Starting phenix.refine on Fri Dec 27 17:58:27 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2359181.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.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" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2359181.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2359181.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } 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 2 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.62, per 1000 atoms: 0.48 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: 0.29 Conformation dependent library (CDL) restraints added in 104.1 milliseconds Time building geometry restraints manager: 0.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.65 - 0.90: 484 0.90 - 1.15: 1140 1.15 - 1.41: 607 1.41 - 1.66: 864 1.66 - 1.91: 58 Bond restraints: 3153 Sorted by residual: bond pdb=" C GLN A 95 " pdb=" O GLN A 95 " ideal model delta sigma weight residual 1.236 0.915 0.321 1.15e-02 7.56e+03 7.78e+02 bond pdb=" C ALA A 6 " pdb=" O ALA A 6 " ideal model delta sigma weight residual 1.235 1.487 -0.252 1.28e-02 6.10e+03 3.87e+02 bond pdb=" N MET A 134 " pdb=" CA MET A 134 " ideal model delta sigma weight residual 1.457 1.677 -0.220 1.32e-02 5.74e+03 2.77e+02 bond pdb=" N BGLU A 90 " pdb=" CA BGLU A 90 " ideal model delta sigma weight residual 1.459 1.651 -0.192 1.17e-02 7.31e+03 2.68e+02 bond pdb=" NE ARG A 156 " pdb=" CZ ARG A 156 " ideal model delta sigma weight residual 1.326 1.503 -0.177 1.10e-02 8.26e+03 2.60e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.32: 3461 5.32 - 10.64: 1796 10.64 - 15.96: 477 15.96 - 21.28: 40 21.28 - 26.60: 3 Bond angle restraints: 5777 Sorted by residual: angle pdb=" N ILE A 21 " pdb=" CA ILE A 21 " pdb=" CB ILE A 21 " ideal model delta sigma weight residual 110.50 123.40 -12.90 6.30e-01 2.52e+00 4.19e+02 angle pdb=" O VAL A 123 " pdb=" C VAL A 123 " pdb=" N THR A 124 " ideal model delta sigma weight residual 123.00 140.57 -17.57 1.14e+00 7.69e-01 2.37e+02 angle pdb=" N VAL A 20 " pdb=" CA VAL A 20 " pdb=" C VAL A 20 " ideal model delta sigma weight residual 110.62 123.94 -13.32 1.02e+00 9.61e-01 1.70e+02 angle pdb=" CA GLY A 174 " pdb=" C GLY A 174 " pdb=" O GLY A 174 " ideal model delta sigma weight residual 122.23 113.29 8.94 6.90e-01 2.10e+00 1.68e+02 angle pdb=" OD1BASN A 97 " pdb=" CG BASN A 97 " pdb=" ND2BASN A 97 " ideal model delta sigma weight residual 122.60 135.43 -12.83 1.00e+00 1.00e+00 1.65e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 944 17.56 - 35.12: 119 35.12 - 52.68: 33 52.68 - 70.23: 13 70.23 - 87.79: 2 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA THR A 125 " pdb=" C THR A 125 " pdb=" N HIS A 126 " pdb=" CA HIS A 126 " ideal model delta harmonic sigma weight residual 180.00 153.94 26.06 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA VAL A 123 " pdb=" C VAL A 123 " pdb=" N THR A 124 " pdb=" CA THR A 124 " ideal model delta harmonic sigma weight residual 180.00 160.87 19.13 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA BLYS A 99 " pdb=" C BLYS A 99 " pdb=" N GLY A 100 " pdb=" CA GLY A 100 " ideal model delta harmonic sigma weight residual 180.00 161.32 18.68 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.210: 102 0.210 - 0.420: 67 0.420 - 0.630: 48 0.630 - 0.840: 18 0.840 - 1.050: 8 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA ASP A 49 " pdb=" N ASP A 49 " pdb=" C ASP A 49 " pdb=" CB ASP A 49 " both_signs ideal model delta sigma weight residual False 2.51 1.46 1.05 2.00e-01 2.50e+01 2.75e+01 chirality pdb=" CB VAL A 70 " pdb=" CA VAL A 70 " pdb=" CG1 VAL A 70 " pdb=" CG2 VAL A 70 " both_signs ideal model delta sigma weight residual False -2.63 -3.62 0.99 2.00e-01 2.50e+01 2.45e+01 chirality pdb=" CA BASN A 76 " pdb=" N BASN A 76 " pdb=" C BASN A 76 " pdb=" CB BASN A 76 " both_signs ideal model delta sigma weight residual False 2.51 1.54 0.97 2.00e-01 2.50e+01 2.35e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.050 2.00e-02 2.50e+03 6.43e-02 1.24e+02 pdb=" CG PHE A 164 " 0.068 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " -0.083 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.028 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.031 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.120 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.041 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.096 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.092 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " 0.033 2.00e-02 2.50e+03 5.07e-02 7.72e+01 pdb=" CG TYR A 139 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " 0.071 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.035 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " -0.093 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.019 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " 0.015 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " -0.066 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.045 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " 0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 98 " -0.068 9.50e-02 1.11e+02 6.18e-02 7.51e+01 pdb=" NE ARG A 98 " -0.069 2.00e-02 2.50e+03 pdb=" CZ ARG A 98 " 0.112 2.00e-02 2.50e+03 pdb=" NH1 ARG A 98 " 0.071 2.00e-02 2.50e+03 pdb=" NH2 ARG A 98 " -0.047 2.00e-02 2.50e+03 pdb="HH11 ARG A 98 " -0.036 2.00e-02 2.50e+03 pdb="HH12 ARG A 98 " -0.038 2.00e-02 2.50e+03 pdb="HH21 ARG A 98 " 0.040 2.00e-02 2.50e+03 pdb="HH22 ARG A 98 " -0.030 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.21: 476 2.21 - 2.81: 7244 2.81 - 3.41: 10799 3.41 - 4.00: 15502 4.00 - 4.60: 22527 Nonbonded interactions: 56548 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.618 2.100 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.721 2.100 nonbonded pdb=" HD3 ARG A 5 " pdb="HH11 ARG A 5 " model vdw 1.761 2.270 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.803 1.850 nonbonded pdb=" O GLY A 75 " pdb=" H ALA A 79 " model vdw 1.831 1.850 ... (remaining 56543 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 6 Type Number sf(0) Gaussians S 10 15.96 2 O1- 2 8.97 3 O 551 7.97 2 N 265 6.97 2 C 957 5.97 2 H 1596 1.00 2 sf(0) = scattering factor at diffraction angle 0. =========================== Regularize ADP if needed ========================== ========================== Anomalous scatterer groups ========================= All atoms refined with f_prime=0 and f_double_prime=0. ====================== Modifying start model if requested ===================== ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 3381 n_use_u_iso = 1596 n_use_u_aniso = 1785 n_grad_site = 0 n_grad_u_iso = 0 n_grad_u_aniso = 0 n_grad_occupancy = 0 n_grad_fp = 0 n_grad_fdp = 0 total number of scatterers = 3381 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (3381 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 1596 aniso = 1785) group_adp = False (0 atoms in 0 groups) tls = False (0 atoms in 0 groups) occupancies = True (876 atoms) group_anomalous = False ============================ Non-default parameters =========================== A complete record of all parameters was written to the .eff file above. Below are only the non-defaults. #phil __ON__ refinement { electron_density_maps { map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT" mtz_label_phases = "PH2FOFCWT" fill_missing_f_obs = True } map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT_no_fill" mtz_label_phases = "PH2FOFCWT_no_fill" } map_coefficients { map_type = "mFo-DFc" mtz_label_amplitudes = "FOFCWT" mtz_label_phases = "PHFOFCWT" } map_coefficients { map_type = "anomalous" mtz_label_amplitudes = "ANOM" mtz_label_phases = "PANOM" } map { map_type = "2mFo-DFc" fill_missing_f_obs = True } map { map_type = "2mFo-DFc" } map { map_type = "mFo-DFc" } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } hydrogens { refine = individual *riding Auto } pdb_interpretation { c_beta_restraints = False 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_2359181_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1596 occupancy sum: 1438.50 (% of total atoms 46.85) Rotatable: count: 507 occupancy sum: 483.00 (% of total atoms 15.73) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2611 r_free= 0.1970 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.797071 | | target function (ml) not normalized (work): 233012.775185 | | target function (ml) not normalized (free): 11890.683060 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 49.25 - 3.58 1.00 2941 171 0.3023 0.2056 7.0457 4.944| | 2: 3.57 - 2.84 1.00 2876 122 0.2446 0.1720 4.3482 4.3455| | 3: 2.84 - 2.48 1.00 2833 165 0.2371 0.1698 4.1352 4.1587| | 4: 2.47 - 2.25 1.00 2825 136 0.2335 0.1410 3.8405 3.838| | 5: 2.25 - 2.09 1.00 2756 127 0.2501 0.1675 3.7991 3.8447| | 6: 2.09 - 1.97 1.00 2846 113 0.2559 0.1835 3.4781 3.6046| | 7: 1.97 - 1.87 1.00 2787 165 0.2537 0.2042 3.1582 3.2241| | 8: 1.87 - 1.79 1.00 2789 144 0.2474 0.2066 3.0859 3.1617| | 9: 1.79 - 1.72 1.00 2745 138 0.2452 0.2122 2.9052 3.0184| | 10: 1.72 - 1.66 1.00 2789 158 0.2361 0.2123 2.8041 2.9569| | 11: 1.66 - 1.61 1.00 2740 147 0.2499 0.1818 2.7633 2.7869| | 12: 1.61 - 1.56 1.00 2787 146 0.2566 0.1877 2.637 2.6006| | 13: 1.56 - 1.52 1.00 2745 130 0.2536 0.1881 2.5698 2.6161| | 14: 1.52 - 1.48 1.00 2803 134 0.2534 0.2063 2.505 2.6034| | 15: 1.48 - 1.45 1.00 2738 128 0.2571 0.2047 2.4305 2.4417| | 16: 1.45 - 1.42 1.00 2756 161 0.2650 0.2215 2.3888 2.4653| | 17: 1.42 - 1.39 1.00 2785 139 0.2713 0.2257 2.3419 2.4338| | 18: 1.39 - 1.36 1.00 2741 179 0.2706 0.2077 2.2887 2.3029| | 19: 1.36 - 1.34 1.00 2807 134 0.2675 0.2567 2.2534 2.3619| | 20: 1.34 - 1.32 1.00 2696 147 0.2677 0.2229 2.2103 2.2163| | 21: 1.32 - 1.30 1.00 2785 112 0.2692 0.2333 2.1743 2.2202| | 22: 1.29 - 1.27 1.00 2704 152 0.2800 0.2692 2.151 2.2953| | 23: 1.27 - 1.26 1.00 2802 156 0.2704 0.2099 2.0962 2.0779| | 24: 1.26 - 1.24 1.00 2744 132 0.2804 0.2482 2.0768 2.1215| | 25: 1.24 - 1.22 1.00 2734 148 0.2855 0.2691 2.0501 2.094| | 26: 1.22 - 1.21 1.00 2727 135 0.2845 0.2375 2.0135 2.086| | 27: 1.21 - 1.19 1.00 2814 148 0.2946 0.2595 2.0162 2.0274| | 28: 1.19 - 1.18 1.00 2671 147 0.3016 0.2695 1.9931 1.9628| | 29: 1.18 - 1.16 1.00 2800 134 0.2984 0.3014 1.9695 2.109| | 30: 1.16 - 1.15 1.00 2740 148 0.3064 0.2912 1.9282 1.9954| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 49.25 - 3.58 2941 171 0.87 18.93 0.76 0.23 1483.00| | 2: 3.57 - 2.84 2876 122 0.80 26.26 1.28 0.23 1483.00| | 3: 2.84 - 2.48 2833 165 0.74 31.96 1.24 0.23 1231.47| | 4: 2.47 - 2.25 2825 136 0.81 25.68 1.26 0.25 578.71| | 5: 2.25 - 2.09 2756 127 0.77 29.60 1.28 0.25 578.71| | 6: 2.09 - 1.97 2846 113 0.83 23.06 1.29 0.25 319.77| | 7: 1.97 - 1.87 2787 165 0.89 17.31 1.28 0.26 98.94| | 8: 1.87 - 1.79 2789 144 0.85 21.98 1.25 0.26 98.94| | 9: 1.79 - 1.72 2745 138 0.87 19.33 1.24 0.25 60.27| | 10: 1.72 - 1.66 2789 158 0.86 20.99 1.22 0.25 52.53| | 11: 1.66 - 1.61 2740 147 0.85 22.17 1.24 0.25 50.53| | 12: 1.61 - 1.56 2787 146 0.88 18.91 1.24 0.25 30.26| | 13: 1.56 - 1.52 2745 130 0.86 20.78 1.24 0.25 30.26| | 14: 1.52 - 1.48 2803 134 0.86 20.99 1.22 0.25 27.01| | 15: 1.48 - 1.45 2738 128 0.87 20.32 1.23 0.25 21.05| | 16: 1.45 - 1.42 2756 161 0.85 21.93 1.23 0.25 21.05| | 17: 1.42 - 1.39 2785 139 0.86 21.18 1.23 0.25 17.97| | 18: 1.39 - 1.36 2741 179 0.86 21.44 1.23 0.25 16.18| | 19: 1.36 - 1.34 2807 134 0.85 22.32 1.22 0.25 16.18| | 20: 1.34 - 1.32 2696 147 0.86 21.51 1.20 0.25 13.68| | 21: 1.32 - 1.30 2785 112 0.85 22.39 1.20 0.25 13.50| | 22: 1.29 - 1.27 2704 152 0.84 23.35 1.21 0.24 13.18| | 23: 1.27 - 1.26 2802 156 0.85 22.53 1.20 0.24 11.54| | 24: 1.26 - 1.24 2744 132 0.84 23.44 1.20 0.24 11.54| | 25: 1.24 - 1.22 2734 148 0.83 24.45 1.20 0.24 11.00| | 26: 1.22 - 1.21 2727 135 0.84 24.42 1.20 0.23 10.40| | 27: 1.21 - 1.19 2814 148 0.83 25.36 1.19 0.23 10.40| | 28: 1.19 - 1.18 2671 147 0.82 25.96 1.18 0.23 9.83| | 29: 1.18 - 1.16 2800 134 0.82 26.40 1.17 0.23 9.62| | 30: 1.16 - 1.15 2740 148 0.80 28.23 1.16 0.23 9.62| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 9.62 max = 1483.00 mean = 217.24| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.97 mean = 23.11| |phase err.(test): min = 0.00 max = 89.91 mean = 23.03| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.082 0.321 1557 Z= 5.432 Angle : 5.425 18.199 2118 Z= 3.832 Chirality : 0.393 1.050 243 Planarity : 0.033 0.107 284 Dihedral : 13.757 87.793 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 1.08 % Allowed : 2.70 % Favored : 96.22 % Rotamer: Outliers : 1.24 % Allowed : 4.35 % Favored : 94.41 % Cbeta Deviations : 44.86 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.28 (0.45), residues: 224 helix: -3.02 (0.38), residues: 109 sheet: -1.50 (0.82), residues: 28 loop : -0.87 (0.53), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.093 0.023 ARG A 98 TYR 0.077 0.038 TYR A 141 PHE 0.090 0.034 PHE A 119 HIS 0.071 0.024 HIS A 126 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2611 r_free= 0.1970 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.797071 | | target function (ml) not normalized (work): 233012.775185 | | target function (ml) not normalized (free): 11890.683060 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2571 0.2612 0.1970 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2571 0.2612 0.1970 n_refl.: 87602 remove outliers: r(all,work,free)=0.1989 0.1992 0.1970 n_refl.: 87594 overall B=0.22 to atoms: r(all,work,free)=0.2016 0.2019 0.1986 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1650 0.1642 0.1788 n_refl.: 87594 remove outliers: r(all,work,free)=0.1648 0.1641 0.1788 n_refl.: 87591 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 97.87 87 5 0.3852 382.080 355.337 0.675 1.003 0.408 11.894-9.307 98.04 96 4 0.1669 616.220 587.718 0.935 1.003 0.400 9.237-7.194 100.00 213 7 0.2131 501.955 493.145 0.959 1.003 0.344 7.162-5.571 100.00 427 22 0.2210 376.689 364.778 0.935 1.003 0.320 5.546-4.326 100.00 867 58 0.1289 517.101 510.369 0.960 1.003 0.229 4.315-3.360 100.00 1859 96 0.1132 491.767 487.639 1.002 1.003 0.209 3.356-2.611 100.00 3867 181 0.1458 323.065 320.043 0.999 1.002 0.043 2.608-2.026 99.99 8198 413 0.1358 214.163 212.152 1.008 1.001 0.000 2.025-1.573 100.00 17313 902 0.1645 104.586 103.888 1.012 0.999 0.000 1.573-1.221 100.00 36679 1900 0.2075 46.378 45.016 1.002 0.996 0.000 1.221-1.150 99.97 13689 708 0.2590 29.221 26.951 0.976 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0017 b_overall=0.0503 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1641 r_free=0.1788 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1641 r_free=0.1788 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.634035 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2020.734996 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1679 0.1803 0.0124 0.002 0.4 4.5 0.0 0.0 0 0.125 0.1530 0.1672 0.0142 0.001 0.4 3.8 0.0 0.0 0 0.250 0.1433 0.1593 0.0160 0.001 0.5 3.8 0.0 0.0 0 0.500 0.1390 0.1568 0.0178 0.002 0.5 3.8 0.0 0.0 0 0.750 0.1366 0.1559 0.0193 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1361 0.1559 0.0198 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1303 0.1523 0.0220 0.002 0.6 3.8 0.5 0.0 0 2.000 0.1267 0.1496 0.0229 0.003 0.6 3.5 0.5 0.0 0 3.000 0.1259 0.1493 0.0234 0.003 0.7 3.8 0.5 0.0 0 4.000 0.1250 0.1489 0.0239 0.004 0.7 3.8 0.5 0.0 0 5.000 0.1242 0.1479 0.0238 0.004 0.8 3.8 0.5 0.0 0 6.000 0.1236 0.1475 0.0240 0.005 0.8 3.5 0.5 0.0 0 7.000 0.1233 0.1473 0.0240 0.005 0.8 3.5 0.5 0.0 0 8.000 0.1231 0.1473 0.0242 0.006 0.9 3.8 0.5 0.0 0 9.000 0.1228 0.1474 0.0246 0.006 0.9 3.5 0.5 0.0 0 10.000 0.1226 0.1470 0.0244 0.007 0.9 3.8 0.5 0.0 0 11.000 0.1226 0.1475 0.0249 0.007 0.9 4.2 0.5 0.0 0 12.000 0.1224 0.1469 0.0245 0.008 1.0 4.2 0.5 0.6 0 13.317 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1224 0.1469 0.0245 0.008 1.0 4.2 0.5 0.6 0 13.317 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.24 14.69 2.45 3.012 19.077 2020.735 0.017 12.24 14.68 2.44 2.988 19.077 60.622 0.017 12.31 14.66 2.35 2.668 19.076 252.592 0.017 12.69 15.33 2.64 2.851 19.319 1010.367 0.016 12.53 15.49 2.96 3.247 19.589 2020.735 0.015 12.33 15.37 3.04 3.235 19.602 3031.102 0.015 12.27 15.34 3.08 3.294 19.632 4041.470 0.015 12.21 15.35 3.14 3.274 19.617 5051.837 0.015 12.21 15.39 3.18 3.391 19.668 6062.205 0.015 12.19 15.45 3.26 3.359 19.640 7072.572 0.015 12.19 15.50 3.31 3.392 19.648 8082.940 0.014 12.14 15.49 3.35 3.518 19.701 9093.307 0.014 12.09 15.43 3.33 3.420 19.641 10103.675 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: 252.592 Accepted refinement result: 12.31 14.66 2.35 2.668 19.076 252.592 0.017 Individual atomic B min max mean iso aniso Overall: 9.08 119.47 20.10 3.31 0 1785 Protein: 9.08 115.01 17.01 3.32 0 1519 Water: 11.48 119.47 38.25 N/A 0 258 Other: 19.74 26.61 22.08 N/A 0 8 Chain A: 9.08 119.47 20.10 N/A 0 1785 Histogram: Values Number of atoms 9.08 - 20.12 1272 20.12 - 31.16 227 31.16 - 42.20 125 42.20 - 53.24 94 53.24 - 64.28 42 64.28 - 75.31 11 75.31 - 86.35 7 86.35 - 97.39 4 97.39 - 108.43 1 108.43 - 119.47 2 =========================== Idealize ADP of riding H ========================== r_work=0.1231 r_free=0.1466 r_work=0.1232 r_free=0.1469 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1232 r_free = 0.1469 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 = 0.1227 r_free = 0.1466 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87591 (all), 4.90 % free)------------| | | | r_work= 0.1227 r_free= 0.1466 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.016523 | | target function (ls_wunit_k1) not normalized (work): 1376.269606 | | target function (ls_wunit_k1) not normalized (free): 110.589083 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1238 0.1227 0.1466 n_refl.: 87591 re-set all scales: r(all,work,free)=0.1672 0.1674 0.1691 n_refl.: 87591 remove outliers: r(all,work,free)=0.1672 0.1674 0.1691 n_refl.: 87591 overall B=0.03 to atoms: r(all,work,free)=0.1677 0.1679 0.1694 n_refl.: 87591 bulk-solvent and scaling: r(all,work,free)=0.1234 0.1223 0.1458 n_refl.: 87591 remove outliers: r(all,work,free)=0.1234 0.1223 0.1458 n_refl.: 87590 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 94.79 86 5 0.3427 297.716 278.667 0.643 1.004 0.380 11.894-9.307 98.04 96 4 0.1519 484.390 473.021 0.937 1.004 0.380 9.237-7.194 100.00 213 7 0.1860 394.570 388.723 0.966 1.004 0.345 7.162-5.571 100.00 427 22 0.1801 296.103 290.714 0.940 1.003 0.300 5.546-4.326 100.00 867 58 0.0996 406.476 403.494 0.963 1.003 0.204 4.315-3.360 100.00 1859 96 0.0866 386.561 385.536 1.007 1.003 0.190 3.356-2.611 100.00 3867 181 0.1168 253.951 252.798 1.010 1.002 0.090 2.608-2.026 99.99 8198 413 0.1028 168.346 167.662 1.019 1.001 0.000 2.025-1.573 100.00 17313 902 0.1110 82.212 82.387 1.027 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1446 36.456 35.965 1.020 0.997 0.000 1.221-1.150 99.97 13689 708 0.2250 22.970 21.462 0.984 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0406 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1223 r_free=0.1458 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=0.1224 r_free=0.1459 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1224 r_free=0.1459 | n_water=258 | time (s): 1.710 (total time: 1.710) Filter (dist) r_work=0.1232 r_free=0.1458 | n_water=252 | time (s): 20.900 (total time: 22.610) Filter (q & B) r_work=0.1234 r_free=0.1458 | n_water=249 | time (s): 2.630 (total time: 25.240) Compute maps r_work=0.1234 r_free=0.1458 | n_water=249 | time (s): 1.080 (total time: 26.320) Filter (map) r_work=0.1249 r_free=0.1462 | n_water=227 | time (s): 2.780 (total time: 29.100) Find peaks r_work=0.1249 r_free=0.1462 | n_water=227 | time (s): 0.460 (total time: 29.560) Add new water r_work=0.1393 r_free=0.1626 | n_water=435 | time (s): 2.390 (total time: 31.950) Refine new water occ: r_work=0.1298 r_free=0.1490 adp: r_work=0.1220 r_free=0.1437 occ: r_work=0.1232 r_free=0.1424 adp: r_work=0.1199 r_free=0.1410 occ: r_work=0.1203 r_free=0.1402 adp: r_work=0.1191 r_free=0.1400 ADP+occupancy (water only), MIN, final r_work=0.1191 r_free=0.1400 r_work=0.1191 r_free=0.1400 | n_water=435 | time (s): 56.020 (total time: 87.970) Filter (q & B) r_work=0.1195 r_free=0.1405 | n_water=418 | time (s): 3.570 (total time: 91.540) Filter (dist only) r_work=0.1195 r_free=0.1404 | n_water=417 | time (s): 35.850 (total time: 127.390) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 29.315470 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1464.727006 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 0.1641 0.1753 0.0112 0.001 0.4 7.7 0.0 0.0 0 0.125 0.1556 0.1679 0.0123 0.001 0.4 7.7 0.0 0.0 0 0.250 0.1422 0.1568 0.0147 0.001 0.4 6.4 0.0 0.0 0 0.500 0.1353 0.1509 0.0156 0.002 0.5 6.4 0.0 0.0 0 0.750 0.1322 0.1495 0.0173 0.002 0.5 5.1 0.0 0.0 0 1.000 0.1324 0.1499 0.0176 0.002 0.5 5.4 0.0 0.0 0 1.000 0.1253 0.1448 0.0194 0.002 0.5 4.8 0.5 0.0 0 2.000 0.1226 0.1434 0.0208 0.003 0.6 4.8 0.5 0.0 0 3.000 0.1208 0.1417 0.0209 0.003 0.7 5.4 0.5 0.0 0 4.000 0.1205 0.1421 0.0216 0.004 0.7 5.1 0.5 0.0 0 5.000 0.1202 0.1414 0.0212 0.004 0.7 6.1 0.5 0.0 0 6.000 0.1197 0.1413 0.0216 0.005 0.8 5.1 0.5 0.0 0 7.000 0.1197 0.1411 0.0214 0.005 0.8 6.1 0.5 0.0 0 8.000 0.1190 0.1405 0.0215 0.006 0.8 5.8 0.5 0.0 0 9.000 0.1187 0.1405 0.0218 0.006 0.9 5.4 0.5 0.0 0 10.000 0.1183 0.1400 0.0217 0.007 0.9 5.8 0.5 0.6 0 11.000 0.1181 0.1401 0.0220 0.007 0.9 4.8 0.5 0.6 0 12.000 0.1181 0.1401 0.0221 0.007 0.9 5.8 0.5 0.6 0 13.000 0.1180 0.1406 0.0226 0.008 1.0 4.8 0.5 0.6 0 14.658 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1183 0.1400 0.0217 0.007 0.9 5.8 0.5 0.6 0 11.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.83 14.00 2.17 3.777 21.765 1464.727 0.016 11.83 14.00 2.17 3.777 21.765 43.942 0.016 11.83 14.00 2.17 3.777 21.765 183.091 0.016 12.05 14.46 2.40 3.612 21.781 732.364 0.015 12.03 14.75 2.71 3.530 21.856 1464.727 0.015 11.90 14.71 2.81 3.470 22.143 2197.091 0.014 11.75 14.58 2.83 3.472 21.981 2929.454 0.014 11.75 14.70 2.95 3.513 22.151 3661.818 0.014 11.70 14.66 2.96 3.525 22.123 4394.181 0.014 11.69 14.70 3.01 3.547 22.131 5126.545 0.014 11.68 14.72 3.04 3.576 22.144 5858.908 0.014 11.62 14.69 3.06 3.564 22.053 6591.272 0.014 11.65 14.89 3.24 3.635 22.183 7323.635 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: 183.091 Accepted refinement result: 11.83 14.00 2.17 3.777 21.765 183.091 0.016 Individual atomic B min max mean iso aniso Overall: 9.11 115.04 22.15 3.31 190 1754 Protein: 9.11 115.04 17.04 3.32 0 1519 Water: 11.50 76.71 40.78 N/A 190 227 Other: 19.77 26.64 22.10 N/A 0 8 Chain A: 9.11 115.04 19.49 N/A 0 1754 Chain S: 13.55 60.00 46.73 N/A 190 0 Histogram: Values Number of atoms 9.11 - 19.70 1261 19.70 - 30.29 242 30.29 - 40.89 165 40.89 - 51.48 133 51.48 - 62.07 120 62.07 - 72.67 12 72.67 - 83.26 5 83.26 - 93.85 4 93.85 - 104.44 0 104.44 - 115.04 2 =========================== Idealize ADP of riding H ========================== r_work=0.1183 r_free=0.1400 r_work=0.1183 r_free=0.1400 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1183 r_free = 0.1400 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 = 0.1188 r_free = 0.1398 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87590 (all), 4.90 % free)------------| | | | r_work= 0.1188 r_free= 0.1398 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.015158 | | target function (ls_wunit_k1) not normalized (work): 1262.538105 | | target function (ls_wunit_k1) not normalized (free): 101.469945 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1198 0.1188 0.1398 n_refl.: 87590 re-set all scales: r(all,work,free)=0.1596 0.1597 0.1613 n_refl.: 87590 remove outliers: r(all,work,free)=0.1596 0.1597 0.1613 n_refl.: 87590 overall B=0.01 to atoms: r(all,work,free)=0.1597 0.1598 0.1614 n_refl.: 87590 bulk-solvent and scaling: r(all,work,free)=0.1195 0.1185 0.1392 n_refl.: 87590 remove outliers: r(all,work,free)=0.1194 0.1184 0.1392 n_refl.: 87588 ======================== 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 0.3292 297.062 272.540 0.580 1.003 0.350 11.894-9.307 98.04 96 4 0.1640 484.390 476.758 0.930 1.003 0.340 9.237-7.194 100.00 213 7 0.1726 394.570 393.191 0.981 1.003 0.310 7.162-5.571 100.00 427 22 0.1650 296.103 291.772 0.938 1.003 0.244 5.546-4.326 100.00 867 58 0.0910 406.476 403.431 0.961 1.003 0.220 4.315-3.360 100.00 1859 96 0.0790 386.561 385.772 1.004 1.003 0.190 3.356-2.611 100.00 3867 181 0.1084 253.951 252.983 1.010 1.002 0.110 2.608-2.026 99.99 8198 413 0.1002 168.346 167.811 1.021 1.001 0.000 2.025-1.573 100.00 17313 902 0.1094 82.212 82.431 1.030 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1437 36.456 35.991 1.025 0.997 0.000 1.221-1.150 99.97 13689 708 0.2255 22.970 21.480 0.988 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0087 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1184 r_free=0.1392 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1184 r_free=0.1392 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1184 r_free=0.1392 | n_water=417 | time (s): 1.640 (total time: 1.640) Filter (dist) r_work=0.1183 r_free=0.1392 | n_water=416 | time (s): 38.620 (total time: 40.260) Filter (q & B) r_work=0.1183 r_free=0.1392 | n_water=416 | time (s): 0.810 (total time: 41.070) Compute maps r_work=0.1183 r_free=0.1392 | n_water=416 | time (s): 1.490 (total time: 42.560) Filter (map) r_work=0.1223 r_free=0.1379 | n_water=285 | time (s): 3.010 (total time: 45.570) Find peaks r_work=0.1223 r_free=0.1379 | n_water=285 | time (s): 0.610 (total time: 46.180) Add new water r_work=0.1348 r_free=0.1496 | n_water=475 | time (s): 2.670 (total time: 48.850) Refine new water occ: r_work=0.1247 r_free=0.1407 adp: r_work=0.1249 r_free=0.1408 occ: r_work=0.1222 r_free=0.1389 adp: r_work=0.1222 r_free=0.1388 occ: r_work=0.1203 r_free=0.1382 adp: r_work=0.1198 r_free=0.1376 ADP+occupancy (water only), MIN, final r_work=0.1198 r_free=0.1376 r_work=0.1198 r_free=0.1376 | n_water=475 | time (s): 221.530 (total time: 270.380) Filter (q & B) r_work=0.1201 r_free=0.1377 | n_water=447 | time (s): 2.690 (total time: 273.070) Filter (dist only) r_work=0.1201 r_free=0.1374 | n_water=446 | time (s): 36.410 (total time: 309.480) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.701606 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 44.479802 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1230 0.1346 0.0116 0.002 0.6 4.8 0.5 0.0 0 0.085 0.1191 0.1319 0.0128 0.003 0.7 3.8 0.5 0.0 0 0.255 0.1173 0.1310 0.0137 0.004 0.8 3.5 0.5 0.0 0 0.510 0.1164 0.1308 0.0144 0.005 0.9 3.8 0.5 0.0 0 0.766 0.1162 0.1310 0.0148 0.006 1.0 3.5 0.5 0.0 0 1.021 0.1159 0.1307 0.0148 0.007 1.0 3.8 0.5 0.0 0 1.276 0.1156 0.1304 0.0149 0.007 1.1 4.2 0.5 0.0 0 1.531 0.1155 0.1305 0.0150 0.008 1.1 4.2 0.5 0.0 0 1.787 0.1164 0.1309 0.0145 0.005 0.9 3.8 0.5 0.0 0 0.851 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1156 0.1304 0.0149 0.007 1.1 4.2 0.5 0.0 0 1.531 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.56 13.04 1.49 3.780 21.283 44.480 3.616 11.56 13.04 1.49 3.779 21.283 1.334 3.616 11.56 13.05 1.48 3.769 21.283 5.560 3.616 11.63 13.17 1.54 3.713 21.267 22.240 3.612 11.61 13.24 1.63 3.736 21.240 44.480 3.610 11.56 13.23 1.68 3.751 21.227 66.720 3.605 11.49 13.18 1.69 3.773 21.225 88.960 3.601 11.45 13.13 1.69 3.781 21.223 111.200 3.597 11.45 13.18 1.73 3.799 21.208 133.439 3.597 11.44 13.18 1.74 3.812 21.199 155.679 3.596 11.42 13.15 1.72 3.820 21.197 177.919 3.594 11.41 13.14 1.74 3.829 21.195 200.159 3.593 11.39 13.12 1.73 3.833 21.197 222.399 3.592 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.334 Accepted refinement result: 11.56 13.04 1.49 3.779 21.283 1.334 3.616 Individual atomic B min max mean iso aniso Overall: 9.11 115.04 21.27 3.31 223 1750 Protein: 9.11 115.04 17.04 3.32 0 1519 Water: 11.51 76.71 35.64 N/A 223 223 Other: 19.78 26.65 22.11 N/A 0 8 Chain A: 9.11 115.04 19.43 N/A 0 1750 Chain S: 13.55 60.01 35.68 N/A 223 0 Histogram: Values Number of atoms 9.11 - 19.71 1265 19.71 - 30.30 289 30.30 - 40.89 211 40.89 - 51.49 133 51.49 - 62.08 52 62.08 - 72.67 12 72.67 - 83.26 5 83.26 - 93.86 4 93.86 - 104.45 0 104.45 - 115.04 2 =========================== Idealize ADP of riding H ========================== r_work=0.1156 r_free=0.1304 r_work=0.1156 r_free=0.1304 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1156 r_free = 0.1304 target_work(ml) = 3.616 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1144 r_free = 0.1311 target_work(ml) = 3.610 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87588 (all), 4.90 % free)------------| | | | r_work= 0.1144 r_free= 0.1311 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.610072 | | target function (ml) not normalized (work): 300690.123138 | | target function (ml) not normalized (free): 15825.852533 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1152 0.1144 0.1311 n_refl.: 87588 re-set all scales: r(all,work,free)=0.1491 0.1491 0.1510 n_refl.: 87588 remove outliers: r(all,work,free)=0.1491 0.1491 0.1510 n_refl.: 87588 overall B=-0.01 to atoms: r(all,work,free)=0.1489 0.1490 0.1509 n_refl.: 87588 bulk-solvent and scaling: r(all,work,free)=0.1146 0.1138 0.1306 n_refl.: 87588 remove outliers: r(all,work,free)=0.1143 0.1135 0.1306 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 91.67 83 5 0.3883 291.616 269.394 0.487 1.001 0.309 11.894-9.307 95.10 93 4 0.2156 477.752 462.715 0.881 1.002 0.294 9.237-7.194 97.73 208 7 0.2229 387.134 387.468 0.945 1.002 0.210 7.162-5.571 100.00 427 22 0.2053 296.103 286.236 0.915 1.002 0.183 5.546-4.326 100.00 867 58 0.1089 406.476 401.987 0.955 1.002 0.149 4.315-3.360 100.00 1859 96 0.0924 386.561 384.013 0.993 1.002 0.133 3.356-2.611 100.00 3867 181 0.1131 253.951 251.827 0.998 1.002 0.100 2.608-2.026 99.99 8198 413 0.0925 168.346 167.609 1.014 1.001 0.000 2.025-1.573 100.00 17313 902 0.0898 82.212 82.484 1.025 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1253 36.456 36.043 1.018 0.998 0.000 1.221-1.150 99.97 13689 708 0.2163 22.970 21.519 0.980 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0209 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1135 r_free=0.1306 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=0.1135 r_free=0.1306 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1135 r_free=0.1306 | n_water=446 | time (s): 2.510 (total time: 2.510) Filter (dist) r_work=0.1134 r_free=0.1305 | n_water=443 | time (s): 49.140 (total time: 51.650) Filter (q & B) r_work=0.1135 r_free=0.1305 | n_water=441 | time (s): 3.980 (total time: 55.630) Compute maps r_work=0.1135 r_free=0.1305 | n_water=441 | time (s): 1.920 (total time: 57.550) Filter (map) r_work=0.1167 r_free=0.1289 | n_water=334 | time (s): 3.990 (total time: 61.540) Find peaks r_work=0.1167 r_free=0.1289 | n_water=334 | time (s): 0.720 (total time: 62.260) Add new water r_work=0.1234 r_free=0.1365 | n_water=501 | time (s): 3.750 (total time: 66.010) Refine new water occ: r_work=0.1161 r_free=0.1317 adp: r_work=0.1162 r_free=0.1318 occ: r_work=0.1145 r_free=0.1301 adp: r_work=0.1145 r_free=0.1301 occ: r_work=0.1134 r_free=0.1287 adp: r_work=0.1130 r_free=0.1286 ADP+occupancy (water only), MIN, final r_work=0.1130 r_free=0.1286 r_work=0.1130 r_free=0.1286 | n_water=501 | time (s): 207.450 (total time: 273.460) Filter (q & B) r_work=0.1139 r_free=0.1294 | n_water=456 | time (s): 4.010 (total time: 277.470) Filter (dist only) r_work=0.1140 r_free=0.1292 | n_water=454 | time (s): 47.620 (total time: 325.090) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.776421 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 45.507533 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1203 0.1330 0.0126 0.002 0.6 4.5 0.5 0.0 0 0.089 0.1165 0.1301 0.0136 0.003 0.7 3.2 0.5 0.0 0 0.266 0.1149 0.1293 0.0144 0.005 0.9 3.5 0.5 0.0 0 0.533 0.1142 0.1289 0.0147 0.006 0.9 3.2 0.5 0.0 0 0.799 0.1139 0.1288 0.0150 0.007 1.0 3.5 0.5 0.0 0 1.066 0.1136 0.1288 0.0151 0.007 1.1 3.5 0.5 0.0 0 1.332 0.1134 0.1287 0.0153 0.008 1.1 3.5 0.5 0.0 0 1.599 0.1132 0.1288 0.0156 0.009 1.1 3.5 0.5 0.0 0 1.865 0.1141 0.1289 0.0148 0.006 1.0 3.5 0.5 0.0 0 0.888 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1134 0.1287 0.0153 0.008 1.1 3.5 0.5 0.0 0 1.599 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.34 12.87 1.53 3.780 21.226 45.508 3.604 11.34 12.87 1.53 3.780 21.226 1.365 3.604 11.34 12.87 1.53 3.775 21.226 5.688 3.604 11.41 12.98 1.57 3.713 21.212 22.754 3.601 11.39 13.03 1.65 3.740 21.193 45.508 3.598 11.36 13.05 1.69 3.758 21.177 68.261 3.596 11.32 13.04 1.72 3.769 21.173 91.015 3.591 11.28 13.01 1.73 3.782 21.170 113.769 3.588 11.26 13.00 1.74 3.792 21.168 136.523 3.587 11.26 13.02 1.75 3.805 21.155 159.276 3.586 11.24 12.99 1.75 3.814 21.154 182.030 3.584 11.23 13.00 1.77 3.822 21.153 204.784 3.583 11.23 13.00 1.77 3.831 21.150 227.538 3.583 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.365 Accepted refinement result: 11.34 12.87 1.53 3.780 21.226 1.365 3.604 Individual atomic B min max mean iso aniso Overall: 9.11 115.03 21.17 3.31 233 1748 Protein: 9.11 115.03 17.03 3.32 0 1519 Water: 11.50 76.70 34.98 N/A 233 221 Other: 19.77 26.64 22.10 N/A 0 8 Chain A: 9.11 115.03 19.39 N/A 0 1748 Chain S: 13.55 60.00 34.47 N/A 233 0 Histogram: Values Number of atoms 9.11 - 19.70 1265 19.70 - 30.29 301 30.29 - 40.88 221 40.88 - 51.48 122 51.48 - 62.07 50 62.07 - 72.66 11 72.66 - 83.26 5 83.26 - 93.85 4 93.85 - 104.44 0 104.44 - 115.03 2 =========================== Idealize ADP of riding H ========================== r_work=0.1134 r_free=0.1287 r_work=0.1134 r_free=0.1287 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1134 r_free = 0.1287 target_work(ml) = 3.604 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1126 r_free = 0.1284 target_work(ml) = 3.600 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87579 (all), 4.91 % free)------------| | | | r_work= 0.1126 r_free= 0.1284 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.600292 | | target function (ml) not normalized (work): 299843.117112 | | target function (ml) not normalized (free): 15796.622247 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1134 0.1126 0.1284 n_refl.: 87579 re-set all scales: r(all,work,free)=0.1464 0.1464 0.1502 n_refl.: 87579 remove outliers: r(all,work,free)=0.1464 0.1464 0.1502 n_refl.: 87579 overall B=-0.01 to atoms: r(all,work,free)=0.1463 0.1463 0.1501 n_refl.: 87579 bulk-solvent and scaling: r(all,work,free)=0.1133 0.1125 0.1285 n_refl.: 87579 remove outliers: r(all,work,free)=0.1131 0.1123 0.1285 n_refl.: 87573 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.3865 294.012 248.213 0.443 1.001 0.313 11.894-9.307 92.16 90 4 0.2294 476.620 458.056 0.869 1.002 0.245 9.237-7.194 97.73 208 7 0.2362 387.134 381.287 0.930 1.002 0.187 7.162-5.571 100.00 427 22 0.2116 296.103 285.767 0.914 1.002 0.140 5.546-4.326 100.00 867 58 0.1100 406.476 402.200 0.965 1.002 0.130 4.315-3.360 100.00 1859 96 0.0906 386.561 384.703 1.004 1.002 0.130 3.356-2.611 100.00 3867 181 0.1100 253.951 252.222 1.010 1.002 0.060 2.608-2.026 99.99 8198 413 0.0906 168.346 167.791 1.026 1.001 0.000 2.025-1.573 100.00 17313 902 0.0880 82.212 82.552 1.036 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1246 36.456 36.064 1.029 0.997 0.000 1.221-1.150 99.97 13689 708 0.2167 22.970 21.523 0.990 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0152 b_overall=-0.0150 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1123 r_free=0.1285 After: r_work=0.1124 r_free=0.1285 ================================== NQH flips ================================== r_work=0.1124 r_free=0.1285 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=0.1124 r_free=0.1285 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1124 r_free=0.1285 | n_water=454 | time (s): 2.410 (total time: 2.410) Filter (dist) r_work=0.1124 r_free=0.1287 | n_water=453 | time (s): 50.900 (total time: 53.310) Filter (q & B) r_work=0.1124 r_free=0.1287 | n_water=453 | time (s): 1.400 (total time: 54.710) Compute maps r_work=0.1124 r_free=0.1287 | n_water=453 | time (s): 1.850 (total time: 56.560) Filter (map) r_work=0.1152 r_free=0.1291 | n_water=361 | time (s): 3.900 (total time: 60.460) Find peaks r_work=0.1152 r_free=0.1291 | n_water=361 | time (s): 0.690 (total time: 61.150) Add new water r_work=0.1200 r_free=0.1331 | n_water=508 | time (s): 4.030 (total time: 65.180) Refine new water occ: r_work=0.1144 r_free=0.1292 adp: r_work=0.1145 r_free=0.1294 occ: r_work=0.1133 r_free=0.1282 adp: r_work=0.1132 r_free=0.1283 occ: r_work=0.1124 r_free=0.1276 adp: r_work=0.1121 r_free=0.1275 ADP+occupancy (water only), MIN, final r_work=0.1121 r_free=0.1275 r_work=0.1121 r_free=0.1275 | n_water=508 | time (s): 176.810 (total time: 241.990) Filter (q & B) r_work=0.1129 r_free=0.1275 | n_water=466 | time (s): 4.020 (total time: 246.010) Filter (dist only) r_work=0.1129 r_free=0.1275 | n_water=463 | time (s): 49.730 (total time: 295.740) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.743904 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 39.014087 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 0.1216 0.1329 0.0113 0.004 0.7 6.1 0.5 0.0 0 0.087 0.1172 0.1299 0.0127 0.004 0.8 5.1 0.5 0.0 0 0.262 0.1151 0.1285 0.0135 0.005 0.9 5.4 0.5 0.0 0 0.523 0.1144 0.1281 0.0138 0.006 1.0 5.4 0.5 0.0 0 0.785 0.1137 0.1278 0.0141 0.006 1.0 5.1 0.5 0.0 0 1.046 0.1131 0.1275 0.0145 0.007 1.1 4.8 0.5 0.0 0 1.308 0.1129 0.1275 0.0146 0.008 1.1 4.8 0.5 0.0 0 1.570 0.1128 0.1275 0.0147 0.008 1.1 4.8 0.5 0.0 0 1.831 0.1143 0.1281 0.0139 0.006 1.0 5.4 0.5 0.0 0 0.872 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1128 0.1275 0.0147 0.008 1.1 4.8 0.5 0.0 0 1.831 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.28 12.75 1.47 3.779 21.229 39.014 3.599 11.28 12.75 1.47 3.779 21.229 1.170 3.599 11.28 12.75 1.47 3.779 21.229 4.877 3.599 11.32 12.79 1.47 3.710 21.221 19.507 3.595 11.40 12.93 1.52 3.723 21.194 39.014 3.599 11.33 12.91 1.58 3.748 21.182 58.521 3.594 11.28 12.89 1.61 3.762 21.177 78.028 3.589 11.25 12.87 1.62 3.776 21.177 97.535 3.587 11.22 12.87 1.64 3.785 21.175 117.042 3.585 11.21 12.88 1.67 3.799 21.169 136.549 3.584 11.20 12.88 1.68 3.810 21.164 156.056 3.583 11.18 12.85 1.67 3.816 21.163 175.563 3.581 11.18 12.84 1.66 3.826 21.159 195.070 3.581 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 4.877 Accepted refinement result: 11.28 12.75 1.47 3.779 21.229 4.877 3.599 Individual atomic B min max mean iso aniso Overall: 9.10 115.03 21.18 3.31 245 1745 Protein: 9.10 115.03 17.03 3.32 0 1519 Water: 11.50 76.70 34.78 N/A 245 218 Other: 19.76 26.63 22.09 N/A 0 8 Chain A: 9.10 115.03 19.33 N/A 0 1745 Chain S: 13.54 60.00 34.35 N/A 245 0 Histogram: Values Number of atoms 9.10 - 19.69 1265 19.69 - 30.29 307 30.29 - 40.88 224 40.88 - 51.47 126 51.47 - 62.06 47 62.06 - 72.66 10 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=0.1128 r_free=0.1275 r_work=0.1128 r_free=0.1275 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1128 r_free = 0.1275 target_work(ml) = 3.599 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1125 r_free = 0.1275 target_work(ml) = 3.598 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87573 (all), 4.91 % free)------------| | | | r_work= 0.1125 r_free= 0.1275 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.597668 | | target function (ml) not normalized (work): 299602.972868 | | target function (ml) not normalized (free): 15782.418563 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2915 171 0.1309 0.1296 5.6164 5.5832| | 2: 3.57 - 2.84 1.00 2888 124 0.1058 0.1364 5.1481 5.2024| | 3: 2.83 - 2.48 1.00 2820 163 0.1094 0.1237 4.9275 4.9721| | 4: 2.47 - 2.25 1.00 2825 136 0.0890 0.0958 4.6115 4.6361| | 5: 2.25 - 2.09 1.00 2756 127 0.0872 0.0954 4.5621 4.6099| | 6: 2.09 - 1.97 1.00 2846 113 0.0849 0.0997 4.2582 4.3544| | 7: 1.97 - 1.87 1.00 2787 165 0.0877 0.1090 3.9719 4.0641| | 8: 1.87 - 1.79 1.00 2789 144 0.0906 0.1115 3.8772 3.9976| | 9: 1.79 - 1.72 1.00 2745 138 0.0871 0.1181 3.6395 3.8204| | 10: 1.72 - 1.66 1.00 2831 160 0.0920 0.1178 3.5633 3.7077| | 11: 1.66 - 1.61 1.00 2712 147 0.0866 0.1043 3.4922 3.5684| | 12: 1.61 - 1.56 1.00 2773 144 0.0906 0.1136 3.326 3.4405| | 13: 1.56 - 1.52 1.00 2745 130 0.0935 0.1032 3.2994 3.3855| | 14: 1.52 - 1.48 1.00 2803 134 0.0982 0.1038 3.2352 3.3106| | 15: 1.48 - 1.45 1.00 2738 128 0.0995 0.1227 3.1475 3.2605| | 16: 1.45 - 1.42 1.00 2756 161 0.1052 0.1260 3.1325 3.2485| | 17: 1.42 - 1.39 1.00 2785 139 0.1132 0.1318 3.1138 3.2333| | 18: 1.39 - 1.36 1.00 2741 179 0.1194 0.1330 3.102 3.2344| | 19: 1.36 - 1.34 1.00 2807 134 0.1256 0.1569 3.11 3.2646| | 20: 1.34 - 1.32 1.00 2696 147 0.1365 0.1445 3.1097 3.1468| | 21: 1.32 - 1.30 1.00 2785 112 0.1465 0.1521 3.112 3.1098| | 22: 1.29 - 1.27 1.00 2704 152 0.1557 0.1989 3.1211 3.2937| | 23: 1.27 - 1.26 1.00 2802 156 0.1646 0.1790 3.1319 3.1987| | 24: 1.26 - 1.24 1.00 2744 132 0.1709 0.1817 3.1262 3.2242| | 25: 1.24 - 1.22 1.00 2733 148 0.1882 0.2174 3.1427 3.2645| | 26: 1.22 - 1.21 1.00 2727 135 0.1908 0.1747 3.1487 3.195| | 27: 1.21 - 1.19 1.00 2814 148 0.2072 0.2176 3.17 3.1628| | 28: 1.19 - 1.18 1.00 2671 147 0.2200 0.2317 3.1652 3.1803| | 29: 1.18 - 1.16 1.00 2800 134 0.2263 0.2391 3.1465 3.2308| | 30: 1.16 - 1.15 1.00 2739 148 0.2449 0.2444 3.1428 3.1649| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.58 2915 171 0.95 8.22 1.00 0.97 5495.90| | 2: 3.57 - 2.84 2888 124 0.93 12.28 1.01 0.97 5495.90| | 3: 2.83 - 2.48 2820 163 0.90 16.18 0.99 0.97 4593.60| | 4: 2.47 - 2.25 2825 136 0.92 13.19 1.00 0.98 2266.86| | 5: 2.25 - 2.09 2756 127 0.91 15.30 1.01 0.98 2266.86| | 6: 2.09 - 1.97 2846 113 0.93 12.16 1.02 0.98 1313.82| | 7: 1.97 - 1.87 2787 165 0.95 9.16 1.02 0.97 501.01| | 8: 1.87 - 1.79 2789 144 0.93 12.55 1.00 0.97 501.01| | 9: 1.79 - 1.72 2745 138 0.94 10.01 0.98 0.97 286.19| | 10: 1.72 - 1.66 2831 160 0.94 11.08 0.98 0.97 243.17| | 11: 1.66 - 1.61 2712 147 0.94 11.67 0.98 0.97 232.96| | 12: 1.61 - 1.56 2773 144 0.95 8.87 0.99 0.97 136.64| | 13: 1.56 - 1.52 2745 130 0.95 10.33 1.02 0.97 136.64| | 14: 1.52 - 1.48 2803 134 0.94 10.73 1.02 0.98 122.63| | 15: 1.48 - 1.45 2738 128 0.95 9.86 1.02 0.98 96.97| | 16: 1.45 - 1.42 2756 161 0.94 11.02 1.02 0.98 96.97| | 17: 1.42 - 1.39 2785 139 0.95 10.91 1.01 0.98 88.55| | 18: 1.39 - 1.36 2741 179 0.94 11.52 1.01 0.98 83.67| | 19: 1.36 - 1.34 2807 134 0.94 11.86 0.99 0.98 83.67| | 20: 1.34 - 1.32 2696 147 0.94 12.12 0.98 0.96 79.91| | 21: 1.32 - 1.30 2785 112 0.94 13.06 0.98 0.96 79.64| | 22: 1.29 - 1.27 2704 152 0.93 13.65 0.98 0.96 80.06| | 23: 1.27 - 1.26 2802 156 0.92 14.84 0.97 0.94 82.20| | 24: 1.26 - 1.24 2744 132 0.92 14.86 0.96 0.94 82.20| | 25: 1.24 - 1.22 2733 148 0.91 16.37 0.96 0.94 84.25| | 26: 1.22 - 1.21 2727 135 0.90 18.14 1.02 0.93 86.51| | 27: 1.21 - 1.19 2814 148 0.89 18.81 1.02 0.93 86.51| | 28: 1.19 - 1.18 2671 147 0.88 20.48 1.01 0.92 90.41| | 29: 1.18 - 1.16 2800 134 0.88 20.61 0.98 0.92 91.87| | 30: 1.16 - 1.15 2739 148 0.86 22.13 0.97 0.92 91.87| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 79.64 max = 5495.90 mean = 853.15| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.94 mean = 13.38| |phase err.(test): min = 0.00 max = 89.60 mean = 13.41| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1132 0.1125 0.1275 n_refl.: 87573 re-set all scales: r(all,work,free)=0.1444 0.1443 0.1496 n_refl.: 87573 remove outliers: r(all,work,free)=0.1444 0.1443 0.1496 n_refl.: 87573 overall B=-0.00 to atoms: r(all,work,free)=0.1443 0.1442 0.1496 n_refl.: 87573 bulk-solvent and scaling: r(all,work,free)=0.1132 0.1124 0.1277 n_refl.: 87573 remove outliers: r(all,work,free)=0.1131 0.1124 0.1277 n_refl.: 87572 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 87.50 79 5 0.4163 289.256 244.992 0.440 1.000 0.314 11.894-9.307 92.16 90 4 0.2339 476.620 458.967 0.875 1.002 0.232 9.237-7.194 97.73 208 7 0.2297 387.134 382.056 0.930 1.002 0.160 7.162-5.571 100.00 427 22 0.2091 296.103 286.614 0.911 1.003 0.126 5.546-4.326 100.00 867 58 0.1108 406.476 402.212 0.963 1.003 0.120 4.315-3.360 100.00 1859 96 0.0910 386.561 384.488 1.004 1.002 0.120 3.356-2.611 100.00 3867 181 0.1096 253.951 252.075 1.010 1.002 0.060 2.608-2.026 99.99 8198 413 0.0905 168.346 167.727 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0884 82.212 82.545 1.035 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1246 36.456 36.058 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2166 22.970 21.521 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=-0.0110 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2611 0.1970 0.082 5.425 8.8 119.3 19.9 258 0.000 1_bss: 0.1641 0.1788 0.082 5.425 9.1 119.5 20.1 258 0.000 1_settarget: 0.1641 0.1788 0.082 5.425 9.1 119.5 20.1 258 0.000 1_nqh: 0.1641 0.1788 0.082 5.425 9.1 119.5 20.1 258 0.000 1_weight: 0.1641 0.1788 0.082 5.425 9.1 119.5 20.1 258 0.000 1_xyzrec: 0.1224 0.1469 0.008 0.966 9.1 119.5 20.1 258 0.137 1_adp: 0.1231 0.1466 0.008 0.966 9.1 119.5 20.1 258 0.137 1_regHadp: 0.1232 0.1469 0.008 0.966 9.1 119.5 20.1 258 0.137 1_occ: 0.1227 0.1466 0.008 0.966 9.1 119.5 20.1 258 0.137 2_bss: 0.1223 0.1458 0.008 0.966 9.1 119.5 20.1 258 0.137 2_settarget: 0.1223 0.1458 0.008 0.966 9.1 119.5 20.1 258 0.137 2_updatecdl: 0.1223 0.1458 0.008 0.966 9.1 119.5 20.1 258 0.137 2_nqh: 0.1224 0.1459 0.008 0.966 9.1 119.5 20.1 258 0.140 2_sol: 0.1195 0.1404 0.008 0.966 9.1 115.0 22.2 417 n/a 2_weight: 0.1195 0.1404 0.008 0.966 9.1 115.0 22.2 417 n/a 2_xyzrec: 0.1183 0.1400 0.007 0.880 9.1 115.0 22.2 417 n/a 2_adp: 0.1183 0.1400 0.007 0.880 9.1 115.0 22.2 417 n/a 2_regHadp: 0.1183 0.1400 0.007 0.880 9.1 115.0 22.2 417 n/a 2_occ: 0.1188 0.1398 0.007 0.880 9.1 115.0 22.2 417 n/a 3_bss: 0.1184 0.1392 0.007 0.880 9.1 115.0 22.2 417 n/a 3_settarget: 0.1184 0.1392 0.007 0.880 9.1 115.0 22.2 417 n/a 3_updatecdl: 0.1184 0.1392 0.007 0.880 9.1 115.0 22.2 417 n/a 3_nqh: 0.1184 0.1392 0.007 0.880 9.1 115.0 22.2 417 n/a 3_sol: 0.1201 0.1374 0.007 0.880 9.1 115.0 21.3 446 n/a 3_weight: 0.1201 0.1374 0.007 0.880 9.1 115.0 21.3 446 n/a 3_xyzrec: 0.1156 0.1304 0.007 1.051 9.1 115.0 21.3 446 n/a 3_adp: 0.1156 0.1304 0.007 1.051 9.1 115.0 21.3 446 n/a 3_regHadp: 0.1156 0.1304 0.007 1.051 9.1 115.0 21.3 446 n/a 3_occ: 0.1144 0.1311 0.007 1.051 9.1 115.0 21.3 446 n/a 4_bss: 0.1135 0.1306 0.007 1.051 9.1 115.0 21.3 446 n/a 4_settarget: 0.1135 0.1306 0.007 1.051 9.1 115.0 21.3 446 n/a 4_updatecdl: 0.1135 0.1306 0.007 1.052 9.1 115.0 21.3 446 n/a 4_nqh: 0.1135 0.1306 0.007 1.052 9.1 115.0 21.3 446 n/a 4_sol: 0.1140 0.1292 0.007 1.052 9.1 115.0 21.2 454 n/a 4_weight: 0.1140 0.1292 0.007 1.052 9.1 115.0 21.2 454 n/a 4_xyzrec: 0.1134 0.1287 0.008 1.095 9.1 115.0 21.2 454 n/a 4_adp: 0.1134 0.1287 0.008 1.095 9.1 115.0 21.2 454 n/a 4_regHadp: 0.1134 0.1287 0.008 1.095 9.1 115.0 21.2 454 n/a 4_occ: 0.1126 0.1284 0.008 1.095 9.1 115.0 21.2 454 n/a 5_bss: 0.1123 0.1285 0.008 1.095 9.1 115.0 21.2 454 n/a 5_settarget: 0.1123 0.1285 0.008 1.095 9.1 115.0 21.2 454 n/a 5_updatecdl: 0.1123 0.1285 0.008 1.096 9.1 115.0 21.2 454 n/a 5_setrh: 0.1124 0.1285 0.008 1.096 9.1 115.0 21.2 454 n/a 5_nqh: 0.1124 0.1285 0.008 1.096 9.1 115.0 21.2 454 n/a 5_sol: 0.1129 0.1275 0.008 1.096 9.1 115.0 21.2 463 n/a 5_weight: 0.1129 0.1275 0.008 1.096 9.1 115.0 21.2 463 n/a 5_xyzrec: 0.1128 0.1275 0.008 1.120 9.1 115.0 21.2 463 n/a 5_adp: 0.1128 0.1275 0.008 1.120 9.1 115.0 21.2 463 n/a 5_regHadp: 0.1128 0.1275 0.008 1.120 9.1 115.0 21.2 463 n/a 5_occ: 0.1125 0.1275 0.008 1.120 9.1 115.0 21.2 463 n/a end: 0.1124 0.1277 0.008 1.120 9.1 115.0 21.2 463 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_2359181_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_2359181_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.8000 Refinement macro-cycles (run) : 14028.3300 Write final files (write_after_run_outputs) : 90.4500 Total : 14122.5800 Total CPU time: 3.93 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:14:54 PST -0800 (1735366494.55 s) Start R-work = 0.1641, R-free = 0.1788 Final R-work = 0.1124, R-free = 0.1277 =============================================================================== Job complete usr+sys time: 14294.89 seconds wall clock time: 258 minutes 57.03 seconds (15537.03 seconds total)