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_1522381.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" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_1522381.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_1522381.pdb" 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" } 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: 2.07, per 1000 atoms: 0.61 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 212.4 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.63 - 0.89: 391 0.89 - 1.14: 1224 1.14 - 1.40: 582 1.40 - 1.66: 894 1.66 - 1.91: 62 Bond restraints: 3153 Sorted by residual: bond pdb=" C GLY A 159 " pdb=" O GLY A 159 " ideal model delta sigma weight residual 1.237 1.436 -0.199 1.07e-02 8.73e+03 3.47e+02 bond pdb=" C CYS A 106 " pdb=" O CYS A 106 " ideal model delta sigma weight residual 1.235 1.470 -0.234 1.26e-02 6.30e+03 3.46e+02 bond pdb=" N GLU A 176 " pdb=" CA GLU A 176 " ideal model delta sigma weight residual 1.459 1.240 0.220 1.19e-02 7.06e+03 3.41e+02 bond pdb=" C ALYS A 99 " pdb=" O ALYS A 99 " ideal model delta sigma weight residual 1.233 1.001 0.232 1.28e-02 6.10e+03 3.28e+02 bond pdb=" C ALA A 183 " pdb=" O ALA A 183 " ideal model delta sigma weight residual 1.244 1.064 0.180 1.00e-02 1.00e+04 3.23e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.91: 3295 4.91 - 9.83: 1855 9.83 - 14.74: 547 14.74 - 19.65: 71 19.65 - 24.57: 9 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA VAL A 25 " pdb=" C VAL A 25 " pdb=" N MET A 26 " ideal model delta sigma weight residual 117.15 134.91 -17.76 1.14e+00 7.69e-01 2.43e+02 angle pdb=" CA THR A 140 " pdb=" C THR A 140 " pdb=" O THR A 140 " ideal model delta sigma weight residual 120.36 104.85 15.51 1.07e+00 8.73e-01 2.10e+02 angle pdb=" CA ASN A 173 " pdb=" C ASN A 173 " pdb=" O ASN A 173 " ideal model delta sigma weight residual 119.05 133.57 -14.52 1.10e+00 8.26e-01 1.74e+02 angle pdb=" C VAL A 25 " pdb=" N MET A 26 " pdb=" CA MET A 26 " ideal model delta sigma weight residual 120.54 137.66 -17.12 1.35e+00 5.49e-01 1.61e+02 angle pdb=" C ASP A 42 " pdb=" N PRO A 43 " pdb=" CA PRO A 43 " ideal model delta sigma weight residual 120.03 107.87 12.16 9.90e-01 1.02e+00 1.51e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.32: 1310 17.32 - 34.63: 119 34.63 - 51.94: 37 51.94 - 69.26: 12 69.26 - 86.57: 3 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C THR A 124 " pdb=" N THR A 124 " pdb=" CA THR A 124 " pdb=" CB THR A 124 " ideal model delta harmonic sigma weight residual -122.00 -144.62 22.62 0 2.50e+00 1.60e-01 8.18e+01 dihedral pdb=" N MET A 26 " pdb=" C MET A 26 " pdb=" CA MET A 26 " pdb=" CB MET A 26 " ideal model delta harmonic sigma weight residual 122.80 144.61 -21.81 0 2.50e+00 1.60e-01 7.61e+01 dihedral pdb=" N THR A 124 " pdb=" C THR A 124 " pdb=" CA THR A 124 " pdb=" CB THR A 124 " ideal model delta harmonic sigma weight residual 123.40 142.70 -19.30 0 2.50e+00 1.60e-01 5.96e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.008 - 0.276: 120 0.276 - 0.544: 80 0.544 - 0.813: 34 0.813 - 1.081: 7 1.081 - 1.349: 2 Chirality restraints: 243 Sorted by residual: chirality pdb=" CG LEU A 172 " pdb=" CB LEU A 172 " pdb=" CD1 LEU A 172 " pdb=" CD2 LEU A 172 " both_signs ideal model delta sigma weight residual False -2.59 -1.24 -1.35 2.00e-01 2.50e+01 4.55e+01 chirality pdb=" CA THR A 124 " pdb=" N THR A 124 " pdb=" C THR A 124 " pdb=" CB THR A 124 " both_signs ideal model delta sigma weight residual False 2.53 1.39 1.14 2.00e-01 2.50e+01 3.24e+01 chirality pdb=" CA ILE A 152 " pdb=" N ILE A 152 " pdb=" C ILE A 152 " pdb=" CB ILE A 152 " both_signs ideal model delta sigma weight residual False 2.43 3.42 -0.99 2.00e-01 2.50e+01 2.43e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " 0.149 2.00e-02 2.50e+03 7.18e-02 1.55e+02 pdb=" CG TYR A 141 " -0.088 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " -0.117 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " -0.058 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " 0.036 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " 0.099 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " 0.040 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " -0.010 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " -0.017 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " 0.017 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " -0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.079 2.00e-02 2.50e+03 6.58e-02 1.30e+02 pdb=" CG PHE A 119 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.089 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.099 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " 0.064 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.126 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.011 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.034 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.019 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " -0.048 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BASN A 76 " -0.012 2.00e-02 2.50e+03 9.14e-02 1.25e+02 pdb=" CG BASN A 76 " 0.111 2.00e-02 2.50e+03 pdb=" OD1BASN A 76 " -0.086 2.00e-02 2.50e+03 pdb=" ND2BASN A 76 " 0.124 2.00e-02 2.50e+03 pdb="HD21BASN A 76 " -0.013 2.00e-02 2.50e+03 pdb="HD22BASN A 76 " -0.122 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.33: 1180 2.33 - 2.90: 8113 2.90 - 3.47: 10476 3.47 - 4.03: 15204 4.03 - 4.60: 21599 Nonbonded interactions: 56572 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.764 2.100 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.769 2.100 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.795 2.450 nonbonded pdb=" H THR A 124 " pdb=" OG1 THR A 154 " model vdw 1.821 2.450 nonbonded pdb=" H THR A 124 " pdb=" HG1 THR A 154 " model vdw 1.831 2.100 ... (remaining 56567 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_1522381_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= 0.3619 r_free= 0.2022 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.468422 | | target function (ml) not normalized (work): 22029.321620 | | target function (ml) not normalized (free): 1143.780924 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3803 0.2272 4.8566 4.8973| | 2: 3.78 - 3.00 1.00 2430 110 0.3394 0.1600 4.069 4.0761| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 48.93 0.83 0.13 6614.49| | 2: 3.78 - 3.00 2430 110 0.94 11.25 1.48 0.26 450.63| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 381.17 max = 12077.75 mean = 3576.32| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 89.98 mean = 30.36| |phase err.(test): min = 0.00 max = 89.96 mean = 33.29| |-----------------------------------------------------------------------------| ----------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 : 0.084 0.253 1557 Z= 5.583 Angle : 5.316 19.200 2118 Z= 3.665 Chirality : 0.401 1.349 243 Planarity : 0.031 0.086 284 Dihedral : 13.837 86.569 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 1.08 % Allowed : 2.70 % Favored : 96.22 % Rotamer: Outliers : 1.24 % Allowed : 5.59 % Favored : 93.17 % Cbeta Deviations : 35.68 % 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: -2.36 (0.49), residues: 224 helix: -2.65 (0.39), residues: 103 sheet: -0.39 (0.73), residues: 38 loop : -0.27 (0.63), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.075 0.016 ARG A 156 TYR 0.143 0.050 TYR A 141 PHE 0.116 0.044 PHE A 119 HIS 0.047 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: 3.00 - 49.25 A, n_refl.=5182 (all), 4.86 % free)-------------| | | | r_work= 0.3619 r_free= 0.2022 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.468422 | | target function (ml) not normalized (work): 22029.321620 | | target function (ml) not normalized (free): 1143.780924 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3574 0.3653 0.2089 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3574 0.3653 0.2089 n_refl.: 5182 remove outliers: r(all,work,free)=0.2528 0.2553 0.2089 n_refl.: 5178 overall B=-2.72 to atoms: r(all,work,free)=0.2424 0.2446 0.2047 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1571 0.1572 0.1553 n_refl.: 5178 remove outliers: r(all,work,free)=0.1569 0.1570 0.1553 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 0.4009 445.050 407.186 0.668 1.023 0.398 11.894-9.307 99.02 97 4 0.1852 714.474 688.103 0.946 1.024 0.382 9.237-7.194 100.00 213 7 0.2205 584.298 570.940 0.975 1.022 0.364 7.162-5.571 100.00 427 22 0.2244 438.444 422.803 0.930 1.017 0.336 5.546-4.326 100.00 867 58 0.1397 601.922 591.566 0.967 1.009 0.257 4.315-3.360 100.00 1859 96 0.1325 572.434 567.413 1.025 0.996 0.189 3.356-3.002 100.00 1373 60 0.1618 440.913 436.254 1.020 0.983 0.075 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9170 b_overall=-4.7368 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1570 r_free=0.1553 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1570 r_free=0.1553 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 18.575033 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.816026 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 0.1166 0.1809 0.0642 0.010 1.0 3.2 0.5 0.0 0 9.288 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.66 18.09 6.42 3.013 16.142 1.816 0.018 10.32 17.91 7.59 4.734 16.342 1.816 0.015 Individual atomic B min max mean iso aniso Overall: 2.30 111.58 17.55 5.14 1785 0 Protein: 2.30 110.95 14.84 5.13 1519 0 Water: 4.15 111.58 33.27 N/A 258 0 Other: 15.79 38.14 23.88 N/A 8 0 Chain A: 2.30 111.58 17.55 N/A 1785 0 Histogram: Values Number of atoms 2.30 - 13.23 917 13.23 - 24.16 481 24.16 - 35.09 191 35.09 - 46.02 110 46.02 - 56.94 56 56.94 - 67.87 13 67.87 - 78.80 8 78.80 - 89.73 5 89.73 - 100.65 1 100.65 - 111.58 3 =========================== Idealize ADP of riding H ========================== r_work=0.1032 r_free=0.1791 r_work=0.1025 r_free=0.1796 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1025 r_free = 0.1796 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1017 r_free = 0.1783 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.11 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= 0.1017 r_free= 0.1783 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ls_wunit_k1) (work): 0.014053 | | target function (ls_wunit_k1) not normalized (work): 69.212198 | | target function (ls_wunit_k1) not normalized (free): 10.454642 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1056 0.1017 0.1783 n_refl.: 5177 re-set all scales: r(all,work,free)=0.2132 0.2133 0.2216 n_refl.: 5177 remove outliers: r(all,work,free)=0.2132 0.2133 0.2216 n_refl.: 5177 overall B=-0.97 to atoms: r(all,work,free)=0.2090 0.2090 0.2206 n_refl.: 5177 bulk-solvent and scaling: r(all,work,free)=0.1053 0.1014 0.1771 n_refl.: 5177 remove outliers: r(all,work,free)=0.1051 0.1012 0.1771 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 0.3398 314.766 296.966 0.645 1.001 0.370 11.894-9.307 99.02 97 4 0.1497 509.668 501.339 0.967 1.002 0.371 9.237-7.194 100.00 213 7 0.1638 416.807 417.652 0.997 1.002 0.326 7.162-5.571 100.00 427 22 0.1637 312.763 308.696 0.953 1.002 0.312 5.546-4.326 100.00 867 58 0.0910 429.379 426.613 0.969 1.001 0.207 4.315-3.360 100.00 1859 96 0.0763 408.344 408.116 1.016 1.000 0.193 3.356-3.002 100.00 1373 60 0.1009 314.524 313.487 0.992 0.999 0.072 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9170 b_overall=-4.3472 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1012 r_free=0.1771 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=0.1013 r_free=0.1773 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1013 r_free=0.1773 | n_water=258 | time (s): 0.650 (total time: 0.650) Filter (dist) r_work=0.1038 r_free=0.1767 | n_water=248 | time (s): 21.330 (total time: 21.980) Filter (q & B) r_work=0.1038 r_free=0.1767 | n_water=245 | time (s): 1.540 (total time: 23.520) Compute maps r_work=0.1038 r_free=0.1767 | n_water=245 | time (s): 0.420 (total time: 23.940) Filter (map) r_work=0.1349 r_free=0.1867 | n_water=140 | time (s): 1.280 (total time: 25.220) Find peaks r_work=0.1349 r_free=0.1867 | n_water=140 | time (s): 0.550 (total time: 25.770) Add new water r_work=0.1716 r_free=0.2163 | n_water=232 | time (s): 1.500 (total time: 27.270) Refine new water occ: r_work=0.1169 r_free=0.1748 adp: r_work=0.1141 r_free=0.1736 occ: r_work=0.1139 r_free=0.1730 adp: r_work=0.1126 r_free=0.1730 occ: r_work=0.1126 r_free=0.1721 adp: r_work=0.1122 r_free=0.1724 ADP+occupancy (water only), MIN, final r_work=0.1122 r_free=0.1724 r_work=0.1122 r_free=0.1724 | n_water=232 | time (s): 7.890 (total time: 35.160) Filter (q & B) r_work=0.1122 r_free=0.1724 | n_water=232 | time (s): 1.130 (total time: 36.290) Filter (dist only) r_work=0.1134 r_free=0.1723 | n_water=229 | time (s): 18.460 (total time: 54.750) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.911448 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.481049 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 0.1011 0.1801 0.0790 0.010 1.0 5.4 0.5 0.6 0 11.956 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.11 18.01 7.90 4.578 16.947 2.481 0.014 9.42 18.29 8.87 5.300 17.371 2.481 0.012 Individual atomic B min max mean iso aniso Overall: 0.00 105.48 16.86 6.22 1756 0 Protein: 0.00 105.48 15.23 6.20 1519 0 Water: 0.00 62.89 27.47 N/A 229 0 Other: 11.03 40.59 23.69 N/A 8 0 Chain A: 0.00 105.48 15.92 N/A 1665 0 Chain S: 2.35 59.32 34.14 N/A 91 0 Histogram: Values Number of atoms 0.00 - 10.55 633 10.55 - 21.10 701 21.10 - 31.64 213 31.64 - 42.19 121 42.19 - 52.74 40 52.74 - 63.29 34 63.29 - 73.84 7 73.84 - 84.39 2 84.39 - 94.93 3 94.93 - 105.48 2 =========================== Idealize ADP of riding H ========================== r_work=0.0942 r_free=0.1829 r_work=0.0939 r_free=0.1831 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0939 r_free = 0.1831 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0939 r_free = 0.1821 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.25 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= 0.0939 r_free= 0.1821 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ls_wunit_k1) (work): 0.012001 | | target function (ls_wunit_k1) not normalized (work): 59.091947 | | target function (ls_wunit_k1) not normalized (free): 9.907748 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0984 0.0939 0.1821 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2147 0.2155 0.2163 n_refl.: 5176 remove outliers: r(all,work,free)=0.2147 0.2155 0.2163 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2147 0.2155 0.2163 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0982 0.0937 0.1817 n_refl.: 5176 remove outliers: r(all,work,free)=0.0982 0.0937 0.1817 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 0.3470 314.766 298.599 0.626 1.006 0.356 11.894-9.307 99.02 97 4 0.1414 509.668 507.096 0.957 1.007 0.353 9.237-7.194 100.00 213 7 0.1456 416.807 416.634 0.986 1.007 0.320 7.162-5.571 100.00 427 22 0.1411 312.763 309.746 0.964 1.006 0.310 5.546-4.326 100.00 867 58 0.0806 429.379 426.995 0.975 1.004 0.230 4.315-3.360 100.00 1859 96 0.0712 408.344 407.789 1.027 1.000 0.190 3.356-3.002 100.00 1373 60 0.0973 314.524 313.413 1.008 0.996 0.080 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-4.9519 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0937 r_free=0.1817 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=0.0939 r_free=0.1818 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0939 r_free=0.1818 | n_water=229 | time (s): 0.650 (total time: 0.650) Filter (dist) r_work=0.0961 r_free=0.1803 | n_water=223 | time (s): 16.990 (total time: 17.640) Filter (q & B) r_work=0.1019 r_free=0.1802 | n_water=221 | time (s): 1.750 (total time: 19.390) Compute maps r_work=0.1019 r_free=0.1802 | n_water=221 | time (s): 0.630 (total time: 20.020) Filter (map) r_work=0.1303 r_free=0.1837 | n_water=147 | time (s): 1.630 (total time: 21.650) Find peaks r_work=0.1303 r_free=0.1837 | n_water=147 | time (s): 0.510 (total time: 22.160) Add new water r_work=0.1672 r_free=0.2202 | n_water=231 | time (s): 1.280 (total time: 23.440) Refine new water occ: r_work=0.1072 r_free=0.1733 adp: r_work=0.1065 r_free=0.1746 occ: r_work=0.1056 r_free=0.1730 adp: r_work=0.1055 r_free=0.1738 occ: r_work=0.1048 r_free=0.1723 adp: r_work=0.1047 r_free=0.1729 ADP+occupancy (water only), MIN, final r_work=0.1047 r_free=0.1729 r_work=0.1047 r_free=0.1729 | n_water=231 | time (s): 6.370 (total time: 29.810) Filter (q & B) r_work=0.1047 r_free=0.1731 | n_water=230 | time (s): 1.380 (total time: 31.190) Filter (dist only) r_work=0.1045 r_free=0.1733 | n_water=229 | time (s): 16.090 (total time: 47.280) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.077239 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.246609 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 0.0948 0.1774 0.0826 0.011 1.1 4.5 0.5 1.2 0 0.539 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.48 17.74 8.26 5.257 17.992 0.247 5.139 9.06 17.68 8.62 7.198 18.016 0.247 5.044 Individual atomic B min max mean iso aniso Overall: 0.00 104.89 16.60 8.86 1756 0 Protein: 0.00 104.89 15.37 8.85 1519 0 Water: 0.00 57.89 24.43 N/A 229 0 Other: 14.18 45.82 25.78 N/A 8 0 Chain A: 0.00 104.89 16.04 N/A 1651 0 Chain S: 0.00 51.89 25.39 N/A 105 0 Histogram: Values Number of atoms 0.00 - 10.49 623 10.49 - 20.98 691 20.98 - 31.47 236 31.47 - 41.95 125 41.95 - 52.44 48 52.44 - 62.93 14 62.93 - 73.42 9 73.42 - 83.91 5 83.91 - 94.40 3 94.40 - 104.89 2 =========================== Idealize ADP of riding H ========================== r_work=0.0906 r_free=0.1768 r_work=0.0913 r_free=0.1778 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0913 r_free = 0.1778 target_work(ml) = 5.049 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0902 r_free = 0.1774 target_work(ml) = 5.041 | | occupancies: max = 1.00 min = 0.26 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= 0.0902 r_free= 0.1774 coordinate error (max.-lik. estimate): 0.26 A | | | | normalized target function (ml) (work): 5.041165 | | target function (ml) not normalized (work): 24822.696634 | | target function (ml) not normalized (free): 1821.824220 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0946 0.0902 0.1774 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2158 0.2169 0.2100 n_refl.: 5176 remove outliers: r(all,work,free)=0.2158 0.2169 0.2100 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2158 0.2169 0.2099 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0941 0.0897 0.1779 n_refl.: 5176 remove outliers: r(all,work,free)=0.0939 0.0895 0.1779 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 0.3698 316.822 283.626 0.593 0.990 0.337 11.894-9.307 99.02 97 4 0.1870 509.668 493.754 0.961 0.994 0.336 9.237-7.194 100.00 213 7 0.1872 416.807 410.145 1.006 0.996 0.310 7.162-5.571 100.00 427 22 0.1911 312.763 303.068 0.991 0.998 0.300 5.546-4.326 100.00 867 58 0.0920 429.379 424.660 1.008 0.999 0.230 4.315-3.360 100.00 1859 96 0.0585 408.344 407.977 1.067 1.002 0.200 3.356-3.002 100.00 1373 60 0.0612 314.524 314.375 1.048 1.005 0.078 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9171 b_overall=-6.9997 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0895 r_free=0.1779 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=0.0897 r_free=0.1779 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0897 r_free=0.1779 | n_water=229 | time (s): 0.600 (total time: 0.600) Filter (dist) r_work=0.0909 r_free=0.1793 | n_water=227 | time (s): 17.560 (total time: 18.160) Filter (q & B) r_work=0.1019 r_free=0.1828 | n_water=223 | time (s): 1.330 (total time: 19.490) Compute maps r_work=0.1019 r_free=0.1828 | n_water=223 | time (s): 0.510 (total time: 20.000) Filter (map) r_work=0.1273 r_free=0.1907 | n_water=155 | time (s): 1.660 (total time: 21.660) Find peaks r_work=0.1273 r_free=0.1907 | n_water=155 | time (s): 0.450 (total time: 22.110) Add new water r_work=0.1583 r_free=0.2202 | n_water=226 | time (s): 1.520 (total time: 23.630) Refine new water occ: r_work=0.1024 r_free=0.1830 adp: r_work=0.1014 r_free=0.1845 occ: r_work=0.1005 r_free=0.1825 adp: r_work=0.1005 r_free=0.1837 occ: r_work=0.0997 r_free=0.1819 adp: r_work=0.0997 r_free=0.1831 ADP+occupancy (water only), MIN, final r_work=0.0997 r_free=0.1831 r_work=0.0997 r_free=0.1831 | n_water=226 | time (s): 11.720 (total time: 35.350) Filter (q & B) r_work=0.0997 r_free=0.1832 | n_water=225 | time (s): 1.640 (total time: 36.990) Filter (dist only) r_work=0.1006 r_free=0.1831 | n_water=223 | time (s): 17.630 (total time: 54.620) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.014076 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.252726 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 0.0918 0.1858 0.0940 0.011 1.0 4.5 0.5 0.0 0 0.507 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.18 18.58 9.40 6.919 18.182 0.253 5.022 8.93 18.52 9.59 8.080 18.291 0.253 4.960 Individual atomic B min max mean iso aniso Overall: 0.00 103.67 16.92 10.48 1750 0 Protein: 0.00 103.67 15.76 10.46 1519 0 Water: 0.00 58.80 24.41 N/A 223 0 Other: 13.94 52.10 27.06 N/A 8 0 Chain A: 0.00 103.67 16.35 N/A 1643 0 Chain S: 0.00 52.19 25.65 N/A 107 0 Histogram: Values Number of atoms 0.00 - 10.37 608 10.37 - 20.73 671 20.73 - 31.10 251 31.10 - 41.47 135 41.47 - 51.84 46 51.84 - 62.20 16 62.20 - 72.57 11 72.57 - 82.94 6 82.94 - 93.31 4 93.31 - 103.67 2 =========================== Idealize ADP of riding H ========================== r_work=0.0893 r_free=0.1852 r_work=0.0897 r_free=0.1856 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0897 r_free = 0.1856 target_work(ml) = 4.965 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0887 r_free = 0.1847 target_work(ml) = 4.959 | | occupancies: max = 1.00 min = 0.26 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= 0.0887 r_free= 0.1847 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 4.958519 | | target function (ml) not normalized (work): 24410.791028 | | target function (ml) not normalized (free): 2145.306340 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0936 0.0887 0.1847 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2120 0.2123 0.2193 n_refl.: 5175 remove outliers: r(all,work,free)=0.2120 0.2123 0.2193 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2120 0.2123 0.2193 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0934 0.0886 0.1849 n_refl.: 5175 remove outliers: r(all,work,free)=0.0934 0.0886 0.1849 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 0.3922 316.822 288.402 0.585 0.991 0.324 11.894-9.307 99.02 97 4 0.1921 509.668 492.310 0.954 0.996 0.320 9.237-7.194 100.00 213 7 0.2070 416.807 409.102 0.999 0.999 0.284 7.162-5.571 100.00 427 22 0.2073 312.763 302.530 0.993 1.000 0.270 5.546-4.326 100.00 867 58 0.0971 429.379 424.953 1.017 1.001 0.220 4.315-3.360 100.00 1859 96 0.0557 408.344 407.970 1.085 1.002 0.210 3.356-3.002 100.00 1373 60 0.0471 314.524 314.231 1.070 1.002 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.8049 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0886 r_free=0.1849 After: r_work=0.0889 r_free=0.1849 ================================== NQH flips ================================== r_work=0.0889 r_free=0.1849 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0889 r_free=0.1849 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0889 r_free=0.1849 | n_water=223 | time (s): 0.650 (total time: 0.650) Filter (dist) r_work=0.0900 r_free=0.1855 | n_water=219 | time (s): 18.770 (total time: 19.420) Filter (q & B) r_work=0.1007 r_free=0.1891 | n_water=216 | time (s): 1.630 (total time: 21.050) Compute maps r_work=0.1007 r_free=0.1891 | n_water=216 | time (s): 0.640 (total time: 21.690) Filter (map) r_work=0.1275 r_free=0.1911 | n_water=154 | time (s): 1.560 (total time: 23.250) Find peaks r_work=0.1275 r_free=0.1911 | n_water=154 | time (s): 0.540 (total time: 23.790) Add new water r_work=0.1540 r_free=0.2104 | n_water=217 | time (s): 1.370 (total time: 25.160) Refine new water occ: r_work=0.0993 r_free=0.1829 adp: r_work=0.0983 r_free=0.1838 occ: r_work=0.0978 r_free=0.1830 adp: r_work=0.0978 r_free=0.1830 occ: r_work=0.0978 r_free=0.1830 adp: r_work=0.0978 r_free=0.1830 ADP+occupancy (water only), MIN, final r_work=0.0978 r_free=0.1830 r_work=0.0978 r_free=0.1830 | n_water=217 | time (s): 6.990 (total time: 32.150) Filter (q & B) r_work=0.0979 r_free=0.1832 | n_water=216 | time (s): 1.540 (total time: 33.690) Filter (dist only) r_work=0.0979 r_free=0.1832 | n_water=216 | time (s): 16.160 (total time: 49.850) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.969081 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.187199 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 0.0924 0.1857 0.0933 0.011 1.1 7.0 0.5 0.6 0 0.485 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.24 18.57 9.33 7.986 18.390 0.187 4.994 9.07 18.64 9.56 8.869 18.475 0.187 4.940 Individual atomic B min max mean iso aniso Overall: 0.00 103.13 16.91 11.62 1743 0 Protein: 0.00 103.13 16.07 11.60 1519 0 Water: 0.42 57.74 22.50 N/A 216 0 Other: 11.05 52.57 26.70 N/A 8 0 Chain A: 0.00 103.13 16.52 N/A 1634 0 Chain S: 0.42 51.35 22.81 N/A 109 0 Histogram: Values Number of atoms 0.00 - 10.31 600 10.31 - 20.63 665 20.63 - 30.94 260 30.94 - 41.25 127 41.25 - 51.57 52 51.57 - 61.88 15 61.88 - 72.19 10 72.19 - 82.50 5 82.50 - 92.82 6 92.82 - 103.13 3 =========================== Idealize ADP of riding H ========================== r_work=0.0907 r_free=0.1864 r_work=0.0911 r_free=0.1870 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0911 r_free = 0.1870 target_work(ml) = 4.945 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0907 r_free = 0.1864 target_work(ml) = 4.943 | | 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= 0.0907 r_free= 0.1864 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ml) (work): 4.942767 | | target function (ml) not normalized (work): 24333.240635 | | target function (ml) not normalized (free): 2297.213885 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1296 0.1829 5.5207 6.1356| | 2: 3.78 - 3.00 1.00 2430 110 0.0432 0.1921 4.3499 12.963| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 12.48 1.00 0.95 13007.05| | 2: 3.78 - 3.00 2430 110 0.99 1.88 1.00 0.97 883.79| |alpha: min = 0.93 max = 0.97 mean = 0.96| |beta: min = 565.37 max = 21887.11 mean = 7022.99| |figures of merit: min = 0.01 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 88.82 mean = 7.25| |phase err.(test): min = 0.00 max = 78.13 mean = 7.06| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0955 0.0907 0.1864 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2183 0.2186 0.2242 n_refl.: 5175 remove outliers: r(all,work,free)=0.2183 0.2186 0.2242 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2183 0.2186 0.2242 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0953 0.0905 0.1863 n_refl.: 5175 remove outliers: r(all,work,free)=0.0953 0.0905 0.1863 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 0.3910 316.822 290.120 0.617 0.983 0.317 11.894-9.307 99.02 97 4 0.1913 509.668 495.581 0.999 0.991 0.308 9.237-7.194 100.00 213 7 0.2225 416.807 406.476 1.050 0.995 0.285 7.162-5.571 100.00 427 22 0.2141 312.763 301.271 1.037 0.997 0.270 5.546-4.326 100.00 867 58 0.1056 429.379 423.927 1.070 0.999 0.220 4.315-3.360 100.00 1859 96 0.0564 408.344 408.026 1.151 1.002 0.210 3.356-3.002 100.00 1373 60 0.0417 314.524 314.158 1.134 1.004 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-8.6538 ================= 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 : 0.3619 0.2022 0.084 5.316 8.8 119.3 19.9 258 0.000 1_bss: 0.1570 0.1553 0.084 5.316 6.1 116.6 17.2 258 0.000 1_settarget: 0.1570 0.1553 0.084 5.316 6.1 116.6 17.2 258 0.000 1_nqh: 0.1570 0.1553 0.084 5.316 6.1 116.6 17.2 258 0.000 1_weight: 0.1570 0.1553 0.084 5.316 6.1 116.6 17.2 258 0.000 1_xyzrec: 0.1166 0.1809 0.010 0.976 6.1 116.6 17.2 258 0.212 1_adp: 0.1032 0.1791 0.010 0.976 2.3 111.6 17.5 258 0.212 1_regHadp: 0.1025 0.1796 0.010 0.976 2.3 111.6 17.5 258 0.212 1_occ: 0.1017 0.1783 0.010 0.976 2.3 111.6 17.5 258 0.212 2_bss: 0.1012 0.1771 0.010 0.976 1.3 110.6 16.6 258 0.212 2_settarget: 0.1012 0.1771 0.010 0.976 1.3 110.6 16.6 258 0.212 2_updatecdl: 0.1012 0.1771 0.010 0.996 1.3 110.6 16.6 258 0.212 2_nqh: 0.1013 0.1773 0.010 0.996 1.3 110.6 16.6 258 0.215 2_sol: 0.1134 0.1723 0.010 0.996 1.0 110.0 16.1 229 n/a 2_weight: 0.1134 0.1723 0.010 0.996 1.0 110.0 16.1 229 n/a 2_xyzrec: 0.1011 0.1801 0.010 1.008 1.0 110.0 16.1 229 n/a 2_adp: 0.0942 0.1829 0.010 1.008 0.0 105.5 16.9 229 n/a 2_regHadp: 0.0939 0.1831 0.010 1.008 0.0 105.5 16.9 229 n/a 2_occ: 0.0939 0.1821 0.010 1.008 0.0 105.5 16.9 229 n/a 3_bss: 0.0937 0.1817 0.010 1.008 0.0 105.5 16.9 229 n/a 3_settarget: 0.0937 0.1817 0.010 1.008 0.0 105.5 16.9 229 n/a 3_updatecdl: 0.0937 0.1817 0.010 1.012 0.0 105.5 16.9 229 n/a 3_nqh: 0.0939 0.1818 0.010 1.012 0.0 105.5 16.9 229 n/a 3_sol: 0.1045 0.1733 0.010 1.012 0.0 105.5 16.6 229 n/a 3_weight: 0.1045 0.1733 0.010 1.012 0.0 105.5 16.6 229 n/a 3_xyzrec: 0.0948 0.1774 0.011 1.050 0.0 105.5 16.6 229 n/a 3_adp: 0.0906 0.1768 0.011 1.050 0.0 104.9 16.6 229 n/a 3_regHadp: 0.0913 0.1778 0.011 1.050 0.0 104.9 16.6 229 n/a 3_occ: 0.0902 0.1774 0.011 1.050 0.0 104.9 16.6 229 n/a 4_bss: 0.0895 0.1779 0.011 1.050 0.0 104.9 16.6 229 n/a 4_settarget: 0.0895 0.1779 0.011 1.050 0.0 104.9 16.6 229 n/a 4_updatecdl: 0.0895 0.1779 0.011 1.064 0.0 104.9 16.6 229 n/a 4_nqh: 0.0897 0.1779 0.011 1.064 0.0 104.9 16.6 229 n/a 4_sol: 0.1006 0.1831 0.011 1.064 0.0 104.9 16.7 223 n/a 4_weight: 0.1006 0.1831 0.011 1.064 0.0 104.9 16.7 223 n/a 4_xyzrec: 0.0918 0.1858 0.011 1.041 0.0 104.9 16.7 223 n/a 4_adp: 0.0893 0.1852 0.011 1.041 0.0 103.7 16.9 223 n/a 4_regHadp: 0.0897 0.1856 0.011 1.041 0.0 103.7 16.9 223 n/a 4_occ: 0.0887 0.1847 0.011 1.041 0.0 103.7 16.9 223 n/a 5_bss: 0.0886 0.1849 0.011 1.041 0.0 103.7 16.9 223 n/a 5_settarget: 0.0886 0.1849 0.011 1.041 0.0 103.7 16.9 223 n/a 5_updatecdl: 0.0886 0.1849 0.011 1.047 0.0 103.7 16.9 223 n/a 5_setrh: 0.0889 0.1849 0.011 1.047 0.0 103.7 16.9 223 n/a 5_nqh: 0.0889 0.1849 0.011 1.047 0.0 103.7 16.9 223 n/a 5_sol: 0.0979 0.1832 0.011 1.047 0.0 103.7 16.7 216 n/a 5_weight: 0.0979 0.1832 0.011 1.047 0.0 103.7 16.7 216 n/a 5_xyzrec: 0.0924 0.1857 0.011 1.139 0.0 103.7 16.7 216 n/a 5_adp: 0.0907 0.1864 0.011 1.139 0.0 103.1 16.9 216 n/a 5_regHadp: 0.0911 0.1870 0.011 1.139 0.0 103.1 16.9 216 n/a 5_occ: 0.0907 0.1864 0.011 1.139 0.0 103.1 16.9 216 n/a end: 0.0905 0.1863 0.011 1.139 0.0 103.1 16.9 216 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_1522381_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_1522381_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.0600 Refinement macro-cycles (run) : 473.7800 Write final files (write_after_run_outputs) : 11.1500 Total : 487.9900 Total CPU time: 8.51 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:18:52 PST -0800 (1735492732.10 s) Start R-work = 0.1570, R-free = 0.1553 Final R-work = 0.0905, R-free = 0.1863 =============================================================================== Job complete usr+sys time: 518.75 seconds wall clock time: 9 minutes 1.17 seconds (541.17 seconds total)