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_2112196.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_2112196.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2112196.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: 1.11, 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: 0.29 Conformation dependent library (CDL) restraints added in 201.8 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.67 - 0.91: 514 0.91 - 1.16: 1113 1.16 - 1.41: 590 1.41 - 1.66: 883 1.66 - 1.90: 53 Bond restraints: 3153 Sorted by residual: bond pdb=" CA ALA A 183 " pdb=" CB ALA A 183 " ideal model delta sigma weight residual 1.536 1.353 0.183 9.10e-03 1.21e+04 4.04e+02 bond pdb=" C PHE A 162 " pdb=" N GLU A 163 " ideal model delta sigma weight residual 1.334 1.111 0.223 1.27e-02 6.20e+03 3.10e+02 bond pdb=" C AASN A 76 " pdb=" N LEU A 77 " ideal model delta sigma weight residual 1.332 1.599 -0.267 1.53e-02 4.27e+03 3.04e+02 bond pdb=" N ACYS A 53 " pdb=" CA ACYS A 53 " ideal model delta sigma weight residual 1.454 1.661 -0.207 1.21e-02 6.83e+03 2.92e+02 bond pdb=" CA SER A 155 " pdb=" C SER A 155 " ideal model delta sigma weight residual 1.523 1.314 0.209 1.24e-02 6.50e+03 2.84e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.76: 3197 4.76 - 9.53: 1848 9.53 - 14.29: 619 14.29 - 19.05: 100 19.05 - 23.81: 13 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA AASN A 76 " pdb=" C AASN A 76 " pdb=" O AASN A 76 " ideal model delta sigma weight residual 120.90 138.71 -17.81 1.07e+00 8.73e-01 2.77e+02 angle pdb=" NE ARG A 48 " pdb=" CZ ARG A 48 " pdb=" NH2 ARG A 48 " ideal model delta sigma weight residual 119.20 133.32 -14.12 9.00e-01 1.23e+00 2.46e+02 angle pdb=" O GLY A 78 " pdb=" C GLY A 78 " pdb=" N ALA A 79 " ideal model delta sigma weight residual 122.19 107.40 14.79 9.60e-01 1.09e+00 2.37e+02 angle pdb=" N BPRO A 66 " pdb=" CA BPRO A 66 " pdb=" CB BPRO A 66 " ideal model delta sigma weight residual 102.60 117.09 -14.49 1.10e+00 8.26e-01 1.74e+02 angle pdb=" CA PHE A 162 " pdb=" C PHE A 162 " pdb=" O PHE A 162 " ideal model delta sigma weight residual 120.42 106.78 13.64 1.06e+00 8.90e-01 1.66e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 15.36: 1270 15.36 - 30.72: 143 30.72 - 46.08: 42 46.08 - 61.44: 22 61.44 - 76.80: 4 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C THR A 110 " pdb=" N THR A 110 " pdb=" CA THR A 110 " pdb=" CB THR A 110 " ideal model delta harmonic sigma weight residual -122.00 -145.58 23.58 0 2.50e+00 1.60e-01 8.90e+01 dihedral pdb=" C ARG A 48 " pdb=" N ARG A 48 " pdb=" CA ARG A 48 " pdb=" CB ARG A 48 " ideal model delta harmonic sigma weight residual -122.60 -145.80 23.20 0 2.50e+00 1.60e-01 8.61e+01 dihedral pdb=" N ARG A 48 " pdb=" C ARG A 48 " pdb=" CA ARG A 48 " pdb=" CB ARG A 48 " ideal model delta harmonic sigma weight residual 122.80 145.79 -22.99 0 2.50e+00 1.60e-01 8.46e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.004 - 0.277: 121 0.277 - 0.550: 77 0.550 - 0.822: 32 0.822 - 1.095: 11 1.095 - 1.368: 2 Chirality restraints: 243 Sorted by residual: chirality pdb=" CG LEU A 172 " pdb=" CB LEU A 172 " pdb=" CD1 LEU A 172 " pdb=" CD2 LEU A 172 " both_signs ideal model delta sigma weight residual False -2.59 -1.22 -1.37 2.00e-01 2.50e+01 4.68e+01 chirality pdb=" CA ARG A 48 " pdb=" N ARG A 48 " pdb=" C ARG A 48 " pdb=" CB ARG A 48 " both_signs ideal model delta sigma weight residual False 2.51 1.29 1.22 2.00e-01 2.50e+01 3.70e+01 chirality pdb=" CA THR A 110 " pdb=" N THR A 110 " pdb=" C THR A 110 " pdb=" CB THR A 110 " both_signs ideal model delta sigma weight residual False 2.53 1.55 0.98 2.00e-01 2.50e+01 2.40e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " -0.004 2.00e-02 2.50e+03 6.87e-02 1.42e+02 pdb=" CG ATYR A 67 " -0.103 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " -0.012 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " 0.101 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " 0.083 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " -0.073 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " 0.077 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " 0.028 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " 0.011 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " 0.056 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " -0.073 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " -0.090 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.094 2.00e-02 2.50e+03 6.84e-02 1.40e+02 pdb=" CG PHE A 119 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.044 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.022 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.047 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.063 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " -0.011 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.114 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.068 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.068 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " -0.086 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " 0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 98 " 0.081 9.50e-02 1.11e+02 7.45e-02 1.09e+02 pdb=" NE ARG A 98 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG A 98 " -0.071 2.00e-02 2.50e+03 pdb=" NH1 ARG A 98 " -0.068 2.00e-02 2.50e+03 pdb=" NH2 ARG A 98 " -0.120 2.00e-02 2.50e+03 pdb="HH11 ARG A 98 " 0.090 2.00e-02 2.50e+03 pdb="HH12 ARG A 98 " 0.002 2.00e-02 2.50e+03 pdb="HH21 ARG A 98 " 0.072 2.00e-02 2.50e+03 pdb="HH22 ARG A 98 " 0.077 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 383 2.19 - 2.79: 7023 2.79 - 3.40: 10961 3.40 - 4.00: 15534 4.00 - 4.60: 22743 Nonbonded interactions: 56644 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.591 2.100 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.758 2.100 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.790 2.100 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.800 2.450 nonbonded pdb=" H GLY A 120 " pdb=" O HIS A 138 " model vdw 1.834 2.450 ... (remaining 56639 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_2112196_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= 0.2784 r_free= 0.1817 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.407914 | | target function (ml) not normalized (work): 71597.745966 | | target function (ml) not normalized (free): 3266.609230 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3208 0.2178 7.6038 5.0409| | 2: 3.63 - 2.88 1.00 2711 122 0.2609 0.1693 4.3172 4.3169| | 3: 2.88 - 2.52 1.00 2682 148 0.2555 0.1591 4.1784 4.1852| | 4: 2.52 - 2.29 1.00 2661 139 0.2554 0.1665 3.4813 3.6047| | 5: 2.29 - 2.13 1.00 2678 122 0.2661 0.1491 3.3903 3.4485| | 6: 2.13 - 2.00 1.00 2692 117 0.2732 0.1766 3.3095 3.3953| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 17.49 0.77 0.23 1285.82| | 2: 3.63 - 2.88 2711 122 0.83 23.55 1.31 0.23 1285.82| | 3: 2.88 - 2.52 2682 148 0.73 32.66 1.29 0.23 1285.82| | 4: 2.52 - 2.29 2661 139 0.93 11.46 1.30 0.26 136.52| | 5: 2.29 - 2.13 2678 122 0.92 13.68 1.32 0.26 136.52| | 6: 2.13 - 2.00 2692 117 0.90 16.39 1.34 0.26 136.52| |alpha: min = 0.23 max = 0.26 mean = 0.25| |beta: min = 136.52 max = 1285.82 mean = 717.57| |figures of merit: min = 0.00 max = 1.00 mean = 0.87| |phase err.(work): min = 0.00 max = 89.94 mean = 19.21| |phase err.(test): min = 0.00 max = 89.88 mean = 19.21| |-----------------------------------------------------------------------------| ----------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 : 0.080 0.267 1557 Z= 5.280 Angle : 5.370 19.386 2118 Z= 3.767 Chirality : 0.421 1.368 243 Planarity : 0.031 0.086 284 Dihedral : 13.675 76.798 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.16 % Favored : 97.30 % Rotamer: Outliers : 1.86 % Allowed : 4.35 % Favored : 93.79 % Cbeta Deviations : 33.51 % 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: -3.07 (0.47), residues: 224 helix: -3.04 (0.35), residues: 108 sheet: -0.35 (0.92), residues: 28 loop : -0.94 (0.58), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.063 0.017 ARG A 145 TYR 0.088 0.033 TYR A 139 PHE 0.078 0.035 PHE A 162 HIS 0.055 0.021 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= 0.2784 r_free= 0.1817 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.407914 | | target function (ml) not normalized (work): 71597.745966 | | target function (ml) not normalized (free): 3266.609230 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.3384 percent. r_work = 0.2918 r_free = 0.1959 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2864 0.2918 0.1959 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2864 0.2918 0.1959 n_refl.: 17050 remove outliers: r(all,work,free)=0.2150 0.2162 0.1959 n_refl.: 17045 overall B=-0.42 to atoms: r(all,work,free)=0.2123 0.2134 0.1942 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1609 0.1608 0.1637 n_refl.: 17045 remove outliers: r(all,work,free)=0.1608 0.1607 0.1637 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 0.4097 394.580 360.514 0.650 1.012 0.393 11.894-9.307 99.02 97 4 0.1949 633.312 614.961 0.931 1.013 0.380 9.237-7.194 100.00 213 7 0.2172 517.986 509.694 0.962 1.013 0.361 7.162-5.571 100.00 427 22 0.2287 388.749 377.339 0.917 1.011 0.274 5.546-4.326 100.00 867 58 0.1403 533.690 528.030 0.966 1.009 0.210 4.315-3.360 100.00 1859 96 0.1292 507.544 503.307 1.016 1.006 0.191 3.356-2.611 100.00 3867 181 0.1654 333.427 328.923 1.014 1.000 0.091 2.608-2.000 99.99 8818 434 0.1629 217.337 213.512 1.032 0.989 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.4971 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1607 r_free=0.1637 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 80 GLN A Total number of N/Q/H flips: 1 r_work=0.1607 r_free=0.1637 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.779927 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.821013 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 0.1353 0.1647 0.0294 0.009 1.0 1.6 0.5 0.0 0 11.390 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.53 16.47 2.94 3.013 18.440 0.821 0.023 12.81 16.65 3.84 3.616 18.730 0.821 0.021 Individual atomic B min max mean iso aniso Overall: 6.47 113.88 20.02 4.04 1785 0 Protein: 6.47 112.76 17.27 4.04 1519 0 Water: 8.92 113.88 35.98 N/A 258 0 Other: 22.14 36.76 26.77 N/A 8 0 Chain A: 6.47 113.88 20.02 N/A 1785 0 Histogram: Values Number of atoms 6.47 - 17.21 1095 17.21 - 27.95 334 27.95 - 38.70 184 38.70 - 49.44 100 49.44 - 60.18 44 60.18 - 70.92 14 70.92 - 81.66 6 81.66 - 92.40 4 92.40 - 103.14 1 103.14 - 113.88 3 =========================== Idealize ADP of riding H ========================== r_work=0.1281 r_free=0.1665 r_work=0.1284 r_free=0.1672 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1284 r_free = 0.1672 target_work(ls_wunit_k1) = 0.021 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1278 r_free = 0.1666 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.26 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= 0.1278 r_free= 0.1666 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.020108 | | target function (ls_wunit_k1) not normalized (work): 326.495307 | | target function (ls_wunit_k1) not normalized (free): 27.464127 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1296 0.1278 0.1666 n_refl.: 17044 re-set all scales: r(all,work,free)=0.1913 0.1912 0.1989 n_refl.: 17044 remove outliers: r(all,work,free)=0.1913 0.1912 0.1989 n_refl.: 17044 overall B=-0.40 to atoms: r(all,work,free)=0.1884 0.1882 0.1972 n_refl.: 17044 bulk-solvent and scaling: r(all,work,free)=0.1295 0.1277 0.1656 n_refl.: 17044 remove outliers: r(all,work,free)=0.1294 0.1276 0.1656 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 0.3556 303.619 278.602 0.621 1.014 0.368 11.894-9.307 99.02 97 4 0.1694 488.324 478.237 0.914 1.015 0.367 9.237-7.194 100.00 213 7 0.1838 399.400 396.186 0.955 1.014 0.351 7.162-5.571 100.00 427 22 0.1840 299.750 294.331 0.926 1.013 0.300 5.546-4.326 100.00 867 58 0.1045 411.508 409.170 0.957 1.010 0.205 4.315-3.360 100.00 1859 96 0.0929 391.349 390.980 1.015 1.006 0.191 3.356-2.611 100.00 3867 181 0.1301 257.094 255.790 1.016 0.999 0.101 2.608-2.000 99.99 8818 434 0.1349 167.581 166.123 1.029 0.987 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.4146 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1276 r_free=0.1656 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A Total number of N/Q/H flips: 1 r_work=0.1276 r_free=0.1656 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1276 r_free=0.1656 | n_water=258 | time (s): 0.660 (total time: 0.660) Filter (dist) r_work=0.1284 r_free=0.1650 | n_water=252 | time (s): 20.740 (total time: 21.400) Filter (q & B) r_work=0.1284 r_free=0.1651 | n_water=250 | time (s): 1.980 (total time: 23.380) Compute maps r_work=0.1284 r_free=0.1651 | n_water=250 | time (s): 0.670 (total time: 24.050) Filter (map) r_work=0.1315 r_free=0.1640 | n_water=214 | time (s): 2.210 (total time: 26.260) Find peaks r_work=0.1315 r_free=0.1640 | n_water=214 | time (s): 0.550 (total time: 26.810) Add new water r_work=0.1525 r_free=0.1850 | n_water=364 | time (s): 1.770 (total time: 28.580) Refine new water occ: r_work=0.1331 r_free=0.1582 adp: r_work=0.1275 r_free=0.1576 occ: r_work=0.1281 r_free=0.1554 adp: r_work=0.1249 r_free=0.1558 occ: r_work=0.1251 r_free=0.1552 adp: r_work=0.1240 r_free=0.1557 ADP+occupancy (water only), MIN, final r_work=0.1240 r_free=0.1557 r_work=0.1240 r_free=0.1557 | n_water=364 | time (s): 12.460 (total time: 41.040) Filter (q & B) r_work=0.1241 r_free=0.1555 | n_water=359 | time (s): 2.250 (total time: 43.290) Filter (dist only) r_work=0.1241 r_free=0.1558 | n_water=358 | time (s): 27.910 (total time: 71.200) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.492830 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.962905 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 0.1214 0.1575 0.0360 0.008 0.9 2.6 0.5 0.0 0 12.246 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.14 15.75 3.60 4.159 21.065 0.963 0.018 12.01 16.08 4.07 4.232 21.335 0.963 0.018 Individual atomic B min max mean iso aniso Overall: 6.89 107.36 21.29 4.28 1885 0 Protein: 6.89 107.36 17.75 4.27 1519 0 Water: 8.94 65.76 35.98 N/A 358 0 Other: 24.64 46.57 36.20 N/A 8 0 Chain A: 6.89 107.36 19.53 N/A 1741 0 Chain S: 18.86 64.48 42.61 N/A 144 0 Histogram: Values Number of atoms 6.89 - 16.94 1034 16.94 - 26.99 371 26.99 - 37.03 223 37.03 - 47.08 154 47.08 - 57.13 63 57.13 - 67.18 29 67.18 - 77.22 4 77.22 - 87.27 4 87.27 - 97.32 1 97.32 - 107.36 2 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1608 r_work=0.1202 r_free=0.1609 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1202 r_free = 0.1609 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 = 0.1604 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= 0.1199 r_free= 0.1604 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.017240 | | target function (ls_wunit_k1) not normalized (work): 279.896225 | | target function (ls_wunit_k1) not normalized (free): 24.886965 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1218 0.1199 0.1604 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1760 0.1753 0.1930 n_refl.: 17042 remove outliers: r(all,work,free)=0.1760 0.1753 0.1930 n_refl.: 17042 overall B=-0.38 to atoms: r(all,work,free)=0.1736 0.1728 0.1914 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1213 0.1193 0.1601 n_refl.: 17042 remove outliers: r(all,work,free)=0.1212 0.1192 0.1601 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 0.3235 300.455 284.742 0.604 1.005 0.350 11.894-9.307 99.02 97 4 0.1531 488.324 486.083 0.920 1.006 0.350 9.237-7.194 100.00 213 7 0.1715 399.400 399.717 0.972 1.006 0.300 7.162-5.571 100.00 427 22 0.1577 299.750 295.766 0.931 1.005 0.281 5.546-4.326 100.00 867 58 0.0888 411.508 408.468 0.961 1.004 0.216 4.315-3.360 100.00 1859 96 0.0813 391.349 390.493 1.015 1.003 0.211 3.356-2.611 100.00 3867 181 0.1216 257.094 256.197 1.012 1.001 0.111 2.608-2.000 99.99 8818 434 0.1326 167.581 166.537 1.017 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.3549 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1192 r_free=0.1601 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=0.1194 r_free=0.1601 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1194 r_free=0.1601 | n_water=358 | time (s): 0.880 (total time: 0.880) Filter (dist) r_work=0.1195 r_free=0.1604 | n_water=356 | time (s): 30.670 (total time: 31.550) Filter (q & B) r_work=0.1195 r_free=0.1604 | n_water=356 | time (s): 1.140 (total time: 32.690) Compute maps r_work=0.1195 r_free=0.1604 | n_water=356 | time (s): 0.600 (total time: 33.290) Filter (map) r_work=0.1255 r_free=0.1610 | n_water=265 | time (s): 1.510 (total time: 34.800) Find peaks r_work=0.1255 r_free=0.1610 | n_water=265 | time (s): 0.420 (total time: 35.220) Add new water r_work=0.1441 r_free=0.1789 | n_water=414 | time (s): 1.380 (total time: 36.600) Refine new water occ: r_work=0.1248 r_free=0.1571 adp: r_work=0.1238 r_free=0.1570 occ: r_work=0.1224 r_free=0.1552 adp: r_work=0.1212 r_free=0.1547 occ: r_work=0.1206 r_free=0.1542 adp: r_work=0.1194 r_free=0.1538 ADP+occupancy (water only), MIN, final r_work=0.1194 r_free=0.1538 r_work=0.1194 r_free=0.1538 | n_water=414 | time (s): 33.860 (total time: 70.460) Filter (q & B) r_work=0.1198 r_free=0.1537 | n_water=403 | time (s): 2.330 (total time: 72.790) Filter (dist only) r_work=0.1198 r_free=0.1537 | n_water=403 | time (s): 29.690 (total time: 102.480) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.973606 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.119702 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 0.1174 0.1558 0.0384 0.009 1.0 4.8 0.5 0.0 0 0.987 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.74 15.58 3.84 4.343 21.566 0.120 5.000 11.55 15.65 4.10 4.871 21.416 0.120 4.977 Individual atomic B min max mean iso aniso Overall: 6.37 103.70 20.81 4.49 1930 0 Protein: 6.37 103.70 16.94 4.48 1519 0 Water: 7.96 65.11 35.10 N/A 403 0 Other: 26.82 46.66 35.56 N/A 8 0 Chain A: 6.37 103.70 18.71 N/A 1737 0 Chain S: 18.41 65.11 39.70 N/A 193 0 Histogram: Values Number of atoms 6.37 - 16.10 1059 16.10 - 25.83 351 25.83 - 35.57 228 35.57 - 45.30 170 45.30 - 55.03 77 55.03 - 64.76 31 64.76 - 74.50 5 74.50 - 84.23 4 84.23 - 93.96 3 93.96 - 103.70 2 =========================== Idealize ADP of riding H ========================== r_work=0.1155 r_free=0.1565 r_work=0.1155 r_free=0.1566 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1155 r_free = 0.1566 target_work(ml) = 4.978 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1147 r_free = 0.1558 target_work(ml) = 4.973 | | occupancies: max = 1.00 min = 0.23 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= 0.1147 r_free= 0.1558 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.973167 | | target function (ml) not normalized (work): 80734.393130 | | target function (ml) not normalized (free): 4192.169080 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1167 0.1147 0.1558 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1676 0.1671 0.1836 n_refl.: 17041 remove outliers: r(all,work,free)=0.1676 0.1671 0.1836 n_refl.: 17041 overall B=-0.37 to atoms: r(all,work,free)=0.1651 0.1645 0.1825 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1166 0.1146 0.1554 n_refl.: 17041 remove outliers: r(all,work,free)=0.1165 0.1145 0.1554 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 0.3564 296.888 278.176 0.567 1.003 0.340 11.894-9.307 99.02 97 4 0.1744 488.324 481.393 0.915 1.004 0.330 9.237-7.194 100.00 213 7 0.1754 399.400 399.439 0.982 1.004 0.269 7.162-5.571 100.00 427 22 0.1599 299.750 294.277 0.938 1.004 0.241 5.546-4.326 100.00 867 58 0.0957 411.508 407.741 0.966 1.004 0.211 4.315-3.360 100.00 1859 96 0.0884 391.349 389.180 1.013 1.003 0.211 3.356-2.611 100.00 3867 181 0.1275 257.094 254.696 1.011 1.002 0.121 2.608-2.000 99.99 8818 434 0.1096 167.581 166.117 1.013 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.3247 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1145 r_free=0.1554 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1145 r_free=0.1554 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1145 r_free=0.1554 | n_water=403 | time (s): 0.720 (total time: 0.720) Filter (dist) r_work=0.1146 r_free=0.1555 | n_water=402 | time (s): 33.250 (total time: 33.970) Filter (q & B) r_work=0.1146 r_free=0.1555 | n_water=402 | time (s): 1.030 (total time: 35.000) Compute maps r_work=0.1146 r_free=0.1555 | n_water=402 | time (s): 0.550 (total time: 35.550) Filter (map) r_work=0.1199 r_free=0.1572 | n_water=317 | time (s): 1.790 (total time: 37.340) Find peaks r_work=0.1199 r_free=0.1572 | n_water=317 | time (s): 0.420 (total time: 37.760) Add new water r_work=0.1343 r_free=0.1699 | n_water=467 | time (s): 1.550 (total time: 39.310) Refine new water occ: r_work=0.1175 r_free=0.1538 adp: r_work=0.1166 r_free=0.1539 occ: r_work=0.1152 r_free=0.1523 adp: r_work=0.1142 r_free=0.1520 occ: r_work=0.1137 r_free=0.1515 adp: r_work=0.1130 r_free=0.1512 ADP+occupancy (water only), MIN, final r_work=0.1130 r_free=0.1512 r_work=0.1130 r_free=0.1512 | n_water=467 | time (s): 35.020 (total time: 74.330) Filter (q & B) r_work=0.1133 r_free=0.1514 | n_water=455 | time (s): 2.100 (total time: 76.430) Filter (dist only) r_work=0.1133 r_free=0.1514 | n_water=455 | time (s): 34.550 (total time: 110.980) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.932519 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.126556 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 0.1120 0.1524 0.0404 0.009 1.0 4.5 0.5 0.0 0 0.966 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.20 15.24 4.04 4.370 21.079 0.127 4.956 11.05 15.24 4.19 4.537 21.088 0.127 4.947 Individual atomic B min max mean iso aniso Overall: 5.63 100.89 21.04 4.60 1982 0 Protein: 5.63 100.89 16.50 4.58 1519 0 Water: 8.11 67.15 36.02 N/A 455 0 Other: 22.35 42.60 30.63 N/A 8 0 Chain A: 5.63 100.89 18.17 N/A 1735 0 Chain S: 17.88 67.15 41.21 N/A 247 0 Histogram: Values Number of atoms 5.63 - 15.15 993 15.15 - 24.68 399 24.68 - 34.20 224 34.20 - 43.73 208 43.73 - 53.26 102 53.26 - 62.78 39 62.78 - 72.31 8 72.31 - 81.84 4 81.84 - 91.36 3 91.36 - 100.89 2 =========================== Idealize ADP of riding H ========================== r_work=0.1105 r_free=0.1524 r_work=0.1105 r_free=0.1525 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1105 r_free = 0.1525 target_work(ml) = 4.947 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1096 r_free = 0.1528 target_work(ml) = 4.944 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1096 r_free= 0.1528 coordinate error (max.-lik. estimate): 0.12 A | | | | normalized target function (ml) (work): 4.944317 | | target function (ml) not normalized (work): 80261.101815 | | target function (ml) not normalized (free): 4181.637490 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1117 0.1096 0.1528 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1569 0.1557 0.1843 n_refl.: 17040 remove outliers: r(all,work,free)=0.1569 0.1557 0.1843 n_refl.: 17040 overall B=-0.28 to atoms: r(all,work,free)=0.1552 0.1540 0.1835 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1115 0.1094 0.1525 n_refl.: 17040 remove outliers: r(all,work,free)=0.1114 0.1093 0.1525 n_refl.: 17039 ======================== 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 92.71 84 5 0.3530 299.056 271.744 0.541 1.003 0.330 11.894-9.307 99.02 97 4 0.1791 488.324 482.837 0.917 1.004 0.299 9.237-7.194 100.00 213 7 0.1706 399.400 400.003 0.985 1.004 0.230 7.162-5.571 100.00 427 22 0.1496 299.750 294.085 0.940 1.004 0.220 5.546-4.326 100.00 867 58 0.0902 411.508 408.314 0.966 1.003 0.191 4.315-3.360 100.00 1859 96 0.0841 391.349 388.737 1.007 1.003 0.191 3.356-2.611 100.00 3867 181 0.1211 257.094 254.769 1.004 1.001 0.058 2.608-2.000 99.99 8818 434 0.1049 167.581 166.453 1.000 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-0.9670 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1093 r_free=0.1525 After: r_work=0.1095 r_free=0.1523 ================================== NQH flips ================================== r_work=0.1095 r_free=0.1523 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1095 r_free=0.1523 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1095 r_free=0.1523 | n_water=455 | time (s): 0.640 (total time: 0.640) Filter (dist) r_work=0.1101 r_free=0.1522 | n_water=452 | time (s): 37.240 (total time: 37.880) Filter (q & B) r_work=0.1102 r_free=0.1522 | n_water=451 | time (s): 2.000 (total time: 39.880) Compute maps r_work=0.1102 r_free=0.1522 | n_water=451 | time (s): 0.790 (total time: 40.670) Filter (map) r_work=0.1175 r_free=0.1552 | n_water=345 | time (s): 1.910 (total time: 42.580) Find peaks r_work=0.1175 r_free=0.1552 | n_water=345 | time (s): 0.520 (total time: 43.100) Add new water r_work=0.1279 r_free=0.1648 | n_water=475 | time (s): 2.110 (total time: 45.210) Refine new water occ: r_work=0.1134 r_free=0.1499 adp: r_work=0.1128 r_free=0.1491 occ: r_work=0.1116 r_free=0.1488 adp: r_work=0.1109 r_free=0.1478 occ: r_work=0.1103 r_free=0.1477 adp: r_work=0.1098 r_free=0.1472 ADP+occupancy (water only), MIN, final r_work=0.1098 r_free=0.1472 r_work=0.1098 r_free=0.1472 | n_water=475 | time (s): 32.560 (total time: 77.770) Filter (q & B) r_work=0.1103 r_free=0.1481 | n_water=464 | time (s): 2.240 (total time: 80.010) Filter (dist only) r_work=0.1103 r_free=0.1481 | n_water=464 | time (s): 37.470 (total time: 117.480) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.984493 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.173059 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 0.1119 0.1503 0.0385 0.011 1.1 6.1 0.5 0.0 0 0.992 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.19 15.03 3.85 4.390 20.757 0.173 4.952 11.06 14.92 3.86 4.569 20.856 0.173 4.943 Individual atomic B min max mean iso aniso Overall: 5.23 101.20 20.98 5.00 1991 0 Protein: 5.23 101.20 16.23 4.99 1519 0 Water: 8.17 69.22 36.40 N/A 464 0 Other: 22.01 40.07 29.63 N/A 8 0 Chain A: 5.23 101.20 17.88 N/A 1734 0 Chain S: 19.50 69.22 41.90 N/A 257 0 Histogram: Values Number of atoms 5.23 - 14.83 998 14.83 - 24.42 405 24.42 - 34.02 207 34.02 - 43.62 201 43.62 - 53.22 125 53.22 - 62.81 34 62.81 - 72.41 12 72.41 - 82.01 2 82.01 - 91.60 3 91.60 - 101.20 4 =========================== Idealize ADP of riding H ========================== r_work=0.1106 r_free=0.1492 r_work=0.1106 r_free=0.1492 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1106 r_free = 0.1492 target_work(ml) = 4.942 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1100 r_free = 0.1497 target_work(ml) = 4.938 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17039 (all), 4.74 % free)------------| | | | r_work= 0.1100 r_free= 0.1497 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ml) (work): 4.938145 | | target function (ml) not normalized (work): 80155.975365 | | target function (ml) not normalized (free): 4170.655297 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.64 1.00 2809 159 0.1100 0.1342 5.4354 5.6241| | 2: 3.63 - 2.88 1.00 2711 122 0.1077 0.1448 5.2029 5.3456| | 3: 2.88 - 2.52 1.00 2681 148 0.1342 0.1721 5.1178 5.2206| | 4: 2.52 - 2.29 1.00 2661 139 0.0934 0.1534 4.6466 4.9745| | 5: 2.29 - 2.13 1.00 2678 122 0.0972 0.1441 4.6026 4.8877| | 6: 2.13 - 2.00 1.00 2692 117 0.1144 0.1813 4.5957 4.8193| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2809 159 0.95 8.75 1.00 0.96 6199.31| | 2: 3.63 - 2.88 2711 122 0.93 12.61 1.01 0.96 6199.31| | 3: 2.88 - 2.52 2681 148 0.88 18.65 0.99 0.96 6199.31| | 4: 2.52 - 2.29 2661 139 0.92 12.59 1.00 0.97 2254.21| | 5: 2.29 - 2.13 2678 122 0.91 14.70 1.00 0.97 2254.21| | 6: 2.13 - 2.00 2692 117 0.89 17.47 0.99 0.97 2254.21| |alpha: min = 0.96 max = 0.97 mean = 0.96| |beta: min = 2254.21 max = 6199.31 mean = 4247.42| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.93 mean = 14.09| |phase err.(test): min = 0.00 max = 87.11 mean = 13.82| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1119 0.1100 0.1497 n_refl.: 17039 re-set all scales: r(all,work,free)=0.1532 0.1519 0.1799 n_refl.: 17039 remove outliers: r(all,work,free)=0.1532 0.1519 0.1799 n_refl.: 17039 overall B=-0.20 to atoms: r(all,work,free)=0.1521 0.1508 0.1794 n_refl.: 17039 bulk-solvent and scaling: r(all,work,free)=0.1120 0.1101 0.1501 n_refl.: 17039 remove outliers: r(all,work,free)=0.1120 0.1101 0.1501 n_refl.: 17039 ======================== 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 92.71 84 5 0.3447 299.056 281.528 0.556 1.005 0.330 11.894-9.307 99.02 97 4 0.1831 488.324 480.530 0.913 1.006 0.287 9.237-7.194 100.00 213 7 0.1698 399.400 400.579 0.980 1.006 0.221 7.162-5.571 100.00 427 22 0.1556 299.750 293.838 0.930 1.006 0.197 5.546-4.326 100.00 867 58 0.0916 411.508 408.196 0.960 1.005 0.190 4.315-3.360 100.00 1859 96 0.0859 391.349 389.119 1.001 1.003 0.191 3.356-2.611 100.00 3867 181 0.1225 257.094 254.823 0.999 1.000 0.058 2.608-2.000 99.99 8818 434 0.1044 167.581 166.306 0.989 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.7052 ================= 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 : 0.2784 0.1817 0.080 5.370 8.8 119.3 19.9 258 0.000 1_bss: 0.1607 0.1637 0.080 5.370 8.4 118.9 19.5 258 0.000 1_settarget: 0.1607 0.1637 0.080 5.370 8.4 118.9 19.5 258 0.000 1_nqh: 0.1607 0.1637 0.080 5.370 8.4 118.9 19.5 258 0.003 1_weight: 0.1607 0.1637 0.080 5.370 8.4 118.9 19.5 258 0.003 1_xyzrec: 0.1353 0.1647 0.009 0.979 8.4 118.9 19.5 258 0.145 1_adp: 0.1281 0.1665 0.009 0.979 6.5 113.9 20.0 258 0.145 1_regHadp: 0.1284 0.1672 0.009 0.979 6.5 113.9 20.0 258 0.145 1_occ: 0.1278 0.1666 0.009 0.979 6.5 113.9 20.0 258 0.145 2_bss: 0.1276 0.1656 0.009 0.979 6.1 113.5 19.6 258 0.145 2_settarget: 0.1276 0.1656 0.009 0.979 6.1 113.5 19.6 258 0.145 2_updatecdl: 0.1276 0.1656 0.009 0.998 6.1 113.5 19.6 258 0.145 2_nqh: 0.1276 0.1656 0.009 0.998 6.1 113.5 19.6 258 0.143 2_sol: 0.1241 0.1558 0.009 0.998 6.1 112.4 20.8 358 n/a 2_weight: 0.1241 0.1558 0.009 0.998 6.1 112.4 20.8 358 n/a 2_xyzrec: 0.1214 0.1575 0.008 0.931 6.1 112.4 20.8 358 n/a 2_adp: 0.1201 0.1608 0.008 0.931 6.9 107.4 21.3 358 n/a 2_regHadp: 0.1202 0.1609 0.008 0.931 6.9 107.4 21.3 358 n/a 2_occ: 0.1199 0.1604 0.008 0.931 6.9 107.4 21.3 358 n/a 3_bss: 0.1192 0.1601 0.008 0.931 6.5 107.0 20.9 358 n/a 3_settarget: 0.1192 0.1601 0.008 0.931 6.5 107.0 20.9 358 n/a 3_updatecdl: 0.1192 0.1601 0.008 0.930 6.5 107.0 20.9 358 n/a 3_nqh: 0.1194 0.1601 0.008 0.930 6.5 107.0 20.9 358 n/a 3_sol: 0.1198 0.1537 0.008 0.930 6.5 107.0 21.1 403 n/a 3_weight: 0.1198 0.1537 0.008 0.930 6.5 107.0 21.1 403 n/a 3_xyzrec: 0.1174 0.1558 0.009 0.972 6.5 107.0 21.1 403 n/a 3_adp: 0.1155 0.1565 0.009 0.972 6.4 103.7 20.8 403 n/a 3_regHadp: 0.1155 0.1566 0.009 0.972 6.4 103.7 20.8 403 n/a 3_occ: 0.1147 0.1558 0.009 0.972 6.4 103.7 20.8 403 n/a 4_bss: 0.1145 0.1554 0.009 0.972 6.0 103.3 20.4 403 n/a 4_settarget: 0.1145 0.1554 0.009 0.972 6.0 103.3 20.4 403 n/a 4_updatecdl: 0.1145 0.1554 0.009 0.974 6.0 103.3 20.4 403 n/a 4_nqh: 0.1145 0.1554 0.009 0.974 6.0 103.3 20.4 403 n/a 4_sol: 0.1133 0.1514 0.009 0.974 6.0 103.3 21.0 455 n/a 4_weight: 0.1133 0.1514 0.009 0.974 6.0 103.3 21.0 455 n/a 4_xyzrec: 0.1120 0.1524 0.009 0.959 6.0 103.3 21.0 455 n/a 4_adp: 0.1105 0.1524 0.009 0.959 5.6 100.9 21.0 455 n/a 4_regHadp: 0.1105 0.1525 0.009 0.959 5.6 100.9 21.0 455 n/a 4_occ: 0.1096 0.1528 0.009 0.959 5.6 100.9 21.0 455 n/a 5_bss: 0.1093 0.1525 0.009 0.959 5.3 100.6 20.8 455 n/a 5_settarget: 0.1093 0.1525 0.009 0.959 5.3 100.6 20.8 455 n/a 5_updatecdl: 0.1093 0.1525 0.009 0.958 5.3 100.6 20.8 455 n/a 5_setrh: 0.1095 0.1523 0.009 0.958 5.3 100.6 20.8 455 n/a 5_nqh: 0.1095 0.1523 0.009 0.958 5.3 100.6 20.8 455 n/a 5_sol: 0.1103 0.1481 0.009 0.958 5.3 100.6 20.8 464 n/a 5_weight: 0.1103 0.1481 0.009 0.958 5.3 100.6 20.8 464 n/a 5_xyzrec: 0.1119 0.1503 0.011 1.081 5.3 100.6 20.8 464 n/a 5_adp: 0.1106 0.1492 0.011 1.081 5.2 101.2 21.0 464 n/a 5_regHadp: 0.1106 0.1492 0.011 1.081 5.2 101.2 21.0 464 n/a 5_occ: 0.1100 0.1497 0.011 1.081 5.2 101.2 21.0 464 n/a end: 0.1101 0.1501 0.011 1.081 5.0 101.0 20.8 464 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_2112196_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_2112196_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.9200 Refinement macro-cycles (run) : 928.8800 Write final files (write_after_run_outputs) : 20.1100 Total : 952.9100 Total CPU time: 16.21 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:13 PST -0800 (1735494073.66 s) Start R-work = 0.1607, R-free = 0.1637 Final R-work = 0.1101, R-free = 0.1501 =============================================================================== Job complete usr+sys time: 995.23 seconds wall clock time: 16 minutes 57.92 seconds (1017.92 seconds total)