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_8954467.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 { 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_8954467.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8954467.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.30, per 1000 atoms: 0.38 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 149.9 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.68 - 0.93: 641 0.93 - 1.18: 1015 1.18 - 1.43: 645 1.43 - 1.68: 820 1.68 - 1.93: 32 Bond restraints: 3153 Sorted by residual: bond pdb=" N GLY A 100 " pdb=" CA GLY A 100 " ideal model delta sigma weight residual 1.444 1.645 -0.201 1.06e-02 8.90e+03 3.60e+02 bond pdb=" CA ILE A 117 " pdb=" CB ILE A 117 " ideal model delta sigma weight residual 1.542 1.779 -0.237 1.26e-02 6.30e+03 3.54e+02 bond pdb=" C GLY A 40 " pdb=" O GLY A 40 " ideal model delta sigma weight residual 1.232 1.384 -0.152 8.20e-03 1.49e+04 3.42e+02 bond pdb=" CA LYS A 130 " pdb=" C LYS A 130 " ideal model delta sigma weight residual 1.524 1.749 -0.225 1.24e-02 6.50e+03 3.29e+02 bond pdb=" N VAL A 146 " pdb=" CA VAL A 146 " ideal model delta sigma weight residual 1.458 1.663 -0.205 1.18e-02 7.18e+03 3.02e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.88: 3324 4.88 - 9.75: 1797 9.75 - 14.63: 571 14.63 - 19.51: 78 19.51 - 24.39: 7 Bond angle restraints: 5777 Sorted by residual: angle pdb=" OE1 GLN A 45 " pdb=" CD GLN A 45 " pdb=" NE2 GLN A 45 " ideal model delta sigma weight residual 122.60 107.17 15.43 1.00e+00 1.00e+00 2.38e+02 angle pdb=" O GLY A 40 " pdb=" C GLY A 40 " pdb=" N BLYS A 41 " ideal model delta sigma weight residual 123.43 111.66 11.77 8.50e-01 1.38e+00 1.92e+02 angle pdb=" CA ALYS A 99 " pdb=" C ALYS A 99 " pdb=" N GLY A 100 " ideal model delta sigma weight residual 115.67 99.67 16.00 1.23e+00 6.61e-01 1.69e+02 angle pdb=" O ILE A 9 " pdb=" C ILE A 9 " pdb=" N LEU A 10 " ideal model delta sigma weight residual 122.94 138.67 -15.73 1.22e+00 6.72e-01 1.66e+02 angle pdb=" CA ALYS A 99 " pdb=" C ALYS A 99 " pdb=" O ALYS A 99 " ideal model delta sigma weight residual 121.65 136.61 -14.96 1.17e+00 7.31e-01 1.64e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.15: 1304 17.15 - 34.31: 131 34.31 - 51.46: 33 51.46 - 68.61: 9 68.61 - 85.76: 4 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C HIS A 115 " pdb=" N HIS A 115 " pdb=" CA HIS A 115 " pdb=" CB HIS A 115 " ideal model delta harmonic sigma weight residual -122.60 -146.76 24.16 0 2.50e+00 1.60e-01 9.34e+01 dihedral pdb=" N HIS A 115 " pdb=" C HIS A 115 " pdb=" CA HIS A 115 " pdb=" CB HIS A 115 " ideal model delta harmonic sigma weight residual 122.80 144.93 -22.13 0 2.50e+00 1.60e-01 7.83e+01 dihedral pdb=" N LEU A 187 " pdb=" C LEU A 187 " pdb=" CA LEU A 187 " pdb=" CB LEU A 187 " ideal model delta harmonic sigma weight residual 122.80 144.66 -21.86 0 2.50e+00 1.60e-01 7.64e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.009 - 0.244: 117 0.244 - 0.480: 77 0.480 - 0.715: 34 0.715 - 0.950: 12 0.950 - 1.185: 3 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA HIS A 115 " pdb=" N HIS A 115 " pdb=" C HIS A 115 " pdb=" CB HIS A 115 " both_signs ideal model delta sigma weight residual False 2.51 1.33 1.18 2.00e-01 2.50e+01 3.51e+01 chirality pdb=" CA LEU A 187 " pdb=" N LEU A 187 " pdb=" C LEU A 187 " pdb=" CB LEU A 187 " both_signs ideal model delta sigma weight residual False 2.51 1.38 1.13 2.00e-01 2.50e+01 3.19e+01 chirality pdb=" CG LEU A 101 " pdb=" CB LEU A 101 " pdb=" CD1 LEU A 101 " pdb=" CD2 LEU A 101 " both_signs ideal model delta sigma weight residual False -2.59 -3.56 0.97 2.00e-01 2.50e+01 2.34e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " -0.051 2.00e-02 2.50e+03 5.87e-02 1.03e+02 pdb=" CG PHE A 162 " 0.082 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " -0.125 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " 0.050 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " 0.054 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " 0.026 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " 0.026 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " 0.044 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " -0.046 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " -0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.050 2.00e-02 2.50e+03 5.52e-02 9.14e+01 pdb=" CG PHE A 164 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.056 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.034 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.019 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.135 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.008 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.064 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.009 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.048 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " -0.050 2.00e-02 2.50e+03 5.51e-02 9.09e+01 pdb=" CG BTYR A 67 " 0.004 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " -0.095 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " 0.055 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " -0.043 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " -0.004 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " 0.056 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " -0.001 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " 0.121 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " 0.016 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " -0.019 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " -0.040 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.37: 1413 2.37 - 2.93: 8349 2.93 - 3.48: 10433 3.48 - 4.04: 15097 4.04 - 4.60: 21277 Nonbonded interactions: 56569 Sorted by model distance: nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.811 2.100 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.826 2.450 nonbonded pdb=" HB2BGLN A 80 " pdb="HE21BGLN A 80 " model vdw 1.840 2.270 nonbonded pdb=" HG SER A 47 " pdb="HH11 ARG A 48 " model vdw 1.860 2.100 nonbonded pdb=" HA AASN A 76 " pdb="HD22AASN A 76 " model vdw 1.873 2.270 ... (remaining 56564 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_8954467_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= 0.3628 r_free= 0.1975 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.467130 | | target function (ml) not normalized (work): 22022.953323 | | target function (ml) not normalized (free): 1146.452856 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3821 0.2133 4.851 4.8934| | 2: 3.78 - 3.00 1.00 2430 110 0.3392 0.1707 4.0722 4.1054| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 6604.57| | 2: 3.78 - 3.00 2430 110 0.94 11.34 1.48 0.26 449.44| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 382.37 max = 12065.15 mean = 3570.70| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 89.98 mean = 30.34| |phase err.(test): min = 0.00 max = 89.99 mean = 33.06| |-----------------------------------------------------------------------------| ----------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 0.237 1557 Z= 5.365 Angle : 5.131 15.998 2118 Z= 3.654 Chirality : 0.383 1.185 243 Planarity : 0.034 0.111 284 Dihedral : 13.667 85.762 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.24 % Favored : 96.22 % Rotamer: Outliers : 1.86 % Allowed : 2.48 % Favored : 95.65 % Cbeta Deviations : 33.51 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.46), residues: 224 helix: -2.43 (0.37), residues: 109 sheet: -0.72 (0.87), residues: 28 loop : -1.20 (0.58), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.116 0.021 ARG A 28 TYR 0.068 0.032 TYR A 139 PHE 0.113 0.037 PHE A 164 HIS 0.045 0.020 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= 0.3628 r_free= 0.1975 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.467130 | | target function (ml) not normalized (work): 22022.953323 | | target function (ml) not normalized (free): 1146.452856 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3587 0.3663 0.2095 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3587 0.3663 0.2095 n_refl.: 5182 remove outliers: r(all,work,free)=0.2537 0.2562 0.2095 n_refl.: 5178 overall B=-2.87 to atoms: r(all,work,free)=0.2426 0.2448 0.2045 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1570 0.1569 0.1591 n_refl.: 5178 remove outliers: r(all,work,free)=0.1566 0.1564 0.1591 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 0.3915 449.434 407.877 0.665 1.082 0.410 11.894-9.307 99.02 97 4 0.1857 713.961 696.187 0.930 1.078 0.392 9.237-7.194 100.00 213 7 0.2197 583.879 573.297 0.950 1.070 0.384 7.162-5.571 100.00 427 22 0.2346 438.130 423.975 0.925 1.054 0.310 5.546-4.326 100.00 867 58 0.1387 601.490 594.270 0.979 1.029 0.223 4.315-3.360 100.00 1859 96 0.1305 572.024 565.482 1.058 0.987 0.190 3.356-3.002 100.00 1373 60 0.1610 440.597 432.227 1.079 0.945 0.107 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9555 b_overall=-3.6714 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1564 r_free=0.1591 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=0.1565 r_free=0.1593 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 19.794603 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.720605 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 0.1165 0.1766 0.0602 0.010 1.0 2.6 0.5 0.0 0 9.897 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.65 17.66 6.02 3.013 15.990 1.721 0.018 10.23 17.60 7.37 4.833 16.192 1.721 0.015 Individual atomic B min max mean iso aniso Overall: 2.26 111.43 17.40 5.18 1785 0 Protein: 2.26 111.04 14.72 5.18 1519 0 Water: 4.02 111.43 33.00 N/A 258 0 Other: 16.36 34.76 23.39 N/A 8 0 Chain A: 2.26 111.43 17.40 N/A 1785 0 Histogram: Values Number of atoms 2.26 - 13.18 936 13.18 - 24.10 469 24.10 - 35.01 187 35.01 - 45.93 109 45.93 - 56.85 50 56.85 - 67.76 17 67.76 - 78.68 8 78.68 - 89.60 5 89.60 - 100.51 1 100.51 - 111.43 3 =========================== Idealize ADP of riding H ========================== r_work=0.1023 r_free=0.1760 r_work=0.1017 r_free=0.1767 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1017 r_free = 0.1767 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 = 0.1013 r_free = 0.1760 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= 0.1013 r_free= 0.1760 coordinate error (max.-lik. estimate): 0.31 A | | | | normalized target function (ls_wunit_k1) (work): 0.014052 | | target function (ls_wunit_k1) not normalized (work): 69.191203 | | target function (ls_wunit_k1) not normalized (free): 10.244315 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1051 0.1013 0.1760 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2097 0.2095 0.2234 n_refl.: 5176 remove outliers: r(all,work,free)=0.2097 0.2095 0.2234 n_refl.: 5176 overall B=-0.96 to atoms: r(all,work,free)=0.2057 0.2054 0.2221 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.1054 0.1016 0.1757 n_refl.: 5176 remove outliers: r(all,work,free)=0.1054 0.1016 0.1757 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 0.3385 330.832 313.626 0.678 1.015 0.387 11.894-9.307 99.02 97 4 0.1516 525.552 516.947 0.976 1.016 0.371 9.237-7.194 100.00 213 7 0.1710 429.797 428.828 1.016 1.015 0.351 7.162-5.571 100.00 427 22 0.1632 322.511 318.688 0.973 1.011 0.264 5.546-4.326 100.00 867 58 0.0908 442.762 439.850 0.996 1.006 0.209 4.315-3.360 100.00 1859 96 0.0767 421.071 421.124 1.045 0.997 0.198 3.356-3.002 100.00 1373 60 0.1004 324.327 322.632 1.021 0.988 0.092 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-3.4433 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1016 r_free=0.1757 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A Total number of N/Q/H flips: 1 r_work=0.1017 r_free=0.1756 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1017 r_free=0.1756 | n_water=258 | time (s): 0.520 (total time: 0.520) Filter (dist) r_work=0.1051 r_free=0.1779 | n_water=247 | time (s): 20.270 (total time: 20.790) Filter (q & B) r_work=0.1051 r_free=0.1781 | n_water=244 | time (s): 1.710 (total time: 22.500) Compute maps r_work=0.1051 r_free=0.1781 | n_water=244 | time (s): 0.560 (total time: 23.060) Filter (map) r_work=0.1381 r_free=0.1824 | n_water=140 | time (s): 1.430 (total time: 24.490) Find peaks r_work=0.1381 r_free=0.1824 | n_water=140 | time (s): 0.490 (total time: 24.980) Add new water r_work=0.1715 r_free=0.2107 | n_water=223 | time (s): 1.490 (total time: 26.470) Refine new water occ: r_work=0.1164 r_free=0.1661 adp: r_work=0.1143 r_free=0.1664 occ: r_work=0.1140 r_free=0.1649 adp: r_work=0.1131 r_free=0.1650 occ: r_work=0.1130 r_free=0.1644 adp: r_work=0.1128 r_free=0.1646 ADP+occupancy (water only), MIN, final r_work=0.1128 r_free=0.1646 r_work=0.1128 r_free=0.1646 | n_water=223 | time (s): 5.150 (total time: 31.620) Filter (q & B) r_work=0.1129 r_free=0.1652 | n_water=222 | time (s): 1.270 (total time: 32.890) Filter (dist only) r_work=0.1135 r_free=0.1646 | n_water=218 | time (s): 16.420 (total time: 49.310) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.132043 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.932235 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 0.1753 0.0731 0.009 1.0 4.8 0.5 0.6 0 11.566 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.22 17.53 7.31 4.598 16.717 2.932 0.014 9.46 18.08 8.62 5.584 17.173 2.932 0.012 Individual atomic B min max mean iso aniso Overall: 0.00 108.18 16.58 6.66 1745 0 Protein: 0.00 108.18 15.15 6.66 1519 0 Water: 0.00 62.75 26.43 N/A 218 0 Other: 10.98 32.40 21.51 N/A 8 0 Chain A: 0.00 108.18 15.87 N/A 1665 0 Chain S: 4.29 62.23 31.51 N/A 80 0 Histogram: Values Number of atoms 0.00 - 10.82 695 10.82 - 21.64 658 21.64 - 32.45 201 32.45 - 43.27 111 43.27 - 54.09 41 54.09 - 64.91 25 64.91 - 75.72 6 75.72 - 86.54 4 86.54 - 97.36 2 97.36 - 108.18 2 =========================== Idealize ADP of riding H ========================== r_work=0.0946 r_free=0.1808 r_work=0.0943 r_free=0.1808 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0943 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 = 0.0941 r_free = 0.1798 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.20 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= 0.0941 r_free= 0.1798 coordinate error (max.-lik. estimate): 0.31 A | | | | normalized target function (ls_wunit_k1) (work): 0.011945 | | target function (ls_wunit_k1) not normalized (work): 58.818043 | | target function (ls_wunit_k1) not normalized (free): 9.958437 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0985 0.0941 0.1798 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2154 0.2161 0.2177 n_refl.: 5176 remove outliers: r(all,work,free)=0.2154 0.2161 0.2177 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2154 0.2161 0.2177 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0986 0.0942 0.1803 n_refl.: 5176 remove outliers: r(all,work,free)=0.0986 0.0942 0.1803 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 0.3171 330.832 319.088 0.695 1.026 0.381 11.894-9.307 99.02 97 4 0.1434 525.552 519.317 0.965 1.026 0.350 9.237-7.194 100.00 213 7 0.1462 429.797 430.243 0.996 1.024 0.340 7.162-5.571 100.00 427 22 0.1421 322.511 319.624 0.973 1.019 0.270 5.546-4.326 100.00 867 58 0.0804 442.762 440.142 0.996 1.010 0.240 4.315-3.360 100.00 1859 96 0.0732 421.071 420.978 1.056 0.995 0.210 3.356-3.002 100.00 1373 60 0.0969 324.327 323.276 1.041 0.980 0.087 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-3.9300 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0942 r_free=0.1803 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN A A 80 GLN A Total number of N/Q/H flips: 3 r_work=0.0946 r_free=0.1806 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0946 r_free=0.1806 | n_water=218 | time (s): 0.560 (total time: 0.560) Filter (dist) r_work=0.0953 r_free=0.1809 | n_water=216 | time (s): 14.970 (total time: 15.530) Filter (q & B) r_work=0.1029 r_free=0.1792 | n_water=213 | time (s): 1.370 (total time: 16.900) Compute maps r_work=0.1029 r_free=0.1792 | n_water=213 | time (s): 0.500 (total time: 17.400) Filter (map) r_work=0.1293 r_free=0.1851 | n_water=141 | time (s): 1.260 (total time: 18.660) Find peaks r_work=0.1293 r_free=0.1851 | n_water=141 | time (s): 0.560 (total time: 19.220) Add new water r_work=0.1711 r_free=0.2233 | n_water=230 | time (s): 1.600 (total time: 20.820) Refine new water occ: r_work=0.1090 r_free=0.1785 adp: r_work=0.1084 r_free=0.1809 occ: r_work=0.1070 r_free=0.1789 adp: r_work=0.1071 r_free=0.1796 occ: r_work=0.1059 r_free=0.1777 adp: r_work=0.1059 r_free=0.1783 ADP+occupancy (water only), MIN, final r_work=0.1059 r_free=0.1783 r_work=0.1059 r_free=0.1783 | n_water=230 | time (s): 14.330 (total time: 35.150) Filter (q & B) r_work=0.1059 r_free=0.1784 | n_water=229 | time (s): 1.390 (total time: 36.540) Filter (dist only) r_work=0.1055 r_free=0.1775 | n_water=227 | time (s): 18.180 (total time: 54.720) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.177665 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.232063 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 0.0948 0.1790 0.0842 0.011 1.1 3.8 0.5 0.6 0 0.589 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.48 17.90 8.42 5.543 17.959 0.232 5.170 9.10 17.76 8.66 7.380 17.915 0.232 5.083 Individual atomic B min max mean iso aniso Overall: 0.00 106.59 16.38 9.04 1754 0 Protein: 0.00 106.59 15.16 9.05 1519 0 Water: 0.00 58.18 24.38 N/A 227 0 Other: 10.55 34.09 21.83 N/A 8 0 Chain A: 0.00 106.59 15.81 N/A 1649 0 Chain S: 0.00 58.18 25.43 N/A 105 0 Histogram: Values Number of atoms 0.00 - 10.66 665 10.66 - 21.32 668 21.32 - 31.98 230 31.98 - 42.64 113 42.64 - 53.30 38 53.30 - 63.96 23 63.96 - 74.62 7 74.62 - 85.27 5 85.27 - 95.93 4 95.93 - 106.59 1 =========================== Idealize ADP of riding H ========================== r_work=0.0910 r_free=0.1776 r_work=0.0916 r_free=0.1787 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0916 r_free = 0.1787 target_work(ml) = 5.088 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0906 r_free = 0.1766 target_work(ml) = 5.080 | | occupancies: max = 1.00 min = 0.21 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= 0.0906 r_free= 0.1766 coordinate error (max.-lik. estimate): 0.26 A | | | | normalized target function (ml) (work): 5.079505 | | target function (ml) not normalized (work): 25011.481188 | | target function (ml) not normalized (free): 1786.856390 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0950 0.0906 0.1766 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2147 0.2166 0.2001 n_refl.: 5176 remove outliers: r(all,work,free)=0.2147 0.2166 0.2001 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2147 0.2166 0.2001 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0942 0.0898 0.1764 n_refl.: 5176 remove outliers: r(all,work,free)=0.0937 0.0894 0.1764 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 0.3562 330.227 301.232 0.605 0.998 0.338 11.894-9.307 99.02 97 4 0.1776 525.552 511.069 0.947 1.001 0.320 9.237-7.194 100.00 213 7 0.1935 429.797 424.395 1.002 1.003 0.310 7.162-5.571 100.00 427 22 0.1808 322.511 313.984 0.977 1.003 0.290 5.546-4.326 100.00 867 58 0.0930 442.762 437.657 0.996 1.003 0.230 4.315-3.360 100.00 1859 96 0.0595 421.071 420.671 1.059 1.002 0.220 3.356-3.002 100.00 1373 60 0.0619 324.327 323.372 1.038 1.001 0.076 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9175 b_overall=-6.4661 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0894 r_free=0.1764 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B A 80 GLN A Total number of N/Q/H flips: 2 r_work=0.0895 r_free=0.1761 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0895 r_free=0.1761 | n_water=227 | time (s): 0.510 (total time: 0.510) Filter (dist) r_work=0.0903 r_free=0.1762 | n_water=225 | time (s): 18.630 (total time: 19.140) Filter (q & B) r_work=0.0945 r_free=0.1770 | n_water=223 | time (s): 1.660 (total time: 20.800) Compute maps r_work=0.0945 r_free=0.1770 | n_water=223 | time (s): 0.640 (total time: 21.440) Filter (map) r_work=0.1196 r_free=0.1873 | n_water=152 | time (s): 1.570 (total time: 23.010) Find peaks r_work=0.1196 r_free=0.1873 | n_water=152 | time (s): 0.510 (total time: 23.520) Add new water r_work=0.1520 r_free=0.2151 | n_water=228 | time (s): 1.180 (total time: 24.700) Refine new water occ: r_work=0.1020 r_free=0.1777 adp: r_work=0.1016 r_free=0.1785 occ: r_work=0.1008 r_free=0.1766 adp: r_work=0.1008 r_free=0.1775 occ: r_work=0.1000 r_free=0.1756 adp: r_work=0.1000 r_free=0.1765 ADP+occupancy (water only), MIN, final r_work=0.1000 r_free=0.1765 r_work=0.1000 r_free=0.1765 | n_water=228 | time (s): 9.820 (total time: 34.520) Filter (q & B) r_work=0.0997 r_free=0.1760 | n_water=225 | time (s): 1.750 (total time: 36.270) Filter (dist only) r_work=0.1001 r_free=0.1745 | n_water=222 | time (s): 16.930 (total time: 53.200) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.055691 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.221689 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.0915 0.1839 0.0924 0.011 1.1 3.5 0.5 0.6 0 0.528 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.15 18.39 9.24 7.035 17.885 0.222 5.059 8.94 18.77 9.83 8.252 17.977 0.222 4.997 Individual atomic B min max mean iso aniso Overall: 0.00 105.26 16.55 10.75 1749 0 Protein: 0.00 105.26 15.54 10.76 1519 0 Water: 0.00 61.16 23.30 N/A 222 0 Other: 15.33 34.13 21.74 N/A 8 0 Chain A: 0.00 105.26 16.08 N/A 1640 0 Chain S: 0.00 56.64 23.63 N/A 109 0 Histogram: Values Number of atoms 0.00 - 10.53 662 10.53 - 21.05 625 21.05 - 31.58 260 31.58 - 42.10 114 42.10 - 52.63 49 52.63 - 63.16 18 63.16 - 73.68 9 73.68 - 84.21 7 84.21 - 94.73 4 94.73 - 105.26 1 =========================== Idealize ADP of riding H ========================== r_work=0.0894 r_free=0.1877 r_work=0.0899 r_free=0.1878 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0899 r_free = 0.1878 target_work(ml) = 5.002 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0889 r_free = 0.1861 target_work(ml) = 4.993 | | 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.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0889 r_free= 0.1861 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 4.993377 | | target function (ml) not normalized (work): 24577.400441 | | target function (ml) not normalized (free): 2101.985684 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0938 0.0889 0.1861 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2098 0.2101 0.2196 n_refl.: 5174 remove outliers: r(all,work,free)=0.2098 0.2101 0.2196 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2098 0.2101 0.2196 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0936 0.0887 0.1859 n_refl.: 5174 remove outliers: r(all,work,free)=0.0936 0.0887 0.1859 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 0.3887 330.227 301.325 0.586 0.990 0.324 11.894-9.307 99.02 97 4 0.1928 525.552 507.466 0.955 0.993 0.320 9.237-7.194 100.00 213 7 0.2115 429.797 421.332 1.005 0.996 0.290 7.162-5.571 100.00 427 22 0.2012 322.511 311.688 0.987 0.998 0.280 5.546-4.326 100.00 867 58 0.0972 442.762 437.302 1.016 1.000 0.232 4.315-3.360 100.00 1859 96 0.0564 421.071 420.810 1.083 1.003 0.224 3.356-3.002 100.00 1373 60 0.0473 324.327 324.204 1.060 1.006 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.6443 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0887 r_free=0.1859 After: r_work=0.0891 r_free=0.1857 ================================== NQH flips ================================== r_work=0.0891 r_free=0.1857 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B Total number of N/Q/H flips: 1 r_work=0.0891 r_free=0.1857 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0891 r_free=0.1857 | n_water=222 | time (s): 0.510 (total time: 0.510) Filter (dist) r_work=0.0895 r_free=0.1859 | n_water=220 | time (s): 18.950 (total time: 19.460) Filter (q & B) r_work=0.0929 r_free=0.1863 | n_water=219 | time (s): 1.430 (total time: 20.890) Compute maps r_work=0.0929 r_free=0.1863 | n_water=219 | time (s): 0.520 (total time: 21.410) Filter (map) r_work=0.1192 r_free=0.1929 | n_water=160 | time (s): 1.730 (total time: 23.140) Find peaks r_work=0.1192 r_free=0.1929 | n_water=160 | time (s): 0.490 (total time: 23.630) Add new water r_work=0.1459 r_free=0.2199 | n_water=223 | time (s): 1.560 (total time: 25.190) Refine new water occ: r_work=0.1000 r_free=0.1885 adp: r_work=0.0998 r_free=0.1894 occ: r_work=0.0990 r_free=0.1877 adp: r_work=0.0990 r_free=0.1885 occ: r_work=0.0983 r_free=0.1868 adp: r_work=0.0983 r_free=0.1876 ADP+occupancy (water only), MIN, final r_work=0.0983 r_free=0.1876 r_work=0.0983 r_free=0.1876 | n_water=223 | time (s): 11.120 (total time: 36.310) Filter (q & B) r_work=0.0983 r_free=0.1876 | n_water=223 | time (s): 1.210 (total time: 37.520) Filter (dist only) r_work=0.0990 r_free=0.1864 | n_water=221 | time (s): 17.630 (total time: 55.150) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.017683 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.238945 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 0.1811 0.0878 0.011 1.2 6.4 0.5 0.0 0 0.509 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.33 18.11 8.78 8.174 18.270 0.239 5.032 9.14 18.63 9.50 9.012 18.357 0.239 4.979 Individual atomic B min max mean iso aniso Overall: 0.00 101.97 16.86 11.87 1748 0 Protein: 0.00 101.97 15.88 11.88 1519 0 Water: 0.00 57.91 23.45 N/A 221 0 Other: 12.92 34.88 21.26 N/A 8 0 Chain A: 0.00 101.97 16.35 N/A 1631 0 Chain S: 0.00 52.32 24.00 N/A 117 0 Histogram: Values Number of atoms 0.00 - 10.20 618 10.20 - 20.39 626 20.39 - 30.59 264 30.59 - 40.79 139 40.79 - 50.98 55 50.98 - 61.18 24 61.18 - 71.38 4 71.38 - 81.58 9 81.58 - 91.77 5 91.77 - 101.97 4 =========================== Idealize ADP of riding H ========================== r_work=0.0914 r_free=0.1863 r_work=0.0918 r_free=0.1874 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0918 r_free = 0.1874 target_work(ml) = 4.984 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0910 r_free = 0.1863 target_work(ml) = 4.979 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0910 r_free= 0.1863 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 4.978770 | | target function (ml) not normalized (work): 24505.505087 | | target function (ml) not normalized (free): 2115.510281 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1291 0.1842 5.5409 6.1723| | 2: 3.78 - 3.00 1.00 2430 110 0.0445 0.1900 4.4023 11.264| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 12.34 1.00 0.98 13424.42| | 2: 3.78 - 3.00 2430 110 0.99 2.04 1.00 1.00 977.76| |alpha: min = 0.96 max = 1.00 mean = 0.99| |beta: min = 631.32 max = 22452.72 mean = 7279.48| |figures of merit: min = 0.00 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.57 mean = 7.25| |phase err.(test): min = 0.00 max = 86.80 mean = 7.41| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0958 0.0910 0.1863 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2148 0.2152 0.2203 n_refl.: 5174 remove outliers: r(all,work,free)=0.2148 0.2152 0.2203 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2148 0.2152 0.2203 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0958 0.0910 0.1868 n_refl.: 5174 remove outliers: r(all,work,free)=0.0958 0.0910 0.1868 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 0.3857 330.227 303.118 0.611 0.985 0.319 11.894-9.307 99.02 97 4 0.1925 525.552 506.983 1.006 0.991 0.318 9.237-7.194 100.00 213 7 0.2215 429.797 418.544 1.047 0.995 0.305 7.162-5.571 100.00 427 22 0.2113 322.511 311.666 1.040 0.997 0.300 5.546-4.326 100.00 867 58 0.1051 442.762 435.856 1.066 0.999 0.234 4.315-3.360 100.00 1859 96 0.0581 421.071 421.380 1.150 1.002 0.228 3.356-3.002 100.00 1373 60 0.0424 324.327 324.535 1.129 1.005 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-8.5783 ================= 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 : 0.3628 0.1975 0.080 5.131 8.8 119.3 19.9 258 0.000 1_bss: 0.1564 0.1591 0.080 5.131 6.0 116.4 17.0 258 0.000 1_settarget: 0.1564 0.1591 0.080 5.131 6.0 116.4 17.0 258 0.000 1_nqh: 0.1565 0.1593 0.080 5.131 6.0 116.4 17.0 258 0.003 1_weight: 0.1565 0.1593 0.080 5.131 6.0 116.4 17.0 258 0.003 1_xyzrec: 0.1165 0.1766 0.010 0.990 6.0 116.4 17.0 258 0.192 1_adp: 0.1023 0.1760 0.010 0.990 2.3 111.4 17.4 258 0.192 1_regHadp: 0.1017 0.1767 0.010 0.990 2.3 111.4 17.4 258 0.192 1_occ: 0.1013 0.1760 0.010 0.990 2.3 111.4 17.4 258 0.192 2_bss: 0.1016 0.1757 0.010 0.990 1.3 110.5 16.4 258 0.192 2_settarget: 0.1016 0.1757 0.010 0.990 1.3 110.5 16.4 258 0.192 2_updatecdl: 0.1016 0.1757 0.010 1.008 1.3 110.5 16.4 258 0.192 2_nqh: 0.1017 0.1756 0.010 1.008 1.3 110.5 16.4 258 0.195 2_sol: 0.1135 0.1646 0.010 1.008 1.0 110.1 15.7 218 n/a 2_weight: 0.1135 0.1646 0.010 1.008 1.0 110.1 15.7 218 n/a 2_xyzrec: 0.1022 0.1753 0.009 0.994 1.0 110.1 15.7 218 n/a 2_adp: 0.0946 0.1808 0.009 0.994 0.0 108.2 16.6 218 n/a 2_regHadp: 0.0943 0.1808 0.009 0.994 0.0 108.2 16.6 218 n/a 2_occ: 0.0941 0.1798 0.009 0.994 0.0 108.2 16.6 218 n/a 3_bss: 0.0942 0.1803 0.009 0.994 0.0 108.2 16.6 218 n/a 3_settarget: 0.0942 0.1803 0.009 0.994 0.0 108.2 16.6 218 n/a 3_updatecdl: 0.0942 0.1803 0.009 1.002 0.0 108.2 16.6 218 n/a 3_nqh: 0.0946 0.1806 0.009 1.002 0.0 108.2 16.6 218 n/a 3_sol: 0.1055 0.1775 0.009 1.002 0.0 108.2 16.5 227 n/a 3_weight: 0.1055 0.1775 0.009 1.002 0.0 108.2 16.5 227 n/a 3_xyzrec: 0.0948 0.1790 0.011 1.094 0.0 108.2 16.5 227 n/a 3_adp: 0.0910 0.1776 0.011 1.094 0.0 106.6 16.4 227 n/a 3_regHadp: 0.0916 0.1787 0.011 1.094 0.0 106.6 16.4 227 n/a 3_occ: 0.0906 0.1766 0.011 1.094 0.0 106.6 16.4 227 n/a 4_bss: 0.0894 0.1764 0.011 1.094 0.0 106.6 16.4 227 n/a 4_settarget: 0.0894 0.1764 0.011 1.094 0.0 106.6 16.4 227 n/a 4_updatecdl: 0.0894 0.1764 0.011 1.104 0.0 106.6 16.4 227 n/a 4_nqh: 0.0895 0.1761 0.011 1.104 0.0 106.6 16.4 227 n/a 4_sol: 0.1001 0.1745 0.011 1.104 0.0 106.6 16.4 222 n/a 4_weight: 0.1001 0.1745 0.011 1.104 0.0 106.6 16.4 222 n/a 4_xyzrec: 0.0915 0.1839 0.011 1.081 0.0 106.6 16.4 222 n/a 4_adp: 0.0894 0.1877 0.011 1.081 0.0 105.3 16.6 222 n/a 4_regHadp: 0.0899 0.1878 0.011 1.081 0.0 105.3 16.6 222 n/a 4_occ: 0.0889 0.1861 0.011 1.081 0.0 105.3 16.6 222 n/a 5_bss: 0.0887 0.1859 0.011 1.081 0.0 105.3 16.6 222 n/a 5_settarget: 0.0887 0.1859 0.011 1.081 0.0 105.3 16.6 222 n/a 5_updatecdl: 0.0887 0.1859 0.011 1.077 0.0 105.3 16.6 222 n/a 5_setrh: 0.0891 0.1857 0.011 1.077 0.0 105.3 16.6 222 n/a 5_nqh: 0.0891 0.1857 0.011 1.077 0.0 105.3 16.6 222 n/a 5_sol: 0.0990 0.1864 0.011 1.077 0.0 105.3 16.7 221 n/a 5_weight: 0.0990 0.1864 0.011 1.077 0.0 105.3 16.7 221 n/a 5_xyzrec: 0.0933 0.1811 0.011 1.171 0.0 105.3 16.7 221 n/a 5_adp: 0.0914 0.1863 0.011 1.171 0.0 102.0 16.9 221 n/a 5_regHadp: 0.0918 0.1874 0.011 1.171 0.0 102.0 16.9 221 n/a 5_occ: 0.0910 0.1863 0.011 1.171 0.0 102.0 16.9 221 n/a end: 0.0910 0.1868 0.011 1.171 0.0 102.0 16.9 221 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_8954467_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_8954467_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 2.8600 Refinement macro-cycles (run) : 479.6800 Write final files (write_after_run_outputs) : 10.2600 Total : 492.8000 Total CPU time: 8.59 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:18:55 PST -0800 (1735492735.95 s) Start R-work = 0.1564, R-free = 0.1591 Final R-work = 0.0910, R-free = 0.1868 =============================================================================== Job complete usr+sys time: 523.46 seconds wall clock time: 9 minutes 5.03 seconds (545.03 seconds total)