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_7848743.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Adding command-line PHIL: ------------------------- xray_data.high_resolution=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_7848743.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7848743.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: 2.15, per 1000 atoms: 0.64 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.38 Conformation dependent library (CDL) restraints added in 121.4 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.92: 524 0.92 - 1.17: 1131 1.17 - 1.42: 627 1.42 - 1.68: 838 1.68 - 1.93: 33 Bond restraints: 3153 Sorted by residual: bond pdb=" N VAL A 23 " pdb=" CA VAL A 23 " ideal model delta sigma weight residual 1.463 1.722 -0.259 1.14e-02 7.69e+03 5.15e+02 bond pdb=" C ALA A 107 " pdb=" N GLY A 108 " ideal model delta sigma weight residual 1.339 1.179 0.160 7.50e-03 1.78e+04 4.57e+02 bond pdb=" C PRO A 43 " pdb=" O PRO A 43 " ideal model delta sigma weight residual 1.233 1.004 0.229 1.10e-02 8.26e+03 4.33e+02 bond pdb=" C VAL A 69 " pdb=" O VAL A 69 " ideal model delta sigma weight residual 1.234 1.001 0.233 1.16e-02 7.43e+03 4.02e+02 bond pdb=" C ALA A 56 " pdb=" O ALA A 56 " ideal model delta sigma weight residual 1.234 1.014 0.220 1.20e-02 6.94e+03 3.36e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.79: 3172 4.79 - 9.58: 1880 9.58 - 14.36: 609 14.36 - 19.15: 107 19.15 - 23.93: 9 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O ARG A 145 " pdb=" C ARG A 145 " pdb=" N VAL A 146 " ideal model delta sigma weight residual 122.07 138.06 -15.99 1.03e+00 9.43e-01 2.41e+02 angle pdb=" O ILE A 117 " pdb=" C ILE A 117 " pdb=" N GLY A 118 " ideal model delta sigma weight residual 123.18 107.34 15.84 1.05e+00 9.07e-01 2.28e+02 angle pdb=" O ILE A 21 " pdb=" C ILE A 21 " pdb=" N PRO A 22 " ideal model delta sigma weight residual 120.07 129.76 -9.69 7.10e-01 1.98e+00 1.86e+02 angle pdb=" CA ILE A 21 " pdb=" C ILE A 21 " pdb=" N PRO A 22 " ideal model delta sigma weight residual 121.00 110.11 10.89 8.30e-01 1.45e+00 1.72e+02 angle pdb=" OD1AASN A 97 " pdb=" CG AASN A 97 " pdb=" ND2AASN A 97 " ideal model delta sigma weight residual 122.60 109.79 12.81 1.00e+00 1.00e+00 1.64e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.05: 1290 16.05 - 32.10: 125 32.10 - 48.15: 45 48.15 - 64.20: 19 64.20 - 80.25: 2 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C APRO A 66 " pdb=" N APRO A 66 " pdb=" CA APRO A 66 " pdb=" CB APRO A 66 " ideal model delta harmonic sigma weight residual -120.70 -141.20 20.50 0 2.50e+00 1.60e-01 6.72e+01 dihedral pdb=" N APRO A 66 " pdb=" C APRO A 66 " pdb=" CA APRO A 66 " pdb=" CB APRO A 66 " ideal model delta harmonic sigma weight residual 115.10 134.63 -19.53 0 2.50e+00 1.60e-01 6.10e+01 dihedral pdb=" C VAL A 71 " pdb=" N VAL A 71 " pdb=" CA VAL A 71 " pdb=" CB VAL A 71 " ideal model delta harmonic sigma weight residual -122.00 -104.01 -17.99 0 2.50e+00 1.60e-01 5.18e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.231: 103 0.231 - 0.460: 79 0.460 - 0.690: 47 0.690 - 0.919: 10 0.919 - 1.148: 4 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA VAL A 71 " pdb=" N VAL A 71 " pdb=" C VAL A 71 " pdb=" CB VAL A 71 " both_signs ideal model delta sigma weight residual False 2.44 3.59 -1.15 2.00e-01 2.50e+01 3.29e+01 chirality pdb=" CA APRO A 66 " pdb=" N APRO A 66 " pdb=" C APRO A 66 " pdb=" CB APRO A 66 " both_signs ideal model delta sigma weight residual False 2.72 1.72 1.00 2.00e-01 2.50e+01 2.49e+01 chirality pdb=" CA PHE A 162 " pdb=" N PHE A 162 " pdb=" C PHE A 162 " pdb=" CB PHE A 162 " both_signs ideal model delta sigma weight residual False 2.51 3.46 -0.95 2.00e-01 2.50e+01 2.26e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.074 2.00e-02 2.50e+03 6.86e-02 1.41e+02 pdb=" CG PHE A 164 " 0.102 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " -0.082 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.088 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " -0.110 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.029 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.076 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.012 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.056 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.063 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " 0.061 2.00e-02 2.50e+03 5.39e-02 8.71e+01 pdb=" CG TYR A 139 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " -0.051 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " -0.025 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " 0.064 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " 0.081 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " -0.018 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " -0.070 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " -0.071 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.028 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " -0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 45 " 0.090 2.00e-02 2.50e+03 7.53e-02 8.51e+01 pdb=" CD GLN A 45 " -0.116 2.00e-02 2.50e+03 pdb=" OE1 GLN A 45 " -0.003 2.00e-02 2.50e+03 pdb=" NE2 GLN A 45 " 0.016 2.00e-02 2.50e+03 pdb="HE21 GLN A 45 " -0.072 2.00e-02 2.50e+03 pdb="HE22 GLN A 45 " 0.084 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.31: 1007 2.31 - 2.88: 7997 2.88 - 3.46: 10546 3.46 - 4.03: 15328 4.03 - 4.60: 21693 Nonbonded interactions: 56571 Sorted by model distance: nonbonded pdb=" H GLY A 120 " pdb=" O HIS A 138 " model vdw 1.741 2.450 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.743 2.100 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.788 2.450 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.803 2.450 nonbonded pdb="HH21 ARG A 145 " pdb=" OE2 GLU A 163 " model vdw 1.811 2.450 ... (remaining 56566 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 6 Type Number sf(0) Gaussians S 10 15.96 2 O1- 2 8.97 2 O 551 7.97 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_7848743_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1596 occupancy sum: 1438.50 (% of total atoms 46.85) Rotatable: count: 507 occupancy sum: 483.00 (% of total atoms 15.73) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.00 - 49.25 A, n_refl.=5182 (all), 4.86 % free)-------------| | | | r_work= 0.3627 r_free= 0.2064 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.467581 | | target function (ml) not normalized (work): 22025.174370 | | target function (ml) not normalized (free): 1155.338385 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3814 0.2235 4.8477 4.9073| | 2: 3.78 - 3.00 1.00 2430 110 0.3399 0.1776 4.0765 4.1682| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 48.80 0.83 0.13 6601.89| | 2: 3.78 - 3.00 2430 110 0.94 11.39 1.48 0.26 453.45| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 389.73 max = 12070.97 mean = 3571.32| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 89.99 mean = 30.36| |phase err.(test): min = 0.00 max = 89.98 mean = 33.40| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.082 0.259 1557 Z= 5.513 Angle : 5.384 15.993 2118 Z= 3.813 Chirality : 0.384 1.148 243 Planarity : 0.032 0.100 284 Dihedral : 13.568 80.246 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.86 % Allowed : 2.48 % Favored : 95.65 % Cbeta Deviations : 31.35 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.49), residues: 224 helix: -2.99 (0.35), residues: 108 sheet: -0.53 (0.99), residues: 30 loop : -0.40 (0.61), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.090 0.021 ARG A 27 TYR 0.071 0.033 TYR A 141 PHE 0.121 0.046 PHE A 164 HIS 0.054 0.030 HIS A 138 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 1785 0 Protein: 8.85 115.78 16.79 3.90 1519 0 Water: 11.36 119.30 38.03 N/A 258 0 Other: 19.04 26.29 21.71 N/A 8 0 Chain A: 8.85 119.30 19.89 N/A 1785 0 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 3.00 - 49.25 A, n_refl.=5182 (all), 4.86 % free)-------------| | | | r_work= 0.3627 r_free= 0.2064 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.467581 | | target function (ml) not normalized (work): 22025.174370 | | target function (ml) not normalized (free): 1155.338385 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3584 0.3659 0.2204 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3584 0.3659 0.2204 n_refl.: 5182 remove outliers: r(all,work,free)=0.2532 0.2554 0.2204 n_refl.: 5178 overall B=-2.42 to atoms: r(all,work,free)=0.2440 0.2459 0.2166 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1560 0.1554 0.1679 n_refl.: 5178 remove outliers: r(all,work,free)=0.1558 0.1551 0.1679 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 0.4005 445.048 409.637 0.628 1.069 0.398 11.894-9.307 99.02 97 4 0.1890 714.469 693.302 0.895 1.065 0.382 9.237-7.194 100.00 213 7 0.2146 584.294 576.098 0.934 1.058 0.374 7.162-5.571 100.00 427 22 0.2312 438.442 424.028 0.901 1.046 0.287 5.546-4.326 100.00 867 58 0.1394 601.918 595.518 0.950 1.025 0.246 4.315-3.360 100.00 1859 96 0.1287 572.431 566.287 1.023 0.990 0.188 3.356-3.002 100.00 1373 60 0.1595 440.910 433.320 1.038 0.955 0.073 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9170 b_overall=-4.2158 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1551 r_free=0.1679 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A A 97 ASN A Total number of N/Q/H flips: 2 r_work=0.1559 r_free=0.1682 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 19.436861 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.945286 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 0.1163 0.1770 0.0607 0.010 1.0 2.9 0.5 0.0 0 9.718 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.63 17.70 6.07 3.013 16.439 1.945 0.018 10.21 17.64 7.43 5.028 16.636 1.945 0.014 Individual atomic B min max mean iso aniso Overall: 1.91 111.89 17.84 5.41 1785 0 Protein: 1.91 111.89 15.15 5.41 1519 0 Water: 4.44 111.88 33.46 N/A 258 0 Other: 17.31 36.61 24.44 N/A 8 0 Chain A: 1.91 111.89 17.84 N/A 1785 0 Histogram: Values Number of atoms 1.91 - 12.91 863 12.91 - 23.91 524 23.91 - 34.90 192 34.90 - 45.90 113 45.90 - 56.90 59 56.90 - 67.90 17 67.90 - 78.89 8 78.89 - 89.89 5 89.89 - 100.89 1 100.89 - 111.89 3 =========================== Idealize ADP of riding H ========================== r_work=0.1021 r_free=0.1764 r_work=0.1015 r_free=0.1769 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1015 r_free = 0.1769 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 = 0.1757 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.27 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= 0.1006 r_free= 0.1757 coordinate error (max.-lik. estimate): 0.31 A | | | | normalized target function (ls_wunit_k1) (work): 0.013783 | | target function (ls_wunit_k1) not normalized (work): 67.879457 | | target function (ls_wunit_k1) not normalized (free): 9.955193 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1044 0.1006 0.1757 n_refl.: 5177 re-set all scales: r(all,work,free)=0.2121 0.2122 0.2221 n_refl.: 5177 remove outliers: r(all,work,free)=0.2121 0.2122 0.2221 n_refl.: 5177 overall B=-1.06 to atoms: r(all,work,free)=0.2075 0.2074 0.2209 n_refl.: 5177 bulk-solvent and scaling: r(all,work,free)=0.1047 0.1010 0.1759 n_refl.: 5177 remove outliers: r(all,work,free)=0.1045 0.1007 0.1759 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 0.3410 311.775 297.101 0.658 1.019 0.370 11.894-9.307 99.02 97 4 0.1529 504.825 497.934 0.978 1.020 0.366 9.237-7.194 100.00 213 7 0.1650 412.846 412.521 1.016 1.018 0.341 7.162-5.571 100.00 427 22 0.1614 309.791 306.557 0.977 1.014 0.295 5.546-4.326 100.00 867 58 0.0902 425.299 422.603 1.000 1.008 0.233 4.315-3.360 100.00 1859 96 0.0758 404.464 404.361 1.052 0.997 0.192 3.356-3.002 100.00 1373 60 0.1003 311.535 309.947 1.031 0.986 0.062 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9552 b_overall=-3.7903 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1007 r_free=0.1759 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN A Total number of N/Q/H flips: 1 r_work=0.1007 r_free=0.1761 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1007 r_free=0.1761 | n_water=258 | time (s): 0.670 (total time: 0.670) Filter (dist) r_work=0.1030 r_free=0.1738 | n_water=250 | time (s): 21.460 (total time: 22.130) Filter (q & B) r_work=0.1031 r_free=0.1740 | n_water=247 | time (s): 1.500 (total time: 23.630) Compute maps r_work=0.1031 r_free=0.1740 | n_water=247 | time (s): 0.630 (total time: 24.260) Filter (map) r_work=0.1297 r_free=0.1856 | n_water=151 | time (s): 1.800 (total time: 26.060) Find peaks r_work=0.1297 r_free=0.1856 | n_water=151 | time (s): 0.570 (total time: 26.630) Add new water r_work=0.1669 r_free=0.2127 | n_water=240 | time (s): 1.860 (total time: 28.490) Refine new water occ: r_work=0.1150 r_free=0.1644 adp: r_work=0.1124 r_free=0.1665 occ: r_work=0.1121 r_free=0.1640 adp: r_work=0.1107 r_free=0.1653 occ: r_work=0.1107 r_free=0.1642 adp: r_work=0.1103 r_free=0.1644 ADP+occupancy (water only), MIN, final r_work=0.1103 r_free=0.1644 r_work=0.1103 r_free=0.1644 | n_water=240 | time (s): 5.120 (total time: 33.610) Filter (q & B) r_work=0.1104 r_free=0.1650 | n_water=238 | time (s): 1.330 (total time: 34.940) Filter (dist only) r_work=0.1110 r_free=0.1651 | n_water=235 | time (s): 18.040 (total time: 52.980) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.384240 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.479678 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 0.1740 0.0737 0.009 1.0 4.8 0.5 0.6 0 11.692 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.04 17.40 7.37 4.768 17.236 2.480 0.014 9.45 17.50 8.05 5.311 17.538 2.480 0.012 Individual atomic B min max mean iso aniso Overall: 0.00 106.58 16.85 6.21 1762 0 Protein: 1.01 106.58 15.14 6.19 1519 0 Water: 0.00 63.10 27.56 N/A 235 0 Other: 16.93 38.95 27.65 N/A 8 0 Chain A: 0.00 106.58 15.90 N/A 1676 0 Chain S: 0.81 59.68 35.40 N/A 86 0 Histogram: Values Number of atoms 0.00 - 10.66 670 10.66 - 21.32 664 21.32 - 31.98 218 31.98 - 42.63 126 42.63 - 53.29 39 53.29 - 63.95 30 63.95 - 74.61 8 74.61 - 85.27 2 85.27 - 95.93 3 95.93 - 106.58 2 =========================== Idealize ADP of riding H ========================== r_work=0.0945 r_free=0.1750 r_work=0.0943 r_free=0.1748 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0943 r_free = 0.1748 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0940 r_free = 0.1733 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.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.0940 r_free= 0.1733 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ls_wunit_k1) (work): 0.012001 | | target function (ls_wunit_k1) not normalized (work): 59.094925 | | target function (ls_wunit_k1) not normalized (free): 8.989465 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0981 0.0940 0.1733 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2137 0.2145 0.2136 n_refl.: 5176 remove outliers: r(all,work,free)=0.2137 0.2145 0.2136 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2137 0.2145 0.2136 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0979 0.0938 0.1732 n_refl.: 5176 remove outliers: r(all,work,free)=0.0977 0.0937 0.1732 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 0.3264 313.812 292.981 0.648 1.012 0.360 11.894-9.307 99.02 97 4 0.1486 504.825 500.318 0.983 1.014 0.350 9.237-7.194 100.00 213 7 0.1450 412.846 412.201 1.016 1.013 0.340 7.162-5.571 100.00 427 22 0.1416 309.791 307.801 0.995 1.010 0.300 5.546-4.326 100.00 867 58 0.0795 425.299 422.927 1.009 1.006 0.240 4.315-3.360 100.00 1859 96 0.0720 404.464 404.436 1.063 0.999 0.199 3.356-3.002 100.00 1373 60 0.0970 311.535 310.537 1.041 0.992 0.090 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9553 b_overall=-4.4489 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0937 r_free=0.1732 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0937 r_free=0.1732 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0937 r_free=0.1732 | n_water=235 | time (s): 0.470 (total time: 0.470) Filter (dist) r_work=0.0950 r_free=0.1733 | n_water=231 | time (s): 19.030 (total time: 19.500) Filter (q & B) r_work=0.0988 r_free=0.1762 | n_water=229 | time (s): 1.510 (total time: 21.010) Compute maps r_work=0.0988 r_free=0.1762 | n_water=229 | time (s): 0.490 (total time: 21.500) Filter (map) r_work=0.1241 r_free=0.1823 | n_water=155 | time (s): 1.610 (total time: 23.110) Find peaks r_work=0.1241 r_free=0.1823 | n_water=155 | time (s): 0.510 (total time: 23.620) Add new water r_work=0.1615 r_free=0.2215 | n_water=240 | time (s): 1.810 (total time: 25.430) Refine new water occ: r_work=0.1048 r_free=0.1718 adp: r_work=0.1046 r_free=0.1737 occ: r_work=0.1034 r_free=0.1713 adp: r_work=0.1035 r_free=0.1722 occ: r_work=0.1024 r_free=0.1705 adp: r_work=0.1023 r_free=0.1714 ADP+occupancy (water only), MIN, final r_work=0.1023 r_free=0.1714 r_work=0.1023 r_free=0.1714 | n_water=240 | time (s): 8.840 (total time: 34.270) Filter (q & B) r_work=0.1023 r_free=0.1714 | n_water=240 | time (s): 0.970 (total time: 35.240) Filter (dist only) r_work=0.1032 r_free=0.1727 | n_water=239 | time (s): 19.110 (total time: 54.350) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.098502 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.200398 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 0.0939 0.1774 0.0835 0.011 1.1 5.4 0.5 0.0 0 0.549 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.39 17.74 8.35 5.249 17.965 0.200 5.115 8.93 18.17 9.24 7.028 17.970 0.200 5.017 Individual atomic B min max mean iso aniso Overall: 0.00 107.58 16.60 8.62 1766 0 Protein: 0.00 107.58 15.28 8.61 1519 0 Water: 0.00 58.10 24.51 N/A 239 0 Other: 21.12 44.65 30.93 N/A 8 0 Chain A: 0.00 107.58 15.99 N/A 1664 0 Chain S: 0.00 57.16 26.65 N/A 102 0 Histogram: Values Number of atoms 0.00 - 10.76 669 10.76 - 21.52 673 21.52 - 32.27 227 32.27 - 43.03 131 43.03 - 53.79 34 53.79 - 64.55 13 64.55 - 75.31 12 75.31 - 86.06 2 86.06 - 96.82 3 96.82 - 107.58 2 =========================== Idealize ADP of riding H ========================== r_work=0.0893 r_free=0.1817 r_work=0.0898 r_free=0.1828 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0898 r_free = 0.1828 target_work(ml) = 5.022 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0890 r_free = 0.1819 target_work(ml) = 5.016 | | occupancies: max = 1.00 min = 0.23 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= 0.0890 r_free= 0.1819 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 5.016075 | | target function (ml) not normalized (work): 24694.136435 | | target function (ml) not normalized (free): 1814.337728 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0937 0.0890 0.1819 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2058 0.2063 0.2101 n_refl.: 5175 remove outliers: r(all,work,free)=0.2058 0.2063 0.2101 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2058 0.2063 0.2101 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0930 0.0883 0.1816 n_refl.: 5175 remove outliers: r(all,work,free)=0.0930 0.0883 0.1816 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 0.3737 313.812 288.731 0.581 0.993 0.320 11.894-9.307 99.02 97 4 0.1913 504.825 489.948 0.949 0.997 0.320 9.237-7.194 100.00 213 7 0.1888 412.846 406.868 1.005 0.999 0.320 7.162-5.571 100.00 427 22 0.1824 309.791 301.067 0.985 1.000 0.290 5.546-4.326 100.00 867 58 0.0902 425.299 420.858 0.999 1.001 0.224 4.315-3.360 100.00 1859 96 0.0581 404.464 404.148 1.056 1.002 0.210 3.356-3.002 100.00 1373 60 0.0604 311.535 311.478 1.033 1.003 0.080 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-6.4268 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0883 r_free=0.1816 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0883 r_free=0.1816 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0883 r_free=0.1816 | n_water=239 | time (s): 0.460 (total time: 0.460) Filter (dist) r_work=0.0895 r_free=0.1800 | n_water=235 | time (s): 20.090 (total time: 20.550) Filter (q & B) r_work=0.0926 r_free=0.1804 | n_water=234 | time (s): 1.380 (total time: 21.930) Compute maps r_work=0.0926 r_free=0.1804 | n_water=234 | time (s): 0.510 (total time: 22.440) Filter (map) r_work=0.1225 r_free=0.1825 | n_water=161 | time (s): 1.600 (total time: 24.040) Find peaks r_work=0.1225 r_free=0.1825 | n_water=161 | time (s): 0.590 (total time: 24.630) Add new water r_work=0.1544 r_free=0.2130 | n_water=237 | time (s): 1.700 (total time: 26.330) Refine new water occ: r_work=0.0998 r_free=0.1774 adp: r_work=0.0994 r_free=0.1786 occ: r_work=0.0986 r_free=0.1777 adp: r_work=0.0985 r_free=0.1782 occ: r_work=0.0978 r_free=0.1772 adp: r_work=0.0977 r_free=0.1778 ADP+occupancy (water only), MIN, final r_work=0.0977 r_free=0.1778 r_work=0.0977 r_free=0.1778 | n_water=237 | time (s): 8.330 (total time: 34.660) Filter (q & B) r_work=0.0978 r_free=0.1776 | n_water=236 | time (s): 1.830 (total time: 36.490) Filter (dist only) r_work=0.0978 r_free=0.1776 | n_water=236 | time (s): 18.310 (total time: 54.800) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.058011 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.206771 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 0.0898 0.1825 0.0928 0.011 1.1 5.8 0.5 1.2 0 0.529 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 8.98 18.25 9.28 6.758 18.089 0.207 4.980 8.71 18.42 9.70 7.988 18.186 0.207 4.911 Individual atomic B min max mean iso aniso Overall: 0.00 107.87 16.84 10.38 1763 0 Protein: 0.00 107.87 15.67 10.36 1519 0 Water: 0.00 55.29 23.86 N/A 236 0 Other: 17.04 50.20 31.95 N/A 8 0 Chain A: 0.00 107.87 16.26 N/A 1655 0 Chain S: 1.75 50.42 25.69 N/A 108 0 Histogram: Values Number of atoms 0.00 - 10.79 676 10.79 - 21.57 632 21.57 - 32.36 248 32.36 - 43.15 133 43.15 - 53.94 43 53.94 - 64.72 9 64.72 - 75.51 12 75.51 - 86.30 6 86.30 - 97.09 2 97.09 - 107.87 2 =========================== Idealize ADP of riding H ========================== r_work=0.0871 r_free=0.1842 r_work=0.0874 r_free=0.1842 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0874 r_free = 0.1842 target_work(ml) = 4.916 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0865 r_free = 0.1826 target_work(ml) = 4.909 | | occupancies: max = 1.00 min = 0.24 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= 0.0865 r_free= 0.1826 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ml) (work): 4.908515 | | target function (ml) not normalized (work): 24164.620996 | | target function (ml) not normalized (free): 2157.149280 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0914 0.0865 0.1826 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2090 0.2089 0.2257 n_refl.: 5175 remove outliers: r(all,work,free)=0.2090 0.2089 0.2257 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2090 0.2089 0.2257 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0914 0.0865 0.1834 n_refl.: 5175 remove outliers: r(all,work,free)=0.0914 0.0865 0.1834 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 0.3897 313.812 284.249 0.573 0.988 0.317 11.894-9.307 99.02 97 4 0.1972 504.825 489.051 0.955 0.993 0.315 9.237-7.194 100.00 213 7 0.2067 412.846 403.686 1.009 0.996 0.304 7.162-5.571 100.00 427 22 0.2049 309.791 298.880 0.996 0.997 0.290 5.546-4.326 100.00 867 58 0.0948 425.299 420.379 1.011 0.999 0.215 4.315-3.360 100.00 1859 96 0.0538 404.464 404.054 1.074 1.002 0.210 3.356-3.002 100.00 1373 60 0.0437 311.535 311.898 1.052 1.005 0.080 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.2499 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0865 r_free=0.1834 After: r_work=0.0868 r_free=0.1833 ================================== NQH flips ================================== r_work=0.0868 r_free=0.1833 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 ASN Total number of N/Q/H flips: 1 r_work=0.0878 r_free=0.1835 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0878 r_free=0.1835 | n_water=236 | time (s): 0.510 (total time: 0.510) Filter (dist) r_work=0.0896 r_free=0.1833 | n_water=231 | time (s): 19.820 (total time: 20.330) Filter (q & B) r_work=0.1009 r_free=0.1878 | n_water=228 | time (s): 1.250 (total time: 21.580) Compute maps r_work=0.1009 r_free=0.1878 | n_water=228 | time (s): 0.510 (total time: 22.090) Filter (map) r_work=0.1285 r_free=0.1824 | n_water=154 | time (s): 1.700 (total time: 23.790) Find peaks r_work=0.1285 r_free=0.1824 | n_water=154 | time (s): 0.600 (total time: 24.390) Add new water r_work=0.1552 r_free=0.2069 | n_water=222 | time (s): 1.830 (total time: 26.220) Refine new water occ: r_work=0.1016 r_free=0.1824 adp: r_work=0.1010 r_free=0.1833 occ: r_work=0.1002 r_free=0.1818 adp: r_work=0.1001 r_free=0.1826 occ: r_work=0.0994 r_free=0.1812 adp: r_work=0.0993 r_free=0.1819 ADP+occupancy (water only), MIN, final r_work=0.0993 r_free=0.1819 r_work=0.0993 r_free=0.1819 | n_water=222 | time (s): 8.420 (total time: 34.640) Filter (q & B) r_work=0.0994 r_free=0.1824 | n_water=219 | time (s): 1.550 (total time: 36.190) Filter (dist only) r_work=0.0999 r_free=0.1829 | n_water=218 | time (s): 17.210 (total time: 53.400) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.031183 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.215039 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 0.0931 0.1877 0.0946 0.011 1.1 9.6 0.5 1.2 0 0.516 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.31 18.77 9.46 7.926 18.368 0.215 5.021 9.03 19.13 10.10 8.844 18.440 0.215 4.952 Individual atomic B min max mean iso aniso Overall: 0.00 108.45 16.96 11.54 1745 0 Protein: 0.00 108.45 15.98 11.51 1519 0 Water: 0.82 56.61 23.21 N/A 218 0 Other: 12.04 49.93 31.47 N/A 8 0 Chain A: 0.00 108.45 16.47 N/A 1640 0 Chain S: 0.90 55.00 24.62 N/A 105 0 Histogram: Values Number of atoms 0.00 - 10.84 661 10.84 - 21.69 620 21.69 - 32.53 268 32.53 - 43.38 116 43.38 - 54.22 43 54.22 - 65.07 15 65.07 - 75.91 12 75.91 - 86.76 4 86.76 - 97.60 4 97.60 - 108.45 2 =========================== Idealize ADP of riding H ========================== r_work=0.0903 r_free=0.1913 r_work=0.0906 r_free=0.1915 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0906 r_free = 0.1915 target_work(ml) = 4.958 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0898 r_free = 0.1912 target_work(ml) = 4.952 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0898 r_free= 0.1912 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ml) (work): 4.951519 | | target function (ml) not normalized (work): 24376.327911 | | target function (ml) not normalized (free): 2148.464881 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1261 0.1873 5.4988 6.0971| | 2: 3.78 - 3.00 1.00 2430 110 0.0456 0.1977 4.3901 11.661| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 0.92 11.98 1.00 0.94 12060.43| | 2: 3.78 - 3.00 2430 110 0.99 2.03 1.00 0.96 954.54| |alpha: min = 0.94 max = 0.97 mean = 0.95| |beta: min = 625.30 max = 20093.59 mean = 6578.55| |figures of merit: min = 0.00 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.90 mean = 7.07| |phase err.(test): min = 0.00 max = 81.94 mean = 7.17| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0950 0.0898 0.1912 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2157 0.2157 0.2319 n_refl.: 5175 remove outliers: r(all,work,free)=0.2157 0.2157 0.2319 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2157 0.2157 0.2319 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0947 0.0895 0.1910 n_refl.: 5175 remove outliers: r(all,work,free)=0.0947 0.0895 0.1910 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 0.3827 313.812 287.167 0.601 0.987 0.328 11.894-9.307 99.02 97 4 0.1836 504.825 491.775 0.968 0.994 0.327 9.237-7.194 100.00 213 7 0.2071 412.846 404.446 1.003 0.997 0.300 7.162-5.571 100.00 427 22 0.2086 309.791 299.410 0.991 0.998 0.290 5.546-4.326 100.00 867 58 0.1026 425.299 420.484 1.009 1.000 0.230 4.315-3.360 100.00 1859 96 0.0575 404.464 404.307 1.084 1.002 0.230 3.356-3.002 100.00 1373 60 0.0444 311.535 311.505 1.063 1.004 0.080 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.6560 ================= 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 : 0.3627 0.2064 0.082 5.384 8.8 119.3 19.9 258 0.000 1_bss: 0.1551 0.1679 0.082 5.384 6.4 116.9 17.5 258 0.000 1_settarget: 0.1551 0.1679 0.082 5.384 6.4 116.9 17.5 258 0.000 1_nqh: 0.1559 0.1682 0.082 5.384 6.4 116.9 17.5 258 0.007 1_weight: 0.1559 0.1682 0.082 5.384 6.4 116.9 17.5 258 0.007 1_xyzrec: 0.1163 0.1770 0.010 0.979 6.4 116.9 17.5 258 0.208 1_adp: 0.1021 0.1764 0.010 0.979 1.9 111.9 17.8 258 0.208 1_regHadp: 0.1015 0.1769 0.010 0.979 1.9 111.9 17.8 258 0.208 1_occ: 0.1006 0.1757 0.010 0.979 1.9 111.9 17.8 258 0.208 2_bss: 0.1007 0.1759 0.010 0.979 0.8 110.8 16.8 258 0.208 2_settarget: 0.1007 0.1759 0.010 0.979 0.8 110.8 16.8 258 0.208 2_updatecdl: 0.1007 0.1759 0.010 1.013 0.8 110.8 16.8 258 0.208 2_nqh: 0.1007 0.1761 0.010 1.013 0.8 110.8 16.8 258 0.205 2_sol: 0.1110 0.1651 0.010 1.013 0.8 110.8 16.3 235 n/a 2_weight: 0.1110 0.1651 0.010 1.013 0.8 110.8 16.3 235 n/a 2_xyzrec: 0.1004 0.1740 0.009 0.996 0.8 110.8 16.3 235 n/a 2_adp: 0.0945 0.1750 0.009 0.996 0.0 106.6 16.9 235 n/a 2_regHadp: 0.0943 0.1748 0.009 0.996 0.0 106.6 16.9 235 n/a 2_occ: 0.0940 0.1733 0.009 0.996 0.0 106.6 16.9 235 n/a 3_bss: 0.0937 0.1732 0.009 0.996 0.0 106.6 16.9 235 n/a 3_settarget: 0.0937 0.1732 0.009 0.996 0.0 106.6 16.9 235 n/a 3_updatecdl: 0.0937 0.1732 0.009 1.001 0.0 106.6 16.9 235 n/a 3_nqh: 0.0937 0.1732 0.009 1.001 0.0 106.6 16.9 235 n/a 3_sol: 0.1032 0.1727 0.009 1.001 1.0 106.6 16.6 239 n/a 3_weight: 0.1032 0.1727 0.009 1.001 1.0 106.6 16.6 239 n/a 3_xyzrec: 0.0939 0.1774 0.011 1.072 1.0 106.6 16.6 239 n/a 3_adp: 0.0893 0.1817 0.011 1.072 0.0 107.6 16.6 239 n/a 3_regHadp: 0.0898 0.1828 0.011 1.072 0.0 107.6 16.6 239 n/a 3_occ: 0.0890 0.1819 0.011 1.072 0.0 107.6 16.6 239 n/a 4_bss: 0.0883 0.1816 0.011 1.072 0.0 107.6 16.6 239 n/a 4_settarget: 0.0883 0.1816 0.011 1.072 0.0 107.6 16.6 239 n/a 4_updatecdl: 0.0883 0.1816 0.011 1.082 0.0 107.6 16.6 239 n/a 4_nqh: 0.0883 0.1816 0.011 1.082 0.0 107.6 16.6 239 n/a 4_sol: 0.0978 0.1776 0.011 1.082 0.0 107.6 16.7 236 n/a 4_weight: 0.0978 0.1776 0.011 1.082 0.0 107.6 16.7 236 n/a 4_xyzrec: 0.0898 0.1825 0.011 1.053 0.0 107.6 16.7 236 n/a 4_adp: 0.0871 0.1842 0.011 1.053 0.0 107.9 16.8 236 n/a 4_regHadp: 0.0874 0.1842 0.011 1.053 0.0 107.9 16.8 236 n/a 4_occ: 0.0865 0.1826 0.011 1.053 0.0 107.9 16.8 236 n/a 5_bss: 0.0865 0.1834 0.011 1.053 0.0 107.9 16.8 236 n/a 5_settarget: 0.0865 0.1834 0.011 1.053 0.0 107.9 16.8 236 n/a 5_updatecdl: 0.0865 0.1834 0.012 1.058 0.0 107.9 16.8 236 n/a 5_setrh: 0.0868 0.1833 0.012 1.058 0.0 107.9 16.8 236 n/a 5_nqh: 0.0878 0.1835 0.012 1.058 0.0 107.9 16.8 236 n/a 5_sol: 0.0999 0.1829 0.012 1.058 0.0 107.9 16.8 218 n/a 5_weight: 0.0999 0.1829 0.012 1.058 0.0 107.9 16.8 218 n/a 5_xyzrec: 0.0931 0.1877 0.011 1.118 0.0 107.9 16.8 218 n/a 5_adp: 0.0903 0.1913 0.011 1.118 0.0 108.4 17.0 218 n/a 5_regHadp: 0.0906 0.1915 0.011 1.118 0.0 108.4 17.0 218 n/a 5_occ: 0.0898 0.1912 0.011 1.118 0.0 108.4 17.0 218 n/a end: 0.0895 0.1910 0.011 1.118 0.0 108.4 17.0 218 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_7848743_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_7848743_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.7300 Refinement macro-cycles (run) : 482.1600 Write final files (write_after_run_outputs) : 10.1200 Total : 496.0100 Total CPU time: 8.67 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:19:01 PST -0800 (1735492741.11 s) Start R-work = 0.1551, R-free = 0.1679 Final R-work = 0.0895, R-free = 0.1910 =============================================================================== Job complete usr+sys time: 527.59 seconds wall clock time: 9 minutes 9.69 seconds (549.69 seconds total)