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_8530786.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 { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8530786.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8530786.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 3 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } 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: 0.42 Conformation dependent library (CDL) restraints added in 107.8 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.63 - 0.89: 390 0.89 - 1.14: 1213 1.14 - 1.39: 566 1.39 - 1.64: 903 1.64 - 1.89: 81 Bond restraints: 3153 Sorted by residual: bond pdb=" C SER A 3 " pdb=" O SER A 3 " ideal model delta sigma weight residual 1.234 0.998 0.235 1.17e-02 7.31e+03 4.05e+02 bond pdb=" ND1 HIS A 138 " pdb=" CE1 HIS A 138 " ideal model delta sigma weight residual 1.321 1.522 -0.201 1.00e-02 1.00e+04 4.04e+02 bond pdb=" C BGLU A 96 " pdb=" O BGLU A 96 " ideal model delta sigma weight residual 1.237 1.455 -0.218 1.17e-02 7.31e+03 3.49e+02 bond pdb=" NE ARG A 28 " pdb=" CZ ARG A 28 " ideal model delta sigma weight residual 1.326 1.144 0.182 1.10e-02 8.26e+03 2.75e+02 bond pdb=" N SER A 3 " pdb=" CA SER A 3 " ideal model delta sigma weight residual 1.454 1.261 0.194 1.17e-02 7.31e+03 2.74e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.94: 3259 4.94 - 9.87: 1874 9.87 - 14.81: 580 14.81 - 19.74: 60 19.74 - 24.67: 4 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CD2 HIS A 138 " pdb=" NE2 HIS A 138 " pdb=" CE1 HIS A 138 " ideal model delta sigma weight residual 109.00 124.34 -15.34 1.00e+00 1.00e+00 2.35e+02 angle pdb=" O ALEU A 153 " pdb=" C ALEU A 153 " pdb=" N THR A 154 " ideal model delta sigma weight residual 123.27 139.65 -16.38 1.16e+00 7.43e-01 1.99e+02 angle pdb=" CA ALEU A 153 " pdb=" C ALEU A 153 " pdb=" N THR A 154 " ideal model delta sigma weight residual 116.39 102.10 14.29 1.17e+00 7.31e-01 1.49e+02 angle pdb=" O ASN A 81 " pdb=" C ASN A 81 " pdb=" N LEU A 82 " ideal model delta sigma weight residual 122.12 109.28 12.84 1.06e+00 8.90e-01 1.47e+02 angle pdb=" CA ASP A 60 " pdb=" C ASP A 60 " pdb=" O ASP A 60 " ideal model delta sigma weight residual 120.70 132.95 -12.25 1.03e+00 9.43e-01 1.41e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.23: 1317 17.23 - 34.46: 108 34.46 - 51.68: 33 51.68 - 68.91: 20 68.91 - 86.13: 3 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C LEU A 172 " pdb=" N LEU A 172 " pdb=" CA LEU A 172 " pdb=" CB LEU A 172 " ideal model delta harmonic sigma weight residual -122.60 -105.65 -16.95 0 2.50e+00 1.60e-01 4.60e+01 dihedral pdb=" N ASP A 60 " pdb=" C ASP A 60 " pdb=" CA ASP A 60 " pdb=" CB ASP A 60 " ideal model delta harmonic sigma weight residual 122.80 139.21 -16.41 0 2.50e+00 1.60e-01 4.31e+01 dihedral pdb=" C THR A 125 " pdb=" N THR A 125 " pdb=" CA THR A 125 " pdb=" CB THR A 125 " ideal model delta harmonic sigma weight residual -122.00 -106.82 -15.18 0 2.50e+00 1.60e-01 3.69e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.214: 105 0.214 - 0.426: 61 0.426 - 0.638: 49 0.638 - 0.850: 21 0.850 - 1.062: 7 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 -1.53 -1.06 2.00e-01 2.50e+01 2.82e+01 chirality pdb=" CB ILE A 105 " pdb=" CA ILE A 105 " pdb=" CG1 ILE A 105 " pdb=" CG2 ILE A 105 " both_signs ideal model delta sigma weight residual False 2.64 1.67 0.98 2.00e-01 2.50e+01 2.38e+01 chirality pdb=" CA AGLN A 80 " pdb=" N AGLN A 80 " pdb=" C AGLN A 80 " pdb=" CB AGLN A 80 " both_signs ideal model delta sigma weight residual False 2.51 3.47 -0.96 2.00e-01 2.50e+01 2.31e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " 0.028 2.00e-02 2.50e+03 5.93e-02 1.05e+02 pdb=" CG PHE A 162 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " 0.046 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " 0.064 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " 0.018 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " -0.111 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " 0.047 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " -0.082 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " -0.021 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " 0.095 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " -0.052 2.00e-02 2.50e+03 5.35e-02 8.59e+01 pdb=" CG BTYR A 67 " 0.040 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " -0.051 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " -0.027 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " -0.042 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " 0.028 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " -0.058 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " -0.030 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " 0.106 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " -0.020 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " 0.017 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " 0.089 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.030 2.00e-02 2.50e+03 5.32e-02 8.50e+01 pdb=" CG PHE A 164 " 0.069 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " -0.054 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.055 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.057 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " -0.100 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.016 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.010 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.026 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.035 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.035 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.074 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.39: 1575 2.39 - 2.94: 8485 2.94 - 3.50: 10405 3.50 - 4.05: 15006 4.05 - 4.60: 21120 Nonbonded interactions: 56591 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.839 2.100 nonbonded pdb=" HG SER A 47 " pdb="HH11 ARG A 48 " model vdw 1.851 2.100 nonbonded pdb=" HG2 LYS A 12 " pdb=" HZ2 LYS A 12 " model vdw 1.865 2.270 nonbonded pdb=" H BTYR A 67 " pdb=" O HOH A 324 " model vdw 1.870 2.450 nonbonded pdb=" HB3 SER A 142 " pdb=" HG SER A 142 " model vdw 1.874 1.816 ... (remaining 56586 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_8530786_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= 0.3616 r_free= 0.2082 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.462402 | | target function (ml) not normalized (work): 21999.641599 | | target function (ml) not normalized (free): 1155.808708 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3808 0.2242 4.8451 4.9167| | 2: 3.78 - 3.00 1.00 2430 110 0.3382 0.1811 4.0687 4.1603| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 48.71 0.83 0.13 6595.01| | 2: 3.78 - 3.00 2430 110 0.94 11.21 1.48 0.26 443.72| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 377.78 max = 12061.67 mean = 3563.03| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 89.98 mean = 30.23| |phase err.(test): min = 0.00 max = 89.93 mean = 33.24| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.083 0.254 1557 Z= 5.582 Angle : 5.191 16.376 2118 Z= 3.628 Chirality : 0.397 1.062 243 Planarity : 0.029 0.101 284 Dihedral : 13.965 86.132 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.16 % Favored : 97.30 % Rotamer: Outliers : 1.86 % Allowed : 2.48 % Favored : 95.65 % Cbeta Deviations : 27.03 % 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: -2.07 (0.48), residues: 224 helix: -2.12 (0.37), residues: 109 sheet: -0.42 (0.91), residues: 28 loop : -0.32 (0.63), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.054 0.014 ARG A 5 TYR 0.083 0.032 TYR A 139 PHE 0.088 0.041 PHE A 162 HIS 0.033 0.013 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= 0.3616 r_free= 0.2082 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.462402 | | target function (ml) not normalized (work): 21999.641599 | | target function (ml) not normalized (free): 1155.808708 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3569 0.3645 0.2144 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3569 0.3645 0.2144 n_refl.: 5182 remove outliers: r(all,work,free)=0.2515 0.2538 0.2144 n_refl.: 5178 overall B=-2.87 to atoms: r(all,work,free)=0.2405 0.2424 0.2094 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1552 0.1547 0.1630 n_refl.: 5178 remove outliers: r(all,work,free)=0.1547 0.1543 0.1630 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 98.94 88 5 0.3804 449.819 410.087 0.666 1.058 0.398 11.894-9.307 99.02 97 4 0.1826 714.574 696.927 0.953 1.055 0.372 9.237-7.194 100.00 213 7 0.2149 584.380 576.908 0.981 1.049 0.364 7.162-5.571 100.00 427 22 0.2331 438.506 423.832 0.937 1.038 0.298 5.546-4.326 100.00 867 58 0.1383 602.006 595.478 0.987 1.020 0.210 4.315-3.360 100.00 1859 96 0.1280 572.515 566.715 1.056 0.990 0.179 3.356-3.002 100.00 1373 60 0.1594 440.975 433.170 1.058 0.961 0.086 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9556 b_overall=-3.6728 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1543 r_free=0.1630 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 80 GLN A Total number of N/Q/H flips: 1 r_work=0.1547 r_free=0.1629 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 18.741903 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.746685 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 0.1153 0.1817 0.0664 0.010 1.0 2.6 0.5 0.0 0 9.371 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.53 18.17 6.64 3.012 15.987 1.747 0.018 10.20 17.94 7.75 4.635 16.137 1.747 0.014 Individual atomic B min max mean iso aniso Overall: 2.30 111.45 17.30 5.07 1785 0 Protein: 2.30 111.45 14.57 5.07 1519 0 Water: 3.99 111.43 33.14 N/A 258 0 Other: 16.93 36.48 23.61 N/A 8 0 Chain A: 2.30 111.45 17.30 N/A 1785 0 Histogram: Values Number of atoms 2.30 - 13.22 950 13.22 - 24.13 460 24.13 - 35.05 178 35.05 - 45.96 110 45.96 - 56.88 56 56.88 - 67.79 14 67.79 - 78.71 8 78.71 - 89.62 5 89.62 - 100.54 1 100.54 - 111.45 3 =========================== Idealize ADP of riding H ========================== r_work=0.1020 r_free=0.1794 r_work=0.1013 r_free=0.1798 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1013 r_free = 0.1798 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1012 r_free = 0.1803 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.1012 r_free= 0.1803 coordinate error (max.-lik. estimate): 0.33 A | | | | normalized target function (ls_wunit_k1) (work): 0.013965 | | target function (ls_wunit_k1) not normalized (work): 68.761412 | | target function (ls_wunit_k1) not normalized (free): 10.890625 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1053 0.1012 0.1803 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2080 0.2077 0.2241 n_refl.: 5176 remove outliers: r(all,work,free)=0.2080 0.2077 0.2241 n_refl.: 5176 overall B=-0.98 to atoms: r(all,work,free)=0.2039 0.2035 0.2232 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.1054 0.1013 0.1806 n_refl.: 5176 remove outliers: r(all,work,free)=0.1054 0.1013 0.1806 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 0.3330 331.069 313.119 0.665 1.020 0.376 11.894-9.307 99.02 97 4 0.1477 525.930 518.480 0.977 1.020 0.351 9.237-7.194 100.00 213 7 0.1672 430.106 430.112 1.013 1.018 0.310 7.162-5.571 100.00 427 22 0.1650 322.743 318.816 0.970 1.014 0.292 5.546-4.326 100.00 867 58 0.0912 443.080 440.042 0.996 1.007 0.192 4.315-3.360 100.00 1859 96 0.0761 421.374 421.391 1.048 0.996 0.183 3.356-3.002 100.00 1373 60 0.1007 324.560 323.195 1.024 0.985 0.072 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-3.4944 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1013 r_free=0.1806 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A Total number of N/Q/H flips: 1 r_work=0.1013 r_free=0.1808 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1013 r_free=0.1808 | n_water=258 | time (s): 0.540 (total time: 0.540) Filter (dist) r_work=0.1052 r_free=0.1807 | n_water=248 | time (s): 19.900 (total time: 20.440) Filter (q & B) r_work=0.1051 r_free=0.1809 | n_water=245 | time (s): 1.360 (total time: 21.800) Compute maps r_work=0.1051 r_free=0.1809 | n_water=245 | time (s): 0.550 (total time: 22.350) Filter (map) r_work=0.1380 r_free=0.1845 | n_water=144 | time (s): 1.410 (total time: 23.760) Find peaks r_work=0.1380 r_free=0.1845 | n_water=144 | time (s): 0.420 (total time: 24.180) Add new water r_work=0.1720 r_free=0.2121 | n_water=234 | time (s): 1.290 (total time: 25.470) Refine new water occ: r_work=0.1174 r_free=0.1695 adp: r_work=0.1153 r_free=0.1698 occ: r_work=0.1152 r_free=0.1666 adp: r_work=0.1141 r_free=0.1675 occ: r_work=0.1141 r_free=0.1656 adp: r_work=0.1137 r_free=0.1663 ADP+occupancy (water only), MIN, final r_work=0.1137 r_free=0.1663 r_work=0.1137 r_free=0.1663 | n_water=234 | time (s): 3.370 (total time: 28.840) Filter (q & B) r_work=0.1137 r_free=0.1663 | n_water=234 | time (s): 0.900 (total time: 29.740) Filter (dist only) r_work=0.1143 r_free=0.1635 | n_water=232 | time (s): 17.740 (total time: 47.480) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 21.612101 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.719338 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 0.1020 0.1732 0.0712 0.009 0.9 3.8 0.5 0.6 0 10.806 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.20 17.32 7.12 4.525 16.648 2.719 0.014 9.48 17.54 8.05 5.387 16.966 2.719 0.013 Individual atomic B min max mean iso aniso Overall: 0.00 108.50 16.38 6.42 1759 0 Protein: 0.00 108.50 14.69 6.40 1519 0 Water: 0.00 63.66 27.19 N/A 232 0 Other: 11.53 37.36 22.73 N/A 8 0 Chain A: 0.00 108.50 15.49 N/A 1669 0 Chain S: 3.56 57.49 32.74 N/A 90 0 Histogram: Values Number of atoms 0.00 - 10.85 723 10.85 - 21.70 637 21.70 - 32.55 209 32.55 - 43.40 108 43.40 - 54.25 44 54.25 - 65.10 26 65.10 - 75.95 6 75.95 - 86.80 2 86.80 - 97.65 2 97.65 - 108.50 2 =========================== Idealize ADP of riding H ========================== r_work=0.0948 r_free=0.1754 r_work=0.0945 r_free=0.1752 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0945 r_free = 0.1752 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0941 r_free = 0.1766 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.20 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= 0.0941 r_free= 0.1766 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ls_wunit_k1) (work): 0.012082 | | target function (ls_wunit_k1) not normalized (work): 59.490703 | | target function (ls_wunit_k1) not normalized (free): 9.867022 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0983 0.0941 0.1766 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2088 0.2092 0.2159 n_refl.: 5176 remove outliers: r(all,work,free)=0.2088 0.2092 0.2159 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2088 0.2092 0.2159 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0982 0.0939 0.1784 n_refl.: 5176 remove outliers: r(all,work,free)=0.0982 0.0939 0.1784 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 0.3253 331.069 315.167 0.693 1.020 0.384 11.894-9.307 99.02 97 4 0.1419 525.930 518.318 0.966 1.021 0.373 9.237-7.194 100.00 213 7 0.1450 430.106 431.887 1.004 1.019 0.310 7.162-5.571 100.00 427 22 0.1477 322.743 319.886 0.974 1.015 0.280 5.546-4.326 100.00 867 58 0.0797 443.080 440.899 0.998 1.008 0.233 4.315-3.360 100.00 1859 96 0.0717 421.374 421.004 1.051 0.997 0.200 3.356-3.002 100.00 1373 60 0.0971 324.560 323.561 1.032 0.985 0.090 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-3.7901 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0939 r_free=0.1784 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=0.1790 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0939 r_free=0.1790 | n_water=232 | time (s): 0.550 (total time: 0.550) Filter (dist) r_work=0.0968 r_free=0.1797 | n_water=226 | time (s): 17.300 (total time: 17.850) Filter (q & B) r_work=0.1050 r_free=0.1843 | n_water=223 | time (s): 1.290 (total time: 19.140) Compute maps r_work=0.1050 r_free=0.1843 | n_water=223 | time (s): 0.510 (total time: 19.650) Filter (map) r_work=0.1302 r_free=0.1914 | n_water=149 | time (s): 1.730 (total time: 21.380) Find peaks r_work=0.1302 r_free=0.1914 | n_water=149 | time (s): 0.590 (total time: 21.970) Add new water r_work=0.1677 r_free=0.2209 | n_water=226 | time (s): 1.730 (total time: 23.700) Refine new water occ: r_work=0.1070 r_free=0.1771 adp: r_work=0.1062 r_free=0.1769 occ: r_work=0.1052 r_free=0.1758 adp: r_work=0.1052 r_free=0.1760 occ: r_work=0.1043 r_free=0.1750 adp: r_work=0.1043 r_free=0.1752 ADP+occupancy (water only), MIN, final r_work=0.1043 r_free=0.1752 r_work=0.1043 r_free=0.1752 | n_water=226 | time (s): 11.450 (total time: 35.150) Filter (q & B) r_work=0.1043 r_free=0.1752 | n_water=226 | time (s): 0.870 (total time: 36.020) Filter (dist only) r_work=0.1053 r_free=0.1763 | n_water=225 | time (s): 17.500 (total time: 53.520) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.051877 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.229783 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 0.0954 0.1832 0.0878 0.010 1.0 4.5 0.5 0.0 0 0.526 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.54 18.32 8.78 5.357 17.441 0.230 5.180 9.07 18.34 9.27 7.317 17.450 0.230 5.078 Individual atomic B min max mean iso aniso Overall: 0.00 109.40 16.09 9.01 1752 0 Protein: 0.00 109.40 14.86 9.00 1519 0 Water: 0.00 54.02 24.08 N/A 225 0 Other: 14.16 39.01 23.82 N/A 8 0 Chain A: 0.00 109.40 15.54 N/A 1653 0 Chain S: 0.00 54.02 25.27 N/A 99 0 Histogram: Values Number of atoms 0.00 - 10.94 733 10.94 - 21.88 619 21.88 - 32.82 225 32.82 - 43.76 110 43.76 - 54.70 33 54.70 - 65.64 17 65.64 - 76.58 9 76.58 - 87.52 1 87.52 - 98.46 3 98.46 - 109.40 2 =========================== Idealize ADP of riding H ========================== r_work=0.0907 r_free=0.1834 r_work=0.0912 r_free=0.1839 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0912 r_free = 0.1839 target_work(ml) = 5.083 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0903 r_free = 0.1830 target_work(ml) = 5.076 | | occupancies: max = 1.00 min = 0.20 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= 0.0903 r_free= 0.1830 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ml) (work): 5.075626 | | target function (ml) not normalized (work): 24992.382461 | | target function (ml) not normalized (free): 1832.056355 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0950 0.0903 0.1830 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2143 0.2152 0.2183 n_refl.: 5176 remove outliers: r(all,work,free)=0.2143 0.2152 0.2183 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2143 0.2152 0.2183 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0945 0.0898 0.1825 n_refl.: 5176 remove outliers: r(all,work,free)=0.0942 0.0896 0.1825 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 0.3680 328.281 308.639 0.627 0.992 0.342 11.894-9.307 99.02 97 4 0.1827 525.930 508.660 0.944 0.996 0.330 9.237-7.194 100.00 213 7 0.1884 430.106 426.743 0.999 0.998 0.304 7.162-5.571 100.00 427 22 0.1866 322.743 315.136 0.969 0.999 0.290 5.546-4.326 100.00 867 58 0.0937 443.080 436.771 0.993 1.000 0.225 4.315-3.360 100.00 1859 96 0.0603 421.374 420.702 1.047 1.002 0.220 3.356-3.002 100.00 1373 60 0.0589 324.560 323.843 1.018 1.003 0.080 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9171 b_overall=-5.8171 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0896 r_free=0.1825 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B Total number of N/Q/H flips: 1 r_work=0.0898 r_free=0.1822 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0898 r_free=0.1822 | n_water=225 | time (s): 0.680 (total time: 0.680) Filter (dist) r_work=0.0933 r_free=0.1838 | n_water=217 | time (s): 16.790 (total time: 17.470) Filter (q & B) r_work=0.0983 r_free=0.1870 | n_water=214 | time (s): 1.560 (total time: 19.030) Compute maps r_work=0.0983 r_free=0.1870 | n_water=214 | time (s): 0.590 (total time: 19.620) Filter (map) r_work=0.1224 r_free=0.1865 | n_water=161 | time (s): 1.280 (total time: 20.900) Find peaks r_work=0.1224 r_free=0.1865 | n_water=161 | time (s): 0.390 (total time: 21.290) Add new water r_work=0.1550 r_free=0.2086 | n_water=231 | time (s): 1.230 (total time: 22.520) Refine new water occ: r_work=0.1001 r_free=0.1795 adp: r_work=0.0998 r_free=0.1806 occ: r_work=0.0988 r_free=0.1783 adp: r_work=0.0988 r_free=0.1793 occ: r_work=0.0978 r_free=0.1769 adp: r_work=0.0978 r_free=0.1780 ADP+occupancy (water only), MIN, final r_work=0.0978 r_free=0.1780 r_work=0.0978 r_free=0.1780 | n_water=231 | time (s): 7.500 (total time: 30.020) Filter (q & B) r_work=0.0978 r_free=0.1785 | n_water=230 | time (s): 1.560 (total time: 31.580) Filter (dist only) r_work=0.0981 r_free=0.1781 | n_water=229 | time (s): 18.170 (total time: 49.750) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.985302 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.252847 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.0901 0.1872 0.0971 0.011 1.0 4.5 0.5 0.0 0 0.493 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.01 18.72 9.71 6.999 17.626 0.253 5.020 8.80 19.00 10.20 8.243 17.720 0.253 4.962 Individual atomic B min max mean iso aniso Overall: 0.00 110.80 16.37 10.82 1756 0 Protein: 0.00 110.80 15.24 10.81 1519 0 Water: 0.00 57.25 23.57 N/A 229 0 Other: 9.16 39.32 24.35 N/A 8 0 Chain A: 0.00 110.80 15.82 N/A 1645 0 Chain S: 0.00 57.25 24.52 N/A 111 0 Histogram: Values Number of atoms 0.00 - 11.08 715 11.08 - 22.16 634 22.16 - 33.24 228 33.24 - 44.32 112 44.32 - 55.40 36 55.40 - 66.48 15 66.48 - 77.56 9 77.56 - 88.64 3 88.64 - 99.72 3 99.72 - 110.80 1 =========================== Idealize ADP of riding H ========================== r_work=0.0880 r_free=0.1900 r_work=0.0884 r_free=0.1903 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0884 r_free = 0.1903 target_work(ml) = 4.966 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0874 r_free = 0.1887 target_work(ml) = 4.958 | | occupancies: max = 1.00 min = 0.21 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= 0.0874 r_free= 0.1887 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 4.958354 | | target function (ml) not normalized (work): 24409.977949 | | target function (ml) not normalized (free): 2117.244513 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0925 0.0874 0.1887 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2166 0.2174 0.2221 n_refl.: 5175 remove outliers: r(all,work,free)=0.2166 0.2174 0.2221 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2166 0.2174 0.2221 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0922 0.0871 0.1887 n_refl.: 5175 remove outliers: r(all,work,free)=0.0922 0.0871 0.1887 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 0.3695 328.281 299.375 0.627 0.989 0.357 11.894-9.307 99.02 97 4 0.1899 525.930 506.658 0.947 0.994 0.340 9.237-7.194 100.00 213 7 0.2107 430.106 422.139 0.998 0.997 0.285 7.162-5.571 100.00 427 22 0.2021 322.743 312.722 0.972 0.998 0.280 5.546-4.326 100.00 867 58 0.0977 443.080 437.324 1.006 1.000 0.225 4.315-3.360 100.00 1859 96 0.0554 421.374 421.389 1.070 1.003 0.220 3.356-3.002 100.00 1373 60 0.0432 324.560 324.458 1.042 1.006 0.080 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-6.9494 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0871 r_free=0.1887 After: r_work=0.0875 r_free=0.1886 ================================== NQH flips ================================== r_work=0.0875 r_free=0.1886 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0875 r_free=0.1886 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0875 r_free=0.1886 | n_water=229 | time (s): 0.670 (total time: 0.670) Filter (dist) r_work=0.0900 r_free=0.1887 | n_water=223 | time (s): 18.660 (total time: 19.330) Filter (q & B) r_work=0.1051 r_free=0.1953 | n_water=219 | time (s): 1.620 (total time: 20.950) Compute maps r_work=0.1051 r_free=0.1953 | n_water=219 | time (s): 0.530 (total time: 21.480) Filter (map) r_work=0.1283 r_free=0.1973 | n_water=154 | time (s): 1.260 (total time: 22.740) Find peaks r_work=0.1283 r_free=0.1973 | n_water=154 | time (s): 0.380 (total time: 23.120) Add new water r_work=0.1581 r_free=0.2249 | n_water=220 | time (s): 1.290 (total time: 24.410) Refine new water occ: r_work=0.1018 r_free=0.1890 adp: r_work=0.1006 r_free=0.1904 occ: r_work=0.0999 r_free=0.1886 adp: r_work=0.0998 r_free=0.1894 occ: r_work=0.0992 r_free=0.1876 adp: r_work=0.0991 r_free=0.1885 ADP+occupancy (water only), MIN, final r_work=0.0991 r_free=0.1885 r_work=0.0991 r_free=0.1885 | n_water=220 | time (s): 13.030 (total time: 37.440) Filter (q & B) r_work=0.0992 r_free=0.1887 | n_water=219 | time (s): 1.840 (total time: 39.280) Filter (dist only) r_work=0.0991 r_free=0.1885 | n_water=216 | time (s): 16.970 (total time: 56.250) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.960471 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.221209 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 0.0936 0.1893 0.0957 0.011 1.1 5.8 0.5 0.0 0 0.480 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.36 18.93 9.57 8.204 17.905 0.221 5.057 9.14 18.99 9.85 8.964 18.031 0.221 5.005 Individual atomic B min max mean iso aniso Overall: 0.00 112.12 16.57 11.88 1743 0 Protein: 0.00 112.12 15.62 11.84 1519 0 Water: 0.00 64.41 23.00 N/A 216 0 Other: 4.16 44.47 24.53 N/A 8 0 Chain A: 0.00 112.12 16.06 N/A 1634 0 Chain S: 0.00 64.41 24.35 N/A 109 0 Histogram: Values Number of atoms 0.00 - 11.21 714 11.21 - 22.42 617 22.42 - 33.63 242 33.63 - 44.85 109 44.85 - 56.06 28 56.06 - 67.27 13 67.27 - 78.48 11 78.48 - 89.69 5 89.69 - 100.90 2 100.90 - 112.12 2 =========================== Idealize ADP of riding H ========================== r_work=0.0914 r_free=0.1899 r_work=0.0917 r_free=0.1899 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0917 r_free = 0.1899 target_work(ml) = 5.009 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0910 r_free = 0.1886 target_work(ml) = 5.005 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0910 r_free= 0.1886 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 5.004960 | | target function (ml) not normalized (work): 24639.415972 | | target function (ml) not normalized (free): 2046.455126 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1284 0.1850 5.5639 6.2548| | 2: 3.78 - 3.00 1.00 2430 110 0.0454 0.1948 4.4315 10.53| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 12.30 1.00 0.98 13482.40| | 2: 3.78 - 3.00 2430 110 0.99 2.22 1.00 1.01 1071.18| |alpha: min = 0.97 max = 1.01 mean = 0.99| |beta: min = 698.08 max = 22322.99 mean = 7356.20| |figures of merit: min = 0.00 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.61 mean = 7.33| |phase err.(test): min = 0.00 max = 75.74 mean = 7.10| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0960 0.0910 0.1886 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2244 0.2251 0.2300 n_refl.: 5175 remove outliers: r(all,work,free)=0.2244 0.2251 0.2300 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2244 0.2251 0.2300 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0957 0.0907 0.1895 n_refl.: 5175 remove outliers: r(all,work,free)=0.0955 0.0905 0.1895 n_refl.: 5174 ======================== 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 0.3703 330.464 295.816 0.605 0.996 0.338 11.894-9.307 99.02 97 4 0.1841 525.930 506.820 0.950 1.002 0.330 9.237-7.194 100.00 213 7 0.2120 430.106 421.065 0.998 1.004 0.305 7.162-5.571 100.00 427 22 0.2032 322.743 315.395 0.977 1.004 0.300 5.546-4.326 100.00 867 58 0.1044 443.080 437.377 1.010 1.003 0.241 4.315-3.360 100.00 1859 96 0.0594 421.374 421.387 1.089 1.002 0.232 3.356-3.002 100.00 1373 60 0.0447 324.560 324.017 1.068 0.999 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9171 b_overall=-7.7311 ================= 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 : 0.3616 0.2082 0.083 5.191 8.8 119.3 19.9 258 0.000 1_bss: 0.1543 0.1630 0.083 5.191 6.0 116.4 17.0 258 0.000 1_settarget: 0.1543 0.1630 0.083 5.191 6.0 116.4 17.0 258 0.000 1_nqh: 0.1547 0.1629 0.083 5.191 6.0 116.4 17.0 258 0.003 1_weight: 0.1547 0.1629 0.083 5.191 6.0 116.4 17.0 258 0.003 1_xyzrec: 0.1153 0.1817 0.010 0.973 6.0 116.4 17.0 258 0.219 1_adp: 0.1020 0.1794 0.010 0.973 2.3 111.5 17.3 258 0.219 1_regHadp: 0.1013 0.1798 0.010 0.973 2.3 111.5 17.3 258 0.219 1_occ: 0.1012 0.1803 0.010 0.973 2.3 111.5 17.3 258 0.219 2_bss: 0.1013 0.1806 0.010 0.973 1.3 110.5 16.3 258 0.219 2_settarget: 0.1013 0.1806 0.010 0.973 1.3 110.5 16.3 258 0.219 2_updatecdl: 0.1013 0.1806 0.010 0.989 1.3 110.5 16.3 258 0.219 2_nqh: 0.1013 0.1808 0.010 0.989 1.3 110.5 16.3 258 0.216 2_sol: 0.1143 0.1635 0.010 0.989 1.0 110.5 15.8 232 n/a 2_weight: 0.1143 0.1635 0.010 0.989 1.0 110.5 15.8 232 n/a 2_xyzrec: 0.1020 0.1732 0.009 0.945 1.0 110.5 15.8 232 n/a 2_adp: 0.0948 0.1754 0.009 0.945 0.0 108.5 16.4 232 n/a 2_regHadp: 0.0945 0.1752 0.009 0.945 0.0 108.5 16.4 232 n/a 2_occ: 0.0941 0.1766 0.009 0.945 0.0 108.5 16.4 232 n/a 3_bss: 0.0939 0.1784 0.009 0.945 0.0 108.5 16.4 232 n/a 3_settarget: 0.0939 0.1784 0.009 0.945 0.0 108.5 16.4 232 n/a 3_updatecdl: 0.0939 0.1784 0.009 0.950 0.0 108.5 16.4 232 n/a 3_nqh: 0.0939 0.1790 0.009 0.950 0.0 108.5 16.4 232 n/a 3_sol: 0.1053 0.1763 0.009 0.950 0.0 108.5 16.1 225 n/a 3_weight: 0.1053 0.1763 0.009 0.950 0.0 108.5 16.1 225 n/a 3_xyzrec: 0.0954 0.1832 0.010 1.031 0.0 108.5 16.1 225 n/a 3_adp: 0.0907 0.1834 0.010 1.031 0.0 109.4 16.1 225 n/a 3_regHadp: 0.0912 0.1839 0.010 1.031 0.0 109.4 16.1 225 n/a 3_occ: 0.0903 0.1830 0.010 1.031 0.0 109.4 16.1 225 n/a 4_bss: 0.0896 0.1825 0.010 1.031 0.0 109.4 16.1 225 n/a 4_settarget: 0.0896 0.1825 0.010 1.031 0.0 109.4 16.1 225 n/a 4_updatecdl: 0.0896 0.1825 0.010 1.035 0.0 109.4 16.1 225 n/a 4_nqh: 0.0898 0.1822 0.010 1.035 0.0 109.4 16.1 225 n/a 4_sol: 0.0981 0.1781 0.010 1.035 0.0 109.4 16.2 229 n/a 4_weight: 0.0981 0.1781 0.010 1.035 0.0 109.4 16.2 229 n/a 4_xyzrec: 0.0901 0.1872 0.011 1.044 0.0 109.4 16.2 229 n/a 4_adp: 0.0880 0.1900 0.011 1.044 0.0 110.8 16.4 229 n/a 4_regHadp: 0.0884 0.1903 0.011 1.044 0.0 110.8 16.4 229 n/a 4_occ: 0.0874 0.1887 0.011 1.044 0.0 110.8 16.4 229 n/a 5_bss: 0.0871 0.1887 0.011 1.044 0.0 110.8 16.4 229 n/a 5_settarget: 0.0871 0.1887 0.011 1.044 0.0 110.8 16.4 229 n/a 5_updatecdl: 0.0871 0.1887 0.011 1.059 0.0 110.8 16.4 229 n/a 5_setrh: 0.0875 0.1886 0.011 1.059 0.0 110.8 16.4 229 n/a 5_nqh: 0.0875 0.1886 0.011 1.059 0.0 110.8 16.4 229 n/a 5_sol: 0.0991 0.1885 0.011 1.059 0.0 110.8 16.3 216 n/a 5_weight: 0.0991 0.1885 0.011 1.059 0.0 110.8 16.3 216 n/a 5_xyzrec: 0.0936 0.1893 0.011 1.136 0.0 110.8 16.3 216 n/a 5_adp: 0.0914 0.1899 0.011 1.136 0.0 112.1 16.6 216 n/a 5_regHadp: 0.0917 0.1899 0.011 1.136 0.0 112.1 16.6 216 n/a 5_occ: 0.0910 0.1886 0.011 1.136 0.0 112.1 16.6 216 n/a end: 0.0905 0.1895 0.011 1.136 0.0 112.1 16.6 216 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_8530786_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_8530786_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.0700 Refinement macro-cycles (run) : 482.7900 Write final files (write_after_run_outputs) : 10.3400 Total : 497.2000 Total CPU time: 8.60 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:18:57 PST -0800 (1735492737.05 s) Start R-work = 0.1543, R-free = 0.1630 Final R-work = 0.0905, R-free = 0.1895 =============================================================================== Job complete usr+sys time: 523.37 seconds wall clock time: 9 minutes 5.08 seconds (545.08 seconds total)