Starting phenix.refine on Sun Dec 29 09:10:02 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2353655.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=3 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 { 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" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 3 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2353655.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2353655.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { 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 =============================================================================== Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 2.12, per 1000 atoms: 0.63 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: 0.52 Conformation dependent library (CDL) restraints added in 167.7 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.91: 532 0.91 - 1.16: 1109 1.16 - 1.42: 624 1.42 - 1.67: 838 1.67 - 1.92: 50 Bond restraints: 3153 Sorted by residual: bond pdb=" C LEU A 7 " pdb=" O LEU A 7 " ideal model delta sigma weight residual 1.236 0.974 0.262 1.19e-02 7.06e+03 4.84e+02 bond pdb=" CA ILE A 21 " pdb=" C ILE A 21 " ideal model delta sigma weight residual 1.523 1.699 -0.176 9.20e-03 1.18e+04 3.64e+02 bond pdb=" C BGLU A 96 " pdb=" O BGLU A 96 " ideal model delta sigma weight residual 1.237 1.011 0.226 1.19e-02 7.06e+03 3.59e+02 bond pdb=" ND1 HIS A 138 " pdb=" CE1 HIS A 138 " ideal model delta sigma weight residual 1.321 1.132 0.189 1.00e-02 1.00e+04 3.57e+02 bond pdb=" CA ILE A 21 " pdb=" CB ILE A 21 " ideal model delta sigma weight residual 1.539 1.639 -0.100 5.40e-03 3.43e+04 3.41e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.38: 3034 4.38 - 8.76: 1829 8.76 - 13.13: 729 13.13 - 17.51: 159 17.51 - 21.89: 26 Bond angle restraints: 5777 Sorted by residual: angle pdb=" NE ARG A 156 " pdb=" CZ ARG A 156 " pdb=" NH1 ARG A 156 " ideal model delta sigma weight residual 121.50 134.62 -13.12 1.00e+00 1.00e+00 1.72e+02 angle pdb=" O LEU A 82 " pdb=" C LEU A 82 " pdb=" N SER A 83 " ideal model delta sigma weight residual 122.15 137.09 -14.94 1.14e+00 7.69e-01 1.72e+02 angle pdb=" CA PHE A 119 " pdb=" CB PHE A 119 " pdb=" CG PHE A 119 " ideal model delta sigma weight residual 113.80 126.88 -13.08 1.00e+00 1.00e+00 1.71e+02 angle pdb=" O BCYS A 53 " pdb=" C BCYS A 53 " pdb=" N PRO A 54 " ideal model delta sigma weight residual 121.19 109.67 11.52 9.40e-01 1.13e+00 1.50e+02 angle pdb=" O PRO A 158 " pdb=" C PRO A 158 " pdb=" N GLY A 159 " ideal model delta sigma weight residual 122.23 136.92 -14.69 1.20e+00 6.94e-01 1.50e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.75: 1289 16.75 - 33.50: 132 33.50 - 50.25: 43 50.25 - 67.00: 15 67.00 - 83.75: 2 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" N ALA A 183 " pdb=" C ALA A 183 " pdb=" CA ALA A 183 " pdb=" CB ALA A 183 " ideal model delta harmonic sigma weight residual 122.90 143.06 -20.16 0 2.50e+00 1.60e-01 6.50e+01 dihedral pdb=" N BLEU A 153 " pdb=" C BLEU A 153 " pdb=" CA BLEU A 153 " pdb=" CB BLEU A 153 " ideal model delta harmonic sigma weight residual 122.80 104.46 18.34 0 2.50e+00 1.60e-01 5.38e+01 dihedral pdb=" N PRO A 22 " pdb=" C PRO A 22 " pdb=" CA PRO A 22 " pdb=" CB PRO A 22 " ideal model delta harmonic sigma weight residual 115.10 132.73 -17.63 0 2.50e+00 1.60e-01 4.98e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.225: 105 0.225 - 0.449: 85 0.449 - 0.673: 38 0.673 - 0.897: 8 0.897 - 1.122: 7 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA ALA A 14 " pdb=" N ALA A 14 " pdb=" C ALA A 14 " pdb=" CB ALA A 14 " both_signs ideal model delta sigma weight residual False 2.48 3.61 -1.12 2.00e-01 2.50e+01 3.15e+01 chirality pdb=" CG LEU A 172 " pdb=" CB LEU A 172 " pdb=" CD1 LEU A 172 " pdb=" CD2 LEU A 172 " both_signs ideal model delta sigma weight residual False -2.59 -1.56 -1.03 2.00e-01 2.50e+01 2.67e+01 chirality pdb=" CB THR A 154 " pdb=" CA THR A 154 " pdb=" OG1 THR A 154 " pdb=" CG2 THR A 154 " both_signs ideal model delta sigma weight residual False 2.55 1.58 0.97 2.00e-01 2.50e+01 2.34e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 156 " -0.090 9.50e-02 1.11e+02 7.28e-02 1.00e+02 pdb=" NE ARG A 156 " 0.037 2.00e-02 2.50e+03 pdb=" CZ ARG A 156 " 0.075 2.00e-02 2.50e+03 pdb=" NH1 ARG A 156 " 0.069 2.00e-02 2.50e+03 pdb=" NH2 ARG A 156 " -0.091 2.00e-02 2.50e+03 pdb="HH11 ARG A 156 " -0.077 2.00e-02 2.50e+03 pdb="HH12 ARG A 156 " -0.034 2.00e-02 2.50e+03 pdb="HH21 ARG A 156 " -0.066 2.00e-02 2.50e+03 pdb="HH22 ARG A 156 " 0.091 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " -0.003 2.00e-02 2.50e+03 5.67e-02 9.65e+01 pdb=" CG BTYR A 67 " 0.047 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " -0.070 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " 0.092 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " -0.001 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " -0.059 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " 0.078 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " 0.023 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " 0.048 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " -0.073 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " -0.072 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 138 " 0.114 2.00e-02 2.50e+03 6.49e-02 9.46e+01 pdb=" CG HIS A 138 " -0.112 2.00e-02 2.50e+03 pdb=" ND1 HIS A 138 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 HIS A 138 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 HIS A 138 " 0.036 2.00e-02 2.50e+03 pdb=" NE2 HIS A 138 " -0.032 2.00e-02 2.50e+03 pdb=" HD1 HIS A 138 " -0.068 2.00e-02 2.50e+03 pdb=" HD2 HIS A 138 " 0.008 2.00e-02 2.50e+03 pdb=" HE1 HIS A 138 " 0.071 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.31: 984 2.31 - 2.88: 8064 2.88 - 3.46: 10527 3.46 - 4.03: 15145 4.03 - 4.60: 21916 Nonbonded interactions: 56636 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.738 2.100 nonbonded pdb=" H THR A 124 " pdb=" HG1 THR A 154 " model vdw 1.766 2.100 nonbonded pdb=" HE3ALYS A 132 " pdb=" HO2ADTT A 201 " model vdw 1.792 2.270 nonbonded pdb=" H LYS A 122 " pdb=" OD2 ASP A 149 " model vdw 1.808 2.450 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.832 2.450 ... (remaining 56631 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 1 N 265 6.97 1 C 957 5.97 2 H 1596 1.00 1 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_2353655_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: 3.00 - 49.25 A, n_refl.=5182 (all), 4.86 % free)-------------| | | | r_work= 0.3617 r_free= 0.2018 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.471422 | | target function (ml) not normalized (work): 22044.112888 | | target function (ml) not normalized (free): 1143.604328 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 49.25 - 3.79 1.00 2500 142 0.3801 0.2255 4.8549 4.9225| | 2: 3.78 - 3.00 1.00 2430 110 0.3393 0.1618 4.0769 4.0418| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 - 3.79 2500 142 0.50 48.85 0.83 0.13 6615.92| | 2: 3.78 - 3.00 2430 110 0.94 11.26 1.48 0.26 451.87| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 383.18 max = 12080.43 mean = 3577.66| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 89.99 mean = 30.32| |phase err.(test): min = 0.00 max = 90.00 mean = 33.49| |-----------------------------------------------------------------------------| ----------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 0.262 1557 Z= 5.579 Angle : 5.302 19.172 2118 Z= 3.691 Chirality : 0.374 1.122 243 Planarity : 0.033 0.109 284 Dihedral : 13.894 83.747 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.86 % Allowed : 3.11 % Favored : 95.03 % Cbeta Deviations : 26.49 % 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: -1.96 (0.51), residues: 224 helix: -2.43 (0.37), residues: 108 sheet: 0.13 (0.94), residues: 28 loop : 0.11 (0.67), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.115 0.027 ARG A 145 TYR 0.086 0.035 TYR A 141 PHE 0.103 0.033 PHE A 119 HIS 0.053 0.028 HIS A 115 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: 3.00 - 49.25 A, n_refl.=5182 (all), 4.86 % free)-------------| | | | r_work= 0.3617 r_free= 0.2018 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.471422 | | target function (ml) not normalized (work): 22044.112888 | | target function (ml) not normalized (free): 1143.604328 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3573 0.3650 0.2140 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3573 0.3650 0.2140 n_refl.: 5182 remove outliers: r(all,work,free)=0.2529 0.2553 0.2140 n_refl.: 5178 overall B=-2.39 to atoms: r(all,work,free)=0.2437 0.2457 0.2097 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1569 0.1570 0.1559 n_refl.: 5178 remove outliers: r(all,work,free)=0.1567 0.1568 0.1559 n_refl.: 5177 ======================== 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 0.4082 444.994 407.108 0.618 1.087 0.394 11.894-9.307 99.02 97 4 0.1884 714.384 694.078 0.891 1.082 0.382 9.237-7.194 100.00 213 7 0.2204 584.224 576.750 0.925 1.073 0.353 7.162-5.571 100.00 427 22 0.2308 438.389 423.865 0.890 1.057 0.287 5.546-4.326 100.00 867 58 0.1407 601.846 594.722 0.939 1.031 0.223 4.315-3.360 100.00 1859 96 0.1311 572.362 565.979 1.024 0.987 0.204 3.356-3.002 100.00 1373 60 0.1596 440.858 433.684 1.050 0.944 0.074 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9170 b_overall=-4.1578 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1568 r_free=0.1559 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN B A 144 ASN Total number of N/Q/H flips: 2 r_work=0.1569 r_free=0.1556 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 19.534868 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.647921 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 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 0.1157 0.1764 0.0608 0.010 1.0 2.6 0.5 0.0 0 9.767 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.57 17.64 6.08 3.013 16.472 1.648 0.018 10.16 17.53 7.37 4.819 16.676 1.648 0.014 Individual atomic B min max mean iso aniso Overall: 2.79 111.91 17.89 5.18 1785 0 Protein: 2.79 111.49 15.21 5.18 1519 0 Water: 4.48 111.91 33.47 N/A 258 0 Other: 17.57 33.78 24.12 N/A 8 0 Chain A: 2.79 111.91 17.89 N/A 1785 0 Histogram: Values Number of atoms 2.79 - 13.70 933 13.70 - 24.61 472 24.61 - 35.53 188 35.53 - 46.44 107 46.44 - 57.35 52 57.35 - 68.26 16 68.26 - 79.17 8 79.17 - 90.09 5 90.09 - 101.00 1 101.00 - 111.91 3 =========================== Idealize ADP of riding H ========================== r_work=0.1016 r_free=0.1753 r_work=0.1009 r_free=0.1760 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1009 r_free = 0.1760 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1014 r_free = 0.1757 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5177 (all), 4.87 % free)-------------| | | | r_work= 0.1014 r_free= 0.1757 coordinate error (max.-lik. estimate): 0.31 A | | | | normalized target function (ls_wunit_k1) (work): 0.014039 | | target function (ls_wunit_k1) not normalized (work): 69.142031 | | target function (ls_wunit_k1) not normalized (free): 9.944207 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1052 0.1014 0.1757 n_refl.: 5177 re-set all scales: r(all,work,free)=0.2120 0.2121 0.2230 n_refl.: 5177 remove outliers: r(all,work,free)=0.2120 0.2121 0.2230 n_refl.: 5177 overall B=-0.92 to atoms: r(all,work,free)=0.2081 0.2079 0.2220 n_refl.: 5177 bulk-solvent and scaling: r(all,work,free)=0.1062 0.1024 0.1775 n_refl.: 5177 remove outliers: r(all,work,free)=0.1060 0.1022 0.1775 n_refl.: 5176 ======================== 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 96.88 88 5 0.3387 311.184 297.677 0.635 1.004 0.365 11.894-9.307 99.02 97 4 0.1509 503.868 497.585 0.956 1.006 0.361 9.237-7.194 100.00 213 7 0.1667 412.064 414.104 0.999 1.005 0.315 7.162-5.571 100.00 427 22 0.1628 309.204 306.339 0.953 1.004 0.292 5.546-4.326 100.00 867 58 0.0918 424.493 421.342 0.964 1.002 0.207 4.315-3.360 100.00 1859 96 0.0776 403.697 403.810 1.013 0.999 0.203 3.356-3.002 100.00 1373 60 0.1015 310.945 308.830 0.987 0.996 0.072 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9170 b_overall=-4.0997 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1022 r_free=0.1775 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN B A 144 ASN Total number of N/Q/H flips: 2 r_work=0.1023 r_free=0.1780 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1023 r_free=0.1780 | n_water=258 | time (s): 0.510 (total time: 0.510) Filter (dist) r_work=0.1048 r_free=0.1767 | n_water=247 | time (s): 20.980 (total time: 21.490) Filter (q & B) r_work=0.1049 r_free=0.1770 | n_water=245 | time (s): 1.460 (total time: 22.950) Compute maps r_work=0.1049 r_free=0.1770 | n_water=245 | time (s): 0.590 (total time: 23.540) Filter (map) r_work=0.1332 r_free=0.1900 | n_water=144 | time (s): 2.030 (total time: 25.570) Find peaks r_work=0.1332 r_free=0.1900 | n_water=144 | time (s): 0.600 (total time: 26.170) Add new water r_work=0.1682 r_free=0.2229 | n_water=230 | time (s): 1.720 (total time: 27.890) Refine new water occ: r_work=0.1160 r_free=0.1701 adp: r_work=0.1137 r_free=0.1713 occ: r_work=0.1134 r_free=0.1683 adp: r_work=0.1124 r_free=0.1691 occ: r_work=0.1124 r_free=0.1678 adp: r_work=0.1120 r_free=0.1683 ADP+occupancy (water only), MIN, final r_work=0.1120 r_free=0.1683 r_work=0.1120 r_free=0.1683 | n_water=230 | time (s): 4.240 (total time: 32.130) Filter (q & B) r_work=0.1121 r_free=0.1687 | n_water=229 | time (s): 1.870 (total time: 34.000) Filter (dist only) r_work=0.1126 r_free=0.1701 | n_water=225 | time (s): 18.190 (total time: 52.190) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.479545 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.623489 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 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 0.1021 0.1819 0.0798 0.009 1.0 4.5 0.5 0.6 0 11.740 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.21 18.19 7.98 4.632 17.293 2.623 0.014 9.50 18.36 8.86 5.478 17.567 2.623 0.013 Individual atomic B min max mean iso aniso Overall: 0.00 107.26 16.78 6.44 1752 0 Protein: 0.00 107.26 15.31 6.43 1519 0 Water: 0.00 63.28 26.54 N/A 225 0 Other: 11.96 29.67 21.52 N/A 8 0 Chain A: 0.00 107.26 16.01 N/A 1669 0 Chain S: 0.00 55.98 32.36 N/A 83 0 Histogram: Values Number of atoms 0.00 - 10.73 658 10.73 - 21.45 675 21.45 - 32.18 223 32.18 - 42.90 116 42.90 - 53.63 44 53.63 - 64.36 23 64.36 - 75.08 6 75.08 - 85.81 3 85.81 - 96.53 2 96.53 - 107.26 2 =========================== Idealize ADP of riding H ========================== r_work=0.0950 r_free=0.1836 r_work=0.0946 r_free=0.1835 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0946 r_free = 0.1835 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0940 r_free = 0.1818 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.0940 r_free= 0.1818 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ls_wunit_k1) (work): 0.012127 | | target function (ls_wunit_k1) not normalized (work): 59.713537 | | target function (ls_wunit_k1) not normalized (free): 9.789678 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0985 0.0940 0.1818 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2150 0.2158 0.2172 n_refl.: 5176 remove outliers: r(all,work,free)=0.2150 0.2158 0.2172 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2150 0.2158 0.2172 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0984 0.0940 0.1826 n_refl.: 5176 remove outliers: r(all,work,free)=0.0984 0.0940 0.1826 n_refl.: 5176 ======================== 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 96.88 88 5 0.3499 311.184 297.764 0.641 1.005 0.352 11.894-9.307 99.02 97 4 0.1461 503.868 499.527 0.991 1.007 0.347 9.237-7.194 100.00 213 7 0.1484 412.064 412.986 1.033 1.007 0.305 7.162-5.571 100.00 427 22 0.1414 309.204 307.394 1.005 1.006 0.300 5.546-4.326 100.00 867 58 0.0802 424.493 422.111 1.016 1.003 0.240 4.315-3.360 100.00 1859 96 0.0713 403.697 403.507 1.068 1.000 0.200 3.356-3.002 100.00 1373 60 0.0971 310.945 309.742 1.045 0.996 0.090 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-4.8183 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0940 r_free=0.1826 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A Total number of N/Q/H flips: 1 r_work=0.0941 r_free=0.1827 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0941 r_free=0.1827 | n_water=225 | time (s): 0.610 (total time: 0.610) Filter (dist) r_work=0.0946 r_free=0.1822 | n_water=223 | time (s): 18.660 (total time: 19.270) Filter (q & B) r_work=0.1019 r_free=0.1840 | n_water=219 | time (s): 1.320 (total time: 20.590) Compute maps r_work=0.1019 r_free=0.1840 | n_water=219 | time (s): 0.540 (total time: 21.130) Filter (map) r_work=0.1261 r_free=0.1888 | n_water=146 | time (s): 1.840 (total time: 22.970) Find peaks r_work=0.1261 r_free=0.1888 | n_water=146 | time (s): 0.610 (total time: 23.580) Add new water r_work=0.1637 r_free=0.2242 | n_water=231 | time (s): 1.500 (total time: 25.080) Refine new water occ: r_work=0.1057 r_free=0.1801 adp: r_work=0.1052 r_free=0.1804 occ: r_work=0.1041 r_free=0.1792 adp: r_work=0.1041 r_free=0.1795 occ: r_work=0.1032 r_free=0.1782 adp: r_work=0.1031 r_free=0.1788 ADP+occupancy (water only), MIN, final r_work=0.1031 r_free=0.1788 r_work=0.1031 r_free=0.1788 | n_water=231 | time (s): 12.680 (total time: 37.760) Filter (q & B) r_work=0.1032 r_free=0.1787 | n_water=230 | time (s): 1.330 (total time: 39.090) Filter (dist only) r_work=0.1032 r_free=0.1798 | n_water=229 | time (s): 17.460 (total time: 56.550) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.137175 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.206392 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 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 0.0932 0.1841 0.0910 0.011 1.1 4.2 0.5 0.0 0 0.569 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.32 18.41 9.10 5.404 18.061 0.206 5.115 8.96 18.37 9.42 7.141 18.063 0.206 5.028 Individual atomic B min max mean iso aniso Overall: 0.00 105.55 16.61 8.78 1756 0 Protein: 0.00 105.55 15.46 8.79 1519 0 Water: 0.00 58.28 24.09 N/A 229 0 Other: 9.41 30.05 20.77 N/A 8 0 Chain A: 0.00 105.55 16.09 N/A 1659 0 Chain S: 0.00 56.40 25.47 N/A 97 0 Histogram: Values Number of atoms 0.00 - 10.56 630 10.56 - 21.11 685 21.11 - 31.66 243 31.66 - 42.22 121 42.22 - 52.77 38 52.77 - 63.33 21 63.33 - 73.88 9 73.88 - 84.44 4 84.44 - 94.99 3 94.99 - 105.55 2 =========================== Idealize ADP of riding H ========================== r_work=0.0896 r_free=0.1837 r_work=0.0900 r_free=0.1844 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0900 r_free = 0.1844 target_work(ml) = 5.031 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0888 r_free = 0.1829 target_work(ml) = 5.023 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.0888 r_free= 0.1829 coordinate error (max.-lik. estimate): 0.27 A | | | | normalized target function (ml) (work): 5.023414 | | target function (ml) not normalized (work): 24735.290108 | | target function (ml) not normalized (free): 1826.673317 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0935 0.0888 0.1829 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2160 0.2172 0.2117 n_refl.: 5176 remove outliers: r(all,work,free)=0.2160 0.2172 0.2117 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2160 0.2172 0.2117 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0930 0.0883 0.1820 n_refl.: 5176 remove outliers: r(all,work,free)=0.0928 0.0881 0.1820 n_refl.: 5175 ======================== 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 0.3747 313.217 285.553 0.603 0.997 0.350 11.894-9.307 99.02 97 4 0.1777 503.868 490.529 0.953 0.999 0.325 9.237-7.194 100.00 213 7 0.1844 412.064 406.393 1.000 1.001 0.300 7.162-5.571 100.00 427 22 0.1748 309.204 301.619 0.979 1.001 0.280 5.546-4.326 100.00 867 58 0.0917 424.493 419.715 0.996 1.002 0.240 4.315-3.360 100.00 1859 96 0.0581 403.697 403.305 1.053 1.002 0.220 3.356-3.002 100.00 1373 60 0.0625 310.945 310.430 1.032 1.002 0.080 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9171 b_overall=-6.2705 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0881 r_free=0.1820 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0881 r_free=0.1820 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0881 r_free=0.1820 | n_water=229 | time (s): 0.590 (total time: 0.590) Filter (dist) r_work=0.0893 r_free=0.1818 | n_water=227 | time (s): 19.280 (total time: 19.870) Filter (q & B) r_work=0.0927 r_free=0.1818 | n_water=226 | time (s): 1.460 (total time: 21.330) Compute maps r_work=0.0927 r_free=0.1818 | n_water=226 | time (s): 0.700 (total time: 22.030) Filter (map) r_work=0.1216 r_free=0.1879 | n_water=157 | time (s): 2.010 (total time: 24.040) Find peaks r_work=0.1216 r_free=0.1879 | n_water=157 | time (s): 0.570 (total time: 24.610) Add new water r_work=0.1544 r_free=0.2165 | n_water=237 | time (s): 1.360 (total time: 25.970) Refine new water occ: r_work=0.0990 r_free=0.1819 adp: r_work=0.0987 r_free=0.1826 occ: r_work=0.0978 r_free=0.1811 adp: r_work=0.0978 r_free=0.1817 occ: r_work=0.0971 r_free=0.1804 adp: r_work=0.0971 r_free=0.1809 ADP+occupancy (water only), MIN, final r_work=0.0971 r_free=0.1809 r_work=0.0971 r_free=0.1809 | n_water=237 | time (s): 9.960 (total time: 35.930) Filter (q & B) r_work=0.0973 r_free=0.1810 | n_water=235 | time (s): 1.820 (total time: 37.750) Filter (dist only) r_work=0.0989 r_free=0.1801 | n_water=233 | time (s): 17.870 (total time: 55.620) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.077854 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.265868 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 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 0.0901 0.1879 0.0978 0.011 1.1 4.5 0.5 0.0 0 0.539 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.01 18.79 9.78 6.878 18.190 0.266 4.994 8.78 19.32 10.54 8.220 18.313 0.266 4.929 Individual atomic B min max mean iso aniso Overall: 0.00 103.55 16.91 10.69 1760 0 Protein: 0.00 103.55 15.89 10.70 1519 0 Water: 0.00 54.10 23.49 N/A 233 0 Other: 9.28 32.34 20.17 N/A 8 0 Chain A: 0.00 103.55 16.44 N/A 1647 0 Chain S: 0.00 47.67 23.82 N/A 113 0 Histogram: Values Number of atoms 0.00 - 10.36 613 10.36 - 20.71 656 20.71 - 31.07 270 31.07 - 41.42 139 41.42 - 51.78 38 51.78 - 62.13 20 62.13 - 72.49 13 72.49 - 82.84 4 82.84 - 93.20 4 93.20 - 103.55 3 =========================== Idealize ADP of riding H ========================== r_work=0.0878 r_free=0.1932 r_work=0.0883 r_free=0.1939 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0883 r_free = 0.1939 target_work(ml) = 4.936 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0870 r_free = 0.1924 target_work(ml) = 4.925 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0870 r_free= 0.1924 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 4.925008 | | target function (ml) not normalized (work): 24245.815295 | | target function (ml) not normalized (free): 2188.014206 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0923 0.0870 0.1924 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2116 0.2117 0.2257 n_refl.: 5175 remove outliers: r(all,work,free)=0.2116 0.2117 0.2257 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2116 0.2117 0.2257 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0920 0.0868 0.1912 n_refl.: 5175 remove outliers: r(all,work,free)=0.0920 0.0868 0.1912 n_refl.: 5175 ======================== 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 0.3793 313.217 284.541 0.574 0.989 0.316 11.894-9.307 99.02 97 4 0.1840 503.868 489.601 0.951 0.993 0.313 9.237-7.194 100.00 213 7 0.2155 412.064 401.588 1.005 0.996 0.290 7.162-5.571 100.00 427 22 0.1975 309.204 300.424 0.998 0.997 0.280 5.546-4.326 100.00 867 58 0.0955 424.493 419.053 1.015 1.000 0.240 4.315-3.360 100.00 1859 96 0.0544 403.697 403.527 1.077 1.003 0.220 3.356-3.002 100.00 1373 60 0.0458 310.945 310.702 1.058 1.006 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.5019 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0868 r_free=0.1912 After: r_work=0.0871 r_free=0.1911 ================================== NQH flips ================================== r_work=0.0871 r_free=0.1911 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A Total number of N/Q/H flips: 1 r_work=0.0873 r_free=0.1911 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0873 r_free=0.1911 | n_water=233 | time (s): 0.680 (total time: 0.680) Filter (dist) r_work=0.0894 r_free=0.1914 | n_water=228 | time (s): 17.380 (total time: 18.060) Filter (q & B) r_work=0.0967 r_free=0.1914 | n_water=226 | time (s): 1.970 (total time: 20.030) Compute maps r_work=0.0967 r_free=0.1914 | n_water=226 | time (s): 0.670 (total time: 20.700) Filter (map) r_work=0.1236 r_free=0.1979 | n_water=155 | time (s): 1.730 (total time: 22.430) Find peaks r_work=0.1236 r_free=0.1979 | n_water=155 | time (s): 0.410 (total time: 22.840) Add new water r_work=0.1530 r_free=0.2277 | n_water=226 | time (s): 1.430 (total time: 24.270) Refine new water occ: r_work=0.1002 r_free=0.1872 adp: r_work=0.0996 r_free=0.1891 occ: r_work=0.0989 r_free=0.1875 adp: r_work=0.0989 r_free=0.1885 occ: r_work=0.0983 r_free=0.1871 adp: r_work=0.0983 r_free=0.1880 ADP+occupancy (water only), MIN, final r_work=0.0983 r_free=0.1880 r_work=0.0983 r_free=0.1880 | n_water=226 | time (s): 12.750 (total time: 37.020) Filter (q & B) r_work=0.0983 r_free=0.1884 | n_water=223 | time (s): 1.820 (total time: 38.840) Filter (dist only) r_work=0.0988 r_free=0.1895 | n_water=222 | time (s): 18.970 (total time: 57.810) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.024280 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.224783 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 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 0.0925 0.1902 0.0977 0.011 1.1 6.4 0.5 0.6 0 0.512 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.25 19.02 9.77 8.141 18.572 0.225 5.001 9.01 19.08 10.07 8.959 18.698 0.225 4.940 Individual atomic B min max mean iso aniso Overall: 0.00 104.53 17.19 11.76 1749 0 Protein: 0.00 104.53 16.31 11.77 1519 0 Water: 0.00 53.88 23.17 N/A 222 0 Other: 8.84 30.90 19.35 N/A 8 0 Chain A: 0.00 104.53 16.71 N/A 1638 0 Chain S: 0.00 50.79 24.28 N/A 111 0 Histogram: Values Number of atoms 0.00 - 10.45 589 10.45 - 20.91 657 20.91 - 31.36 290 31.36 - 41.81 131 41.81 - 52.27 38 52.27 - 62.72 18 62.72 - 73.17 14 73.17 - 83.63 5 83.63 - 94.08 2 94.08 - 104.53 5 =========================== Idealize ADP of riding H ========================== r_work=0.0901 r_free=0.1908 r_work=0.0904 r_free=0.1910 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0904 r_free = 0.1910 target_work(ml) = 4.946 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0896 r_free = 0.1896 target_work(ml) = 4.939 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0896 r_free= 0.1896 coordinate error (max.-lik. estimate): 0.27 A | | | | normalized target function (ml) (work): 4.939230 | | target function (ml) not normalized (work): 24315.828839 | | target function (ml) not normalized (free): 2276.146771 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.79 1.00 2493 142 0.1265 0.1827 5.5069 6.1758| | 2: 3.78 - 3.00 1.00 2430 110 0.0445 0.2012 4.3569 12.72| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 - 3.79 2493 142 0.91 12.35 1.00 0.94 12448.16| | 2: 3.78 - 3.00 2430 110 0.99 1.93 1.00 0.96 885.64| |alpha: min = 0.93 max = 0.97 mean = 0.95| |beta: min = 565.98 max = 20764.41 mean = 6740.88| |figures of merit: min = 0.01 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.51 mean = 7.20| |phase err.(test): min = 0.00 max = 87.12 mean = 7.65| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0946 0.0896 0.1896 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2170 0.2170 0.2291 n_refl.: 5175 remove outliers: r(all,work,free)=0.2170 0.2170 0.2291 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2170 0.2170 0.2291 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0946 0.0895 0.1902 n_refl.: 5175 remove outliers: r(all,work,free)=0.0946 0.0895 0.1902 n_refl.: 5175 ======================== 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 0.3908 313.217 282.623 0.595 0.987 0.330 11.894-9.307 99.02 97 4 0.1860 503.868 489.449 0.968 0.993 0.330 9.237-7.194 100.00 213 7 0.2207 412.064 402.092 1.003 0.996 0.289 7.162-5.571 100.00 427 22 0.2019 309.204 300.135 0.996 0.998 0.274 5.546-4.326 100.00 867 58 0.1006 424.493 418.915 1.019 1.000 0.235 4.315-3.360 100.00 1859 96 0.0587 403.697 403.738 1.094 1.002 0.230 3.356-3.002 100.00 1373 60 0.0423 310.945 310.862 1.077 1.005 0.065 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-8.1945 ================= 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 : 0.3617 0.2018 0.083 5.302 8.8 119.3 19.9 258 0.000 1_bss: 0.1568 0.1559 0.083 5.302 6.5 116.9 17.5 258 0.000 1_settarget: 0.1568 0.1559 0.083 5.302 6.5 116.9 17.5 258 0.000 1_nqh: 0.1569 0.1556 0.083 5.302 6.5 116.9 17.5 258 0.006 1_weight: 0.1569 0.1556 0.083 5.302 6.5 116.9 17.5 258 0.006 1_xyzrec: 0.1157 0.1764 0.010 0.995 6.5 116.9 17.5 258 0.204 1_adp: 0.1016 0.1753 0.010 0.995 2.8 111.9 17.9 258 0.204 1_regHadp: 0.1009 0.1760 0.010 0.995 2.8 111.9 17.9 258 0.204 1_occ: 0.1014 0.1757 0.010 0.995 2.8 111.9 17.9 258 0.204 2_bss: 0.1022 0.1775 0.010 0.995 1.9 111.0 17.0 258 0.204 2_settarget: 0.1022 0.1775 0.010 0.995 1.9 111.0 17.0 258 0.204 2_updatecdl: 0.1022 0.1775 0.010 1.010 1.9 111.0 17.0 258 0.204 2_nqh: 0.1023 0.1780 0.010 1.010 1.9 111.0 17.0 258 0.199 2_sol: 0.1126 0.1701 0.010 1.010 1.0 110.6 16.3 225 n/a 2_weight: 0.1126 0.1701 0.010 1.010 1.0 110.6 16.3 225 n/a 2_xyzrec: 0.1021 0.1819 0.009 0.999 1.0 110.6 16.3 225 n/a 2_adp: 0.0950 0.1836 0.009 0.999 0.0 107.3 16.8 225 n/a 2_regHadp: 0.0946 0.1835 0.009 0.999 0.0 107.3 16.8 225 n/a 2_occ: 0.0940 0.1818 0.009 0.999 0.0 107.3 16.8 225 n/a 3_bss: 0.0940 0.1826 0.009 0.999 0.0 107.3 16.8 225 n/a 3_settarget: 0.0940 0.1826 0.009 0.999 0.0 107.3 16.8 225 n/a 3_updatecdl: 0.0940 0.1826 0.009 1.009 0.0 107.3 16.8 225 n/a 3_nqh: 0.0941 0.1827 0.009 1.009 0.0 107.3 16.8 225 n/a 3_sol: 0.1032 0.1798 0.009 1.009 0.0 107.3 16.6 229 n/a 3_weight: 0.1032 0.1798 0.009 1.009 0.0 107.3 16.6 229 n/a 3_xyzrec: 0.0932 0.1841 0.011 1.105 0.0 107.3 16.6 229 n/a 3_adp: 0.0896 0.1837 0.011 1.105 0.0 105.5 16.6 229 n/a 3_regHadp: 0.0900 0.1844 0.011 1.105 0.0 105.5 16.6 229 n/a 3_occ: 0.0888 0.1829 0.011 1.105 0.0 105.5 16.6 229 n/a 4_bss: 0.0881 0.1820 0.011 1.105 0.0 105.5 16.6 229 n/a 4_settarget: 0.0881 0.1820 0.011 1.105 0.0 105.5 16.6 229 n/a 4_updatecdl: 0.0881 0.1820 0.011 1.110 0.0 105.5 16.6 229 n/a 4_nqh: 0.0881 0.1820 0.011 1.110 0.0 105.5 16.6 229 n/a 4_sol: 0.0989 0.1801 0.011 1.110 0.0 105.5 16.7 233 n/a 4_weight: 0.0989 0.1801 0.011 1.110 0.0 105.5 16.7 233 n/a 4_xyzrec: 0.0901 0.1879 0.011 1.077 0.0 105.5 16.7 233 n/a 4_adp: 0.0878 0.1932 0.011 1.077 0.0 103.5 16.9 233 n/a 4_regHadp: 0.0883 0.1939 0.011 1.077 0.0 103.5 16.9 233 n/a 4_occ: 0.0870 0.1924 0.011 1.077 0.0 103.5 16.9 233 n/a 5_bss: 0.0868 0.1912 0.011 1.077 0.0 103.5 16.9 233 n/a 5_settarget: 0.0868 0.1912 0.011 1.077 0.0 103.5 16.9 233 n/a 5_updatecdl: 0.0868 0.1912 0.011 1.083 0.0 103.5 16.9 233 n/a 5_setrh: 0.0871 0.1911 0.011 1.083 0.0 103.5 16.9 233 n/a 5_nqh: 0.0873 0.1911 0.011 1.083 0.0 103.5 16.9 233 n/a 5_sol: 0.0988 0.1895 0.011 1.083 0.0 103.5 17.0 222 n/a 5_weight: 0.0988 0.1895 0.011 1.083 0.0 103.5 17.0 222 n/a 5_xyzrec: 0.0925 0.1902 0.011 1.144 0.0 103.5 17.0 222 n/a 5_adp: 0.0901 0.1908 0.011 1.144 0.0 104.5 17.2 222 n/a 5_regHadp: 0.0904 0.1910 0.011 1.144 0.0 104.5 17.2 222 n/a 5_occ: 0.0896 0.1896 0.011 1.144 0.0 104.5 17.2 222 n/a end: 0.0895 0.1902 0.011 1.144 0.0 104.5 17.2 222 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_2353655_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_2353655_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.2000 Refinement macro-cycles (run) : 493.1800 Write final files (write_after_run_outputs) : 9.7200 Total : 506.1000 Total CPU time: 8.83 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:19:11 PST -0800 (1735492751.67 s) Start R-work = 0.1568, R-free = 0.1559 Final R-work = 0.0895, R-free = 0.1902 =============================================================================== Job complete usr+sys time: 537.02 seconds wall clock time: 9 minutes 19.65 seconds (559.65 seconds total)