Starting phenix.refine on Sun Dec 29 09:10:02 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6462862.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" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 3 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6462862.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6462862.pdb" } 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: 1.45, per 1000 atoms: 0.43 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: 0.30 Conformation dependent library (CDL) restraints added in 117.3 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.92: 532 0.92 - 1.17: 1105 1.17 - 1.43: 688 1.43 - 1.69: 810 1.69 - 1.95: 18 Bond restraints: 3153 Sorted by residual: bond pdb=" N ALEU A 153 " pdb=" CA ALEU A 153 " ideal model delta sigma weight residual 1.456 1.726 -0.269 1.21e-02 6.83e+03 4.96e+02 bond pdb=" C VAL A 69 " pdb=" O VAL A 69 " ideal model delta sigma weight residual 1.235 1.423 -0.188 1.02e-02 9.61e+03 3.40e+02 bond pdb=" N BLYS A 132 " pdb=" CA BLYS A 132 " ideal model delta sigma weight residual 1.459 1.669 -0.210 1.19e-02 7.06e+03 3.12e+02 bond pdb=" N ASP A 60 " pdb=" CA ASP A 60 " ideal model delta sigma weight residual 1.459 1.255 0.204 1.17e-02 7.31e+03 3.03e+02 bond pdb=" N LEU A 72 " pdb=" CA LEU A 72 " ideal model delta sigma weight residual 1.454 1.661 -0.207 1.21e-02 6.83e+03 2.91e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.22: 2904 4.22 - 8.44: 1893 8.44 - 12.65: 760 12.65 - 16.87: 193 16.87 - 21.09: 27 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA ILE A 117 " pdb=" C ILE A 117 " pdb=" O ILE A 117 " ideal model delta sigma weight residual 120.84 136.82 -15.98 1.16e+00 7.43e-01 1.90e+02 angle pdb=" CA LYS A 12 " pdb=" C LYS A 12 " pdb=" O LYS A 12 " ideal model delta sigma weight residual 120.96 105.98 14.98 1.09e+00 8.42e-01 1.89e+02 angle pdb=" O VAL A 169 " pdb=" C VAL A 169 " pdb=" N GLU A 170 " ideal model delta sigma weight residual 121.91 135.32 -13.41 9.80e-01 1.04e+00 1.87e+02 angle pdb=" O ARG A 28 " pdb=" C ARG A 28 " pdb=" N ALA A 29 " ideal model delta sigma weight residual 122.12 107.87 14.25 1.06e+00 8.90e-01 1.81e+02 angle pdb=" C LEU A 72 " pdb=" CA LEU A 72 " pdb=" CB LEU A 72 " ideal model delta sigma weight residual 110.17 123.12 -12.95 9.90e-01 1.02e+00 1.71e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 1322 17.98 - 35.96: 108 35.96 - 53.93: 38 53.93 - 71.91: 10 71.91 - 89.89: 3 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C ASP A 49 " pdb=" N ASP A 49 " pdb=" CA ASP A 49 " pdb=" CB ASP A 49 " ideal model delta harmonic sigma weight residual -122.60 -147.92 25.32 0 2.50e+00 1.60e-01 1.03e+02 dihedral pdb=" C ALA A 86 " pdb=" N ALA A 86 " pdb=" CA ALA A 86 " pdb=" CB ALA A 86 " ideal model delta harmonic sigma weight residual -122.60 -146.84 24.24 0 2.50e+00 1.60e-01 9.40e+01 dihedral pdb=" N ASP A 49 " pdb=" C ASP A 49 " pdb=" CA ASP A 49 " pdb=" CB ASP A 49 " ideal model delta harmonic sigma weight residual 122.80 146.09 -23.29 0 2.50e+00 1.60e-01 8.68e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.272: 117 0.272 - 0.544: 84 0.544 - 0.815: 28 0.815 - 1.086: 12 1.086 - 1.358: 2 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA ASP A 49 " pdb=" N ASP A 49 " pdb=" C ASP A 49 " pdb=" CB ASP A 49 " both_signs ideal model delta sigma weight residual False 2.51 1.15 1.36 2.00e-01 2.50e+01 4.61e+01 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 -1.35 -1.24 2.00e-01 2.50e+01 3.83e+01 chirality pdb=" CA ALA A 86 " pdb=" N ALA A 86 " pdb=" C ALA A 86 " pdb=" CB ALA A 86 " both_signs ideal model delta sigma weight residual False 2.48 1.47 1.01 2.00e-01 2.50e+01 2.57e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.072 2.00e-02 2.50e+03 6.94e-02 1.44e+02 pdb=" CG PHE A 164 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.134 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.038 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.017 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.079 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.065 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.034 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.066 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.058 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.110 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " -0.016 2.00e-02 2.50e+03 6.26e-02 1.18e+02 pdb=" CG PHE A 162 " 0.069 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " 0.096 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " -0.089 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " -0.013 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " 0.010 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " -0.095 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " -0.085 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " 0.019 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " 0.085 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " -0.079 2.00e-02 2.50e+03 5.99e-02 1.08e+02 pdb=" CG ATYR A 67 " -0.065 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " 0.035 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " 0.069 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " 0.115 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " 0.027 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " -0.011 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " -0.042 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " 0.043 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " 0.021 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " -0.088 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " -0.026 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 398 2.19 - 2.80: 7074 2.80 - 3.40: 10882 3.40 - 4.00: 15533 4.00 - 4.60: 22718 Nonbonded interactions: 56605 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.592 2.100 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.789 2.450 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.803 2.450 nonbonded pdb=" H THR A 125 " pdb=" HH TYR A 141 " model vdw 1.810 2.100 nonbonded pdb=" H THR A 124 " pdb=" HG1 THR A 154 " model vdw 1.823 2.100 ... (remaining 56600 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_6462862_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= 0.3613 r_free= 0.2028 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.475315 | | target function (ml) not normalized (work): 22063.303446 | | target function (ml) not normalized (free): 1151.981902 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3798 0.2205 4.8563 4.923| | 2: 3.78 - 3.00 1.00 2430 110 0.3387 0.1729 4.0834 4.1174| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 48.87 0.83 0.13 6615.01| | 2: 3.78 - 3.00 2430 110 0.94 11.37 1.48 0.26 456.90| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 389.24 max = 12078.36 mean = 3579.67| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 89.99 mean = 30.39| |phase err.(test): min = 0.00 max = 89.96 mean = 33.44| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.081 0.269 1557 Z= 5.407 Angle : 5.189 18.284 2118 Z= 3.660 Chirality : 0.408 1.358 243 Planarity : 0.032 0.088 284 Dihedral : 13.844 89.886 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.54 % Allowed : 5.41 % Favored : 94.05 % Rotamer: Outliers : 1.24 % Allowed : 3.73 % Favored : 95.03 % Cbeta Deviations : 35.14 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.21 (0.42), residues: 224 helix: -2.76 (0.33), residues: 107 sheet: -2.02 (0.79), residues: 24 loop : -1.05 (0.51), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.093 0.026 ARG A 98 TYR 0.072 0.044 TYR A 139 PHE 0.095 0.041 PHE A 164 HIS 0.045 0.026 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= 0.3613 r_free= 0.2028 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.475315 | | target function (ml) not normalized (work): 22063.303446 | | target function (ml) not normalized (free): 1151.981902 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3568 0.3644 0.2160 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3568 0.3644 0.2160 n_refl.: 5182 remove outliers: r(all,work,free)=0.2523 0.2547 0.2160 n_refl.: 5178 overall B=-2.86 to atoms: r(all,work,free)=0.2414 0.2434 0.2122 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1574 0.1570 0.1650 n_refl.: 5178 remove outliers: r(all,work,free)=0.1570 0.1566 0.1650 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 0.3904 449.846 407.448 0.642 1.092 0.398 11.894-9.307 99.02 97 4 0.1880 714.616 693.219 0.919 1.087 0.372 9.237-7.194 100.00 213 7 0.2190 584.414 576.360 0.954 1.077 0.343 7.162-5.571 100.00 427 22 0.2335 438.532 423.760 0.922 1.060 0.326 5.546-4.326 100.00 867 58 0.1387 602.042 595.288 0.971 1.033 0.220 4.315-3.360 100.00 1859 96 0.1312 572.548 566.939 1.060 0.986 0.189 3.356-3.002 100.00 1373 60 0.1607 441.001 433.140 1.085 0.940 0.118 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9556 b_overall=-3.6540 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1566 r_free=0.1650 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN Total number of N/Q/H flips: 1 r_work=0.1565 r_free=0.1648 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 18.426712 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.710998 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 0.1151 0.1779 0.0628 0.009 1.0 2.9 0.5 0.0 0 9.213 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.51 17.79 6.28 3.013 16.000 1.711 0.018 10.15 17.77 7.62 4.845 16.242 1.711 0.014 Individual atomic B min max mean iso aniso Overall: 2.32 111.44 17.49 5.19 1785 0 Protein: 2.32 110.57 14.78 5.18 1519 0 Water: 4.01 111.44 33.20 N/A 258 0 Other: 16.55 38.75 23.76 N/A 8 0 Chain A: 2.32 111.44 17.49 N/A 1785 0 Histogram: Values Number of atoms 2.32 - 13.23 926 13.23 - 24.14 472 24.14 - 35.05 191 35.05 - 45.97 110 45.97 - 56.88 55 56.88 - 67.79 13 67.79 - 78.70 8 78.70 - 89.62 5 89.62 - 100.53 1 100.53 - 111.44 4 =========================== Idealize ADP of riding H ========================== r_work=0.1015 r_free=0.1777 r_work=0.1009 r_free=0.1783 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1009 r_free = 0.1783 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1009 r_free = 0.1786 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.24 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= 0.1009 r_free= 0.1786 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ls_wunit_k1) (work): 0.013851 | | target function (ls_wunit_k1) not normalized (work): 68.202483 | | target function (ls_wunit_k1) not normalized (free): 10.375964 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1049 0.1009 0.1786 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2085 0.2083 0.2242 n_refl.: 5176 remove outliers: r(all,work,free)=0.2085 0.2083 0.2242 n_refl.: 5176 overall B=-0.97 to atoms: r(all,work,free)=0.2045 0.2040 0.2229 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.1049 0.1011 0.1779 n_refl.: 5176 remove outliers: r(all,work,free)=0.1049 0.1011 0.1779 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 0.3256 330.183 312.394 0.652 1.034 0.376 11.894-9.307 99.02 97 4 0.1523 524.523 515.953 0.959 1.033 0.351 9.237-7.194 100.00 213 7 0.1656 428.955 429.381 1.001 1.030 0.321 7.162-5.571 100.00 427 22 0.1634 321.879 318.462 0.968 1.023 0.312 5.546-4.326 100.00 867 58 0.0914 441.894 438.973 0.988 1.012 0.202 4.315-3.360 100.00 1859 96 0.0762 420.246 420.168 1.049 0.994 0.193 3.356-3.002 100.00 1373 60 0.1000 323.691 322.346 1.035 0.976 0.092 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-3.4758 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1011 r_free=0.1779 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN Total number of N/Q/H flips: 1 r_work=0.1012 r_free=0.1783 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1012 r_free=0.1783 | n_water=258 | time (s): 0.720 (total time: 0.720) Filter (dist) r_work=0.1045 r_free=0.1779 | n_water=246 | time (s): 21.900 (total time: 22.620) Filter (q & B) r_work=0.1047 r_free=0.1771 | n_water=243 | time (s): 1.800 (total time: 24.420) Compute maps r_work=0.1047 r_free=0.1771 | n_water=243 | time (s): 0.690 (total time: 25.110) Filter (map) r_work=0.1371 r_free=0.1801 | n_water=140 | time (s): 1.940 (total time: 27.050) Find peaks r_work=0.1371 r_free=0.1801 | n_water=140 | time (s): 0.500 (total time: 27.550) Add new water r_work=0.1719 r_free=0.2168 | n_water=228 | time (s): 1.250 (total time: 28.800) Refine new water occ: r_work=0.1176 r_free=0.1638 adp: r_work=0.1156 r_free=0.1651 occ: r_work=0.1151 r_free=0.1614 adp: r_work=0.1151 r_free=0.1614 occ: r_work=0.1151 r_free=0.1614 adp: r_work=0.1151 r_free=0.1614 ADP+occupancy (water only), MIN, final r_work=0.1151 r_free=0.1614 r_work=0.1151 r_free=0.1614 | n_water=228 | time (s): 3.880 (total time: 32.680) Filter (q & B) r_work=0.1151 r_free=0.1614 | n_water=228 | time (s): 0.780 (total time: 33.460) Filter (dist only) r_work=0.1151 r_free=0.1609 | n_water=226 | time (s): 18.700 (total time: 52.160) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.367359 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.984673 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 0.1024 0.1793 0.0769 0.009 1.0 3.2 0.5 0.6 0 11.184 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.24 17.93 7.69 4.604 16.576 2.985 0.014 9.52 18.30 8.78 5.628 16.914 2.985 0.013 Individual atomic B min max mean iso aniso Overall: 0.00 106.99 16.07 6.68 1753 0 Protein: 0.00 106.99 14.83 6.66 1519 0 Water: 0.00 62.97 24.15 N/A 226 0 Other: 10.78 40.12 24.37 N/A 8 0 Chain A: 0.00 106.99 15.58 N/A 1666 0 Chain S: 4.86 50.70 25.43 N/A 87 0 Histogram: Values Number of atoms 0.00 - 10.70 703 10.70 - 21.40 649 21.40 - 32.10 220 32.10 - 42.80 119 42.80 - 53.50 31 53.50 - 64.19 17 64.19 - 74.89 6 74.89 - 85.59 3 85.59 - 96.29 3 96.29 - 106.99 2 =========================== Idealize ADP of riding H ========================== r_work=0.0952 r_free=0.1830 r_work=0.0948 r_free=0.1830 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0948 r_free = 0.1830 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0946 r_free = 0.1826 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.26 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= 0.0946 r_free= 0.1826 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ls_wunit_k1) (work): 0.012192 | | target function (ls_wunit_k1) not normalized (work): 60.035840 | | target function (ls_wunit_k1) not normalized (free): 10.199722 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0991 0.0946 0.1826 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2133 0.2137 0.2229 n_refl.: 5176 remove outliers: r(all,work,free)=0.2133 0.2137 0.2229 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2133 0.2137 0.2229 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0994 0.0949 0.1843 n_refl.: 5176 remove outliers: r(all,work,free)=0.0990 0.0945 0.1843 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 0.3141 329.580 308.082 0.660 1.000 0.354 11.894-9.307 99.02 97 4 0.1513 524.523 514.306 0.983 1.003 0.335 9.237-7.194 100.00 213 7 0.1463 428.955 427.979 1.032 1.004 0.315 7.162-5.571 100.00 427 22 0.1444 321.879 317.404 1.004 1.003 0.310 5.546-4.326 100.00 867 58 0.0802 441.894 438.734 1.016 1.002 0.240 4.315-3.360 100.00 1859 96 0.0733 420.246 420.408 1.064 1.000 0.213 3.356-3.002 100.00 1373 60 0.0972 323.691 324.168 1.040 0.998 0.120 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9557 b_overall=-4.6327 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0945 r_free=0.1843 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A A 76 ASN B Total number of N/Q/H flips: 2 r_work=0.0946 r_free=0.1844 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0946 r_free=0.1844 | n_water=226 | time (s): 0.710 (total time: 0.710) Filter (dist) r_work=0.0975 r_free=0.1868 | n_water=220 | time (s): 17.400 (total time: 18.110) Filter (q & B) r_work=0.1030 r_free=0.1894 | n_water=218 | time (s): 1.470 (total time: 19.580) Compute maps r_work=0.1030 r_free=0.1894 | n_water=218 | time (s): 0.470 (total time: 20.050) Filter (map) r_work=0.1298 r_free=0.1878 | n_water=144 | time (s): 1.290 (total time: 21.340) Find peaks r_work=0.1298 r_free=0.1878 | n_water=144 | time (s): 0.470 (total time: 21.810) Add new water r_work=0.1708 r_free=0.2253 | n_water=236 | time (s): 1.690 (total time: 23.500) Refine new water occ: r_work=0.1093 r_free=0.1738 adp: r_work=0.1086 r_free=0.1757 occ: r_work=0.1078 r_free=0.1740 adp: r_work=0.1076 r_free=0.1749 occ: r_work=0.1069 r_free=0.1733 adp: r_work=0.1069 r_free=0.1743 ADP+occupancy (water only), MIN, final r_work=0.1069 r_free=0.1743 r_work=0.1069 r_free=0.1743 | n_water=236 | time (s): 13.070 (total time: 36.570) Filter (q & B) r_work=0.1069 r_free=0.1743 | n_water=236 | time (s): 1.140 (total time: 37.710) Filter (dist only) r_work=0.1076 r_free=0.1742 | n_water=233 | time (s): 18.280 (total time: 55.990) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.127398 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.201458 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 0.0960 0.1814 0.0854 0.011 1.0 4.8 0.5 0.6 0 0.564 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.60 18.14 8.54 5.532 17.571 0.201 5.180 9.12 18.24 9.11 7.304 17.630 0.201 5.082 Individual atomic B min max mean iso aniso Overall: 0.00 107.19 16.20 9.03 1760 0 Protein: 0.00 107.19 15.03 9.01 1519 0 Water: 0.00 58.10 23.48 N/A 233 0 Other: 9.01 42.09 25.75 N/A 8 0 Chain A: 0.00 107.19 15.63 N/A 1645 0 Chain S: 0.00 58.10 24.32 N/A 115 0 Histogram: Values Number of atoms 0.00 - 10.72 685 10.72 - 21.44 646 21.44 - 32.16 246 32.16 - 42.88 114 42.88 - 53.59 38 53.59 - 64.31 15 64.31 - 75.03 9 75.03 - 85.75 2 85.75 - 96.47 4 96.47 - 107.19 1 =========================== Idealize ADP of riding H ========================== r_work=0.0912 r_free=0.1824 r_work=0.0916 r_free=0.1834 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0916 r_free = 0.1834 target_work(ml) = 5.086 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0904 r_free = 0.1833 target_work(ml) = 5.078 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0904 r_free= 0.1833 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ml) (work): 5.078241 | | target function (ml) not normalized (work): 24995.103263 | | target function (ml) not normalized (free): 1816.655886 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0951 0.0904 0.1833 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2067 0.2069 0.2149 n_refl.: 5174 remove outliers: r(all,work,free)=0.2067 0.2069 0.2149 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2067 0.2069 0.2149 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0946 0.0900 0.1827 n_refl.: 5174 remove outliers: r(all,work,free)=0.0946 0.0900 0.1827 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 0.3703 329.580 304.020 0.604 0.990 0.328 11.894-9.307 99.02 97 4 0.1882 524.523 508.810 0.939 0.995 0.318 9.237-7.194 100.00 213 7 0.1903 428.955 422.232 1.005 0.998 0.305 7.162-5.571 100.00 427 22 0.1847 321.879 312.612 0.979 0.999 0.300 5.546-4.326 100.00 867 58 0.0942 441.894 436.502 1.001 1.000 0.240 4.315-3.360 100.00 1859 96 0.0600 420.246 419.706 1.057 1.002 0.230 3.356-3.002 100.00 1373 60 0.0604 323.691 323.713 1.033 1.003 0.098 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-6.4273 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0900 r_free=0.1827 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B Total number of N/Q/H flips: 1 r_work=0.0901 r_free=0.1828 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0901 r_free=0.1828 | n_water=233 | time (s): 0.500 (total time: 0.500) Filter (dist) r_work=0.0914 r_free=0.1833 | n_water=229 | time (s): 18.660 (total time: 19.160) Filter (q & B) r_work=0.0953 r_free=0.1846 | n_water=226 | time (s): 1.930 (total time: 21.090) Compute maps r_work=0.0953 r_free=0.1846 | n_water=226 | time (s): 0.690 (total time: 21.780) Filter (map) r_work=0.1207 r_free=0.1905 | n_water=158 | time (s): 1.740 (total time: 23.520) Find peaks r_work=0.1207 r_free=0.1905 | n_water=158 | time (s): 0.400 (total time: 23.920) Add new water r_work=0.1561 r_free=0.2182 | n_water=233 | time (s): 1.200 (total time: 25.120) Refine new water r_work=0.1561 r_free=0.2182 | n_water=233 | time (s): 0.060 (total time: 25.180) Filter (q & B) r_work=0.1207 r_free=0.1905 | n_water=158 | time (s): 1.450 (total time: 26.630) Filter (dist only) r_work=0.1212 r_free=0.1908 | n_water=155 | time (s): 12.090 (total time: 38.720) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.322898 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.285750 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 0.1092 0.1926 0.0834 0.011 1.1 4.8 0.5 0.6 0 0.661 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.92 19.26 8.34 7.022 17.633 0.286 5.323 10.30 19.26 8.96 8.488 17.727 0.286 5.235 Individual atomic B min max mean iso aniso Overall: 0.00 104.47 15.97 10.70 1682 0 Protein: 0.00 104.47 15.31 10.69 1519 0 Water: 0.92 52.03 21.99 N/A 155 0 Other: 12.49 37.09 24.82 N/A 8 0 Chain A: 0.00 104.47 15.75 N/A 1636 0 Chain S: 1.83 45.97 23.83 N/A 46 0 Histogram: Values Number of atoms 0.00 - 10.45 640 10.45 - 20.89 609 20.89 - 31.34 269 31.34 - 41.79 92 41.79 - 52.24 38 52.24 - 62.68 14 62.68 - 73.13 10 73.13 - 83.58 5 83.58 - 94.02 3 94.02 - 104.47 2 =========================== Idealize ADP of riding H ========================== r_work=0.1030 r_free=0.1926 r_work=0.1035 r_free=0.1933 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1035 r_free = 0.1933 target_work(ml) = 5.238 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1031 r_free = 0.1938 target_work(ml) = 5.235 | | occupancies: max = 1.00 min = 0.25 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= 0.1031 r_free= 0.1938 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ml) (work): 5.235449 | | target function (ml) not normalized (work): 25768.881245 | | target function (ml) not normalized (free): 1777.885656 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1077 0.1031 0.1938 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2334 0.2330 0.2501 n_refl.: 5174 remove outliers: r(all,work,free)=0.2334 0.2330 0.2501 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2334 0.2330 0.2501 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.1066 0.1019 0.1940 n_refl.: 5174 remove outliers: r(all,work,free)=0.1066 0.1019 0.1940 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 0.3668 329.580 303.726 0.702 0.995 0.360 11.894-9.307 99.02 97 4 0.1610 524.523 513.594 1.015 1.000 0.353 9.237-7.194 100.00 213 7 0.2004 428.955 420.971 1.041 1.002 0.347 7.162-5.571 100.00 427 22 0.1869 321.879 316.238 1.012 1.002 0.320 5.546-4.326 100.00 867 58 0.1099 441.894 435.936 1.027 1.002 0.269 4.315-3.360 100.00 1859 96 0.0742 420.246 418.430 1.102 1.001 0.259 3.356-3.002 100.00 1373 60 0.0737 323.691 322.639 1.091 1.000 0.090 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-6.5543 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1019 r_free=0.1940 After: r_work=0.1022 r_free=0.1939 ================================== NQH flips ================================== r_work=0.1022 r_free=0.1939 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1022 r_free=0.1939 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1022 r_free=0.1939 | n_water=155 | time (s): 0.580 (total time: 0.580) Filter (dist) r_work=0.1053 r_free=0.1955 | n_water=150 | time (s): 12.810 (total time: 13.390) Filter (q & B) r_work=0.1074 r_free=0.1955 | n_water=149 | time (s): 1.640 (total time: 15.030) Compute maps r_work=0.1074 r_free=0.1955 | n_water=149 | time (s): 0.530 (total time: 15.560) Filter (map) r_work=0.1142 r_free=0.1989 | n_water=137 | time (s): 1.420 (total time: 16.980) Find peaks r_work=0.1142 r_free=0.1989 | n_water=137 | time (s): 0.420 (total time: 17.400) Add new water r_work=0.1430 r_free=0.2339 | n_water=197 | time (s): 1.340 (total time: 18.740) Refine new water occ: r_work=0.1110 r_free=0.1970 adp: r_work=0.1110 r_free=0.1991 occ: r_work=0.1097 r_free=0.1953 adp: r_work=0.1098 r_free=0.1971 occ: r_work=0.1085 r_free=0.1933 adp: r_work=0.1086 r_free=0.1951 ADP+occupancy (water only), MIN, final r_work=0.1086 r_free=0.1951 r_work=0.1086 r_free=0.1951 | n_water=197 | time (s): 11.700 (total time: 30.440) Filter (q & B) r_work=0.1085 r_free=0.1956 | n_water=193 | time (s): 1.400 (total time: 31.840) Filter (dist only) r_work=0.1081 r_free=0.1948 | n_water=191 | time (s): 14.790 (total time: 46.630) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.161622 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.246500 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 0.1051 0.2004 0.0953 0.011 1.1 8.0 0.5 0.6 0 0.581 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.51 20.04 9.53 8.116 18.049 0.246 5.195 10.27 20.23 9.96 8.988 18.123 0.246 5.140 Individual atomic B min max mean iso aniso Overall: 0.00 101.91 16.60 11.68 1718 0 Protein: 0.00 101.91 15.61 11.67 1519 0 Water: 0.00 58.18 24.14 N/A 191 0 Other: 11.56 37.83 24.07 N/A 8 0 Chain A: 0.00 101.91 15.95 N/A 1624 0 Chain S: 1.21 58.18 27.80 N/A 94 0 Histogram: Values Number of atoms 0.00 - 10.19 594 10.19 - 20.38 631 20.38 - 30.57 280 30.57 - 40.76 117 40.76 - 50.95 56 50.95 - 61.15 18 61.15 - 71.34 5 71.34 - 81.53 12 81.53 - 91.72 1 91.72 - 101.91 4 =========================== Idealize ADP of riding H ========================== r_work=0.1027 r_free=0.2023 r_work=0.1032 r_free=0.2027 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1032 r_free = 0.2027 target_work(ml) = 5.147 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1004 r_free = 0.1988 target_work(ml) = 5.125 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.1004 r_free= 0.1988 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ml) (work): 5.125086 | | target function (ml) not normalized (work): 25225.673703 | | target function (ml) not normalized (free): 1927.250541 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1364 0.1962 5.6196 6.1729| | 2: 3.78 - 3.00 1.00 2430 110 0.0564 0.2031 4.6179 9.5519| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 13.05 1.00 0.95 14076.88| | 2: 3.78 - 3.00 2430 110 0.98 3.04 1.01 0.98 1489.85| |alpha: min = 0.93 max = 0.98 mean = 0.96| |beta: min = 986.29 max = 22375.25 mean = 7862.64| |figures of merit: min = 0.00 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.68 mean = 8.11| |phase err.(test): min = 0.00 max = 79.79 mean = 7.78| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1054 0.1004 0.1988 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2307 0.2309 0.2400 n_refl.: 5174 remove outliers: r(all,work,free)=0.2307 0.2309 0.2400 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2307 0.2309 0.2400 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.1049 0.1000 0.1969 n_refl.: 5174 remove outliers: r(all,work,free)=0.1049 0.1000 0.1969 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 0.3926 329.580 287.974 0.621 0.987 0.330 11.894-9.307 99.02 97 4 0.1961 524.523 515.169 1.024 0.992 0.332 9.237-7.194 100.00 213 7 0.2171 428.955 422.036 1.066 0.996 0.316 7.162-5.571 100.00 427 22 0.2054 321.879 314.940 1.030 0.997 0.300 5.546-4.326 100.00 867 58 0.1142 441.894 433.768 1.061 1.000 0.270 4.315-3.360 100.00 1859 96 0.0703 420.246 419.489 1.149 1.003 0.270 3.356-3.002 100.00 1373 60 0.0536 323.691 323.063 1.131 1.006 0.090 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-8.5888 ================= 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 : 0.3613 0.2028 0.081 5.189 8.8 119.3 19.9 258 0.000 1_bss: 0.1566 0.1650 0.081 5.189 6.0 116.4 17.0 258 0.000 1_settarget: 0.1566 0.1650 0.081 5.189 6.0 116.4 17.0 258 0.000 1_nqh: 0.1565 0.1648 0.081 5.189 6.0 116.4 17.0 258 0.003 1_weight: 0.1565 0.1648 0.081 5.189 6.0 116.4 17.0 258 0.003 1_xyzrec: 0.1151 0.1779 0.009 0.956 6.0 116.4 17.0 258 0.216 1_adp: 0.1015 0.1777 0.009 0.956 2.3 111.4 17.5 258 0.216 1_regHadp: 0.1009 0.1783 0.009 0.956 2.3 111.4 17.5 258 0.216 1_occ: 0.1009 0.1786 0.009 0.956 2.3 111.4 17.5 258 0.216 2_bss: 0.1011 0.1779 0.009 0.956 1.3 110.5 16.5 258 0.216 2_settarget: 0.1011 0.1779 0.009 0.956 1.3 110.5 16.5 258 0.216 2_updatecdl: 0.1011 0.1779 0.010 0.985 1.3 110.5 16.5 258 0.216 2_nqh: 0.1012 0.1783 0.010 0.985 1.3 110.5 16.5 258 0.213 2_sol: 0.1151 0.1609 0.010 0.985 1.3 109.6 15.4 226 n/a 2_weight: 0.1151 0.1609 0.010 0.985 1.3 109.6 15.4 226 n/a 2_xyzrec: 0.1024 0.1793 0.009 0.963 1.3 109.6 15.4 226 n/a 2_adp: 0.0952 0.1830 0.009 0.963 0.0 107.0 16.1 226 n/a 2_regHadp: 0.0948 0.1830 0.009 0.963 0.0 107.0 16.1 226 n/a 2_occ: 0.0946 0.1826 0.009 0.963 0.0 107.0 16.1 226 n/a 3_bss: 0.0945 0.1843 0.009 0.963 0.0 107.0 16.1 226 n/a 3_settarget: 0.0945 0.1843 0.009 0.963 0.0 107.0 16.1 226 n/a 3_updatecdl: 0.0945 0.1843 0.009 0.966 0.0 107.0 16.1 226 n/a 3_nqh: 0.0946 0.1844 0.009 0.966 0.0 107.0 16.1 226 n/a 3_sol: 0.1076 0.1742 0.009 0.966 0.0 107.0 16.1 233 n/a 3_weight: 0.1076 0.1742 0.009 0.966 0.0 107.0 16.1 233 n/a 3_xyzrec: 0.0960 0.1814 0.011 1.018 0.0 107.0 16.1 233 n/a 3_adp: 0.0912 0.1824 0.011 1.018 0.0 107.2 16.2 233 n/a 3_regHadp: 0.0916 0.1834 0.011 1.018 0.0 107.2 16.2 233 n/a 3_occ: 0.0904 0.1833 0.011 1.018 0.0 107.2 16.2 233 n/a 4_bss: 0.0900 0.1827 0.011 1.018 0.0 107.2 16.2 233 n/a 4_settarget: 0.0900 0.1827 0.011 1.018 0.0 107.2 16.2 233 n/a 4_updatecdl: 0.0900 0.1827 0.011 1.024 0.0 107.2 16.2 233 n/a 4_nqh: 0.0901 0.1828 0.011 1.024 0.0 107.2 16.2 233 n/a 4_sol: 0.1212 0.1908 0.011 1.024 0.0 107.2 15.8 155 n/a 4_weight: 0.1212 0.1908 0.011 1.024 0.0 107.2 15.8 155 n/a 4_xyzrec: 0.1092 0.1926 0.011 1.065 0.0 107.2 15.8 155 n/a 4_adp: 0.1030 0.1926 0.011 1.065 0.0 104.5 16.0 155 n/a 4_regHadp: 0.1035 0.1933 0.011 1.065 0.0 104.5 16.0 155 n/a 4_occ: 0.1031 0.1938 0.011 1.065 0.0 104.5 16.0 155 n/a 5_bss: 0.1019 0.1940 0.011 1.065 0.0 104.5 16.0 155 n/a 5_settarget: 0.1019 0.1940 0.011 1.065 0.0 104.5 16.0 155 n/a 5_updatecdl: 0.1019 0.1940 0.011 1.069 0.0 104.5 16.0 155 n/a 5_setrh: 0.1022 0.1939 0.011 1.069 0.0 104.5 16.0 155 n/a 5_nqh: 0.1022 0.1939 0.011 1.069 0.0 104.5 16.0 155 n/a 5_sol: 0.1081 0.1948 0.011 1.069 0.0 104.5 16.5 191 n/a 5_weight: 0.1081 0.1948 0.011 1.069 0.0 104.5 16.5 191 n/a 5_xyzrec: 0.1051 0.2004 0.011 1.136 0.0 104.5 16.5 191 n/a 5_adp: 0.1027 0.2023 0.011 1.136 0.0 101.9 16.6 191 n/a 5_regHadp: 0.1032 0.2027 0.011 1.136 0.0 101.9 16.6 191 n/a 5_occ: 0.1004 0.1988 0.011 1.136 0.0 101.9 16.6 191 n/a end: 0.1000 0.1969 0.011 1.136 0.0 101.9 16.6 191 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_6462862_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_6462862_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.7600 Refinement macro-cycles (run) : 473.0000 Write final files (write_after_run_outputs) : 10.7900 Total : 487.5500 Total CPU time: 8.46 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:18:49 PST -0800 (1735492729.79 s) Start R-work = 0.1566, R-free = 0.1650 Final R-work = 0.1000, R-free = 0.1969 =============================================================================== Job complete usr+sys time: 515.58 seconds wall clock time: 8 minutes 58.53 seconds (538.53 seconds total)