Starting phenix.refine on Sun Dec 29 09:10:03 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6727304.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" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6727304.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6727304.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 3 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.73, per 1000 atoms: 0.51 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: 0.37 Conformation dependent library (CDL) restraints added in 135.9 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.60 - 0.87: 330 0.87 - 1.15: 1271 1.15 - 1.42: 675 1.42 - 1.69: 851 1.69 - 1.96: 26 Bond restraints: 3153 Sorted by residual: bond pdb=" CA ILE A 91 " pdb=" CB ILE A 91 " ideal model delta sigma weight residual 1.540 1.756 -0.217 1.11e-02 8.12e+03 3.80e+02 bond pdb=" C ALA A 61 " pdb=" O ALA A 61 " ideal model delta sigma weight residual 1.237 1.459 -0.223 1.19e-02 7.06e+03 3.51e+02 bond pdb=" CA VAL A 177 " pdb=" C VAL A 177 " ideal model delta sigma weight residual 1.523 1.744 -0.221 1.27e-02 6.20e+03 3.03e+02 bond pdb=" CA ILE A 117 " pdb=" CB ILE A 117 " ideal model delta sigma weight residual 1.537 1.336 0.202 1.17e-02 7.31e+03 2.97e+02 bond pdb=" N LYS A 130 " pdb=" CA LYS A 130 " ideal model delta sigma weight residual 1.459 1.261 0.198 1.16e-02 7.43e+03 2.91e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.00: 3270 5.00 - 9.99: 1905 9.99 - 14.98: 523 14.98 - 19.98: 74 19.98 - 24.97: 5 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 121.77 106.55 15.22 1.00e+00 1.00e+00 2.32e+02 angle pdb=" CA PHE A 164 " pdb=" CB PHE A 164 " pdb=" CG PHE A 164 " ideal model delta sigma weight residual 113.80 127.87 -14.07 1.00e+00 1.00e+00 1.98e+02 angle pdb=" O ALA A 104 " pdb=" C ALA A 104 " pdb=" N ILE A 105 " ideal model delta sigma weight residual 123.31 108.07 15.24 1.17e+00 7.31e-01 1.70e+02 angle pdb=" O ILE A 168 " pdb=" C ILE A 168 " pdb=" N VAL A 169 " ideal model delta sigma weight residual 121.80 107.45 14.35 1.13e+00 7.83e-01 1.61e+02 angle pdb=" CA LYS A 89 " pdb=" C LYS A 89 " pdb=" O LYS A 89 " ideal model delta sigma weight residual 120.20 106.35 13.85 1.12e+00 7.97e-01 1.53e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.96: 1312 17.96 - 35.91: 120 35.91 - 53.86: 36 53.86 - 71.81: 10 71.81 - 89.76: 3 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" N LEU A 112 " pdb=" C LEU A 112 " pdb=" CA LEU A 112 " pdb=" CB LEU A 112 " ideal model delta harmonic sigma weight residual 122.80 143.52 -20.72 0 2.50e+00 1.60e-01 6.87e+01 dihedral pdb=" N VAL A 186 " pdb=" C VAL A 186 " pdb=" CA VAL A 186 " pdb=" CB VAL A 186 " ideal model delta harmonic sigma weight residual 123.40 142.70 -19.30 0 2.50e+00 1.60e-01 5.96e+01 dihedral pdb=" C LEU A 112 " pdb=" N LEU A 112 " pdb=" CA LEU A 112 " pdb=" CB LEU A 112 " ideal model delta harmonic sigma weight residual -122.60 -141.87 19.27 0 2.50e+00 1.60e-01 5.94e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.214: 99 0.214 - 0.428: 81 0.428 - 0.641: 46 0.641 - 0.855: 13 0.855 - 1.068: 4 Chirality restraints: 243 Sorted by residual: chirality pdb=" C3 ADTT A 201 " pdb=" C2 ADTT A 201 " pdb=" C4 ADTT A 201 " pdb=" O3 ADTT A 201 " both_signs ideal model delta sigma weight residual False 2.56 3.62 -1.07 2.00e-01 2.50e+01 2.85e+01 chirality pdb=" CA LEU A 185 " pdb=" N LEU A 185 " pdb=" C LEU A 185 " pdb=" CB LEU A 185 " both_signs ideal model delta sigma weight residual False 2.51 1.54 0.97 2.00e-01 2.50e+01 2.34e+01 chirality pdb=" CA LEU A 112 " pdb=" N LEU A 112 " pdb=" C LEU A 112 " pdb=" CB LEU A 112 " both_signs ideal model delta sigma weight residual False 2.51 1.58 0.93 2.00e-01 2.50e+01 2.18e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.064 2.00e-02 2.50e+03 6.92e-02 1.44e+02 pdb=" CG PHE A 119 " -0.145 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.052 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.043 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.101 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.060 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.069 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.020 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " -0.066 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.039 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " 0.033 2.00e-02 2.50e+03 5.55e-02 9.25e+01 pdb=" CG TYR A 139 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " 0.067 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " 0.021 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.083 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " 0.034 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.082 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " 0.013 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " 0.006 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " -0.120 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.010 2.00e-02 2.50e+03 5.50e-02 9.07e+01 pdb=" CG PHE A 164 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.069 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " -0.043 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.069 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.081 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.030 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.025 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.039 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.065 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.061 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.071 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.31: 990 2.31 - 2.88: 7948 2.88 - 3.45: 10630 3.45 - 4.03: 15219 4.03 - 4.60: 21827 Nonbonded interactions: 56614 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.737 2.100 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.796 2.450 nonbonded pdb=" H LYS A 122 " pdb=" OD2 ASP A 149 " model vdw 1.810 2.450 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.825 2.100 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.840 2.450 ... (remaining 56609 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_6727304_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= 0.3629 r_free= 0.2067 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.468080 | | target function (ml) not normalized (work): 22027.635015 | | target function (ml) not normalized (free): 1157.672196 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3812 0.2230 4.8518 4.9023| | 2: 3.78 - 3.00 1.00 2430 110 0.3406 0.1790 4.0733 4.1959| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 48.81 0.83 0.13 6602.87| | 2: 3.78 - 3.00 2430 110 0.93 11.48 1.48 0.26 454.65| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 390.76 max = 12068.89 mean = 3572.41| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 90.00 mean = 30.41| |phase err.(test): min = 0.00 max = 89.90 mean = 33.65| |-----------------------------------------------------------------------------| ----------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 : 0.081 0.275 1557 Z= 5.356 Angle : 5.237 16.778 2118 Z= 3.690 Chirality : 0.368 1.068 243 Planarity : 0.032 0.087 284 Dihedral : 14.189 89.760 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.24 % Allowed : 2.48 % Favored : 96.27 % Cbeta Deviations : 30.27 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.64 (0.43), residues: 224 helix: -3.42 (0.30), residues: 109 sheet: -2.32 (0.88), residues: 28 loop : -0.61 (0.53), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.057 0.019 ARG A 98 TYR 0.061 0.031 TYR A 141 PHE 0.123 0.036 PHE A 119 HIS 0.033 0.016 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= 0.3629 r_free= 0.2067 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.468080 | | target function (ml) not normalized (work): 22027.635015 | | target function (ml) not normalized (free): 1157.672196 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3584 0.3659 0.2180 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3584 0.3659 0.2180 n_refl.: 5182 remove outliers: r(all,work,free)=0.2534 0.2555 0.2180 n_refl.: 5178 overall B=-2.85 to atoms: r(all,work,free)=0.2427 0.2445 0.2130 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1567 0.1564 0.1638 n_refl.: 5178 remove outliers: r(all,work,free)=0.1563 0.1559 0.1638 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 0.3796 449.424 410.833 0.650 1.103 0.406 11.894-9.307 99.02 97 4 0.1852 713.947 690.641 0.912 1.096 0.384 9.237-7.194 100.00 213 7 0.2236 583.867 573.387 0.946 1.085 0.374 7.162-5.571 100.00 427 22 0.2316 438.121 423.464 0.915 1.067 0.357 5.546-4.326 100.00 867 58 0.1384 601.478 594.314 0.970 1.036 0.248 4.315-3.360 100.00 1859 96 0.1301 572.012 565.453 1.057 0.985 0.179 3.356-3.002 100.00 1373 60 0.1609 440.588 432.151 1.095 0.934 0.054 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9555 b_overall=-3.6487 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1559 r_free=0.1638 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 ASN Total number of N/Q/H flips: 1 r_work=0.1559 r_free=0.1635 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 19.462536 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.842963 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 0.1169 0.1788 0.0620 0.010 1.0 2.2 0.5 0.0 0 9.731 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.69 17.88 6.20 3.013 16.006 1.843 0.018 10.31 17.73 7.42 4.760 16.154 1.843 0.015 Individual atomic B min max mean iso aniso Overall: 1.95 111.45 17.31 5.19 1785 0 Protein: 1.95 111.02 14.60 5.18 1519 0 Water: 4.02 111.45 33.09 N/A 258 0 Other: 16.22 35.81 23.58 N/A 8 0 Chain A: 1.95 111.45 17.31 N/A 1785 0 Histogram: Values Number of atoms 1.95 - 12.90 923 12.90 - 23.85 483 23.85 - 34.80 184 34.80 - 45.75 107 45.75 - 56.70 58 56.70 - 67.65 13 67.65 - 78.60 8 78.60 - 89.55 5 89.55 - 100.50 1 100.50 - 111.45 3 =========================== Idealize ADP of riding H ========================== r_work=0.1031 r_free=0.1773 r_work=0.1025 r_free=0.1783 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1025 r_free = 0.1783 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1026 r_free = 0.1798 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.20 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= 0.1026 r_free= 0.1798 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ls_wunit_k1) (work): 0.014279 | | target function (ls_wunit_k1) not normalized (work): 70.309728 | | target function (ls_wunit_k1) not normalized (free): 10.519989 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1065 0.1026 0.1798 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2108 0.2107 0.2236 n_refl.: 5176 remove outliers: r(all,work,free)=0.2108 0.2107 0.2236 n_refl.: 5176 overall B=-0.97 to atoms: r(all,work,free)=0.2067 0.2065 0.2224 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.1062 0.1024 0.1784 n_refl.: 5176 remove outliers: r(all,work,free)=0.1062 0.1024 0.1784 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 0.3372 330.602 313.222 0.657 1.039 0.381 11.894-9.307 99.02 97 4 0.1524 525.187 516.574 0.959 1.038 0.360 9.237-7.194 100.00 213 7 0.1717 429.499 427.590 0.999 1.034 0.341 7.162-5.571 100.00 427 22 0.1659 322.287 318.235 0.958 1.027 0.322 5.546-4.326 100.00 867 58 0.0931 442.454 439.009 0.988 1.014 0.232 4.315-3.360 100.00 1859 96 0.0768 420.778 420.852 1.048 0.993 0.193 3.356-3.002 100.00 1373 60 0.1003 324.101 322.521 1.041 0.972 0.055 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-3.4715 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1024 r_free=0.1784 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A A 144 ASN Total number of N/Q/H flips: 2 r_work=0.1026 r_free=0.1787 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1026 r_free=0.1787 | n_water=258 | time (s): 0.670 (total time: 0.670) Filter (dist) r_work=0.1051 r_free=0.1786 | n_water=249 | time (s): 21.120 (total time: 21.790) Filter (q & B) r_work=0.1051 r_free=0.1791 | n_water=246 | time (s): 1.250 (total time: 23.040) Compute maps r_work=0.1051 r_free=0.1791 | n_water=246 | time (s): 0.440 (total time: 23.480) Filter (map) r_work=0.1328 r_free=0.1804 | n_water=145 | time (s): 1.620 (total time: 25.100) Find peaks r_work=0.1328 r_free=0.1804 | n_water=145 | time (s): 0.410 (total time: 25.510) Add new water r_work=0.1687 r_free=0.2098 | n_water=233 | time (s): 1.180 (total time: 26.690) Refine new water occ: r_work=0.1155 r_free=0.1672 adp: r_work=0.1134 r_free=0.1674 occ: r_work=0.1131 r_free=0.1651 adp: r_work=0.1120 r_free=0.1655 occ: r_work=0.1120 r_free=0.1645 adp: r_work=0.1117 r_free=0.1649 ADP+occupancy (water only), MIN, final r_work=0.1117 r_free=0.1649 r_work=0.1117 r_free=0.1649 | n_water=233 | time (s): 3.310 (total time: 30.000) Filter (q & B) r_work=0.1117 r_free=0.1649 | n_water=233 | time (s): 0.920 (total time: 30.920) Filter (dist only) r_work=0.1127 r_free=0.1650 | n_water=228 | time (s): 17.660 (total time: 48.580) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.542980 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.883378 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 0.1015 0.1787 0.0772 0.009 1.0 4.8 0.5 0.6 0 11.771 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.15 17.87 7.72 4.590 16.649 2.883 0.014 9.45 18.06 8.60 5.490 17.053 2.883 0.012 Individual atomic B min max mean iso aniso Overall: 0.00 107.98 16.51 6.52 1755 0 Protein: 0.00 107.98 14.90 6.52 1519 0 Water: 0.00 62.76 27.08 N/A 228 0 Other: 11.89 29.84 20.42 N/A 8 0 Chain A: 0.00 107.98 15.61 N/A 1668 0 Chain S: 0.01 60.64 33.86 N/A 87 0 Histogram: Values Number of atoms 0.00 - 10.80 685 10.80 - 21.60 670 21.60 - 32.40 201 32.40 - 43.19 118 43.19 - 53.99 42 53.99 - 64.79 27 64.79 - 75.59 4 75.59 - 86.39 4 86.39 - 97.19 2 97.19 - 107.98 2 =========================== Idealize ADP of riding H ========================== r_work=0.0945 r_free=0.1806 r_work=0.0943 r_free=0.1805 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0943 r_free = 0.1805 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0942 r_free = 0.1788 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.17 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= 0.0942 r_free= 0.1788 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ls_wunit_k1) (work): 0.012142 | | target function (ls_wunit_k1) not normalized (work): 59.786090 | | target function (ls_wunit_k1) not normalized (free): 9.741782 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0986 0.0942 0.1788 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2154 0.2160 0.2194 n_refl.: 5176 remove outliers: r(all,work,free)=0.2154 0.2160 0.2194 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2154 0.2160 0.2194 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0987 0.0944 0.1793 n_refl.: 5176 remove outliers: r(all,work,free)=0.0987 0.0944 0.1793 n_refl.: 5176 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 96.88 88 5 0.3293 330.602 316.057 0.664 1.037 0.381 11.894-9.307 99.02 97 4 0.1440 525.187 519.887 0.956 1.037 0.345 9.237-7.194 100.00 213 7 0.1458 429.499 430.381 0.996 1.033 0.330 7.162-5.571 100.00 427 22 0.1452 322.287 319.647 0.966 1.026 0.310 5.546-4.326 100.00 867 58 0.0814 442.454 439.528 0.996 1.014 0.250 4.315-3.360 100.00 1859 96 0.0722 420.778 420.457 1.058 0.994 0.200 3.356-3.002 100.00 1373 60 0.0970 324.101 322.655 1.052 0.973 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-4.0285 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0944 r_free=0.1793 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A Total number of N/Q/H flips: 1 r_work=0.0944 r_free=0.1794 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0944 r_free=0.1794 | n_water=228 | time (s): 0.550 (total time: 0.550) Filter (dist) r_work=0.0946 r_free=0.1758 | n_water=225 | time (s): 18.770 (total time: 19.320) Filter (q & B) r_work=0.1016 r_free=0.1761 | n_water=222 | time (s): 1.650 (total time: 20.970) Compute maps r_work=0.1016 r_free=0.1761 | n_water=222 | time (s): 0.650 (total time: 21.620) Filter (map) r_work=0.1290 r_free=0.1863 | n_water=147 | time (s): 1.870 (total time: 23.490) Find peaks r_work=0.1290 r_free=0.1863 | n_water=147 | time (s): 0.380 (total time: 23.870) Add new water r_work=0.1657 r_free=0.2155 | n_water=227 | time (s): 1.510 (total time: 25.380) Refine new water occ: r_work=0.1062 r_free=0.1776 adp: r_work=0.1054 r_free=0.1784 occ: r_work=0.1043 r_free=0.1766 adp: r_work=0.1043 r_free=0.1772 occ: r_work=0.1033 r_free=0.1754 adp: r_work=0.1032 r_free=0.1761 ADP+occupancy (water only), MIN, final r_work=0.1032 r_free=0.1761 r_work=0.1032 r_free=0.1761 | n_water=227 | time (s): 10.180 (total time: 35.560) Filter (q & B) r_work=0.1032 r_free=0.1761 | n_water=227 | time (s): 0.980 (total time: 36.540) Filter (dist only) r_work=0.1054 r_free=0.1762 | n_water=223 | time (s): 17.050 (total time: 53.590) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.086926 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.262548 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 0.0954 0.1853 0.0898 0.011 1.0 4.2 0.5 0.6 0 0.543 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.54 18.53 8.98 5.431 17.656 0.263 5.176 9.16 18.61 9.45 7.115 17.662 0.263 5.088 Individual atomic B min max mean iso aniso Overall: 0.00 108.73 16.22 8.77 1750 0 Protein: 0.00 108.73 15.04 8.76 1519 0 Water: 0.00 57.76 24.03 N/A 223 0 Other: 6.89 32.54 20.98 N/A 8 0 Chain A: 0.00 108.73 15.62 N/A 1650 0 Chain S: 0.00 57.69 25.99 N/A 100 0 Histogram: Values Number of atoms 0.00 - 10.87 687 10.87 - 21.75 673 21.75 - 32.62 216 32.62 - 43.49 109 43.49 - 54.37 29 54.37 - 65.24 18 65.24 - 76.11 12 76.11 - 86.99 1 86.99 - 97.86 4 97.86 - 108.73 1 =========================== Idealize ADP of riding H ========================== r_work=0.0916 r_free=0.1861 r_work=0.0921 r_free=0.1868 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0921 r_free = 0.1868 target_work(ml) = 5.091 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0911 r_free = 0.1853 target_work(ml) = 5.084 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.0911 r_free= 0.1853 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 5.084233 | | target function (ml) not normalized (work): 25034.764784 | | target function (ml) not normalized (free): 1824.604633 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0958 0.0911 0.1853 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2180 0.2190 0.2150 n_refl.: 5176 remove outliers: r(all,work,free)=0.2180 0.2190 0.2150 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2180 0.2190 0.2150 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0956 0.0909 0.1859 n_refl.: 5176 remove outliers: r(all,work,free)=0.0954 0.0907 0.1859 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 0.3799 327.817 303.774 0.608 1.003 0.348 11.894-9.307 99.02 97 4 0.1755 525.187 512.833 0.942 1.007 0.338 9.237-7.194 100.00 213 7 0.1837 429.499 422.671 0.991 1.008 0.336 7.162-5.571 100.00 427 22 0.1887 322.287 314.255 0.968 1.007 0.310 5.546-4.326 100.00 867 58 0.0932 442.454 437.715 0.991 1.004 0.250 4.315-3.360 100.00 1859 96 0.0611 420.778 420.148 1.047 1.001 0.210 3.356-3.002 100.00 1373 60 0.0627 324.101 322.737 1.030 0.997 0.062 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9171 b_overall=-5.9288 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0907 r_free=0.1859 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A A 80 GLN A Total number of N/Q/H flips: 2 r_work=0.0908 r_free=0.1855 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0908 r_free=0.1855 | n_water=223 | time (s): 0.540 (total time: 0.540) Filter (dist) r_work=0.0908 r_free=0.1855 | n_water=223 | time (s): 15.870 (total time: 16.410) Filter (q & B) r_work=0.0947 r_free=0.1857 | n_water=222 | time (s): 1.350 (total time: 17.760) Compute maps r_work=0.0947 r_free=0.1857 | n_water=222 | time (s): 0.460 (total time: 18.220) Filter (map) r_work=0.1227 r_free=0.1908 | n_water=153 | time (s): 1.460 (total time: 19.680) Find peaks r_work=0.1227 r_free=0.1908 | n_water=153 | time (s): 0.400 (total time: 20.080) Add new water r_work=0.1552 r_free=0.2227 | n_water=231 | time (s): 1.220 (total time: 21.300) Refine new water occ: r_work=0.1013 r_free=0.1795 adp: r_work=0.1007 r_free=0.1813 occ: r_work=0.0999 r_free=0.1786 adp: r_work=0.0997 r_free=0.1799 occ: r_work=0.0990 r_free=0.1770 adp: r_work=0.0988 r_free=0.1782 ADP+occupancy (water only), MIN, final r_work=0.0988 r_free=0.1782 r_work=0.0988 r_free=0.1782 | n_water=231 | time (s): 9.600 (total time: 30.900) Filter (q & B) r_work=0.0988 r_free=0.1780 | n_water=229 | time (s): 1.340 (total time: 32.240) Filter (dist only) r_work=0.0987 r_free=0.1785 | n_water=228 | time (s): 17.890 (total time: 50.130) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.978864 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.273457 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 0.0913 0.1852 0.0939 0.011 1.0 4.2 0.5 0.6 0 0.489 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.13 18.52 9.39 6.849 17.794 0.273 5.042 8.93 18.72 9.79 7.929 17.867 0.273 4.986 Individual atomic B min max mean iso aniso Overall: 0.00 109.21 16.44 10.36 1755 0 Protein: 0.00 109.21 15.34 10.35 1519 0 Water: 0.00 59.69 23.61 N/A 228 0 Other: 5.87 33.38 20.76 N/A 8 0 Chain A: 0.00 109.21 15.83 N/A 1643 0 Chain S: 0.00 59.69 25.33 N/A 112 0 Histogram: Values Number of atoms 0.00 - 10.92 690 10.92 - 21.84 644 21.84 - 32.76 246 32.76 - 43.69 104 43.69 - 54.61 36 54.61 - 65.53 16 65.53 - 76.45 10 76.45 - 87.37 4 87.37 - 98.29 4 98.29 - 109.21 1 =========================== Idealize ADP of riding H ========================== r_work=0.0893 r_free=0.1872 r_work=0.0898 r_free=0.1875 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0898 r_free = 0.1875 target_work(ml) = 4.990 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0887 r_free = 0.1861 target_work(ml) = 4.983 | | occupancies: max = 1.00 min = 0.20 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= 0.0887 r_free= 0.1861 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ml) (work): 4.983010 | | target function (ml) not normalized (work): 24531.358086 | | target function (ml) not normalized (free): 2139.737769 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0936 0.0887 0.1861 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2213 0.2219 0.2250 n_refl.: 5175 remove outliers: r(all,work,free)=0.2213 0.2219 0.2250 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2213 0.2219 0.2250 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0934 0.0885 0.1871 n_refl.: 5175 remove outliers: r(all,work,free)=0.0933 0.0883 0.1871 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 0.3789 329.998 293.857 0.607 0.989 0.350 11.894-9.307 99.02 97 4 0.1847 525.187 510.160 0.953 0.994 0.343 9.237-7.194 100.00 213 7 0.2063 429.499 417.311 1.002 0.997 0.314 7.162-5.571 100.00 427 22 0.2034 322.287 312.991 0.984 0.998 0.300 5.546-4.326 100.00 867 58 0.0995 442.454 436.551 1.011 1.000 0.270 4.315-3.360 100.00 1859 96 0.0562 420.778 420.757 1.072 1.002 0.210 3.356-3.002 100.00 1373 60 0.0457 324.101 323.897 1.052 1.005 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9171 b_overall=-7.1715 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0883 r_free=0.1871 After: r_work=0.0886 r_free=0.1870 ================================== NQH flips ================================== r_work=0.0886 r_free=0.1870 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B A 135 ASN Total number of N/Q/H flips: 2 r_work=0.0898 r_free=0.1868 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0898 r_free=0.1868 | n_water=228 | time (s): 0.510 (total time: 0.510) Filter (dist) r_work=0.0910 r_free=0.1863 | n_water=225 | time (s): 19.180 (total time: 19.690) Filter (q & B) r_work=0.0991 r_free=0.1895 | n_water=223 | time (s): 1.510 (total time: 21.200) Compute maps r_work=0.0991 r_free=0.1895 | n_water=223 | time (s): 0.650 (total time: 21.850) Filter (map) r_work=0.1238 r_free=0.1944 | n_water=155 | time (s): 1.380 (total time: 23.230) Find peaks r_work=0.1238 r_free=0.1944 | n_water=155 | time (s): 0.420 (total time: 23.650) Add new water r_work=0.1546 r_free=0.2222 | n_water=227 | time (s): 1.380 (total time: 25.030) Refine new water occ: r_work=0.1014 r_free=0.1897 adp: r_work=0.1004 r_free=0.1905 occ: r_work=0.0996 r_free=0.1886 adp: r_work=0.0995 r_free=0.1893 occ: r_work=0.0988 r_free=0.1875 adp: r_work=0.0987 r_free=0.1883 ADP+occupancy (water only), MIN, final r_work=0.0987 r_free=0.1883 r_work=0.0987 r_free=0.1883 | n_water=227 | time (s): 12.460 (total time: 37.490) Filter (q & B) r_work=0.0987 r_free=0.1882 | n_water=225 | time (s): 2.020 (total time: 39.510) Filter (dist only) r_work=0.0993 r_free=0.1882 | n_water=224 | time (s): 17.530 (total time: 57.040) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.019650 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.222375 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 0.0935 0.1893 0.0958 0.011 1.2 7.4 0.5 1.2 0 0.510 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.35 18.93 9.58 7.902 18.055 0.222 5.051 9.16 19.03 9.87 8.784 18.168 0.222 4.997 Individual atomic B min max mean iso aniso Overall: 0.00 107.77 16.70 11.51 1751 0 Protein: 0.00 107.77 15.64 11.51 1519 0 Water: 0.00 65.03 23.72 N/A 224 0 Other: 8.60 35.48 22.41 N/A 8 0 Chain A: 0.00 107.77 16.09 N/A 1635 0 Chain S: 0.00 65.03 25.37 N/A 116 0 Histogram: Values Number of atoms 0.00 - 10.78 664 10.78 - 21.55 641 21.55 - 32.33 254 32.33 - 43.11 114 43.11 - 53.89 37 53.89 - 64.66 18 64.66 - 75.44 10 75.44 - 86.22 9 86.22 - 97.00 2 97.00 - 107.77 2 =========================== Idealize ADP of riding H ========================== r_work=0.0916 r_free=0.1903 r_work=0.0919 r_free=0.1905 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0919 r_free = 0.1905 target_work(ml) = 5.002 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0908 r_free = 0.1899 target_work(ml) = 4.995 | | occupancies: max = 1.00 min = 0.20 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= 0.1899 coordinate error (max.-lik. estimate): 0.31 A | | | | normalized target function (ml) (work): 4.994811 | | target function (ml) not normalized (work): 24584.458877 | | target function (ml) not normalized (free): 2225.458410 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1281 0.1870 5.5504 6.1975| | 2: 3.78 - 3.00 1.00 2430 110 0.0454 0.1949 4.425 12.231| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 12.23 1.00 0.98 13192.52| | 2: 3.78 - 3.00 2430 110 0.99 2.19 1.00 1.00 1040.32| |alpha: min = 0.97 max = 1.00 mean = 0.99| |beta: min = 678.41 max = 21907.47 mean = 7192.96| |figures of merit: min = 0.01 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.51 mean = 7.27| |phase err.(test): min = 0.00 max = 81.70 mean = 7.29| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0959 0.0908 0.1899 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2169 0.2167 0.2307 n_refl.: 5174 remove outliers: r(all,work,free)=0.2169 0.2167 0.2307 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2169 0.2167 0.2307 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0958 0.0908 0.1897 n_refl.: 5174 remove outliers: r(all,work,free)=0.0958 0.0908 0.1897 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 329.998 300.147 0.596 0.986 0.326 11.894-9.307 99.02 97 4 0.1816 525.187 513.122 0.960 0.992 0.324 9.237-7.194 100.00 213 7 0.2145 429.499 418.203 1.007 0.995 0.308 7.162-5.571 100.00 427 22 0.2134 322.287 312.648 0.991 0.997 0.280 5.546-4.326 100.00 867 58 0.1057 442.454 436.292 1.021 0.999 0.260 4.315-3.360 100.00 1859 96 0.0578 420.778 420.676 1.095 1.002 0.210 3.356-3.002 100.00 1373 60 0.0445 324.101 323.810 1.076 1.005 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-8.2057 ================= 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 : 0.3629 0.2067 0.081 5.237 8.8 119.3 19.9 258 0.000 1_bss: 0.1559 0.1638 0.081 5.237 6.0 116.4 17.0 258 0.000 1_settarget: 0.1559 0.1638 0.081 5.237 6.0 116.4 17.0 258 0.000 1_nqh: 0.1559 0.1635 0.081 5.237 6.0 116.4 17.0 258 0.003 1_weight: 0.1559 0.1635 0.081 5.237 6.0 116.4 17.0 258 0.003 1_xyzrec: 0.1169 0.1788 0.010 1.007 6.0 116.4 17.0 258 0.196 1_adp: 0.1031 0.1773 0.010 1.007 1.9 111.4 17.3 258 0.196 1_regHadp: 0.1025 0.1783 0.010 1.007 1.9 111.4 17.3 258 0.196 1_occ: 0.1026 0.1798 0.010 1.007 1.9 111.4 17.3 258 0.196 2_bss: 0.1024 0.1784 0.010 1.007 1.0 110.5 16.3 258 0.196 2_settarget: 0.1024 0.1784 0.010 1.007 1.0 110.5 16.3 258 0.196 2_updatecdl: 0.1024 0.1784 0.010 1.023 1.0 110.5 16.3 258 0.196 2_nqh: 0.1026 0.1787 0.010 1.023 1.0 110.5 16.3 258 0.196 2_sol: 0.1127 0.1650 0.010 1.023 1.0 110.0 15.7 228 n/a 2_weight: 0.1127 0.1650 0.010 1.023 1.0 110.0 15.7 228 n/a 2_xyzrec: 0.1015 0.1787 0.009 0.979 1.0 110.0 15.7 228 n/a 2_adp: 0.0945 0.1806 0.009 0.979 0.0 108.0 16.5 228 n/a 2_regHadp: 0.0943 0.1805 0.009 0.979 0.0 108.0 16.5 228 n/a 2_occ: 0.0942 0.1788 0.009 0.979 0.0 108.0 16.5 228 n/a 3_bss: 0.0944 0.1793 0.009 0.979 0.0 108.0 16.5 228 n/a 3_settarget: 0.0944 0.1793 0.009 0.979 0.0 108.0 16.5 228 n/a 3_updatecdl: 0.0944 0.1793 0.009 0.987 0.0 108.0 16.5 228 n/a 3_nqh: 0.0944 0.1794 0.009 0.987 0.0 108.0 16.5 228 n/a 3_sol: 0.1054 0.1762 0.009 0.987 0.0 108.0 16.2 223 n/a 3_weight: 0.1054 0.1762 0.009 0.987 0.0 108.0 16.2 223 n/a 3_xyzrec: 0.0954 0.1853 0.011 1.036 0.0 108.0 16.2 223 n/a 3_adp: 0.0916 0.1861 0.011 1.036 0.0 108.7 16.2 223 n/a 3_regHadp: 0.0921 0.1868 0.011 1.036 0.0 108.7 16.2 223 n/a 3_occ: 0.0911 0.1853 0.011 1.036 0.0 108.7 16.2 223 n/a 4_bss: 0.0907 0.1859 0.011 1.036 0.0 108.7 16.2 223 n/a 4_settarget: 0.0907 0.1859 0.011 1.036 0.0 108.7 16.2 223 n/a 4_updatecdl: 0.0907 0.1859 0.011 1.043 0.0 108.7 16.2 223 n/a 4_nqh: 0.0908 0.1855 0.011 1.043 0.0 108.7 16.2 223 n/a 4_sol: 0.0987 0.1785 0.011 1.043 0.0 108.7 16.3 228 n/a 4_weight: 0.0987 0.1785 0.011 1.043 0.0 108.7 16.3 228 n/a 4_xyzrec: 0.0913 0.1852 0.011 1.025 0.0 108.7 16.3 228 n/a 4_adp: 0.0893 0.1872 0.011 1.025 0.0 109.2 16.4 228 n/a 4_regHadp: 0.0898 0.1875 0.011 1.025 0.0 109.2 16.4 228 n/a 4_occ: 0.0887 0.1861 0.011 1.025 0.0 109.2 16.4 228 n/a 5_bss: 0.0883 0.1871 0.011 1.025 0.0 109.2 16.4 228 n/a 5_settarget: 0.0883 0.1871 0.011 1.025 0.0 109.2 16.4 228 n/a 5_updatecdl: 0.0883 0.1871 0.011 1.037 0.0 109.2 16.4 228 n/a 5_setrh: 0.0886 0.1870 0.011 1.037 0.0 109.2 16.4 228 n/a 5_nqh: 0.0898 0.1868 0.011 1.037 0.0 109.2 16.4 228 n/a 5_sol: 0.0993 0.1882 0.011 1.037 0.0 109.2 16.5 224 n/a 5_weight: 0.0993 0.1882 0.011 1.037 0.0 109.2 16.5 224 n/a 5_xyzrec: 0.0935 0.1893 0.011 1.156 0.0 109.2 16.5 224 n/a 5_adp: 0.0916 0.1903 0.011 1.156 0.0 107.8 16.7 224 n/a 5_regHadp: 0.0919 0.1905 0.011 1.156 0.0 107.8 16.7 224 n/a 5_occ: 0.0908 0.1899 0.011 1.156 0.0 107.8 16.7 224 n/a end: 0.0908 0.1897 0.011 1.156 0.0 107.8 16.7 224 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_6727304_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_6727304_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.1700 Refinement macro-cycles (run) : 476.8400 Write final files (write_after_run_outputs) : 11.4300 Total : 491.4400 Total CPU time: 8.58 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:18:56 PST -0800 (1735492736.22 s) Start R-work = 0.1559, R-free = 0.1638 Final R-work = 0.0908, R-free = 0.1897 =============================================================================== Job complete usr+sys time: 523.54 seconds wall clock time: 9 minutes 5.69 seconds (545.69 seconds total)