Starting phenix.refine on Sun Dec 29 09:24:42 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_4735076.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Adding command-line PHIL: ------------------------- xray_data.high_resolution=2 ordered_solvent.low_resolution=4 No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_4735076.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_4735076.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 2 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.13, per 1000 atoms: 0.33 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: 0.28 Conformation dependent library (CDL) restraints added in 109.6 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.63 - 0.89: 390 0.89 - 1.15: 1214 1.15 - 1.40: 614 1.40 - 1.66: 889 1.66 - 1.92: 46 Bond restraints: 3153 Sorted by residual: bond pdb=" N ALA A 36 " pdb=" CA ALA A 36 " ideal model delta sigma weight residual 1.456 1.690 -0.233 1.23e-02 6.61e+03 3.60e+02 bond pdb=" C GLN A 180 " pdb=" O GLN A 180 " ideal model delta sigma weight residual 1.236 0.997 0.239 1.29e-02 6.01e+03 3.42e+02 bond pdb=" C GLY A 78 " pdb=" O GLY A 78 " ideal model delta sigma weight residual 1.234 1.455 -0.222 1.21e-02 6.83e+03 3.36e+02 bond pdb=" C LYS A 12 " pdb=" O LYS A 12 " ideal model delta sigma weight residual 1.234 1.016 0.219 1.20e-02 6.94e+03 3.33e+02 bond pdb=" C GLY A 157 " pdb=" O GLY A 157 " ideal model delta sigma weight residual 1.235 1.479 -0.244 1.35e-02 5.49e+03 3.26e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.47: 3088 4.47 - 8.94: 1853 8.94 - 13.41: 670 13.41 - 17.88: 152 17.88 - 22.35: 14 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA ILE A 21 " pdb=" C ILE A 21 " pdb=" N PRO A 22 " ideal model delta sigma weight residual 120.83 109.48 11.35 5.90e-01 2.87e+00 3.70e+02 angle pdb=" O ILE A 21 " pdb=" C ILE A 21 " pdb=" N PRO A 22 " ideal model delta sigma weight residual 120.42 130.43 -10.01 6.40e-01 2.44e+00 2.45e+02 angle pdb=" CA GLU A 116 " pdb=" C GLU A 116 " pdb=" O GLU A 116 " ideal model delta sigma weight residual 120.98 104.33 16.65 1.24e+00 6.50e-01 1.80e+02 angle pdb=" O ALEU A 153 " pdb=" C ALEU A 153 " pdb=" N THR A 154 " ideal model delta sigma weight residual 123.12 140.58 -17.46 1.32e+00 5.74e-01 1.75e+02 angle pdb=" CG HIS A 115 " pdb=" CD2 HIS A 115 " pdb=" NE2 HIS A 115 " ideal model delta sigma weight residual 107.20 94.55 12.65 1.00e+00 1.00e+00 1.60e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.87: 1300 16.87 - 33.74: 126 33.74 - 50.61: 35 50.61 - 67.47: 17 67.47 - 84.34: 3 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" N BLYS A 99 " pdb=" C BLYS A 99 " pdb=" CA BLYS A 99 " pdb=" CB BLYS A 99 " ideal model delta harmonic sigma weight residual 122.80 143.36 -20.56 0 2.50e+00 1.60e-01 6.76e+01 dihedral pdb=" C VAL A 20 " pdb=" N VAL A 20 " pdb=" CA VAL A 20 " pdb=" CB VAL A 20 " ideal model delta harmonic sigma weight residual -122.00 -142.42 20.42 0 2.50e+00 1.60e-01 6.67e+01 dihedral pdb=" C ALYS A 99 " pdb=" N ALYS A 99 " pdb=" CA ALYS A 99 " pdb=" CB ALYS A 99 " ideal model delta harmonic sigma weight residual -122.60 -142.20 19.60 0 2.50e+00 1.60e-01 6.14e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.003 - 0.198: 89 0.198 - 0.393: 77 0.393 - 0.588: 43 0.588 - 0.783: 25 0.783 - 0.978: 9 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA LEU A 58 " pdb=" N LEU A 58 " pdb=" C LEU A 58 " pdb=" CB LEU A 58 " both_signs ideal model delta sigma weight residual False 2.51 1.53 0.98 2.00e-01 2.50e+01 2.39e+01 chirality pdb=" CA ALA A 183 " pdb=" N ALA A 183 " pdb=" C ALA A 183 " pdb=" CB ALA A 183 " both_signs ideal model delta sigma weight residual False 2.48 1.52 0.97 2.00e-01 2.50e+01 2.34e+01 chirality pdb=" CA BLYS A 99 " pdb=" N BLYS A 99 " pdb=" C BLYS A 99 " pdb=" CB BLYS A 99 " both_signs ideal model delta sigma weight residual False 2.51 1.55 0.96 2.00e-01 2.50e+01 2.29e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.018 2.00e-02 2.50e+03 6.78e-02 1.38e+02 pdb=" CG PHE A 119 " -0.170 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " 0.038 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " -0.102 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.066 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.083 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.035 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.007 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " -0.013 2.00e-02 2.50e+03 6.68e-02 1.34e+02 pdb=" CG TYR A 139 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " 0.083 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " 0.084 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " -0.080 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.071 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " -0.065 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.015 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " -0.099 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " -0.020 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.108 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 5 " 0.035 9.50e-02 1.11e+02 7.54e-02 1.25e+02 pdb=" NE ARG A 5 " -0.063 2.00e-02 2.50e+03 pdb=" CZ ARG A 5 " -0.022 2.00e-02 2.50e+03 pdb=" NH1 ARG A 5 " -0.063 2.00e-02 2.50e+03 pdb=" NH2 ARG A 5 " -0.072 2.00e-02 2.50e+03 pdb="HH11 ARG A 5 " 0.096 2.00e-02 2.50e+03 pdb="HH12 ARG A 5 " 0.021 2.00e-02 2.50e+03 pdb="HH21 ARG A 5 " 0.154 2.00e-02 2.50e+03 pdb="HH22 ARG A 5 " -0.053 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.28: 759 2.28 - 2.86: 7804 2.86 - 3.44: 10629 3.44 - 4.02: 15316 4.02 - 4.60: 22095 Nonbonded interactions: 56603 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.695 2.100 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.721 2.100 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.781 2.450 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.801 2.100 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.835 2.450 ... (remaining 56598 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 2 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 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } output { prefix = "shake_4735076_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: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2791 r_free= 0.1820 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.401961 | | target function (ml) not normalized (work): 71501.057143 | | target function (ml) not normalized (free): 3267.421659 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 49.25 - 3.64 1.00 2819 159 0.3203 0.2126 7.5225 5.0297| | 2: 3.63 - 2.88 1.00 2711 122 0.2634 0.1781 4.329 4.3247| | 3: 2.88 - 2.52 1.00 2682 148 0.2573 0.1669 4.1856 4.1977| | 4: 2.52 - 2.29 1.00 2661 139 0.2554 0.1492 3.4986 3.5217| | 5: 2.29 - 2.13 1.00 2678 122 0.2647 0.1543 3.3958 3.5043| | 6: 2.13 - 2.00 1.00 2692 117 0.2745 0.1879 3.3172 3.4342| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 - 3.64 2819 159 0.88 17.63 0.77 0.23 1307.08| | 2: 3.63 - 2.88 2711 122 0.83 23.95 1.32 0.23 1307.08| | 3: 2.88 - 2.52 2682 148 0.73 32.85 1.28 0.23 1307.08| | 4: 2.52 - 2.29 2661 139 0.93 11.43 1.30 0.26 136.89| | 5: 2.29 - 2.13 2678 122 0.92 13.57 1.31 0.26 136.89| | 6: 2.13 - 2.00 2692 117 0.90 16.37 1.33 0.26 136.89| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 136.89 max = 1307.08 mean = 728.51| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 89.98 mean = 19.30| |phase err.(test): min = 0.00 max = 88.52 mean = 19.39| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.083 0.244 1557 Z= 5.545 Angle : 5.417 18.814 2118 Z= 3.858 Chirality : 0.388 0.978 243 Planarity : 0.031 0.133 284 Dihedral : 14.032 84.343 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.86 % Allowed : 1.86 % Favored : 96.27 % Cbeta Deviations : 34.05 % 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: -1.98 (0.49), residues: 224 helix: -2.23 (0.41), residues: 109 sheet: 0.06 (0.95), residues: 28 loop : -0.17 (0.55), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.066 0.020 ARG A 48 TYR 0.077 0.042 TYR A 139 PHE 0.142 0.046 PHE A 119 HIS 0.057 0.028 HIS A 126 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 1785 0 Protein: 8.85 115.78 16.79 3.90 1519 0 Water: 11.36 119.30 38.03 N/A 258 0 Other: 19.04 26.29 21.71 N/A 8 0 Chain A: 8.85 119.30 19.89 N/A 1785 0 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: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2791 r_free= 0.1820 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.401961 | | target function (ml) not normalized (work): 71501.057143 | | target function (ml) not normalized (free): 3267.421659 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.3104 percent. r_work = 0.2922 r_free = 0.1975 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2867 0.2922 0.1975 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2867 0.2922 0.1975 n_refl.: 17050 remove outliers: r(all,work,free)=0.2159 0.2171 0.1975 n_refl.: 17045 overall B=-0.39 to atoms: r(all,work,free)=0.2133 0.2145 0.1956 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1624 0.1623 0.1652 n_refl.: 17045 remove outliers: r(all,work,free)=0.1624 0.1622 0.1652 n_refl.: 17044 ======================== 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 32.574-12.150 100.00 89 5 0.4087 394.641 362.437 0.655 1.013 0.399 11.894-9.307 99.02 97 4 0.1884 633.411 614.788 0.926 1.013 0.390 9.237-7.194 100.00 213 7 0.2190 518.066 508.860 0.959 1.013 0.365 7.162-5.571 100.00 427 22 0.2308 388.809 376.835 0.931 1.012 0.341 5.546-4.326 100.00 867 58 0.1413 533.773 528.067 0.959 1.009 0.223 4.315-3.360 100.00 1859 96 0.1310 507.623 503.764 1.018 1.006 0.191 3.356-2.611 100.00 3867 181 0.1649 333.479 328.709 1.009 1.000 0.051 2.608-2.000 99.99 8818 434 0.1661 217.371 213.527 1.029 0.988 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.4109 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1622 r_free=0.1652 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN Total number of N/Q/H flips: 1 r_work=0.1626 r_free=0.1666 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.301039 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.794191 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1352 0.1625 0.0272 0.009 1.0 1.0 0.5 0.0 0 11.651 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.52 16.25 2.72 3.012 18.464 0.794 0.023 12.80 16.52 3.72 3.536 18.673 0.794 0.021 Individual atomic B min max mean iso aniso Overall: 6.16 113.90 19.89 4.04 1785 0 Protein: 6.16 112.94 17.13 4.04 1519 0 Water: 7.89 113.90 35.94 N/A 258 0 Other: 21.53 36.53 25.67 N/A 8 0 Chain A: 6.16 113.90 19.89 N/A 1785 0 Histogram: Values Number of atoms 6.16 - 16.94 1090 16.94 - 27.71 342 27.71 - 38.49 182 38.49 - 49.26 93 49.26 - 60.03 52 60.03 - 70.81 11 70.81 - 81.58 7 81.58 - 92.36 4 92.36 - 103.13 1 103.13 - 113.90 3 =========================== Idealize ADP of riding H ========================== r_work=0.1280 r_free=0.1652 r_work=0.1283 r_free=0.1659 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1283 r_free = 0.1659 target_work(ls_wunit_k1) = 0.021 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1279 r_free = 0.1652 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17044 (all), 4.73 % free)------------| | | | r_work= 0.1279 r_free= 0.1652 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.020115 | | target function (ls_wunit_k1) not normalized (work): 326.600056 | | target function (ls_wunit_k1) not normalized (free): 26.823796 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1297 0.1279 0.1652 n_refl.: 17044 re-set all scales: r(all,work,free)=0.1916 0.1916 0.1981 n_refl.: 17044 remove outliers: r(all,work,free)=0.1916 0.1916 0.1981 n_refl.: 17044 overall B=-0.51 to atoms: r(all,work,free)=0.1880 0.1879 0.1961 n_refl.: 17044 bulk-solvent and scaling: r(all,work,free)=0.1293 0.1275 0.1640 n_refl.: 17044 remove outliers: r(all,work,free)=0.1291 0.1274 0.1640 n_refl.: 17042 ======================== 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 0.3537 303.359 280.989 0.627 1.005 0.370 11.894-9.307 99.02 97 4 0.1663 487.905 476.708 0.918 1.006 0.370 9.237-7.194 100.00 213 7 0.1797 399.057 396.179 0.964 1.006 0.335 7.162-5.571 100.00 427 22 0.1823 299.493 294.218 0.934 1.006 0.321 5.546-4.326 100.00 867 58 0.1041 411.156 408.333 0.957 1.005 0.210 4.315-3.360 100.00 1859 96 0.0933 391.013 390.244 1.017 1.004 0.192 3.356-2.611 100.00 3867 181 0.1302 256.873 255.516 1.008 1.001 0.102 2.608-2.000 99.99 8818 434 0.1348 167.437 166.097 1.011 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9583 b_overall=-1.1436 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1274 r_free=0.1640 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN Total number of N/Q/H flips: 1 r_work=0.1276 r_free=0.1643 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1276 r_free=0.1643 | n_water=258 | time (s): 0.660 (total time: 0.660) Filter (dist) r_work=0.1283 r_free=0.1629 | n_water=252 | time (s): 21.160 (total time: 21.820) Filter (q & B) r_work=0.1283 r_free=0.1628 | n_water=250 | time (s): 1.650 (total time: 23.470) Compute maps r_work=0.1283 r_free=0.1628 | n_water=250 | time (s): 0.660 (total time: 24.130) Filter (map) r_work=0.1319 r_free=0.1617 | n_water=212 | time (s): 2.250 (total time: 26.380) Find peaks r_work=0.1319 r_free=0.1617 | n_water=212 | time (s): 0.470 (total time: 26.850) Add new water r_work=0.1550 r_free=0.1848 | n_water=376 | time (s): 2.160 (total time: 29.010) Refine new water occ: r_work=0.1342 r_free=0.1585 adp: r_work=0.1280 r_free=0.1579 occ: r_work=0.1284 r_free=0.1549 adp: r_work=0.1251 r_free=0.1558 occ: r_work=0.1251 r_free=0.1542 adp: r_work=0.1242 r_free=0.1546 ADP+occupancy (water only), MIN, final r_work=0.1242 r_free=0.1546 r_work=0.1242 r_free=0.1546 | n_water=376 | time (s): 14.860 (total time: 43.870) Filter (q & B) r_work=0.1247 r_free=0.1554 | n_water=363 | time (s): 1.950 (total time: 45.820) Filter (dist only) r_work=0.1247 r_free=0.1556 | n_water=362 | time (s): 28.320 (total time: 74.140) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.725492 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.008411 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1219 0.1630 0.0411 0.008 0.9 1.9 0.5 0.0 0 12.363 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.19 16.30 4.11 4.139 20.887 1.008 0.018 12.01 16.35 4.34 4.190 21.099 1.008 0.018 Individual atomic B min max mean iso aniso Overall: 6.39 107.43 21.16 4.24 1889 0 Protein: 6.39 107.43 17.46 4.23 1519 0 Water: 8.33 68.35 36.53 N/A 362 0 Other: 21.98 36.02 27.11 N/A 8 0 Chain A: 6.39 107.43 19.20 N/A 1739 0 Chain S: 18.98 65.56 43.88 N/A 150 0 Histogram: Values Number of atoms 6.39 - 16.50 1029 16.50 - 26.60 381 26.60 - 36.71 211 36.71 - 46.81 155 46.81 - 56.91 77 56.91 - 67.02 25 67.02 - 77.12 4 77.12 - 87.22 4 87.22 - 97.33 1 97.33 - 107.43 2 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1635 r_work=0.1203 r_free=0.1636 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1203 r_free = 0.1636 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1199 r_free = 0.1634 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17042 (all), 4.74 % free)------------| | | | r_work= 0.1199 r_free= 0.1634 coordinate error (max.-lik. estimate): 0.12 A | | | | normalized target function (ls_wunit_k1) (work): 0.017114 | | target function (ls_wunit_k1) not normalized (work): 277.841501 | | target function (ls_wunit_k1) not normalized (free): 25.453999 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1220 0.1199 0.1634 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1751 0.1743 0.1959 n_refl.: 17042 remove outliers: r(all,work,free)=0.1751 0.1743 0.1959 n_refl.: 17042 overall B=-0.34 to atoms: r(all,work,free)=0.1730 0.1721 0.1947 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1216 0.1195 0.1626 n_refl.: 17042 remove outliers: r(all,work,free)=0.1216 0.1195 0.1626 n_refl.: 17042 ======================== 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 0.3336 303.359 285.416 0.598 1.006 0.350 11.894-9.307 99.02 97 4 0.1556 487.905 484.840 0.915 1.007 0.340 9.237-7.194 100.00 213 7 0.1693 399.057 397.868 0.974 1.007 0.300 7.162-5.571 100.00 427 22 0.1550 299.493 296.181 0.938 1.006 0.291 5.546-4.326 100.00 867 58 0.0882 411.156 408.202 0.959 1.005 0.210 4.315-3.360 100.00 1859 96 0.0832 391.013 390.362 1.016 1.004 0.201 3.356-2.611 100.00 3867 181 0.1203 256.873 256.217 1.010 1.001 0.131 2.608-2.000 99.99 8818 434 0.1334 167.437 166.369 1.012 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-1.1663 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1195 r_free=0.1626 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN Total number of N/Q/H flips: 1 r_work=0.1196 r_free=0.1628 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1628 | n_water=362 | time (s): 0.670 (total time: 0.670) Filter (dist) r_work=0.1197 r_free=0.1629 | n_water=361 | time (s): 28.040 (total time: 28.710) Filter (q & B) r_work=0.1197 r_free=0.1629 | n_water=361 | time (s): 0.940 (total time: 29.650) Compute maps r_work=0.1197 r_free=0.1629 | n_water=361 | time (s): 0.720 (total time: 30.370) Filter (map) r_work=0.1268 r_free=0.1634 | n_water=252 | time (s): 2.100 (total time: 32.470) Find peaks r_work=0.1268 r_free=0.1634 | n_water=252 | time (s): 0.590 (total time: 33.060) Add new water r_work=0.1475 r_free=0.1808 | n_water=411 | time (s): 1.650 (total time: 34.710) Refine new water occ: r_work=0.1265 r_free=0.1585 adp: r_work=0.1256 r_free=0.1584 occ: r_work=0.1239 r_free=0.1559 adp: r_work=0.1226 r_free=0.1557 occ: r_work=0.1219 r_free=0.1547 adp: r_work=0.1208 r_free=0.1544 ADP+occupancy (water only), MIN, final r_work=0.1208 r_free=0.1544 r_work=0.1208 r_free=0.1544 | n_water=411 | time (s): 33.290 (total time: 68.000) Filter (q & B) r_work=0.1211 r_free=0.1558 | n_water=399 | time (s): 1.550 (total time: 69.550) Filter (dist only) r_work=0.1210 r_free=0.1559 | n_water=398 | time (s): 31.990 (total time: 101.540) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.890557 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.148603 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1190 0.1549 0.0359 0.009 1.0 3.2 0.5 0.0 0 0.945 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.90 15.49 3.59 4.290 21.216 0.149 5.003 11.71 15.65 3.94 4.844 21.074 0.149 4.983 Individual atomic B min max mean iso aniso Overall: 6.00 106.49 20.47 4.61 1925 0 Protein: 6.00 106.49 16.73 4.61 1519 0 Water: 8.30 60.72 34.63 N/A 398 0 Other: 19.43 37.00 26.14 N/A 8 0 Chain A: 6.00 106.49 18.39 N/A 1733 0 Chain S: 18.17 60.72 39.22 N/A 192 0 Histogram: Values Number of atoms 6.00 - 16.05 1075 16.05 - 26.10 352 26.10 - 36.15 215 36.15 - 46.20 180 46.20 - 56.25 70 56.25 - 66.29 21 66.29 - 76.34 6 76.34 - 86.39 3 86.39 - 96.44 1 96.44 - 106.49 2 =========================== Idealize ADP of riding H ========================== r_work=0.1171 r_free=0.1565 r_work=0.1172 r_free=0.1567 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1172 r_free = 0.1567 target_work(ml) = 4.983 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1164 r_free = 0.1572 target_work(ml) = 4.981 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17042 (all), 4.74 % free)------------| | | | r_work= 0.1164 r_free= 0.1572 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ml) (work): 4.980802 | | target function (ml) not normalized (work): 80863.321727 | | target function (ml) not normalized (free): 4203.808935 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1184 0.1164 0.1572 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1663 0.1653 0.1899 n_refl.: 17042 remove outliers: r(all,work,free)=0.1663 0.1653 0.1899 n_refl.: 17042 overall B=-0.33 to atoms: r(all,work,free)=0.1642 0.1631 0.1888 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1181 0.1162 0.1573 n_refl.: 17042 remove outliers: r(all,work,free)=0.1181 0.1161 0.1573 n_refl.: 17041 ======================== 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 0.3645 299.869 279.892 0.555 1.006 0.330 11.894-9.307 99.02 97 4 0.1786 487.905 479.848 0.914 1.007 0.317 9.237-7.194 100.00 213 7 0.1825 399.057 399.133 0.983 1.007 0.265 7.162-5.571 100.00 427 22 0.1638 299.493 293.246 0.939 1.006 0.251 5.546-4.326 100.00 867 58 0.0962 411.156 406.981 0.965 1.006 0.211 4.315-3.360 100.00 1859 96 0.0922 391.013 388.671 1.013 1.004 0.201 3.356-2.611 100.00 3867 181 0.1289 256.873 254.583 1.012 1.001 0.131 2.608-2.000 99.99 8818 434 0.1096 167.437 165.992 1.012 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-1.1530 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1161 r_free=0.1573 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN Total number of N/Q/H flips: 1 r_work=0.1161 r_free=0.1571 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1161 r_free=0.1571 | n_water=398 | time (s): 0.720 (total time: 0.720) Filter (dist) r_work=0.1161 r_free=0.1571 | n_water=398 | time (s): 30.870 (total time: 31.590) Filter (q & B) r_work=0.1162 r_free=0.1574 | n_water=397 | time (s): 2.120 (total time: 33.710) Compute maps r_work=0.1162 r_free=0.1574 | n_water=397 | time (s): 0.680 (total time: 34.390) Filter (map) r_work=0.1204 r_free=0.1572 | n_water=308 | time (s): 1.790 (total time: 36.180) Find peaks r_work=0.1204 r_free=0.1572 | n_water=308 | time (s): 0.430 (total time: 36.610) Add new water r_work=0.1358 r_free=0.1683 | n_water=449 | time (s): 1.380 (total time: 37.990) Refine new water occ: r_work=0.1188 r_free=0.1521 adp: r_work=0.1179 r_free=0.1522 occ: r_work=0.1165 r_free=0.1500 adp: r_work=0.1155 r_free=0.1500 occ: r_work=0.1149 r_free=0.1489 adp: r_work=0.1141 r_free=0.1490 ADP+occupancy (water only), MIN, final r_work=0.1141 r_free=0.1490 r_work=0.1141 r_free=0.1490 | n_water=449 | time (s): 36.610 (total time: 74.600) Filter (q & B) r_work=0.1146 r_free=0.1493 | n_water=438 | time (s): 1.870 (total time: 76.470) Filter (dist only) r_work=0.1145 r_free=0.1494 | n_water=437 | time (s): 35.560 (total time: 112.030) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.934526 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.151117 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1122 0.1551 0.0429 0.010 1.0 4.2 0.5 0.0 0 0.967 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.22 15.51 4.29 4.423 20.753 0.151 4.963 11.09 15.49 4.40 4.632 20.747 0.151 4.955 Individual atomic B min max mean iso aniso Overall: 5.23 103.40 20.60 4.83 1964 0 Protein: 5.23 103.40 16.31 4.83 1519 0 Water: 8.22 66.73 35.39 N/A 437 0 Other: 20.74 37.45 27.70 N/A 8 0 Chain A: 5.23 103.40 17.95 N/A 1733 0 Chain S: 16.84 66.73 40.50 N/A 231 0 Histogram: Values Number of atoms 5.23 - 15.05 1018 15.05 - 24.86 391 24.86 - 34.68 221 34.68 - 44.50 197 44.50 - 54.32 88 54.32 - 64.13 33 64.13 - 73.95 9 73.95 - 83.77 3 83.77 - 93.59 2 93.59 - 103.40 2 =========================== Idealize ADP of riding H ========================== r_work=0.1109 r_free=0.1549 r_work=0.1109 r_free=0.1549 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1109 r_free = 0.1549 target_work(ml) = 4.955 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1103 r_free = 0.1564 target_work(ml) = 4.955 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1103 r_free= 0.1564 coordinate error (max.-lik. estimate): 0.12 A | | | | normalized target function (ml) (work): 4.954885 | | target function (ml) not normalized (work): 80437.599197 | | target function (ml) not normalized (free): 4192.221107 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1125 0.1103 0.1564 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1568 0.1551 0.1907 n_refl.: 17041 remove outliers: r(all,work,free)=0.1568 0.1551 0.1907 n_refl.: 17041 overall B=-0.24 to atoms: r(all,work,free)=0.1554 0.1537 0.1899 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1124 0.1102 0.1560 n_refl.: 17041 remove outliers: r(all,work,free)=0.1123 0.1101 0.1560 n_refl.: 17040 ======================== 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 0.3724 302.047 269.761 0.536 1.001 0.320 11.894-9.307 99.02 97 4 0.1743 487.905 483.330 0.927 1.001 0.294 9.237-7.194 100.00 213 7 0.1667 399.057 400.734 0.992 1.002 0.230 7.162-5.571 100.00 427 22 0.1549 299.493 293.742 0.939 1.002 0.230 5.546-4.326 100.00 867 58 0.0900 411.156 407.911 0.966 1.002 0.192 4.315-3.360 100.00 1859 96 0.0833 391.013 389.015 1.007 1.001 0.177 3.356-2.611 100.00 3867 181 0.1215 256.873 254.758 1.002 1.001 0.141 2.608-2.000 99.99 8818 434 0.1065 167.437 166.195 0.992 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9583 b_overall=-0.8384 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1101 r_free=0.1560 After: r_work=0.1103 r_free=0.1559 ================================== NQH flips ================================== r_work=0.1103 r_free=0.1559 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN Total number of N/Q/H flips: 1 r_work=0.1104 r_free=0.1559 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1104 r_free=0.1559 | n_water=437 | time (s): 0.710 (total time: 0.710) Filter (dist) r_work=0.1104 r_free=0.1559 | n_water=437 | time (s): 34.340 (total time: 35.050) Filter (q & B) r_work=0.1104 r_free=0.1559 | n_water=437 | time (s): 1.130 (total time: 36.180) Compute maps r_work=0.1104 r_free=0.1559 | n_water=437 | time (s): 0.750 (total time: 36.930) Filter (map) r_work=0.1175 r_free=0.1544 | n_water=335 | time (s): 1.580 (total time: 38.510) Find peaks r_work=0.1175 r_free=0.1544 | n_water=335 | time (s): 0.410 (total time: 38.920) Add new water r_work=0.1286 r_free=0.1633 | n_water=476 | time (s): 1.520 (total time: 40.440) Refine new water occ: r_work=0.1130 r_free=0.1507 adp: r_work=0.1122 r_free=0.1509 occ: r_work=0.1112 r_free=0.1492 adp: r_work=0.1104 r_free=0.1492 occ: r_work=0.1099 r_free=0.1486 adp: r_work=0.1093 r_free=0.1487 ADP+occupancy (water only), MIN, final r_work=0.1093 r_free=0.1487 r_work=0.1093 r_free=0.1487 | n_water=476 | time (s): 34.600 (total time: 75.040) Filter (q & B) r_work=0.1100 r_free=0.1500 | n_water=456 | time (s): 1.710 (total time: 76.750) Filter (dist only) r_work=0.1100 r_free=0.1501 | n_water=455 | time (s): 38.150 (total time: 114.900) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.873162 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.170260 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1124 0.1511 0.0386 0.010 1.0 7.0 0.5 0.0 0 0.937 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.24 15.11 3.86 4.517 20.513 0.170 4.956 11.11 15.09 3.98 4.645 20.554 0.170 4.946 Individual atomic B min max mean iso aniso Overall: 5.30 102.93 20.56 5.02 1982 0 Protein: 5.30 102.93 16.01 5.01 1519 0 Water: 7.81 67.68 35.56 N/A 455 0 Other: 23.13 38.99 29.48 N/A 8 0 Chain A: 5.30 102.93 17.63 N/A 1733 0 Chain S: 13.94 67.68 40.90 N/A 249 0 Histogram: Values Number of atoms 5.30 - 15.07 1054 15.07 - 24.83 365 24.83 - 34.59 215 34.59 - 44.36 185 44.36 - 54.12 117 54.12 - 63.88 31 63.88 - 73.65 5 73.65 - 83.41 5 83.41 - 93.17 2 93.17 - 102.93 3 =========================== Idealize ADP of riding H ========================== r_work=0.1111 r_free=0.1509 r_work=0.1111 r_free=0.1508 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1111 r_free = 0.1508 target_work(ml) = 4.946 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1108 r_free = 0.1522 target_work(ml) = 4.946 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1108 r_free= 0.1522 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ml) (work): 4.945803 | | target function (ml) not normalized (work): 80285.227333 | | target function (ml) not normalized (free): 4175.898915 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.64 1.00 2810 159 0.1115 0.1364 5.4557 5.6523| | 2: 3.63 - 2.88 1.00 2711 122 0.1078 0.1465 5.2075 5.3407| | 3: 2.88 - 2.52 1.00 2681 148 0.1335 0.1691 5.1167 5.1871| | 4: 2.52 - 2.29 1.00 2661 139 0.0962 0.1625 4.6591 5.0129| | 5: 2.29 - 2.13 1.00 2678 122 0.0992 0.1508 4.6103 4.9034| | 6: 2.13 - 2.00 1.00 2692 117 0.1136 0.1810 4.5969 4.8113| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 - 3.64 2810 159 0.95 8.86 1.00 0.95 6206.22| | 2: 3.63 - 2.88 2711 122 0.92 12.75 1.01 0.95 6206.22| | 3: 2.88 - 2.52 2681 148 0.88 18.67 0.99 0.95 6206.22| | 4: 2.52 - 2.29 2661 139 0.92 12.70 1.01 0.97 2279.40| | 5: 2.29 - 2.13 2678 122 0.91 14.82 1.00 0.97 2279.40| | 6: 2.13 - 2.00 2692 117 0.89 17.58 0.99 0.97 2279.40| |alpha: min = 0.95 max = 0.97 mean = 0.96| |beta: min = 2279.40 max = 6206.22 mean = 4263.49| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.99 mean = 14.19| |phase err.(test): min = 0.00 max = 89.54 mean = 13.77| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1128 0.1108 0.1522 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1548 0.1535 0.1825 n_refl.: 17040 remove outliers: r(all,work,free)=0.1548 0.1535 0.1825 n_refl.: 17040 overall B=-0.17 to atoms: r(all,work,free)=0.1539 0.1526 0.1820 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1128 0.1108 0.1525 n_refl.: 17040 remove outliers: r(all,work,free)=0.1128 0.1108 0.1525 n_refl.: 17040 ======================== 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 0.3522 302.047 283.305 0.561 1.005 0.324 11.894-9.307 99.02 97 4 0.1740 487.905 482.521 0.925 1.006 0.319 9.237-7.194 100.00 213 7 0.1757 399.057 400.076 0.989 1.006 0.236 7.162-5.571 100.00 427 22 0.1568 299.493 294.019 0.941 1.005 0.217 5.546-4.326 100.00 867 58 0.0930 411.156 408.123 0.967 1.005 0.210 4.315-3.360 100.00 1859 96 0.0854 391.013 388.655 1.007 1.003 0.184 3.356-2.611 100.00 3867 181 0.1224 256.873 254.699 1.002 1.000 0.151 2.608-2.000 99.99 8818 434 0.1058 167.437 166.029 0.990 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.6007 ================= 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 : 0.2791 0.1820 0.083 5.417 8.8 119.3 19.9 258 0.000 1_bss: 0.1622 0.1652 0.083 5.417 8.5 118.9 19.5 258 0.000 1_settarget: 0.1622 0.1652 0.083 5.417 8.5 118.9 19.5 258 0.000 1_nqh: 0.1626 0.1666 0.083 5.417 8.5 118.9 19.5 258 0.003 1_weight: 0.1626 0.1666 0.083 5.417 8.5 118.9 19.5 258 0.003 1_xyzrec: 0.1352 0.1625 0.009 1.001 8.5 118.9 19.5 258 0.145 1_adp: 0.1280 0.1652 0.009 1.001 6.2 113.9 19.9 258 0.145 1_regHadp: 0.1283 0.1659 0.009 1.001 6.2 113.9 19.9 258 0.145 1_occ: 0.1279 0.1652 0.009 1.001 6.2 113.9 19.9 258 0.145 2_bss: 0.1274 0.1640 0.009 1.001 5.7 113.4 19.4 258 0.145 2_settarget: 0.1274 0.1640 0.009 1.001 5.7 113.4 19.4 258 0.145 2_updatecdl: 0.1274 0.1640 0.009 0.999 5.7 113.4 19.4 258 0.145 2_nqh: 0.1276 0.1643 0.009 0.999 5.7 113.4 19.4 258 0.142 2_sol: 0.1247 0.1556 0.009 0.999 5.7 112.4 20.8 362 n/a 2_weight: 0.1247 0.1556 0.009 0.999 5.7 112.4 20.8 362 n/a 2_xyzrec: 0.1219 0.1630 0.008 0.935 5.7 112.4 20.8 362 n/a 2_adp: 0.1201 0.1635 0.008 0.935 6.4 107.4 21.2 362 n/a 2_regHadp: 0.1203 0.1636 0.008 0.935 6.4 107.4 21.2 362 n/a 2_occ: 0.1199 0.1634 0.008 0.935 6.4 107.4 21.2 362 n/a 3_bss: 0.1195 0.1626 0.008 0.935 6.1 107.1 20.8 362 n/a 3_settarget: 0.1195 0.1626 0.008 0.935 6.1 107.1 20.8 362 n/a 3_updatecdl: 0.1195 0.1626 0.008 0.938 6.1 107.1 20.8 362 n/a 3_nqh: 0.1196 0.1628 0.008 0.938 6.1 107.1 20.8 362 n/a 3_sol: 0.1210 0.1559 0.008 0.938 6.1 107.1 20.7 398 n/a 3_weight: 0.1210 0.1559 0.008 0.938 6.1 107.1 20.7 398 n/a 3_xyzrec: 0.1190 0.1549 0.009 0.960 6.1 107.1 20.7 398 n/a 3_adp: 0.1171 0.1565 0.009 0.960 6.0 106.5 20.5 398 n/a 3_regHadp: 0.1172 0.1567 0.009 0.960 6.0 106.5 20.5 398 n/a 3_occ: 0.1164 0.1572 0.009 0.960 6.0 106.5 20.5 398 n/a 4_bss: 0.1161 0.1573 0.009 0.960 5.7 106.2 20.1 398 n/a 4_settarget: 0.1161 0.1573 0.009 0.960 5.7 106.2 20.1 398 n/a 4_updatecdl: 0.1161 0.1573 0.009 0.960 5.7 106.2 20.1 398 n/a 4_nqh: 0.1161 0.1571 0.009 0.960 5.7 106.2 20.1 398 n/a 4_sol: 0.1145 0.1494 0.009 0.960 5.7 106.2 20.6 437 n/a 4_weight: 0.1145 0.1494 0.009 0.960 5.7 106.2 20.6 437 n/a 4_xyzrec: 0.1122 0.1551 0.010 0.988 5.7 106.2 20.6 437 n/a 4_adp: 0.1109 0.1549 0.010 0.988 5.2 103.4 20.6 437 n/a 4_regHadp: 0.1109 0.1549 0.010 0.988 5.2 103.4 20.6 437 n/a 4_occ: 0.1103 0.1564 0.010 0.988 5.2 103.4 20.6 437 n/a 5_bss: 0.1101 0.1560 0.010 0.988 5.0 103.2 20.4 437 n/a 5_settarget: 0.1101 0.1560 0.010 0.988 5.0 103.2 20.4 437 n/a 5_updatecdl: 0.1101 0.1560 0.010 0.989 5.0 103.2 20.4 437 n/a 5_setrh: 0.1103 0.1559 0.010 0.989 5.0 103.2 20.4 437 n/a 5_nqh: 0.1104 0.1559 0.010 0.989 5.0 103.2 20.4 437 n/a 5_sol: 0.1100 0.1501 0.010 0.989 5.0 103.2 20.5 455 n/a 5_weight: 0.1100 0.1501 0.010 0.989 5.0 103.2 20.5 455 n/a 5_xyzrec: 0.1124 0.1511 0.010 1.023 5.0 103.2 20.5 455 n/a 5_adp: 0.1111 0.1509 0.010 1.023 5.3 102.9 20.6 455 n/a 5_regHadp: 0.1111 0.1508 0.010 1.023 5.3 102.9 20.6 455 n/a 5_occ: 0.1108 0.1522 0.010 1.023 5.3 102.9 20.6 455 n/a end: 0.1108 0.1525 0.010 1.023 5.1 102.8 20.4 455 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_4735076_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_4735076_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 2.8800 Refinement macro-cycles (run) : 925.9300 Write final files (write_after_run_outputs) : 20.2300 Total : 949.0400 Total CPU time: 16.19 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:12 PST -0800 (1735494072.62 s) Start R-work = 0.1622, R-free = 0.1652 Final R-work = 0.1108, R-free = 0.1525 =============================================================================== Job complete usr+sys time: 992.09 seconds wall clock time: 16 minutes 55.07 seconds (1015.07 seconds total)