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_6218374.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_6218374.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6218374.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: 2.03, per 1000 atoms: 0.60 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: 0.30 Conformation dependent library (CDL) restraints added in 160.8 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.91: 534 0.91 - 1.17: 1108 1.17 - 1.42: 643 1.42 - 1.68: 837 1.68 - 1.94: 31 Bond restraints: 3153 Sorted by residual: bond pdb=" N LEU A 166 " pdb=" CA LEU A 166 " ideal model delta sigma weight residual 1.459 1.686 -0.227 1.25e-02 6.40e+03 3.31e+02 bond pdb=" C PRO A 73 " pdb=" O PRO A 73 " ideal model delta sigma weight residual 1.232 0.999 0.232 1.31e-02 5.83e+03 3.14e+02 bond pdb=" C GLY A 159 " pdb=" O GLY A 159 " ideal model delta sigma weight residual 1.236 1.049 0.187 1.08e-02 8.57e+03 2.99e+02 bond pdb=" CA VAL A 8 " pdb=" CB VAL A 8 " ideal model delta sigma weight residual 1.537 1.745 -0.208 1.26e-02 6.30e+03 2.72e+02 bond pdb=" N ALA A 6 " pdb=" CA ALA A 6 " ideal model delta sigma weight residual 1.455 1.657 -0.202 1.25e-02 6.40e+03 2.60e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.60: 3130 4.60 - 9.21: 1832 9.21 - 13.81: 657 13.81 - 18.41: 147 18.41 - 23.02: 11 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O GLY A 157 " pdb=" C GLY A 157 " pdb=" N PRO A 158 " ideal model delta sigma weight residual 121.77 106.15 15.62 1.00e+00 1.00e+00 2.44e+02 angle pdb=" O THR A 125 " pdb=" C THR A 125 " pdb=" N HIS A 126 " ideal model delta sigma weight residual 122.92 106.88 16.04 1.17e+00 7.31e-01 1.88e+02 angle pdb=" CA GLY A 40 " pdb=" C GLY A 40 " pdb=" N BLYS A 41 " ideal model delta sigma weight residual 114.75 128.25 -13.50 9.90e-01 1.02e+00 1.86e+02 angle pdb=" O ALA A 167 " pdb=" C ALA A 167 " pdb=" N ILE A 168 " ideal model delta sigma weight residual 122.15 137.42 -15.27 1.14e+00 7.69e-01 1.79e+02 angle pdb=" CA GLY A 100 " pdb=" C GLY A 100 " pdb=" O GLY A 100 " ideal model delta sigma weight residual 121.23 135.40 -14.17 1.08e+00 8.57e-01 1.72e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.69: 1294 16.69 - 33.37: 129 33.37 - 50.05: 40 50.05 - 66.73: 15 66.73 - 83.41: 3 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C GLU A 116 " pdb=" N GLU A 116 " pdb=" CA GLU A 116 " pdb=" CB GLU A 116 " ideal model delta harmonic sigma weight residual -122.60 -141.52 18.92 0 2.50e+00 1.60e-01 5.73e+01 dihedral pdb=" N GLN A 45 " pdb=" C GLN A 45 " pdb=" CA GLN A 45 " pdb=" CB GLN A 45 " ideal model delta harmonic sigma weight residual 122.80 105.07 17.73 0 2.50e+00 1.60e-01 5.03e+01 dihedral pdb=" N THR A 125 " pdb=" C THR A 125 " pdb=" CA THR A 125 " pdb=" CB THR A 125 " ideal model delta harmonic sigma weight residual 123.40 106.19 17.21 0 2.50e+00 1.60e-01 4.74e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.270: 112 0.270 - 0.538: 96 0.538 - 0.806: 26 0.806 - 1.074: 7 1.074 - 1.342: 2 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA VAL A 8 " pdb=" N VAL A 8 " pdb=" C VAL A 8 " pdb=" CB VAL A 8 " both_signs ideal model delta sigma weight residual False 2.44 3.78 -1.34 2.00e-01 2.50e+01 4.50e+01 chirality pdb=" CG LEU A 172 " pdb=" CB LEU A 172 " pdb=" CD1 LEU A 172 " pdb=" CD2 LEU A 172 " both_signs ideal model delta sigma weight residual False -2.59 -1.45 -1.14 2.00e-01 2.50e+01 3.24e+01 chirality pdb=" CA GLU A 176 " pdb=" N GLU A 176 " pdb=" C GLU A 176 " pdb=" CB GLU A 176 " both_signs ideal model delta sigma weight residual False 2.51 3.55 -1.04 2.00e-01 2.50e+01 2.72e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " 0.037 2.00e-02 2.50e+03 6.00e-02 1.08e+02 pdb=" CG PHE A 164 " 0.091 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " -0.060 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.029 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " -0.030 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.092 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.000 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.059 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.109 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.057 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.019 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " 0.066 2.00e-02 2.50e+03 5.74e-02 9.88e+01 pdb=" CG PHE A 162 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " 0.024 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " -0.045 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " 0.120 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " -0.065 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " -0.021 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " -0.110 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " 0.013 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " -0.007 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " 0.065 2.00e-02 2.50e+03 4.96e-02 7.37e+01 pdb=" CG TYR A 139 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " -0.056 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " 0.089 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.066 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " 0.026 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " -0.003 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " -0.051 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " -0.026 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " -0.026 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " 0.055 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.31: 952 2.31 - 2.88: 8002 2.88 - 3.45: 10574 3.45 - 4.03: 15252 4.03 - 4.60: 21810 Nonbonded interactions: 56590 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.733 2.100 nonbonded pdb=" HE2 HIS A 126 " pdb=" O PRO A 184 " model vdw sym.op. 1.828 2.450 x-y,-y,-z-4/3 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.834 2.450 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.834 2.450 nonbonded pdb=" HD3 ARG A 28 " pdb="HH11 ARG A 28 " model vdw 1.837 2.270 ... (remaining 56585 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_6218374_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1596 occupancy sum: 1438.50 (% of total atoms 46.85) Rotatable: count: 507 occupancy sum: 483.00 (% of total atoms 15.73) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.00 - 49.25 A, n_refl.=5182 (all), 4.86 % free)-------------| | | | r_work= 0.3613 r_free= 0.2063 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.473470 | | target function (ml) not normalized (work): 22054.208630 | | target function (ml) not normalized (free): 1148.849205 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3780 0.2256 4.8525 4.9087| | 2: 3.78 - 3.00 1.00 2430 110 0.3410 0.1737 4.0835 4.1074| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 48.70 0.83 0.13 6599.01| | 2: 3.78 - 3.00 2430 110 0.93 11.47 1.48 0.26 455.19| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 388.93 max = 12055.91 mean = 3570.72| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 89.98 mean = 30.35| |phase err.(test): min = 0.00 max = 89.93 mean = 33.43| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.080 0.239 1557 Z= 5.325 Angle : 5.304 16.901 2118 Z= 3.669 Chirality : 0.395 1.342 243 Planarity : 0.032 0.089 284 Dihedral : 13.779 83.411 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.54 % Allowed : 1.62 % Favored : 97.84 % Rotamer: Outliers : 1.24 % Allowed : 2.48 % Favored : 96.27 % Cbeta Deviations : 28.11 % 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: -2.32 (0.48), residues: 224 helix: -2.65 (0.40), residues: 103 sheet: 0.21 (0.88), residues: 28 loop : -0.45 (0.56), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.072 0.020 ARG A 48 TYR 0.089 0.035 TYR A 139 PHE 0.077 0.029 PHE A 162 HIS 0.060 0.028 HIS A 126 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 1785 0 Protein: 8.85 115.78 16.79 3.90 1519 0 Water: 11.36 119.30 38.03 N/A 258 0 Other: 19.04 26.29 21.71 N/A 8 0 Chain A: 8.85 119.30 19.89 N/A 1785 0 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 3.00 - 49.25 A, n_refl.=5182 (all), 4.86 % free)-------------| | | | r_work= 0.3613 r_free= 0.2063 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.473470 | | target function (ml) not normalized (work): 22054.208630 | | target function (ml) not normalized (free): 1148.849205 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3575 0.3649 0.2191 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3575 0.3649 0.2191 n_refl.: 5182 remove outliers: r(all,work,free)=0.2532 0.2554 0.2191 n_refl.: 5178 overall B=-2.85 to atoms: r(all,work,free)=0.2423 0.2441 0.2140 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1577 0.1574 0.1647 n_refl.: 5178 remove outliers: r(all,work,free)=0.1573 0.1569 0.1647 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 98.94 88 5 0.3830 449.831 411.481 0.674 1.057 0.401 11.894-9.307 99.02 97 4 0.1863 714.592 694.903 0.945 1.055 0.383 9.237-7.194 100.00 213 7 0.2217 584.394 576.849 0.979 1.049 0.343 7.162-5.571 100.00 427 22 0.2331 438.517 423.665 0.950 1.038 0.336 5.546-4.326 100.00 867 58 0.1403 602.021 594.792 0.978 1.021 0.221 4.315-3.360 100.00 1859 96 0.1319 572.529 566.008 1.055 0.991 0.200 3.356-3.002 100.00 1373 60 0.1601 440.986 433.063 1.059 0.961 0.097 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9555 b_overall=-3.6503 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1569 r_free=0.1647 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=0.1569 r_free=0.1648 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 19.242704 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.962243 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 0.1160 0.1770 0.0610 0.010 1.0 2.6 0.5 0.0 0 9.621 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.60 17.70 6.10 3.013 16.004 1.962 0.018 10.21 17.62 7.40 4.856 16.164 1.962 0.014 Individual atomic B min max mean iso aniso Overall: 2.20 111.57 17.33 5.27 1785 0 Protein: 2.20 111.57 14.62 5.26 1519 0 Water: 4.01 111.44 33.07 N/A 258 0 Other: 15.98 36.99 24.23 N/A 8 0 Chain A: 2.20 111.57 17.33 N/A 1785 0 Histogram: Values Number of atoms 2.20 - 13.14 914 13.14 - 24.08 489 24.08 - 35.01 192 35.01 - 45.95 102 45.95 - 56.89 57 56.89 - 67.82 14 67.82 - 78.76 8 78.76 - 89.70 5 89.70 - 100.63 1 100.63 - 111.57 3 =========================== Idealize ADP of riding H ========================== r_work=0.1021 r_free=0.1762 r_work=0.1016 r_free=0.1768 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1016 r_free = 0.1768 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 = 0.1018 r_free = 0.1767 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.1018 r_free= 0.1767 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ls_wunit_k1) (work): 0.014039 | | target function (ls_wunit_k1) not normalized (work): 69.128566 | | target function (ls_wunit_k1) not normalized (free): 10.229270 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1057 0.1018 0.1767 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2096 0.2095 0.2217 n_refl.: 5176 remove outliers: r(all,work,free)=0.2096 0.2095 0.2217 n_refl.: 5176 overall B=-0.97 to atoms: r(all,work,free)=0.2056 0.2053 0.2206 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.1058 0.1020 0.1762 n_refl.: 5176 remove outliers: r(all,work,free)=0.1058 0.1020 0.1762 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 0.3295 330.508 313.431 0.668 1.013 0.376 11.894-9.307 99.02 97 4 0.1511 525.039 517.248 0.979 1.014 0.351 9.237-7.194 100.00 213 7 0.1694 429.378 429.271 1.019 1.013 0.321 7.162-5.571 100.00 427 22 0.1641 322.196 318.824 0.983 1.010 0.312 5.546-4.326 100.00 867 58 0.0923 442.329 439.162 0.992 1.005 0.206 4.315-3.360 100.00 1859 96 0.0766 420.660 420.624 1.046 0.997 0.202 3.356-3.002 100.00 1373 60 0.1012 324.010 322.400 1.019 0.989 0.092 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-3.4661 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1020 r_free=0.1762 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1020 r_free=0.1762 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1020 r_free=0.1762 | n_water=258 | time (s): 0.500 (total time: 0.500) Filter (dist) r_work=0.1059 r_free=0.1753 | n_water=245 | time (s): 20.810 (total time: 21.310) Filter (q & B) r_work=0.1059 r_free=0.1759 | n_water=242 | time (s): 1.870 (total time: 23.180) Compute maps r_work=0.1059 r_free=0.1759 | n_water=242 | time (s): 0.660 (total time: 23.840) Filter (map) r_work=0.1372 r_free=0.1851 | n_water=140 | time (s): 1.720 (total time: 25.560) Find peaks r_work=0.1372 r_free=0.1851 | n_water=140 | time (s): 0.510 (total time: 26.070) Add new water r_work=0.1724 r_free=0.2183 | n_water=232 | time (s): 1.830 (total time: 27.900) Refine new water occ: r_work=0.1156 r_free=0.1681 adp: r_work=0.1134 r_free=0.1694 occ: r_work=0.1129 r_free=0.1662 adp: r_work=0.1118 r_free=0.1675 occ: r_work=0.1118 r_free=0.1660 adp: r_work=0.1114 r_free=0.1665 ADP+occupancy (water only), MIN, final r_work=0.1114 r_free=0.1665 r_work=0.1114 r_free=0.1665 | n_water=232 | time (s): 4.750 (total time: 32.650) Filter (q & B) r_work=0.1114 r_free=0.1665 | n_water=232 | time (s): 1.000 (total time: 33.650) Filter (dist only) r_work=0.1126 r_free=0.1649 | n_water=227 | time (s): 18.600 (total time: 52.250) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.760161 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.880301 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 0.1022 0.1785 0.0763 0.009 1.0 4.5 0.5 0.6 0 11.380 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.22 17.85 7.63 4.644 16.672 2.880 0.014 9.51 18.06 8.55 5.607 17.133 2.880 0.013 Individual atomic B min max mean iso aniso Overall: 0.00 107.99 16.61 6.69 1754 0 Protein: 0.00 107.99 15.08 6.68 1519 0 Water: 0.00 62.80 26.71 N/A 227 0 Other: 12.46 31.03 21.32 N/A 8 0 Chain A: 0.00 107.99 15.74 N/A 1663 0 Chain S: 2.45 58.87 32.49 N/A 91 0 Histogram: Values Number of atoms 0.00 - 10.80 695 10.80 - 21.60 659 21.60 - 32.40 199 32.40 - 43.20 120 43.20 - 54.00 39 54.00 - 64.80 28 64.80 - 75.60 8 75.60 - 86.39 3 86.39 - 97.19 1 97.19 - 107.99 2 =========================== Idealize ADP of riding H ========================== r_work=0.0951 r_free=0.1806 r_work=0.0947 r_free=0.1808 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0947 r_free = 0.1808 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0943 r_free = 0.1792 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= 0.0943 r_free= 0.1792 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ls_wunit_k1) (work): 0.012121 | | target function (ls_wunit_k1) not normalized (work): 59.684990 | | target function (ls_wunit_k1) not normalized (free): 9.618967 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0987 0.0943 0.1792 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2131 0.2134 0.2198 n_refl.: 5176 remove outliers: r(all,work,free)=0.2131 0.2134 0.2198 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2131 0.2134 0.2198 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0989 0.0945 0.1795 n_refl.: 5176 remove outliers: r(all,work,free)=0.0986 0.0943 0.1795 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 0.3268 327.725 313.446 0.659 1.011 0.358 11.894-9.307 99.02 97 4 0.1432 525.039 521.127 0.979 1.013 0.340 9.237-7.194 100.00 213 7 0.1447 429.378 429.342 1.017 1.012 0.314 7.162-5.571 100.00 427 22 0.1408 322.196 320.287 0.996 1.010 0.300 5.546-4.326 100.00 867 58 0.0798 442.329 440.015 1.003 1.005 0.220 4.315-3.360 100.00 1859 96 0.0737 420.660 420.387 1.060 0.998 0.210 3.356-3.002 100.00 1373 60 0.0974 324.010 322.467 1.036 0.991 0.096 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9553 b_overall=-4.2074 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0943 r_free=0.1795 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN B Total number of N/Q/H flips: 2 r_work=0.0946 r_free=0.1793 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0946 r_free=0.1793 | n_water=227 | time (s): 0.520 (total time: 0.520) Filter (dist) r_work=0.0976 r_free=0.1801 | n_water=220 | time (s): 18.990 (total time: 19.510) Filter (q & B) r_work=0.1031 r_free=0.1792 | n_water=218 | time (s): 1.650 (total time: 21.160) Compute maps r_work=0.1031 r_free=0.1792 | n_water=218 | time (s): 0.490 (total time: 21.650) Filter (map) r_work=0.1286 r_free=0.1810 | n_water=148 | time (s): 1.380 (total time: 23.030) Find peaks r_work=0.1286 r_free=0.1810 | n_water=148 | time (s): 0.400 (total time: 23.430) Add new water r_work=0.1667 r_free=0.2110 | n_water=234 | time (s): 1.390 (total time: 24.820) Refine new water occ: r_work=0.1089 r_free=0.1695 adp: r_work=0.1083 r_free=0.1715 occ: r_work=0.1074 r_free=0.1700 adp: r_work=0.1072 r_free=0.1707 occ: r_work=0.1064 r_free=0.1693 adp: r_work=0.1062 r_free=0.1699 ADP+occupancy (water only), MIN, final r_work=0.1062 r_free=0.1699 r_work=0.1062 r_free=0.1699 | n_water=234 | time (s): 8.130 (total time: 32.950) Filter (q & B) r_work=0.1062 r_free=0.1699 | n_water=234 | time (s): 0.790 (total time: 33.740) Filter (dist only) r_work=0.1076 r_free=0.1719 | n_water=231 | time (s): 16.580 (total time: 50.320) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.151488 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.188067 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 0.0968 0.1736 0.0768 0.011 1.1 4.2 0.5 0.6 0 0.576 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.68 17.36 7.68 5.546 17.839 0.188 5.183 9.19 17.12 7.93 7.113 17.792 0.188 5.088 Individual atomic B min max mean iso aniso Overall: 0.00 107.32 16.30 8.61 1758 0 Protein: 0.00 107.32 15.09 8.60 1519 0 Water: 0.00 57.80 24.08 N/A 231 0 Other: 7.98 35.45 21.21 N/A 8 0 Chain A: 0.00 107.32 15.67 N/A 1645 0 Chain S: 0.00 50.76 25.47 N/A 113 0 Histogram: Values Number of atoms 0.00 - 10.73 675 10.73 - 21.46 662 21.46 - 32.20 234 32.20 - 42.93 116 42.93 - 53.66 37 53.66 - 64.39 16 64.39 - 75.12 12 75.12 - 85.85 1 85.85 - 96.59 4 96.59 - 107.32 1 =========================== Idealize ADP of riding H ========================== r_work=0.0919 r_free=0.1712 r_work=0.0924 r_free=0.1722 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0924 r_free = 0.1722 target_work(ml) = 5.092 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0913 r_free = 0.1714 target_work(ml) = 5.084 | | occupancies: max = 1.00 min = 0.24 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= 0.0913 r_free= 0.1714 coordinate error (max.-lik. estimate): 0.25 A | | | | normalized target function (ml) (work): 5.084477 | | target function (ml) not normalized (work): 25030.880648 | | target function (ml) not normalized (free): 1758.389562 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0953 0.0913 0.1714 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2131 0.2137 0.2137 n_refl.: 5175 remove outliers: r(all,work,free)=0.2131 0.2137 0.2137 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2131 0.2137 0.2137 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0946 0.0906 0.1711 n_refl.: 5175 remove outliers: r(all,work,free)=0.0944 0.0904 0.1711 n_refl.: 5174 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 94.79 86 5 0.3733 329.905 298.441 0.602 0.995 0.344 11.894-9.307 99.02 97 4 0.1803 525.039 510.368 0.939 0.999 0.315 9.237-7.194 100.00 213 7 0.1966 429.378 421.663 0.996 1.001 0.290 7.162-5.571 100.00 427 22 0.1874 322.196 313.856 0.979 1.001 0.290 5.546-4.326 100.00 867 58 0.0932 442.329 437.729 0.998 1.001 0.230 4.315-3.360 100.00 1859 96 0.0599 420.660 419.891 1.057 1.002 0.220 3.356-3.002 100.00 1373 60 0.0613 324.010 323.668 1.033 1.002 0.090 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9171 b_overall=-6.3261 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0904 r_free=0.1711 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN A Total number of N/Q/H flips: 2 r_work=0.0905 r_free=0.1716 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0905 r_free=0.1716 | n_water=231 | time (s): 0.530 (total time: 0.530) Filter (dist) r_work=0.0919 r_free=0.1739 | n_water=227 | time (s): 19.240 (total time: 19.770) Filter (q & B) r_work=0.0993 r_free=0.1774 | n_water=224 | time (s): 1.790 (total time: 21.560) Compute maps r_work=0.0993 r_free=0.1774 | n_water=224 | time (s): 0.520 (total time: 22.080) Filter (map) r_work=0.1251 r_free=0.1794 | n_water=153 | time (s): 1.610 (total time: 23.690) Find peaks r_work=0.1251 r_free=0.1794 | n_water=153 | time (s): 0.410 (total time: 24.100) Add new water r_work=0.1602 r_free=0.2090 | n_water=239 | time (s): 1.230 (total time: 25.330) Refine new water occ: r_work=0.1029 r_free=0.1674 adp: r_work=0.1026 r_free=0.1685 occ: r_work=0.1016 r_free=0.1670 adp: r_work=0.1016 r_free=0.1681 occ: r_work=0.1007 r_free=0.1664 adp: r_work=0.1007 r_free=0.1675 ADP+occupancy (water only), MIN, final r_work=0.1007 r_free=0.1675 r_work=0.1007 r_free=0.1675 | n_water=239 | time (s): 10.870 (total time: 36.200) Filter (q & B) r_work=0.1008 r_free=0.1672 | n_water=235 | time (s): 1.490 (total time: 37.690) Filter (dist only) r_work=0.1008 r_free=0.1672 | n_water=235 | time (s): 17.320 (total time: 55.010) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.999750 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.243339 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 0.0916 0.1721 0.0805 0.011 1.0 5.4 0.5 0.0 0 0.500 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.16 17.21 8.05 6.749 17.874 0.243 5.033 8.90 17.38 8.47 8.113 17.915 0.243 4.967 Individual atomic B min max mean iso aniso Overall: 0.00 106.13 16.48 10.50 1762 0 Protein: 0.00 106.13 15.38 10.49 1519 0 Water: 0.00 52.82 23.44 N/A 235 0 Other: 7.15 36.80 22.22 N/A 8 0 Chain A: 0.00 106.13 15.87 N/A 1636 0 Chain S: 0.00 52.12 24.39 N/A 126 0 Histogram: Values Number of atoms 0.00 - 10.61 672 10.61 - 21.23 651 21.23 - 31.84 244 31.84 - 42.45 115 42.45 - 53.07 47 53.07 - 63.68 13 63.68 - 74.29 11 74.29 - 84.91 4 84.91 - 95.52 4 95.52 - 106.13 1 =========================== Idealize ADP of riding H ========================== r_work=0.0890 r_free=0.1738 r_work=0.0894 r_free=0.1746 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0894 r_free = 0.1746 target_work(ml) = 4.972 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0885 r_free = 0.1739 target_work(ml) = 4.964 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0885 r_free= 0.1739 coordinate error (max.-lik. estimate): 0.24 A | | | | normalized target function (ml) (work): 4.964118 | | target function (ml) not normalized (work): 24433.390767 | | target function (ml) not normalized (free): 2058.086781 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0928 0.0885 0.1739 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2073 0.2072 0.2196 n_refl.: 5174 remove outliers: r(all,work,free)=0.2073 0.2072 0.2196 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2073 0.2072 0.2196 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0925 0.0882 0.1743 n_refl.: 5174 remove outliers: r(all,work,free)=0.0925 0.0882 0.1743 n_refl.: 5174 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 94.79 86 5 0.3742 329.905 301.647 0.583 0.986 0.316 11.894-9.307 99.02 97 4 0.1906 525.039 507.469 0.947 0.991 0.313 9.237-7.194 100.00 213 7 0.2202 429.378 418.362 1.005 0.994 0.281 7.162-5.571 100.00 427 22 0.2082 322.196 311.174 0.991 0.996 0.263 5.546-4.326 100.00 867 58 0.0979 442.329 437.134 1.020 0.999 0.240 4.315-3.360 100.00 1859 96 0.0558 420.660 420.181 1.084 1.002 0.220 3.356-3.002 100.00 1373 60 0.0429 324.010 323.972 1.060 1.005 0.090 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.6768 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0882 r_free=0.1743 After: r_work=0.0885 r_free=0.1741 ================================== NQH flips ================================== r_work=0.0885 r_free=0.1741 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 135 ASN Total number of N/Q/H flips: 2 r_work=0.0891 r_free=0.1740 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0891 r_free=0.1740 | n_water=235 | time (s): 0.690 (total time: 0.690) Filter (dist) r_work=0.0922 r_free=0.1764 | n_water=224 | time (s): 20.300 (total time: 20.990) Filter (q & B) r_work=0.1000 r_free=0.1793 | n_water=221 | time (s): 1.280 (total time: 22.270) Compute maps r_work=0.1000 r_free=0.1793 | n_water=221 | time (s): 0.570 (total time: 22.840) Filter (map) r_work=0.1274 r_free=0.1875 | n_water=151 | time (s): 1.590 (total time: 24.430) Find peaks r_work=0.1274 r_free=0.1875 | n_water=151 | time (s): 0.460 (total time: 24.890) Add new water r_work=0.1564 r_free=0.2119 | n_water=223 | time (s): 1.260 (total time: 26.150) Refine new water occ: r_work=0.1013 r_free=0.1740 adp: r_work=0.1009 r_free=0.1748 occ: r_work=0.1004 r_free=0.1739 adp: r_work=0.1003 r_free=0.1745 occ: r_work=0.0998 r_free=0.1736 adp: r_work=0.0997 r_free=0.1742 ADP+occupancy (water only), MIN, final r_work=0.0997 r_free=0.1742 r_work=0.0997 r_free=0.1742 | n_water=223 | time (s): 14.290 (total time: 40.440) Filter (q & B) r_work=0.0997 r_free=0.1742 | n_water=223 | time (s): 0.870 (total time: 41.310) Filter (dist only) r_work=0.0997 r_free=0.1742 | n_water=223 | time (s): 15.700 (total time: 57.010) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.973112 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.219152 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 0.0933 0.1742 0.0809 0.011 1.1 7.0 0.5 0.6 0 0.487 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.33 17.42 8.09 7.993 18.078 0.219 5.041 9.12 17.53 8.42 8.792 18.208 0.219 4.983 Individual atomic B min max mean iso aniso Overall: 0.00 106.48 16.76 11.63 1750 0 Protein: 0.00 106.48 15.80 11.62 1519 0 Water: 0.40 57.96 23.10 N/A 223 0 Other: 7.63 37.51 23.50 N/A 8 0 Chain A: 0.00 106.48 16.23 N/A 1626 0 Chain S: 0.40 57.96 23.80 N/A 124 0 Histogram: Values Number of atoms 0.00 - 10.65 656 10.65 - 21.30 638 21.30 - 31.95 252 31.95 - 42.59 115 42.59 - 53.24 51 53.24 - 63.89 18 63.89 - 74.54 9 74.54 - 85.19 5 85.19 - 95.84 4 95.84 - 106.48 2 =========================== Idealize ADP of riding H ========================== r_work=0.0912 r_free=0.1753 r_work=0.0914 r_free=0.1756 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0914 r_free = 0.1756 target_work(ml) = 4.988 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0908 r_free = 0.1750 target_work(ml) = 4.983 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0908 r_free= 0.1750 coordinate error (max.-lik. estimate): 0.24 A | | | | normalized target function (ml) (work): 4.982911 | | target function (ml) not normalized (work): 24525.888037 | | target function (ml) not normalized (free): 2060.382590 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.79 1.00 2492 142 0.1295 0.1717 5.5636 6.0517| | 2: 3.78 - 3.00 1.00 2430 110 0.0437 0.1805 4.3874 10.919| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2492 142 0.91 12.41 1.00 0.97 13395.37| | 2: 3.78 - 3.00 2430 110 0.99 1.97 1.00 0.99 972.12| |alpha: min = 0.97 max = 0.99 mean = 0.98| |beta: min = 614.30 max = 22116.76 mean = 7261.99| |figures of merit: min = 0.01 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 88.75 mean = 7.26| |phase err.(test): min = 0.00 max = 88.08 mean = 7.51| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0950 0.0908 0.1750 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2139 0.2138 0.2239 n_refl.: 5174 remove outliers: r(all,work,free)=0.2139 0.2138 0.2239 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2139 0.2138 0.2239 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0951 0.0909 0.1758 n_refl.: 5174 remove outliers: r(all,work,free)=0.0951 0.0909 0.1758 n_refl.: 5174 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 94.79 86 5 0.3730 329.905 302.888 0.582 0.987 0.313 11.894-9.307 99.02 97 4 0.1939 525.039 510.249 0.950 0.994 0.308 9.237-7.194 100.00 213 7 0.2216 429.378 419.330 1.003 0.997 0.280 7.162-5.571 100.00 427 22 0.2085 322.196 312.828 0.992 0.999 0.280 5.546-4.326 100.00 867 58 0.1051 442.329 436.645 1.018 1.000 0.260 4.315-3.360 100.00 1859 96 0.0593 420.660 420.181 1.092 1.002 0.220 3.356-3.002 100.00 1373 60 0.0414 324.010 323.518 1.069 1.003 0.080 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.9615 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.3613 0.2063 0.080 5.304 8.8 119.3 19.9 258 0.000 1_bss: 0.1569 0.1647 0.080 5.304 6.0 116.4 17.0 258 0.000 1_settarget: 0.1569 0.1647 0.080 5.304 6.0 116.4 17.0 258 0.000 1_nqh: 0.1569 0.1648 0.080 5.304 6.0 116.4 17.0 258 0.003 1_weight: 0.1569 0.1648 0.080 5.304 6.0 116.4 17.0 258 0.003 1_xyzrec: 0.1160 0.1770 0.010 0.997 6.0 116.4 17.0 258 0.206 1_adp: 0.1021 0.1762 0.010 0.997 2.2 111.6 17.3 258 0.206 1_regHadp: 0.1016 0.1768 0.010 0.997 2.2 111.6 17.3 258 0.206 1_occ: 0.1018 0.1767 0.010 0.997 2.2 111.6 17.3 258 0.206 2_bss: 0.1020 0.1762 0.010 0.997 1.2 110.6 16.4 258 0.206 2_settarget: 0.1020 0.1762 0.010 0.997 1.2 110.6 16.4 258 0.206 2_updatecdl: 0.1020 0.1762 0.010 1.016 1.2 110.6 16.4 258 0.206 2_nqh: 0.1020 0.1762 0.010 1.016 1.2 110.6 16.4 258 0.206 2_sol: 0.1126 0.1649 0.010 1.016 1.0 110.6 15.7 227 n/a 2_weight: 0.1126 0.1649 0.010 1.016 1.0 110.6 15.7 227 n/a 2_xyzrec: 0.1022 0.1785 0.009 0.981 1.0 110.6 15.7 227 n/a 2_adp: 0.0951 0.1806 0.009 0.981 0.0 108.0 16.6 227 n/a 2_regHadp: 0.0947 0.1808 0.009 0.981 0.0 108.0 16.6 227 n/a 2_occ: 0.0943 0.1792 0.009 0.981 0.0 108.0 16.6 227 n/a 3_bss: 0.0943 0.1795 0.009 0.981 0.0 108.0 16.6 227 n/a 3_settarget: 0.0943 0.1795 0.009 0.981 0.0 108.0 16.6 227 n/a 3_updatecdl: 0.0943 0.1795 0.009 0.990 0.0 108.0 16.6 227 n/a 3_nqh: 0.0946 0.1793 0.009 0.990 0.0 108.0 16.6 227 n/a 3_sol: 0.1076 0.1719 0.009 0.990 0.0 108.0 16.4 231 n/a 3_weight: 0.1076 0.1719 0.009 0.990 0.0 108.0 16.4 231 n/a 3_xyzrec: 0.0968 0.1736 0.011 1.085 0.0 108.0 16.4 231 n/a 3_adp: 0.0919 0.1712 0.011 1.085 0.0 107.3 16.3 231 n/a 3_regHadp: 0.0924 0.1722 0.011 1.085 0.0 107.3 16.3 231 n/a 3_occ: 0.0913 0.1714 0.011 1.085 0.0 107.3 16.3 231 n/a 4_bss: 0.0904 0.1711 0.011 1.085 0.0 107.3 16.3 231 n/a 4_settarget: 0.0904 0.1711 0.011 1.085 0.0 107.3 16.3 231 n/a 4_updatecdl: 0.0904 0.1711 0.011 1.089 0.0 107.3 16.3 231 n/a 4_nqh: 0.0905 0.1716 0.011 1.089 0.0 107.3 16.3 231 n/a 4_sol: 0.1008 0.1672 0.011 1.089 0.0 107.3 16.4 235 n/a 4_weight: 0.1008 0.1672 0.011 1.089 0.0 107.3 16.4 235 n/a 4_xyzrec: 0.0916 0.1721 0.011 1.049 0.0 107.3 16.4 235 n/a 4_adp: 0.0890 0.1738 0.011 1.049 0.0 106.1 16.5 235 n/a 4_regHadp: 0.0894 0.1746 0.011 1.049 0.0 106.1 16.5 235 n/a 4_occ: 0.0885 0.1739 0.011 1.049 0.0 106.1 16.5 235 n/a 5_bss: 0.0882 0.1743 0.011 1.049 0.0 106.1 16.5 235 n/a 5_settarget: 0.0882 0.1743 0.011 1.049 0.0 106.1 16.5 235 n/a 5_updatecdl: 0.0882 0.1743 0.011 1.055 0.0 106.1 16.5 235 n/a 5_setrh: 0.0885 0.1741 0.011 1.055 0.0 106.1 16.5 235 n/a 5_nqh: 0.0891 0.1740 0.011 1.055 0.0 106.1 16.5 235 n/a 5_sol: 0.0997 0.1742 0.011 1.055 0.0 106.1 16.5 223 n/a 5_weight: 0.0997 0.1742 0.011 1.055 0.0 106.1 16.5 223 n/a 5_xyzrec: 0.0933 0.1742 0.011 1.113 0.0 106.1 16.5 223 n/a 5_adp: 0.0912 0.1753 0.011 1.113 0.0 106.5 16.8 223 n/a 5_regHadp: 0.0914 0.1756 0.011 1.113 0.0 106.5 16.8 223 n/a 5_occ: 0.0908 0.1750 0.011 1.113 0.0 106.5 16.8 223 n/a end: 0.0909 0.1758 0.011 1.113 0.0 106.5 16.8 223 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_6218374_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_6218374_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 2.8600 Refinement macro-cycles (run) : 490.5700 Write final files (write_after_run_outputs) : 10.7600 Total : 504.1900 Total CPU time: 8.76 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:19:07 PST -0800 (1735492747.18 s) Start R-work = 0.1569, R-free = 0.1647 Final R-work = 0.0909, R-free = 0.1758 =============================================================================== Job complete usr+sys time: 532.94 seconds wall clock time: 9 minutes 15.28 seconds (555.28 seconds total)