.1 3.5 0.5 0.6 0 1.609 0.1152 0.1313 0.0161 0.008 1.1 3.5 0.5 0.6 0 1.877 0.1161 0.1310 0.0148 0.006 0.9 3.2 0.5 0.0 0 0.894 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1156 0.1307 0.0151 0.007 1.0 3.5 0.5 0.6 0 1.341 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.56 13.07 1.51 3.778 21.275 48.189 3.621 11.56 13.07 1.51 3.778 21.275 1.446 3.621 11.57 13.08 1.51 3.763 21.275 6.024 3.621 11.62 13.21 1.58 3.710 21.261 24.094 3.617 11.63 13.26 1.64 3.730 21.230 48.189 3.615 11.55 13.23 1.68 3.755 21.220 72.283 3.609 11.52 13.22 1.71 3.765 21.214 96.377 3.606 11.48 13.22 1.74 3.784 21.202 120.471 3.603 11.47 13.24 1.77 3.799 21.196 144.566 3.602 11.44 13.21 1.77 3.809 21.192 168.660 3.600 11.44 13.22 1.79 3.822 21.184 192.754 3.599 11.41 13.18 1.77 3.826 21.183 216.848 3.597 11.41 13.21 1.79 3.837 21.180 240.943 3.598 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.446 Accepted refinement result: 11.56 13.07 1.51 3.778 21.275 1.446 3.621 Individual atomic B min max mean iso aniso Overall: 9.09 115.03 21.26 3.31 209 1748 Protein: 9.09 115.03 17.03 3.32 0 1519 Water: 11.50 76.71 36.19 N/A 209 221 Other: 19.74 26.63 22.09 N/A 0 8 Chain A: 9.09 115.03 19.38 N/A 0 1748 Chain S: 14.37 60.01 36.99 N/A 209 0 Histogram: Values Number of atoms 9.09 - 19.68 1261 19.68 - 30.28 281 30.28 - 40.87 208 40.87 - 51.47 125 51.47 - 62.06 60 62.06 - 72.66 11 72.66 - 83.25 5 83.25 - 93.84 4 93.84 - 104.44 0 104.44 - 115.03 2 =========================== Idealize ADP of riding H ========================== r_work=0.1156 r_free=0.1307 r_work=0.1156 r_free=0.1307 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1156 r_free = 0.1307 target_work(ml) = 3.621 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1148 r_free = 0.1312 target_work(ml) = 3.615 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87590 (all), 4.90 % free)------------| | | | r_work= 0.1148 r_free= 0.1312 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.615472 | | target function (ml) not normalized (work): 301147.138051 | | target function (ml) not normalized (free): 15855.465786 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1156 0.1148 0.1312 n_refl.: 87590 re-set all scales: r(all,work,free)=0.1499 0.1498 0.1553 n_refl.: 87590 remove outliers: r(all,work,free)=0.1499 0.1498 0.1553 n_refl.: 87590 overall B=-0.00 to atoms: r(all,work,free)=0.1498 0.1497 0.1553 n_refl.: 87590 bulk-solvent and scaling: r(all,work,free)=0.1153 0.1145 0.1310 n_refl.: 87590 remove outliers: r(all,work,free)=0.1151 0.1143 0.1310 n_refl.: 87584 ======================== 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 0.3741 297.963 274.519 0.518 1.001 0.310 11.894-9.307 98.04 96 4 0.2140 484.022 466.744 0.886 1.002 0.297 9.237-7.194 98.18 209 7 0.2219 387.223 387.598 0.962 1.002 0.220 7.162-5.571 100.00 427 22 0.2072 297.002 286.914 0.924 1.003 0.186 5.546-4.326 100.00 867 58 0.1079 407.710 403.277 0.965 1.002 0.165 4.315-3.360 100.00 1859 96 0.0937 387.735 385.145 1.003 1.002 0.160 3.356-2.611 100.00 3867 181 0.1151 254.722 252.655 1.007 1.002 0.034 2.608-2.026 99.99 8198 413 0.0934 168.857 168.048 1.023 1.001 0.000 2.025-1.573 100.00 17313 902 0.0902 82.461 82.777 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1260 36.567 36.155 1.027 0.997 0.000 1.221-1.150 99.97 13689 708 0.2165 23.040 21.580 0.989 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0107 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1143 r_free=0.1310 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=0.1143 r_free=0.1310 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1143 r_free=0.1310 | n_water=430 | time (s): 2.570 (total time: 2.570) Filter (dist) r_work=0.1143 r_free=0.1310 | n_water=430 | time (s): 44.060 (total time: 46.630) Filter (q & B) r_work=0.1143 r_free=0.1309 | n_water=429 | time (s): 3.960 (total time: 50.590) Compute maps r_work=0.1143 r_free=0.1309 | n_water=429 | time (s): 1.910 (total time: 52.500) Filter (map) r_work=0.1174 r_free=0.1312 | n_water=315 | time (s): 4.080 (total time: 56.580) Find peaks r_work=0.1174 r_free=0.1312 | n_water=315 | time (s): 0.710 (total time: 57.290) Add new water r_work=0.1251 r_free=0.1403 | n_water=479 | time (s): 3.750 (total time: 61.040) Refine new water occ: r_work=0.1172 r_free=0.1338 adp: r_work=0.1173 r_free=0.1339 occ: r_work=0.1155 r_free=0.1321 adp: r_work=0.1155 r_free=0.1321 occ: r_work=0.1142 r_free=0.1306 adp: r_work=0.1139 r_free=0.1305 ADP+occupancy (water only), MIN, final r_work=0.1139 r_free=0.1305 r_work=0.1139 r_free=0.1305 | n_water=479 | time (s): 308.220 (total time: 369.260) Filter (q & B) r_work=0.1145 r_free=0.1310 | n_water=444 | time (s): 3.950 (total time: 373.210) Filter (dist only) r_work=0.1146 r_free=0.1308 | n_water=443 | time (s): 46.680 (total time: 419.890) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.820100 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 46.999565 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1209 0.1348 0.0139 0.002 0.6 4.2 0.5 0.0 0 0.091 0.1171 0.1325 0.0154 0.003 0.8 3.5 0.5 0.0 0 0.273 0.1157 0.1315 0.0158 0.005 0.9 3.8 0.5 0.0 0 0.546 0.1151 0.1314 0.0163 0.006 1.0 3.8 0.5 0.0 0 0.819 0.1146 0.1314 0.0168 0.006 1.0 3.8 0.5 0.0 0 1.092 0.1144 0.1312 0.0168 0.007 1.1 3.8 0.5 0.0 0 1.365 0.1142 0.1314 0.0172 0.008 1.1 3.8 0.5 0.0 0 1.638 0.1141 0.1315 0.0175 0.009 1.1 3.8 0.5 0.0 0 1.911 0.1149 0.1314 0.0164 0.006 1.0 3.5 0.5 0.0 0 0.910 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1144 0.1312 0.0168 0.007 1.1 3.8 0.5 0.0 0 1.365 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.44 13.12 1.68 3.779 21.182 47.000 3.614 11.44 13.12 1.68 3.779 21.182 1.410 3.614 11.45 13.13 1.68 3.769 21.182 5.875 3.614 11.52 13.22 1.70 3.711 21.169 23.500 3.612 11.49 13.24 1.75 3.737 21.153 47.000 3.609 11.48 13.27 1.79 3.754 21.133 70.499 3.606 11.41 13.21 1.80 3.769 21.133 93.999 3.602 11.38 13.20 1.82 3.780 21.128 117.499 3.599 11.39 13.25 1.86 3.798 21.112 140.999 3.599 11.37 13.24 1.87 3.810 21.107 164.498 3.598 11.35 13.22 1.87 3.817 21.107 187.998 3.596 11.34 13.22 1.88 3.826 21.104 211.498 3.596 11.33 13.21 1.88 3.832 21.103 234.998 3.594 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.410 Accepted refinement result: 11.44 13.12 1.68 3.779 21.182 1.410 3.614 Individual atomic B min max mean iso aniso Overall: 9.09 115.03 21.10 3.31 224 1746 Protein: 9.09 115.03 17.03 3.32 0 1519 Water: 11.50 76.70 35.03 N/A 224 219 Other: 19.74 26.63 22.09 N/A 0 8 Chain A: 9.09 115.03 19.37 N/A 0 1746 Chain S: 14.37 60.01 34.54 N/A 224 0 Histogram: Values Number of atoms 9.09 - 19.68 1264 19.68 - 30.28 293 30.28 - 40.87 223 40.87 - 51.46 120 51.46 - 62.06 48 62.06 - 72.65 11 72.65 - 83.25 5 83.25 - 93.84 4 93.84 - 104.43 0 104.43 - 115.03 2 =========================== Idealize ADP of riding H ========================== r_work=0.1144 r_free=0.1312 r_work=0.1144 r_free=0.1312 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1144 r_free = 0.1312 target_work(ml) = 3.614 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1138 r_free = 0.1310 target_work(ml) = 3.611 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87584 (all), 4.91 % free)------------| | | | r_work= 0.1138 r_free= 0.1310 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.611468 | | target function (ml) not normalized (work): 300791.938240 | | target function (ml) not normalized (free): 15858.278492 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1146 0.1138 0.1310 n_refl.: 87584 re-set all scales: r(all,work,free)=0.1472 0.1472 0.1508 n_refl.: 87584 remove outliers: r(all,work,free)=0.1472 0.1472 0.1508 n_refl.: 87584 overall B=-0.01 to atoms: r(all,work,free)=0.1471 0.1471 0.1507 n_refl.: 87584 bulk-solvent and scaling: r(all,work,free)=0.1143 0.1135 0.1308 n_refl.: 87584 remove outliers: r(all,work,free)=0.1141 0.1133 0.1308 n_refl.: 87579 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 90.62 82 5 0.3953 289.127 261.446 0.473 1.001 0.312 11.894-9.307 95.10 93 4 0.2370 472.136 464.730 0.864 1.002 0.254 9.237-7.194 98.18 209 7 0.2347 387.223 379.704 0.927 1.003 0.210 7.162-5.571 100.00 427 22 0.2132 297.002 286.519 0.915 1.003 0.125 5.546-4.326 100.00 867 58 0.1134 407.710 403.020 0.962 1.003 0.120 4.315-3.360 100.00 1859 96 0.0918 387.735 385.398 1.003 1.003 0.120 3.356-2.611 100.00 3867 181 0.1109 254.722 252.755 1.010 1.002 0.024 2.608-2.026 99.99 8198 413 0.0919 168.857 168.129 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0882 82.461 82.797 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1251 36.567 36.172 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2166 23.040 21.586 0.990 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0152 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1133 r_free=0.1308 After: r_work=0.1134 r_free=0.1308 ================================== NQH flips ================================== r_work=0.1134 r_free=0.1308 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=0.1134 r_free=0.1308 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1134 r_free=0.1308 | n_water=443 | time (s): 2.600 (total time: 2.600) Filter (dist) r_work=0.1133 r_free=0.1310 | n_water=442 | time (s): 46.490 (total time: 49.090) Filter (q & B) r_work=0.1134 r_free=0.1311 | n_water=439 | time (s): 3.950 (total time: 53.040) Compute maps r_work=0.1134 r_free=0.1311 | n_water=439 | time (s): 1.910 (total time: 54.950) Filter (map) r_work=0.1160 r_free=0.1316 | n_water=341 | time (s): 4.030 (total time: 58.980) Find peaks r_work=0.1160 r_free=0.1316 | n_water=341 | time (s): 0.750 (total time: 59.730) Add new water r_work=0.1211 r_free=0.1368 | n_water=499 | time (s): 3.910 (total time: 63.640) Refine new water occ: r_work=0.1152 r_free=0.1317 adp: r_work=0.1153 r_free=0.1320 occ: r_work=0.1139 r_free=0.1300 adp: r_work=0.1138 r_free=0.1303 occ: r_work=0.1129 r_free=0.1285 adp: r_work=0.1126 r_free=0.1288 ADP+occupancy (water only), MIN, final r_work=0.1126 r_free=0.1288 r_work=0.1126 r_free=0.1288 | n_water=499 | time (s): 307.630 (total time: 371.270) Filter (q & B) r_work=0.1134 r_free=0.1296 | n_water=451 | time (s): 4.070 (total time: 375.340) Filter (dist only) r_work=0.1135 r_free=0.1295 | n_water=450 | time (s): 47.600 (total time: 422.940) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.770767 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 46.068521 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 0.1219 0.1346 0.0127 0.004 0.7 6.7 0.0 0.0 0 0.089 0.1170 0.1316 0.0146 0.004 0.8 6.7 0.0 0.0 0 0.266 0.1151 0.1305 0.0154 0.005 0.9 6.1 0.5 0.0 0 0.531 0.1143 0.1300 0.0156 0.006 1.0 5.8 0.5 0.0 0 0.797 0.1137 0.1296 0.0158 0.006 1.1 5.8 0.5 0.0 0 1.062 0.1135 0.1295 0.0160 0.007 1.1 5.4 0.5 0.0 0 1.328 0.1134 0.1295 0.0161 0.008 1.1 5.4 0.5 0.0 0 1.594 0.1133 0.1295 0.0162 0.008 1.1 5.8 0.5 0.0 0 1.859 0.1141 0.1298 0.0157 0.006 1.0 5.8 0.5 0.0 0 0.885 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1133 0.1295 0.0162 0.008 1.1 5.8 0.5 0.0 0 1.859 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.33 12.95 1.62 3.779 21.208 46.069 3.607 11.33 12.95 1.62 3.779 21.208 1.382 3.607 11.34 12.95 1.61 3.771 21.208 5.759 3.607 11.40 13.02 1.63 3.711 21.196 23.034 3.604 11.38 13.06 1.68 3.738 21.178 46.069 3.603 11.35 13.08 1.72 3.757 21.161 69.103 3.599 11.30 13.04 1.74 3.771 21.157 92.137 3.595 11.27 13.01 1.74 3.779 21.157 115.171 3.592 11.25 13.02 1.77 3.792 21.152 138.206 3.591 11.24 13.03 1.79 3.806 21.145 161.240 3.590 11.23 13.04 1.81 3.817 21.140 184.274 3.589 11.23 13.04 1.81 3.829 21.135 207.308 3.589 11.21 13.02 1.81 3.834 21.135 230.343 3.588 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 5.759 Accepted refinement result: 11.34 12.95 1.61 3.771 21.208 5.759 3.607 Individual atomic B min max mean iso aniso Overall: 9.09 114.94 21.15 3.29 233 1744 Protein: 9.09 114.94 17.02 3.29 0 1519 Water: 11.50 76.69 35.06 N/A 233 217 Other: 19.72 26.60 22.08 N/A 0 8 Chain A: 9.09 114.94 19.33 N/A 0 1744 Chain S: 14.36 60.00 34.76 N/A 233 0 Histogram: Values Number of atoms 9.09 - 19.67 1266 19.67 - 30.26 298 30.26 - 40.84 217 40.84 - 51.43 122 51.43 - 62.01 52 62.01 - 72.60 10 72.60 - 83.18 6 83.18 - 93.77 4 93.77 - 104.35 0 104.35 - 114.94 2 =========================== Idealize ADP of riding H ========================== r_work=0.1134 r_free=0.1295 r_work=0.1134 r_free=0.1295 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1134 r_free = 0.1295 target_work(ml) = 3.607 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1130 r_free = 0.1293 target_work(ml) = 3.606 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87579 (all), 4.91 % free)------------| | | | r_work= 0.1130 r_free= 0.1293 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.605568 | | target function (ml) not normalized (work): 300282.546928 | | target function (ml) not normalized (free): 15823.225517 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2921 171 0.1334 0.1324 5.648 5.6069| | 2: 3.57 - 2.84 1.00 2888 124 0.1062 0.1414 5.1626 5.235| | 3: 2.83 - 2.48 1.00 2820 163 0.1087 0.1211 4.9456 4.9723| | 4: 2.47 - 2.25 1.00 2825 136 0.0897 0.1049 4.6327 4.6806| | 5: 2.25 - 2.09 1.00 2756 127 0.0868 0.0975 4.5805 4.6353| | 6: 2.09 - 1.97 1.00 2846 113 0.0857 0.0986 4.2706 4.3608| | 7: 1.97 - 1.87 1.00 2787 165 0.0885 0.1115 3.9796 4.089| | 8: 1.87 - 1.79 1.00 2789 144 0.0911 0.1107 3.8922 3.9909| | 9: 1.79 - 1.72 1.00 2745 138 0.0864 0.1194 3.6469 3.8366| | 10: 1.72 - 1.66 1.00 2831 160 0.0913 0.1218 3.5667 3.7359| | 11: 1.66 - 1.61 1.00 2712 147 0.0866 0.1023 3.498 3.5586| | 12: 1.61 - 1.56 1.00 2773 144 0.0901 0.1171 3.3303 3.4723| | 13: 1.56 - 1.52 1.00 2745 130 0.0946 0.1041 3.3107 3.3983| | 14: 1.52 - 1.48 1.00 2803 134 0.0982 0.1051 3.242 3.3319| | 15: 1.48 - 1.45 1.00 2738 128 0.1004 0.1217 3.1553 3.2654| | 16: 1.45 - 1.42 1.00 2756 161 0.1055 0.1236 3.1379 3.2349| | 17: 1.42 - 1.39 1.00 2785 139 0.1138 0.1278 3.1195 3.2189| | 18: 1.39 - 1.36 1.00 2741 179 0.1196 0.1327 3.1039 3.2434| | 19: 1.36 - 1.34 1.00 2807 134 0.1260 0.1569 3.1128 3.2703| | 20: 1.34 - 1.32 1.00 2696 147 0.1364 0.1449 3.1136 3.1499| | 21: 1.32 - 1.30 1.00 2785 112 0.1466 0.1529 3.1142 3.1135| | 22: 1.29 - 1.27 1.00 2704 152 0.1557 0.1996 3.1238 3.3021| | 23: 1.27 - 1.26 1.00 2802 156 0.1644 0.1787 3.1352 3.1994| | 24: 1.26 - 1.24 1.00 2744 132 0.1703 0.1853 3.129 3.2373| | 25: 1.24 - 1.22 1.00 2733 148 0.1876 0.2171 3.1439 3.2692| | 26: 1.22 - 1.21 1.00 2727 135 0.1908 0.1760 3.1507 3.206| | 27: 1.21 - 1.19 1.00 2814 148 0.2069 0.2166 3.1723 3.1664| | 28: 1.19 - 1.18 1.00 2671 147 0.2199 0.2305 3.1681 3.1768| | 29: 1.18 - 1.16 1.00 2800 134 0.2264 0.2381 3.15 3.2301| | 30: 1.16 - 1.15 1.00 2739 148 0.2441 0.2438 3.1448 3.1664| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.58 2921 171 0.95 8.54 1.00 0.97 5768.09| | 2: 3.57 - 2.84 2888 124 0.93 12.53 1.01 0.97 5768.09| | 3: 2.83 - 2.48 2820 163 0.90 16.43 0.99 0.98 4819.44| | 4: 2.47 - 2.25 2825 136 0.92 13.44 1.00 0.98 2373.17| | 5: 2.25 - 2.09 2756 127 0.90 15.64 1.01 0.98 2373.17| | 6: 2.09 - 1.97 2846 113 0.92 12.37 1.02 0.98 1371.85| | 7: 1.97 - 1.87 2787 165 0.95 9.31 1.02 0.98 517.86| | 8: 1.87 - 1.79 2789 144 0.93 12.68 1.00 0.98 517.86| | 9: 1.79 - 1.72 2745 138 0.94 10.08 0.98 0.98 293.53| | 10: 1.72 - 1.66 2831 160 0.94 11.21 0.98 0.98 248.60| | 11: 1.66 - 1.61 2712 147 0.93 11.83 0.98 0.98 238.09| | 12: 1.61 - 1.56 2773 144 0.95 8.94 0.99 0.98 138.97| | 13: 1.56 - 1.52 2745 130 0.95 10.44 1.03 0.98 138.97| | 14: 1.52 - 1.48 2803 134 0.94 10.76 1.02 0.98 124.54| | 15: 1.48 - 1.45 2738 128 0.95 9.90 1.02 0.98 98.14| | 16: 1.45 - 1.42 2756 161 0.94 11.05 1.02 0.98 98.14| | 17: 1.42 - 1.39 2785 139 0.95 10.89 1.01 0.98 89.18| | 18: 1.39 - 1.36 2741 179 0.94 11.50 1.01 0.98 84.00| | 19: 1.36 - 1.34 2807 134 0.94 11.83 1.00 0.98 84.00| | 20: 1.34 - 1.32 2696 147 0.94 12.11 0.98 0.97 80.27| | 21: 1.32 - 1.30 2785 112 0.94 13.10 0.98 0.97 80.01| | 22: 1.29 - 1.27 2704 152 0.93 13.64 0.98 0.96 80.45| | 23: 1.27 - 1.26 2802 156 0.92 14.85 0.97 0.95 82.72| | 24: 1.26 - 1.24 2744 132 0.92 14.86 0.96 0.95 82.72| | 25: 1.24 - 1.22 2733 148 0.91 16.37 0.96 0.94 84.69| | 26: 1.22 - 1.21 2727 135 0.90 18.11 1.03 0.93 86.89| | 27: 1.21 - 1.19 2814 148 0.89 18.76 1.02 0.93 86.89| | 28: 1.19 - 1.18 2671 147 0.88 20.35 1.01 0.93 90.23| | 29: 1.18 - 1.16 2800 134 0.88 20.44 0.99 0.93 91.49| | 30: 1.16 - 1.15 2739 148 0.86 21.97 0.98 0.93 91.49| |alpha: min = 0.93 max = 0.98 mean = 0.97| |beta: min = 80.01 max = 5768.09 mean = 891.36| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.99 mean = 13.45| |phase err.(test): min = 0.00 max = 89.95 mean = 13.45| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1138 0.1130 0.1293 n_refl.: 87579 re-set all scales: r(all,work,free)=0.1462 0.1463 0.1481 n_refl.: 87579 remove outliers: r(all,work,free)=0.1462 0.1463 0.1481 n_refl.: 87579 overall B=-0.01 to atoms: r(all,work,free)=0.1461 0.1462 0.1481 n_refl.: 87579 bulk-solvent and scaling: r(all,work,free)=0.1138 0.1130 0.1293 n_refl.: 87579 remove outliers: r(all,work,free)=0.1136 0.1128 0.1293 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 0.4043 286.534 248.783 0.433 1.002 0.300 11.894-9.307 93.14 91 4 0.2281 476.061 454.491 0.852 1.003 0.228 9.237-7.194 97.73 208 7 0.2317 388.949 380.168 0.923 1.003 0.160 7.162-5.571 100.00 427 22 0.2131 297.002 286.465 0.910 1.003 0.108 5.546-4.326 100.00 867 58 0.1115 407.710 403.386 0.961 1.003 0.100 4.315-3.360 100.00 1859 96 0.0920 387.735 385.666 1.002 1.003 0.087 3.356-2.611 100.00 3867 181 0.1103 254.722 253.066 1.011 1.002 0.024 2.608-2.026 99.99 8198 413 0.0908 168.857 168.312 1.026 1.001 0.000 2.025-1.573 100.00 17313 902 0.0884 82.461 82.844 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1250 36.567 36.193 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2168 23.040 21.596 0.989 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0146 ================= 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: 0.1221 0.1470 0.008 0.980 9.0 119.5 20.1 258 0.130 1_adp: 0.1228 0.1467 0.008 0.980 9.0 119.4 20.1 258 0.130 1_regHadp: 0.1230 0.1471 0.008 0.980 9.0 119.4 20.1 258 0.130 1_occ: 0.1224 0.1461 0.008 0.980 9.0 119.4 20.1 258 0.130 2_bss: 0.1221 0.1452 0.008 0.980 9.1 119.5 20.1 258 0.130 2_settarget: 0.1221 0.1452 0.008 0.980 9.1 119.5 20.1 258 0.130 2_updatecdl: 0.1221 0.1452 0.008 0.985 9.1 119.5 20.1 258 0.130 2_nqh: 0.1223 0.1453 0.008 0.985 9.1 119.5 20.1 258 0.133 2_sol: 0.1196 0.1401 0.008 0.985 9.1 115.0 22.1 413 n/a 2_weight: 0.1196 0.1401 0.008 0.985 9.1 115.0 22.1 413 n/a 2_xyzrec: 0.1190 0.1406 0.007 0.894 9.1 115.0 22.1 413 n/a 2_adp: 0.1190 0.1406 0.007 0.894 9.1 115.0 22.1 413 n/a 2_regHadp: 0.1190 0.1406 0.007 0.894 9.1 115.0 22.1 413 n/a 2_occ: 0.1189 0.1406 0.007 0.894 9.1 115.0 22.1 413 n/a 3_bss: 0.1186 0.1398 0.007 0.894 9.1 115.0 22.1 413 n/a 3_settarget: 0.1186 0.1398 0.007 0.894 9.1 115.0 22.1 413 n/a 3_updatecdl: 0.1186 0.1398 0.007 0.893 9.1 115.0 22.1 413 n/a 3_nqh: 0.1186 0.1398 0.007 0.893 9.1 115.0 22.1 413 n/a 3_sol: 0.1204 0.1386 0.007 0.893 9.1 115.0 21.3 430 n/a 3_weight: 0.1204 0.1386 0.007 0.893 9.1 115.0 21.3 430 n/a 3_xyzrec: 0.1156 0.1307 0.007 1.021 9.1 115.0 21.3 430 n/a 3_adp: 0.1156 0.1307 0.007 1.021 9.1 115.0 21.3 430 n/a 3_regHadp: 0.1156 0.1307 0.007 1.021 9.1 115.0 21.3 430 n/a 3_occ: 0.1148 0.1312 0.007 1.021 9.1 115.0 21.3 430 n/a 4_bss: 0.1143 0.1310 0.007 1.021 9.1 115.0 21.3 430 n/a 4_settarget: 0.1143 0.1310 0.007 1.021 9.1 115.0 21.3 430 n/a 4_updatecdl: 0.1143 0.1310 0.007 1.024 9.1 115.0 21.3 430 n/a 4_nqh: 0.1143 0.1310 0.007 1.024 9.1 115.0 21.3 430 n/a 4_sol: 0.1146 0.1308 0.007 1.024 9.1 115.0 21.1 443 n/a 4_weight: 0.1146 0.1308 0.007 1.024 9.1 115.0 21.1 443 n/a 4_xyzrec: 0.1144 0.1312 0.007 1.058 9.1 115.0 21.1 443 n/a 4_adp: 0.1144 0.1312 0.007 1.058 9.1 115.0 21.1 443 n/a 4_regHadp: 0.1144 0.1312 0.007 1.058 9.1 115.0 21.1 443 n/a 4_occ: 0.1138 0.1310 0.007 1.058 9.1 115.0 21.1 443 n/a 5_bss: 0.1133 0.1308 0.007 1.058 9.1 115.0 21.1 443 n/a 5_settarget: 0.1133 0.1308 0.007 1.058 9.1 115.0 21.1 443 n/a 5_updatecdl: 0.1133 0.1308 0.007 1.059 9.1 115.0 21.1 443 n/a 5_setrh: 0.1134 0.1308 0.007 1.059 9.1 115.0 21.1 443 n/a 5_nqh: 0.1134 0.1308 0.007 1.059 9.1 115.0 21.1 443 n/a 5_sol: 0.1135 0.1295 0.007 1.059 9.1 115.0 21.1 450 n/a 5_weight: 0.1135 0.1295 0.007 1.059 9.1 115.0 21.1 450 n/a 5_xyzrec: 0.1133 0.1295 0.008 1.093 9.1 115.0 21.1 450 n/a 5_adp: 0.1134 0.1295 0.008 1.093 9.1 114.9 21.1 450 n/a 5_regHadp: 0.1134 0.1295 0.008 1.093 9.1 114.9 21.1 450 n/a 5_occ: 0.1130 0.1293 0.008 1.093 9.1 114.9 21.1 450 n/a end: 0.1128 0.1293 0.008 1.093 9.1 114.9 21.1 450 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_6109584_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_6109584_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.6700 Refinement macro-cycles (run) : 14566.2900 Write final files (write_after_run_outputs) : 66.1400 Total : 14636.1000 Total CPU time: 4.07 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:23:47 PST -0800 (1735367027.85 s) Start R-work = 0.1639, R-free = 0.1766 Final R-work = 0.1128, R-free = 0.1293 =============================================================================== Job complete usr+sys time: 14770.21 seconds wall clock time: 267 minutes 11.84 seconds (16031.84 seconds total)