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_5431713.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_5431713.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_5431713.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: 1.18, per 1000 atoms: 0.35 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 107.5 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.65 - 0.90: 481 0.90 - 1.16: 1143 1.16 - 1.41: 623 1.41 - 1.67: 871 1.67 - 1.92: 35 Bond restraints: 3153 Sorted by residual: bond pdb=" C VAL A 8 " pdb=" O VAL A 8 " ideal model delta sigma weight residual 1.237 1.004 0.233 1.08e-02 8.57e+03 4.67e+02 bond pdb=" N ALA A 178 " pdb=" CA ALA A 178 " ideal model delta sigma weight residual 1.459 1.706 -0.247 1.20e-02 6.94e+03 4.23e+02 bond pdb=" ND1 HIS A 126 " pdb=" CE1 HIS A 126 " ideal model delta sigma weight residual 1.321 1.526 -0.205 1.00e-02 1.00e+04 4.20e+02 bond pdb=" NE ARG A 28 " pdb=" CZ ARG A 28 " ideal model delta sigma weight residual 1.326 1.123 0.203 1.10e-02 8.26e+03 3.40e+02 bond pdb=" N LEU A 72 " pdb=" CA LEU A 72 " ideal model delta sigma weight residual 1.460 1.266 0.194 1.10e-02 8.26e+03 3.10e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.76: 3189 4.76 - 9.52: 1851 9.52 - 14.29: 626 14.29 - 19.05: 104 19.05 - 23.81: 7 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O BASN A 97 " pdb=" C BASN A 97 " pdb=" N ARG A 98 " ideal model delta sigma weight residual 122.12 137.77 -15.65 1.06e+00 8.90e-01 2.18e+02 angle pdb=" N MET A 26 " pdb=" CA MET A 26 " pdb=" C MET A 26 " ideal model delta sigma weight residual 111.28 125.26 -13.98 1.09e+00 8.42e-01 1.64e+02 angle pdb=" CA LEU A 101 " pdb=" C LEU A 101 " pdb=" O LEU A 101 " ideal model delta sigma weight residual 121.05 135.61 -14.56 1.14e+00 7.69e-01 1.63e+02 angle pdb=" CA ACYS A 53 " pdb=" C ACYS A 53 " pdb=" O ACYS A 53 " ideal model delta sigma weight residual 119.29 111.03 8.26 6.50e-01 2.37e+00 1.62e+02 angle pdb=" O ACYS A 53 " pdb=" C ACYS A 53 " pdb=" N PRO A 54 " ideal model delta sigma weight residual 121.23 131.43 -10.20 8.10e-01 1.52e+00 1.59e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.00: 1300 17.00 - 34.00: 124 34.00 - 51.00: 40 51.00 - 68.00: 16 68.00 - 85.00: 1 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 -151.44 28.84 0 2.50e+00 1.60e-01 1.33e+02 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 122.80 147.76 -24.96 0 2.50e+00 1.60e-01 9.97e+01 dihedral pdb=" C THR A 140 " pdb=" N THR A 140 " pdb=" CA THR A 140 " pdb=" CB THR A 140 " ideal model delta harmonic sigma weight residual -122.00 -140.71 18.71 0 2.50e+00 1.60e-01 5.60e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.003 - 0.239: 107 0.239 - 0.476: 85 0.476 - 0.712: 34 0.712 - 0.949: 14 0.949 - 1.185: 3 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 1.33 1.18 2.00e-01 2.50e+01 3.51e+01 chirality pdb=" CA ASP A 55 " pdb=" N ASP A 55 " pdb=" C ASP A 55 " pdb=" CB ASP A 55 " both_signs ideal model delta sigma weight residual False 2.51 3.50 -0.98 2.00e-01 2.50e+01 2.42e+01 chirality pdb=" CA LEU A 113 " pdb=" N LEU A 113 " pdb=" C LEU A 113 " pdb=" CB LEU A 113 " both_signs ideal model delta sigma weight residual False 2.51 3.47 -0.96 2.00e-01 2.50e+01 2.30e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " 0.003 2.00e-02 2.50e+03 6.39e-02 1.23e+02 pdb=" CG ATYR A 67 " -0.012 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " 0.034 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " 0.124 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " -0.059 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " -0.026 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " 0.132 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " -0.004 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " -0.019 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " -0.071 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " -0.038 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " -0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " -0.032 2.00e-02 2.50e+03 5.32e-02 8.49e+01 pdb=" CG TYR A 141 " 0.099 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " -0.064 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " -0.105 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " -0.035 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " 0.024 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " 0.050 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " 0.041 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " 0.016 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " 0.028 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " -0.021 2.00e-02 2.50e+03 5.13e-02 7.88e+01 pdb=" CG PHE A 119 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.077 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " -0.061 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.016 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.050 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.033 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.106 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " -0.015 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.050 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.030 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.33: 1083 2.33 - 2.90: 8181 2.90 - 3.46: 10442 3.46 - 4.03: 15295 4.03 - 4.60: 21653 Nonbonded interactions: 56654 Sorted by model distance: nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.759 2.100 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.793 2.450 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.794 2.100 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.814 2.450 nonbonded pdb=" O GLU A 147 " pdb=" H BTHR A 154 " model vdw 1.839 2.450 ... (remaining 56649 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_5431713_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= 0.3616 r_free= 0.2023 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.464415 | | target function (ml) not normalized (work): 22009.567007 | | target function (ml) not normalized (free): 1146.666430 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3794 0.2226 4.8487 4.9068| | 2: 3.78 - 3.00 1.00 2430 110 0.3400 0.1679 4.069 4.0901| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 48.76 0.83 0.13 6600.42| | 2: 3.78 - 3.00 2430 110 0.94 11.20 1.48 0.26 444.97| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 378.22 max = 12057.90 mean = 3566.40| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 90.00 mean = 30.25| |phase err.(test): min = 0.00 max = 90.00 mean = 33.13| |-----------------------------------------------------------------------------| ----------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 0.248 1557 Z= 5.412 Angle : 5.242 17.749 2118 Z= 3.615 Chirality : 0.385 1.185 243 Planarity : 0.031 0.077 284 Dihedral : 13.529 84.996 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.70 % Favored : 96.76 % Rotamer: Outliers : 0.62 % Allowed : 3.11 % Favored : 96.27 % Cbeta Deviations : 29.19 % 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: -3.03 (0.46), residues: 224 helix: -3.13 (0.35), residues: 102 sheet: -0.48 (0.95), residues: 28 loop : -0.87 (0.54), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.061 0.017 ARG A 27 TYR 0.110 0.034 TYR A 141 PHE 0.102 0.042 PHE A 162 HIS 0.067 0.029 HIS A 126 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 1785 0 Protein: 8.85 115.78 16.79 3.90 1519 0 Water: 11.36 119.30 38.03 N/A 258 0 Other: 19.04 26.29 21.71 N/A 8 0 Chain A: 8.85 119.30 19.89 N/A 1785 0 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 3.00 - 49.25 A, n_refl.=5182 (all), 4.86 % free)-------------| | | | r_work= 0.3616 r_free= 0.2023 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.464415 | | target function (ml) not normalized (work): 22009.567007 | | target function (ml) not normalized (free): 1146.666430 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3576 0.3651 0.2143 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3576 0.3651 0.2143 n_refl.: 5182 remove outliers: r(all,work,free)=0.2526 0.2549 0.2143 n_refl.: 5178 overall B=-2.94 to atoms: r(all,work,free)=0.2413 0.2433 0.2095 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1558 0.1555 0.1622 n_refl.: 5178 remove outliers: r(all,work,free)=0.1554 0.1550 0.1622 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 0.3890 449.871 404.975 0.664 1.062 0.394 11.894-9.307 99.02 97 4 0.1844 714.656 694.781 0.939 1.059 0.383 9.237-7.194 100.00 213 7 0.2173 584.447 575.547 0.979 1.053 0.354 7.162-5.571 100.00 427 22 0.2318 438.556 424.834 0.946 1.041 0.326 5.546-4.326 100.00 867 58 0.1400 602.075 595.577 0.985 1.022 0.268 4.315-3.360 100.00 1859 96 0.1284 572.580 566.236 1.053 0.991 0.200 3.356-3.002 100.00 1373 60 0.1592 441.025 433.227 1.066 0.959 0.075 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9556 b_overall=-3.7552 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1550 r_free=0.1622 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 80 GLN A A 144 ASN A 180 GLN Total number of N/Q/H flips: 3 r_work=0.1552 r_free=0.1620 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 18.647754 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.822393 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 0.1164 0.1774 0.0610 0.010 1.0 2.6 0.5 0.0 0 9.324 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.64 17.74 6.10 3.013 15.923 1.822 0.018 10.23 17.66 7.42 4.924 16.151 1.822 0.014 Individual atomic B min max mean iso aniso Overall: 2.14 111.36 17.38 5.27 1785 0 Protein: 2.14 110.60 14.71 5.26 1519 0 Water: 4.26 111.36 32.94 N/A 258 0 Other: 16.72 38.61 23.98 N/A 8 0 Chain A: 2.14 111.36 17.38 N/A 1785 0 Histogram: Values Number of atoms 2.14 - 13.07 914 13.07 - 23.99 490 23.99 - 34.91 184 34.91 - 45.83 110 45.83 - 56.75 56 56.75 - 67.68 14 67.68 - 78.60 8 78.60 - 89.52 5 89.52 - 100.44 1 100.44 - 111.36 3 =========================== Idealize ADP of riding H ========================== r_work=0.1023 r_free=0.1766 r_work=0.1017 r_free=0.1771 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1017 r_free = 0.1771 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 = 0.1014 r_free = 0.1772 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.1014 r_free= 0.1772 coordinate error (max.-lik. estimate): 0.31 A | | | | normalized target function (ls_wunit_k1) (work): 0.013906 | | target function (ls_wunit_k1) not normalized (work): 68.472934 | | target function (ls_wunit_k1) not normalized (free): 10.157085 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1051 0.1014 0.1772 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2095 0.2096 0.2196 n_refl.: 5176 remove outliers: r(all,work,free)=0.2095 0.2096 0.2196 n_refl.: 5176 overall B=-1.00 to atoms: r(all,work,free)=0.2053 0.2052 0.2185 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.1049 0.1011 0.1764 n_refl.: 5176 remove outliers: r(all,work,free)=0.1049 0.1011 0.1764 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 0.3351 330.403 312.941 0.680 1.004 0.384 11.894-9.307 99.02 97 4 0.1499 524.872 516.837 0.989 1.006 0.352 9.237-7.194 100.00 213 7 0.1647 429.241 429.261 1.025 1.006 0.330 7.162-5.571 100.00 427 22 0.1630 322.093 318.132 0.987 1.005 0.320 5.546-4.326 100.00 867 58 0.0909 442.189 438.962 1.001 1.003 0.232 4.315-3.360 100.00 1859 96 0.0763 420.526 420.507 1.042 0.998 0.198 3.356-3.002 100.00 1373 60 0.1006 323.907 322.524 1.019 0.994 0.051 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-3.5660 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1011 r_free=0.1764 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 144 ASN A 180 GLN Total number of N/Q/H flips: 3 r_work=0.1016 r_free=0.1774 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1016 r_free=0.1774 | n_water=258 | time (s): 0.460 (total time: 0.460) Filter (dist) r_work=0.1038 r_free=0.1754 | n_water=249 | time (s): 19.510 (total time: 19.970) Filter (q & B) r_work=0.1037 r_free=0.1755 | n_water=246 | time (s): 1.340 (total time: 21.310) Compute maps r_work=0.1037 r_free=0.1755 | n_water=246 | time (s): 0.510 (total time: 21.820) Filter (map) r_work=0.1336 r_free=0.1816 | n_water=145 | time (s): 1.560 (total time: 23.380) Find peaks r_work=0.1336 r_free=0.1816 | n_water=145 | time (s): 0.550 (total time: 23.930) Add new water r_work=0.1694 r_free=0.2130 | n_water=232 | time (s): 1.780 (total time: 25.710) Refine new water occ: r_work=0.1159 r_free=0.1686 adp: r_work=0.1136 r_free=0.1693 occ: r_work=0.1134 r_free=0.1670 adp: r_work=0.1123 r_free=0.1679 occ: r_work=0.1121 r_free=0.1655 adp: r_work=0.1117 r_free=0.1665 ADP+occupancy (water only), MIN, final r_work=0.1117 r_free=0.1665 r_work=0.1117 r_free=0.1665 | n_water=232 | time (s): 4.410 (total time: 30.120) Filter (q & B) r_work=0.1117 r_free=0.1665 | n_water=232 | time (s): 0.980 (total time: 31.100) Filter (dist only) r_work=0.1122 r_free=0.1650 | n_water=229 | time (s): 17.160 (total time: 48.260) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.762408 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.712598 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 0.1015 0.1789 0.0774 0.009 1.0 4.2 0.5 0.6 0 11.381 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.15 17.89 7.74 4.648 16.739 2.713 0.014 9.47 18.05 8.58 5.315 17.034 2.713 0.013 Individual atomic B min max mean iso aniso Overall: 0.00 107.81 16.38 6.29 1756 0 Protein: 0.00 107.81 14.76 6.29 1519 0 Water: 0.00 62.65 27.01 N/A 229 0 Other: 10.72 34.12 21.25 N/A 8 0 Chain A: 0.00 107.81 15.48 N/A 1670 0 Chain S: 3.28 59.08 33.91 N/A 86 0 Histogram: Values Number of atoms 0.00 - 10.78 698 10.78 - 21.56 662 21.56 - 32.34 206 32.34 - 43.13 111 43.13 - 53.91 39 53.91 - 64.69 28 64.69 - 75.47 5 75.47 - 86.25 4 86.25 - 97.03 1 97.03 - 107.81 2 =========================== Idealize ADP of riding H ========================== r_work=0.0947 r_free=0.1805 r_work=0.0944 r_free=0.1804 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0944 r_free = 0.1804 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0941 r_free = 0.1791 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.13 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= 0.1791 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ls_wunit_k1) (work): 0.012137 | | target function (ls_wunit_k1) not normalized (work): 59.763920 | | target function (ls_wunit_k1) not normalized (free): 9.789616 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0983 0.0941 0.1791 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2112 0.2121 0.2118 n_refl.: 5176 remove outliers: r(all,work,free)=0.2112 0.2121 0.2118 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2112 0.2121 0.2118 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0985 0.0944 0.1789 n_refl.: 5176 remove outliers: r(all,work,free)=0.0981 0.0939 0.1789 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 0.3150 329.800 309.676 0.658 1.011 0.360 11.894-9.307 99.02 97 4 0.1457 524.872 520.197 0.978 1.014 0.340 9.237-7.194 100.00 213 7 0.1482 429.241 430.348 1.022 1.013 0.314 7.162-5.571 100.00 427 22 0.1478 322.093 319.233 0.991 1.011 0.300 5.546-4.326 100.00 867 58 0.0793 442.189 439.258 1.008 1.006 0.240 4.315-3.360 100.00 1859 96 0.0719 420.526 420.152 1.056 0.999 0.200 3.356-3.002 100.00 1373 60 0.0972 323.907 322.927 1.039 0.991 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9556 b_overall=-4.2385 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0939 r_free=0.1789 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN A A 80 GLN A Total number of N/Q/H flips: 3 r_work=0.0942 r_free=0.1785 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0942 r_free=0.1785 | n_water=229 | time (s): 0.550 (total time: 0.550) Filter (dist) r_work=0.0956 r_free=0.1774 | n_water=225 | time (s): 20.060 (total time: 20.610) Filter (q & B) r_work=0.1019 r_free=0.1790 | n_water=223 | time (s): 1.440 (total time: 22.050) Compute maps r_work=0.1019 r_free=0.1790 | n_water=223 | time (s): 0.550 (total time: 22.600) Filter (map) r_work=0.1292 r_free=0.1892 | n_water=144 | time (s): 1.900 (total time: 24.500) Find peaks r_work=0.1292 r_free=0.1892 | n_water=144 | time (s): 0.560 (total time: 25.060) Add new water r_work=0.1671 r_free=0.2245 | n_water=229 | time (s): 1.430 (total time: 26.490) Refine new water r_work=0.1671 r_free=0.2245 | n_water=229 | time (s): 0.100 (total time: 26.590) Filter (q & B) r_work=0.1292 r_free=0.1892 | n_water=144 | time (s): 1.860 (total time: 28.450) Filter (dist only) r_work=0.1304 r_free=0.1855 | n_water=137 | time (s): 12.620 (total time: 41.070) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.567795 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.327908 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 0.1159 0.1915 0.0756 0.012 1.1 3.8 0.5 0.6 0 0.784 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.59 19.15 7.56 5.274 17.211 0.328 5.419 10.90 19.68 8.78 7.265 17.154 0.328 5.331 Individual atomic B min max mean iso aniso Overall: 0.00 107.04 15.38 8.68 1664 0 Protein: 0.00 107.04 14.66 8.68 1519 0 Water: 0.90 57.65 22.87 N/A 137 0 Other: 13.28 36.33 22.50 N/A 8 0 Chain A: 0.00 107.04 15.24 N/A 1646 0 Chain S: 5.24 50.84 27.46 N/A 18 0 Histogram: Values Number of atoms 0.00 - 10.70 691 10.70 - 21.41 621 21.41 - 32.11 204 32.11 - 42.82 85 42.82 - 53.52 31 53.52 - 64.22 14 64.22 - 74.93 10 74.93 - 85.63 4 85.63 - 96.34 3 96.34 - 107.04 1 =========================== Idealize ADP of riding H ========================== r_work=0.1090 r_free=0.1968 r_work=0.1096 r_free=0.1977 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1096 r_free = 0.1977 target_work(ml) = 5.333 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1094 r_free = 0.1977 target_work(ml) = 5.332 | | occupancies: max = 1.00 min = 0.17 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= 0.1094 r_free= 0.1977 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ml) (work): 5.331811 | | target function (ml) not normalized (work): 26243.175152 | | target function (ml) not normalized (free): 1670.094548 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1139 0.1094 0.1977 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2307 0.2303 0.2500 n_refl.: 5174 remove outliers: r(all,work,free)=0.2307 0.2303 0.2500 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2307 0.2303 0.2500 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.1120 0.1074 0.1978 n_refl.: 5174 remove outliers: r(all,work,free)=0.1120 0.1074 0.1978 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 0.3634 329.800 307.724 0.690 0.996 0.370 11.894-9.307 99.02 97 4 0.1669 524.872 510.201 0.986 1.002 0.363 9.237-7.194 100.00 213 7 0.1781 429.241 423.496 0.996 1.003 0.341 7.162-5.571 100.00 427 22 0.1803 322.093 316.277 0.965 1.003 0.327 5.546-4.326 100.00 867 58 0.1072 442.189 436.432 0.981 1.002 0.259 4.315-3.360 100.00 1859 96 0.0798 420.526 418.761 1.048 1.000 0.240 3.356-3.002 100.00 1373 60 0.0960 323.907 321.387 1.042 0.998 0.043 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-6.1961 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1074 r_free=0.1978 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B A 138 HIS Total number of N/Q/H flips: 2 r_work=0.1087 r_free=0.1985 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1087 r_free=0.1985 | n_water=137 | time (s): 0.570 (total time: 0.570) Filter (dist) r_work=0.1094 r_free=0.1989 | n_water=135 | time (s): 11.270 (total time: 11.840) Filter (q & B) r_work=0.1114 r_free=0.1996 | n_water=134 | time (s): 1.520 (total time: 13.360) Compute maps r_work=0.1114 r_free=0.1996 | n_water=134 | time (s): 0.610 (total time: 13.970) Filter (map) r_work=0.1182 r_free=0.1975 | n_water=124 | time (s): 1.750 (total time: 15.720) Find peaks r_work=0.1182 r_free=0.1975 | n_water=124 | time (s): 0.430 (total time: 16.150) Add new water r_work=0.1515 r_free=0.2285 | n_water=201 | time (s): 1.270 (total time: 17.420) Refine new water occ: r_work=0.1145 r_free=0.1997 adp: r_work=0.1146 r_free=0.2015 occ: r_work=0.1126 r_free=0.1979 adp: r_work=0.1128 r_free=0.2000 occ: r_work=0.1108 r_free=0.1963 adp: r_work=0.1109 r_free=0.1982 ADP+occupancy (water only), MIN, final r_work=0.1109 r_free=0.1982 r_work=0.1109 r_free=0.1982 | n_water=201 | time (s): 7.060 (total time: 24.480) Filter (q & B) r_work=0.1110 r_free=0.1982 | n_water=199 | time (s): 1.580 (total time: 26.060) Filter (dist only) r_work=0.1109 r_free=0.1986 | n_water=198 | time (s): 16.360 (total time: 42.420) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.180175 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.244878 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 0.1041 0.2048 0.1006 0.011 1.1 5.4 0.5 0.6 0 0.590 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.41 20.48 10.06 6.771 17.464 0.245 5.223 10.13 20.42 10.29 8.022 17.524 0.245 5.159 Individual atomic B min max mean iso aniso Overall: 0.00 105.96 16.32 10.29 1725 0 Protein: 0.00 105.96 14.96 10.29 1519 0 Water: 0.00 62.46 26.45 N/A 198 0 Other: 14.77 38.88 23.55 N/A 8 0 Chain A: 0.00 105.96 15.52 N/A 1636 0 Chain S: 3.38 62.46 31.04 N/A 89 0 Histogram: Values Number of atoms 0.00 - 10.60 670 10.60 - 21.19 616 21.19 - 31.79 254 31.79 - 42.38 103 42.38 - 52.98 43 52.98 - 63.57 19 63.57 - 74.17 10 74.17 - 84.77 5 84.77 - 95.36 3 95.36 - 105.96 2 =========================== Idealize ADP of riding H ========================== r_work=0.1013 r_free=0.2042 r_work=0.1017 r_free=0.2043 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1017 r_free = 0.2043 target_work(ml) = 5.163 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0980 r_free = 0.1986 target_work(ml) = 5.137 | | occupancies: max = 1.00 min = 0.11 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= 0.0980 r_free= 0.1986 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ml) (work): 5.137096 | | target function (ml) not normalized (work): 25284.787522 | | target function (ml) not normalized (free): 1899.014222 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1031 0.0980 0.1986 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2220 0.2218 0.2401 n_refl.: 5174 remove outliers: r(all,work,free)=0.2220 0.2218 0.2401 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2220 0.2218 0.2401 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.1026 0.0976 0.1982 n_refl.: 5174 remove outliers: r(all,work,free)=0.1026 0.0976 0.1982 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 0.3820 329.800 299.283 0.623 0.987 0.310 11.894-9.307 99.02 97 4 0.1947 524.872 506.296 1.018 0.994 0.330 9.237-7.194 100.00 213 7 0.2069 429.241 420.656 1.061 0.997 0.334 7.162-5.571 100.00 427 22 0.2009 322.093 313.365 1.038 0.999 0.330 5.546-4.326 100.00 867 58 0.1074 442.189 436.477 1.059 1.000 0.250 4.315-3.360 100.00 1859 96 0.0659 420.526 419.341 1.138 1.003 0.240 3.356-3.002 100.00 1373 60 0.0614 323.907 323.206 1.132 1.004 0.040 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-8.3745 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0976 r_free=0.1982 After: r_work=0.0979 r_free=0.1982 ================================== NQH flips ================================== r_work=0.0979 r_free=0.1982 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 r_work=0.0979 r_free=0.1982 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0979 r_free=0.1982 | n_water=198 | time (s): 0.580 (total time: 0.580) Filter (dist) r_work=0.0988 r_free=0.1988 | n_water=195 | time (s): 16.330 (total time: 16.910) Filter (q & B) r_work=0.1039 r_free=0.1980 | n_water=192 | time (s): 1.430 (total time: 18.340) Compute maps r_work=0.1039 r_free=0.1980 | n_water=192 | time (s): 0.440 (total time: 18.780) Filter (map) r_work=0.1221 r_free=0.1943 | n_water=129 | time (s): 1.460 (total time: 20.240) Find peaks r_work=0.1221 r_free=0.1943 | n_water=129 | time (s): 0.410 (total time: 20.650) Add new water r_work=0.1474 r_free=0.2191 | n_water=191 | time (s): 1.130 (total time: 21.780) Refine new water occ: r_work=0.1068 r_free=0.1970 adp: r_work=0.1065 r_free=0.1987 occ: r_work=0.1054 r_free=0.1975 adp: r_work=0.1055 r_free=0.1980 occ: r_work=0.1046 r_free=0.1969 adp: r_work=0.1046 r_free=0.1973 ADP+occupancy (water only), MIN, final r_work=0.1046 r_free=0.1973 r_work=0.1046 r_free=0.1973 | n_water=191 | time (s): 11.770 (total time: 33.550) Filter (q & B) r_work=0.1046 r_free=0.1970 | n_water=189 | time (s): 1.720 (total time: 35.270) Filter (dist only) r_work=0.1046 r_free=0.1952 | n_water=187 | time (s): 13.890 (total time: 49.160) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.134631 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.244115 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 0.1001 0.1981 0.0980 0.011 1.2 8.3 0.5 0.6 0 0.567 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.01 19.81 9.80 7.821 17.578 0.244 5.151 9.81 19.89 10.08 8.795 17.715 0.244 5.103 Individual atomic B min max mean iso aniso Overall: 0.00 104.81 16.43 11.59 1714 0 Protein: 0.00 104.81 15.43 11.59 1519 0 Water: 0.00 60.30 24.18 N/A 187 0 Other: 13.23 38.06 24.49 N/A 8 0 Chain A: 0.00 104.81 15.86 N/A 1624 0 Chain S: 0.00 60.30 26.61 N/A 90 0 Histogram: Values Number of atoms 0.00 - 10.48 645 10.48 - 20.96 600 20.96 - 31.44 282 31.44 - 41.92 109 41.92 - 52.40 41 52.40 - 62.89 15 62.89 - 73.37 8 73.37 - 83.85 10 83.85 - 94.33 1 94.33 - 104.81 3 =========================== Idealize ADP of riding H ========================== r_work=0.0981 r_free=0.1989 r_work=0.0985 r_free=0.1993 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0985 r_free = 0.1993 target_work(ml) = 5.108 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0972 r_free = 0.1975 target_work(ml) = 5.099 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0972 r_free= 0.1975 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 5.098978 | | target function (ml) not normalized (work): 25097.167750 | | target function (ml) not normalized (free): 1990.347026 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1325 0.1856 5.5932 6.078| | 2: 3.78 - 3.00 1.00 2430 110 0.0542 0.2175 4.5922 10.248| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 12.57 1.00 0.93 13654.72| | 2: 3.78 - 3.00 2430 110 0.98 2.91 1.00 0.95 1412.23| |alpha: min = 0.92 max = 0.95 mean = 0.94| |beta: min = 946.78 max = 21939.97 mean = 7610.58| |figures of merit: min = 0.00 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.87 mean = 7.80| |phase err.(test): min = 0.00 max = 84.51 mean = 7.50| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1022 0.0972 0.1975 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2291 0.2285 0.2469 n_refl.: 5174 remove outliers: r(all,work,free)=0.2291 0.2285 0.2469 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2291 0.2285 0.2469 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.1020 0.0970 0.1982 n_refl.: 5174 remove outliers: r(all,work,free)=0.1020 0.0970 0.1982 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 0.3797 329.800 302.167 0.648 0.989 0.330 11.894-9.307 99.02 97 4 0.1930 524.872 508.019 1.028 0.995 0.350 9.237-7.194 100.00 213 7 0.2089 429.241 419.978 1.054 0.999 0.350 7.162-5.571 100.00 427 22 0.2074 322.093 314.533 1.037 1.000 0.340 5.546-4.326 100.00 867 58 0.1109 442.189 436.537 1.055 1.001 0.256 4.315-3.360 100.00 1859 96 0.0666 420.526 419.309 1.141 1.001 0.252 3.356-3.002 100.00 1373 60 0.0526 323.907 323.025 1.142 1.001 0.040 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-8.5027 ================= 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 : 0.3616 0.2023 0.082 5.242 8.8 119.3 19.9 258 0.000 1_bss: 0.1550 0.1622 0.082 5.242 5.9 116.4 16.9 258 0.000 1_settarget: 0.1550 0.1622 0.082 5.242 5.9 116.4 16.9 258 0.000 1_nqh: 0.1552 0.1620 0.082 5.242 5.9 116.4 16.9 258 0.010 1_weight: 0.1552 0.1620 0.082 5.242 5.9 116.4 16.9 258 0.010 1_xyzrec: 0.1164 0.1774 0.010 0.961 5.9 116.4 16.9 258 0.216 1_adp: 0.1023 0.1766 0.010 0.961 2.1 111.4 17.4 258 0.216 1_regHadp: 0.1017 0.1771 0.010 0.961 2.1 111.4 17.4 258 0.216 1_occ: 0.1014 0.1772 0.010 0.961 2.1 111.4 17.4 258 0.216 2_bss: 0.1011 0.1764 0.010 0.961 1.1 110.4 16.4 258 0.216 2_settarget: 0.1011 0.1764 0.010 0.961 1.1 110.4 16.4 258 0.216 2_updatecdl: 0.1011 0.1764 0.010 0.994 1.1 110.4 16.4 258 0.216 2_nqh: 0.1016 0.1774 0.010 0.994 1.1 110.4 16.4 258 0.213 2_sol: 0.1122 0.1650 0.010 0.994 1.0 109.6 15.8 229 n/a 2_weight: 0.1122 0.1650 0.010 0.994 1.0 109.6 15.8 229 n/a 2_xyzrec: 0.1015 0.1789 0.009 0.974 1.0 109.6 15.8 229 n/a 2_adp: 0.0947 0.1805 0.009 0.974 0.0 107.8 16.4 229 n/a 2_regHadp: 0.0944 0.1804 0.009 0.974 0.0 107.8 16.4 229 n/a 2_occ: 0.0941 0.1791 0.009 0.974 0.0 107.8 16.4 229 n/a 3_bss: 0.0939 0.1789 0.009 0.974 0.0 107.8 16.4 229 n/a 3_settarget: 0.0939 0.1789 0.009 0.974 0.0 107.8 16.4 229 n/a 3_updatecdl: 0.0939 0.1789 0.009 0.981 0.0 107.8 16.4 229 n/a 3_nqh: 0.0942 0.1785 0.009 0.981 0.0 107.8 16.4 229 n/a 3_sol: 0.1304 0.1855 0.009 0.981 0.0 107.8 15.5 137 n/a 3_weight: 0.1304 0.1855 0.009 0.981 0.0 107.8 15.5 137 n/a 3_xyzrec: 0.1159 0.1915 0.012 1.142 0.0 107.8 15.5 137 n/a 3_adp: 0.1090 0.1968 0.012 1.142 0.0 107.0 15.4 137 n/a 3_regHadp: 0.1096 0.1977 0.012 1.142 0.0 107.0 15.4 137 n/a 3_occ: 0.1094 0.1977 0.012 1.142 0.0 107.0 15.4 137 n/a 4_bss: 0.1074 0.1978 0.012 1.142 0.0 107.0 15.4 137 n/a 4_settarget: 0.1074 0.1978 0.012 1.142 0.0 107.0 15.4 137 n/a 4_updatecdl: 0.1074 0.1978 0.012 1.154 0.0 107.0 15.4 137 n/a 4_nqh: 0.1087 0.1985 0.012 1.154 0.0 107.0 15.4 137 n/a 4_sol: 0.1109 0.1986 0.012 1.154 0.0 107.0 16.2 198 n/a 4_weight: 0.1109 0.1986 0.012 1.154 0.0 107.0 16.2 198 n/a 4_xyzrec: 0.1041 0.2048 0.011 1.102 0.0 107.0 16.2 198 n/a 4_adp: 0.1013 0.2042 0.011 1.102 0.0 106.0 16.3 198 n/a 4_regHadp: 0.1017 0.2043 0.011 1.102 0.0 106.0 16.3 198 n/a 4_occ: 0.0980 0.1986 0.011 1.102 0.0 106.0 16.3 198 n/a 5_bss: 0.0976 0.1982 0.011 1.102 0.0 106.0 16.3 198 n/a 5_settarget: 0.0976 0.1982 0.011 1.102 0.0 106.0 16.3 198 n/a 5_updatecdl: 0.0976 0.1982 0.011 1.117 0.0 106.0 16.3 198 n/a 5_setrh: 0.0979 0.1982 0.011 1.117 0.0 106.0 16.3 198 n/a 5_nqh: 0.0979 0.1982 0.011 1.117 0.0 106.0 16.3 198 n/a 5_sol: 0.1046 0.1952 0.011 1.117 0.0 106.0 16.2 187 n/a 5_weight: 0.1046 0.1952 0.011 1.117 0.0 106.0 16.2 187 n/a 5_xyzrec: 0.1001 0.1981 0.011 1.249 0.0 106.0 16.2 187 n/a 5_adp: 0.0981 0.1989 0.011 1.249 0.0 104.8 16.4 187 n/a 5_regHadp: 0.0985 0.1993 0.011 1.249 0.0 104.8 16.4 187 n/a 5_occ: 0.0972 0.1975 0.011 1.249 0.0 104.8 16.4 187 n/a end: 0.0970 0.1982 0.011 1.249 0.0 104.8 16.4 187 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_5431713_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_5431713_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.0600 Refinement macro-cycles (run) : 442.4000 Write final files (write_after_run_outputs) : 11.1500 Total : 456.6100 Total CPU time: 7.96 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:18:19 PST -0800 (1735492699.03 s) Start R-work = 0.1550, R-free = 0.1622 Final R-work = 0.0970, R-free = 0.1982 =============================================================================== Job complete usr+sys time: 487.09 seconds wall clock time: 8 minutes 29.45 seconds (509.45 seconds total)