Starting phenix.refine on Sun Dec 29 09:24:42 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_4426565.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=2 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_4426565.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_4426565.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 2 } } 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 3 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 2.02, per 1000 atoms: 0.60 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.43 Conformation dependent library (CDL) restraints added in 151.8 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.60 - 0.86: 293 0.86 - 1.12: 1283 1.12 - 1.38: 539 1.38 - 1.64: 957 1.64 - 1.90: 81 Bond restraints: 3153 Sorted by residual: bond pdb=" C ILE A 152 " pdb=" N BLEU A 153 " ideal model delta sigma weight residual 1.331 1.591 -0.260 1.34e-02 5.57e+03 3.77e+02 bond pdb=" C ILE A 168 " pdb=" N VAL A 169 " ideal model delta sigma weight residual 1.334 1.104 0.230 1.25e-02 6.40e+03 3.38e+02 bond pdb=" NE ARG A 28 " pdb=" CZ ARG A 28 " ideal model delta sigma weight residual 1.326 1.130 0.196 1.10e-02 8.26e+03 3.16e+02 bond pdb=" CG HIS A 115 " pdb=" ND1 HIS A 115 " ideal model delta sigma weight residual 1.378 1.183 0.195 1.10e-02 8.26e+03 3.15e+02 bond pdb=" C MET A 17 " pdb=" O MET A 17 " ideal model delta sigma weight residual 1.236 1.034 0.202 1.15e-02 7.56e+03 3.08e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.40: 2974 4.40 - 8.80: 1886 8.80 - 13.20: 737 13.20 - 17.60: 160 17.60 - 22.00: 20 Bond angle restraints: 5777 Sorted by residual: angle pdb=" NE ARG A 27 " pdb=" CZ ARG A 27 " pdb=" NH2 ARG A 27 " ideal model delta sigma weight residual 119.20 105.02 14.18 9.00e-01 1.23e+00 2.48e+02 angle pdb=" O GLY A 157 " pdb=" C GLY A 157 " pdb=" N PRO A 158 " ideal model delta sigma weight residual 121.77 137.48 -15.71 1.00e+00 1.00e+00 2.47e+02 angle pdb=" O SER A 57 " pdb=" C SER A 57 " pdb=" N LEU A 58 " ideal model delta sigma weight residual 122.96 105.96 17.00 1.13e+00 7.83e-01 2.26e+02 angle pdb=" O LYS A 182 " pdb=" C LYS A 182 " pdb=" N ALA A 183 " ideal model delta sigma weight residual 122.07 106.73 15.34 1.03e+00 9.43e-01 2.22e+02 angle pdb=" CA ACYS A 53 " pdb=" C ACYS A 53 " pdb=" O ACYS A 53 " ideal model delta sigma weight residual 119.32 135.38 -16.06 1.12e+00 7.97e-01 2.06e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.02 - 17.43: 1317 17.43 - 34.84: 110 34.84 - 52.25: 36 52.25 - 69.65: 16 69.65 - 87.06: 2 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C BLYS A 99 " pdb=" N BLYS A 99 " pdb=" CA BLYS A 99 " pdb=" CB BLYS A 99 " ideal model delta harmonic sigma weight residual -122.60 -139.89 17.29 0 2.50e+00 1.60e-01 4.78e+01 dihedral pdb=" C LYS A 62 " pdb=" N LYS A 62 " pdb=" CA LYS A 62 " pdb=" CB LYS A 62 " ideal model delta harmonic sigma weight residual -122.60 -139.75 17.15 0 2.50e+00 1.60e-01 4.70e+01 dihedral pdb=" C BASN A 76 " pdb=" N BASN A 76 " pdb=" CA BASN A 76 " pdb=" CB BASN A 76 " ideal model delta harmonic sigma weight residual -122.60 -139.41 16.81 0 2.50e+00 1.60e-01 4.52e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.193: 92 0.193 - 0.385: 70 0.385 - 0.577: 51 0.577 - 0.769: 23 0.769 - 0.961: 7 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA BASN A 76 " pdb=" N BASN A 76 " pdb=" C BASN A 76 " pdb=" CB BASN A 76 " both_signs ideal model delta sigma weight residual False 2.51 1.55 0.96 2.00e-01 2.50e+01 2.31e+01 chirality pdb=" CA BLYS A 93 " pdb=" N BLYS A 93 " pdb=" C BLYS A 93 " pdb=" CB BLYS A 93 " both_signs ideal model delta sigma weight residual False 2.51 3.43 -0.92 2.00e-01 2.50e+01 2.12e+01 chirality pdb=" CA ALA A 2 " pdb=" N ALA A 2 " pdb=" C ALA A 2 " pdb=" CB ALA A 2 " both_signs ideal model delta sigma weight residual False 2.48 3.40 -0.92 2.00e-01 2.50e+01 2.10e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " -0.053 2.00e-02 2.50e+03 6.76e-02 1.37e+02 pdb=" CG PHE A 162 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " 0.114 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " -0.085 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " 0.053 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " -0.013 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " -0.011 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " 0.045 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " 0.117 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " -0.108 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " -0.029 2.00e-02 2.50e+03 6.67e-02 1.33e+02 pdb=" CG BTYR A 67 " -0.097 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " 0.142 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " 0.055 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " -0.065 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " -0.045 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " 0.107 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " -0.030 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " -0.007 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " 0.015 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " -0.033 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 126 " 0.015 2.00e-02 2.50e+03 6.98e-02 1.10e+02 pdb=" CG HIS A 126 " -0.018 2.00e-02 2.50e+03 pdb=" ND1 HIS A 126 " 0.059 2.00e-02 2.50e+03 pdb=" CD2 HIS A 126 " 0.020 2.00e-02 2.50e+03 pdb=" CE1 HIS A 126 " 0.044 2.00e-02 2.50e+03 pdb=" NE2 HIS A 126 " -0.034 2.00e-02 2.50e+03 pdb=" HD2 HIS A 126 " -0.089 2.00e-02 2.50e+03 pdb=" HE1 HIS A 126 " -0.118 2.00e-02 2.50e+03 pdb=" HE2 HIS A 126 " 0.121 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.33: 1105 2.33 - 2.90: 8231 2.90 - 3.47: 10484 3.47 - 4.03: 15091 4.03 - 4.60: 21643 Nonbonded interactions: 56554 Sorted by model distance: nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.767 2.100 nonbonded pdb="HD22BASN A 76 " pdb=" HB2 PHE A 119 " model vdw sym.op. 1.802 2.270 -y,x-y-1,z+1/3 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.815 2.450 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.827 2.450 x-y,-y,-z-4/3 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.828 2.100 ... (remaining 56549 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 2 N 265 6.97 2 C 957 5.97 2 H 1596 1.00 2 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_4426565_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: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2789 r_free= 0.1848 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.390472 | | target function (ml) not normalized (work): 71314.439768 | | target function (ml) not normalized (free): 3249.722912 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 49.25 - 3.64 1.00 2819 159 0.3203 0.2170 7.4642 5.0343| | 2: 3.63 - 2.88 1.00 2711 122 0.2638 0.1771 4.3356 4.3365| | 3: 2.88 - 2.52 1.00 2682 148 0.2579 0.1819 4.193 4.2134| | 4: 2.52 - 2.29 1.00 2661 139 0.2564 0.1409 3.4956 3.4504| | 5: 2.29 - 2.13 1.00 2678 122 0.2643 0.1528 3.3928 3.4361| | 6: 2.13 - 2.00 1.00 2692 117 0.2704 0.1928 3.3008 3.4002| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 - 3.64 2819 159 0.88 17.82 0.77 0.23 1334.10| | 2: 3.63 - 2.88 2711 122 0.82 24.14 1.31 0.23 1334.10| | 3: 2.88 - 2.52 2682 148 0.73 33.23 1.29 0.23 1334.10| | 4: 2.52 - 2.29 2661 139 0.94 10.82 1.30 0.26 124.77| | 5: 2.29 - 2.13 2678 122 0.92 12.82 1.31 0.26 124.77| | 6: 2.13 - 2.00 2692 117 0.91 15.46 1.33 0.26 124.77| |alpha: min = 0.23 max = 0.26 mean = 0.25| |beta: min = 124.77 max = 1334.10 mean = 736.17| |figures of merit: min = 0.00 max = 1.00 mean = 0.87| |phase err.(work): min = 0.00 max = 89.98 mean = 19.06| |phase err.(test): min = 0.00 max = 89.21 mean = 19.19| |-----------------------------------------------------------------------------| ----------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 : 0.083 0.260 1557 Z= 5.645 Angle : 5.327 18.348 2118 Z= 3.706 Chirality : 0.379 0.961 243 Planarity : 0.029 0.128 284 Dihedral : 13.731 87.063 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.78 % Favored : 95.68 % Rotamer: Outliers : 2.48 % Allowed : 1.24 % Favored : 96.27 % Cbeta Deviations : 25.41 % 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: -2.74 (0.46), residues: 224 helix: -2.53 (0.34), residues: 109 sheet: -0.74 (0.77), residues: 40 loop : -0.85 (0.65), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.095 0.025 ARG A 28 TYR 0.079 0.025 TYR A 139 PHE 0.093 0.035 PHE A 119 HIS 0.067 0.030 HIS A 138 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 1785 0 Protein: 8.85 115.78 16.79 3.90 1519 0 Water: 11.36 119.30 38.03 N/A 258 0 Other: 19.04 26.29 21.71 N/A 8 0 Chain A: 8.85 119.30 19.89 N/A 1785 0 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2789 r_free= 0.1848 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.390472 | | target function (ml) not normalized (work): 71314.439768 | | target function (ml) not normalized (free): 3249.722912 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.3229 percent. r_work = 0.2921 r_free = 0.2057 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2871 0.2921 0.2057 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2871 0.2921 0.2057 n_refl.: 17050 remove outliers: r(all,work,free)=0.2166 0.2174 0.2057 n_refl.: 17045 overall B=-0.38 to atoms: r(all,work,free)=0.2141 0.2148 0.2040 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1627 0.1622 0.1717 n_refl.: 17045 remove outliers: r(all,work,free)=0.1626 0.1621 0.1717 n_refl.: 17044 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 100.00 89 5 0.4115 394.770 363.817 0.655 1.019 0.403 11.894-9.307 99.02 97 4 0.1915 633.618 616.317 0.924 1.020 0.380 9.237-7.194 100.00 213 7 0.2181 518.236 509.820 0.955 1.019 0.351 7.162-5.571 100.00 427 22 0.2325 388.937 374.050 0.914 1.017 0.290 5.546-4.326 100.00 867 58 0.1385 533.948 529.008 0.949 1.014 0.220 4.315-3.360 100.00 1859 96 0.1312 507.789 503.394 1.015 1.008 0.191 3.356-2.611 100.00 3867 181 0.1649 333.589 329.038 1.012 0.998 0.061 2.608-2.000 99.99 8818 434 0.1663 217.443 213.350 1.034 0.981 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.3706 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1621 r_free=0.1717 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 80 GLN B Total number of N/Q/H flips: 2 r_work=0.1622 r_free=0.1729 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.600218 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.867234 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 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 0.1351 0.1644 0.0293 0.009 1.0 1.3 0.5 0.0 0 11.300 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.51 16.44 2.93 3.013 18.475 0.867 0.023 12.77 16.57 3.80 3.617 18.701 0.867 0.020 Individual atomic B min max mean iso aniso Overall: 6.04 113.92 19.93 4.10 1785 0 Protein: 6.04 113.14 17.15 4.10 1519 0 Water: 8.44 113.92 36.11 N/A 258 0 Other: 21.66 38.00 26.40 N/A 8 0 Chain A: 6.04 113.92 19.93 N/A 1785 0 Histogram: Values Number of atoms 6.04 - 16.83 1082 16.83 - 27.62 340 27.62 - 38.41 189 38.41 - 49.19 96 49.19 - 59.98 51 59.98 - 70.77 12 70.77 - 81.55 7 81.55 - 92.34 4 92.34 - 103.13 1 103.13 - 113.92 3 =========================== Idealize ADP of riding H ========================== r_work=0.1277 r_free=0.1657 r_work=0.1281 r_free=0.1662 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1281 r_free = 0.1662 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1275 r_free = 0.1657 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17044 (all), 4.73 % free)------------| | | | r_work= 0.1275 r_free= 0.1657 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.019954 | | target function (ls_wunit_k1) not normalized (work): 323.998191 | | target function (ls_wunit_k1) not normalized (free): 27.200538 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1293 0.1275 0.1657 n_refl.: 17044 re-set all scales: r(all,work,free)=0.1910 0.1909 0.1991 n_refl.: 17044 remove outliers: r(all,work,free)=0.1910 0.1909 0.1991 n_refl.: 17044 overall B=-0.50 to atoms: r(all,work,free)=0.1874 0.1872 0.1970 n_refl.: 17044 bulk-solvent and scaling: r(all,work,free)=0.1292 0.1274 0.1652 n_refl.: 17044 remove outliers: r(all,work,free)=0.1290 0.1272 0.1652 n_refl.: 17042 ======================== 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 0.3494 303.123 279.233 0.630 1.007 0.370 11.894-9.307 99.02 97 4 0.1684 487.526 476.831 0.920 1.007 0.367 9.237-7.194 100.00 213 7 0.1810 398.747 395.569 0.962 1.007 0.351 7.162-5.571 100.00 427 22 0.1815 299.260 294.412 0.931 1.007 0.301 5.546-4.326 100.00 867 58 0.1041 410.836 408.312 0.957 1.006 0.210 4.315-3.360 100.00 1859 96 0.0926 390.709 390.182 1.015 1.004 0.192 3.356-2.611 100.00 3867 181 0.1300 256.674 255.380 1.009 1.001 0.081 2.608-2.000 99.99 8818 434 0.1349 167.307 165.953 1.011 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9583 b_overall=-1.1369 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1272 r_free=0.1652 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 80 GLN B Total number of N/Q/H flips: 2 r_work=0.1273 r_free=0.1651 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1273 r_free=0.1651 | n_water=258 | time (s): 0.940 (total time: 0.940) Filter (dist) r_work=0.1277 r_free=0.1643 | n_water=253 | time (s): 20.360 (total time: 21.300) Filter (q & B) r_work=0.1278 r_free=0.1644 | n_water=251 | time (s): 2.050 (total time: 23.350) Compute maps r_work=0.1278 r_free=0.1644 | n_water=251 | time (s): 0.750 (total time: 24.100) Filter (map) r_work=0.1313 r_free=0.1623 | n_water=210 | time (s): 1.670 (total time: 25.770) Find peaks r_work=0.1313 r_free=0.1623 | n_water=210 | time (s): 0.530 (total time: 26.300) Add new water r_work=0.1536 r_free=0.1875 | n_water=367 | time (s): 2.030 (total time: 28.330) Refine new water occ: r_work=0.1326 r_free=0.1585 adp: r_work=0.1269 r_free=0.1582 occ: r_work=0.1273 r_free=0.1558 adp: r_work=0.1242 r_free=0.1561 occ: r_work=0.1243 r_free=0.1555 adp: r_work=0.1232 r_free=0.1551 ADP+occupancy (water only), MIN, final r_work=0.1232 r_free=0.1551 r_work=0.1232 r_free=0.1551 | n_water=367 | time (s): 16.680 (total time: 45.010) Filter (q & B) r_work=0.1234 r_free=0.1560 | n_water=361 | time (s): 1.560 (total time: 46.570) Filter (dist only) r_work=0.1234 r_free=0.1563 | n_water=360 | time (s): 30.370 (total time: 76.940) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.800582 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.995543 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 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 0.1207 0.1620 0.0413 0.008 0.9 2.2 0.5 0.0 0 11.900 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.07 16.20 4.13 4.178 20.880 0.996 0.018 11.93 16.49 4.57 4.193 21.094 0.996 0.017 Individual atomic B min max mean iso aniso Overall: 6.58 107.64 21.08 4.22 1887 0 Protein: 6.58 107.64 17.46 4.21 1519 0 Water: 8.41 65.69 36.07 N/A 360 0 Other: 24.19 43.11 33.36 N/A 8 0 Chain A: 6.58 107.64 19.16 N/A 1737 0 Chain S: 17.66 65.10 43.25 N/A 150 0 Histogram: Values Number of atoms 6.58 - 16.69 1050 16.69 - 26.79 357 26.79 - 36.90 223 36.90 - 47.00 153 47.00 - 57.11 67 57.11 - 67.21 27 67.21 - 77.32 3 77.32 - 87.43 3 87.43 - 97.53 2 97.53 - 107.64 2 =========================== Idealize ADP of riding H ========================== r_work=0.1193 r_free=0.1649 r_work=0.1194 r_free=0.1650 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1194 r_free = 0.1650 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1190 r_free = 0.1643 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17042 (all), 4.74 % free)------------| | | | r_work= 0.1190 r_free= 0.1643 coordinate error (max.-lik. estimate): 0.12 A | | | | normalized target function (ls_wunit_k1) (work): 0.016757 | | target function (ls_wunit_k1) not normalized (work): 272.056566 | | target function (ls_wunit_k1) not normalized (free): 25.335796 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1212 0.1190 0.1643 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1758 0.1749 0.1968 n_refl.: 17042 remove outliers: r(all,work,free)=0.1758 0.1749 0.1968 n_refl.: 17042 overall B=-0.37 to atoms: r(all,work,free)=0.1735 0.1725 0.1953 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1209 0.1186 0.1641 n_refl.: 17042 remove outliers: r(all,work,free)=0.1208 0.1185 0.1641 n_refl.: 17041 ======================== 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 0.3229 299.964 284.423 0.613 1.003 0.350 11.894-9.307 99.02 97 4 0.1406 487.526 485.073 0.924 1.003 0.350 9.237-7.194 100.00 213 7 0.1599 398.747 401.255 0.978 1.003 0.300 7.162-5.571 100.00 427 22 0.1543 299.260 295.555 0.938 1.003 0.281 5.546-4.326 100.00 867 58 0.0858 410.836 409.182 0.964 1.003 0.215 4.315-3.360 100.00 1859 96 0.0821 390.709 389.873 1.016 1.002 0.201 3.356-2.611 100.00 3867 181 0.1205 256.674 255.578 1.009 1.001 0.121 2.608-2.000 99.99 8818 434 0.1332 167.307 166.208 1.009 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-1.1550 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1185 r_free=0.1641 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=0.1187 r_free=0.1644 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1187 r_free=0.1644 | n_water=360 | time (s): 0.650 (total time: 0.650) Filter (dist) r_work=0.1187 r_free=0.1644 | n_water=360 | time (s): 28.010 (total time: 28.660) Filter (q & B) r_work=0.1187 r_free=0.1644 | n_water=360 | time (s): 1.170 (total time: 29.830) Compute maps r_work=0.1187 r_free=0.1644 | n_water=360 | time (s): 0.610 (total time: 30.440) Filter (map) r_work=0.1256 r_free=0.1648 | n_water=263 | time (s): 1.540 (total time: 31.980) Find peaks r_work=0.1256 r_free=0.1648 | n_water=263 | time (s): 0.500 (total time: 32.480) Add new water r_work=0.1456 r_free=0.1827 | n_water=416 | time (s): 1.810 (total time: 34.290) Refine new water occ: r_work=0.1245 r_free=0.1596 adp: r_work=0.1237 r_free=0.1598 occ: r_work=0.1217 r_free=0.1578 adp: r_work=0.1205 r_free=0.1574 occ: r_work=0.1197 r_free=0.1574 adp: r_work=0.1186 r_free=0.1567 ADP+occupancy (water only), MIN, final r_work=0.1186 r_free=0.1567 r_work=0.1186 r_free=0.1567 | n_water=416 | time (s): 35.020 (total time: 69.310) Filter (q & B) r_work=0.1189 r_free=0.1572 | n_water=408 | time (s): 1.590 (total time: 70.900) Filter (dist only) r_work=0.1190 r_free=0.1574 | n_water=407 | time (s): 31.660 (total time: 102.560) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.838994 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.160823 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 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 0.1176 0.1568 0.0392 0.009 0.9 6.1 0.5 0.0 0 0.919 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.76 15.68 3.92 4.283 21.255 0.161 4.996 11.55 15.86 4.31 4.873 21.146 0.161 4.975 Individual atomic B min max mean iso aniso Overall: 6.08 104.64 20.64 4.65 1934 0 Protein: 6.08 104.64 16.70 4.64 1519 0 Water: 8.68 62.77 35.12 N/A 407 0 Other: 26.85 43.50 33.84 N/A 8 0 Chain A: 6.08 104.64 18.47 N/A 1736 0 Chain S: 14.71 62.77 39.66 N/A 198 0 Histogram: Values Number of atoms 6.08 - 15.93 1072 15.93 - 25.79 343 25.79 - 35.64 218 35.64 - 45.50 182 45.50 - 55.36 80 55.36 - 65.21 27 65.21 - 75.07 3 75.07 - 84.93 4 84.93 - 94.78 3 94.78 - 104.64 2 =========================== Idealize ADP of riding H ========================== r_work=0.1155 r_free=0.1586 r_work=0.1156 r_free=0.1589 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1156 r_free = 0.1589 target_work(ml) = 4.976 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1148 r_free = 0.1599 target_work(ml) = 4.973 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1148 r_free= 0.1599 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ml) (work): 4.973223 | | target function (ml) not normalized (work): 80735.298220 | | target function (ml) not normalized (free): 4202.887888 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1170 0.1148 0.1599 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1672 0.1663 0.1899 n_refl.: 17041 remove outliers: r(all,work,free)=0.1672 0.1663 0.1899 n_refl.: 17041 overall B=-0.32 to atoms: r(all,work,free)=0.1652 0.1641 0.1889 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1169 0.1147 0.1597 n_refl.: 17041 remove outliers: r(all,work,free)=0.1168 0.1146 0.1597 n_refl.: 17040 ======================== 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 93.75 85 5 0.3425 296.403 279.471 0.573 1.006 0.340 11.894-9.307 99.02 97 4 0.1706 487.526 479.708 0.920 1.007 0.340 9.237-7.194 100.00 213 7 0.1737 398.747 401.091 0.984 1.007 0.290 7.162-5.571 100.00 427 22 0.1625 299.260 294.278 0.942 1.006 0.261 5.546-4.326 100.00 867 58 0.0931 410.836 407.388 0.965 1.006 0.221 4.315-3.360 100.00 1859 96 0.0896 390.709 388.730 1.011 1.004 0.201 3.356-2.611 100.00 3867 181 0.1289 256.674 254.382 1.008 1.000 0.141 2.608-2.000 99.99 8818 434 0.1091 167.307 165.877 1.009 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-1.0942 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1146 r_free=0.1597 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1146 r_free=0.1597 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1146 r_free=0.1597 | n_water=407 | time (s): 0.850 (total time: 0.850) Filter (dist) r_work=0.1146 r_free=0.1597 | n_water=407 | time (s): 31.910 (total time: 32.760) Filter (q & B) r_work=0.1146 r_free=0.1594 | n_water=404 | time (s): 2.360 (total time: 35.120) Compute maps r_work=0.1146 r_free=0.1594 | n_water=404 | time (s): 0.630 (total time: 35.750) Filter (map) r_work=0.1199 r_free=0.1608 | n_water=313 | time (s): 2.390 (total time: 38.140) Find peaks r_work=0.1199 r_free=0.1608 | n_water=313 | time (s): 0.610 (total time: 38.750) Add new water r_work=0.1352 r_free=0.1733 | n_water=455 | time (s): 1.680 (total time: 40.430) Refine new water occ: r_work=0.1181 r_free=0.1531 adp: r_work=0.1175 r_free=0.1541 occ: r_work=0.1156 r_free=0.1505 adp: r_work=0.1148 r_free=0.1513 occ: r_work=0.1139 r_free=0.1493 adp: r_work=0.1132 r_free=0.1498 ADP+occupancy (water only), MIN, final r_work=0.1132 r_free=0.1498 r_work=0.1132 r_free=0.1498 | n_water=455 | time (s): 32.440 (total time: 72.870) Filter (q & B) r_work=0.1135 r_free=0.1505 | n_water=447 | time (s): 1.440 (total time: 74.310) Filter (dist only) r_work=0.1135 r_free=0.1505 | n_water=447 | time (s): 33.780 (total time: 108.090) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.920848 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.175591 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 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 0.1117 0.1580 0.0462 0.010 1.0 4.8 0.5 0.0 0 0.960 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.17 15.80 4.62 4.437 20.835 0.176 4.957 11.02 15.61 4.58 4.648 20.803 0.176 4.944 Individual atomic B min max mean iso aniso Overall: 5.40 102.11 20.72 4.85 1974 0 Protein: 5.40 102.11 16.19 4.84 1519 0 Water: 8.14 64.16 35.83 N/A 447 0 Other: 28.68 47.46 36.31 N/A 8 0 Chain A: 5.40 102.11 17.91 N/A 1735 0 Chain S: 14.65 64.16 41.06 N/A 239 0 Histogram: Values Number of atoms 5.40 - 15.07 1031 15.07 - 24.74 375 24.74 - 34.41 219 34.41 - 44.08 190 44.08 - 53.75 113 53.75 - 63.42 31 63.42 - 73.10 7 73.10 - 82.77 4 82.77 - 92.44 2 92.44 - 102.11 2 =========================== Idealize ADP of riding H ========================== r_work=0.1102 r_free=0.1561 r_work=0.1102 r_free=0.1561 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1102 r_free = 0.1561 target_work(ml) = 4.944 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1095 r_free = 0.1560 target_work(ml) = 4.937 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1095 r_free= 0.1560 coordinate error (max.-lik. estimate): 0.12 A | | | | normalized target function (ml) (work): 4.937482 | | target function (ml) not normalized (work): 80150.141423 | | target function (ml) not normalized (free): 4176.952638 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1118 0.1095 0.1560 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1580 0.1569 0.1847 n_refl.: 17040 remove outliers: r(all,work,free)=0.1580 0.1569 0.1847 n_refl.: 17040 overall B=-0.23 to atoms: r(all,work,free)=0.1567 0.1555 0.1842 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1116 0.1094 0.1556 n_refl.: 17040 remove outliers: r(all,work,free)=0.1116 0.1094 0.1556 n_refl.: 17040 ======================== 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 93.75 85 5 0.3621 296.403 276.624 0.547 1.003 0.318 11.894-9.307 99.02 97 4 0.1678 487.526 481.785 0.926 1.004 0.310 9.237-7.194 100.00 213 7 0.1684 398.747 400.903 0.996 1.005 0.250 7.162-5.571 100.00 427 22 0.1546 299.260 293.134 0.936 1.004 0.240 5.546-4.326 100.00 867 58 0.0904 410.836 407.778 0.964 1.004 0.211 4.315-3.360 100.00 1859 96 0.0850 390.709 388.961 1.004 1.003 0.191 3.356-2.611 100.00 3867 181 0.1229 256.674 254.423 0.998 1.001 0.151 2.608-2.000 99.99 8818 434 0.1033 167.307 166.139 0.992 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.7873 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1094 r_free=0.1556 After: r_work=0.1096 r_free=0.1554 ================================== NQH flips ================================== r_work=0.1096 r_free=0.1554 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1096 r_free=0.1554 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1096 r_free=0.1554 | n_water=447 | time (s): 0.770 (total time: 0.770) Filter (dist) r_work=0.1099 r_free=0.1556 | n_water=446 | time (s): 37.440 (total time: 38.210) Filter (q & B) r_work=0.1099 r_free=0.1556 | n_water=446 | time (s): 1.210 (total time: 39.420) Compute maps r_work=0.1099 r_free=0.1556 | n_water=446 | time (s): 0.740 (total time: 40.160) Filter (map) r_work=0.1179 r_free=0.1573 | n_water=339 | time (s): 2.290 (total time: 42.450) Find peaks r_work=0.1179 r_free=0.1573 | n_water=339 | time (s): 0.540 (total time: 42.990) Add new water r_work=0.1307 r_free=0.1678 | n_water=477 | time (s): 1.490 (total time: 44.480) Refine new water occ: r_work=0.1141 r_free=0.1523 adp: r_work=0.1134 r_free=0.1526 occ: r_work=0.1118 r_free=0.1507 adp: r_work=0.1110 r_free=0.1508 occ: r_work=0.1103 r_free=0.1498 adp: r_work=0.1096 r_free=0.1497 ADP+occupancy (water only), MIN, final r_work=0.1096 r_free=0.1497 r_work=0.1096 r_free=0.1497 | n_water=477 | time (s): 31.980 (total time: 76.460) Filter (q & B) r_work=0.1099 r_free=0.1509 | n_water=466 | time (s): 2.160 (total time: 78.620) Filter (dist only) r_work=0.1099 r_free=0.1509 | n_water=466 | time (s): 38.230 (total time: 116.850) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.001780 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.187625 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 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 0.1119 0.1538 0.0419 0.010 1.1 6.7 0.5 0.0 0 1.001 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.19 15.38 4.19 4.514 20.570 0.188 4.946 11.08 15.26 4.18 4.583 20.607 0.188 4.936 Individual atomic B min max mean iso aniso Overall: 5.16 102.07 20.72 4.98 1993 0 Protein: 5.16 102.07 15.90 4.96 1519 0 Water: 7.67 64.92 36.18 N/A 466 0 Other: 28.27 46.46 36.16 N/A 8 0 Chain A: 5.16 102.07 17.61 N/A 1734 0 Chain S: 13.44 64.92 41.61 N/A 259 0 Histogram: Values Number of atoms 5.16 - 14.85 1045 14.85 - 24.55 361 24.55 - 34.24 208 34.24 - 43.93 201 43.93 - 53.62 131 53.62 - 63.31 30 63.31 - 73.00 8 73.00 - 82.69 5 82.69 - 92.38 1 92.38 - 102.07 3 =========================== Idealize ADP of riding H ========================== r_work=0.1108 r_free=0.1526 r_work=0.1108 r_free=0.1527 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1108 r_free = 0.1527 target_work(ml) = 4.936 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1104 r_free = 0.1533 target_work(ml) = 4.933 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1104 r_free= 0.1533 coordinate error (max.-lik. estimate): 0.12 A | | | | normalized target function (ml) (work): 4.932820 | | target function (ml) not normalized (work): 80074.466323 | | target function (ml) not normalized (free): 4168.931040 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.64 1.00 2810 159 0.1109 0.1439 5.4522 5.6679| | 2: 3.63 - 2.88 1.00 2711 122 0.1097 0.1538 5.2293 5.3691| | 3: 2.88 - 2.52 1.00 2681 148 0.1370 0.1674 5.1373 5.2136| | 4: 2.52 - 2.29 1.00 2661 139 0.0917 0.1509 4.6149 4.937| | 5: 2.29 - 2.13 1.00 2678 122 0.0955 0.1516 4.5701 4.8957| | 6: 2.13 - 2.00 1.00 2692 117 0.1116 0.1684 4.5635 4.7656| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 - 3.64 2810 159 0.94 9.29 1.00 0.95 6541.41| | 2: 3.63 - 2.88 2711 122 0.92 13.11 1.01 0.95 6541.41| | 3: 2.88 - 2.52 2681 148 0.87 19.24 0.99 0.95 6541.41| | 4: 2.52 - 2.29 2661 139 0.93 12.03 1.01 0.96 2084.59| | 5: 2.29 - 2.13 2678 122 0.92 14.03 1.00 0.96 2084.59| | 6: 2.13 - 2.00 2692 117 0.89 16.72 0.99 0.96 2084.59| |alpha: min = 0.95 max = 0.96 mean = 0.96| |beta: min = 2084.59 max = 6541.41 mean = 4336.47| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.94 mean = 14.04| |phase err.(test): min = 0.00 max = 85.84 mean = 13.53| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1125 0.1104 0.1533 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1560 0.1544 0.1872 n_refl.: 17040 remove outliers: r(all,work,free)=0.1560 0.1544 0.1872 n_refl.: 17040 overall B=-0.16 to atoms: r(all,work,free)=0.1551 0.1535 0.1867 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1125 0.1104 0.1534 n_refl.: 17040 remove outliers: r(all,work,free)=0.1125 0.1104 0.1534 n_refl.: 17040 ======================== 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 93.75 85 5 0.3589 296.403 278.989 0.550 1.004 0.314 11.894-9.307 99.02 97 4 0.1735 487.526 479.965 0.931 1.005 0.303 9.237-7.194 100.00 213 7 0.1668 398.747 401.263 0.997 1.005 0.230 7.162-5.571 100.00 427 22 0.1543 299.260 293.676 0.940 1.005 0.220 5.546-4.326 100.00 867 58 0.0915 410.836 408.116 0.969 1.004 0.213 4.315-3.360 100.00 1859 96 0.0876 390.709 388.603 1.007 1.003 0.191 3.356-2.611 100.00 3867 181 0.1252 256.674 254.178 0.999 1.000 0.131 2.608-2.000 99.99 8818 434 0.1028 167.307 166.023 0.989 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.5600 ================= 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 : 0.2789 0.1848 0.083 5.327 8.8 119.3 19.9 258 0.000 1_bss: 0.1621 0.1717 0.083 5.327 8.5 118.9 19.5 258 0.000 1_settarget: 0.1621 0.1717 0.083 5.327 8.5 118.9 19.5 258 0.000 1_nqh: 0.1622 0.1729 0.083 5.327 8.5 118.9 19.5 258 0.006 1_weight: 0.1622 0.1729 0.083 5.327 8.5 118.9 19.5 258 0.006 1_xyzrec: 0.1351 0.1644 0.009 0.960 8.5 118.9 19.5 258 0.154 1_adp: 0.1277 0.1657 0.009 0.960 6.0 113.9 19.9 258 0.154 1_regHadp: 0.1281 0.1662 0.009 0.960 6.0 113.9 19.9 258 0.154 1_occ: 0.1275 0.1657 0.009 0.960 6.0 113.9 19.9 258 0.154 2_bss: 0.1272 0.1652 0.009 0.960 5.5 113.4 19.4 258 0.154 2_settarget: 0.1272 0.1652 0.009 0.960 5.5 113.4 19.4 258 0.154 2_updatecdl: 0.1272 0.1652 0.009 0.987 5.5 113.4 19.4 258 0.154 2_nqh: 0.1273 0.1651 0.009 0.987 5.5 113.4 19.4 258 0.148 2_sol: 0.1234 0.1563 0.009 0.987 5.5 112.6 20.7 360 n/a 2_weight: 0.1234 0.1563 0.009 0.987 5.5 112.6 20.7 360 n/a 2_xyzrec: 0.1207 0.1620 0.008 0.913 5.5 112.6 20.7 360 n/a 2_adp: 0.1193 0.1649 0.008 0.913 6.6 107.6 21.1 360 n/a 2_regHadp: 0.1194 0.1650 0.008 0.913 6.6 107.6 21.1 360 n/a 2_occ: 0.1190 0.1643 0.008 0.913 6.6 107.6 21.1 360 n/a 3_bss: 0.1185 0.1641 0.008 0.913 6.2 107.3 20.7 360 n/a 3_settarget: 0.1185 0.1641 0.008 0.913 6.2 107.3 20.7 360 n/a 3_updatecdl: 0.1185 0.1641 0.008 0.909 6.2 107.3 20.7 360 n/a 3_nqh: 0.1187 0.1644 0.008 0.909 6.2 107.3 20.7 360 n/a 3_sol: 0.1190 0.1574 0.008 0.909 6.2 107.3 20.8 407 n/a 3_weight: 0.1190 0.1574 0.008 0.909 6.2 107.3 20.8 407 n/a 3_xyzrec: 0.1176 0.1568 0.009 0.941 6.2 107.3 20.8 407 n/a 3_adp: 0.1155 0.1586 0.009 0.941 6.1 104.6 20.6 407 n/a 3_regHadp: 0.1156 0.1589 0.009 0.941 6.1 104.6 20.6 407 n/a 3_occ: 0.1148 0.1599 0.009 0.941 6.1 104.6 20.6 407 n/a 4_bss: 0.1146 0.1597 0.009 0.941 5.8 104.3 20.3 407 n/a 4_settarget: 0.1146 0.1597 0.009 0.941 5.8 104.3 20.3 407 n/a 4_updatecdl: 0.1146 0.1597 0.009 0.942 5.8 104.3 20.3 407 n/a 4_nqh: 0.1146 0.1597 0.009 0.942 5.8 104.3 20.3 407 n/a 4_sol: 0.1135 0.1505 0.009 0.942 5.8 104.3 20.8 447 n/a 4_weight: 0.1135 0.1505 0.009 0.942 5.8 104.3 20.8 447 n/a 4_xyzrec: 0.1117 0.1580 0.010 0.982 5.8 104.3 20.8 447 n/a 4_adp: 0.1102 0.1561 0.010 0.982 5.4 102.1 20.7 447 n/a 4_regHadp: 0.1102 0.1561 0.010 0.982 5.4 102.1 20.7 447 n/a 4_occ: 0.1095 0.1560 0.010 0.982 5.4 102.1 20.7 447 n/a 5_bss: 0.1094 0.1556 0.010 0.982 5.2 101.9 20.5 447 n/a 5_settarget: 0.1094 0.1556 0.010 0.982 5.2 101.9 20.5 447 n/a 5_updatecdl: 0.1094 0.1556 0.010 0.981 5.2 101.9 20.5 447 n/a 5_setrh: 0.1096 0.1554 0.010 0.981 5.2 101.9 20.5 447 n/a 5_nqh: 0.1096 0.1554 0.010 0.981 5.2 101.9 20.5 447 n/a 5_sol: 0.1099 0.1509 0.010 0.981 5.2 101.9 20.7 466 n/a 5_weight: 0.1099 0.1509 0.010 0.981 5.2 101.9 20.7 466 n/a 5_xyzrec: 0.1119 0.1538 0.010 1.075 5.2 101.9 20.7 466 n/a 5_adp: 0.1108 0.1526 0.010 1.075 5.2 102.1 20.7 466 n/a 5_regHadp: 0.1108 0.1527 0.010 1.075 5.2 102.1 20.7 466 n/a 5_occ: 0.1104 0.1533 0.010 1.075 5.2 102.1 20.7 466 n/a end: 0.1104 0.1534 0.010 1.075 5.0 101.9 20.6 466 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_4426565_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_4426565_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.4100 Refinement macro-cycles (run) : 947.5500 Write final files (write_after_run_outputs) : 18.9000 Total : 969.8600 Total CPU time: 16.57 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:35 PST -0800 (1735494095.60 s) Start R-work = 0.1621, R-free = 0.1717 Final R-work = 0.1104, R-free = 0.1534 =============================================================================== Job complete usr+sys time: 1014.89 seconds wall clock time: 17 minutes 17.90 seconds (1037.90 seconds total)