Starting phenix.refine on Sun Dec 29 09:24:41 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6218374.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 { 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" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6218374.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6218374.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 =============================================================================== 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: 1.46, per 1000 atoms: 0.43 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.29 Conformation dependent library (CDL) restraints added in 125.1 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.91: 534 0.91 - 1.17: 1108 1.17 - 1.42: 643 1.42 - 1.68: 837 1.68 - 1.94: 31 Bond restraints: 3153 Sorted by residual: bond pdb=" N LEU A 166 " pdb=" CA LEU A 166 " ideal model delta sigma weight residual 1.459 1.686 -0.227 1.25e-02 6.40e+03 3.31e+02 bond pdb=" C PRO A 73 " pdb=" O PRO A 73 " ideal model delta sigma weight residual 1.232 0.999 0.232 1.31e-02 5.83e+03 3.14e+02 bond pdb=" C GLY A 159 " pdb=" O GLY A 159 " ideal model delta sigma weight residual 1.236 1.049 0.187 1.08e-02 8.57e+03 2.99e+02 bond pdb=" CA VAL A 8 " pdb=" CB VAL A 8 " ideal model delta sigma weight residual 1.537 1.745 -0.208 1.26e-02 6.30e+03 2.72e+02 bond pdb=" N ALA A 6 " pdb=" CA ALA A 6 " ideal model delta sigma weight residual 1.455 1.657 -0.202 1.25e-02 6.40e+03 2.60e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.60: 3130 4.60 - 9.21: 1832 9.21 - 13.81: 657 13.81 - 18.41: 147 18.41 - 23.02: 11 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O GLY A 157 " pdb=" C GLY A 157 " pdb=" N PRO A 158 " ideal model delta sigma weight residual 121.77 106.15 15.62 1.00e+00 1.00e+00 2.44e+02 angle pdb=" O THR A 125 " pdb=" C THR A 125 " pdb=" N HIS A 126 " ideal model delta sigma weight residual 122.92 106.88 16.04 1.17e+00 7.31e-01 1.88e+02 angle pdb=" CA GLY A 40 " pdb=" C GLY A 40 " pdb=" N BLYS A 41 " ideal model delta sigma weight residual 114.75 128.25 -13.50 9.90e-01 1.02e+00 1.86e+02 angle pdb=" O ALA A 167 " pdb=" C ALA A 167 " pdb=" N ILE A 168 " ideal model delta sigma weight residual 122.15 137.42 -15.27 1.14e+00 7.69e-01 1.79e+02 angle pdb=" CA GLY A 100 " pdb=" C GLY A 100 " pdb=" O GLY A 100 " ideal model delta sigma weight residual 121.23 135.40 -14.17 1.08e+00 8.57e-01 1.72e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.69: 1294 16.69 - 33.37: 129 33.37 - 50.05: 40 50.05 - 66.73: 15 66.73 - 83.41: 3 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C GLU A 116 " pdb=" N GLU A 116 " pdb=" CA GLU A 116 " pdb=" CB GLU A 116 " ideal model delta harmonic sigma weight residual -122.60 -141.52 18.92 0 2.50e+00 1.60e-01 5.73e+01 dihedral pdb=" N GLN A 45 " pdb=" C GLN A 45 " pdb=" CA GLN A 45 " pdb=" CB GLN A 45 " ideal model delta harmonic sigma weight residual 122.80 105.07 17.73 0 2.50e+00 1.60e-01 5.03e+01 dihedral pdb=" N THR A 125 " pdb=" C THR A 125 " pdb=" CA THR A 125 " pdb=" CB THR A 125 " ideal model delta harmonic sigma weight residual 123.40 106.19 17.21 0 2.50e+00 1.60e-01 4.74e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.270: 112 0.270 - 0.538: 96 0.538 - 0.806: 26 0.806 - 1.074: 7 1.074 - 1.342: 2 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA VAL A 8 " pdb=" N VAL A 8 " pdb=" C VAL A 8 " pdb=" CB VAL A 8 " both_signs ideal model delta sigma weight residual False 2.44 3.78 -1.34 2.00e-01 2.50e+01 4.50e+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 -1.45 -1.14 2.00e-01 2.50e+01 3.24e+01 chirality pdb=" CA GLU A 176 " pdb=" N GLU A 176 " pdb=" C GLU A 176 " pdb=" CB GLU A 176 " both_signs ideal model delta sigma weight residual False 2.51 3.55 -1.04 2.00e-01 2.50e+01 2.72e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " 0.037 2.00e-02 2.50e+03 6.00e-02 1.08e+02 pdb=" CG PHE A 164 " 0.091 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " -0.060 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.029 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " -0.030 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.092 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.000 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.059 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.109 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.057 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.019 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " 0.066 2.00e-02 2.50e+03 5.74e-02 9.88e+01 pdb=" CG PHE A 162 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " 0.024 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " -0.045 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " 0.120 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " -0.065 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " -0.021 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " -0.110 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " 0.013 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " -0.007 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " 0.065 2.00e-02 2.50e+03 4.96e-02 7.37e+01 pdb=" CG TYR A 139 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " -0.056 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " 0.089 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.066 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " 0.026 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " -0.003 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " -0.051 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " -0.026 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " -0.026 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " 0.055 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.31: 952 2.31 - 2.88: 8002 2.88 - 3.45: 10574 3.45 - 4.03: 15252 4.03 - 4.60: 21810 Nonbonded interactions: 56590 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.733 2.100 nonbonded pdb=" HE2 HIS A 126 " pdb=" O PRO A 184 " model vdw sym.op. 1.828 2.450 x-y,-y,-z-4/3 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.834 2.450 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.834 2.450 nonbonded pdb=" HD3 ARG A 28 " pdb="HH11 ARG A 28 " model vdw 1.837 2.270 ... (remaining 56585 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_6218374_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= 0.2792 r_free= 0.1859 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.397521 | | target function (ml) not normalized (work): 71428.938429 | | target function (ml) not normalized (free): 3257.366999 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3177 0.2189 7.4606 5.0361| | 2: 3.63 - 2.88 1.00 2711 122 0.2668 0.1763 4.3373 4.3237| | 3: 2.88 - 2.52 1.00 2682 148 0.2544 0.1855 4.1912 4.2126| | 4: 2.52 - 2.29 1.00 2661 139 0.2563 0.1532 3.5046 3.5746| | 5: 2.29 - 2.13 1.00 2678 122 0.2680 0.1454 3.4159 3.4166| | 6: 2.13 - 2.00 1.00 2692 117 0.2749 0.1828 3.3153 3.3504| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 17.70 0.77 0.23 1335.51| | 2: 3.63 - 2.88 2711 122 0.82 24.23 1.32 0.23 1335.51| | 3: 2.88 - 2.52 2682 148 0.73 33.23 1.29 0.23 1335.51| | 4: 2.52 - 2.29 2661 139 0.93 11.32 1.30 0.26 135.34| | 5: 2.29 - 2.13 2678 122 0.92 13.65 1.32 0.26 135.34| | 6: 2.13 - 2.00 2692 117 0.90 16.37 1.34 0.26 135.34| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 135.34 max = 1335.51 mean = 742.11| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 89.96 mean = 19.42| |phase err.(test): min = 0.00 max = 89.03 mean = 19.71| |-----------------------------------------------------------------------------| ----------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 : 0.080 0.239 1557 Z= 5.325 Angle : 5.304 16.901 2118 Z= 3.669 Chirality : 0.395 1.342 243 Planarity : 0.032 0.089 284 Dihedral : 13.779 83.411 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.54 % Allowed : 1.62 % Favored : 97.84 % Rotamer: Outliers : 1.24 % Allowed : 2.48 % Favored : 96.27 % Cbeta Deviations : 28.11 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.48), residues: 224 helix: -2.65 (0.40), residues: 103 sheet: 0.21 (0.88), residues: 28 loop : -0.45 (0.56), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.072 0.020 ARG A 48 TYR 0.089 0.035 TYR A 139 PHE 0.077 0.029 PHE A 162 HIS 0.060 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= 0.2792 r_free= 0.1859 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.397521 | | target function (ml) not normalized (work): 71428.938429 | | target function (ml) not normalized (free): 3257.366999 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.3408 percent. r_work = 0.2926 r_free = 0.2010 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2873 0.2926 0.2010 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2873 0.2926 0.2010 n_refl.: 17050 remove outliers: r(all,work,free)=0.2170 0.2181 0.2010 n_refl.: 17045 overall B=-0.41 to atoms: r(all,work,free)=0.2143 0.2153 0.1992 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1626 0.1623 0.1681 n_refl.: 17045 remove outliers: r(all,work,free)=0.1624 0.1621 0.1681 n_refl.: 17043 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 98.94 88 5 0.3881 399.107 362.895 0.654 1.018 0.397 11.894-9.307 99.02 97 4 0.1859 633.876 614.789 0.921 1.018 0.380 9.237-7.194 100.00 213 7 0.2216 518.446 510.154 0.953 1.017 0.340 7.162-5.571 100.00 427 22 0.2330 389.095 375.544 0.923 1.015 0.284 5.546-4.326 100.00 867 58 0.1409 534.164 528.465 0.952 1.012 0.220 4.315-3.360 100.00 1859 96 0.1308 507.996 503.445 1.016 1.008 0.201 3.356-2.611 100.00 3867 181 0.1657 333.724 329.443 1.013 1.000 0.091 2.608-2.000 99.99 8818 434 0.1658 217.531 213.608 1.034 0.986 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.4499 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1621 r_free=0.1681 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=0.1621 r_free=0.1681 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.633377 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.956094 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 0.1350 0.1632 0.0282 0.009 1.0 1.0 0.5 0.0 0 11.817 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.50 16.32 2.82 3.013 18.452 0.956 0.023 12.77 16.53 3.75 3.581 18.684 0.956 0.020 Individual atomic B min max mean iso aniso Overall: 6.22 113.89 19.92 4.11 1785 0 Protein: 6.22 113.45 17.13 4.11 1519 0 Water: 8.25 113.89 36.15 N/A 258 0 Other: 21.83 36.71 25.97 N/A 8 0 Chain A: 6.22 113.89 19.92 N/A 1785 0 Histogram: Values Number of atoms 6.22 - 16.99 1092 16.99 - 27.75 337 27.75 - 38.52 183 38.52 - 49.29 94 49.29 - 60.06 52 60.06 - 70.82 13 70.82 - 81.59 6 81.59 - 92.36 4 92.36 - 103.12 1 103.12 - 113.89 3 =========================== Idealize ADP of riding H ========================== r_work=0.1277 r_free=0.1653 r_work=0.1280 r_free=0.1660 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1280 r_free = 0.1660 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1275 r_free = 0.1655 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17043 (all), 4.74 % free)------------| | | | r_work= 0.1275 r_free= 0.1655 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.019995 | | target function (ls_wunit_k1) not normalized (work): 324.644356 | | target function (ls_wunit_k1) not normalized (free): 27.110416 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1293 0.1275 0.1655 n_refl.: 17043 re-set all scales: r(all,work,free)=0.1899 0.1897 0.1985 n_refl.: 17043 remove outliers: r(all,work,free)=0.1899 0.1897 0.1985 n_refl.: 17043 overall B=-0.51 to atoms: r(all,work,free)=0.1862 0.1860 0.1965 n_refl.: 17043 bulk-solvent and scaling: r(all,work,free)=0.1292 0.1274 0.1650 n_refl.: 17043 remove outliers: r(all,work,free)=0.1291 0.1273 0.1650 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 0.3568 304.992 283.297 0.642 1.007 0.379 11.894-9.307 99.02 97 4 0.1696 488.515 476.784 0.918 1.007 0.364 9.237-7.194 100.00 213 7 0.1842 399.556 396.020 0.959 1.007 0.351 7.162-5.571 100.00 427 22 0.1869 299.867 294.151 0.932 1.006 0.291 5.546-4.326 100.00 867 58 0.1053 411.670 408.660 0.955 1.005 0.206 4.315-3.360 100.00 1859 96 0.0935 391.502 390.885 1.015 1.004 0.192 3.356-2.611 100.00 3867 181 0.1290 257.194 255.870 1.010 1.001 0.102 2.608-2.000 99.99 8818 434 0.1343 167.647 166.340 1.012 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-1.1617 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1273 r_free=0.1650 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1273 r_free=0.1650 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1273 r_free=0.1650 | n_water=258 | time (s): 0.890 (total time: 0.890) Filter (dist) r_work=0.1279 r_free=0.1641 | n_water=253 | time (s): 21.650 (total time: 22.540) Filter (q & B) r_work=0.1279 r_free=0.1642 | n_water=251 | time (s): 1.930 (total time: 24.470) Compute maps r_work=0.1279 r_free=0.1642 | n_water=251 | time (s): 0.740 (total time: 25.210) Filter (map) r_work=0.1319 r_free=0.1635 | n_water=209 | time (s): 1.710 (total time: 26.920) Find peaks r_work=0.1319 r_free=0.1635 | n_water=209 | time (s): 0.440 (total time: 27.360) Add new water r_work=0.1532 r_free=0.1871 | n_water=366 | time (s): 1.370 (total time: 28.730) Refine new water occ: r_work=0.1328 r_free=0.1585 adp: r_work=0.1273 r_free=0.1583 occ: r_work=0.1279 r_free=0.1556 adp: r_work=0.1247 r_free=0.1563 occ: r_work=0.1249 r_free=0.1552 adp: r_work=0.1238 r_free=0.1554 ADP+occupancy (water only), MIN, final r_work=0.1238 r_free=0.1554 r_work=0.1238 r_free=0.1554 | n_water=366 | time (s): 17.090 (total time: 45.820) Filter (q & B) r_work=0.1240 r_free=0.1561 | n_water=357 | time (s): 1.570 (total time: 47.390) Filter (dist only) r_work=0.1240 r_free=0.1564 | n_water=356 | time (s): 27.910 (total time: 75.300) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.320298 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.038927 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 0.1220 0.1606 0.0385 0.009 0.9 2.6 0.5 0.0 0 12.660 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.20 16.06 3.85 4.180 20.797 1.039 0.019 12.03 16.22 4.20 4.285 21.044 1.039 0.018 Individual atomic B min max mean iso aniso Overall: 6.68 107.94 21.00 4.35 1883 0 Protein: 6.68 107.94 17.48 4.34 1519 0 Water: 8.51 68.72 35.76 N/A 356 0 Other: 26.22 43.92 34.28 N/A 8 0 Chain A: 6.68 107.94 19.20 N/A 1736 0 Chain S: 17.71 63.81 42.30 N/A 147 0 Histogram: Values Number of atoms 6.68 - 16.80 1060 16.80 - 26.93 354 26.93 - 37.05 218 37.05 - 47.18 145 47.18 - 57.31 72 57.31 - 67.43 23 67.43 - 77.56 4 77.56 - 87.69 3 87.69 - 97.81 2 97.81 - 107.94 2 =========================== Idealize ADP of riding H ========================== r_work=0.1203 r_free=0.1622 r_work=0.1204 r_free=0.1624 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1204 r_free = 0.1624 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 = 0.1202 r_free = 0.1626 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.23 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= 0.1202 r_free= 0.1626 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.017316 | | target function (ls_wunit_k1) not normalized (work): 281.132084 | | target function (ls_wunit_k1) not normalized (free): 25.540308 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1222 0.1202 0.1626 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1791 0.1786 0.1955 n_refl.: 17042 remove outliers: r(all,work,free)=0.1791 0.1786 0.1955 n_refl.: 17042 overall B=-0.37 to atoms: r(all,work,free)=0.1766 0.1760 0.1939 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1220 0.1199 0.1623 n_refl.: 17042 remove outliers: r(all,work,free)=0.1219 0.1198 0.1623 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 0.3284 307.020 280.456 0.613 1.009 0.370 11.894-9.307 99.02 97 4 0.1617 488.515 483.656 0.913 1.009 0.360 9.237-7.194 100.00 213 7 0.1714 399.556 399.147 0.967 1.009 0.304 7.162-5.571 100.00 427 22 0.1620 299.867 296.462 0.934 1.008 0.280 5.546-4.326 100.00 867 58 0.0892 411.670 409.282 0.957 1.007 0.206 4.315-3.360 100.00 1859 96 0.0839 391.502 390.783 1.013 1.005 0.201 3.356-2.611 100.00 3867 181 0.1207 257.194 256.554 1.010 1.001 0.063 2.608-2.000 99.99 8818 434 0.1326 167.647 166.561 1.011 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-1.1517 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1198 r_free=0.1623 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1198 r_free=0.1623 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1198 r_free=0.1623 | n_water=356 | time (s): 0.680 (total time: 0.680) Filter (dist) r_work=0.1198 r_free=0.1623 | n_water=355 | time (s): 29.560 (total time: 30.240) Filter (q & B) r_work=0.1198 r_free=0.1623 | n_water=355 | time (s): 1.190 (total time: 31.430) Compute maps r_work=0.1198 r_free=0.1623 | n_water=355 | time (s): 0.850 (total time: 32.280) Filter (map) r_work=0.1264 r_free=0.1656 | n_water=255 | time (s): 1.600 (total time: 33.880) Find peaks r_work=0.1264 r_free=0.1656 | n_water=255 | time (s): 0.610 (total time: 34.490) Add new water r_work=0.1456 r_free=0.1822 | n_water=417 | time (s): 2.000 (total time: 36.490) Refine new water occ: r_work=0.1246 r_free=0.1612 adp: r_work=0.1239 r_free=0.1610 occ: r_work=0.1220 r_free=0.1588 adp: r_work=0.1210 r_free=0.1584 occ: r_work=0.1201 r_free=0.1572 adp: r_work=0.1191 r_free=0.1571 ADP+occupancy (water only), MIN, final r_work=0.1191 r_free=0.1571 r_work=0.1191 r_free=0.1571 | n_water=417 | time (s): 35.680 (total time: 72.170) Filter (q & B) r_work=0.1193 r_free=0.1581 | n_water=405 | time (s): 1.980 (total time: 74.150) Filter (dist only) r_work=0.1193 r_free=0.1581 | n_water=405 | time (s): 30.600 (total time: 104.750) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.915333 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.166712 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 0.1176 0.1556 0.0380 0.009 1.0 4.2 0.5 0.0 0 0.958 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.76 15.56 3.80 4.356 21.230 0.167 4.995 11.60 15.77 4.17 4.867 21.184 0.167 4.975 Individual atomic B min max mean iso aniso Overall: 5.73 105.00 20.69 4.81 1932 0 Protein: 5.73 105.00 16.85 4.81 1519 0 Water: 8.30 63.13 34.81 N/A 405 0 Other: 27.09 47.17 35.28 N/A 8 0 Chain A: 5.73 105.00 18.53 N/A 1731 0 Chain S: 15.51 63.13 39.30 N/A 201 0 Histogram: Values Number of atoms 5.73 - 15.66 1036 15.66 - 25.58 373 25.58 - 35.51 235 35.51 - 45.44 164 45.44 - 55.37 81 55.37 - 65.29 29 65.29 - 75.22 5 75.22 - 85.15 5 85.15 - 95.08 2 95.08 - 105.00 2 =========================== Idealize ADP of riding H ========================== r_work=0.1160 r_free=0.1577 r_work=0.1161 r_free=0.1580 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1161 r_free = 0.1580 target_work(ml) = 4.976 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1148 r_free = 0.1595 target_work(ml) = 4.973 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1148 r_free= 0.1595 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.973241 | | target function (ml) not normalized (work): 80735.601994 | | target function (ml) not normalized (free): 4198.282447 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1170 0.1148 0.1595 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1650 0.1642 0.1858 n_refl.: 17041 remove outliers: r(all,work,free)=0.1650 0.1642 0.1858 n_refl.: 17041 overall B=-0.34 to atoms: r(all,work,free)=0.1628 0.1619 0.1849 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1166 0.1145 0.1587 n_refl.: 17041 remove outliers: r(all,work,free)=0.1166 0.1145 0.1587 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 0.3462 307.020 281.831 0.584 1.008 0.350 11.894-9.307 99.02 97 4 0.1710 488.515 480.959 0.912 1.008 0.340 9.237-7.194 100.00 213 7 0.1845 399.556 399.934 0.985 1.008 0.280 7.162-5.571 100.00 427 22 0.1623 299.867 295.088 0.941 1.007 0.241 5.546-4.326 100.00 867 58 0.0945 411.670 408.017 0.963 1.006 0.200 4.315-3.360 100.00 1859 96 0.0901 391.502 388.937 1.010 1.004 0.191 3.356-2.611 100.00 3867 181 0.1283 257.194 254.842 1.010 1.001 0.131 2.608-2.000 99.99 8818 434 0.1079 167.647 166.275 1.013 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-1.1665 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1145 r_free=0.1587 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=0.1147 r_free=0.1584 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1147 r_free=0.1584 | n_water=405 | time (s): 0.660 (total time: 0.660) Filter (dist) r_work=0.1147 r_free=0.1584 | n_water=405 | time (s): 31.830 (total time: 32.490) Filter (q & B) r_work=0.1147 r_free=0.1584 | n_water=404 | time (s): 1.610 (total time: 34.100) Compute maps r_work=0.1147 r_free=0.1584 | n_water=404 | time (s): 0.690 (total time: 34.790) Filter (map) r_work=0.1205 r_free=0.1612 | n_water=312 | time (s): 1.820 (total time: 36.610) Find peaks r_work=0.1205 r_free=0.1612 | n_water=312 | time (s): 0.620 (total time: 37.230) Add new water r_work=0.1357 r_free=0.1749 | n_water=468 | time (s): 1.530 (total time: 38.760) Refine new water occ: r_work=0.1182 r_free=0.1532 adp: r_work=0.1172 r_free=0.1540 occ: r_work=0.1156 r_free=0.1511 adp: r_work=0.1146 r_free=0.1512 occ: r_work=0.1139 r_free=0.1496 adp: r_work=0.1130 r_free=0.1497 ADP+occupancy (water only), MIN, final r_work=0.1130 r_free=0.1497 r_work=0.1130 r_free=0.1497 | n_water=468 | time (s): 23.340 (total time: 62.100) Filter (q & B) r_work=0.1134 r_free=0.1505 | n_water=456 | time (s): 1.640 (total time: 63.740) Filter (dist only) r_work=0.1134 r_free=0.1505 | n_water=456 | time (s): 35.690 (total time: 99.430) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.892822 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.147128 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 0.1119 0.1555 0.0436 0.009 1.0 3.2 0.5 0.0 0 0.946 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.19 15.55 4.36 4.558 21.031 0.147 4.958 11.05 15.47 4.41 4.705 21.061 0.147 4.948 Individual atomic B min max mean iso aniso Overall: 5.59 103.67 21.00 4.85 1983 0 Protein: 5.59 103.67 16.47 4.84 1519 0 Water: 8.46 64.38 35.86 N/A 456 0 Other: 25.59 45.21 33.38 N/A 8 0 Chain A: 5.59 103.67 18.10 N/A 1731 0 Chain S: 17.93 64.38 40.91 N/A 252 0 Histogram: Values Number of atoms 5.59 - 15.39 1036 15.39 - 25.20 376 25.20 - 35.01 223 35.01 - 44.82 199 44.82 - 54.63 105 54.63 - 64.43 28 64.43 - 74.24 8 74.24 - 84.05 2 84.05 - 93.86 4 93.86 - 103.67 2 =========================== Idealize ADP of riding H ========================== r_work=0.1105 r_free=0.1547 r_work=0.1105 r_free=0.1547 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1105 r_free = 0.1547 target_work(ml) = 4.949 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1098 r_free = 0.1546 target_work(ml) = 4.944 | | 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= 0.1098 r_free= 0.1546 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.944110 | | target function (ml) not normalized (work): 80262.674484 | | target function (ml) not normalized (free): 4177.742799 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1119 0.1098 0.1546 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1562 0.1548 0.1863 n_refl.: 17041 remove outliers: r(all,work,free)=0.1562 0.1548 0.1863 n_refl.: 17041 overall B=-0.25 to atoms: r(all,work,free)=0.1546 0.1532 0.1854 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1117 0.1095 0.1545 n_refl.: 17041 remove outliers: r(all,work,free)=0.1116 0.1094 0.1545 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 0.3620 303.523 282.461 0.566 1.004 0.340 11.894-9.307 99.02 97 4 0.1782 488.515 480.898 0.910 1.005 0.334 9.237-7.194 100.00 213 7 0.1781 399.556 401.203 0.988 1.005 0.240 7.162-5.571 100.00 427 22 0.1592 299.867 293.961 0.938 1.004 0.210 5.546-4.326 100.00 867 58 0.0920 411.670 408.380 0.963 1.004 0.201 4.315-3.360 100.00 1859 96 0.0833 391.502 389.154 1.004 1.003 0.191 3.356-2.611 100.00 3867 181 0.1218 257.194 255.024 1.001 1.001 0.053 2.608-2.000 99.99 8818 434 0.1033 167.647 166.437 0.996 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-0.8785 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1094 r_free=0.1545 After: r_work=0.1097 r_free=0.1544 ================================== NQH flips ================================== r_work=0.1097 r_free=0.1544 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1097 r_free=0.1544 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1097 r_free=0.1544 | n_water=456 | time (s): 0.870 (total time: 0.870) Filter (dist) r_work=0.1099 r_free=0.1543 | n_water=455 | time (s): 37.210 (total time: 38.080) Filter (q & B) r_work=0.1099 r_free=0.1543 | n_water=455 | time (s): 0.970 (total time: 39.050) Compute maps r_work=0.1099 r_free=0.1543 | n_water=455 | time (s): 0.600 (total time: 39.650) Filter (map) r_work=0.1180 r_free=0.1574 | n_water=345 | time (s): 1.520 (total time: 41.170) Find peaks r_work=0.1180 r_free=0.1574 | n_water=345 | time (s): 0.430 (total time: 41.600) Add new water r_work=0.1303 r_free=0.1694 | n_water=486 | time (s): 1.480 (total time: 43.080) Refine new water occ: r_work=0.1144 r_free=0.1498 adp: r_work=0.1139 r_free=0.1505 occ: r_work=0.1122 r_free=0.1472 adp: r_work=0.1115 r_free=0.1477 occ: r_work=0.1108 r_free=0.1455 adp: r_work=0.1102 r_free=0.1460 ADP+occupancy (water only), MIN, final r_work=0.1102 r_free=0.1460 r_work=0.1102 r_free=0.1460 | n_water=486 | time (s): 36.210 (total time: 79.290) Filter (q & B) r_work=0.1106 r_free=0.1475 | n_water=474 | time (s): 1.860 (total time: 81.150) Filter (dist only) r_work=0.1106 r_free=0.1475 | n_water=472 | time (s): 40.580 (total time: 121.730) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.951936 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.186667 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 0.1116 0.1513 0.0397 0.010 1.0 3.5 0.5 0.0 0 0.976 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.16 15.13 3.97 4.542 20.824 0.187 4.947 11.06 14.99 3.93 4.628 20.925 0.187 4.937 Individual atomic B min max mean iso aniso Overall: 5.06 102.92 21.07 5.10 1999 0 Protein: 5.06 102.92 16.28 5.09 1519 0 Water: 8.09 65.67 36.29 N/A 472 0 Other: 25.36 44.92 33.52 N/A 8 0 Chain A: 5.06 102.92 17.91 N/A 1731 0 Chain S: 15.38 65.67 41.49 N/A 268 0 Histogram: Values Number of atoms 5.06 - 14.85 1005 14.85 - 24.63 400 24.63 - 34.42 213 34.42 - 44.20 201 44.20 - 53.99 133 53.99 - 63.77 29 63.77 - 73.56 9 73.56 - 83.35 2 83.35 - 93.13 3 93.13 - 102.92 4 =========================== Idealize ADP of riding H ========================== r_work=0.1106 r_free=0.1499 r_work=0.1106 r_free=0.1500 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1106 r_free = 0.1500 target_work(ml) = 4.938 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1099 r_free = 0.1487 target_work(ml) = 4.930 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1099 r_free= 0.1487 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.929993 | | target function (ml) not normalized (work): 80028.576808 | | target function (ml) not normalized (free): 4160.234330 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1128 0.1362 5.4596 5.6507| | 2: 3.63 - 2.88 1.00 2711 122 0.1072 0.1486 5.2032 5.3589| | 3: 2.88 - 2.52 1.00 2681 148 0.1329 0.1636 5.1187 5.1875| | 4: 2.52 - 2.29 1.00 2661 139 0.0921 0.1468 4.6199 4.9328| | 5: 2.29 - 2.13 1.00 2678 122 0.0957 0.1544 4.5774 4.9158| | 6: 2.13 - 2.00 1.00 2692 117 0.1119 0.1664 4.5713 4.7422| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 8.82 1.00 0.97 6265.08| | 2: 3.63 - 2.88 2711 122 0.93 12.59 1.01 0.97 6265.08| | 3: 2.88 - 2.52 2681 148 0.88 18.77 0.99 0.97 6265.08| | 4: 2.52 - 2.29 2661 139 0.93 12.09 1.01 0.98 2114.89| | 5: 2.29 - 2.13 2678 122 0.91 14.10 1.00 0.98 2114.89| | 6: 2.13 - 2.00 2692 117 0.89 16.82 0.99 0.98 2114.89| |alpha: min = 0.97 max = 0.98 mean = 0.97| |beta: min = 2114.89 max = 6265.08 mean = 4211.85| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.70 mean = 13.83| |phase err.(test): min = 0.00 max = 86.71 mean = 13.46| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1118 0.1099 0.1487 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1539 0.1528 0.1785 n_refl.: 17040 remove outliers: r(all,work,free)=0.1539 0.1528 0.1785 n_refl.: 17040 overall B=-0.22 to atoms: r(all,work,free)=0.1527 0.1516 0.1779 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1118 0.1099 0.1490 n_refl.: 17040 remove outliers: r(all,work,free)=0.1118 0.1099 0.1490 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 0.3627 303.523 281.488 0.544 1.005 0.324 11.894-9.307 99.02 97 4 0.1808 488.515 480.433 0.912 1.006 0.320 9.237-7.194 100.00 213 7 0.1756 399.556 402.680 0.983 1.006 0.213 7.162-5.571 100.00 427 22 0.1605 299.867 294.288 0.939 1.005 0.210 5.546-4.326 100.00 867 58 0.0938 411.670 408.598 0.960 1.005 0.195 4.315-3.360 100.00 1859 96 0.0863 391.502 389.295 1.003 1.003 0.191 3.356-2.611 100.00 3867 181 0.1214 257.194 254.862 0.999 1.001 0.091 2.608-2.000 99.99 8818 434 0.1028 167.647 166.427 0.991 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.7493 ================= 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 : 0.2792 0.1859 0.080 5.304 8.8 119.3 19.9 258 0.000 1_bss: 0.1621 0.1681 0.080 5.304 8.4 118.9 19.5 258 0.000 1_settarget: 0.1621 0.1681 0.080 5.304 8.4 118.9 19.5 258 0.000 1_nqh: 0.1621 0.1681 0.080 5.304 8.4 118.9 19.5 258 0.003 1_weight: 0.1621 0.1681 0.080 5.304 8.4 118.9 19.5 258 0.003 1_xyzrec: 0.1350 0.1632 0.009 0.988 8.4 118.9 19.5 258 0.145 1_adp: 0.1277 0.1653 0.009 0.988 6.2 113.9 19.9 258 0.145 1_regHadp: 0.1280 0.1660 0.009 0.988 6.2 113.9 19.9 258 0.145 1_occ: 0.1275 0.1655 0.009 0.988 6.2 113.9 19.9 258 0.145 2_bss: 0.1273 0.1650 0.009 0.988 5.7 113.4 19.4 258 0.145 2_settarget: 0.1273 0.1650 0.009 0.988 5.7 113.4 19.4 258 0.145 2_updatecdl: 0.1273 0.1650 0.009 1.005 5.7 113.4 19.4 258 0.145 2_nqh: 0.1273 0.1650 0.009 1.005 5.7 113.4 19.4 258 0.145 2_sol: 0.1240 0.1564 0.009 1.005 5.7 112.9 20.5 356 n/a 2_weight: 0.1240 0.1564 0.009 1.005 5.7 112.9 20.5 356 n/a 2_xyzrec: 0.1220 0.1606 0.009 0.936 5.7 112.9 20.5 356 n/a 2_adp: 0.1203 0.1622 0.009 0.936 6.7 107.9 21.0 356 n/a 2_regHadp: 0.1204 0.1624 0.009 0.936 6.7 107.9 21.0 356 n/a 2_occ: 0.1202 0.1626 0.009 0.936 6.7 107.9 21.0 356 n/a 3_bss: 0.1198 0.1623 0.009 0.936 6.3 107.6 20.6 356 n/a 3_settarget: 0.1198 0.1623 0.009 0.936 6.3 107.6 20.6 356 n/a 3_updatecdl: 0.1198 0.1623 0.009 0.943 6.3 107.6 20.6 356 n/a 3_nqh: 0.1198 0.1623 0.009 0.943 6.3 107.6 20.6 356 n/a 3_sol: 0.1193 0.1581 0.009 0.943 6.3 107.6 20.8 405 n/a 3_weight: 0.1193 0.1581 0.009 0.943 6.3 107.6 20.8 405 n/a 3_xyzrec: 0.1176 0.1556 0.009 0.953 6.3 107.6 20.8 405 n/a 3_adp: 0.1160 0.1577 0.009 0.953 5.7 105.0 20.7 405 n/a 3_regHadp: 0.1161 0.1580 0.009 0.953 5.7 105.0 20.7 405 n/a 3_occ: 0.1148 0.1595 0.009 0.953 5.7 105.0 20.7 405 n/a 4_bss: 0.1145 0.1587 0.009 0.953 5.4 104.7 20.4 405 n/a 4_settarget: 0.1145 0.1587 0.009 0.953 5.4 104.7 20.4 405 n/a 4_updatecdl: 0.1145 0.1587 0.009 0.952 5.4 104.7 20.4 405 n/a 4_nqh: 0.1147 0.1584 0.009 0.952 5.4 104.7 20.4 405 n/a 4_sol: 0.1134 0.1505 0.009 0.952 5.4 104.7 20.9 456 n/a 4_weight: 0.1134 0.1505 0.009 0.952 5.4 104.7 20.9 456 n/a 4_xyzrec: 0.1119 0.1555 0.009 0.961 5.4 104.7 20.9 456 n/a 4_adp: 0.1105 0.1547 0.009 0.961 5.6 103.7 21.0 456 n/a 4_regHadp: 0.1105 0.1547 0.009 0.961 5.6 103.7 21.0 456 n/a 4_occ: 0.1098 0.1546 0.009 0.961 5.6 103.7 21.0 456 n/a 5_bss: 0.1094 0.1545 0.009 0.961 5.3 103.4 20.7 456 n/a 5_settarget: 0.1094 0.1545 0.009 0.961 5.3 103.4 20.7 456 n/a 5_updatecdl: 0.1094 0.1545 0.009 0.961 5.3 103.4 20.7 456 n/a 5_setrh: 0.1097 0.1544 0.009 0.961 5.3 103.4 20.7 456 n/a 5_nqh: 0.1097 0.1544 0.009 0.961 5.3 103.4 20.7 456 n/a 5_sol: 0.1106 0.1475 0.009 0.961 5.3 103.4 20.9 472 n/a 5_weight: 0.1106 0.1475 0.009 0.961 5.3 103.4 20.9 472 n/a 5_xyzrec: 0.1116 0.1513 0.010 1.036 5.3 103.4 20.9 472 n/a 5_adp: 0.1106 0.1499 0.010 1.036 5.1 102.9 21.1 472 n/a 5_regHadp: 0.1106 0.1500 0.010 1.036 5.1 102.9 21.1 472 n/a 5_occ: 0.1099 0.1487 0.010 1.036 5.1 102.9 21.1 472 n/a end: 0.1099 0.1490 0.010 1.036 4.8 102.7 20.9 472 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_6218374_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_6218374_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.3500 Refinement macro-cycles (run) : 926.1300 Write final files (write_after_run_outputs) : 20.7700 Total : 950.2500 Total CPU time: 16.21 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:12 PST -0800 (1735494072.40 s) Start R-work = 0.1621, R-free = 0.1681 Final R-work = 0.1099, R-free = 0.1490 =============================================================================== Job complete usr+sys time: 994.80 seconds wall clock time: 16 minutes 56.63 seconds (1016.63 seconds total)