Starting phenix.refine on Sun Dec 29 09:10:03 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3850167.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_3850167.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3850167.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 1 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: 2.14, per 1000 atoms: 0.63 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.33 Conformation dependent library (CDL) restraints added in 133.4 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.65 - 0.92: 601 0.92 - 1.19: 1081 1.19 - 1.46: 774 1.46 - 1.73: 684 1.73 - 2.00: 13 Bond restraints: 3153 Sorted by residual: bond pdb=" C ALA A 107 " pdb=" N GLY A 108 " ideal model delta sigma weight residual 1.339 1.486 -0.147 7.50e-03 1.78e+04 3.83e+02 bond pdb=" N GLU A 143 " pdb=" CA GLU A 143 " ideal model delta sigma weight residual 1.456 1.688 -0.232 1.22e-02 6.72e+03 3.61e+02 bond pdb=" C ALYS A 175 " pdb=" N GLU A 176 " ideal model delta sigma weight residual 1.334 1.114 0.220 1.20e-02 6.94e+03 3.38e+02 bond pdb=" N LEU A 151 " pdb=" CA LEU A 151 " ideal model delta sigma weight residual 1.456 1.235 0.221 1.26e-02 6.30e+03 3.08e+02 bond pdb=" C ILE A 91 " pdb=" O ILE A 91 " ideal model delta sigma weight residual 1.236 1.419 -0.182 1.10e-02 8.26e+03 2.75e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.25: 2932 4.25 - 8.50: 1862 8.50 - 12.74: 764 12.74 - 16.99: 190 16.99 - 21.24: 29 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O ARG A 28 " pdb=" C ARG A 28 " pdb=" N ALA A 29 " ideal model delta sigma weight residual 122.12 138.52 -16.40 1.06e+00 8.90e-01 2.39e+02 angle pdb=" CA LEU A 72 " pdb=" C LEU A 72 " pdb=" O LEU A 72 " ideal model delta sigma weight residual 119.99 106.88 13.11 8.70e-01 1.32e+00 2.27e+02 angle pdb=" O ILE A 102 " pdb=" C ILE A 102 " pdb=" N ALA A 103 " ideal model delta sigma weight residual 123.20 139.27 -16.07 1.08e+00 8.57e-01 2.21e+02 angle pdb=" O GLU A 16 " pdb=" C GLU A 16 " pdb=" N MET A 17 " ideal model delta sigma weight residual 122.22 105.67 16.55 1.17e+00 7.31e-01 2.00e+02 angle pdb=" O ASN A 81 " pdb=" C ASN A 81 " pdb=" N LEU A 82 " ideal model delta sigma weight residual 122.12 135.60 -13.48 1.06e+00 8.90e-01 1.62e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.94: 1304 16.94 - 33.88: 119 33.88 - 50.81: 40 50.81 - 67.75: 16 67.75 - 84.69: 2 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C VAL A 25 " pdb=" N VAL A 25 " pdb=" CA VAL A 25 " pdb=" CB VAL A 25 " ideal model delta harmonic sigma weight residual -122.00 -141.71 19.71 0 2.50e+00 1.60e-01 6.22e+01 dihedral pdb=" C BLYS A 99 " pdb=" N BLYS A 99 " pdb=" CA BLYS A 99 " pdb=" CB BLYS A 99 " ideal model delta harmonic sigma weight residual -122.60 -141.96 19.36 0 2.50e+00 1.60e-01 6.00e+01 dihedral pdb=" C GLU A 176 " pdb=" N GLU A 176 " pdb=" CA GLU A 176 " pdb=" CB GLU A 176 " ideal model delta harmonic sigma weight residual -122.60 -141.30 18.70 0 2.50e+00 1.60e-01 5.60e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.194: 76 0.194 - 0.387: 73 0.387 - 0.580: 61 0.580 - 0.773: 21 0.773 - 0.966: 12 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA GLU A 16 " pdb=" N GLU A 16 " pdb=" C GLU A 16 " pdb=" CB GLU A 16 " both_signs ideal model delta sigma weight residual False 2.51 1.54 0.97 2.00e-01 2.50e+01 2.33e+01 chirality pdb=" CA BLYS A 99 " pdb=" N BLYS A 99 " pdb=" C BLYS A 99 " pdb=" CB BLYS A 99 " both_signs ideal model delta sigma weight residual False 2.51 1.55 0.97 2.00e-01 2.50e+01 2.33e+01 chirality pdb=" CG LEU A 92 " pdb=" CB LEU A 92 " pdb=" CD1 LEU A 92 " pdb=" CD2 LEU A 92 " both_signs ideal model delta sigma weight residual False -2.59 -3.53 0.94 2.00e-01 2.50e+01 2.21e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " 0.001 2.00e-02 2.50e+03 5.84e-02 1.02e+02 pdb=" CG PHE A 162 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " 0.104 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " 0.090 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " -0.070 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " -0.054 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " -0.058 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " 0.012 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " 0.043 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " -0.090 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 126 " 0.059 2.00e-02 2.50e+03 6.54e-02 9.62e+01 pdb=" CG HIS A 126 " -0.046 2.00e-02 2.50e+03 pdb=" ND1 HIS A 126 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 HIS A 126 " -0.118 2.00e-02 2.50e+03 pdb=" CE1 HIS A 126 " 0.020 2.00e-02 2.50e+03 pdb=" NE2 HIS A 126 " 0.122 2.00e-02 2.50e+03 pdb=" HD2 HIS A 126 " 0.034 2.00e-02 2.50e+03 pdb=" HE1 HIS A 126 " -0.003 2.00e-02 2.50e+03 pdb=" HE2 HIS A 126 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 173 " -0.049 2.00e-02 2.50e+03 7.85e-02 9.24e+01 pdb=" CG ASN A 173 " -0.056 2.00e-02 2.50e+03 pdb=" OD1 ASN A 173 " 0.076 2.00e-02 2.50e+03 pdb=" ND2 ASN A 173 " 0.075 2.00e-02 2.50e+03 pdb="HD21 ASN A 173 " -0.120 2.00e-02 2.50e+03 pdb="HD22 ASN A 173 " 0.075 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.38: 1486 2.38 - 2.93: 8395 2.93 - 3.49: 10385 3.49 - 4.04: 15036 4.04 - 4.60: 21272 Nonbonded interactions: 56574 Sorted by model distance: nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.823 2.450 nonbonded pdb="HH21 ARG A 145 " pdb=" OE2 GLU A 163 " model vdw 1.829 2.450 nonbonded pdb=" O LEU A 7 " pdb=" H VAL A 71 " model vdw 1.832 2.450 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.845 2.100 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.863 2.450 ... (remaining 56569 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_3850167_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= 0.3628 r_free= 0.2041 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.475147 | | target function (ml) not normalized (work): 22062.472395 | | target function (ml) not normalized (free): 1151.917774 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 49.25 - 3.79 1.00 2500 142 0.3801 0.2209 4.8564 4.9023| | 2: 3.78 - 3.00 1.00 2430 110 0.3417 0.1755 4.0829 4.1436| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 0.49 49.06 0.83 0.13 6626.02| | 2: 3.78 - 3.00 2430 110 0.94 11.36 1.48 0.26 452.50| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 379.14 max = 12074.77 mean = 3583.08| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 89.99 mean = 30.48| |phase err.(test): min = 0.00 max = 90.00 mean = 33.35| |-----------------------------------------------------------------------------| ----------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 0.233 1557 Z= 5.612 Angle : 5.255 16.549 2118 Z= 3.695 Chirality : 0.399 0.966 243 Planarity : 0.030 0.087 284 Dihedral : 13.955 84.687 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.16 % Favored : 97.30 % Rotamer: Outliers : 1.24 % Allowed : 2.48 % Favored : 96.27 % Cbeta Deviations : 30.27 % 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: -2.58 (0.46), residues: 224 helix: -2.82 (0.34), residues: 115 sheet: -0.73 (0.81), residues: 28 loop : 0.16 (0.59), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.112 0.018 ARG A 98 TYR 0.084 0.034 TYR A 141 PHE 0.101 0.038 PHE A 162 HIS 0.086 0.052 HIS A 115 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 1785 0 Protein: 8.85 115.78 16.79 3.90 1519 0 Water: 11.36 119.30 38.03 N/A 258 0 Other: 19.04 26.29 21.71 N/A 8 0 Chain A: 8.85 119.30 19.89 N/A 1785 0 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 3.00 - 49.25 A, n_refl.=5182 (all), 4.86 % free)-------------| | | | r_work= 0.3628 r_free= 0.2041 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.475147 | | target function (ml) not normalized (work): 22062.472395 | | target function (ml) not normalized (free): 1151.917774 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3586 0.3663 0.2147 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3586 0.3663 0.2147 n_refl.: 5182 remove outliers: r(all,work,free)=0.2543 0.2568 0.2147 n_refl.: 5178 overall B=-2.43 to atoms: r(all,work,free)=0.2449 0.2471 0.2102 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1579 0.1579 0.1591 n_refl.: 5178 remove outliers: r(all,work,free)=0.1575 0.1574 0.1591 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 0.3855 449.637 405.767 0.620 1.089 0.398 11.894-9.307 99.02 97 4 0.1806 714.285 697.120 0.889 1.084 0.372 9.237-7.194 100.00 213 7 0.2186 584.143 573.845 0.922 1.075 0.363 7.162-5.571 100.00 427 22 0.2330 438.328 423.737 0.887 1.058 0.288 5.546-4.326 100.00 867 58 0.1421 601.763 594.668 0.942 1.032 0.257 4.315-3.360 100.00 1859 96 0.1334 572.283 564.832 1.026 0.987 0.198 3.356-3.002 100.00 1373 60 0.1589 440.796 432.426 1.053 0.942 0.106 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9173 b_overall=-4.2082 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1574 r_free=0.1591 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** Total number of N/Q/H flips: 0 r_work=0.1574 r_free=0.1591 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 19.314141 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.747859 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 0.1162 0.1794 0.0632 0.010 1.0 2.9 0.5 0.0 0 9.657 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.62 17.94 6.32 3.013 16.433 1.748 0.018 10.24 17.98 7.74 4.702 16.568 1.748 0.015 Individual atomic B min max mean iso aniso Overall: 2.66 112.20 17.72 5.11 1785 0 Protein: 2.66 112.20 15.01 5.11 1519 0 Water: 4.44 111.87 33.44 N/A 258 0 Other: 17.83 36.46 23.81 N/A 8 0 Chain A: 2.66 112.20 17.72 N/A 1785 0 Histogram: Values Number of atoms 2.66 - 13.62 941 13.62 - 24.57 465 24.57 - 35.52 185 35.52 - 46.48 108 46.48 - 57.43 56 57.43 - 68.39 14 68.39 - 79.34 7 79.34 - 90.30 5 90.30 - 101.25 1 101.25 - 112.20 3 =========================== Idealize ADP of riding H ========================== r_work=0.1024 r_free=0.1798 r_work=0.1017 r_free=0.1802 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1017 r_free = 0.1802 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 = 0.1794 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.12 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= 0.1794 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ls_wunit_k1) (work): 0.013941 | | target function (ls_wunit_k1) not normalized (work): 68.643810 | | target function (ls_wunit_k1) not normalized (free): 10.567602 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1052 0.1012 0.1794 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2102 0.2101 0.2248 n_refl.: 5176 remove outliers: r(all,work,free)=0.2102 0.2101 0.2248 n_refl.: 5176 overall B=-1.06 to atoms: r(all,work,free)=0.2058 0.2054 0.2235 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.1057 0.1017 0.1803 n_refl.: 5176 remove outliers: r(all,work,free)=0.1057 0.1017 0.1803 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 0.3306 318.141 309.083 0.705 0.999 0.381 11.894-9.307 99.02 97 4 0.1529 505.392 498.325 0.997 1.001 0.361 9.237-7.194 100.00 213 7 0.1652 413.310 414.616 1.034 1.001 0.316 7.162-5.571 100.00 427 22 0.1634 310.139 306.957 0.985 1.001 0.265 5.546-4.326 100.00 867 58 0.0914 425.777 422.015 1.002 1.000 0.212 4.315-3.360 100.00 1859 96 0.0773 404.918 404.738 1.049 0.999 0.194 3.356-3.002 100.00 1373 60 0.1001 311.885 310.191 1.020 0.998 0.072 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-3.7814 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1017 r_free=0.1803 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=0.1019 r_free=0.1804 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1019 r_free=0.1804 | n_water=258 | time (s): 0.500 (total time: 0.500) Filter (dist) r_work=0.1040 r_free=0.1782 | n_water=248 | time (s): 21.080 (total time: 21.580) Filter (q & B) r_work=0.1041 r_free=0.1786 | n_water=246 | time (s): 1.650 (total time: 23.230) Compute maps r_work=0.1041 r_free=0.1786 | n_water=246 | time (s): 0.680 (total time: 23.910) Filter (map) r_work=0.1340 r_free=0.1838 | n_water=147 | time (s): 1.700 (total time: 25.610) Find peaks r_work=0.1340 r_free=0.1838 | n_water=147 | time (s): 0.420 (total time: 26.030) Add new water r_work=0.1693 r_free=0.2166 | n_water=235 | time (s): 1.150 (total time: 27.180) Refine new water occ: r_work=0.1169 r_free=0.1669 adp: r_work=0.1142 r_free=0.1698 occ: r_work=0.1139 r_free=0.1654 adp: r_work=0.1128 r_free=0.1676 occ: r_work=0.1126 r_free=0.1661 adp: r_work=0.1124 r_free=0.1666 ADP+occupancy (water only), MIN, final r_work=0.1124 r_free=0.1666 r_work=0.1124 r_free=0.1666 | n_water=235 | time (s): 3.320 (total time: 30.500) Filter (q & B) r_work=0.1124 r_free=0.1666 | n_water=235 | time (s): 1.230 (total time: 31.730) Filter (dist only) r_work=0.1126 r_free=0.1661 | n_water=233 | time (s): 18.930 (total time: 50.660) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.752819 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.662828 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 0.1013 0.1804 0.0792 0.009 1.0 4.5 0.5 0.6 0 11.376 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.13 18.04 7.92 4.580 17.038 2.663 0.014 9.41 18.48 9.07 5.500 17.466 2.663 0.012 Individual atomic B min max mean iso aniso Overall: 0.00 109.42 16.93 6.53 1760 0 Protein: 0.00 109.42 15.27 6.50 1519 0 Water: 0.00 64.34 27.39 N/A 233 0 Other: 13.12 47.82 28.73 N/A 8 0 Chain A: 0.00 109.42 16.08 N/A 1672 0 Chain S: 1.96 59.21 33.14 N/A 88 0 Histogram: Values Number of atoms 0.00 - 10.94 695 10.94 - 21.88 657 21.88 - 32.83 208 32.83 - 43.77 121 43.77 - 54.71 39 54.71 - 65.65 25 65.65 - 76.59 8 76.59 - 87.54 4 87.54 - 98.48 2 98.48 - 109.42 1 =========================== Idealize ADP of riding H ========================== r_work=0.0941 r_free=0.1848 r_work=0.0938 r_free=0.1849 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0938 r_free = 0.1849 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0935 r_free = 0.1843 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.26 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= 0.0935 r_free= 0.1843 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ls_wunit_k1) (work): 0.011950 | | target function (ls_wunit_k1) not normalized (work): 58.842003 | | target function (ls_wunit_k1) not normalized (free): 10.251739 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0980 0.0935 0.1843 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2133 0.2136 0.2230 n_refl.: 5176 remove outliers: r(all,work,free)=0.2133 0.2136 0.2230 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2133 0.2136 0.2230 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0982 0.0937 0.1851 n_refl.: 5176 remove outliers: r(all,work,free)=0.0980 0.0934 0.1851 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 0.3344 315.461 299.913 0.658 1.006 0.354 11.894-9.307 99.02 97 4 0.1437 505.392 501.199 0.991 1.008 0.350 9.237-7.194 100.00 213 7 0.1470 413.310 414.372 1.033 1.008 0.310 7.162-5.571 100.00 427 22 0.1403 310.139 308.993 0.995 1.006 0.261 5.546-4.326 100.00 867 58 0.0789 425.777 422.744 1.015 1.004 0.244 4.315-3.360 100.00 1859 96 0.0720 404.918 404.452 1.066 1.000 0.200 3.356-3.002 100.00 1373 60 0.0966 311.885 310.847 1.044 0.996 0.090 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9553 b_overall=-4.7260 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0934 r_free=0.1851 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN A Total number of N/Q/H flips: 2 r_work=0.0935 r_free=0.1856 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0935 r_free=0.1856 | n_water=233 | time (s): 0.710 (total time: 0.710) Filter (dist) r_work=0.0954 r_free=0.1873 | n_water=228 | time (s): 17.940 (total time: 18.650) Filter (q & B) r_work=0.1016 r_free=0.1866 | n_water=226 | time (s): 1.900 (total time: 20.550) Compute maps r_work=0.1016 r_free=0.1866 | n_water=226 | time (s): 0.660 (total time: 21.210) Filter (map) r_work=0.1284 r_free=0.1899 | n_water=149 | time (s): 1.740 (total time: 22.950) Find peaks r_work=0.1284 r_free=0.1899 | n_water=149 | time (s): 0.540 (total time: 23.490) Add new water r_work=0.1678 r_free=0.2287 | n_water=238 | time (s): 1.310 (total time: 24.800) Refine new water occ: r_work=0.1079 r_free=0.1841 adp: r_work=0.1076 r_free=0.1858 occ: r_work=0.1061 r_free=0.1830 adp: r_work=0.1063 r_free=0.1842 occ: r_work=0.1049 r_free=0.1814 adp: r_work=0.1051 r_free=0.1826 ADP+occupancy (water only), MIN, final r_work=0.1051 r_free=0.1826 r_work=0.1051 r_free=0.1826 | n_water=238 | time (s): 11.330 (total time: 36.130) Filter (q & B) r_work=0.1051 r_free=0.1820 | n_water=237 | time (s): 1.220 (total time: 37.350) Filter (dist only) r_work=0.1062 r_free=0.1828 | n_water=235 | time (s): 17.310 (total time: 54.660) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.102677 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.238951 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 0.0965 0.1830 0.0865 0.011 1.0 3.8 0.5 0.6 0 0.551 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.65 18.30 8.65 5.458 18.090 0.239 5.138 9.20 18.20 9.00 7.327 18.064 0.239 5.037 Individual atomic B min max mean iso aniso Overall: 0.00 107.69 16.65 8.99 1762 0 Protein: 0.00 107.69 15.37 8.96 1519 0 Water: 0.00 59.34 24.58 N/A 235 0 Other: 8.12 45.74 28.24 N/A 8 0 Chain A: 0.00 107.69 16.10 N/A 1655 0 Chain S: 0.00 58.71 25.21 N/A 107 0 Histogram: Values Number of atoms 0.00 - 10.77 658 10.77 - 21.54 679 21.54 - 32.31 236 32.31 - 43.08 113 43.08 - 53.85 40 53.85 - 64.61 16 64.61 - 75.38 13 75.38 - 86.15 2 86.15 - 96.92 4 96.92 - 107.69 1 =========================== Idealize ADP of riding H ========================== r_work=0.0920 r_free=0.1820 r_work=0.0927 r_free=0.1826 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0927 r_free = 0.1826 target_work(ml) = 5.042 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0912 r_free = 0.1793 target_work(ml) = 5.030 | | 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.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0912 r_free= 0.1793 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 5.029998 | | target function (ml) not normalized (work): 24762.679288 | | target function (ml) not normalized (free): 1841.549948 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0957 0.0912 0.1793 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2135 0.2148 0.2027 n_refl.: 5175 remove outliers: r(all,work,free)=0.2135 0.2148 0.2027 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2135 0.2148 0.2027 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0946 0.0902 0.1780 n_refl.: 5175 remove outliers: r(all,work,free)=0.0944 0.0899 0.1780 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 0.3661 317.559 284.333 0.580 0.995 0.326 11.894-9.307 99.02 97 4 0.1930 505.392 490.116 0.952 0.999 0.310 9.237-7.194 100.00 213 7 0.1981 413.310 406.798 1.006 1.001 0.310 7.162-5.571 100.00 427 22 0.1921 310.139 301.397 0.985 1.001 0.280 5.546-4.326 100.00 867 58 0.0914 425.777 419.867 1.009 1.002 0.214 4.315-3.360 100.00 1859 96 0.0592 404.918 404.569 1.071 1.002 0.200 3.356-3.002 100.00 1373 60 0.0593 311.885 311.402 1.052 1.003 0.090 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9171 b_overall=-7.1164 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0899 r_free=0.1780 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0899 r_free=0.1780 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0899 r_free=0.1780 | n_water=235 | time (s): 0.570 (total time: 0.570) Filter (dist) r_work=0.0907 r_free=0.1793 | n_water=233 | time (s): 17.430 (total time: 18.000) Filter (q & B) r_work=0.0962 r_free=0.1789 | n_water=230 | time (s): 1.290 (total time: 19.290) Compute maps r_work=0.0962 r_free=0.1789 | n_water=230 | time (s): 0.540 (total time: 19.830) Filter (map) r_work=0.1231 r_free=0.1877 | n_water=160 | time (s): 1.480 (total time: 21.310) Find peaks r_work=0.1231 r_free=0.1877 | n_water=160 | time (s): 0.380 (total time: 21.690) Add new water r_work=0.1526 r_free=0.2100 | n_water=234 | time (s): 1.180 (total time: 22.870) Refine new water occ: r_work=0.1012 r_free=0.1811 adp: r_work=0.1009 r_free=0.1823 occ: r_work=0.1000 r_free=0.1809 adp: r_work=0.1001 r_free=0.1816 occ: r_work=0.0993 r_free=0.1803 adp: r_work=0.0993 r_free=0.1809 ADP+occupancy (water only), MIN, final r_work=0.0993 r_free=0.1809 r_work=0.0993 r_free=0.1809 | n_water=234 | time (s): 9.780 (total time: 32.650) Filter (q & B) r_work=0.0994 r_free=0.1807 | n_water=232 | time (s): 1.300 (total time: 33.950) Filter (dist only) r_work=0.1001 r_free=0.1806 | n_water=230 | time (s): 18.290 (total time: 52.240) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.997048 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.241747 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 0.0904 0.1853 0.0949 0.011 1.0 4.5 0.5 0.6 0 0.499 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.04 18.53 9.49 7.007 18.145 0.242 4.990 8.80 18.76 9.96 8.389 18.270 0.242 4.925 Individual atomic B min max mean iso aniso Overall: 0.00 106.34 16.94 10.98 1757 0 Protein: 0.00 106.34 15.84 10.97 1519 0 Water: 0.00 58.74 23.81 N/A 230 0 Other: 11.16 40.74 28.29 N/A 8 0 Chain A: 0.00 106.34 16.44 N/A 1645 0 Chain S: 0.00 54.48 24.31 N/A 112 0 Histogram: Values Number of atoms 0.00 - 10.63 651 10.63 - 21.27 645 21.27 - 31.90 256 31.90 - 42.53 115 42.53 - 53.17 53 53.17 - 63.80 13 63.80 - 74.43 12 74.43 - 85.07 7 85.07 - 95.70 3 95.70 - 106.34 2 =========================== Idealize ADP of riding H ========================== r_work=0.0880 r_free=0.1876 r_work=0.0885 r_free=0.1881 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0885 r_free = 0.1881 target_work(ml) = 4.931 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0874 r_free = 0.1870 target_work(ml) = 4.921 | | 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.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0874 r_free= 0.1870 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ml) (work): 4.920909 | | target function (ml) not normalized (work): 24220.715636 | | target function (ml) not normalized (free): 2182.638742 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0925 0.0874 0.1870 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2099 0.2100 0.2235 n_refl.: 5174 remove outliers: r(all,work,free)=0.2099 0.2100 0.2235 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2099 0.2100 0.2235 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0923 0.0873 0.1873 n_refl.: 5174 remove outliers: r(all,work,free)=0.0923 0.0873 0.1873 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 0.3726 317.559 289.356 0.596 0.986 0.324 11.894-9.307 99.02 97 4 0.1929 505.392 490.144 0.960 0.992 0.320 9.237-7.194 100.00 213 7 0.2133 413.310 403.144 1.009 0.995 0.300 7.162-5.571 100.00 427 22 0.2019 310.139 300.783 0.989 0.997 0.280 5.546-4.326 100.00 867 58 0.0981 425.777 419.645 1.014 0.999 0.220 4.315-3.360 100.00 1859 96 0.0555 404.918 404.712 1.081 1.003 0.210 3.356-3.002 100.00 1373 60 0.0425 311.885 311.851 1.062 1.006 0.086 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.6416 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0873 r_free=0.1873 After: r_work=0.0876 r_free=0.1871 ================================== NQH flips ================================== r_work=0.0876 r_free=0.1871 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 ASN Total number of N/Q/H flips: 1 r_work=0.0883 r_free=0.1872 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0883 r_free=0.1872 | n_water=230 | time (s): 0.540 (total time: 0.540) Filter (dist) r_work=0.0890 r_free=0.1878 | n_water=227 | time (s): 17.810 (total time: 18.350) Filter (q & B) r_work=0.1002 r_free=0.1875 | n_water=224 | time (s): 1.340 (total time: 19.690) Compute maps r_work=0.1002 r_free=0.1875 | n_water=224 | time (s): 0.570 (total time: 20.260) Filter (map) r_work=0.1276 r_free=0.1979 | n_water=154 | time (s): 1.620 (total time: 21.880) Find peaks r_work=0.1276 r_free=0.1979 | n_water=154 | time (s): 0.600 (total time: 22.480) Add new water r_work=0.1541 r_free=0.2211 | n_water=223 | time (s): 1.750 (total time: 24.230) Refine new water occ: r_work=0.0994 r_free=0.1873 adp: r_work=0.0982 r_free=0.1891 occ: r_work=0.0977 r_free=0.1875 adp: r_work=0.0976 r_free=0.1885 occ: r_work=0.0971 r_free=0.1871 adp: r_work=0.0971 r_free=0.1871 ADP+occupancy (water only), MIN, final r_work=0.0971 r_free=0.1871 r_work=0.0971 r_free=0.1871 | n_water=223 | time (s): 9.250 (total time: 33.480) Filter (q & B) r_work=0.0971 r_free=0.1874 | n_water=222 | time (s): 1.330 (total time: 34.810) Filter (dist only) r_work=0.0971 r_free=0.1874 | n_water=222 | time (s): 15.530 (total time: 50.340) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.901897 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.244374 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 0.0911 0.1850 0.0940 0.011 1.1 6.4 0.5 0.6 0 0.451 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.11 18.50 9.40 8.331 18.515 0.244 4.979 8.93 18.49 9.56 9.222 18.660 0.244 4.926 Individual atomic B min max mean iso aniso Overall: 0.00 107.47 17.17 12.27 1749 0 Protein: 0.00 107.47 16.27 12.26 1519 0 Water: 0.00 60.47 22.94 N/A 222 0 Other: 10.41 39.61 26.82 N/A 8 0 Chain A: 0.00 107.47 16.74 N/A 1636 0 Chain S: 0.00 60.47 23.34 N/A 113 0 Histogram: Values Number of atoms 0.00 - 10.75 636 10.75 - 21.49 634 21.49 - 32.24 282 32.24 - 42.99 110 42.99 - 53.74 47 53.74 - 64.48 17 64.48 - 75.23 11 75.23 - 85.98 6 85.98 - 96.73 4 96.73 - 107.47 2 =========================== Idealize ADP of riding H ========================== r_work=0.0893 r_free=0.1849 r_work=0.0896 r_free=0.1852 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0896 r_free = 0.1852 target_work(ml) = 4.931 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0890 r_free = 0.1844 target_work(ml) = 4.927 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0890 r_free= 0.1844 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 4.926657 | | target function (ml) not normalized (work): 24249.007735 | | target function (ml) not normalized (free): 2148.698607 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.79 1.00 2492 142 0.1266 0.1847 5.5023 6.24| | 2: 3.78 - 3.00 1.00 2430 110 0.0432 0.1840 4.3363 11.478| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2492 142 0.92 12.15 1.00 0.94 12229.38| | 2: 3.78 - 3.00 2430 110 0.99 1.86 1.00 0.96 857.93| |alpha: min = 0.93 max = 0.96 mean = 0.95| |beta: min = 546.64 max = 20393.92 mean = 6615.28| |figures of merit: min = 0.00 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.77 mean = 7.07| |phase err.(test): min = 0.00 max = 86.88 mean = 7.16| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0939 0.0890 0.1844 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2151 0.2153 0.2265 n_refl.: 5174 remove outliers: r(all,work,free)=0.2151 0.2153 0.2265 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2151 0.2153 0.2265 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0939 0.0890 0.1857 n_refl.: 5174 remove outliers: r(all,work,free)=0.0939 0.0890 0.1857 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 0.3839 317.559 288.881 0.602 0.985 0.324 11.894-9.307 99.02 97 4 0.1892 505.392 492.080 0.962 0.993 0.305 9.237-7.194 100.00 213 7 0.2144 413.310 402.799 1.005 0.996 0.290 7.162-5.571 100.00 427 22 0.2024 310.139 301.059 0.990 0.998 0.290 5.546-4.326 100.00 867 58 0.1037 425.777 419.809 1.020 1.000 0.240 4.315-3.360 100.00 1859 96 0.0573 404.918 404.743 1.093 1.003 0.209 3.356-3.002 100.00 1373 60 0.0412 311.885 311.893 1.078 1.005 0.090 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-8.2101 ================= 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 : 0.3628 0.2041 0.084 5.255 8.8 119.3 19.9 258 0.000 1_bss: 0.1574 0.1591 0.084 5.255 6.4 116.9 17.5 258 0.000 1_settarget: 0.1574 0.1591 0.084 5.255 6.4 116.9 17.5 258 0.000 1_nqh: 0.1574 0.1591 0.084 5.255 6.4 116.9 17.5 258 0.000 1_weight: 0.1574 0.1591 0.084 5.255 6.4 116.9 17.5 258 0.000 1_xyzrec: 0.1162 0.1794 0.010 0.968 6.4 116.9 17.5 258 0.207 1_adp: 0.1024 0.1798 0.010 0.968 2.7 112.2 17.7 258 0.207 1_regHadp: 0.1017 0.1802 0.010 0.968 2.7 112.2 17.7 258 0.207 1_occ: 0.1012 0.1794 0.010 0.968 2.7 112.2 17.7 258 0.207 2_bss: 0.1017 0.1803 0.010 0.968 1.6 111.1 16.7 258 0.207 2_settarget: 0.1017 0.1803 0.010 0.968 1.6 111.1 16.7 258 0.207 2_updatecdl: 0.1017 0.1803 0.010 0.991 1.6 111.1 16.7 258 0.207 2_nqh: 0.1019 0.1804 0.010 0.991 1.6 111.1 16.7 258 0.209 2_sol: 0.1126 0.1661 0.010 0.991 1.0 111.1 16.1 233 n/a 2_weight: 0.1126 0.1661 0.010 0.991 1.0 111.1 16.1 233 n/a 2_xyzrec: 0.1013 0.1804 0.009 0.973 1.0 111.1 16.1 233 n/a 2_adp: 0.0941 0.1848 0.009 0.973 0.0 109.4 16.9 233 n/a 2_regHadp: 0.0938 0.1849 0.009 0.973 0.0 109.4 16.9 233 n/a 2_occ: 0.0935 0.1843 0.009 0.973 0.0 109.4 16.9 233 n/a 3_bss: 0.0934 0.1851 0.009 0.973 0.0 109.4 16.9 233 n/a 3_settarget: 0.0934 0.1851 0.009 0.973 0.0 109.4 16.9 233 n/a 3_updatecdl: 0.0934 0.1851 0.009 0.981 0.0 109.4 16.9 233 n/a 3_nqh: 0.0935 0.1856 0.009 0.981 0.0 109.4 16.9 233 n/a 3_sol: 0.1062 0.1828 0.009 0.981 0.0 109.4 16.7 235 n/a 3_weight: 0.1062 0.1828 0.009 0.981 0.0 109.4 16.7 235 n/a 3_xyzrec: 0.0965 0.1830 0.011 1.042 0.0 109.4 16.7 235 n/a 3_adp: 0.0920 0.1820 0.011 1.042 0.0 107.7 16.7 235 n/a 3_regHadp: 0.0927 0.1826 0.011 1.042 0.0 107.7 16.7 235 n/a 3_occ: 0.0912 0.1793 0.011 1.042 0.0 107.7 16.7 235 n/a 4_bss: 0.0899 0.1780 0.011 1.042 0.0 107.7 16.7 235 n/a 4_settarget: 0.0899 0.1780 0.011 1.042 0.0 107.7 16.7 235 n/a 4_updatecdl: 0.0899 0.1780 0.011 1.053 0.0 107.7 16.7 235 n/a 4_nqh: 0.0899 0.1780 0.011 1.053 0.0 107.7 16.7 235 n/a 4_sol: 0.1001 0.1806 0.011 1.053 0.0 107.7 16.7 230 n/a 4_weight: 0.1001 0.1806 0.011 1.053 0.0 107.7 16.7 230 n/a 4_xyzrec: 0.0904 0.1853 0.011 1.034 0.0 107.7 16.7 230 n/a 4_adp: 0.0880 0.1876 0.011 1.034 0.0 106.3 16.9 230 n/a 4_regHadp: 0.0885 0.1881 0.011 1.034 0.0 106.3 16.9 230 n/a 4_occ: 0.0874 0.1870 0.011 1.034 0.0 106.3 16.9 230 n/a 5_bss: 0.0873 0.1873 0.011 1.034 0.0 106.3 16.9 230 n/a 5_settarget: 0.0873 0.1873 0.011 1.034 0.0 106.3 16.9 230 n/a 5_updatecdl: 0.0873 0.1873 0.011 1.045 0.0 106.3 16.9 230 n/a 5_setrh: 0.0876 0.1871 0.011 1.045 0.0 106.3 16.9 230 n/a 5_nqh: 0.0883 0.1872 0.011 1.045 0.0 106.3 16.9 230 n/a 5_sol: 0.0971 0.1874 0.011 1.045 0.0 106.3 16.9 222 n/a 5_weight: 0.0971 0.1874 0.011 1.045 0.0 106.3 16.9 222 n/a 5_xyzrec: 0.0911 0.1850 0.011 1.089 0.0 106.3 16.9 222 n/a 5_adp: 0.0893 0.1849 0.011 1.089 0.0 107.5 17.2 222 n/a 5_regHadp: 0.0896 0.1852 0.011 1.089 0.0 107.5 17.2 222 n/a 5_occ: 0.0890 0.1844 0.011 1.089 0.0 107.5 17.2 222 n/a end: 0.0890 0.1857 0.011 1.089 0.0 107.5 17.2 222 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_3850167_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_3850167_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.2300 Refinement macro-cycles (run) : 484.6500 Write final files (write_after_run_outputs) : 10.4800 Total : 498.3600 Total CPU time: 8.66 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:19:02 PST -0800 (1735492742.31 s) Start R-work = 0.1574, R-free = 0.1591 Final R-work = 0.0890, R-free = 0.1857 =============================================================================== Job complete usr+sys time: 527.93 seconds wall clock time: 9 minutes 11.23 seconds (551.23 seconds total)