Starting phenix.refine on Sun Dec 29 09:24:41 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7848743.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 { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7848743.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7848743.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 = 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: 1.60, per 1000 atoms: 0.47 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: 0.56 Conformation dependent library (CDL) restraints added in 159.5 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.92: 524 0.92 - 1.17: 1131 1.17 - 1.42: 627 1.42 - 1.68: 838 1.68 - 1.93: 33 Bond restraints: 3153 Sorted by residual: bond pdb=" N VAL A 23 " pdb=" CA VAL A 23 " ideal model delta sigma weight residual 1.463 1.722 -0.259 1.14e-02 7.69e+03 5.15e+02 bond pdb=" C ALA A 107 " pdb=" N GLY A 108 " ideal model delta sigma weight residual 1.339 1.179 0.160 7.50e-03 1.78e+04 4.57e+02 bond pdb=" C PRO A 43 " pdb=" O PRO A 43 " ideal model delta sigma weight residual 1.233 1.004 0.229 1.10e-02 8.26e+03 4.33e+02 bond pdb=" C VAL A 69 " pdb=" O VAL A 69 " ideal model delta sigma weight residual 1.234 1.001 0.233 1.16e-02 7.43e+03 4.02e+02 bond pdb=" C ALA A 56 " pdb=" O ALA A 56 " ideal model delta sigma weight residual 1.234 1.014 0.220 1.20e-02 6.94e+03 3.36e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.79: 3172 4.79 - 9.58: 1880 9.58 - 14.36: 609 14.36 - 19.15: 107 19.15 - 23.93: 9 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O ARG A 145 " pdb=" C ARG A 145 " pdb=" N VAL A 146 " ideal model delta sigma weight residual 122.07 138.06 -15.99 1.03e+00 9.43e-01 2.41e+02 angle pdb=" O ILE A 117 " pdb=" C ILE A 117 " pdb=" N GLY A 118 " ideal model delta sigma weight residual 123.18 107.34 15.84 1.05e+00 9.07e-01 2.28e+02 angle pdb=" O ILE A 21 " pdb=" C ILE A 21 " pdb=" N PRO A 22 " ideal model delta sigma weight residual 120.07 129.76 -9.69 7.10e-01 1.98e+00 1.86e+02 angle pdb=" CA ILE A 21 " pdb=" C ILE A 21 " pdb=" N PRO A 22 " ideal model delta sigma weight residual 121.00 110.11 10.89 8.30e-01 1.45e+00 1.72e+02 angle pdb=" OD1AASN A 97 " pdb=" CG AASN A 97 " pdb=" ND2AASN A 97 " ideal model delta sigma weight residual 122.60 109.79 12.81 1.00e+00 1.00e+00 1.64e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.05: 1290 16.05 - 32.10: 125 32.10 - 48.15: 45 48.15 - 64.20: 19 64.20 - 80.25: 2 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C APRO A 66 " pdb=" N APRO A 66 " pdb=" CA APRO A 66 " pdb=" CB APRO A 66 " ideal model delta harmonic sigma weight residual -120.70 -141.20 20.50 0 2.50e+00 1.60e-01 6.72e+01 dihedral pdb=" N APRO A 66 " pdb=" C APRO A 66 " pdb=" CA APRO A 66 " pdb=" CB APRO A 66 " ideal model delta harmonic sigma weight residual 115.10 134.63 -19.53 0 2.50e+00 1.60e-01 6.10e+01 dihedral pdb=" C VAL A 71 " pdb=" N VAL A 71 " pdb=" CA VAL A 71 " pdb=" CB VAL A 71 " ideal model delta harmonic sigma weight residual -122.00 -104.01 -17.99 0 2.50e+00 1.60e-01 5.18e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.231: 103 0.231 - 0.460: 79 0.460 - 0.690: 47 0.690 - 0.919: 10 0.919 - 1.148: 4 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA VAL A 71 " pdb=" N VAL A 71 " pdb=" C VAL A 71 " pdb=" CB VAL A 71 " both_signs ideal model delta sigma weight residual False 2.44 3.59 -1.15 2.00e-01 2.50e+01 3.29e+01 chirality pdb=" CA APRO A 66 " pdb=" N APRO A 66 " pdb=" C APRO A 66 " pdb=" CB APRO A 66 " both_signs ideal model delta sigma weight residual False 2.72 1.72 1.00 2.00e-01 2.50e+01 2.49e+01 chirality pdb=" CA PHE A 162 " pdb=" N PHE A 162 " pdb=" C PHE A 162 " pdb=" CB PHE A 162 " both_signs ideal model delta sigma weight residual False 2.51 3.46 -0.95 2.00e-01 2.50e+01 2.26e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.074 2.00e-02 2.50e+03 6.86e-02 1.41e+02 pdb=" CG PHE A 164 " 0.102 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " -0.082 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.088 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " -0.110 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.029 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.076 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.012 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.056 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.063 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " 0.061 2.00e-02 2.50e+03 5.39e-02 8.71e+01 pdb=" CG TYR A 139 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " -0.051 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " -0.025 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " 0.064 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " 0.081 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " -0.018 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " -0.070 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " -0.071 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.028 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " -0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 45 " 0.090 2.00e-02 2.50e+03 7.53e-02 8.51e+01 pdb=" CD GLN A 45 " -0.116 2.00e-02 2.50e+03 pdb=" OE1 GLN A 45 " -0.003 2.00e-02 2.50e+03 pdb=" NE2 GLN A 45 " 0.016 2.00e-02 2.50e+03 pdb="HE21 GLN A 45 " -0.072 2.00e-02 2.50e+03 pdb="HE22 GLN A 45 " 0.084 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.31: 1007 2.31 - 2.88: 7997 2.88 - 3.46: 10546 3.46 - 4.03: 15328 4.03 - 4.60: 21693 Nonbonded interactions: 56571 Sorted by model distance: nonbonded pdb=" H GLY A 120 " pdb=" O HIS A 138 " model vdw 1.741 2.450 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.743 2.100 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.788 2.450 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.803 2.450 nonbonded pdb="HH21 ARG A 145 " pdb=" OE2 GLU A 163 " model vdw 1.811 2.450 ... (remaining 56566 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_7848743_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= 0.2791 r_free= 0.1855 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.406996 | | target function (ml) not normalized (work): 71582.834390 | | target function (ml) not normalized (free): 3278.379239 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3194 0.2138 7.5109 5.0328| | 2: 3.63 - 2.88 1.00 2711 122 0.2640 0.1869 4.3318 4.3461| | 3: 2.88 - 2.52 1.00 2682 148 0.2567 0.1626 4.1838 4.178| | 4: 2.52 - 2.29 1.00 2661 139 0.2552 0.1680 3.5032 3.6744| | 5: 2.29 - 2.13 1.00 2678 122 0.2704 0.1517 3.4205 3.4632| | 6: 2.13 - 2.00 1.00 2692 117 0.2712 0.1871 3.3296 3.3877| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 17.67 0.77 0.23 1310.66| | 2: 3.63 - 2.88 2711 122 0.83 23.91 1.32 0.23 1310.66| | 3: 2.88 - 2.52 2682 148 0.73 33.11 1.29 0.23 1310.66| | 4: 2.52 - 2.29 2661 139 0.93 11.87 1.30 0.26 140.68| | 5: 2.29 - 2.13 2678 122 0.92 13.97 1.32 0.26 140.68| | 6: 2.13 - 2.00 2692 117 0.90 16.55 1.33 0.26 140.68| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 140.68 max = 1310.66 mean = 732.19| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 89.96 mean = 19.51| |phase err.(test): min = 0.00 max = 89.33 mean = 19.76| |-----------------------------------------------------------------------------| ----------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 : 0.082 0.259 1557 Z= 5.513 Angle : 5.384 15.993 2118 Z= 3.813 Chirality : 0.384 1.148 243 Planarity : 0.032 0.100 284 Dihedral : 13.568 80.246 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.86 % Allowed : 2.48 % Favored : 95.65 % Cbeta Deviations : 31.35 % 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: -2.80 (0.49), residues: 224 helix: -2.99 (0.35), residues: 108 sheet: -0.53 (0.99), residues: 30 loop : -0.40 (0.61), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.090 0.021 ARG A 27 TYR 0.071 0.033 TYR A 141 PHE 0.121 0.046 PHE A 164 HIS 0.054 0.030 HIS A 138 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= 0.2791 r_free= 0.1855 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.406996 | | target function (ml) not normalized (work): 71582.834390 | | target function (ml) not normalized (free): 3278.379239 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.2805 percent. r_work = 0.2920 r_free = 0.2012 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2867 0.2920 0.2012 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2867 0.2920 0.2012 n_refl.: 17050 remove outliers: r(all,work,free)=0.2156 0.2165 0.2012 n_refl.: 17045 overall B=-0.41 to atoms: r(all,work,free)=0.2129 0.2138 0.1994 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1612 0.1608 0.1685 n_refl.: 17045 remove outliers: r(all,work,free)=0.1611 0.1607 0.1685 n_refl.: 17044 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 100.00 89 5 0.4039 394.814 361.759 0.640 1.017 0.397 11.894-9.307 99.02 97 4 0.1884 633.688 614.285 0.918 1.018 0.380 9.237-7.194 100.00 213 7 0.2148 518.293 510.157 0.953 1.018 0.371 7.162-5.571 100.00 427 22 0.2315 388.980 376.030 0.917 1.016 0.284 5.546-4.326 100.00 867 58 0.1402 534.007 528.803 0.957 1.013 0.220 4.315-3.360 100.00 1859 96 0.1272 507.845 503.686 1.016 1.008 0.191 3.356-2.611 100.00 3867 181 0.1643 333.625 328.940 1.014 0.999 0.081 2.608-2.000 99.99 8818 434 0.1651 217.467 213.704 1.037 0.983 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.4607 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1607 r_free=0.1685 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A A 97 ASN A Total number of N/Q/H flips: 2 r_work=0.1612 r_free=0.1690 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.956743 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.944833 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 0.1628 0.0280 0.009 1.0 1.3 0.5 0.0 0 11.978 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.48 16.28 2.80 3.013 18.450 0.945 0.023 12.75 16.50 3.75 3.644 18.706 0.945 0.020 Individual atomic B min max mean iso aniso Overall: 5.91 113.89 19.96 4.13 1785 0 Protein: 5.91 112.97 17.19 4.14 1519 0 Water: 8.74 113.89 36.09 N/A 258 0 Other: 21.31 37.32 26.44 N/A 8 0 Chain A: 5.91 113.89 19.96 N/A 1785 0 Histogram: Values Number of atoms 5.91 - 16.70 1068 16.70 - 27.50 351 27.50 - 38.30 190 38.30 - 49.10 95 49.10 - 59.90 52 59.90 - 70.70 14 70.70 - 81.49 7 81.49 - 92.29 4 92.29 - 103.09 1 103.09 - 113.89 3 =========================== Idealize ADP of riding H ========================== r_work=0.1275 r_free=0.1650 r_work=0.1278 r_free=0.1659 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1278 r_free = 0.1659 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 = 0.1274 r_free = 0.1652 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17044 (all), 4.73 % free)------------| | | | r_work= 0.1274 r_free= 0.1652 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.020010 | | target function (ls_wunit_k1) not normalized (work): 324.894920 | | target function (ls_wunit_k1) not normalized (free): 26.911364 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1292 0.1274 0.1652 n_refl.: 17044 re-set all scales: r(all,work,free)=0.1910 0.1909 0.1975 n_refl.: 17044 remove outliers: r(all,work,free)=0.1910 0.1909 0.1975 n_refl.: 17044 overall B=-0.39 to atoms: r(all,work,free)=0.1881 0.1880 0.1959 n_refl.: 17044 bulk-solvent and scaling: r(all,work,free)=0.1293 0.1276 0.1646 n_refl.: 17044 remove outliers: r(all,work,free)=0.1292 0.1274 0.1646 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 0.3527 303.592 279.670 0.624 1.009 0.369 11.894-9.307 99.02 97 4 0.1689 488.280 477.799 0.919 1.010 0.369 9.237-7.194 100.00 213 7 0.1836 399.363 395.970 0.959 1.010 0.357 7.162-5.571 100.00 427 22 0.1845 299.723 294.494 0.931 1.009 0.301 5.546-4.326 100.00 867 58 0.1044 411.471 409.294 0.960 1.007 0.221 4.315-3.360 100.00 1859 96 0.0926 391.313 391.069 1.017 1.004 0.181 3.356-2.611 100.00 3867 181 0.1299 257.070 255.775 1.015 1.000 0.091 2.608-2.000 99.99 8818 434 0.1348 167.566 166.095 1.023 0.991 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.3899 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1274 r_free=0.1646 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A ** A 97 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 r_work=0.1276 r_free=0.1645 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1276 r_free=0.1645 | n_water=258 | time (s): 0.730 (total time: 0.730) Filter (dist) r_work=0.1281 r_free=0.1634 | n_water=254 | time (s): 21.030 (total time: 21.760) Filter (q & B) r_work=0.1281 r_free=0.1634 | n_water=252 | time (s): 1.340 (total time: 23.100) Compute maps r_work=0.1281 r_free=0.1634 | n_water=252 | time (s): 0.510 (total time: 23.610) Filter (map) r_work=0.1317 r_free=0.1637 | n_water=212 | time (s): 2.020 (total time: 25.630) Find peaks r_work=0.1317 r_free=0.1637 | n_water=212 | time (s): 0.520 (total time: 26.150) Add new water r_work=0.1535 r_free=0.1872 | n_water=371 | time (s): 1.700 (total time: 27.850) Refine new water occ: r_work=0.1330 r_free=0.1570 adp: r_work=0.1271 r_free=0.1559 occ: r_work=0.1277 r_free=0.1540 adp: r_work=0.1243 r_free=0.1540 occ: r_work=0.1244 r_free=0.1535 adp: r_work=0.1234 r_free=0.1533 ADP+occupancy (water only), MIN, final r_work=0.1234 r_free=0.1533 r_work=0.1234 r_free=0.1533 | n_water=371 | time (s): 9.790 (total time: 37.640) Filter (q & B) r_work=0.1236 r_free=0.1536 | n_water=362 | time (s): 2.260 (total time: 39.900) Filter (dist only) r_work=0.1237 r_free=0.1537 | n_water=361 | time (s): 27.460 (total time: 67.360) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.195298 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.983398 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 0.1210 0.1580 0.0370 0.008 0.9 2.9 0.5 0.0 0 12.598 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.10 15.80 3.70 4.201 21.075 0.983 0.018 11.96 16.06 4.10 4.198 21.325 0.983 0.018 Individual atomic B min max mean iso aniso Overall: 7.04 107.58 21.35 4.21 1888 0 Protein: 7.04 107.58 17.68 4.20 1519 0 Water: 8.71 65.78 36.44 N/A 361 0 Other: 24.61 46.34 35.50 N/A 8 0 Chain A: 7.04 107.58 19.43 N/A 1739 0 Chain S: 18.96 62.61 43.71 N/A 149 0 Histogram: Values Number of atoms 7.04 - 17.09 1047 17.09 - 27.15 361 27.15 - 37.20 221 37.20 - 47.25 153 47.25 - 57.31 71 57.31 - 67.36 25 67.36 - 77.42 3 77.42 - 87.47 3 87.47 - 97.52 2 97.52 - 107.58 2 =========================== Idealize ADP of riding H ========================== r_work=0.1196 r_free=0.1606 r_work=0.1198 r_free=0.1607 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1198 r_free = 0.1607 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1192 r_free = 0.1611 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.24 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= 0.1192 r_free= 0.1611 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.017018 | | target function (ls_wunit_k1) not normalized (work): 276.293752 | | target function (ls_wunit_k1) not normalized (free): 24.516958 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1212 0.1192 0.1611 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1753 0.1743 0.1968 n_refl.: 17042 remove outliers: r(all,work,free)=0.1753 0.1743 0.1968 n_refl.: 17042 overall B=-0.38 to atoms: r(all,work,free)=0.1728 0.1719 0.1949 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1207 0.1187 0.1599 n_refl.: 17042 remove outliers: r(all,work,free)=0.1206 0.1186 0.1599 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 0.3289 300.428 283.599 0.604 1.002 0.348 11.894-9.307 99.02 97 4 0.1554 488.280 486.214 0.919 1.003 0.347 9.237-7.194 100.00 213 7 0.1686 399.363 398.746 0.969 1.003 0.330 7.162-5.571 100.00 427 22 0.1559 299.723 295.948 0.938 1.003 0.271 5.546-4.326 100.00 867 58 0.0881 411.471 409.154 0.963 1.003 0.205 4.315-3.360 100.00 1859 96 0.0807 391.313 390.299 1.016 1.002 0.191 3.356-2.611 100.00 3867 181 0.1190 257.070 256.316 1.011 1.001 0.058 2.608-2.000 99.99 8818 434 0.1332 167.566 166.548 1.014 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.3467 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1186 r_free=0.1599 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 97 ASN A Total number of N/Q/H flips: 2 r_work=0.1187 r_free=0.1601 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1187 r_free=0.1601 | n_water=361 | time (s): 0.650 (total time: 0.650) Filter (dist) r_work=0.1188 r_free=0.1601 | n_water=360 | time (s): 29.100 (total time: 29.750) Filter (q & B) r_work=0.1188 r_free=0.1601 | n_water=360 | time (s): 0.920 (total time: 30.670) Compute maps r_work=0.1188 r_free=0.1601 | n_water=360 | time (s): 0.770 (total time: 31.440) Filter (map) r_work=0.1253 r_free=0.1639 | n_water=264 | time (s): 2.070 (total time: 33.510) Find peaks r_work=0.1253 r_free=0.1639 | n_water=264 | time (s): 0.500 (total time: 34.010) Add new water r_work=0.1444 r_free=0.1807 | n_water=419 | time (s): 1.490 (total time: 35.500) Refine new water occ: r_work=0.1242 r_free=0.1585 adp: r_work=0.1233 r_free=0.1588 occ: r_work=0.1219 r_free=0.1569 adp: r_work=0.1206 r_free=0.1568 occ: r_work=0.1202 r_free=0.1561 adp: r_work=0.1191 r_free=0.1561 ADP+occupancy (water only), MIN, final r_work=0.1191 r_free=0.1561 r_work=0.1191 r_free=0.1561 | n_water=419 | time (s): 42.080 (total time: 77.580) Filter (q & B) r_work=0.1193 r_free=0.1565 | n_water=410 | time (s): 1.680 (total time: 79.260) Filter (dist only) r_work=0.1193 r_free=0.1565 | n_water=410 | time (s): 31.510 (total time: 110.770) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.944689 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.140032 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 0.1175 0.1573 0.0399 0.009 1.0 3.5 0.5 0.0 0 0.972 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.75 15.73 3.99 4.300 21.542 0.140 5.003 11.57 15.87 4.30 4.790 21.450 0.140 4.983 Individual atomic B min max mean iso aniso Overall: 6.45 105.22 20.96 4.53 1937 0 Protein: 6.45 105.22 16.98 4.53 1519 0 Water: 8.98 61.82 35.41 N/A 410 0 Other: 27.17 44.28 35.31 N/A 8 0 Chain A: 6.45 105.22 18.76 N/A 1737 0 Chain S: 15.57 61.82 40.02 N/A 200 0 Histogram: Values Number of atoms 6.45 - 16.33 1070 16.33 - 26.20 344 26.20 - 36.08 226 36.08 - 45.96 182 45.96 - 55.83 75 55.83 - 65.71 27 65.71 - 75.59 4 75.59 - 85.46 4 85.46 - 95.34 3 95.34 - 105.22 2 =========================== Idealize ADP of riding H ========================== r_work=0.1157 r_free=0.1587 r_work=0.1157 r_free=0.1588 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1157 r_free = 0.1588 target_work(ml) = 4.984 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1149 r_free = 0.1595 target_work(ml) = 4.980 | | 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= 0.1149 r_free= 0.1595 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.979645 | | target function (ml) not normalized (work): 80839.557697 | | target function (ml) not normalized (free): 4205.174384 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1171 0.1149 0.1595 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1681 0.1672 0.1907 n_refl.: 17041 remove outliers: r(all,work,free)=0.1681 0.1672 0.1907 n_refl.: 17041 overall B=-0.38 to atoms: r(all,work,free)=0.1655 0.1645 0.1894 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1167 0.1146 0.1593 n_refl.: 17041 remove outliers: r(all,work,free)=0.1166 0.1145 0.1593 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 0.3403 296.861 279.403 0.565 1.005 0.333 11.894-9.307 99.02 97 4 0.1749 488.280 481.058 0.904 1.006 0.328 9.237-7.194 100.00 213 7 0.1817 399.363 399.071 0.983 1.006 0.273 7.162-5.571 100.00 427 22 0.1637 299.723 293.787 0.942 1.006 0.249 5.546-4.326 100.00 867 58 0.0961 411.471 406.651 0.964 1.005 0.216 4.315-3.360 100.00 1859 96 0.0882 391.313 389.038 1.011 1.004 0.211 3.356-2.611 100.00 3867 181 0.1284 257.070 254.870 1.012 1.001 0.142 2.608-2.000 99.99 8818 434 0.1085 167.566 166.146 1.018 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.3538 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1145 r_free=0.1593 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1145 r_free=0.1593 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1145 r_free=0.1593 | n_water=410 | time (s): 0.890 (total time: 0.890) Filter (dist) r_work=0.1145 r_free=0.1593 | n_water=410 | time (s): 32.300 (total time: 33.190) Filter (q & B) r_work=0.1145 r_free=0.1590 | n_water=408 | time (s): 1.770 (total time: 34.960) Compute maps r_work=0.1145 r_free=0.1590 | n_water=408 | time (s): 0.780 (total time: 35.740) Filter (map) r_work=0.1203 r_free=0.1602 | n_water=309 | time (s): 2.240 (total time: 37.980) Find peaks r_work=0.1203 r_free=0.1602 | n_water=309 | time (s): 0.650 (total time: 38.630) Add new water r_work=0.1366 r_free=0.1745 | n_water=461 | time (s): 1.570 (total time: 40.200) Refine new water occ: r_work=0.1181 r_free=0.1570 adp: r_work=0.1171 r_free=0.1569 occ: r_work=0.1152 r_free=0.1540 adp: r_work=0.1141 r_free=0.1540 occ: r_work=0.1132 r_free=0.1529 adp: r_work=0.1124 r_free=0.1526 ADP+occupancy (water only), MIN, final r_work=0.1124 r_free=0.1526 r_work=0.1124 r_free=0.1526 | n_water=461 | time (s): 37.650 (total time: 77.850) Filter (q & B) r_work=0.1126 r_free=0.1531 | n_water=453 | time (s): 1.570 (total time: 79.420) Filter (dist only) r_work=0.1131 r_free=0.1533 | n_water=452 | time (s): 35.860 (total time: 115.280) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.990821 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.161587 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 0.1113 0.1583 0.0470 0.010 1.0 3.8 0.5 0.0 0 0.995 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.13 15.83 4.70 4.407 21.161 0.162 4.959 11.00 15.80 4.80 4.559 21.205 0.162 4.950 Individual atomic B min max mean iso aniso Overall: 6.09 103.12 21.19 4.75 1979 0 Protein: 6.09 103.12 16.60 4.74 1519 0 Water: 8.62 65.84 36.38 N/A 452 0 Other: 24.80 42.07 32.56 N/A 8 0 Chain A: 6.09 103.12 18.33 N/A 1736 0 Chain S: 13.75 65.84 41.59 N/A 243 0 Histogram: Values Number of atoms 6.09 - 15.80 1062 15.80 - 25.50 345 25.50 - 35.20 226 35.20 - 44.90 200 44.90 - 54.61 91 54.61 - 64.31 39 64.31 - 74.01 9 74.01 - 83.71 2 83.71 - 93.42 3 93.42 - 103.12 2 =========================== Idealize ADP of riding H ========================== r_work=0.1100 r_free=0.1580 r_work=0.1100 r_free=0.1580 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1100 r_free = 0.1580 target_work(ml) = 4.950 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1092 r_free = 0.1584 target_work(ml) = 4.949 | | occupancies: max = 1.00 min = 0.13 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= 0.1092 r_free= 0.1584 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.948725 | | target function (ml) not normalized (work): 80332.645470 | | target function (ml) not normalized (free): 4193.109146 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1116 0.1092 0.1584 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1599 0.1587 0.1874 n_refl.: 17040 remove outliers: r(all,work,free)=0.1599 0.1587 0.1874 n_refl.: 17040 overall B=-0.30 to atoms: r(all,work,free)=0.1580 0.1568 0.1864 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1113 0.1090 0.1574 n_refl.: 17040 remove outliers: r(all,work,free)=0.1113 0.1090 0.1574 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 0.3574 296.861 275.330 0.562 1.002 0.340 11.894-9.307 99.02 97 4 0.1684 488.280 478.858 0.917 1.003 0.305 9.237-7.194 100.00 213 7 0.1645 399.363 400.695 0.991 1.003 0.270 7.162-5.571 100.00 427 22 0.1486 299.723 293.958 0.945 1.003 0.210 5.546-4.326 100.00 867 58 0.0892 411.471 407.151 0.965 1.003 0.201 4.315-3.360 100.00 1859 96 0.0837 391.313 389.264 1.007 1.002 0.201 3.356-2.611 100.00 3867 181 0.1227 257.070 254.866 1.004 1.002 0.161 2.608-2.000 99.99 8818 434 0.1042 167.566 166.307 1.001 1.000 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-1.0239 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1090 r_free=0.1574 After: r_work=0.1092 r_free=0.1573 ================================== NQH flips ================================== r_work=0.1092 r_free=0.1573 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1092 r_free=0.1573 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1092 r_free=0.1573 | n_water=452 | time (s): 0.630 (total time: 0.630) Filter (dist) r_work=0.1093 r_free=0.1571 | n_water=451 | time (s): 35.850 (total time: 36.480) Filter (q & B) r_work=0.1094 r_free=0.1569 | n_water=449 | time (s): 1.950 (total time: 38.430) Compute maps r_work=0.1094 r_free=0.1569 | n_water=449 | time (s): 0.580 (total time: 39.010) Filter (map) r_work=0.1170 r_free=0.1595 | n_water=346 | time (s): 1.550 (total time: 40.560) Find peaks r_work=0.1170 r_free=0.1595 | n_water=346 | time (s): 0.450 (total time: 41.010) Add new water r_work=0.1288 r_free=0.1695 | n_water=493 | time (s): 1.560 (total time: 42.570) Refine new water occ: r_work=0.1126 r_free=0.1501 adp: r_work=0.1119 r_free=0.1511 occ: r_work=0.1103 r_free=0.1479 adp: r_work=0.1096 r_free=0.1490 occ: r_work=0.1088 r_free=0.1468 adp: r_work=0.1082 r_free=0.1478 ADP+occupancy (water only), MIN, final r_work=0.1082 r_free=0.1478 r_work=0.1082 r_free=0.1478 | n_water=493 | time (s): 29.240 (total time: 71.810) Filter (q & B) r_work=0.1087 r_free=0.1501 | n_water=477 | time (s): 1.570 (total time: 73.380) Filter (dist only) r_work=0.1087 r_free=0.1503 | n_water=476 | time (s): 41.070 (total time: 114.450) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.864111 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.149892 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 0.1109 0.1532 0.0423 0.011 1.0 6.7 0.5 0.0 0 0.932 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.09 15.32 4.23 4.493 20.970 0.150 4.938 10.99 15.16 4.17 4.558 21.059 0.150 4.928 Individual atomic B min max mean iso aniso Overall: 5.58 102.37 21.21 4.86 2003 0 Protein: 5.58 102.37 16.36 4.85 1519 0 Water: 8.76 67.61 36.49 N/A 476 0 Other: 25.64 42.30 32.90 N/A 8 0 Chain A: 5.58 102.37 18.06 N/A 1736 0 Chain S: 15.29 67.61 41.65 N/A 267 0 Histogram: Values Number of atoms 5.58 - 15.26 1033 15.26 - 24.94 373 24.94 - 34.62 228 34.62 - 44.30 197 44.30 - 53.97 121 53.97 - 63.65 35 63.65 - 73.33 8 73.33 - 83.01 3 83.01 - 92.69 1 92.69 - 102.37 4 =========================== Idealize ADP of riding H ========================== r_work=0.1099 r_free=0.1516 r_work=0.1099 r_free=0.1516 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1099 r_free = 0.1516 target_work(ml) = 4.928 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1090 r_free = 0.1513 target_work(ml) = 4.925 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1090 r_free= 0.1513 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.924554 | | target function (ml) not normalized (work): 79940.280145 | | target function (ml) not normalized (free): 4161.975598 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1098 0.1417 5.4399 5.6489| | 2: 3.63 - 2.88 1.00 2711 122 0.1071 0.1563 5.2159 5.3839| | 3: 2.88 - 2.52 1.00 2681 148 0.1337 0.1607 5.1333 5.1992| | 4: 2.52 - 2.29 1.00 2661 139 0.0921 0.1531 4.6058 4.9511| | 5: 2.29 - 2.13 1.00 2678 122 0.0947 0.1434 4.5635 4.8507| | 6: 2.13 - 2.00 1.00 2692 117 0.1120 0.1680 4.5597 4.7649| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 0.94 9.27 1.00 0.96 6496.49| | 2: 3.63 - 2.88 2711 122 0.92 12.95 1.01 0.96 6496.49| | 3: 2.88 - 2.52 2681 148 0.87 19.10 0.99 0.96 6496.49| | 4: 2.52 - 2.29 2661 139 0.93 11.86 1.01 0.98 2034.10| | 5: 2.29 - 2.13 2678 122 0.92 13.70 1.00 0.98 2034.10| | 6: 2.13 - 2.00 2692 117 0.90 16.50 1.00 0.98 2034.10| |alpha: min = 0.96 max = 0.98 mean = 0.97| |beta: min = 2034.10 max = 6496.49 mean = 4288.80| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.94 mean = 13.86| |phase err.(test): min = 0.00 max = 87.50 mean = 13.47| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1111 0.1090 0.1513 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1582 0.1570 0.1818 n_refl.: 17040 remove outliers: r(all,work,free)=0.1582 0.1570 0.1818 n_refl.: 17040 overall B=-0.26 to atoms: r(all,work,free)=0.1565 0.1554 0.1808 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1111 0.1090 0.1511 n_refl.: 17040 remove outliers: r(all,work,free)=0.1111 0.1090 0.1511 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 0.3475 296.861 279.547 0.543 1.004 0.318 11.894-9.307 99.02 97 4 0.1837 488.280 480.537 0.905 1.005 0.310 9.237-7.194 100.00 213 7 0.1699 399.363 401.423 0.994 1.005 0.250 7.162-5.571 100.00 427 22 0.1512 299.723 294.281 0.940 1.005 0.210 5.546-4.326 100.00 867 58 0.0912 411.471 406.974 0.965 1.004 0.201 4.315-3.360 100.00 1859 96 0.0856 391.313 389.083 1.004 1.003 0.181 3.356-2.611 100.00 3867 181 0.1217 257.070 254.962 1.003 1.001 0.141 2.608-2.000 99.99 8818 434 0.1027 167.566 166.292 0.999 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.9145 ================= 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 : 0.2791 0.1855 0.082 5.384 8.8 119.3 19.9 258 0.000 1_bss: 0.1607 0.1685 0.082 5.384 8.4 118.9 19.5 258 0.000 1_settarget: 0.1607 0.1685 0.082 5.384 8.4 118.9 19.5 258 0.000 1_nqh: 0.1612 0.1690 0.082 5.384 8.4 118.9 19.5 258 0.007 1_weight: 0.1612 0.1690 0.082 5.384 8.4 118.9 19.5 258 0.007 1_xyzrec: 0.1348 0.1628 0.009 0.980 8.4 118.9 19.5 258 0.149 1_adp: 0.1275 0.1650 0.009 0.980 5.9 113.9 20.0 258 0.149 1_regHadp: 0.1278 0.1659 0.009 0.980 5.9 113.9 20.0 258 0.149 1_occ: 0.1274 0.1652 0.009 0.980 5.9 113.9 20.0 258 0.149 2_bss: 0.1274 0.1646 0.009 0.980 5.5 113.5 19.6 258 0.149 2_settarget: 0.1274 0.1646 0.009 0.980 5.5 113.5 19.6 258 0.149 2_updatecdl: 0.1274 0.1646 0.009 0.992 5.5 113.5 19.6 258 0.149 2_nqh: 0.1276 0.1645 0.009 0.992 5.5 113.5 19.6 258 0.146 2_sol: 0.1237 0.1537 0.009 0.992 5.5 112.6 20.9 361 n/a 2_weight: 0.1237 0.1537 0.009 0.992 5.5 112.6 20.9 361 n/a 2_xyzrec: 0.1210 0.1580 0.008 0.931 5.5 112.6 20.9 361 n/a 2_adp: 0.1196 0.1606 0.008 0.931 7.0 107.6 21.3 361 n/a 2_regHadp: 0.1198 0.1607 0.008 0.931 7.0 107.6 21.3 361 n/a 2_occ: 0.1192 0.1611 0.008 0.931 7.0 107.6 21.3 361 n/a 3_bss: 0.1186 0.1599 0.008 0.931 6.7 107.2 21.0 361 n/a 3_settarget: 0.1186 0.1599 0.008 0.931 6.7 107.2 21.0 361 n/a 3_updatecdl: 0.1186 0.1599 0.008 0.937 6.7 107.2 21.0 361 n/a 3_nqh: 0.1187 0.1601 0.008 0.937 6.7 107.2 21.0 361 n/a 3_sol: 0.1193 0.1565 0.008 0.937 6.7 107.2 21.1 410 n/a 3_weight: 0.1193 0.1565 0.008 0.937 6.7 107.2 21.1 410 n/a 3_xyzrec: 0.1175 0.1573 0.009 0.965 6.7 107.2 21.1 410 n/a 3_adp: 0.1157 0.1587 0.009 0.965 6.5 105.2 21.0 410 n/a 3_regHadp: 0.1157 0.1588 0.009 0.965 6.5 105.2 21.0 410 n/a 3_occ: 0.1149 0.1595 0.009 0.965 6.5 105.2 21.0 410 n/a 4_bss: 0.1145 0.1593 0.009 0.965 6.1 104.8 20.6 410 n/a 4_settarget: 0.1145 0.1593 0.009 0.965 6.1 104.8 20.6 410 n/a 4_updatecdl: 0.1145 0.1593 0.009 0.963 6.1 104.8 20.6 410 n/a 4_nqh: 0.1145 0.1593 0.009 0.963 6.1 104.8 20.6 410 n/a 4_sol: 0.1131 0.1533 0.009 0.963 6.1 104.8 21.1 452 n/a 4_weight: 0.1131 0.1533 0.009 0.963 6.1 104.8 21.1 452 n/a 4_xyzrec: 0.1113 0.1583 0.010 0.979 6.1 104.8 21.1 452 n/a 4_adp: 0.1100 0.1580 0.010 0.979 6.1 103.1 21.2 452 n/a 4_regHadp: 0.1100 0.1580 0.010 0.979 6.1 103.1 21.2 452 n/a 4_occ: 0.1092 0.1584 0.010 0.979 6.1 103.1 21.2 452 n/a 5_bss: 0.1090 0.1574 0.010 0.979 5.8 102.8 20.9 452 n/a 5_settarget: 0.1090 0.1574 0.010 0.979 5.8 102.8 20.9 452 n/a 5_updatecdl: 0.1090 0.1574 0.010 0.980 5.8 102.8 20.9 452 n/a 5_setrh: 0.1092 0.1573 0.010 0.980 5.8 102.8 20.9 452 n/a 5_nqh: 0.1092 0.1573 0.010 0.980 5.8 102.8 20.9 452 n/a 5_sol: 0.1087 0.1503 0.010 0.980 5.8 102.8 21.0 476 n/a 5_weight: 0.1087 0.1503 0.010 0.980 5.8 102.8 21.0 476 n/a 5_xyzrec: 0.1109 0.1532 0.011 1.025 5.8 102.8 21.0 476 n/a 5_adp: 0.1099 0.1516 0.011 1.025 5.6 102.4 21.2 476 n/a 5_regHadp: 0.1099 0.1516 0.011 1.025 5.6 102.4 21.2 476 n/a 5_occ: 0.1090 0.1513 0.011 1.025 5.6 102.4 21.2 476 n/a end: 0.1090 0.1511 0.011 1.025 5.3 102.1 20.9 476 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_7848743_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_7848743_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.2300 Refinement macro-cycles (run) : 937.0000 Write final files (write_after_run_outputs) : 19.2500 Total : 959.4800 Total CPU time: 16.38 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:23 PST -0800 (1735494083.28 s) Start R-work = 0.1607, R-free = 0.1685 Final R-work = 0.1090, R-free = 0.1511 =============================================================================== Job complete usr+sys time: 1003.54 seconds wall clock time: 17 minutes 5.72 seconds (1025.72 seconds total)