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_9049096.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 { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_9049096.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_9049096.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" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== 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: 1.28, 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: 0.31 Conformation dependent library (CDL) restraints added in 168.8 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.63 - 0.89: 396 0.89 - 1.15: 1225 1.15 - 1.41: 621 1.41 - 1.67: 874 1.67 - 1.93: 37 Bond restraints: 3153 Sorted by residual: bond pdb=" C ILE A 168 " pdb=" O ILE A 168 " ideal model delta sigma weight residual 1.236 1.432 -0.195 9.70e-03 1.06e+04 4.05e+02 bond pdb=" C LYS A 122 " pdb=" O LYS A 122 " ideal model delta sigma weight residual 1.235 1.015 0.221 1.21e-02 6.83e+03 3.32e+02 bond pdb=" C LEU A 172 " pdb=" N ASN A 173 " ideal model delta sigma weight residual 1.332 1.581 -0.249 1.39e-02 5.18e+03 3.22e+02 bond pdb=" N ILE A 105 " pdb=" CA ILE A 105 " ideal model delta sigma weight residual 1.457 1.659 -0.202 1.14e-02 7.69e+03 3.13e+02 bond pdb=" CA VAL A 51 " pdb=" CB VAL A 51 " ideal model delta sigma weight residual 1.537 1.331 0.206 1.17e-02 7.31e+03 3.10e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.32: 2954 4.32 - 8.63: 1867 8.63 - 12.95: 762 12.95 - 17.26: 172 17.26 - 21.58: 22 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA ACYS A 53 " pdb=" C ACYS A 53 " pdb=" O ACYS A 53 " ideal model delta sigma weight residual 119.29 108.55 10.74 6.50e-01 2.37e+00 2.73e+02 angle pdb=" N ILE A 168 " pdb=" CA ILE A 168 " pdb=" C ILE A 168 " ideal model delta sigma weight residual 110.74 95.89 14.85 9.10e-01 1.21e+00 2.66e+02 angle pdb=" C ALA A 107 " pdb=" N GLY A 108 " pdb=" CA GLY A 108 " ideal model delta sigma weight residual 121.13 132.71 -11.58 7.30e-01 1.88e+00 2.52e+02 angle pdb=" NE ARG A 5 " pdb=" CZ ARG A 5 " pdb=" NH1 ARG A 5 " ideal model delta sigma weight residual 121.50 135.02 -13.52 1.00e+00 1.00e+00 1.83e+02 angle pdb=" O ACYS A 53 " pdb=" C ACYS A 53 " pdb=" N PRO A 54 " ideal model delta sigma weight residual 121.23 131.75 -10.52 8.10e-01 1.52e+00 1.69e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 16.49: 1291 16.49 - 32.96: 123 32.96 - 49.44: 51 49.44 - 65.91: 14 65.91 - 82.39: 2 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C ARG A 48 " pdb=" N ARG A 48 " pdb=" CA ARG A 48 " pdb=" CB ARG A 48 " ideal model delta harmonic sigma weight residual -122.60 -141.31 18.71 0 2.50e+00 1.60e-01 5.60e+01 dihedral pdb=" C THR A 110 " pdb=" N THR A 110 " pdb=" CA THR A 110 " pdb=" CB THR A 110 " ideal model delta harmonic sigma weight residual -122.00 -140.31 18.31 0 2.50e+00 1.60e-01 5.36e+01 dihedral pdb=" C VAL A 51 " pdb=" N VAL A 51 " pdb=" CA VAL A 51 " pdb=" CB VAL A 51 " ideal model delta harmonic sigma weight residual -122.00 -139.83 17.83 0 2.50e+00 1.60e-01 5.09e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.005 - 0.229: 92 0.229 - 0.454: 87 0.454 - 0.679: 45 0.679 - 0.904: 16 0.904 - 1.129: 3 Chirality restraints: 243 Sorted by residual: chirality pdb=" CG LEU A 172 " pdb=" CB LEU A 172 " pdb=" CD1 LEU A 172 " pdb=" CD2 LEU A 172 " both_signs ideal model delta sigma weight residual False -2.59 -1.46 -1.13 2.00e-01 2.50e+01 3.19e+01 chirality pdb=" CB THR A 124 " pdb=" CA THR A 124 " pdb=" OG1 THR A 124 " pdb=" CG2 THR A 124 " both_signs ideal model delta sigma weight residual False 2.55 1.42 1.13 2.00e-01 2.50e+01 3.18e+01 chirality pdb=" CA ILE A 168 " pdb=" N ILE A 168 " pdb=" C ILE A 168 " pdb=" CB ILE A 168 " both_signs ideal model delta sigma weight residual False 2.43 3.36 -0.92 2.00e-01 2.50e+01 2.13e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 156 " -0.186 9.50e-02 1.11e+02 9.10e-02 1.03e+02 pdb=" NE ARG A 156 " -0.093 2.00e-02 2.50e+03 pdb=" CZ ARG A 156 " 0.109 2.00e-02 2.50e+03 pdb=" NH1 ARG A 156 " -0.054 2.00e-02 2.50e+03 pdb=" NH2 ARG A 156 " 0.055 2.00e-02 2.50e+03 pdb="HH11 ARG A 156 " 0.074 2.00e-02 2.50e+03 pdb="HH12 ARG A 156 " -0.030 2.00e-02 2.50e+03 pdb="HH21 ARG A 156 " 0.026 2.00e-02 2.50e+03 pdb="HH22 ARG A 156 " -0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 48 " -0.046 9.50e-02 1.11e+02 6.85e-02 1.01e+02 pdb=" NE ARG A 48 " 0.093 2.00e-02 2.50e+03 pdb=" CZ ARG A 48 " -0.037 2.00e-02 2.50e+03 pdb=" NH1 ARG A 48 " 0.070 2.00e-02 2.50e+03 pdb=" NH2 ARG A 48 " -0.011 2.00e-02 2.50e+03 pdb="HH11 ARG A 48 " -0.122 2.00e-02 2.50e+03 pdb="HH12 ARG A 48 " 0.041 2.00e-02 2.50e+03 pdb="HH21 ARG A 48 " -0.078 2.00e-02 2.50e+03 pdb="HH22 ARG A 48 " 0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " 0.009 2.00e-02 2.50e+03 5.53e-02 9.18e+01 pdb=" CG TYR A 141 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " 0.142 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " -0.063 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " -0.057 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " 0.053 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " -0.015 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " -0.010 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " -0.034 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " 0.020 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " 0.006 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " 0.015 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.35: 1220 2.35 - 2.91: 8224 2.91 - 3.47: 10514 3.47 - 4.04: 15150 4.04 - 4.60: 21582 Nonbonded interactions: 56690 Sorted by model distance: nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.783 2.100 nonbonded pdb=" HD3 ARG A 5 " pdb="HH11 ARG A 5 " model vdw 1.840 2.270 nonbonded pdb=" H ASP A 49 " pdb=" HA ASP A 49 " model vdw 1.852 1.816 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.852 2.450 nonbonded pdb=" H THR A 124 " pdb=" HG1 THR A 154 " model vdw 1.852 2.100 ... (remaining 56685 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_9049096_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= 0.3611 r_free= 0.2069 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.463976 | | target function (ml) not normalized (work): 22007.399950 | | target function (ml) not normalized (free): 1155.183722 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3790 0.2311 4.8426 4.9355| | 2: 3.78 - 3.00 1.00 2430 110 0.3392 0.1661 4.0745 4.1304| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 48.86 0.83 0.13 6609.56| | 2: 3.78 - 3.00 2430 110 0.94 11.26 1.48 0.26 445.41| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 378.29 max = 12083.09 mean = 3571.25| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 89.97 mean = 30.33| |phase err.(test): min = 0.00 max = 90.00 mean = 33.30| |-----------------------------------------------------------------------------| ----------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 : 0.082 0.250 1557 Z= 5.564 Angle : 5.272 17.218 2118 Z= 3.760 Chirality : 0.389 1.129 243 Planarity : 0.032 0.084 284 Dihedral : 13.915 82.386 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.54 % Allowed : 1.62 % Favored : 97.84 % Rotamer: Outliers : 1.24 % Allowed : 3.73 % Favored : 95.03 % Cbeta Deviations : 31.89 % 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: -2.93 (0.44), residues: 224 helix: -2.86 (0.37), residues: 109 sheet: -0.74 (0.76), residues: 28 loop : -0.74 (0.51), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.103 0.025 ARG A 156 TYR 0.115 0.046 TYR A 141 PHE 0.110 0.045 PHE A 164 HIS 0.058 0.032 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= 0.3611 r_free= 0.2069 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.463976 | | target function (ml) not normalized (work): 22007.399950 | | target function (ml) not normalized (free): 1155.183722 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3569 0.3645 0.2180 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3569 0.3645 0.2180 n_refl.: 5182 remove outliers: r(all,work,free)=0.2516 0.2538 0.2180 n_refl.: 5178 overall B=-2.81 to atoms: r(all,work,free)=0.2412 0.2430 0.2137 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1562 0.1557 0.1668 n_refl.: 5178 remove outliers: r(all,work,free)=0.1558 0.1552 0.1668 n_refl.: 5176 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 98.94 88 5 0.3846 449.758 408.031 0.682 1.043 0.401 11.894-9.307 99.02 97 4 0.1872 714.476 695.845 0.965 1.041 0.388 9.237-7.194 100.00 213 7 0.2188 584.299 575.115 0.992 1.036 0.374 7.162-5.571 100.00 427 22 0.2331 438.446 425.007 0.952 1.029 0.289 5.546-4.326 100.00 867 58 0.1367 601.924 595.301 0.986 1.016 0.236 4.315-3.360 100.00 1859 96 0.1295 572.436 566.338 1.052 0.994 0.210 3.356-3.002 100.00 1373 60 0.1604 440.914 432.933 1.044 0.972 0.064 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9555 b_overall=-3.5928 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1552 r_free=0.1668 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN A A 80 GLN A A 80 GLN B Total number of N/Q/H flips: 4 r_work=0.1560 r_free=0.1678 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 19.583966 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.804927 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 0.1170 0.1798 0.0628 0.010 1.0 3.2 0.5 0.0 0 9.792 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.70 17.98 6.28 3.013 16.049 1.805 0.018 10.30 18.02 7.73 4.729 16.190 1.805 0.015 Individual atomic B min max mean iso aniso Overall: 1.99 111.88 17.34 5.15 1785 0 Protein: 1.99 111.88 14.63 5.15 1519 0 Water: 4.06 111.49 33.10 N/A 258 0 Other: 17.19 35.09 23.76 N/A 8 0 Chain A: 1.99 111.88 17.34 N/A 1785 0 Histogram: Values Number of atoms 1.99 - 12.98 911 12.98 - 23.97 493 23.97 - 34.96 187 34.96 - 45.95 106 45.95 - 56.94 56 56.94 - 67.93 16 67.93 - 78.92 7 78.92 - 89.90 5 89.90 - 100.89 1 100.89 - 111.88 3 =========================== Idealize ADP of riding H ========================== r_work=0.1030 r_free=0.1802 r_work=0.1023 r_free=0.1811 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1023 r_free = 0.1811 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 = 0.1017 r_free = 0.1809 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.1017 r_free= 0.1809 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ls_wunit_k1) (work): 0.014189 | | target function (ls_wunit_k1) not normalized (work): 69.864623 | | target function (ls_wunit_k1) not normalized (free): 10.866773 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1058 0.1017 0.1809 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2096 0.2094 0.2253 n_refl.: 5176 remove outliers: r(all,work,free)=0.2096 0.2094 0.2253 n_refl.: 5176 overall B=-0.95 to atoms: r(all,work,free)=0.2057 0.2052 0.2242 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.1056 0.1016 0.1804 n_refl.: 5176 remove outliers: r(all,work,free)=0.1056 0.1016 0.1804 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 0.3423 330.254 312.079 0.672 1.014 0.385 11.894-9.307 99.02 97 4 0.1520 524.635 515.449 0.978 1.014 0.354 9.237-7.194 100.00 213 7 0.1674 429.047 428.561 1.017 1.013 0.341 7.162-5.571 100.00 427 22 0.1613 321.948 318.281 0.979 1.010 0.282 5.546-4.326 100.00 867 58 0.0913 441.988 438.812 0.994 1.005 0.217 4.315-3.360 100.00 1859 96 0.0767 420.336 420.373 1.045 0.997 0.203 3.356-3.002 100.00 1373 60 0.1006 323.760 322.218 1.017 0.990 0.061 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-3.4035 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1016 r_free=0.1804 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN B Total number of N/Q/H flips: 1 r_work=0.1017 r_free=0.1805 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1017 r_free=0.1805 | n_water=258 | time (s): 0.470 (total time: 0.470) Filter (dist) r_work=0.1043 r_free=0.1805 | n_water=247 | time (s): 20.060 (total time: 20.530) Filter (q & B) r_work=0.1043 r_free=0.1806 | n_water=244 | time (s): 1.370 (total time: 21.900) Compute maps r_work=0.1043 r_free=0.1806 | n_water=244 | time (s): 0.570 (total time: 22.470) Filter (map) r_work=0.1367 r_free=0.1828 | n_water=139 | time (s): 2.060 (total time: 24.530) Find peaks r_work=0.1367 r_free=0.1828 | n_water=139 | time (s): 0.620 (total time: 25.150) Add new water r_work=0.1726 r_free=0.2069 | n_water=228 | time (s): 1.790 (total time: 26.940) Refine new water occ: r_work=0.1167 r_free=0.1693 adp: r_work=0.1142 r_free=0.1718 occ: r_work=0.1139 r_free=0.1672 adp: r_work=0.1129 r_free=0.1692 occ: r_work=0.1128 r_free=0.1676 adp: r_work=0.1126 r_free=0.1682 ADP+occupancy (water only), MIN, final r_work=0.1126 r_free=0.1682 r_work=0.1126 r_free=0.1682 | n_water=228 | time (s): 7.510 (total time: 34.450) Filter (q & B) r_work=0.1127 r_free=0.1690 | n_water=227 | time (s): 1.520 (total time: 35.970) Filter (dist only) r_work=0.1132 r_free=0.1690 | n_water=224 | time (s): 16.460 (total time: 52.430) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.559444 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.839442 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 0.1016 0.1798 0.0783 0.009 1.0 4.8 0.5 0.6 0 11.280 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.16 17.98 7.83 4.577 16.693 2.839 0.014 9.48 18.44 8.96 5.524 17.162 2.839 0.012 Individual atomic B min max mean iso aniso Overall: 0.00 108.56 16.67 6.57 1751 0 Protein: 0.00 108.56 15.11 6.56 1519 0 Water: 0.00 62.82 27.05 N/A 224 0 Other: 11.96 33.34 22.55 N/A 8 0 Chain A: 0.00 108.56 15.80 N/A 1663 0 Chain S: 0.00 61.87 33.21 N/A 88 0 Histogram: Values Number of atoms 0.00 - 10.86 682 10.86 - 21.71 666 21.71 - 32.57 212 32.57 - 43.42 106 43.42 - 54.28 44 54.28 - 65.13 28 65.13 - 75.99 6 75.99 - 86.85 3 86.85 - 97.70 2 97.70 - 108.56 2 =========================== Idealize ADP of riding H ========================== r_work=0.0948 r_free=0.1844 r_work=0.0945 r_free=0.1845 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0945 r_free = 0.1845 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0941 r_free = 0.1830 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.0941 r_free= 0.1830 coordinate error (max.-lik. estimate): 0.31 A | | | | normalized target function (ls_wunit_k1) (work): 0.011949 | | target function (ls_wunit_k1) not normalized (work): 58.838185 | | target function (ls_wunit_k1) not normalized (free): 10.299034 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0986 0.0941 0.1830 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2137 0.2144 0.2177 n_refl.: 5176 remove outliers: r(all,work,free)=0.2137 0.2144 0.2177 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2137 0.2144 0.2177 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0988 0.0943 0.1843 n_refl.: 5176 remove outliers: r(all,work,free)=0.0986 0.0941 0.1843 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 0.3286 327.472 310.020 0.681 1.001 0.364 11.894-9.307 99.02 97 4 0.1380 524.635 518.245 0.993 1.004 0.360 9.237-7.194 100.00 213 7 0.1445 429.047 426.234 1.023 1.004 0.330 7.162-5.571 100.00 427 22 0.1384 321.948 318.370 0.997 1.003 0.270 5.546-4.326 100.00 867 58 0.0801 441.988 438.576 1.009 1.003 0.250 4.315-3.360 100.00 1859 96 0.0735 420.336 420.621 1.061 1.001 0.213 3.356-3.002 100.00 1373 60 0.0980 323.760 323.766 1.031 0.999 0.090 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9552 b_overall=-4.3987 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0941 r_free=0.1843 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=0.0943 r_free=0.1839 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0943 r_free=0.1839 | n_water=224 | time (s): 0.500 (total time: 0.500) Filter (dist) r_work=0.0967 r_free=0.1858 | n_water=219 | time (s): 18.010 (total time: 18.510) Filter (q & B) r_work=0.1051 r_free=0.1816 | n_water=215 | time (s): 1.390 (total time: 19.900) Compute maps r_work=0.1051 r_free=0.1816 | n_water=215 | time (s): 0.490 (total time: 20.390) Filter (map) r_work=0.1279 r_free=0.1837 | n_water=145 | time (s): 1.700 (total time: 22.090) Find peaks r_work=0.1279 r_free=0.1837 | n_water=145 | time (s): 0.590 (total time: 22.680) Add new water r_work=0.1676 r_free=0.2179 | n_water=231 | time (s): 1.570 (total time: 24.250) Refine new water occ: r_work=0.1066 r_free=0.1788 adp: r_work=0.1059 r_free=0.1805 occ: r_work=0.1050 r_free=0.1797 adp: r_work=0.1049 r_free=0.1798 occ: r_work=0.1040 r_free=0.1790 adp: r_work=0.1040 r_free=0.1792 ADP+occupancy (water only), MIN, final r_work=0.1040 r_free=0.1792 r_work=0.1040 r_free=0.1792 | n_water=231 | time (s): 8.290 (total time: 32.540) Filter (q & B) r_work=0.1040 r_free=0.1792 | n_water=231 | time (s): 1.110 (total time: 33.650) Filter (dist only) r_work=0.1039 r_free=0.1794 | n_water=230 | time (s): 19.120 (total time: 52.770) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.094272 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.232325 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 0.0938 0.1853 0.0915 0.011 1.1 5.1 0.5 0.6 0 0.547 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.38 18.53 9.15 5.474 17.870 0.232 5.159 8.93 18.56 9.63 7.368 17.904 0.232 5.060 Individual atomic B min max mean iso aniso Overall: 0.00 106.96 16.48 9.13 1757 0 Protein: 0.00 106.96 15.28 9.12 1519 0 Water: 0.00 57.82 24.17 N/A 230 0 Other: 9.44 38.31 23.90 N/A 8 0 Chain A: 0.00 106.96 15.88 N/A 1646 0 Chain S: 0.00 54.24 25.39 N/A 111 0 Histogram: Values Number of atoms 0.00 - 10.70 672 10.70 - 21.39 654 21.39 - 32.09 243 32.09 - 42.79 121 42.79 - 53.48 28 53.48 - 64.18 19 64.18 - 74.88 10 74.88 - 85.57 5 85.57 - 96.27 4 96.27 - 106.96 1 =========================== Idealize ADP of riding H ========================== r_work=0.0893 r_free=0.1856 r_work=0.0898 r_free=0.1858 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0898 r_free = 0.1858 target_work(ml) = 5.064 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0888 r_free = 0.1836 target_work(ml) = 5.057 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0888 r_free= 0.1836 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ml) (work): 5.057461 | | target function (ml) not normalized (work): 24897.878824 | | target function (ml) not normalized (free): 1896.124743 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0936 0.0888 0.1836 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2120 0.2131 0.2099 n_refl.: 5175 remove outliers: r(all,work,free)=0.2120 0.2131 0.2099 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2120 0.2131 0.2099 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0928 0.0880 0.1838 n_refl.: 5175 remove outliers: r(all,work,free)=0.0926 0.0878 0.1838 n_refl.: 5174 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 94.79 86 5 0.3600 329.650 298.170 0.607 0.994 0.350 11.894-9.307 99.02 97 4 0.1759 524.635 510.503 0.943 0.998 0.325 9.237-7.194 100.00 213 7 0.1953 429.047 421.273 0.995 1.000 0.300 7.162-5.571 100.00 427 22 0.1797 321.948 313.958 0.977 1.001 0.290 5.546-4.326 100.00 867 58 0.0908 441.988 436.849 0.996 1.001 0.235 4.315-3.360 100.00 1859 96 0.0578 420.336 420.127 1.059 1.002 0.230 3.356-3.002 100.00 1373 60 0.0599 323.760 323.519 1.031 1.003 0.080 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9171 b_overall=-6.3719 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0878 r_free=0.1838 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0878 r_free=0.1838 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0878 r_free=0.1838 | n_water=230 | time (s): 0.510 (total time: 0.510) Filter (dist) r_work=0.0913 r_free=0.1857 | n_water=224 | time (s): 16.830 (total time: 17.340) Filter (q & B) r_work=0.0985 r_free=0.1878 | n_water=221 | time (s): 1.600 (total time: 18.940) Compute maps r_work=0.0985 r_free=0.1878 | n_water=221 | time (s): 0.520 (total time: 19.460) Filter (map) r_work=0.1232 r_free=0.1919 | n_water=154 | time (s): 1.650 (total time: 21.110) Find peaks r_work=0.1232 r_free=0.1919 | n_water=154 | time (s): 0.450 (total time: 21.560) Add new water r_work=0.1561 r_free=0.2157 | n_water=229 | time (s): 1.540 (total time: 23.100) Refine new water occ: r_work=0.1019 r_free=0.1831 adp: r_work=0.1013 r_free=0.1838 occ: r_work=0.1005 r_free=0.1830 adp: r_work=0.1004 r_free=0.1832 occ: r_work=0.0996 r_free=0.1825 adp: r_work=0.0996 r_free=0.1830 ADP+occupancy (water only), MIN, final r_work=0.0996 r_free=0.1830 r_work=0.0996 r_free=0.1830 | n_water=229 | time (s): 11.610 (total time: 34.710) Filter (q & B) r_work=0.0997 r_free=0.1830 | n_water=228 | time (s): 1.730 (total time: 36.440) Filter (dist only) r_work=0.1006 r_free=0.1836 | n_water=226 | time (s): 17.030 (total time: 53.470) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.965543 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.284232 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 0.0917 0.1841 0.0925 0.010 1.0 4.8 0.5 0.0 0 0.483 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.17 18.41 9.25 7.098 18.071 0.284 5.059 8.92 18.89 9.98 8.698 18.240 0.284 4.991 Individual atomic B min max mean iso aniso Overall: 0.00 107.04 16.85 11.42 1753 0 Protein: 0.00 107.04 15.79 11.42 1519 0 Water: 0.00 55.43 23.69 N/A 226 0 Other: 13.45 41.10 25.47 N/A 8 0 Chain A: 0.00 107.04 16.29 N/A 1635 0 Chain S: 0.00 55.43 24.68 N/A 118 0 Histogram: Values Number of atoms 0.00 - 10.70 661 10.70 - 21.41 623 21.41 - 32.11 265 32.11 - 42.81 122 42.81 - 53.52 44 53.52 - 64.22 17 64.22 - 74.93 9 74.93 - 85.63 7 85.63 - 96.33 3 96.33 - 107.04 2 =========================== Idealize ADP of riding H ========================== r_work=0.0892 r_free=0.1889 r_work=0.0898 r_free=0.1893 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0898 r_free = 0.1893 target_work(ml) = 4.999 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0887 r_free = 0.1889 target_work(ml) = 4.991 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0887 r_free= 0.1889 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ml) (work): 4.991390 | | target function (ml) not normalized (work): 24567.621976 | | target function (ml) not normalized (free): 2181.844630 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0938 0.0887 0.1889 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2082 0.2082 0.2214 n_refl.: 5174 remove outliers: r(all,work,free)=0.2082 0.2082 0.2214 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2082 0.2082 0.2214 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0938 0.0887 0.1884 n_refl.: 5174 remove outliers: r(all,work,free)=0.0938 0.0887 0.1884 n_refl.: 5174 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 94.79 86 5 0.3766 329.650 300.241 0.582 0.987 0.317 11.894-9.307 99.02 97 4 0.1886 524.635 507.610 0.949 0.992 0.316 9.237-7.194 100.00 213 7 0.2179 429.047 418.444 1.005 0.995 0.290 7.162-5.571 100.00 427 22 0.1977 321.948 312.798 0.992 0.996 0.264 5.546-4.326 100.00 867 58 0.0984 441.988 435.307 1.018 0.999 0.240 4.315-3.360 100.00 1859 96 0.0560 420.336 420.286 1.086 1.002 0.230 3.356-3.002 100.00 1373 60 0.0479 323.760 324.061 1.061 1.005 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.7061 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0887 r_free=0.1884 After: r_work=0.0890 r_free=0.1882 ================================== NQH flips ================================== r_work=0.0890 r_free=0.1882 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0890 r_free=0.1882 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0890 r_free=0.1882 | n_water=226 | time (s): 0.530 (total time: 0.530) Filter (dist) r_work=0.0907 r_free=0.1890 | n_water=222 | time (s): 17.900 (total time: 18.430) Filter (q & B) r_work=0.1065 r_free=0.1935 | n_water=216 | time (s): 1.460 (total time: 19.890) Compute maps r_work=0.1065 r_free=0.1935 | n_water=216 | time (s): 0.600 (total time: 20.490) Filter (map) r_work=0.1302 r_free=0.1966 | n_water=153 | time (s): 1.780 (total time: 22.270) Find peaks r_work=0.1302 r_free=0.1966 | n_water=153 | time (s): 0.600 (total time: 22.870) Add new water r_work=0.1590 r_free=0.2229 | n_water=221 | time (s): 1.620 (total time: 24.490) Refine new water occ: r_work=0.1013 r_free=0.1840 adp: r_work=0.1002 r_free=0.1843 occ: r_work=0.0994 r_free=0.1835 adp: r_work=0.0993 r_free=0.1839 occ: r_work=0.0987 r_free=0.1832 adp: r_work=0.0986 r_free=0.1837 ADP+occupancy (water only), MIN, final r_work=0.0986 r_free=0.1837 r_work=0.0986 r_free=0.1837 | n_water=221 | time (s): 13.210 (total time: 37.700) Filter (q & B) r_work=0.0986 r_free=0.1836 | n_water=220 | time (s): 1.500 (total time: 39.200) Filter (dist only) r_work=0.0986 r_free=0.1836 | n_water=220 | time (s): 15.570 (total time: 54.770) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.973845 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.235587 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 0.0923 0.1827 0.0904 0.011 1.1 8.3 0.5 0.0 0 0.487 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.23 18.27 9.04 8.637 18.602 0.236 5.019 9.02 18.35 9.33 9.415 18.712 0.236 4.968 Individual atomic B min max mean iso aniso Overall: 0.00 108.09 17.13 12.49 1747 0 Protein: 0.00 108.09 16.17 12.50 1519 0 Water: 0.30 59.18 23.40 N/A 220 0 Other: 15.09 41.88 26.39 N/A 8 0 Chain A: 0.00 108.09 16.63 N/A 1630 0 Chain S: 0.30 59.18 24.05 N/A 117 0 Histogram: Values Number of atoms 0.00 - 10.81 637 10.81 - 21.62 643 21.62 - 32.43 274 32.43 - 43.24 104 43.24 - 54.04 48 54.04 - 64.85 18 64.85 - 75.66 9 75.66 - 86.47 7 86.47 - 97.28 4 97.28 - 108.09 3 =========================== Idealize ADP of riding H ========================== r_work=0.0902 r_free=0.1835 r_work=0.0904 r_free=0.1835 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0904 r_free = 0.1835 target_work(ml) = 4.973 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0899 r_free = 0.1819 target_work(ml) = 4.969 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0899 r_free= 0.1819 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 4.968698 | | target function (ml) not normalized (work): 24455.929514 | | target function (ml) not normalized (free): 2268.341564 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.79 1.00 2492 142 0.1281 0.1761 5.5429 6.25| | 2: 3.78 - 3.00 1.00 2430 110 0.0433 0.1917 4.3798 12.553| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.79 2492 142 0.91 12.31 1.00 0.97 13406.96| | 2: 3.78 - 3.00 2430 110 0.99 1.91 1.00 1.00 954.60| |alpha: min = 0.96 max = 1.00 mean = 0.99| |beta: min = 615.95 max = 22486.82 mean = 7259.21| |figures of merit: min = 0.00 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.81 mean = 7.18| |phase err.(test): min = 0.00 max = 85.72 mean = 7.64| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0946 0.0899 0.1819 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2118 0.2120 0.2175 n_refl.: 5174 remove outliers: r(all,work,free)=0.2118 0.2120 0.2175 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2118 0.2120 0.2175 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0947 0.0900 0.1829 n_refl.: 5174 remove outliers: r(all,work,free)=0.0947 0.0900 0.1829 n_refl.: 5174 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 94.79 86 5 0.3867 329.650 291.341 0.592 0.986 0.317 11.894-9.307 99.02 97 4 0.1907 524.635 513.398 1.007 0.992 0.314 9.237-7.194 100.00 213 7 0.2239 429.047 419.461 1.055 0.995 0.295 7.162-5.571 100.00 427 22 0.2039 321.948 313.132 1.041 0.997 0.290 5.546-4.326 100.00 867 58 0.1050 441.988 433.592 1.064 0.999 0.240 4.315-3.360 100.00 1859 96 0.0565 420.336 420.831 1.150 1.002 0.240 3.356-3.002 100.00 1373 60 0.0425 323.760 323.820 1.125 1.005 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-8.4725 ================= 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 : 0.3611 0.2069 0.082 5.272 8.8 119.3 19.9 258 0.000 1_bss: 0.1552 0.1668 0.082 5.272 6.0 116.5 17.1 258 0.000 1_settarget: 0.1552 0.1668 0.082 5.272 6.0 116.5 17.1 258 0.000 1_nqh: 0.1560 0.1678 0.082 5.272 6.0 116.5 17.1 258 0.013 1_weight: 0.1560 0.1678 0.082 5.272 6.0 116.5 17.1 258 0.013 1_xyzrec: 0.1170 0.1798 0.010 0.981 6.0 116.5 17.1 258 0.208 1_adp: 0.1030 0.1802 0.010 0.981 2.0 111.9 17.3 258 0.208 1_regHadp: 0.1023 0.1811 0.010 0.981 2.0 111.9 17.3 258 0.208 1_occ: 0.1017 0.1809 0.010 0.981 2.0 111.9 17.3 258 0.208 2_bss: 0.1016 0.1804 0.010 0.981 1.0 110.9 16.4 258 0.208 2_settarget: 0.1016 0.1804 0.010 0.981 1.0 110.9 16.4 258 0.208 2_updatecdl: 0.1016 0.1804 0.010 1.008 1.0 110.9 16.4 258 0.208 2_nqh: 0.1017 0.1805 0.010 1.008 1.0 110.9 16.4 258 0.206 2_sol: 0.1132 0.1690 0.010 1.008 1.0 110.9 15.8 224 n/a 2_weight: 0.1132 0.1690 0.010 1.008 1.0 110.9 15.8 224 n/a 2_xyzrec: 0.1016 0.1798 0.009 0.969 1.0 110.9 15.8 224 n/a 2_adp: 0.0948 0.1844 0.009 0.969 0.0 108.6 16.7 224 n/a 2_regHadp: 0.0945 0.1845 0.009 0.969 0.0 108.6 16.7 224 n/a 2_occ: 0.0941 0.1830 0.009 0.969 0.0 108.6 16.7 224 n/a 3_bss: 0.0941 0.1843 0.009 0.969 0.0 108.6 16.7 224 n/a 3_settarget: 0.0941 0.1843 0.009 0.969 0.0 108.6 16.7 224 n/a 3_updatecdl: 0.0941 0.1843 0.009 0.976 0.0 108.6 16.7 224 n/a 3_nqh: 0.0943 0.1839 0.009 0.976 0.0 108.6 16.7 224 n/a 3_sol: 0.1039 0.1794 0.009 0.976 0.0 108.6 16.4 230 n/a 3_weight: 0.1039 0.1794 0.009 0.976 0.0 108.6 16.4 230 n/a 3_xyzrec: 0.0938 0.1853 0.011 1.065 0.0 108.6 16.4 230 n/a 3_adp: 0.0893 0.1856 0.011 1.065 0.0 107.0 16.5 230 n/a 3_regHadp: 0.0898 0.1858 0.011 1.065 0.0 107.0 16.5 230 n/a 3_occ: 0.0888 0.1836 0.011 1.065 0.0 107.0 16.5 230 n/a 4_bss: 0.0878 0.1838 0.011 1.065 0.0 107.0 16.5 230 n/a 4_settarget: 0.0878 0.1838 0.011 1.065 0.0 107.0 16.5 230 n/a 4_updatecdl: 0.0878 0.1838 0.011 1.076 0.0 107.0 16.5 230 n/a 4_nqh: 0.0878 0.1838 0.011 1.076 0.0 107.0 16.5 230 n/a 4_sol: 0.1006 0.1836 0.011 1.076 0.0 107.0 16.5 226 n/a 4_weight: 0.1006 0.1836 0.011 1.076 0.0 107.0 16.5 226 n/a 4_xyzrec: 0.0917 0.1841 0.010 1.011 0.0 107.0 16.5 226 n/a 4_adp: 0.0892 0.1889 0.010 1.011 0.0 107.0 16.9 226 n/a 4_regHadp: 0.0898 0.1893 0.010 1.011 0.0 107.0 16.9 226 n/a 4_occ: 0.0887 0.1889 0.010 1.011 0.0 107.0 16.9 226 n/a 5_bss: 0.0887 0.1884 0.010 1.011 0.0 107.0 16.9 226 n/a 5_settarget: 0.0887 0.1884 0.010 1.011 0.0 107.0 16.9 226 n/a 5_updatecdl: 0.0887 0.1884 0.010 1.017 0.0 107.0 16.9 226 n/a 5_setrh: 0.0890 0.1882 0.010 1.017 0.0 107.0 16.9 226 n/a 5_nqh: 0.0890 0.1882 0.010 1.017 0.0 107.0 16.9 226 n/a 5_sol: 0.0986 0.1836 0.010 1.017 0.0 107.0 16.9 220 n/a 5_weight: 0.0986 0.1836 0.010 1.017 0.0 107.0 16.9 220 n/a 5_xyzrec: 0.0923 0.1827 0.011 1.121 0.0 107.0 16.9 220 n/a 5_adp: 0.0902 0.1835 0.011 1.121 0.0 108.1 17.1 220 n/a 5_regHadp: 0.0904 0.1835 0.011 1.121 0.0 108.1 17.1 220 n/a 5_occ: 0.0899 0.1819 0.011 1.121 0.0 108.1 17.1 220 n/a end: 0.0900 0.1829 0.011 1.121 0.0 108.1 17.1 220 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_9049096_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_9049096_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.8200 Refinement macro-cycles (run) : 488.4600 Write final files (write_after_run_outputs) : 10.8600 Total : 503.1400 Total CPU time: 8.75 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:19:04 PST -0800 (1735492744.65 s) Start R-work = 0.1552, R-free = 0.1668 Final R-work = 0.0900, R-free = 0.1829 =============================================================================== Job complete usr+sys time: 532.75 seconds wall clock time: 9 minutes 13.31 seconds (553.31 seconds total)