Starting phenix.refine on Sun Dec 29 09:10:02 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_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=3 ordered_solvent.low_resolution=4 No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 3 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" 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" } 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: 1.25, per 1000 atoms: 0.37 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.33 Conformation dependent library (CDL) restraints added in 115.7 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.44 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 1 N 265 6.97 1 C 957 5.97 2 H 1596 1.00 1 sf(0) = scattering factor at diffraction angle 0. =========================== Regularize ADP if needed ========================== ========================== Anomalous scatterer groups ========================= All atoms refined with f_prime=0 and f_double_prime=0. ====================== Modifying start model if requested ===================== ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 3381 n_use_u_iso = 1596 n_use_u_aniso = 1785 n_grad_site = 0 n_grad_u_iso = 0 n_grad_u_aniso = 0 n_grad_occupancy = 0 n_grad_fp = 0 n_grad_fdp = 0 total number of scatterers = 3381 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (3381 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 1596 aniso = 1785) group_adp = False (0 atoms in 0 groups) tls = False (0 atoms in 0 groups) occupancies = True (876 atoms) group_anomalous = False ============================ Non-default parameters =========================== A complete record of all parameters was written to the .eff file above. Below are only the non-defaults. #phil __ON__ refinement { electron_density_maps { map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT" mtz_label_phases = "PH2FOFCWT" fill_missing_f_obs = True } map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT_no_fill" mtz_label_phases = "PH2FOFCWT_no_fill" } map_coefficients { map_type = "mFo-DFc" mtz_label_amplitudes = "FOFCWT" mtz_label_phases = "PHFOFCWT" } map_coefficients { map_type = "anomalous" mtz_label_amplitudes = "ANOM" mtz_label_phases = "PANOM" } map { map_type = "2mFo-DFc" fill_missing_f_obs = True } map { map_type = "2mFo-DFc" } map { map_type = "mFo-DFc" } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } hydrogens { refine = individual *riding Auto } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } output { prefix = "shake_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: 3.00 - 49.25 A, n_refl.=5182 (all), 4.86 % free)-------------| | | | r_work= 0.3613 r_free= 0.2039 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.464696 | | target function (ml) not normalized (work): 22010.952742 | | target function (ml) not normalized (free): 1144.920401 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 49.25 - 3.79 1.00 2500 142 0.3820 0.2249 4.8478 4.9102| | 2: 3.78 - 3.00 1.00 2430 110 0.3359 0.1682 4.0706 4.0697| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 49.25 - 3.79 2500 142 0.50 48.83 0.83 0.13 6606.63| | 2: 3.78 - 3.00 2430 110 0.94 11.31 1.48 0.26 449.31| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 383.40 max = 12076.07 mean = 3571.68| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 89.99 mean = 30.34| |phase err.(test): min = 0.00 max = 89.98 mean = 33.61| |-----------------------------------------------------------------------------| ----------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: 3.00 - 49.25 A, n_refl.=5182 (all), 4.86 % free)-------------| | | | r_work= 0.3613 r_free= 0.2039 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.464696 | | target function (ml) not normalized (work): 22010.952742 | | target function (ml) not normalized (free): 1144.920401 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3573 0.3649 0.2144 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3573 0.3649 0.2144 n_refl.: 5182 remove outliers: r(all,work,free)=0.2525 0.2548 0.2144 n_refl.: 5178 overall B=-2.53 to atoms: r(all,work,free)=0.2427 0.2447 0.2102 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1565 0.1564 0.1600 n_refl.: 5178 remove outliers: r(all,work,free)=0.1563 0.1562 0.1600 n_refl.: 5177 ======================== 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 0.4083 445.008 405.079 0.642 1.065 0.405 11.894-9.307 99.02 97 4 0.1943 714.406 687.890 0.906 1.062 0.402 9.237-7.194 100.00 213 7 0.2182 584.243 571.310 0.937 1.055 0.364 7.162-5.571 100.00 427 22 0.2295 438.403 422.845 0.896 1.043 0.277 5.546-4.326 100.00 867 58 0.1395 601.865 592.797 0.955 1.023 0.236 4.315-3.360 100.00 1859 96 0.1306 572.380 566.860 1.024 0.990 0.188 3.356-3.002 100.00 1373 60 0.1593 440.871 436.472 1.041 0.958 0.085 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9170 b_overall=-4.4169 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1562 r_free=0.1600 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=0.1562 r_free=0.1600 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 18.792637 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.661057 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1164 0.1813 0.0649 0.010 1.0 2.6 0.5 0.0 0 9.396 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.64 18.13 6.49 3.013 16.324 1.661 0.018 10.22 17.80 7.58 4.828 16.560 1.661 0.015 Individual atomic B min max mean iso aniso Overall: 2.55 111.76 17.80 5.17 1785 0 Protein: 2.55 111.46 15.11 5.17 1519 0 Water: 4.33 111.76 33.40 N/A 258 0 Other: 17.07 37.07 24.68 N/A 8 0 Chain A: 2.55 111.76 17.80 N/A 1785 0 Histogram: Values Number of atoms 2.55 - 13.47 924 13.47 - 24.39 482 24.39 - 35.31 184 35.31 - 46.23 107 46.23 - 57.16 54 57.16 - 68.08 17 68.08 - 79.00 8 79.00 - 89.92 5 89.92 - 100.84 1 100.84 - 111.76 3 =========================== Idealize ADP of riding H ========================== r_work=0.1022 r_free=0.1780 r_work=0.1015 r_free=0.1785 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1015 r_free = 0.1785 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1014 r_free = 0.1791 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5177 (all), 4.87 % free)-------------| | | | r_work= 0.1014 r_free= 0.1791 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ls_wunit_k1) (work): 0.014072 | | target function (ls_wunit_k1) not normalized (work): 69.305601 | | target function (ls_wunit_k1) not normalized (free): 10.561819 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1054 0.1014 0.1791 n_refl.: 5177 re-set all scales: r(all,work,free)=0.2126 0.2127 0.2234 n_refl.: 5177 remove outliers: r(all,work,free)=0.2126 0.2127 0.2234 n_refl.: 5177 overall B=-0.95 to atoms: r(all,work,free)=0.2085 0.2084 0.2222 n_refl.: 5177 bulk-solvent and scaling: r(all,work,free)=0.1056 0.1017 0.1793 n_refl.: 5177 remove outliers: r(all,work,free)=0.1054 0.1015 0.1793 n_refl.: 5176 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 96.88 88 5 0.3439 312.729 296.233 0.638 1.011 0.370 11.894-9.307 99.02 97 4 0.1521 506.369 499.273 0.949 1.012 0.371 9.237-7.194 100.00 213 7 0.1677 414.109 414.008 0.983 1.011 0.315 7.162-5.571 100.00 427 22 0.1645 310.739 307.265 0.945 1.009 0.292 5.546-4.326 100.00 867 58 0.0910 426.600 423.753 0.969 1.005 0.212 4.315-3.360 100.00 1859 96 0.0768 405.701 405.501 1.015 0.998 0.193 3.356-3.002 100.00 1373 60 0.0995 312.488 310.782 0.997 0.991 0.064 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9170 b_overall=-4.2389 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1015 r_free=0.1793 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1015 r_free=0.1793 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1015 r_free=0.1793 | n_water=258 | time (s): 0.500 (total time: 0.500) Filter (dist) r_work=0.1034 r_free=0.1800 | n_water=250 | time (s): 21.570 (total time: 22.070) Filter (q & B) r_work=0.1033 r_free=0.1802 | n_water=247 | time (s): 1.780 (total time: 23.850) Compute maps r_work=0.1033 r_free=0.1802 | n_water=247 | time (s): 0.420 (total time: 24.270) Filter (map) r_work=0.1308 r_free=0.1874 | n_water=152 | time (s): 1.600 (total time: 25.870) Find peaks r_work=0.1308 r_free=0.1874 | n_water=152 | time (s): 0.410 (total time: 26.280) Add new water r_work=0.1640 r_free=0.2161 | n_water=236 | time (s): 1.380 (total time: 27.660) Refine new water occ: r_work=0.1152 r_free=0.1712 adp: r_work=0.1129 r_free=0.1719 occ: r_work=0.1125 r_free=0.1694 adp: r_work=0.1114 r_free=0.1702 occ: r_work=0.1112 r_free=0.1686 adp: r_work=0.1109 r_free=0.1691 ADP+occupancy (water only), MIN, final r_work=0.1109 r_free=0.1691 r_work=0.1109 r_free=0.1691 | n_water=236 | time (s): 4.510 (total time: 32.170) Filter (q & B) r_work=0.1109 r_free=0.1691 | n_water=236 | time (s): 0.780 (total time: 32.950) Filter (dist only) r_work=0.1109 r_free=0.1688 | n_water=235 | time (s): 19.210 (total time: 52.160) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.676613 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.626171 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1011 0.1820 0.0810 0.009 1.0 3.8 0.5 0.0 0 11.338 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.11 18.20 8.10 4.626 17.278 2.626 0.014 9.43 18.65 9.22 5.593 17.759 2.626 0.012 Individual atomic B min max mean iso aniso Overall: 0.00 106.31 17.24 6.67 1762 0 Protein: 0.00 106.31 15.63 6.65 1519 0 Water: 0.00 63.10 27.34 N/A 235 0 Other: 11.62 40.13 26.47 N/A 8 0 Chain A: 0.00 106.31 16.41 N/A 1678 0 Chain S: 1.90 59.85 33.86 N/A 84 0 Histogram: Values Number of atoms 0.00 - 10.63 612 10.63 - 21.26 711 21.26 - 31.89 226 31.89 - 42.52 123 42.52 - 53.16 49 53.16 - 63.79 24 63.79 - 74.42 10 74.42 - 85.05 2 85.05 - 95.68 3 95.68 - 106.31 2 =========================== Idealize ADP of riding H ========================== r_work=0.0943 r_free=0.1865 r_work=0.0941 r_free=0.1865 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0941 r_free = 0.1865 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0935 r_free = 0.1848 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.0935 r_free= 0.1848 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ls_wunit_k1) (work): 0.012008 | | target function (ls_wunit_k1) not normalized (work): 59.127392 | | target function (ls_wunit_k1) not normalized (free): 10.674187 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0982 0.0935 0.1848 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2162 0.2162 0.2296 n_refl.: 5176 remove outliers: r(all,work,free)=0.2162 0.2162 0.2296 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2162 0.2162 0.2296 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0981 0.0934 0.1849 n_refl.: 5176 remove outliers: r(all,work,free)=0.0981 0.0934 0.1849 n_refl.: 5176 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 96.88 88 5 0.3368 312.729 296.842 0.646 1.014 0.354 11.894-9.307 99.02 97 4 0.1440 506.369 501.701 0.982 1.015 0.350 9.237-7.194 100.00 213 7 0.1424 414.109 414.952 1.022 1.014 0.310 7.162-5.571 100.00 427 22 0.1414 310.739 308.495 0.998 1.011 0.290 5.546-4.326 100.00 867 58 0.0805 426.600 424.100 1.015 1.006 0.220 4.315-3.360 100.00 1859 96 0.0728 405.701 405.436 1.071 0.998 0.203 3.356-3.002 100.00 1373 60 0.0941 312.488 311.244 1.056 0.990 0.080 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-4.9222 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0934 r_free=0.1849 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=0.0935 r_free=0.1852 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0935 r_free=0.1852 | n_water=235 | time (s): 0.710 (total time: 0.710) Filter (dist) r_work=0.0976 r_free=0.1870 | n_water=225 | time (s): 18.280 (total time: 18.990) Filter (q & B) r_work=0.1037 r_free=0.1874 | n_water=223 | time (s): 1.870 (total time: 20.860) Compute maps r_work=0.1037 r_free=0.1874 | n_water=223 | time (s): 0.680 (total time: 21.540) Filter (map) r_work=0.1303 r_free=0.1924 | n_water=146 | time (s): 1.720 (total time: 23.260) Find peaks r_work=0.1303 r_free=0.1924 | n_water=146 | time (s): 0.410 (total time: 23.670) Add new water r_work=0.1686 r_free=0.2285 | n_water=232 | time (s): 1.470 (total time: 25.140) Refine new water occ: r_work=0.1063 r_free=0.1794 adp: r_work=0.1058 r_free=0.1802 occ: r_work=0.1047 r_free=0.1790 adp: r_work=0.1047 r_free=0.1796 occ: r_work=0.1038 r_free=0.1783 adp: r_work=0.1038 r_free=0.1788 ADP+occupancy (water only), MIN, final r_work=0.1038 r_free=0.1788 r_work=0.1038 r_free=0.1788 | n_water=232 | time (s): 12.390 (total time: 37.530) Filter (q & B) r_work=0.1039 r_free=0.1791 | n_water=229 | time (s): 1.530 (total time: 39.060) Filter (dist only) r_work=0.1039 r_free=0.1797 | n_water=228 | time (s): 17.310 (total time: 56.370) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.104471 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.193382 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.0941 0.1827 0.0887 0.011 1.1 4.5 0.5 0.6 0 0.552 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.41 18.27 8.87 5.575 18.412 0.193 5.123 9.01 18.26 9.25 7.248 18.394 0.193 5.031 Individual atomic B min max mean iso aniso Overall: 0.00 105.84 16.80 8.87 1755 0 Protein: 0.00 105.84 15.68 8.86 1519 0 Water: 0.00 58.10 23.90 N/A 228 0 Other: 9.07 39.76 26.78 N/A 8 0 Chain A: 0.00 105.84 16.37 N/A 1660 0 Chain S: 0.00 52.73 24.33 N/A 95 0 Histogram: Values Number of atoms 0.00 - 10.58 626 10.58 - 21.17 684 21.17 - 31.75 246 31.75 - 42.34 123 42.34 - 52.92 41 52.92 - 63.50 15 63.50 - 74.09 8 74.09 - 84.67 7 84.67 - 95.25 3 95.25 - 105.84 2 =========================== Idealize ADP of riding H ========================== r_work=0.0901 r_free=0.1826 r_work=0.0906 r_free=0.1826 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0906 r_free = 0.1826 target_work(ml) = 5.033 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0898 r_free = 0.1813 target_work(ml) = 5.029 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.0898 r_free= 0.1813 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ml) (work): 5.029057 | | target function (ml) not normalized (work): 24763.077406 | | target function (ml) not normalized (free): 1812.196399 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0946 0.0898 0.1813 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2164 0.2174 0.2132 n_refl.: 5176 remove outliers: r(all,work,free)=0.2164 0.2174 0.2132 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2164 0.2174 0.2132 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0935 0.0889 0.1805 n_refl.: 5176 remove outliers: r(all,work,free)=0.0933 0.0887 0.1805 n_refl.: 5175 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3696 314.772 284.374 0.589 0.993 0.330 11.894-9.307 99.02 97 4 0.1906 506.369 489.772 0.951 0.997 0.314 9.237-7.194 100.00 213 7 0.1857 414.109 408.687 1.014 0.998 0.305 7.162-5.571 100.00 427 22 0.1788 310.739 302.633 0.987 0.999 0.286 5.546-4.326 100.00 867 58 0.0912 426.600 420.812 1.011 1.000 0.220 4.315-3.360 100.00 1859 96 0.0591 405.701 405.471 1.073 1.002 0.210 3.356-3.002 100.00 1373 60 0.0609 312.488 312.599 1.057 1.004 0.082 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9171 b_overall=-7.3055 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0887 r_free=0.1805 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A Total number of N/Q/H flips: 1 r_work=0.0888 r_free=0.1814 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0888 r_free=0.1814 | n_water=228 | time (s): 0.600 (total time: 0.600) Filter (dist) r_work=0.0895 r_free=0.1822 | n_water=225 | time (s): 18.440 (total time: 19.040) Filter (q & B) r_work=0.0944 r_free=0.1844 | n_water=222 | time (s): 1.510 (total time: 20.550) Compute maps r_work=0.0944 r_free=0.1844 | n_water=222 | time (s): 0.580 (total time: 21.130) Filter (map) r_work=0.1207 r_free=0.1886 | n_water=158 | time (s): 1.960 (total time: 23.090) Find peaks r_work=0.1207 r_free=0.1886 | n_water=158 | time (s): 0.600 (total time: 23.690) Add new water r_work=0.1527 r_free=0.2146 | n_water=231 | time (s): 1.490 (total time: 25.180) Refine new water occ: r_work=0.1008 r_free=0.1786 adp: r_work=0.1006 r_free=0.1793 occ: r_work=0.0997 r_free=0.1778 adp: r_work=0.0997 r_free=0.1784 occ: r_work=0.0989 r_free=0.1770 adp: r_work=0.0989 r_free=0.1778 ADP+occupancy (water only), MIN, final r_work=0.0989 r_free=0.1778 r_work=0.0989 r_free=0.1778 | n_water=231 | time (s): 11.420 (total time: 36.600) Filter (q & B) r_work=0.0989 r_free=0.1778 | n_water=231 | time (s): 0.850 (total time: 37.450) Filter (dist only) r_work=0.0999 r_free=0.1789 | n_water=229 | time (s): 19.330 (total time: 56.780) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.027337 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.223876 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.0915 0.1830 0.0915 0.011 1.1 5.1 0.5 0.6 0 0.514 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.15 18.30 9.15 6.951 18.475 0.224 5.011 8.86 18.62 9.76 7.999 18.563 0.224 4.944 Individual atomic B min max mean iso aniso Overall: 0.00 105.94 17.10 10.35 1756 0 Protein: 0.00 105.94 16.04 10.35 1519 0 Water: 0.17 55.94 23.78 N/A 229 0 Other: 10.07 40.29 27.43 N/A 8 0 Chain A: 0.00 105.94 16.58 N/A 1647 0 Chain S: 0.35 55.94 24.94 N/A 109 0 Histogram: Values Number of atoms 0.00 - 10.59 619 10.59 - 21.19 658 21.19 - 31.78 280 31.78 - 42.38 123 42.38 - 52.97 40 52.97 - 63.56 14 63.56 - 74.16 10 74.16 - 84.75 7 84.75 - 95.35 3 95.35 - 105.94 2 =========================== Idealize ADP of riding H ========================== r_work=0.0886 r_free=0.1862 r_work=0.0890 r_free=0.1864 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0890 r_free = 0.1864 target_work(ml) = 4.948 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0878 r_free = 0.1858 target_work(ml) = 4.940 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0878 r_free= 0.1858 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ml) (work): 4.939774 | | target function (ml) not normalized (work): 24318.507257 | | target function (ml) not normalized (free): 2076.747947 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0928 0.0878 0.1858 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2116 0.2114 0.2270 n_refl.: 5175 remove outliers: r(all,work,free)=0.2116 0.2114 0.2270 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2116 0.2114 0.2270 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0927 0.0878 0.1857 n_refl.: 5175 remove outliers: r(all,work,free)=0.0927 0.0878 0.1857 n_refl.: 5175 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3859 314.772 280.325 0.569 0.986 0.317 11.894-9.307 99.02 97 4 0.1942 506.369 492.266 0.963 0.992 0.314 9.237-7.194 100.00 213 7 0.2058 414.109 409.950 1.023 0.995 0.290 7.162-5.571 100.00 427 22 0.1974 310.739 302.001 1.000 0.997 0.280 5.546-4.326 100.00 867 58 0.0983 426.600 419.352 1.018 0.999 0.215 4.315-3.360 100.00 1859 96 0.0554 405.701 405.619 1.093 1.002 0.210 3.356-3.002 100.00 1373 60 0.0461 312.488 312.053 1.075 1.005 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-8.1659 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0878 r_free=0.1857 After: r_work=0.0881 r_free=0.1855 ================================== NQH flips ================================== r_work=0.0881 r_free=0.1855 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0881 r_free=0.1855 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0881 r_free=0.1855 | n_water=229 | time (s): 0.490 (total time: 0.490) Filter (dist) r_work=0.0894 r_free=0.1860 | n_water=226 | time (s): 20.010 (total time: 20.500) Filter (q & B) r_work=0.0998 r_free=0.1883 | n_water=223 | time (s): 1.820 (total time: 22.320) Compute maps r_work=0.0998 r_free=0.1883 | n_water=223 | time (s): 0.590 (total time: 22.910) Filter (map) r_work=0.1276 r_free=0.1988 | n_water=159 | time (s): 1.410 (total time: 24.320) Find peaks r_work=0.1276 r_free=0.1988 | n_water=159 | time (s): 0.400 (total time: 24.720) Add new water r_work=0.1555 r_free=0.2224 | n_water=228 | time (s): 1.400 (total time: 26.120) Refine new water occ: r_work=0.0987 r_free=0.1832 adp: r_work=0.0980 r_free=0.1837 occ: r_work=0.0975 r_free=0.1823 adp: r_work=0.0974 r_free=0.1830 occ: r_work=0.0969 r_free=0.1819 adp: r_work=0.0968 r_free=0.1826 ADP+occupancy (water only), MIN, final r_work=0.0968 r_free=0.1826 r_work=0.0968 r_free=0.1826 | n_water=228 | time (s): 17.170 (total time: 43.290) Filter (q & B) r_work=0.0968 r_free=0.1828 | n_water=227 | time (s): 1.330 (total time: 44.620) Filter (dist only) r_work=0.0970 r_free=0.1820 | n_water=226 | time (s): 17.630 (total time: 62.250) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.008640 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.241995 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.0910 0.1820 0.0910 0.011 1.1 7.7 0.5 0.6 0 0.504 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.10 18.20 9.10 7.926 18.752 0.242 4.967 8.93 18.35 9.42 9.081 18.903 0.242 4.914 Individual atomic B min max mean iso aniso Overall: 0.00 107.44 17.42 12.01 1753 0 Protein: 0.00 107.44 16.52 12.01 1519 0 Water: 0.30 49.17 23.18 N/A 226 0 Other: 10.10 36.77 25.25 N/A 8 0 Chain A: 0.00 107.44 16.99 N/A 1638 0 Chain S: 0.30 46.87 23.53 N/A 115 0 Histogram: Values Number of atoms 0.00 - 10.74 623 10.74 - 21.49 617 21.49 - 32.23 311 32.23 - 42.97 117 42.97 - 53.72 48 53.72 - 64.46 12 64.46 - 75.21 12 75.21 - 85.95 6 85.95 - 96.69 3 96.69 - 107.44 4 =========================== Idealize ADP of riding H ========================== r_work=0.0893 r_free=0.1835 r_work=0.0898 r_free=0.1839 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0898 r_free = 0.1839 target_work(ml) = 4.922 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0889 r_free = 0.1823 target_work(ml) = 4.916 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0889 r_free= 0.1823 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 4.915606 | | target function (ml) not normalized (work): 24199.529378 | | target function (ml) not normalized (free): 2101.940587 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.79 1.00 2493 142 0.1270 0.1845 5.4915 6.2887| | 2: 3.78 - 3.00 1.00 2430 110 0.0425 0.1786 4.3248 10.99| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.79 2493 142 0.91 12.21 1.00 0.94 12313.79| | 2: 3.78 - 3.00 2430 110 0.99 1.93 1.00 0.96 859.29| |alpha: min = 0.93 max = 0.96 mean = 0.95| |beta: min = 556.56 max = 20770.50 mean = 6659.83| |figures of merit: min = 0.01 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.41 mean = 7.13| |phase err.(test): min = 0.00 max = 86.91 mean = 7.32| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0937 0.0889 0.1823 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2166 0.2168 0.2242 n_refl.: 5175 remove outliers: r(all,work,free)=0.2166 0.2168 0.2242 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2166 0.2168 0.2242 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0936 0.0890 0.1828 n_refl.: 5175 remove outliers: r(all,work,free)=0.0936 0.0890 0.1828 n_refl.: 5175 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3979 314.772 285.968 0.603 0.983 0.320 11.894-9.307 99.02 97 4 0.2023 506.369 487.502 1.000 0.990 0.320 9.237-7.194 100.00 213 7 0.2056 414.109 406.238 1.059 0.994 0.294 7.162-5.571 100.00 427 22 0.2098 310.739 300.301 1.045 0.996 0.288 5.546-4.326 100.00 867 58 0.1037 426.600 420.323 1.070 0.999 0.220 4.315-3.360 100.00 1859 96 0.0555 405.701 405.810 1.156 1.003 0.210 3.356-3.002 100.00 1373 60 0.0412 312.488 312.533 1.137 1.006 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-8.8736 ================= 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 : 0.3613 0.2039 0.080 5.370 8.8 119.3 19.9 258 0.000 1_bss: 0.1562 0.1600 0.080 5.370 6.3 116.8 17.4 258 0.000 1_settarget: 0.1562 0.1600 0.080 5.370 6.3 116.8 17.4 258 0.000 1_nqh: 0.1562 0.1600 0.080 5.370 6.3 116.8 17.4 258 0.003 1_weight: 0.1562 0.1600 0.080 5.370 6.3 116.8 17.4 258 0.003 1_xyzrec: 0.1164 0.1813 0.010 0.976 6.3 116.8 17.4 258 0.198 1_adp: 0.1022 0.1780 0.010 0.976 2.5 111.8 17.8 258 0.198 1_regHadp: 0.1015 0.1785 0.010 0.976 2.5 111.8 17.8 258 0.198 1_occ: 0.1014 0.1791 0.010 0.976 2.5 111.8 17.8 258 0.198 2_bss: 0.1015 0.1793 0.010 0.976 1.6 110.8 16.9 258 0.198 2_settarget: 0.1015 0.1793 0.010 0.976 1.6 110.8 16.9 258 0.198 2_updatecdl: 0.1015 0.1793 0.010 1.007 1.6 110.8 16.9 258 0.198 2_nqh: 0.1015 0.1793 0.010 1.007 1.6 110.8 16.9 258 0.198 2_sol: 0.1109 0.1688 0.010 1.007 1.0 110.5 16.3 235 n/a 2_weight: 0.1109 0.1688 0.010 1.007 1.0 110.5 16.3 235 n/a 2_xyzrec: 0.1011 0.1820 0.009 0.991 1.0 110.5 16.3 235 n/a 2_adp: 0.0943 0.1865 0.009 0.991 0.0 106.3 17.2 235 n/a 2_regHadp: 0.0941 0.1865 0.009 0.991 0.0 106.3 17.2 235 n/a 2_occ: 0.0935 0.1848 0.009 0.991 0.0 106.3 17.2 235 n/a 3_bss: 0.0934 0.1849 0.009 0.991 0.0 106.3 17.2 235 n/a 3_settarget: 0.0934 0.1849 0.009 0.991 0.0 106.3 17.2 235 n/a 3_updatecdl: 0.0934 0.1849 0.009 0.996 0.0 106.3 17.2 235 n/a 3_nqh: 0.0935 0.1852 0.009 0.996 0.0 106.3 17.2 235 n/a 3_sol: 0.1039 0.1797 0.009 0.996 0.0 106.3 16.8 228 n/a 3_weight: 0.1039 0.1797 0.009 0.996 0.0 106.3 16.8 228 n/a 3_xyzrec: 0.0941 0.1827 0.011 1.066 0.0 106.3 16.8 228 n/a 3_adp: 0.0901 0.1826 0.011 1.066 0.0 105.8 16.8 228 n/a 3_regHadp: 0.0906 0.1826 0.011 1.066 0.0 105.8 16.8 228 n/a 3_occ: 0.0898 0.1813 0.011 1.066 0.0 105.8 16.8 228 n/a 4_bss: 0.0887 0.1805 0.011 1.066 0.0 105.8 16.8 228 n/a 4_settarget: 0.0887 0.1805 0.011 1.066 0.0 105.8 16.8 228 n/a 4_updatecdl: 0.0887 0.1805 0.011 1.073 0.0 105.8 16.8 228 n/a 4_nqh: 0.0888 0.1814 0.011 1.073 0.0 105.8 16.8 228 n/a 4_sol: 0.0999 0.1789 0.011 1.073 0.0 105.8 16.9 229 n/a 4_weight: 0.0999 0.1789 0.011 1.073 0.0 105.8 16.9 229 n/a 4_xyzrec: 0.0915 0.1830 0.011 1.051 0.0 105.8 16.9 229 n/a 4_adp: 0.0886 0.1862 0.011 1.051 0.0 105.9 17.1 229 n/a 4_regHadp: 0.0890 0.1864 0.011 1.051 0.0 105.9 17.1 229 n/a 4_occ: 0.0878 0.1858 0.011 1.051 0.0 105.9 17.1 229 n/a 5_bss: 0.0878 0.1857 0.011 1.051 0.0 105.9 17.1 229 n/a 5_settarget: 0.0878 0.1857 0.011 1.051 0.0 105.9 17.1 229 n/a 5_updatecdl: 0.0878 0.1857 0.011 1.059 0.0 105.9 17.1 229 n/a 5_setrh: 0.0881 0.1855 0.011 1.059 0.0 105.9 17.1 229 n/a 5_nqh: 0.0881 0.1855 0.011 1.059 0.0 105.9 17.1 229 n/a 5_sol: 0.0970 0.1820 0.011 1.059 0.0 105.9 17.1 226 n/a 5_weight: 0.0970 0.1820 0.011 1.059 0.0 105.9 17.1 226 n/a 5_xyzrec: 0.0910 0.1820 0.011 1.127 0.0 105.9 17.1 226 n/a 5_adp: 0.0893 0.1835 0.011 1.127 0.0 107.4 17.4 226 n/a 5_regHadp: 0.0898 0.1839 0.011 1.127 0.0 107.4 17.4 226 n/a 5_occ: 0.0889 0.1823 0.011 1.127 0.0 107.4 17.4 226 n/a end: 0.0890 0.1828 0.011 1.127 0.0 107.4 17.4 226 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_2112196_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_2112196_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.7400 Refinement macro-cycles (run) : 503.6800 Write final files (write_after_run_outputs) : 9.3300 Total : 516.7500 Total CPU time: 8.96 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:19:18 PST -0800 (1735492758.91 s) Start R-work = 0.1562, R-free = 0.1600 Final R-work = 0.0890, R-free = 0.1828 =============================================================================== Job complete usr+sys time: 545.12 seconds wall clock time: 9 minutes 27.12 seconds (567.12 seconds total)