Starting phenix.refine on Sun Dec 29 09:24:42 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3031784.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Adding command-line PHIL: ------------------------- xray_data.high_resolution=2 ordered_solvent.low_resolution=4 No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3031784.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3031784.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 2 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } 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: 1.10, per 1000 atoms: 0.33 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: 0.38 Conformation dependent library (CDL) restraints added in 121.4 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.52 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: 395 0.89 - 1.15: 1224 1.15 - 1.41: 630 1.41 - 1.67: 858 1.67 - 1.93: 46 Bond restraints: 3153 Sorted by residual: bond pdb=" N ALA A 183 " pdb=" CA ALA A 183 " ideal model delta sigma weight residual 1.462 1.608 -0.146 7.70e-03 1.69e+04 3.58e+02 bond pdb=" CG HIS A 138 " pdb=" ND1 HIS A 138 " ideal model delta sigma weight residual 1.378 1.172 0.206 1.10e-02 8.26e+03 3.52e+02 bond pdb=" C ILE A 52 " pdb=" O ILE A 52 " ideal model delta sigma weight residual 1.237 1.034 0.204 1.10e-02 8.26e+03 3.42e+02 bond pdb=" C VAL A 123 " pdb=" O VAL A 123 " ideal model delta sigma weight residual 1.233 1.040 0.193 1.08e-02 8.57e+03 3.18e+02 bond pdb=" CA ASP A 60 " pdb=" C ASP A 60 " ideal model delta sigma weight residual 1.524 1.745 -0.221 1.26e-02 6.30e+03 3.08e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.46: 3113 4.46 - 8.92: 1829 8.92 - 13.38: 687 13.38 - 17.84: 133 17.84 - 22.30: 15 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA ARG A 98 " pdb=" C ARG A 98 " pdb=" O ARG A 98 " ideal model delta sigma weight residual 119.43 137.78 -18.35 1.21e+00 6.83e-01 2.30e+02 angle pdb=" OE1AGLN A 80 " pdb=" CD AGLN A 80 " pdb=" NE2AGLN A 80 " ideal model delta sigma weight residual 122.60 136.28 -13.68 1.00e+00 1.00e+00 1.87e+02 angle pdb=" O AGLU A 90 " pdb=" C AGLU A 90 " pdb=" N ILE A 91 " ideal model delta sigma weight residual 122.07 135.83 -13.76 1.03e+00 9.43e-01 1.78e+02 angle pdb=" N VAL A 23 " pdb=" CA VAL A 23 " pdb=" CB VAL A 23 " ideal model delta sigma weight residual 110.62 124.46 -13.84 1.05e+00 9.07e-01 1.74e+02 angle pdb=" CA LEU A 92 " pdb=" C LEU A 92 " pdb=" O LEU A 92 " ideal model delta sigma weight residual 120.19 134.73 -14.54 1.15e+00 7.56e-01 1.60e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.65: 1281 16.65 - 33.30: 143 33.30 - 49.95: 36 49.95 - 66.59: 19 66.59 - 83.24: 2 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: 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 -148.83 26.23 0 2.50e+00 1.60e-01 1.10e+02 dihedral pdb=" N BLYS A 99 " pdb=" C BLYS A 99 " pdb=" CA BLYS A 99 " pdb=" CB BLYS A 99 " ideal model delta harmonic sigma weight residual 122.80 146.02 -23.22 0 2.50e+00 1.60e-01 8.63e+01 dihedral pdb=" N AASN A 76 " pdb=" C AASN A 76 " pdb=" CA AASN A 76 " pdb=" CB AASN A 76 " ideal model delta harmonic sigma weight residual 122.80 100.77 22.03 0 2.50e+00 1.60e-01 7.76e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.213: 98 0.213 - 0.427: 68 0.427 - 0.640: 44 0.640 - 0.853: 27 0.853 - 1.066: 6 Chirality restraints: 243 Sorted by residual: chirality pdb=" CB THR A 110 " pdb=" CA THR A 110 " pdb=" OG1 THR A 110 " pdb=" CG2 THR A 110 " both_signs ideal model delta sigma weight residual False 2.55 1.49 1.07 2.00e-01 2.50e+01 2.84e+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 1.52 0.99 2.00e-01 2.50e+01 2.46e+01 chirality pdb=" CA ASP A 68 " pdb=" N ASP A 68 " pdb=" C ASP A 68 " pdb=" CB ASP A 68 " both_signs ideal model delta sigma weight residual False 2.51 1.55 0.96 2.00e-01 2.50e+01 2.32e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " 0.089 2.00e-02 2.50e+03 5.87e-02 1.04e+02 pdb=" CG PHE A 164 " 0.070 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " -0.050 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " -0.098 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.000 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.072 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.053 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.053 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.006 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 126 " 0.015 2.00e-02 2.50e+03 6.29e-02 8.91e+01 pdb=" CG HIS A 126 " -0.119 2.00e-02 2.50e+03 pdb=" ND1 HIS A 126 " 0.061 2.00e-02 2.50e+03 pdb=" CD2 HIS A 126 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 HIS A 126 " 0.094 2.00e-02 2.50e+03 pdb=" NE2 HIS A 126 " 0.031 2.00e-02 2.50e+03 pdb=" HD2 HIS A 126 " 0.041 2.00e-02 2.50e+03 pdb=" HE1 HIS A 126 " -0.066 2.00e-02 2.50e+03 pdb=" HE2 HIS A 126 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 5 " 0.060 9.50e-02 1.11e+02 6.44e-02 8.46e+01 pdb=" NE ARG A 5 " -0.090 2.00e-02 2.50e+03 pdb=" CZ ARG A 5 " 0.032 2.00e-02 2.50e+03 pdb=" NH1 ARG A 5 " 0.054 2.00e-02 2.50e+03 pdb=" NH2 ARG A 5 " -0.063 2.00e-02 2.50e+03 pdb="HH11 ARG A 5 " 0.050 2.00e-02 2.50e+03 pdb="HH12 ARG A 5 " -0.064 2.00e-02 2.50e+03 pdb="HH21 ARG A 5 " 0.102 2.00e-02 2.50e+03 pdb="HH22 ARG A 5 " -0.025 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.33: 1120 2.33 - 2.90: 8110 2.90 - 3.47: 10544 3.47 - 4.03: 15209 4.03 - 4.60: 21683 Nonbonded interactions: 56666 Sorted by model distance: nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.763 2.100 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.823 2.100 nonbonded pdb=" O ILE A 102 " pdb=" H ALEU A 153 " model vdw 1.838 2.450 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.838 2.450 nonbonded pdb=" H LEU A 10 " pdb=" O ALA A 36 " model vdw 1.842 2.450 ... (remaining 56661 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 6 Type Number sf(0) Gaussians S 10 15.96 2 O1- 2 8.97 2 O 551 7.97 2 N 265 6.97 2 C 957 5.97 2 H 1596 1.00 2 sf(0) = scattering factor at diffraction angle 0. =========================== Regularize ADP if needed ========================== ========================== Anomalous scatterer groups ========================= All atoms refined with f_prime=0 and f_double_prime=0. ====================== Modifying start model if requested ===================== ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 3381 n_use_u_iso = 1596 n_use_u_aniso = 1785 n_grad_site = 0 n_grad_u_iso = 0 n_grad_u_aniso = 0 n_grad_occupancy = 0 n_grad_fp = 0 n_grad_fdp = 0 total number of scatterers = 3381 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (3381 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 1596 aniso = 1785) group_adp = False (0 atoms in 0 groups) tls = False (0 atoms in 0 groups) occupancies = True (876 atoms) group_anomalous = False ============================ Non-default parameters =========================== A complete record of all parameters was written to the .eff file above. Below are only the non-defaults. #phil __ON__ refinement { electron_density_maps { map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT" mtz_label_phases = "PH2FOFCWT" fill_missing_f_obs = True } map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT_no_fill" mtz_label_phases = "PH2FOFCWT_no_fill" } map_coefficients { map_type = "mFo-DFc" mtz_label_amplitudes = "FOFCWT" mtz_label_phases = "PHFOFCWT" } map_coefficients { map_type = "anomalous" mtz_label_amplitudes = "ANOM" mtz_label_phases = "PANOM" } map { map_type = "2mFo-DFc" fill_missing_f_obs = True } map { map_type = "2mFo-DFc" } map { map_type = "mFo-DFc" } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } hydrogens { refine = individual *riding Auto } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } output { prefix = "shake_3031784_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1596 occupancy sum: 1438.50 (% of total atoms 46.85) Rotatable: count: 507 occupancy sum: 483.00 (% of total atoms 15.73) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2787 r_free= 0.1820 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.406797 | | target function (ml) not normalized (work): 71579.597438 | | target function (ml) not normalized (free): 3259.689324 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 49.25 - 3.64 1.00 2819 159 0.3196 0.2061 7.5853 5.016| | 2: 3.63 - 2.88 1.00 2711 122 0.2644 0.1826 4.33 4.3414| | 3: 2.88 - 2.52 1.00 2682 148 0.2570 0.1674 4.1771 4.1647| | 4: 2.52 - 2.29 1.00 2661 139 0.2577 0.1588 3.5015 3.5454| | 5: 2.29 - 2.13 1.00 2678 122 0.2621 0.1471 3.3704 3.4235| | 6: 2.13 - 2.00 1.00 2692 117 0.2713 0.1974 3.3105 3.4671| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 49.25 - 3.64 2819 159 0.88 17.48 0.77 0.23 1277.05| | 2: 3.63 - 2.88 2711 122 0.83 23.61 1.31 0.23 1277.05| | 3: 2.88 - 2.52 2682 148 0.73 32.58 1.29 0.23 1277.05| | 4: 2.52 - 2.29 2661 139 0.94 11.13 1.30 0.26 132.36| | 5: 2.29 - 2.13 2678 122 0.92 13.25 1.31 0.26 132.36| | 6: 2.13 - 2.00 2692 117 0.90 15.93 1.33 0.26 132.36| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 132.36 max = 1277.05 mean = 711.08| |figures of merit: min = 0.00 max = 1.00 mean = 0.87| |phase err.(work): min = 0.00 max = 89.93 mean = 19.00| |phase err.(test): min = 0.00 max = 87.94 mean = 19.37| |-----------------------------------------------------------------------------| ----------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 0.232 1557 Z= 5.599 Angle : 5.167 19.341 2118 Z= 3.645 Chirality : 0.398 1.066 243 Planarity : 0.030 0.086 284 Dihedral : 14.193 83.240 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.24 % Favored : 96.22 % Rotamer: Outliers : 3.73 % Allowed : 1.86 % Favored : 94.41 % Cbeta Deviations : 31.89 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.53), residues: 224 helix: -2.16 (0.45), residues: 102 sheet: -1.71 (0.83), residues: 30 loop : 0.61 (0.65), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.063 0.016 ARG A 27 TYR 0.089 0.035 TYR A 141 PHE 0.108 0.037 PHE A 162 HIS 0.084 0.030 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: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2787 r_free= 0.1820 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.406797 | | target function (ml) not normalized (work): 71579.597438 | | target function (ml) not normalized (free): 3259.689324 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.3293 percent. r_work = 0.2920 r_free = 0.1979 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2866 0.2920 0.1979 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2866 0.2920 0.1979 n_refl.: 17050 remove outliers: r(all,work,free)=0.2160 0.2172 0.1979 n_refl.: 17045 overall B=-0.39 to atoms: r(all,work,free)=0.2134 0.2145 0.1961 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1620 0.1618 0.1668 n_refl.: 17045 remove outliers: r(all,work,free)=0.1618 0.1616 0.1668 n_refl.: 17043 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 98.94 88 5 0.3879 398.954 359.469 0.647 1.013 0.397 11.894-9.307 99.02 97 4 0.1875 633.634 615.096 0.927 1.014 0.375 9.237-7.194 100.00 213 7 0.2179 518.248 511.265 0.965 1.013 0.360 7.162-5.571 100.00 427 22 0.2355 388.946 374.594 0.921 1.012 0.298 5.546-4.326 100.00 867 58 0.1365 533.960 528.276 0.959 1.010 0.225 4.315-3.360 100.00 1859 96 0.1303 507.802 504.343 1.017 1.006 0.201 3.356-2.611 100.00 3867 181 0.1665 333.597 328.836 1.011 0.999 0.061 2.608-2.000 99.99 8818 434 0.1649 217.448 213.430 1.028 0.988 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.3964 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1616 r_free=0.1668 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=0.1620 r_free=0.1669 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.762396 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.980305 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1348 0.1625 0.0277 0.009 1.0 1.3 0.5 0.0 0 11.881 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.48 16.25 2.77 3.013 18.467 0.980 0.023 12.74 16.47 3.72 3.643 18.690 0.980 0.020 Individual atomic B min max mean iso aniso Overall: 6.01 113.91 19.92 4.14 1785 0 Protein: 6.01 113.15 17.14 4.14 1519 0 Water: 8.21 113.91 36.06 N/A 258 0 Other: 21.60 36.20 26.27 N/A 8 0 Chain A: 6.01 113.91 19.92 N/A 1785 0 Histogram: Values Number of atoms 6.01 - 16.80 1079 16.80 - 27.59 346 27.59 - 38.38 183 38.38 - 49.17 97 49.17 - 59.96 53 59.96 - 70.75 12 70.75 - 81.54 7 81.54 - 92.33 4 92.33 - 103.12 1 103.12 - 113.91 3 =========================== Idealize ADP of riding H ========================== r_work=0.1274 r_free=0.1647 r_work=0.1278 r_free=0.1654 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1278 r_free = 0.1654 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1272 r_free = 0.1646 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17043 (all), 4.74 % free)------------| | | | r_work= 0.1272 r_free= 0.1646 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.019930 | | target function (ls_wunit_k1) not normalized (work): 323.576572 | | target function (ls_wunit_k1) not normalized (free): 26.809096 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1290 0.1272 0.1646 n_refl.: 17043 re-set all scales: r(all,work,free)=0.1898 0.1897 0.1974 n_refl.: 17043 remove outliers: r(all,work,free)=0.1898 0.1897 0.1974 n_refl.: 17043 overall B=-0.46 to atoms: r(all,work,free)=0.1865 0.1863 0.1955 n_refl.: 17043 bulk-solvent and scaling: r(all,work,free)=0.1289 0.1271 0.1641 n_refl.: 17043 remove outliers: r(all,work,free)=0.1288 0.1270 0.1641 n_refl.: 17042 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3546 304.793 282.832 0.639 1.007 0.374 11.894-9.307 99.02 97 4 0.1674 488.196 477.293 0.920 1.007 0.370 9.237-7.194 100.00 213 7 0.1824 399.295 395.433 0.963 1.007 0.351 7.162-5.571 100.00 427 22 0.1865 299.671 294.125 0.930 1.007 0.301 5.546-4.326 100.00 867 58 0.1048 411.401 408.523 0.957 1.006 0.210 4.315-3.360 100.00 1859 96 0.0925 391.246 390.632 1.015 1.004 0.192 3.356-2.611 100.00 3867 181 0.1294 257.026 255.663 1.009 1.001 0.091 2.608-2.000 99.99 8818 434 0.1341 167.537 166.222 1.012 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-1.1602 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1270 r_free=0.1641 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=0.1272 r_free=0.1640 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1272 r_free=0.1640 | n_water=258 | time (s): 0.920 (total time: 0.920) Filter (dist) r_work=0.1281 r_free=0.1629 | n_water=252 | time (s): 20.550 (total time: 21.470) Filter (q & B) r_work=0.1280 r_free=0.1629 | n_water=250 | time (s): 1.760 (total time: 23.230) Compute maps r_work=0.1280 r_free=0.1629 | n_water=250 | time (s): 0.550 (total time: 23.780) Filter (map) r_work=0.1318 r_free=0.1627 | n_water=211 | time (s): 1.420 (total time: 25.200) Find peaks r_work=0.1318 r_free=0.1627 | n_water=211 | time (s): 0.570 (total time: 25.770) Add new water r_work=0.1538 r_free=0.1861 | n_water=364 | time (s): 1.840 (total time: 27.610) Refine new water occ: r_work=0.1334 r_free=0.1587 adp: r_work=0.1279 r_free=0.1585 occ: r_work=0.1283 r_free=0.1558 adp: r_work=0.1251 r_free=0.1559 occ: r_work=0.1251 r_free=0.1557 adp: r_work=0.1241 r_free=0.1555 ADP+occupancy (water only), MIN, final r_work=0.1241 r_free=0.1555 r_work=0.1241 r_free=0.1555 | n_water=364 | time (s): 14.850 (total time: 42.460) Filter (q & B) r_work=0.1243 r_free=0.1557 | n_water=356 | time (s): 1.830 (total time: 44.290) Filter (dist only) r_work=0.1243 r_free=0.1559 | n_water=355 | time (s): 25.030 (total time: 69.320) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.537776 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.003391 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1213 0.1611 0.0398 0.008 0.9 2.6 0.5 0.0 0 12.269 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.13 16.11 3.98 4.201 20.872 1.003 0.018 11.98 16.30 4.32 4.243 21.069 1.003 0.018 Individual atomic B min max mean iso aniso Overall: 6.60 107.68 20.98 4.25 1882 0 Protein: 6.60 107.68 17.43 4.25 1519 0 Water: 8.45 68.14 35.86 N/A 355 0 Other: 24.43 46.67 34.78 N/A 8 0 Chain A: 6.60 107.68 19.17 N/A 1738 0 Chain S: 18.02 63.66 42.83 N/A 144 0 Histogram: Values Number of atoms 6.60 - 16.71 1043 16.71 - 26.82 366 26.82 - 36.93 216 36.93 - 47.03 154 47.03 - 57.14 72 57.14 - 67.25 20 67.25 - 77.36 4 77.36 - 87.47 4 87.47 - 97.57 1 97.57 - 107.68 2 =========================== Idealize ADP of riding H ========================== r_work=0.1198 r_free=0.1630 r_work=0.1200 r_free=0.1632 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1632 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1199 r_free = 0.1644 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17042 (all), 4.74 % free)------------| | | | r_work= 0.1199 r_free= 0.1644 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.017374 | | target function (ls_wunit_k1) not normalized (work): 282.074708 | | target function (ls_wunit_k1) not normalized (free): 26.047549 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1220 0.1199 0.1644 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1796 0.1791 0.1968 n_refl.: 17042 remove outliers: r(all,work,free)=0.1796 0.1791 0.1968 n_refl.: 17042 overall B=-0.37 to atoms: r(all,work,free)=0.1771 0.1765 0.1952 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1219 0.1198 0.1642 n_refl.: 17042 remove outliers: r(all,work,free)=0.1218 0.1197 0.1642 n_refl.: 17041 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 94.79 86 5 0.3352 306.820 278.392 0.617 1.004 0.370 11.894-9.307 99.02 97 4 0.1575 488.196 482.703 0.919 1.004 0.370 9.237-7.194 100.00 213 7 0.1720 399.295 398.832 0.976 1.004 0.320 7.162-5.571 100.00 427 22 0.1627 299.671 295.762 0.938 1.004 0.281 5.546-4.326 100.00 867 58 0.0903 411.401 408.789 0.960 1.003 0.210 4.315-3.360 100.00 1859 96 0.0831 391.246 390.926 1.017 1.003 0.185 3.356-2.611 100.00 3867 181 0.1205 257.026 256.064 1.009 1.001 0.058 2.608-2.000 99.99 8818 434 0.1323 167.537 166.392 1.008 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-1.1543 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1197 r_free=0.1642 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=0.1199 r_free=0.1644 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1199 r_free=0.1644 | n_water=355 | time (s): 0.870 (total time: 0.870) Filter (dist) r_work=0.1200 r_free=0.1644 | n_water=352 | time (s): 26.070 (total time: 26.940) Filter (q & B) r_work=0.1200 r_free=0.1644 | n_water=352 | time (s): 0.980 (total time: 27.920) Compute maps r_work=0.1200 r_free=0.1644 | n_water=352 | time (s): 0.640 (total time: 28.560) Filter (map) r_work=0.1257 r_free=0.1636 | n_water=261 | time (s): 1.650 (total time: 30.210) Find peaks r_work=0.1257 r_free=0.1636 | n_water=261 | time (s): 0.480 (total time: 30.690) Add new water r_work=0.1447 r_free=0.1844 | n_water=422 | time (s): 1.650 (total time: 32.340) Refine new water occ: r_work=0.1248 r_free=0.1595 adp: r_work=0.1241 r_free=0.1601 occ: r_work=0.1224 r_free=0.1566 adp: r_work=0.1212 r_free=0.1571 occ: r_work=0.1205 r_free=0.1552 adp: r_work=0.1194 r_free=0.1553 ADP+occupancy (water only), MIN, final r_work=0.1194 r_free=0.1553 r_work=0.1194 r_free=0.1553 | n_water=422 | time (s): 35.910 (total time: 68.250) Filter (q & B) r_work=0.1198 r_free=0.1556 | n_water=409 | time (s): 2.230 (total time: 70.480) Filter (dist only) r_work=0.1197 r_free=0.1554 | n_water=407 | time (s): 32.290 (total time: 102.770) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.938104 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.174527 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1180 0.1557 0.0376 0.009 1.0 5.4 0.5 0.0 0 0.969 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.80 15.57 3.76 4.298 21.180 0.175 5.000 11.60 15.64 4.04 4.872 21.129 0.175 4.978 Individual atomic B min max mean iso aniso Overall: 6.33 104.69 20.62 4.81 1934 0 Protein: 6.33 104.69 16.77 4.80 1519 0 Water: 8.18 66.97 34.71 N/A 407 0 Other: 25.51 45.37 34.12 N/A 8 0 Chain A: 6.33 104.69 18.52 N/A 1734 0 Chain S: 15.88 66.97 38.87 N/A 200 0 Histogram: Values Number of atoms 6.33 - 16.16 1078 16.16 - 26.00 347 26.00 - 35.84 226 35.84 - 45.67 161 45.67 - 55.51 85 55.51 - 65.35 23 65.35 - 75.18 5 75.18 - 85.02 4 85.02 - 94.86 3 94.86 - 104.69 2 =========================== Idealize ADP of riding H ========================== r_work=0.1160 r_free=0.1564 r_work=0.1160 r_free=0.1566 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1160 r_free = 0.1566 target_work(ml) = 4.978 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1150 r_free = 0.1548 target_work(ml) = 4.970 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1150 r_free= 0.1548 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.969832 | | target function (ml) not normalized (work): 80680.258698 | | target function (ml) not normalized (free): 4187.831287 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1169 0.1150 0.1548 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1649 0.1643 0.1820 n_refl.: 17041 remove outliers: r(all,work,free)=0.1649 0.1643 0.1820 n_refl.: 17041 overall B=-0.38 to atoms: r(all,work,free)=0.1624 0.1618 0.1811 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1165 0.1146 0.1541 n_refl.: 17041 remove outliers: r(all,work,free)=0.1164 0.1145 0.1541 n_refl.: 17040 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 93.75 85 5 0.3512 303.325 281.394 0.572 1.006 0.334 11.894-9.307 99.02 97 4 0.1741 488.196 481.453 0.910 1.007 0.330 9.237-7.194 100.00 213 7 0.1902 399.295 397.435 0.986 1.007 0.310 7.162-5.571 100.00 427 22 0.1652 299.671 293.856 0.942 1.007 0.241 5.546-4.326 100.00 867 58 0.0949 411.401 407.503 0.964 1.006 0.201 4.315-3.360 100.00 1859 96 0.0890 391.246 388.697 1.013 1.004 0.201 3.356-2.611 100.00 3867 181 0.1288 257.026 254.725 1.009 1.001 0.142 2.608-2.000 99.99 8818 434 0.1074 167.537 166.182 1.012 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-1.1655 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1145 r_free=0.1541 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1145 r_free=0.1541 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1145 r_free=0.1541 | n_water=407 | time (s): 0.690 (total time: 0.690) Filter (dist) r_work=0.1145 r_free=0.1541 | n_water=407 | time (s): 31.340 (total time: 32.030) Filter (q & B) r_work=0.1145 r_free=0.1542 | n_water=406 | time (s): 2.330 (total time: 34.360) Compute maps r_work=0.1145 r_free=0.1542 | n_water=406 | time (s): 0.620 (total time: 34.980) Filter (map) r_work=0.1206 r_free=0.1583 | n_water=307 | time (s): 2.090 (total time: 37.070) Find peaks r_work=0.1206 r_free=0.1583 | n_water=307 | time (s): 0.650 (total time: 37.720) Add new water r_work=0.1360 r_free=0.1706 | n_water=449 | time (s): 1.870 (total time: 39.590) Refine new water occ: r_work=0.1186 r_free=0.1530 adp: r_work=0.1175 r_free=0.1534 occ: r_work=0.1162 r_free=0.1512 adp: r_work=0.1149 r_free=0.1512 occ: r_work=0.1145 r_free=0.1496 adp: r_work=0.1135 r_free=0.1498 ADP+occupancy (water only), MIN, final r_work=0.1135 r_free=0.1498 r_work=0.1135 r_free=0.1498 | n_water=449 | time (s): 42.160 (total time: 81.750) Filter (q & B) r_work=0.1140 r_free=0.1502 | n_water=439 | time (s): 1.640 (total time: 83.390) Filter (dist only) r_work=0.1143 r_free=0.1506 | n_water=438 | time (s): 33.950 (total time: 117.340) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.988523 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.154934 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1126 0.1554 0.0428 0.010 1.0 5.8 0.5 0.0 0 0.994 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.26 15.54 4.28 4.546 20.839 0.155 4.966 11.15 15.46 4.31 4.598 20.876 0.155 4.957 Individual atomic B min max mean iso aniso Overall: 5.85 101.98 20.77 4.81 1965 0 Protein: 5.85 101.98 16.38 4.81 1519 0 Water: 8.77 65.36 35.74 N/A 438 0 Other: 25.82 44.61 33.90 N/A 8 0 Chain A: 5.85 101.98 18.04 N/A 1732 0 Chain S: 16.20 65.36 41.03 N/A 233 0 Histogram: Values Number of atoms 5.85 - 15.47 1052 15.47 - 25.08 356 25.08 - 34.69 218 34.69 - 44.30 184 44.30 - 53.92 102 53.92 - 63.53 37 63.53 - 73.14 7 73.14 - 82.76 3 82.76 - 92.37 4 92.37 - 101.98 2 =========================== Idealize ADP of riding H ========================== r_work=0.1115 r_free=0.1546 r_work=0.1115 r_free=0.1546 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1115 r_free = 0.1546 target_work(ml) = 4.957 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1108 r_free = 0.1552 target_work(ml) = 4.954 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1108 r_free= 0.1552 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.954067 | | target function (ml) not normalized (work): 80419.374592 | | target function (ml) not normalized (free): 4181.181512 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1130 0.1108 0.1552 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1586 0.1575 0.1839 n_refl.: 17040 remove outliers: r(all,work,free)=0.1586 0.1575 0.1839 n_refl.: 17040 overall B=-0.27 to atoms: r(all,work,free)=0.1569 0.1558 0.1830 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1126 0.1104 0.1543 n_refl.: 17040 remove outliers: r(all,work,free)=0.1126 0.1104 0.1543 n_refl.: 17040 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 93.75 85 5 0.3684 303.325 278.781 0.555 1.004 0.328 11.894-9.307 99.02 97 4 0.1837 488.196 479.933 0.911 1.005 0.320 9.237-7.194 100.00 213 7 0.1776 399.295 401.367 0.994 1.005 0.260 7.162-5.571 100.00 427 22 0.1549 299.671 293.761 0.938 1.004 0.200 5.546-4.326 100.00 867 58 0.0906 411.401 408.646 0.963 1.004 0.185 4.315-3.360 100.00 1859 96 0.0852 391.246 388.901 1.007 1.003 0.181 3.356-2.611 100.00 3867 181 0.1224 257.026 254.933 1.002 1.001 0.141 2.608-2.000 99.99 8818 434 0.1050 167.537 166.233 0.999 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.9436 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1104 r_free=0.1543 After: r_work=0.1107 r_free=0.1542 ================================== NQH flips ================================== r_work=0.1107 r_free=0.1542 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1107 r_free=0.1542 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1107 r_free=0.1542 | n_water=438 | time (s): 0.920 (total time: 0.920) Filter (dist) r_work=0.1107 r_free=0.1542 | n_water=438 | time (s): 36.110 (total time: 37.030) Filter (q & B) r_work=0.1107 r_free=0.1542 | n_water=438 | time (s): 1.330 (total time: 38.360) Compute maps r_work=0.1107 r_free=0.1542 | n_water=438 | time (s): 0.730 (total time: 39.090) Filter (map) r_work=0.1189 r_free=0.1574 | n_water=332 | time (s): 2.230 (total time: 41.320) Find peaks r_work=0.1189 r_free=0.1574 | n_water=332 | time (s): 0.510 (total time: 41.830) Add new water r_work=0.1310 r_free=0.1702 | n_water=471 | time (s): 1.620 (total time: 43.450) Refine new water occ: r_work=0.1148 r_free=0.1522 adp: r_work=0.1140 r_free=0.1529 occ: r_work=0.1126 r_free=0.1498 adp: r_work=0.1117 r_free=0.1504 occ: r_work=0.1111 r_free=0.1483 adp: r_work=0.1104 r_free=0.1490 ADP+occupancy (water only), MIN, final r_work=0.1104 r_free=0.1490 r_work=0.1104 r_free=0.1490 | n_water=471 | time (s): 19.380 (total time: 62.830) Filter (q & B) r_work=0.1108 r_free=0.1490 | n_water=462 | time (s): 1.820 (total time: 64.650) Filter (dist only) r_work=0.1107 r_free=0.1489 | n_water=459 | time (s): 36.980 (total time: 101.630) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.921377 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.150390 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1114 0.1515 0.0401 0.010 1.0 5.1 0.5 0.0 0 0.961 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.14 15.15 4.01 4.522 20.668 0.150 4.945 11.05 15.04 3.99 4.588 20.719 0.150 4.937 Individual atomic B min max mean iso aniso Overall: 5.54 100.56 20.75 4.96 1986 0 Protein: 5.54 100.56 16.17 4.95 1519 0 Water: 8.34 64.38 35.72 N/A 459 0 Other: 25.79 44.49 33.36 N/A 8 0 Chain A: 5.54 100.56 17.79 N/A 1731 0 Chain S: 19.36 64.38 40.85 N/A 255 0 Histogram: Values Number of atoms 5.54 - 15.05 1052 15.05 - 24.55 354 24.55 - 34.05 215 34.05 - 43.55 198 43.55 - 53.05 113 53.05 - 62.55 33 62.55 - 72.06 11 72.06 - 81.56 3 81.56 - 91.06 3 91.06 - 100.56 4 =========================== Idealize ADP of riding H ========================== r_work=0.1105 r_free=0.1504 r_work=0.1105 r_free=0.1505 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1105 r_free = 0.1505 target_work(ml) = 4.937 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1101 r_free = 0.1510 target_work(ml) = 4.932 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1101 r_free= 0.1510 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.932494 | | target function (ml) not normalized (work): 80069.171083 | | target function (ml) not normalized (free): 4156.149292 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.64 1.00 2810 159 0.1117 0.1333 5.4565 5.5969| | 2: 3.63 - 2.88 1.00 2711 122 0.1069 0.1540 5.1965 5.3567| | 3: 2.88 - 2.52 1.00 2681 148 0.1337 0.1661 5.1072 5.1819| | 4: 2.52 - 2.29 1.00 2661 139 0.0942 0.1545 4.6341 4.9401| | 5: 2.29 - 2.13 1.00 2678 122 0.0963 0.1520 4.5882 4.8884| | 6: 2.13 - 2.00 1.00 2692 117 0.1127 0.1791 4.5831 4.8098| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.64 2810 159 0.95 8.56 1.00 0.96 5990.87| | 2: 3.63 - 2.88 2711 122 0.93 12.34 1.01 0.96 5990.87| | 3: 2.88 - 2.52 2681 148 0.88 18.36 0.99 0.96 5990.87| | 4: 2.52 - 2.29 2661 139 0.93 12.27 1.01 0.97 2161.70| | 5: 2.29 - 2.13 2678 122 0.91 14.21 1.00 0.97 2161.70| | 6: 2.13 - 2.00 2692 117 0.89 17.00 0.99 0.97 2161.70| |alpha: min = 0.96 max = 0.97 mean = 0.97| |beta: min = 2161.70 max = 5990.87 mean = 4096.46| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.82 mean = 13.75| |phase err.(test): min = 0.00 max = 88.42 mean = 13.42| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1120 0.1101 0.1510 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1564 0.1554 0.1802 n_refl.: 17040 remove outliers: r(all,work,free)=0.1564 0.1554 0.1802 n_refl.: 17040 overall B=-0.22 to atoms: r(all,work,free)=0.1551 0.1541 0.1795 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1121 0.1101 0.1513 n_refl.: 17040 remove outliers: r(all,work,free)=0.1121 0.1101 0.1513 n_refl.: 17040 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 93.75 85 5 0.3643 303.325 279.661 0.562 1.003 0.350 11.894-9.307 99.02 97 4 0.1685 488.196 482.157 0.909 1.003 0.340 9.237-7.194 100.00 213 7 0.1828 399.295 402.555 0.993 1.003 0.220 7.162-5.571 100.00 427 22 0.1571 299.671 294.347 0.940 1.003 0.210 5.546-4.326 100.00 867 58 0.0914 411.401 408.444 0.962 1.003 0.178 4.315-3.360 100.00 1859 96 0.0855 391.246 389.325 1.004 1.002 0.167 3.356-2.611 100.00 3867 181 0.1221 257.026 254.818 0.998 1.001 0.141 2.608-2.000 99.99 8818 434 0.1040 167.537 166.130 0.988 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.7619 ================= 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 : 0.2787 0.1820 0.083 5.167 8.8 119.3 19.9 258 0.000 1_bss: 0.1616 0.1668 0.083 5.167 8.5 118.9 19.5 258 0.000 1_settarget: 0.1616 0.1668 0.083 5.167 8.5 118.9 19.5 258 0.000 1_nqh: 0.1620 0.1669 0.083 5.167 8.5 118.9 19.5 258 0.003 1_weight: 0.1620 0.1669 0.083 5.167 8.5 118.9 19.5 258 0.003 1_xyzrec: 0.1348 0.1625 0.009 0.986 8.5 118.9 19.5 258 0.142 1_adp: 0.1274 0.1647 0.009 0.986 6.0 113.9 19.9 258 0.142 1_regHadp: 0.1278 0.1654 0.009 0.986 6.0 113.9 19.9 258 0.142 1_occ: 0.1272 0.1646 0.009 0.986 6.0 113.9 19.9 258 0.142 2_bss: 0.1270 0.1641 0.009 0.986 5.5 113.4 19.5 258 0.142 2_settarget: 0.1270 0.1641 0.009 0.986 5.5 113.4 19.5 258 0.142 2_updatecdl: 0.1270 0.1641 0.009 0.998 5.5 113.4 19.5 258 0.142 2_nqh: 0.1272 0.1640 0.009 0.998 5.5 113.4 19.5 258 0.139 2_sol: 0.1243 0.1559 0.009 0.998 5.5 112.7 20.6 355 n/a 2_weight: 0.1243 0.1559 0.009 0.998 5.5 112.7 20.6 355 n/a 2_xyzrec: 0.1213 0.1611 0.008 0.930 5.5 112.7 20.6 355 n/a 2_adp: 0.1198 0.1630 0.008 0.930 6.6 107.7 21.0 355 n/a 2_regHadp: 0.1200 0.1632 0.008 0.930 6.6 107.7 21.0 355 n/a 2_occ: 0.1199 0.1644 0.008 0.930 6.6 107.7 21.0 355 n/a 3_bss: 0.1197 0.1642 0.008 0.930 6.2 107.3 20.6 355 n/a 3_settarget: 0.1197 0.1642 0.008 0.930 6.2 107.3 20.6 355 n/a 3_updatecdl: 0.1197 0.1642 0.008 0.931 6.2 107.3 20.6 355 n/a 3_nqh: 0.1199 0.1644 0.008 0.931 6.2 107.3 20.6 355 n/a 3_sol: 0.1197 0.1554 0.008 0.931 6.2 107.3 20.7 407 n/a 3_weight: 0.1197 0.1554 0.008 0.931 6.2 107.3 20.7 407 n/a 3_xyzrec: 0.1180 0.1557 0.009 0.972 6.2 107.3 20.7 407 n/a 3_adp: 0.1160 0.1564 0.009 0.972 6.3 104.7 20.6 407 n/a 3_regHadp: 0.1160 0.1566 0.009 0.972 6.3 104.7 20.6 407 n/a 3_occ: 0.1150 0.1548 0.009 0.972 6.3 104.7 20.6 407 n/a 4_bss: 0.1145 0.1541 0.009 0.972 6.0 104.3 20.2 407 n/a 4_settarget: 0.1145 0.1541 0.009 0.972 6.0 104.3 20.2 407 n/a 4_updatecdl: 0.1145 0.1541 0.009 0.973 6.0 104.3 20.2 407 n/a 4_nqh: 0.1145 0.1541 0.009 0.973 6.0 104.3 20.2 407 n/a 4_sol: 0.1143 0.1506 0.009 0.973 6.0 104.3 20.7 438 n/a 4_weight: 0.1143 0.1506 0.009 0.973 6.0 104.3 20.7 438 n/a 4_xyzrec: 0.1126 0.1554 0.010 0.994 6.0 104.3 20.7 438 n/a 4_adp: 0.1115 0.1546 0.010 0.994 5.9 102.0 20.8 438 n/a 4_regHadp: 0.1115 0.1546 0.010 0.994 5.9 102.0 20.8 438 n/a 4_occ: 0.1108 0.1552 0.010 0.994 5.9 102.0 20.8 438 n/a 5_bss: 0.1104 0.1543 0.010 0.994 5.6 101.7 20.5 438 n/a 5_settarget: 0.1104 0.1543 0.010 0.994 5.6 101.7 20.5 438 n/a 5_updatecdl: 0.1104 0.1543 0.010 0.994 5.6 101.7 20.5 438 n/a 5_setrh: 0.1107 0.1542 0.010 0.994 5.6 101.7 20.5 438 n/a 5_nqh: 0.1107 0.1542 0.010 0.994 5.6 101.7 20.5 438 n/a 5_sol: 0.1107 0.1489 0.010 0.994 5.6 101.7 20.7 459 n/a 5_weight: 0.1107 0.1489 0.010 0.994 5.6 101.7 20.7 459 n/a 5_xyzrec: 0.1114 0.1515 0.010 1.022 5.6 101.7 20.7 459 n/a 5_adp: 0.1105 0.1504 0.010 1.022 5.5 100.6 20.8 459 n/a 5_regHadp: 0.1105 0.1505 0.010 1.022 5.5 100.6 20.8 459 n/a 5_occ: 0.1101 0.1510 0.010 1.022 5.5 100.6 20.8 459 n/a end: 0.1101 0.1513 0.010 1.022 5.3 100.3 20.5 459 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_3031784_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_3031784_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.1000 Refinement macro-cycles (run) : 920.8300 Write final files (write_after_run_outputs) : 20.9400 Total : 944.8700 Total CPU time: 16.14 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:09 PST -0800 (1735494069.09 s) Start R-work = 0.1616, R-free = 0.1668 Final R-work = 0.1101, R-free = 0.1513 =============================================================================== Job complete usr+sys time: 989.93 seconds wall clock time: 16 minutes 52.13 seconds (1012.13 seconds total)