Starting phenix.refine on Sun Dec 29 09:10:03 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_5239121.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Adding command-line PHIL: ------------------------- xray_data.high_resolution=3 ordered_solvent.low_resolution=4 No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_5239121.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_5239121.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 3 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== 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: 0.47 Conformation dependent library (CDL) restraints added in 155.3 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.64 - 0.89: 412 0.89 - 1.14: 1190 1.14 - 1.40: 598 1.40 - 1.65: 883 1.65 - 1.90: 70 Bond restraints: 3153 Sorted by residual: bond pdb=" N ILE A 31 " pdb=" CA ILE A 31 " ideal model delta sigma weight residual 1.459 1.193 0.266 1.24e-02 6.50e+03 4.60e+02 bond pdb=" N ILE A 105 " pdb=" CA ILE A 105 " ideal model delta sigma weight residual 1.458 1.223 0.235 1.19e-02 7.06e+03 3.89e+02 bond pdb=" C GLU A 16 " pdb=" O GLU A 16 " ideal model delta sigma weight residual 1.236 1.000 0.236 1.25e-02 6.40e+03 3.58e+02 bond pdb=" C AGLU A 96 " pdb=" O AGLU A 96 " ideal model delta sigma weight residual 1.237 1.443 -0.206 1.17e-02 7.31e+03 3.10e+02 bond pdb=" N VAL A 44 " pdb=" CA VAL A 44 " ideal model delta sigma weight residual 1.458 1.253 0.205 1.17e-02 7.31e+03 3.07e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.15: 2745 4.15 - 8.30: 1953 8.30 - 12.44: 831 12.44 - 16.59: 224 16.59 - 20.74: 24 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O BGLY A 65 " pdb=" C BGLY A 65 " pdb=" N BPRO A 66 " ideal model delta sigma weight residual 121.77 137.73 -15.96 1.00e+00 1.00e+00 2.55e+02 angle pdb=" CA LYS A 182 " pdb=" C LYS A 182 " pdb=" O LYS A 182 " ideal model delta sigma weight residual 121.07 137.12 -16.05 1.10e+00 8.26e-01 2.13e+02 angle pdb=" O ILE A 102 " pdb=" C ILE A 102 " pdb=" N ALA A 103 " ideal model delta sigma weight residual 123.20 137.69 -14.49 1.06e+00 8.90e-01 1.87e+02 angle pdb=" NE ARG A 156 " pdb=" CZ ARG A 156 " pdb=" NH2 ARG A 156 " ideal model delta sigma weight residual 119.20 131.37 -12.17 9.00e-01 1.23e+00 1.83e+02 angle pdb=" O ILE A 52 " pdb=" C ILE A 52 " pdb=" N ACYS A 53 " ideal model delta sigma weight residual 123.03 137.34 -14.31 1.11e+00 8.12e-01 1.66e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.32: 1280 15.32 - 30.63: 131 30.63 - 45.95: 45 45.95 - 61.27: 21 61.27 - 76.58: 4 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C VAL A 25 " pdb=" N VAL A 25 " pdb=" CA VAL A 25 " pdb=" CB VAL A 25 " ideal model delta harmonic sigma weight residual -122.00 -146.63 24.63 0 2.50e+00 1.60e-01 9.71e+01 dihedral pdb=" C LYS A 182 " pdb=" N LYS A 182 " pdb=" CA LYS A 182 " pdb=" CB LYS A 182 " ideal model delta harmonic sigma weight residual -122.60 -143.33 20.73 0 2.50e+00 1.60e-01 6.88e+01 dihedral pdb=" N VAL A 25 " pdb=" C VAL A 25 " pdb=" CA VAL A 25 " pdb=" CB VAL A 25 " ideal model delta harmonic sigma weight residual 123.40 143.55 -20.15 0 2.50e+00 1.60e-01 6.49e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.003 - 0.242: 102 0.242 - 0.482: 75 0.482 - 0.721: 44 0.721 - 0.960: 18 0.960 - 1.199: 4 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA VAL A 25 " pdb=" N VAL A 25 " pdb=" C VAL A 25 " pdb=" CB VAL A 25 " both_signs ideal model delta sigma weight residual False 2.44 1.24 1.20 2.00e-01 2.50e+01 3.60e+01 chirality pdb=" CA LYS A 182 " pdb=" N LYS A 182 " pdb=" C LYS A 182 " pdb=" CB LYS A 182 " both_signs ideal model delta sigma weight residual False 2.51 1.39 1.12 2.00e-01 2.50e+01 3.12e+01 chirality pdb=" CA ALA A 6 " pdb=" N ALA A 6 " pdb=" C ALA A 6 " pdb=" CB ALA A 6 " both_signs ideal model delta sigma weight residual False 2.48 3.47 -0.98 2.00e-01 2.50e+01 2.40e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " -0.002 2.00e-02 2.50e+03 6.68e-02 1.34e+02 pdb=" CG BTYR A 67 " 0.103 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " -0.081 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " -0.056 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " 0.070 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " -0.077 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " 0.094 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " 0.005 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " -0.067 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " 0.071 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " 0.004 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " -0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " -0.088 2.00e-02 2.50e+03 6.13e-02 1.13e+02 pdb=" CG TYR A 141 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " -0.069 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " 0.069 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " 0.091 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " -0.087 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " 0.027 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " 0.047 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " -0.075 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 68 " -0.042 2.00e-02 2.50e+03 8.69e-02 7.54e+01 pdb=" CG ASP A 68 " 0.150 2.00e-02 2.50e+03 pdb=" OD1 ASP A 68 " -0.051 2.00e-02 2.50e+03 pdb=" OD2 ASP A 68 " -0.057 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.29: 851 2.29 - 2.87: 7855 2.87 - 3.44: 10617 3.44 - 4.02: 15259 4.02 - 4.60: 22059 Nonbonded interactions: 56641 Sorted by model distance: nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.711 2.450 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.771 2.450 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.808 2.450 nonbonded pdb=" H LEU A 10 " pdb=" O ALA A 36 " model vdw 1.812 2.450 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.812 2.100 ... (remaining 56636 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_5239121_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= 0.3630 r_free= 0.2011 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.477192 | | target function (ml) not normalized (work): 22072.555426 | | target function (ml) not normalized (free): 1154.964911 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3816 0.2190 4.8499 4.9084| | 2: 3.78 - 3.00 1.00 2430 110 0.3404 0.1710 4.0937 4.1633| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 48.91 0.83 0.13 6615.23| | 2: 3.78 - 3.00 2430 110 0.93 11.52 1.48 0.26 461.97| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 395.65 max = 12075.97 mean = 3582.28| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 89.98 mean = 30.48| |phase err.(test): min = 0.00 max = 89.91 mean = 33.46| |-----------------------------------------------------------------------------| ----------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 0.266 1557 Z= 5.538 Angle : 5.610 17.491 2118 Z= 3.877 Chirality : 0.426 1.199 243 Planarity : 0.033 0.128 284 Dihedral : 13.512 76.582 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.24 % Favored : 96.22 % Rotamer: Outliers : 1.24 % Allowed : 2.48 % Favored : 96.27 % Cbeta Deviations : 32.43 % 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: -2.34 (0.51), residues: 224 helix: -3.09 (0.35), residues: 102 sheet: -0.83 (0.90), residues: 30 loop : 0.48 (0.66), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.075 0.013 ARG A 156 TYR 0.100 0.040 TYR A 141 PHE 0.087 0.036 PHE A 164 HIS 0.054 0.018 HIS A 115 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= 0.3630 r_free= 0.2011 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.477192 | | target function (ml) not normalized (work): 22072.555426 | | target function (ml) not normalized (free): 1154.964911 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3584 0.3661 0.2135 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3584 0.3661 0.2135 n_refl.: 5182 remove outliers: r(all,work,free)=0.2533 0.2557 0.2135 n_refl.: 5178 overall B=-2.88 to atoms: r(all,work,free)=0.2423 0.2444 0.2092 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1569 0.1565 0.1637 n_refl.: 5178 remove outliers: r(all,work,free)=0.1567 0.1563 0.1637 n_refl.: 5177 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 100.00 89 5 0.4036 444.773 409.395 0.660 1.062 0.394 11.894-9.307 99.02 97 4 0.1844 714.029 696.688 0.943 1.059 0.383 9.237-7.194 100.00 213 7 0.2172 583.934 575.827 0.977 1.052 0.359 7.162-5.571 100.00 427 22 0.2345 438.172 424.463 0.942 1.041 0.298 5.546-4.326 100.00 867 58 0.1349 601.547 594.937 0.985 1.022 0.232 4.315-3.360 100.00 1859 96 0.1327 572.078 565.142 1.053 0.990 0.221 3.356-3.002 100.00 1373 60 0.1596 440.639 432.534 1.063 0.959 0.093 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9552 b_overall=-3.6959 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1563 r_free=0.1637 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1563 r_free=0.1637 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 19.128633 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.949126 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1169 0.1768 0.0599 0.010 1.0 2.9 0.5 0.0 0 9.564 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.69 17.68 5.99 3.013 15.983 1.949 0.018 10.24 17.77 7.53 5.041 16.187 1.949 0.015 Individual atomic B min max mean iso aniso Overall: 2.16 111.42 17.40 5.39 1785 0 Protein: 2.16 110.76 14.71 5.38 1519 0 Water: 4.34 111.42 32.99 N/A 258 0 Other: 16.44 37.08 24.06 N/A 8 0 Chain A: 2.16 111.42 17.40 N/A 1785 0 Histogram: Values Number of atoms 2.16 - 13.09 917 13.09 - 24.02 479 24.02 - 34.94 192 34.94 - 45.87 109 45.87 - 56.79 53 56.79 - 67.72 18 67.72 - 78.65 8 78.65 - 89.57 5 89.57 - 100.50 1 100.50 - 111.42 3 =========================== Idealize ADP of riding H ========================== r_work=0.1024 r_free=0.1777 r_work=0.1018 r_free=0.1784 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1018 r_free = 0.1784 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1018 r_free = 0.1776 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5177 (all), 4.87 % free)-------------| | | | r_work= 0.1018 r_free= 0.1776 coordinate error (max.-lik. estimate): 0.31 A | | | | normalized target function (ls_wunit_k1) (work): 0.014308 | | target function (ls_wunit_k1) not normalized (work): 70.465203 | | target function (ls_wunit_k1) not normalized (free): 10.210445 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1057 0.1018 0.1776 n_refl.: 5177 re-set all scales: r(all,work,free)=0.2105 0.2104 0.2211 n_refl.: 5177 remove outliers: r(all,work,free)=0.2105 0.2104 0.2211 n_refl.: 5177 overall B=-1.01 to atoms: r(all,work,free)=0.2062 0.2061 0.2200 n_refl.: 5177 bulk-solvent and scaling: r(all,work,free)=0.1062 0.1024 0.1786 n_refl.: 5177 remove outliers: r(all,work,free)=0.1060 0.1022 0.1786 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 0.3443 324.502 307.020 0.664 1.002 0.365 11.894-9.307 99.02 97 4 0.1540 525.432 519.001 0.992 1.004 0.361 9.237-7.194 100.00 213 7 0.1684 429.699 430.460 1.033 1.004 0.315 7.162-5.571 100.00 427 22 0.1637 322.437 318.708 0.991 1.003 0.292 5.546-4.326 100.00 867 58 0.0918 442.660 439.208 1.002 1.002 0.207 4.315-3.360 100.00 1859 96 0.0773 420.974 420.842 1.045 1.000 0.204 3.356-3.002 100.00 1373 60 0.1007 324.252 322.357 1.014 0.998 0.082 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9552 b_overall=-3.6056 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1022 r_free=0.1786 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1022 r_free=0.1786 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1022 r_free=0.1786 | n_water=258 | time (s): 0.440 (total time: 0.440) Filter (dist) r_work=0.1060 r_free=0.1791 | n_water=244 | time (s): 21.930 (total time: 22.370) Filter (q & B) r_work=0.1059 r_free=0.1791 | n_water=241 | time (s): 1.660 (total time: 24.030) Compute maps r_work=0.1059 r_free=0.1791 | n_water=241 | time (s): 0.620 (total time: 24.650) Filter (map) r_work=0.1315 r_free=0.1910 | n_water=148 | time (s): 1.820 (total time: 26.470) Find peaks r_work=0.1315 r_free=0.1910 | n_water=148 | time (s): 0.450 (total time: 26.920) Add new water r_work=0.1658 r_free=0.2173 | n_water=236 | time (s): 1.210 (total time: 28.130) Refine new water occ: r_work=0.1147 r_free=0.1690 adp: r_work=0.1120 r_free=0.1699 occ: r_work=0.1119 r_free=0.1676 adp: r_work=0.1107 r_free=0.1686 occ: r_work=0.1107 r_free=0.1675 adp: r_work=0.1104 r_free=0.1678 ADP+occupancy (water only), MIN, final r_work=0.1104 r_free=0.1678 r_work=0.1104 r_free=0.1678 | n_water=236 | time (s): 6.230 (total time: 34.360) Filter (q & B) r_work=0.1105 r_free=0.1680 | n_water=234 | time (s): 1.450 (total time: 35.810) Filter (dist only) r_work=0.1112 r_free=0.1681 | n_water=231 | time (s): 18.520 (total time: 54.330) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.179833 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.898761 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 0.1003 0.1800 0.0797 0.009 1.0 5.4 0.5 0.6 0 11.590 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.03 18.00 7.97 4.727 16.753 2.899 0.014 9.33 18.10 8.77 5.609 17.193 2.899 0.012 Individual atomic B min max mean iso aniso Overall: 0.00 105.24 16.63 6.67 1758 0 Protein: 0.00 105.24 15.06 6.65 1519 0 Water: 0.00 62.86 26.64 N/A 231 0 Other: 10.77 41.58 26.35 N/A 8 0 Chain A: 0.00 105.24 15.77 N/A 1673 0 Chain S: 3.76 62.86 33.64 N/A 85 0 Histogram: Values Number of atoms 0.00 - 10.52 647 10.52 - 21.05 688 21.05 - 31.57 213 31.57 - 42.10 121 42.10 - 52.62 46 52.62 - 63.15 26 63.15 - 73.67 9 73.67 - 84.19 3 84.19 - 94.72 3 94.72 - 105.24 2 =========================== Idealize ADP of riding H ========================== r_work=0.0933 r_free=0.1810 r_work=0.0930 r_free=0.1810 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0930 r_free = 0.1810 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0926 r_free = 0.1799 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.25 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= 0.0926 r_free= 0.1799 coordinate error (max.-lik. estimate): 0.31 A | | | | normalized target function (ls_wunit_k1) (work): 0.011632 | | target function (ls_wunit_k1) not normalized (work): 57.274583 | | target function (ls_wunit_k1) not normalized (free): 9.980169 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0971 0.0926 0.1799 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2121 0.2125 0.2185 n_refl.: 5176 remove outliers: r(all,work,free)=0.2121 0.2125 0.2185 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2121 0.2125 0.2185 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0970 0.0925 0.1802 n_refl.: 5176 remove outliers: r(all,work,free)=0.0970 0.0925 0.1802 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 0.3338 324.502 307.330 0.673 1.010 0.369 11.894-9.307 99.02 97 4 0.1445 525.432 519.466 0.979 1.012 0.339 9.237-7.194 100.00 213 7 0.1439 429.699 430.181 1.020 1.011 0.305 7.162-5.571 100.00 427 22 0.1353 322.437 320.874 0.991 1.009 0.300 5.546-4.326 100.00 867 58 0.0791 442.660 440.036 1.001 1.005 0.215 4.315-3.360 100.00 1859 96 0.0714 420.974 420.960 1.055 0.999 0.210 3.356-3.002 100.00 1373 60 0.0957 324.252 323.099 1.031 0.992 0.078 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-4.0768 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0925 r_free=0.1802 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A Total number of N/Q/H flips: 1 r_work=0.0926 r_free=0.1802 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0926 r_free=0.1802 | n_water=231 | time (s): 0.630 (total time: 0.630) Filter (dist) r_work=0.0945 r_free=0.1823 | n_water=226 | time (s): 18.590 (total time: 19.220) Filter (q & B) r_work=0.1034 r_free=0.1840 | n_water=223 | time (s): 1.460 (total time: 20.680) Compute maps r_work=0.1034 r_free=0.1840 | n_water=223 | time (s): 0.520 (total time: 21.200) Filter (map) r_work=0.1301 r_free=0.1888 | n_water=147 | time (s): 1.770 (total time: 22.970) Find peaks r_work=0.1301 r_free=0.1888 | n_water=147 | time (s): 0.430 (total time: 23.400) Add new water r_work=0.1678 r_free=0.2199 | n_water=233 | time (s): 1.490 (total time: 24.890) Refine new water occ: r_work=0.1058 r_free=0.1762 adp: r_work=0.1051 r_free=0.1774 occ: r_work=0.1040 r_free=0.1759 adp: r_work=0.1040 r_free=0.1768 occ: r_work=0.1030 r_free=0.1755 adp: r_work=0.1030 r_free=0.1763 ADP+occupancy (water only), MIN, final r_work=0.1030 r_free=0.1763 r_work=0.1030 r_free=0.1763 | n_water=233 | time (s): 9.420 (total time: 34.310) Filter (q & B) r_work=0.1030 r_free=0.1769 | n_water=232 | time (s): 1.860 (total time: 36.170) Filter (dist only) r_work=0.1030 r_free=0.1771 | n_water=231 | time (s): 19.080 (total time: 55.250) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.073552 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.224277 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 0.0922 0.1810 0.0888 0.011 1.0 4.8 0.5 0.0 0 0.537 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.22 18.10 8.88 5.538 17.868 0.224 5.136 8.83 18.05 9.22 7.304 17.871 0.224 5.043 Individual atomic B min max mean iso aniso Overall: 0.00 103.43 16.39 9.04 1758 0 Protein: 0.00 103.43 15.18 9.02 1519 0 Water: 0.00 57.92 23.98 N/A 231 0 Other: 12.00 43.86 27.32 N/A 8 0 Chain A: 0.00 103.43 15.87 N/A 1660 0 Chain S: 0.00 57.92 25.27 N/A 98 0 Histogram: Values Number of atoms 0.00 - 10.34 657 10.34 - 20.69 654 20.69 - 31.03 238 31.03 - 41.37 120 41.37 - 51.72 48 51.72 - 62.06 20 62.06 - 72.40 11 72.40 - 82.75 4 82.75 - 93.09 3 93.09 - 103.43 3 =========================== Idealize ADP of riding H ========================== r_work=0.0883 r_free=0.1805 r_work=0.0888 r_free=0.1807 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0888 r_free = 0.1807 target_work(ml) = 5.047 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0877 r_free = 0.1799 target_work(ml) = 5.041 | | occupancies: max = 1.00 min = 0.25 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= 0.0877 r_free= 0.1799 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ml) (work): 5.041189 | | target function (ml) not normalized (work): 24822.816452 | | target function (ml) not normalized (free): 1846.992773 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0925 0.0877 0.1799 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2121 0.2131 0.2094 n_refl.: 5176 remove outliers: r(all,work,free)=0.2121 0.2131 0.2094 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2121 0.2131 0.2094 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0917 0.0870 0.1798 n_refl.: 5176 remove outliers: r(all,work,free)=0.0915 0.0868 0.1798 n_refl.: 5175 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3666 326.622 294.387 0.604 0.995 0.350 11.894-9.307 99.02 97 4 0.1824 525.432 509.908 0.952 0.998 0.335 9.237-7.194 100.00 213 7 0.1853 429.699 423.248 1.001 0.999 0.320 7.162-5.571 100.00 427 22 0.1754 322.437 314.193 0.979 1.000 0.290 5.546-4.326 100.00 867 58 0.0902 442.660 437.984 0.995 1.001 0.231 4.315-3.360 100.00 1859 96 0.0578 420.974 420.646 1.052 1.002 0.220 3.356-3.002 100.00 1373 60 0.0586 324.252 323.987 1.026 1.003 0.080 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9171 b_overall=-6.1389 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0868 r_free=0.1798 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=0.0871 r_free=0.1791 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0871 r_free=0.1791 | n_water=231 | time (s): 0.500 (total time: 0.500) Filter (dist) r_work=0.0886 r_free=0.1798 | n_water=225 | time (s): 18.430 (total time: 18.930) Filter (q & B) r_work=0.0958 r_free=0.1836 | n_water=222 | time (s): 1.910 (total time: 20.840) Compute maps r_work=0.0958 r_free=0.1836 | n_water=222 | time (s): 0.620 (total time: 21.460) Filter (map) r_work=0.1214 r_free=0.1890 | n_water=155 | time (s): 1.780 (total time: 23.240) Find peaks r_work=0.1214 r_free=0.1890 | n_water=155 | time (s): 0.580 (total time: 23.820) Add new water r_work=0.1544 r_free=0.2241 | n_water=234 | time (s): 1.650 (total time: 25.470) Refine new water occ: r_work=0.0992 r_free=0.1784 adp: r_work=0.0989 r_free=0.1794 occ: r_work=0.0977 r_free=0.1772 adp: r_work=0.0978 r_free=0.1783 occ: r_work=0.0967 r_free=0.1761 adp: r_work=0.0967 r_free=0.1773 ADP+occupancy (water only), MIN, final r_work=0.0967 r_free=0.1773 r_work=0.0967 r_free=0.1773 | n_water=234 | time (s): 11.120 (total time: 36.590) Filter (q & B) r_work=0.0968 r_free=0.1775 | n_water=232 | time (s): 1.400 (total time: 37.990) Filter (dist only) r_work=0.0984 r_free=0.1779 | n_water=230 | time (s): 18.490 (total time: 56.480) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.983733 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.230253 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 0.0896 0.1876 0.0980 0.011 1.0 4.8 0.5 0.6 0 0.492 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 8.96 18.76 9.80 7.037 18.019 0.230 5.030 8.75 18.80 10.04 8.100 18.142 0.230 4.965 Individual atomic B min max mean iso aniso Overall: 0.00 103.19 16.75 10.56 1757 0 Protein: 0.00 103.19 15.61 10.55 1519 0 Water: 0.00 55.10 23.82 N/A 230 0 Other: 17.89 46.74 29.46 N/A 8 0 Chain A: 0.00 103.19 16.20 N/A 1651 0 Chain S: 1.15 55.10 25.24 N/A 106 0 Histogram: Values Number of atoms 0.00 - 10.32 641 10.32 - 20.64 639 20.64 - 30.96 264 30.96 - 41.28 115 41.28 - 51.59 61 51.59 - 61.91 14 61.91 - 72.23 9 72.23 - 82.55 7 82.55 - 92.87 5 92.87 - 103.19 2 =========================== Idealize ADP of riding H ========================== r_work=0.0875 r_free=0.1880 r_work=0.0880 r_free=0.1883 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0880 r_free = 0.1883 target_work(ml) = 4.971 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0869 r_free = 0.1867 target_work(ml) = 4.964 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0869 r_free= 0.1867 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 4.963616 | | target function (ml) not normalized (work): 24435.882924 | | target function (ml) not normalized (free): 2142.261992 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0919 0.0869 0.1867 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2084 0.2088 0.2152 n_refl.: 5175 remove outliers: r(all,work,free)=0.2084 0.2088 0.2152 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2084 0.2088 0.2152 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0918 0.0867 0.1873 n_refl.: 5175 remove outliers: r(all,work,free)=0.0918 0.0867 0.1873 n_refl.: 5175 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3762 326.622 298.339 0.597 0.989 0.330 11.894-9.307 99.02 97 4 0.1944 525.432 509.998 0.957 0.994 0.340 9.237-7.194 100.00 213 7 0.2013 429.699 421.393 1.007 0.996 0.340 7.162-5.571 100.00 427 22 0.1947 322.437 312.632 0.987 0.998 0.280 5.546-4.326 100.00 867 58 0.0959 442.660 437.331 1.003 1.000 0.230 4.315-3.360 100.00 1859 96 0.0563 420.974 420.872 1.068 1.003 0.220 3.356-3.002 100.00 1373 60 0.0446 324.252 324.255 1.044 1.005 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-6.9343 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0867 r_free=0.1873 After: r_work=0.0870 r_free=0.1873 ================================== NQH flips ================================== r_work=0.0870 r_free=0.1873 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN B Total number of N/Q/H flips: 2 r_work=0.0871 r_free=0.1870 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0871 r_free=0.1870 | n_water=230 | time (s): 0.510 (total time: 0.510) Filter (dist) r_work=0.0873 r_free=0.1880 | n_water=229 | time (s): 18.560 (total time: 19.070) Filter (q & B) r_work=0.0949 r_free=0.1881 | n_water=226 | time (s): 1.480 (total time: 20.550) Compute maps r_work=0.0949 r_free=0.1881 | n_water=226 | time (s): 0.630 (total time: 21.180) Filter (map) r_work=0.1224 r_free=0.1960 | n_water=159 | time (s): 1.950 (total time: 23.130) Find peaks r_work=0.1224 r_free=0.1960 | n_water=159 | time (s): 0.580 (total time: 23.710) Add new water r_work=0.1469 r_free=0.2228 | n_water=226 | time (s): 1.540 (total time: 25.250) Refine new water occ: r_work=0.0973 r_free=0.1862 adp: r_work=0.0968 r_free=0.1871 occ: r_work=0.0961 r_free=0.1865 adp: r_work=0.0961 r_free=0.1865 occ: r_work=0.0956 r_free=0.1857 adp: r_work=0.0956 r_free=0.1858 ADP+occupancy (water only), MIN, final r_work=0.0956 r_free=0.1858 r_work=0.0956 r_free=0.1858 | n_water=226 | time (s): 10.230 (total time: 35.480) Filter (q & B) r_work=0.0957 r_free=0.1865 | n_water=223 | time (s): 1.750 (total time: 37.230) Filter (dist only) r_work=0.0963 r_free=0.1875 | n_water=222 | time (s): 18.920 (total time: 56.150) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.931355 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.258009 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.0913 0.1886 0.0974 0.010 1.1 6.4 0.5 0.0 0 0.466 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.13 18.86 9.74 8.053 18.378 0.258 5.016 8.91 19.14 10.23 9.197 18.521 0.258 4.961 Individual atomic B min max mean iso aniso Overall: 0.00 105.35 17.00 12.24 1749 0 Protein: 0.00 105.35 16.05 12.21 1519 0 Water: 0.00 55.93 23.08 N/A 222 0 Other: 12.89 47.74 28.34 N/A 8 0 Chain A: 0.00 105.35 16.54 N/A 1641 0 Chain S: 0.00 53.27 24.00 N/A 108 0 Histogram: Values Number of atoms 0.00 - 10.54 658 10.54 - 21.07 586 21.07 - 31.61 295 31.61 - 42.14 115 42.14 - 52.68 58 52.68 - 63.21 10 63.21 - 73.75 14 73.75 - 84.28 5 84.28 - 94.82 6 94.82 - 105.35 2 =========================== Idealize ADP of riding H ========================== r_work=0.0891 r_free=0.1914 r_work=0.0895 r_free=0.1919 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0895 r_free = 0.1919 target_work(ml) = 4.967 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0888 r_free = 0.1904 target_work(ml) = 4.963 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0888 r_free= 0.1904 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 4.962650 | | target function (ml) not normalized (work): 24431.126711 | | target function (ml) not normalized (free): 2153.978425 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.79 1.00 2493 142 0.1256 0.1865 5.5251 6.2232| | 2: 3.78 - 3.00 1.00 2430 110 0.0438 0.1970 4.3857 11.548| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.79 2493 142 0.92 11.92 1.00 0.99 12673.07| | 2: 3.78 - 3.00 2430 110 0.99 1.88 1.00 1.01 954.00| |alpha: min = 0.98 max = 1.01 mean = 1.00| |beta: min = 615.22 max = 21046.44 mean = 6888.52| |figures of merit: min = 0.01 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.39 mean = 6.96| |phase err.(test): min = 0.00 max = 82.88 mean = 7.44| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0939 0.0888 0.1904 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2164 0.2169 0.2244 n_refl.: 5175 remove outliers: r(all,work,free)=0.2164 0.2169 0.2244 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2164 0.2169 0.2244 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0939 0.0888 0.1909 n_refl.: 5175 remove outliers: r(all,work,free)=0.0939 0.0888 0.1909 n_refl.: 5175 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3757 326.622 300.752 0.607 0.989 0.330 11.894-9.307 99.02 97 4 0.1966 525.432 510.235 0.954 0.995 0.330 9.237-7.194 100.00 213 7 0.2105 429.699 421.372 1.006 0.998 0.330 7.162-5.571 100.00 427 22 0.2011 322.437 313.014 0.988 0.999 0.290 5.546-4.326 100.00 867 58 0.1032 442.660 436.762 1.008 1.001 0.235 4.315-3.360 100.00 1859 96 0.0572 420.974 420.829 1.082 1.003 0.230 3.356-3.002 100.00 1373 60 0.0417 324.252 323.764 1.062 1.004 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.6135 ================= 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 : 0.3630 0.2011 0.083 5.610 8.8 119.3 19.9 258 0.000 1_bss: 0.1563 0.1637 0.083 5.610 6.0 116.4 17.0 258 0.000 1_settarget: 0.1563 0.1637 0.083 5.610 6.0 116.4 17.0 258 0.000 1_nqh: 0.1563 0.1637 0.083 5.610 6.0 116.4 17.0 258 0.000 1_weight: 0.1563 0.1637 0.083 5.610 6.0 116.4 17.0 258 0.000 1_xyzrec: 0.1169 0.1768 0.010 0.982 6.0 116.4 17.0 258 0.194 1_adp: 0.1024 0.1777 0.010 0.982 2.2 111.4 17.4 258 0.194 1_regHadp: 0.1018 0.1784 0.010 0.982 2.2 111.4 17.4 258 0.194 1_occ: 0.1018 0.1776 0.010 0.982 2.2 111.4 17.4 258 0.194 2_bss: 0.1022 0.1786 0.010 0.982 1.2 110.4 16.4 258 0.194 2_settarget: 0.1022 0.1786 0.010 0.982 1.2 110.4 16.4 258 0.194 2_updatecdl: 0.1022 0.1786 0.010 1.001 1.2 110.4 16.4 258 0.194 2_nqh: 0.1022 0.1786 0.010 1.001 1.2 110.4 16.4 258 0.194 2_sol: 0.1112 0.1681 0.010 1.001 1.0 109.7 15.8 231 n/a 2_weight: 0.1112 0.1681 0.010 1.001 1.0 109.7 15.8 231 n/a 2_xyzrec: 0.1003 0.1800 0.009 0.985 1.0 109.7 15.8 231 n/a 2_adp: 0.0933 0.1810 0.009 0.985 0.0 105.2 16.6 231 n/a 2_regHadp: 0.0930 0.1810 0.009 0.985 0.0 105.2 16.6 231 n/a 2_occ: 0.0926 0.1799 0.009 0.985 0.0 105.2 16.6 231 n/a 3_bss: 0.0925 0.1802 0.009 0.985 0.0 105.2 16.6 231 n/a 3_settarget: 0.0925 0.1802 0.009 0.985 0.0 105.2 16.6 231 n/a 3_updatecdl: 0.0925 0.1802 0.009 0.993 0.0 105.2 16.6 231 n/a 3_nqh: 0.0926 0.1802 0.009 0.993 0.0 105.2 16.6 231 n/a 3_sol: 0.1030 0.1771 0.009 0.993 0.0 105.2 16.4 231 n/a 3_weight: 0.1030 0.1771 0.009 0.993 0.0 105.2 16.4 231 n/a 3_xyzrec: 0.0922 0.1810 0.011 1.042 0.0 105.2 16.4 231 n/a 3_adp: 0.0883 0.1805 0.011 1.042 0.0 103.4 16.4 231 n/a 3_regHadp: 0.0888 0.1807 0.011 1.042 0.0 103.4 16.4 231 n/a 3_occ: 0.0877 0.1799 0.011 1.042 0.0 103.4 16.4 231 n/a 4_bss: 0.0868 0.1798 0.011 1.042 0.0 103.4 16.4 231 n/a 4_settarget: 0.0868 0.1798 0.011 1.042 0.0 103.4 16.4 231 n/a 4_updatecdl: 0.0868 0.1798 0.011 1.056 0.0 103.4 16.4 231 n/a 4_nqh: 0.0871 0.1791 0.011 1.056 0.0 103.4 16.4 231 n/a 4_sol: 0.0984 0.1779 0.011 1.056 0.0 103.4 16.5 230 n/a 4_weight: 0.0984 0.1779 0.011 1.056 0.0 103.4 16.5 230 n/a 4_xyzrec: 0.0896 0.1876 0.011 1.022 0.0 103.4 16.5 230 n/a 4_adp: 0.0875 0.1880 0.011 1.022 0.0 103.2 16.7 230 n/a 4_regHadp: 0.0880 0.1883 0.011 1.022 0.0 103.2 16.7 230 n/a 4_occ: 0.0869 0.1867 0.011 1.022 0.0 103.2 16.7 230 n/a 5_bss: 0.0867 0.1873 0.011 1.022 0.0 103.2 16.7 230 n/a 5_settarget: 0.0867 0.1873 0.011 1.022 0.0 103.2 16.7 230 n/a 5_updatecdl: 0.0867 0.1873 0.011 1.027 0.0 103.2 16.7 230 n/a 5_setrh: 0.0870 0.1873 0.011 1.027 0.0 103.2 16.7 230 n/a 5_nqh: 0.0871 0.1870 0.011 1.027 0.0 103.2 16.7 230 n/a 5_sol: 0.0963 0.1875 0.011 1.027 0.0 103.2 16.7 222 n/a 5_weight: 0.0963 0.1875 0.011 1.027 0.0 103.2 16.7 222 n/a 5_xyzrec: 0.0913 0.1886 0.010 1.103 0.0 103.2 16.7 222 n/a 5_adp: 0.0891 0.1914 0.010 1.103 0.0 105.4 17.0 222 n/a 5_regHadp: 0.0895 0.1919 0.010 1.103 0.0 105.4 17.0 222 n/a 5_occ: 0.0888 0.1904 0.010 1.103 0.0 105.4 17.0 222 n/a end: 0.0888 0.1909 0.010 1.103 0.0 105.4 17.0 222 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_5239121_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_5239121_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.0800 Refinement macro-cycles (run) : 490.3200 Write final files (write_after_run_outputs) : 9.4500 Total : 503.8500 Total CPU time: 8.81 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:19:09 PST -0800 (1735492749.59 s) Start R-work = 0.1563, R-free = 0.1637 Final R-work = 0.0888, R-free = 0.1909 =============================================================================== Job complete usr+sys time: 535.46 seconds wall clock time: 9 minutes 17.48 seconds (557.48 seconds total)