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_6824987.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Adding command-line PHIL: ------------------------- xray_data.high_resolution=3 ordered_solvent.low_resolution=4 No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6824987.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6824987.pdb" 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" 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" } 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 =============================================================================== 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: 1.84, per 1000 atoms: 0.54 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: 0.59 Conformation dependent library (CDL) restraints added in 114.1 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.92: 585 0.92 - 1.18: 1063 1.18 - 1.44: 702 1.44 - 1.70: 781 1.70 - 1.96: 22 Bond restraints: 3153 Sorted by residual: bond pdb=" CA ILE A 9 " pdb=" C ILE A 9 " ideal model delta sigma weight residual 1.526 1.308 0.217 1.13e-02 7.83e+03 3.70e+02 bond pdb=" C VAL A 20 " pdb=" N ILE A 21 " ideal model delta sigma weight residual 1.329 1.527 -0.198 1.13e-02 7.83e+03 3.06e+02 bond pdb=" CA PHE A 164 " pdb=" C PHE A 164 " ideal model delta sigma weight residual 1.524 1.748 -0.224 1.29e-02 6.01e+03 3.02e+02 bond pdb=" N ARG A 27 " pdb=" CA ARG A 27 " ideal model delta sigma weight residual 1.459 1.671 -0.213 1.28e-02 6.10e+03 2.76e+02 bond pdb=" C ALA A 29 " pdb=" N GLY A 30 " ideal model delta sigma weight residual 1.330 1.131 0.199 1.23e-02 6.61e+03 2.63e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.29: 2984 4.29 - 8.57: 1820 8.57 - 12.86: 780 12.86 - 17.14: 180 17.14 - 21.42: 13 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA LEU A 187 " pdb=" C LEU A 187 " pdb=" O LEU A 187 " ideal model delta sigma weight residual 121.47 106.45 15.02 1.15e+00 7.56e-01 1.71e+02 angle pdb=" CA BLYS A 132 " pdb=" C BLYS A 132 " pdb=" O BLYS A 132 " ideal model delta sigma weight residual 120.42 106.68 13.74 1.06e+00 8.90e-01 1.68e+02 angle pdb=" O GLY A 100 " pdb=" C GLY A 100 " pdb=" N LEU A 101 " ideal model delta sigma weight residual 123.21 107.82 15.39 1.20e+00 6.94e-01 1.65e+02 angle pdb=" CA BASN A 76 " pdb=" C BASN A 76 " pdb=" O BASN A 76 " ideal model delta sigma weight residual 120.90 134.44 -13.54 1.07e+00 8.73e-01 1.60e+02 angle pdb=" C ILE A 9 " pdb=" CA ILE A 9 " pdb=" CB ILE A 9 " ideal model delta sigma weight residual 111.23 124.79 -13.56 1.08e+00 8.57e-01 1.58e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.85: 1312 17.85 - 35.69: 122 35.69 - 53.53: 35 53.53 - 71.37: 10 71.37 - 89.21: 2 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" N PRO A 184 " pdb=" C PRO A 184 " pdb=" CA PRO A 184 " pdb=" CB PRO A 184 " ideal model delta harmonic sigma weight residual 115.10 146.83 -31.73 0 2.50e+00 1.60e-01 1.61e+02 dihedral pdb=" C PRO A 184 " pdb=" N PRO A 184 " pdb=" CA PRO A 184 " pdb=" CB PRO A 184 " ideal model delta harmonic sigma weight residual -120.70 -146.85 26.15 0 2.50e+00 1.60e-01 1.09e+02 dihedral pdb=" C ILE A 9 " pdb=" N ILE A 9 " pdb=" CA ILE A 9 " pdb=" CB ILE A 9 " ideal model delta harmonic sigma weight residual -122.00 -139.48 17.48 0 2.50e+00 1.60e-01 4.89e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.286: 132 0.286 - 0.571: 69 0.571 - 0.856: 36 0.856 - 1.141: 5 1.141 - 1.426: 1 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA PRO A 184 " pdb=" N PRO A 184 " pdb=" C PRO A 184 " pdb=" CB PRO A 184 " both_signs ideal model delta sigma weight residual False 2.72 1.29 1.43 2.00e-01 2.50e+01 5.08e+01 chirality pdb=" CA SER A 3 " pdb=" N SER A 3 " pdb=" C SER A 3 " pdb=" CB SER A 3 " both_signs ideal model delta sigma weight residual False 2.51 1.51 1.00 2.00e-01 2.50e+01 2.49e+01 chirality pdb=" CA GLU A 163 " pdb=" N GLU A 163 " pdb=" C GLU A 163 " pdb=" CB GLU A 163 " both_signs ideal model delta sigma weight residual False 2.51 3.44 -0.93 2.00e-01 2.50e+01 2.15e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " 0.012 2.00e-02 2.50e+03 6.63e-02 1.32e+02 pdb=" CG BTYR A 67 " 0.023 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " 0.086 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " -0.120 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " -0.088 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " 0.090 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " -0.001 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " 0.032 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " -0.062 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " 0.060 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " 0.037 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " -0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.130 2.00e-02 2.50e+03 6.55e-02 1.29e+02 pdb=" CG PHE A 164 " 0.123 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.052 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.034 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " 0.015 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.026 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.004 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.096 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.069 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.036 2.00e-02 2.50e+03 6.23e-02 1.17e+02 pdb=" CG PHE A 119 " -0.073 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " 0.132 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.032 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.021 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " 0.044 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " -0.059 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.060 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.048 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.004 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.085 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.050 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.30: 903 2.30 - 2.88: 8054 2.88 - 3.45: 10531 3.45 - 4.03: 15257 4.03 - 4.60: 21875 Nonbonded interactions: 56620 Sorted by model distance: nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.728 2.450 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.750 2.450 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.776 2.100 nonbonded pdb=" HG SER A 47 " pdb="HH11 ARG A 48 " model vdw 1.819 2.100 nonbonded pdb=" H THR A 125 " pdb=" HH TYR A 141 " model vdw 1.821 2.100 ... (remaining 56615 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_6824987_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= 0.3619 r_free= 0.2034 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.469620 | | target function (ml) not normalized (work): 22035.226269 | | target function (ml) not normalized (free): 1155.733799 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3805 0.2204 4.8503 4.8958| | 2: 3.78 - 3.00 1.00 2430 110 0.3393 0.1746 4.078 4.1866| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 48.69 0.83 0.13 6597.65| | 2: 3.78 - 3.00 2430 110 0.93 11.43 1.48 0.26 453.81| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 391.22 max = 12069.03 mean = 3569.35| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 89.99 mean = 30.32| |phase err.(test): min = 0.00 max = 89.97 mean = 33.47| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.082 0.241 1557 Z= 5.406 Angle : 5.285 16.769 2118 Z= 3.659 Chirality : 0.394 1.426 243 Planarity : 0.033 0.126 284 Dihedral : 14.106 89.210 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.24 % Allowed : 3.11 % Favored : 95.65 % Cbeta Deviations : 30.81 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.45), residues: 224 helix: -2.54 (0.38), residues: 101 sheet: -0.64 (0.92), residues: 28 loop : -0.37 (0.50), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.062 0.015 ARG A 98 TYR 0.072 0.026 TYR A 139 PHE 0.125 0.045 PHE A 164 HIS 0.042 0.025 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= 0.3619 r_free= 0.2034 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.469620 | | target function (ml) not normalized (work): 22035.226269 | | target function (ml) not normalized (free): 1155.733799 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3578 0.3654 0.2138 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3578 0.3654 0.2138 n_refl.: 5182 remove outliers: r(all,work,free)=0.2529 0.2552 0.2138 n_refl.: 5178 overall B=-2.48 to atoms: r(all,work,free)=0.2433 0.2454 0.2102 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1583 0.1579 0.1651 n_refl.: 5178 remove outliers: r(all,work,free)=0.1577 0.1573 0.1651 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 97.87 87 5 0.3866 443.974 394.711 0.652 1.010 0.383 11.894-9.307 99.02 97 4 0.1859 714.215 700.236 0.962 1.012 0.392 9.237-7.194 100.00 213 7 0.2214 584.086 578.345 0.983 1.011 0.357 7.162-5.571 100.00 427 22 0.2356 438.285 423.512 0.939 1.009 0.293 5.546-4.326 100.00 867 58 0.1386 601.704 596.213 0.968 1.005 0.230 4.315-3.360 100.00 1859 96 0.1310 572.227 566.161 1.018 0.999 0.199 3.356-3.002 100.00 1373 60 0.1636 440.753 431.491 0.997 0.992 0.117 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9177 b_overall=-4.2816 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1573 r_free=0.1651 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=0.1574 r_free=0.1643 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 18.261111 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.813962 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 0.1154 0.1821 0.0666 0.010 1.0 2.9 0.5 0.0 0 9.131 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.54 18.21 6.66 3.013 16.379 1.814 0.018 10.18 18.26 8.08 4.916 16.586 1.814 0.014 Individual atomic B min max mean iso aniso Overall: 2.30 112.13 17.80 5.33 1785 0 Protein: 2.30 112.13 15.08 5.32 1519 0 Water: 4.39 111.82 33.62 N/A 258 0 Other: 16.10 39.36 23.95 N/A 8 0 Chain A: 2.30 112.13 17.80 N/A 1785 0 Histogram: Values Number of atoms 2.30 - 13.28 898 13.28 - 24.27 504 24.27 - 35.25 184 35.25 - 46.23 112 46.23 - 57.22 56 57.22 - 68.20 13 68.20 - 79.18 8 79.18 - 90.16 6 90.16 - 101.15 1 101.15 - 112.13 3 =========================== Idealize ADP of riding H ========================== r_work=0.1018 r_free=0.1826 r_work=0.1013 r_free=0.1830 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1013 r_free = 0.1830 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 = 0.1006 r_free = 0.1844 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.1006 r_free= 0.1844 coordinate error (max.-lik. estimate): 0.31 A | | | | normalized target function (ls_wunit_k1) (work): 0.013820 | | target function (ls_wunit_k1) not normalized (work): 68.033656 | | target function (ls_wunit_k1) not normalized (free): 10.570504 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1049 0.1006 0.1844 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2028 0.2020 0.2265 n_refl.: 5175 remove outliers: r(all,work,free)=0.2028 0.2020 0.2265 n_refl.: 5175 overall B=-0.92 to atoms: r(all,work,free)=0.1992 0.1982 0.2255 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.1043 0.1002 0.1826 n_refl.: 5175 remove outliers: r(all,work,free)=0.1043 0.1002 0.1826 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 0.3267 314.450 297.502 0.634 1.001 0.360 11.894-9.307 99.02 97 4 0.1501 505.850 497.686 0.955 1.004 0.354 9.237-7.194 100.00 213 7 0.1634 413.685 413.049 0.989 1.004 0.313 7.162-5.571 100.00 427 22 0.1590 310.420 307.430 0.952 1.003 0.298 5.546-4.326 100.00 867 58 0.0901 426.163 423.229 0.967 1.002 0.213 4.315-3.360 100.00 1859 96 0.0757 405.286 405.262 1.015 0.999 0.205 3.356-3.002 100.00 1373 60 0.1004 312.168 311.190 0.986 0.997 0.091 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-4.1268 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1002 r_free=0.1826 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=0.1003 r_free=0.1824 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1003 r_free=0.1824 | n_water=258 | time (s): 0.680 (total time: 0.680) Filter (dist) r_work=0.1025 r_free=0.1793 | n_water=247 | time (s): 21.360 (total time: 22.040) Filter (q & B) r_work=0.1027 r_free=0.1798 | n_water=245 | time (s): 1.730 (total time: 23.770) Compute maps r_work=0.1027 r_free=0.1798 | n_water=245 | time (s): 0.590 (total time: 24.360) Filter (map) r_work=0.1323 r_free=0.1932 | n_water=152 | time (s): 2.030 (total time: 26.390) Find peaks r_work=0.1323 r_free=0.1932 | n_water=152 | time (s): 0.540 (total time: 26.930) Add new water r_work=0.1681 r_free=0.2215 | n_water=239 | time (s): 1.580 (total time: 28.510) Refine new water occ: r_work=0.1148 r_free=0.1714 adp: r_work=0.1123 r_free=0.1732 occ: r_work=0.1117 r_free=0.1703 adp: r_work=0.1108 r_free=0.1714 occ: r_work=0.1105 r_free=0.1696 adp: r_work=0.1103 r_free=0.1704 ADP+occupancy (water only), MIN, final r_work=0.1103 r_free=0.1704 r_work=0.1103 r_free=0.1704 | n_water=239 | time (s): 5.840 (total time: 34.350) Filter (q & B) r_work=0.1103 r_free=0.1704 | n_water=239 | time (s): 1.010 (total time: 35.360) Filter (dist only) r_work=0.1109 r_free=0.1703 | n_water=236 | time (s): 17.700 (total time: 53.060) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.155538 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.549267 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 0.1004 0.1809 0.0805 0.009 1.0 5.4 0.5 0.6 0 12.078 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.04 18.09 8.05 4.708 17.291 2.549 0.014 9.42 18.14 8.72 5.315 17.585 2.549 0.012 Individual atomic B min max mean iso aniso Overall: 0.00 107.61 16.92 6.26 1763 0 Protein: 0.00 107.61 15.21 6.25 1519 0 Water: 0.00 74.59 27.70 N/A 236 0 Other: 10.98 37.00 23.41 N/A 8 0 Chain A: 0.00 107.61 16.03 N/A 1677 0 Chain S: 6.37 57.41 34.34 N/A 86 0 Histogram: Values Number of atoms 0.00 - 10.76 646 10.76 - 21.52 693 21.52 - 32.28 223 32.28 - 43.04 117 43.04 - 53.80 43 53.80 - 64.56 28 64.56 - 75.32 7 75.32 - 86.08 1 86.08 - 96.84 3 96.84 - 107.61 2 =========================== Idealize ADP of riding H ========================== r_work=0.0942 r_free=0.1814 r_work=0.0939 r_free=0.1813 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0939 r_free = 0.1813 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 = 0.0938 r_free = 0.1805 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0938 r_free= 0.1805 coordinate error (max.-lik. estimate): 0.31 A | | | | normalized target function (ls_wunit_k1) (work): 0.011968 | | target function (ls_wunit_k1) not normalized (work): 58.917202 | | target function (ls_wunit_k1) not normalized (free): 10.172800 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0981 0.0938 0.1805 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2048 0.2044 0.2207 n_refl.: 5175 remove outliers: r(all,work,free)=0.2048 0.2044 0.2207 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2048 0.2044 0.2207 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0981 0.0938 0.1799 n_refl.: 5175 remove outliers: r(all,work,free)=0.0981 0.0938 0.1799 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 0.3300 314.450 297.975 0.646 1.000 0.347 11.894-9.307 99.02 97 4 0.1543 505.850 498.642 0.990 1.002 0.338 9.237-7.194 100.00 213 7 0.1465 413.685 415.590 1.036 1.003 0.295 7.162-5.571 100.00 427 22 0.1448 310.420 307.982 1.002 1.003 0.273 5.546-4.326 100.00 867 58 0.0799 426.163 423.431 1.018 1.002 0.225 4.315-3.360 100.00 1859 96 0.0723 405.286 404.745 1.070 0.999 0.220 3.356-3.002 100.00 1373 60 0.0947 312.168 311.342 1.045 0.997 0.100 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-4.8556 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0938 r_free=0.1799 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN A A 80 GLN A Total number of N/Q/H flips: 3 r_work=0.0939 r_free=0.1807 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0939 r_free=0.1807 | n_water=236 | time (s): 0.600 (total time: 0.600) Filter (dist) r_work=0.0960 r_free=0.1812 | n_water=232 | time (s): 17.170 (total time: 17.770) Filter (q & B) r_work=0.1015 r_free=0.1819 | n_water=230 | time (s): 1.430 (total time: 19.200) Compute maps r_work=0.1015 r_free=0.1819 | n_water=230 | time (s): 0.580 (total time: 19.780) Filter (map) r_work=0.1270 r_free=0.1889 | n_water=156 | time (s): 1.820 (total time: 21.600) Find peaks r_work=0.1270 r_free=0.1889 | n_water=156 | time (s): 0.600 (total time: 22.200) Add new water r_work=0.1612 r_free=0.2219 | n_water=232 | time (s): 1.680 (total time: 23.880) Refine new water occ: r_work=0.1071 r_free=0.1801 adp: r_work=0.1064 r_free=0.1814 occ: r_work=0.1053 r_free=0.1788 adp: r_work=0.1052 r_free=0.1798 occ: r_work=0.1042 r_free=0.1772 adp: r_work=0.1041 r_free=0.1781 ADP+occupancy (water only), MIN, final r_work=0.1041 r_free=0.1781 r_work=0.1041 r_free=0.1781 | n_water=232 | time (s): 14.100 (total time: 37.980) Filter (q & B) r_work=0.1041 r_free=0.1781 | n_water=232 | time (s): 1.100 (total time: 39.080) Filter (dist only) r_work=0.1041 r_free=0.1786 | n_water=231 | time (s): 17.640 (total time: 56.720) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.127737 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.227959 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 0.0945 0.1785 0.0840 0.011 1.1 4.8 0.5 0.0 0 0.564 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.45 17.85 8.40 5.281 18.008 0.228 5.129 9.00 17.90 8.90 7.282 18.044 0.228 5.030 Individual atomic B min max mean iso aniso Overall: 0.00 105.81 16.71 8.95 1758 0 Protein: 0.00 105.81 15.40 8.95 1519 0 Water: 0.00 58.18 25.00 N/A 231 0 Other: 9.92 40.69 25.90 N/A 8 0 Chain A: 0.00 105.81 16.12 N/A 1663 0 Chain S: 0.00 55.89 27.08 N/A 95 0 Histogram: Values Number of atoms 0.00 - 10.58 640 10.58 - 21.16 677 21.16 - 31.74 239 31.74 - 42.33 120 42.33 - 52.91 45 52.91 - 63.49 19 63.49 - 74.07 10 74.07 - 84.65 3 84.65 - 95.23 3 95.23 - 105.81 2 =========================== Idealize ADP of riding H ========================== r_work=0.0900 r_free=0.1790 r_work=0.0905 r_free=0.1795 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0905 r_free = 0.1795 target_work(ml) = 5.034 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0897 r_free = 0.1782 target_work(ml) = 5.028 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0897 r_free= 0.1782 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ml) (work): 5.028447 | | target function (ml) not normalized (work): 24755.043105 | | target function (ml) not normalized (free): 1814.252281 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0942 0.0897 0.1782 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2056 0.2054 0.2174 n_refl.: 5175 remove outliers: r(all,work,free)=0.2056 0.2054 0.2174 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2056 0.2054 0.2174 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0938 0.0894 0.1774 n_refl.: 5175 remove outliers: r(all,work,free)=0.0938 0.0894 0.1774 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 0.3746 314.450 288.283 0.581 0.992 0.324 11.894-9.307 99.02 97 4 0.1898 505.850 491.736 0.952 0.996 0.320 9.237-7.194 100.00 213 7 0.1895 413.685 411.881 1.011 0.998 0.290 7.162-5.571 100.00 427 22 0.1844 310.420 303.562 0.985 0.999 0.280 5.546-4.326 100.00 867 58 0.0922 426.163 420.562 1.002 1.000 0.220 4.315-3.360 100.00 1859 96 0.0596 405.286 404.785 1.062 1.001 0.220 3.356-3.002 100.00 1373 60 0.0595 312.168 311.697 1.039 1.003 0.080 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-6.6327 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0894 r_free=0.1774 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0894 r_free=0.1774 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0894 r_free=0.1774 | n_water=231 | time (s): 0.570 (total time: 0.570) Filter (dist) r_work=0.0914 r_free=0.1784 | n_water=226 | time (s): 17.050 (total time: 17.620) Filter (q & B) r_work=0.0983 r_free=0.1818 | n_water=224 | time (s): 1.540 (total time: 19.160) Compute maps r_work=0.0983 r_free=0.1818 | n_water=224 | time (s): 0.620 (total time: 19.780) Filter (map) r_work=0.1233 r_free=0.1894 | n_water=166 | time (s): 1.920 (total time: 21.700) Find peaks r_work=0.1233 r_free=0.1894 | n_water=166 | time (s): 0.490 (total time: 22.190) Add new water r_work=0.1524 r_free=0.2151 | n_water=229 | time (s): 1.560 (total time: 23.750) Refine new water occ: r_work=0.0976 r_free=0.1840 adp: r_work=0.0968 r_free=0.1847 occ: r_work=0.0961 r_free=0.1837 adp: r_work=0.0960 r_free=0.1840 occ: r_work=0.0955 r_free=0.1831 adp: r_work=0.0953 r_free=0.1833 ADP+occupancy (water only), MIN, final r_work=0.0953 r_free=0.1833 r_work=0.0953 r_free=0.1833 | n_water=229 | time (s): 8.320 (total time: 32.070) Filter (q & B) r_work=0.0953 r_free=0.1832 | n_water=227 | time (s): 1.240 (total time: 33.310) Filter (dist only) r_work=0.0953 r_free=0.1832 | n_water=227 | time (s): 17.170 (total time: 50.480) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.961634 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.193676 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 0.0881 0.1846 0.0965 0.011 1.1 4.5 0.5 0.6 0 0.481 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 8.81 18.46 9.65 6.978 18.158 0.194 4.963 8.62 18.79 10.17 8.101 18.274 0.194 4.902 Individual atomic B min max mean iso aniso Overall: 0.00 107.24 16.89 10.56 1754 0 Protein: 0.00 107.24 15.77 10.55 1519 0 Water: 0.00 58.68 24.09 N/A 227 0 Other: 12.21 40.96 26.60 N/A 8 0 Chain A: 0.00 107.24 16.37 N/A 1654 0 Chain S: 0.00 58.68 25.55 N/A 100 0 Histogram: Values Number of atoms 0.00 - 10.72 647 10.72 - 21.45 639 21.45 - 32.17 277 32.17 - 42.90 115 42.90 - 53.62 38 53.62 - 64.35 20 64.35 - 75.07 7 75.07 - 85.79 7 85.79 - 96.52 0 96.52 - 107.24 4 =========================== Idealize ADP of riding H ========================== r_work=0.0862 r_free=0.1879 r_work=0.0865 r_free=0.1880 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0865 r_free = 0.1880 target_work(ml) = 4.907 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0860 r_free = 0.1868 target_work(ml) = 4.903 | | occupancies: max = 1.00 min = 0.27 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= 0.0860 r_free= 0.1868 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ml) (work): 4.902754 | | target function (ml) not normalized (work): 24136.260096 | | target function (ml) not normalized (free): 2216.528177 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0911 0.0860 0.1868 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2095 0.2089 0.2303 n_refl.: 5175 remove outliers: r(all,work,free)=0.2095 0.2089 0.2303 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2095 0.2089 0.2303 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0910 0.0859 0.1868 n_refl.: 5175 remove outliers: r(all,work,free)=0.0910 0.0859 0.1868 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 0.3852 314.450 284.347 0.571 0.988 0.317 11.894-9.307 99.02 97 4 0.1983 505.850 488.777 0.955 0.993 0.314 9.237-7.194 100.00 213 7 0.2064 413.685 405.674 1.013 0.996 0.295 7.162-5.571 100.00 427 22 0.1974 310.420 301.443 0.993 0.997 0.290 5.546-4.326 100.00 867 58 0.0959 426.163 420.694 1.015 0.999 0.230 4.315-3.360 100.00 1859 96 0.0545 405.286 405.200 1.082 1.002 0.220 3.356-3.002 100.00 1373 60 0.0414 312.168 312.536 1.060 1.004 0.076 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.5780 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0859 r_free=0.1868 After: r_work=0.0862 r_free=0.1867 ================================== NQH flips ================================== r_work=0.0862 r_free=0.1867 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0862 r_free=0.1867 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0862 r_free=0.1867 | n_water=227 | time (s): 0.550 (total time: 0.550) Filter (dist) r_work=0.0869 r_free=0.1867 | n_water=226 | time (s): 19.590 (total time: 20.140) Filter (q & B) r_work=0.1020 r_free=0.1931 | n_water=222 | time (s): 1.980 (total time: 22.120) Compute maps r_work=0.1020 r_free=0.1931 | n_water=222 | time (s): 0.620 (total time: 22.740) Filter (map) r_work=0.1267 r_free=0.1966 | n_water=159 | time (s): 1.760 (total time: 24.500) Find peaks r_work=0.1267 r_free=0.1966 | n_water=159 | time (s): 0.600 (total time: 25.100) Add new water r_work=0.1541 r_free=0.2193 | n_water=220 | time (s): 1.760 (total time: 26.860) Refine new water occ: r_work=0.1006 r_free=0.1870 adp: r_work=0.0995 r_free=0.1876 occ: r_work=0.0988 r_free=0.1865 adp: r_work=0.0988 r_free=0.1872 occ: r_work=0.0982 r_free=0.1860 adp: r_work=0.0981 r_free=0.1866 ADP+occupancy (water only), MIN, final r_work=0.0981 r_free=0.1866 r_work=0.0981 r_free=0.1866 | n_water=220 | time (s): 8.950 (total time: 35.810) Filter (q & B) r_work=0.0981 r_free=0.1872 | n_water=218 | time (s): 1.810 (total time: 37.620) Filter (dist only) r_work=0.0992 r_free=0.1891 | n_water=216 | time (s): 17.010 (total time: 54.630) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.966204 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.231985 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 0.0930 0.1911 0.0981 0.010 1.1 6.7 0.5 0.6 0 0.483 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.30 19.11 9.81 8.045 18.422 0.232 5.007 9.08 19.20 10.13 8.888 18.478 0.232 4.949 Individual atomic B min max mean iso aniso Overall: 0.00 110.23 16.98 11.62 1743 0 Protein: 0.00 110.23 16.01 11.61 1519 0 Water: 0.00 53.68 23.47 N/A 216 0 Other: 9.84 39.46 27.38 N/A 8 0 Chain A: 0.00 110.23 16.50 N/A 1640 0 Chain S: 0.00 53.68 24.67 N/A 103 0 Histogram: Values Number of atoms 0.00 - 11.02 676 11.02 - 22.05 609 22.05 - 33.07 280 33.07 - 44.09 110 44.09 - 55.12 34 55.12 - 66.14 16 66.14 - 77.16 7 77.16 - 88.18 6 88.18 - 99.21 2 99.21 - 110.23 3 =========================== Idealize ADP of riding H ========================== r_work=0.0908 r_free=0.1920 r_work=0.0911 r_free=0.1918 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0911 r_free = 0.1918 target_work(ml) = 4.954 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0906 r_free = 0.1908 target_work(ml) = 4.951 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0906 r_free= 0.1908 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ml) (work): 4.950617 | | target function (ml) not normalized (work): 24371.889392 | | target function (ml) not normalized (free): 2147.213384 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1275 0.1897 5.508 6.2825| | 2: 3.78 - 3.00 1.00 2430 110 0.0455 0.1927 4.3787 11.41| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 12.27 1.00 0.94 12361.57| | 2: 3.78 - 3.00 2430 110 0.99 2.15 1.00 0.96 938.84| |alpha: min = 0.93 max = 0.97 mean = 0.95| |beta: min = 609.17 max = 20583.24 mean = 6723.29| |figures of merit: min = 0.00 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.77 mean = 7.27| |phase err.(test): min = 0.00 max = 82.83 mean = 6.83| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0957 0.0906 0.1908 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2171 0.2165 0.2382 n_refl.: 5175 remove outliers: r(all,work,free)=0.2171 0.2165 0.2382 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2171 0.2165 0.2382 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0955 0.0904 0.1913 n_refl.: 5175 remove outliers: r(all,work,free)=0.0955 0.0904 0.1913 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 0.3941 314.450 285.225 0.604 0.986 0.320 11.894-9.307 99.02 97 4 0.1912 505.850 491.285 1.009 0.993 0.320 9.237-7.194 100.00 213 7 0.2162 413.685 403.703 1.051 0.996 0.313 7.162-5.571 100.00 427 22 0.2012 310.420 302.521 1.034 0.998 0.307 5.546-4.326 100.00 867 58 0.1046 426.163 420.592 1.065 1.000 0.235 4.315-3.360 100.00 1859 96 0.0581 405.286 404.871 1.146 1.001 0.230 3.356-3.002 100.00 1373 60 0.0438 312.168 312.069 1.126 1.002 0.080 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-8.3375 ================= 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 : 0.3619 0.2034 0.082 5.285 8.8 119.3 19.9 258 0.000 1_bss: 0.1573 0.1651 0.082 5.285 6.4 116.8 17.4 258 0.000 1_settarget: 0.1573 0.1651 0.082 5.285 6.4 116.8 17.4 258 0.000 1_nqh: 0.1574 0.1643 0.082 5.285 6.4 116.8 17.4 258 0.003 1_weight: 0.1574 0.1643 0.082 5.285 6.4 116.8 17.4 258 0.003 1_xyzrec: 0.1154 0.1821 0.010 0.956 6.4 116.8 17.4 258 0.214 1_adp: 0.1018 0.1826 0.010 0.956 2.3 112.1 17.8 258 0.214 1_regHadp: 0.1013 0.1830 0.010 0.956 2.3 112.1 17.8 258 0.214 1_occ: 0.1006 0.1844 0.010 0.956 2.3 112.1 17.8 258 0.214 2_bss: 0.1002 0.1826 0.010 0.956 1.4 111.2 16.9 258 0.214 2_settarget: 0.1002 0.1826 0.010 0.956 1.4 111.2 16.9 258 0.214 2_updatecdl: 0.1002 0.1826 0.010 0.979 1.4 111.2 16.9 258 0.214 2_nqh: 0.1003 0.1824 0.010 0.979 1.4 111.2 16.9 258 0.217 2_sol: 0.1109 0.1703 0.010 0.979 1.0 111.2 16.4 236 n/a 2_weight: 0.1109 0.1703 0.010 0.979 1.0 111.2 16.4 236 n/a 2_xyzrec: 0.1004 0.1809 0.009 0.999 1.0 111.2 16.4 236 n/a 2_adp: 0.0942 0.1814 0.009 0.999 0.0 107.6 16.9 236 n/a 2_regHadp: 0.0939 0.1813 0.009 0.999 0.0 107.6 16.9 236 n/a 2_occ: 0.0938 0.1805 0.009 0.999 0.0 107.6 16.9 236 n/a 3_bss: 0.0938 0.1799 0.009 0.999 0.0 107.6 16.9 236 n/a 3_settarget: 0.0938 0.1799 0.009 0.999 0.0 107.6 16.9 236 n/a 3_updatecdl: 0.0938 0.1799 0.009 1.005 0.0 107.6 16.9 236 n/a 3_nqh: 0.0939 0.1807 0.009 1.005 0.0 107.6 16.9 236 n/a 3_sol: 0.1041 0.1786 0.009 1.005 0.0 107.6 16.6 231 n/a 3_weight: 0.1041 0.1786 0.009 1.005 0.0 107.6 16.6 231 n/a 3_xyzrec: 0.0945 0.1785 0.011 1.096 0.0 107.6 16.6 231 n/a 3_adp: 0.0900 0.1790 0.011 1.096 0.0 105.8 16.7 231 n/a 3_regHadp: 0.0905 0.1795 0.011 1.096 0.0 105.8 16.7 231 n/a 3_occ: 0.0897 0.1782 0.011 1.096 0.0 105.8 16.7 231 n/a 4_bss: 0.0894 0.1774 0.011 1.096 0.0 105.8 16.7 231 n/a 4_settarget: 0.0894 0.1774 0.011 1.096 0.0 105.8 16.7 231 n/a 4_updatecdl: 0.0894 0.1774 0.011 1.117 0.0 105.8 16.7 231 n/a 4_nqh: 0.0894 0.1774 0.011 1.117 0.0 105.8 16.7 231 n/a 4_sol: 0.0953 0.1832 0.011 1.117 0.0 105.8 16.7 227 n/a 4_weight: 0.0953 0.1832 0.011 1.117 0.0 105.8 16.7 227 n/a 4_xyzrec: 0.0881 0.1846 0.011 1.070 0.0 105.8 16.7 227 n/a 4_adp: 0.0862 0.1879 0.011 1.070 0.0 107.2 16.9 227 n/a 4_regHadp: 0.0865 0.1880 0.011 1.070 0.0 107.2 16.9 227 n/a 4_occ: 0.0860 0.1868 0.011 1.070 0.0 107.2 16.9 227 n/a 5_bss: 0.0859 0.1868 0.011 1.070 0.0 107.2 16.9 227 n/a 5_settarget: 0.0859 0.1868 0.011 1.070 0.0 107.2 16.9 227 n/a 5_updatecdl: 0.0859 0.1868 0.011 1.070 0.0 107.2 16.9 227 n/a 5_setrh: 0.0862 0.1867 0.011 1.070 0.0 107.2 16.9 227 n/a 5_nqh: 0.0862 0.1867 0.011 1.070 0.0 107.2 16.9 227 n/a 5_sol: 0.0992 0.1891 0.011 1.070 0.0 107.2 16.9 216 n/a 5_weight: 0.0992 0.1891 0.011 1.070 0.0 107.2 16.9 216 n/a 5_xyzrec: 0.0930 0.1911 0.010 1.105 0.0 107.2 16.9 216 n/a 5_adp: 0.0908 0.1920 0.010 1.105 0.0 110.2 17.0 216 n/a 5_regHadp: 0.0911 0.1918 0.010 1.105 0.0 110.2 17.0 216 n/a 5_occ: 0.0906 0.1908 0.010 1.105 0.0 110.2 17.0 216 n/a end: 0.0904 0.1913 0.010 1.105 0.0 110.2 17.0 216 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_6824987_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_6824987_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.8500 Refinement macro-cycles (run) : 485.8100 Write final files (write_after_run_outputs) : 10.1100 Total : 499.7700 Total CPU time: 8.69 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:19:02 PST -0800 (1735492742.94 s) Start R-work = 0.1573, R-free = 0.1651 Final R-work = 0.0904, R-free = 0.1913 =============================================================================== Job complete usr+sys time: 528.76 seconds wall clock time: 9 minutes 10.95 seconds (550.95 seconds total)