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_8960824.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_8960824.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8960824.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 4 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: 1.50, per 1000 atoms: 0.44 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: 0.40 Conformation dependent library (CDL) restraints added in 132.8 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.63 - 0.89: 431 0.89 - 1.16: 1194 1.16 - 1.42: 654 1.42 - 1.68: 837 1.68 - 1.94: 37 Bond restraints: 3153 Sorted by residual: bond pdb=" N LEU A 112 " pdb=" CA LEU A 112 " ideal model delta sigma weight residual 1.459 1.687 -0.229 1.16e-02 7.43e+03 3.89e+02 bond pdb=" C LEU A 82 " pdb=" N SER A 83 " ideal model delta sigma weight residual 1.335 1.593 -0.258 1.35e-02 5.49e+03 3.65e+02 bond pdb=" N LEU A 101 " pdb=" CA LEU A 101 " ideal model delta sigma weight residual 1.456 1.673 -0.217 1.22e-02 6.72e+03 3.17e+02 bond pdb=" N SER A 161 " pdb=" CA SER A 161 " ideal model delta sigma weight residual 1.459 1.661 -0.202 1.20e-02 6.94e+03 2.84e+02 bond pdb=" CA VAL A 35 " pdb=" C VAL A 35 " ideal model delta sigma weight residual 1.526 1.338 0.188 1.13e-02 7.83e+03 2.77e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.69: 3126 4.69 - 9.38: 1925 9.38 - 14.07: 595 14.07 - 18.76: 114 18.76 - 23.44: 17 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA ACYS A 53 " pdb=" C ACYS A 53 " pdb=" O ACYS A 53 " ideal model delta sigma weight residual 119.32 131.10 -11.78 7.40e-01 1.83e+00 2.53e+02 angle pdb=" CA MET A 133 " pdb=" C MET A 133 " pdb=" O MET A 133 " ideal model delta sigma weight residual 120.55 137.01 -16.46 1.06e+00 8.90e-01 2.41e+02 angle pdb=" NE ARG A 145 " pdb=" CZ ARG A 145 " pdb=" NH1 ARG A 145 " ideal model delta sigma weight residual 121.50 135.28 -13.78 1.00e+00 1.00e+00 1.90e+02 angle pdb=" NE ARG A 27 " pdb=" CZ ARG A 27 " pdb=" NH1 ARG A 27 " ideal model delta sigma weight residual 121.50 108.76 12.74 1.00e+00 1.00e+00 1.62e+02 angle pdb=" CA ALA A 107 " pdb=" C ALA A 107 " pdb=" O ALA A 107 " ideal model delta sigma weight residual 119.18 134.20 -15.02 1.19e+00 7.06e-01 1.59e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 19.06: 1320 19.06 - 38.11: 114 38.11 - 57.16: 39 57.16 - 76.20: 7 76.20 - 95.25: 1 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" N GLU A 116 " pdb=" C GLU A 116 " pdb=" CA GLU A 116 " pdb=" CB GLU A 116 " ideal model delta harmonic sigma weight residual 122.80 141.08 -18.28 0 2.50e+00 1.60e-01 5.34e+01 dihedral pdb=" C AGLU A 94 " pdb=" N AGLU A 94 " pdb=" CA AGLU A 94 " pdb=" CB AGLU A 94 " ideal model delta harmonic sigma weight residual -122.60 -140.50 17.90 0 2.50e+00 1.60e-01 5.13e+01 dihedral pdb=" N AGLU A 94 " pdb=" C AGLU A 94 " pdb=" CA AGLU A 94 " pdb=" CB AGLU A 94 " ideal model delta harmonic sigma weight residual 122.80 140.61 -17.81 0 2.50e+00 1.60e-01 5.08e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.182: 80 0.182 - 0.362: 69 0.362 - 0.543: 54 0.543 - 0.724: 21 0.724 - 0.905: 19 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA ARG A 156 " pdb=" N ARG A 156 " pdb=" C ARG A 156 " pdb=" CB ARG A 156 " both_signs ideal model delta sigma weight residual False 2.51 1.61 0.90 2.00e-01 2.50e+01 2.05e+01 chirality pdb=" CB VAL A 169 " pdb=" CA VAL A 169 " pdb=" CG1 VAL A 169 " pdb=" CG2 VAL A 169 " both_signs ideal model delta sigma weight residual False -2.63 -3.53 0.90 2.00e-01 2.50e+01 2.03e+01 chirality pdb=" CA ARG A 98 " pdb=" N ARG A 98 " pdb=" C ARG A 98 " pdb=" CB ARG A 98 " both_signs ideal model delta sigma weight residual False 2.51 1.61 0.90 2.00e-01 2.50e+01 2.02e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " -0.055 2.00e-02 2.50e+03 6.39e-02 1.22e+02 pdb=" CG TYR A 141 " -0.125 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " 0.040 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " 0.071 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " 0.073 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " 0.017 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " -0.106 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " 0.023 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " 0.063 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " 0.024 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " -0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.058 2.00e-02 2.50e+03 6.29e-02 1.19e+02 pdb=" CG PHE A 164 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.106 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " -0.105 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.078 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.088 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.018 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.055 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.037 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.042 2.00e-02 2.50e+03 6.06e-02 1.10e+02 pdb=" CG PHE A 119 " -0.063 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.029 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " -0.141 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " 0.037 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.044 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.037 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.023 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.086 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.054 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.047 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.32: 1020 2.32 - 2.89: 8040 2.89 - 3.46: 10588 3.46 - 4.03: 15216 4.03 - 4.60: 21742 Nonbonded interactions: 56606 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.749 2.100 nonbonded pdb=" H GLY A 120 " pdb=" O HIS A 138 " model vdw 1.812 2.450 nonbonded pdb=" HD3 ARG A 5 " pdb="HH11 ARG A 5 " model vdw 1.831 2.270 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.832 2.450 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.839 2.450 ... (remaining 56601 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_8960824_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= 0.2097 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.467650 | | target function (ml) not normalized (work): 22025.516814 | | target function (ml) not normalized (free): 1155.781030 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3800 0.2327 4.8486 4.9522| | 2: 3.78 - 3.00 1.00 2430 110 0.3391 0.1707 4.0757 4.1142| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 48.71 0.83 0.13 6601.27| | 2: 3.78 - 3.00 2430 110 0.94 11.30 1.48 0.26 450.11| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 385.67 max = 12072.35 mean = 3569.36| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 90.00 mean = 30.27| |phase err.(test): min = 0.00 max = 89.96 mean = 32.97| |-----------------------------------------------------------------------------| ----------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 0.267 1557 Z= 5.430 Angle : 5.342 16.459 2118 Z= 3.797 Chirality : 0.396 0.905 243 Planarity : 0.033 0.105 284 Dihedral : 14.246 95.252 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.24 % Favored : 96.22 % Rotamer: Outliers : 1.24 % Allowed : 3.11 % Favored : 95.65 % Cbeta Deviations : 32.43 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.45), residues: 224 helix: -3.06 (0.33), residues: 103 sheet: -1.10 (0.76), residues: 38 loop : -0.48 (0.58), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.058 0.012 ARG A 28 TYR 0.112 0.051 TYR A 141 PHE 0.123 0.054 PHE A 164 HIS 0.063 0.030 HIS A 138 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 1785 0 Protein: 8.85 115.78 16.79 3.90 1519 0 Water: 11.36 119.30 38.03 N/A 258 0 Other: 19.04 26.29 21.71 N/A 8 0 Chain A: 8.85 119.30 19.89 N/A 1785 0 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 3.00 - 49.25 A, n_refl.=5182 (all), 4.86 % free)-------------| | | | r_work= 0.3616 r_free= 0.2097 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.467650 | | target function (ml) not normalized (work): 22025.516814 | | target function (ml) not normalized (free): 1155.781030 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3569 0.3646 0.2195 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3569 0.3646 0.2195 n_refl.: 5182 remove outliers: r(all,work,free)=0.2522 0.2545 0.2195 n_refl.: 5178 overall B=-2.78 to atoms: r(all,work,free)=0.2417 0.2436 0.2145 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1562 0.1560 0.1606 n_refl.: 5178 remove outliers: r(all,work,free)=0.1558 0.1555 0.1606 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 0.3819 449.991 409.920 0.660 1.079 0.404 11.894-9.307 99.02 97 4 0.1832 714.847 692.136 0.926 1.076 0.393 9.237-7.194 100.00 213 7 0.2182 584.603 576.272 0.964 1.067 0.379 7.162-5.571 100.00 427 22 0.2332 438.673 424.203 0.923 1.053 0.315 5.546-4.326 100.00 867 58 0.1356 602.236 595.202 0.978 1.028 0.263 4.315-3.360 100.00 1859 96 0.1294 572.733 567.479 1.055 0.987 0.204 3.356-3.002 100.00 1373 60 0.1636 441.143 433.245 1.075 0.947 0.097 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9555 b_overall=-3.5604 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1555 r_free=0.1606 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1555 r_free=0.1606 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 19.115547 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.943480 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 0.1163 0.1820 0.0657 0.010 1.0 2.9 0.5 0.0 0 9.558 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.63 18.20 6.57 3.013 16.074 1.943 0.018 10.24 18.02 7.77 5.016 16.245 1.943 0.015 Individual atomic B min max mean iso aniso Overall: 1.91 111.51 17.42 5.38 1785 0 Protein: 1.91 111.36 14.74 5.38 1519 0 Water: 4.08 111.51 33.01 N/A 258 0 Other: 18.32 37.84 24.62 N/A 8 0 Chain A: 1.91 111.51 17.42 N/A 1785 0 Histogram: Values Number of atoms 1.91 - 12.87 901 12.87 - 23.83 494 23.83 - 34.79 192 34.79 - 45.75 112 45.75 - 56.71 54 56.71 - 67.67 15 67.67 - 78.63 8 78.63 - 89.59 5 89.59 - 100.55 1 100.55 - 111.51 3 =========================== Idealize ADP of riding H ========================== r_work=0.1024 r_free=0.1802 r_work=0.1018 r_free=0.1810 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1018 r_free = 0.1810 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 = 0.1013 r_free = 0.1814 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.13 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= 0.1013 r_free= 0.1814 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ls_wunit_k1) (work): 0.014041 | | target function (ls_wunit_k1) not normalized (work): 69.137781 | | target function (ls_wunit_k1) not normalized (free): 10.833838 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1053 0.1013 0.1814 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2091 0.2090 0.2215 n_refl.: 5176 remove outliers: r(all,work,free)=0.2091 0.2090 0.2215 n_refl.: 5176 overall B=-0.94 to atoms: r(all,work,free)=0.2052 0.2050 0.2204 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.1052 0.1012 0.1802 n_refl.: 5176 remove outliers: r(all,work,free)=0.1052 0.1012 0.1802 n_refl.: 5176 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 96.88 88 5 0.3317 329.841 311.210 0.664 1.027 0.381 11.894-9.307 99.02 97 4 0.1509 523.979 516.165 0.967 1.027 0.361 9.237-7.194 100.00 213 7 0.1718 428.511 427.182 1.008 1.024 0.331 7.162-5.571 100.00 427 22 0.1666 321.545 317.304 0.966 1.019 0.302 5.546-4.326 100.00 867 58 0.0909 441.436 438.135 0.990 1.010 0.211 4.315-3.360 100.00 1859 96 0.0757 419.810 419.629 1.044 0.996 0.193 3.356-3.002 100.00 1373 60 0.0995 323.356 321.894 1.027 0.981 0.077 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-3.3515 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1012 r_free=0.1802 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A Total number of N/Q/H flips: 1 r_work=0.1012 r_free=0.1800 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1012 r_free=0.1800 | n_water=258 | time (s): 0.510 (total time: 0.510) Filter (dist) r_work=0.1045 r_free=0.1798 | n_water=247 | time (s): 19.010 (total time: 19.520) Filter (q & B) r_work=0.1045 r_free=0.1798 | n_water=244 | time (s): 1.830 (total time: 21.350) Compute maps r_work=0.1045 r_free=0.1798 | n_water=244 | time (s): 0.500 (total time: 21.850) Filter (map) r_work=0.1338 r_free=0.1847 | n_water=146 | time (s): 1.770 (total time: 23.620) Find peaks r_work=0.1338 r_free=0.1847 | n_water=146 | time (s): 0.600 (total time: 24.220) Add new water r_work=0.1693 r_free=0.2145 | n_water=235 | time (s): 1.480 (total time: 25.700) Refine new water occ: r_work=0.1148 r_free=0.1699 adp: r_work=0.1126 r_free=0.1701 occ: r_work=0.1122 r_free=0.1680 adp: r_work=0.1112 r_free=0.1691 occ: r_work=0.1111 r_free=0.1679 adp: r_work=0.1109 r_free=0.1681 ADP+occupancy (water only), MIN, final r_work=0.1109 r_free=0.1681 r_work=0.1109 r_free=0.1681 | n_water=235 | time (s): 3.710 (total time: 29.410) Filter (q & B) r_work=0.1109 r_free=0.1681 | n_water=235 | time (s): 0.920 (total time: 30.330) Filter (dist only) r_work=0.1111 r_free=0.1675 | n_water=233 | time (s): 19.150 (total time: 49.480) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.739323 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.682024 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 0.0998 0.1765 0.0766 0.009 1.0 4.2 0.5 0.6 0 11.870 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.98 17.65 7.66 4.723 16.901 2.682 0.013 9.34 17.74 8.40 5.430 17.347 2.682 0.012 Individual atomic B min max mean iso aniso Overall: 0.00 107.69 16.82 6.42 1760 0 Protein: 0.00 107.69 15.17 6.41 1519 0 Water: 0.00 62.86 27.29 N/A 233 0 Other: 13.04 37.90 24.79 N/A 8 0 Chain A: 0.00 107.69 15.96 N/A 1671 0 Chain S: 0.00 59.77 33.00 N/A 89 0 Histogram: Values Number of atoms 0.00 - 10.77 655 10.77 - 21.54 689 21.54 - 32.31 210 32.31 - 43.08 122 43.08 - 53.85 43 53.85 - 64.62 28 64.62 - 75.38 6 75.38 - 86.15 2 86.15 - 96.92 3 96.92 - 107.69 2 =========================== Idealize ADP of riding H ========================== r_work=0.0934 r_free=0.1774 r_work=0.0932 r_free=0.1777 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0932 r_free = 0.1777 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 = 0.0929 r_free = 0.1773 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.23 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= 0.0929 r_free= 0.1773 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ls_wunit_k1) (work): 0.011675 | | target function (ls_wunit_k1) not normalized (work): 57.489530 | | target function (ls_wunit_k1) not normalized (free): 9.772739 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0973 0.0929 0.1773 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2135 0.2137 0.2236 n_refl.: 5176 remove outliers: r(all,work,free)=0.2135 0.2137 0.2236 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2135 0.2137 0.2236 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0976 0.0931 0.1791 n_refl.: 5176 remove outliers: r(all,work,free)=0.0976 0.0931 0.1791 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 0.3158 329.841 315.960 0.716 0.998 0.387 11.894-9.307 99.02 97 4 0.1387 523.979 516.744 0.984 1.001 0.345 9.237-7.194 100.00 213 7 0.1448 428.511 427.668 1.023 1.002 0.320 7.162-5.571 100.00 427 22 0.1437 321.545 317.625 0.994 1.001 0.290 5.546-4.326 100.00 867 58 0.0771 441.436 438.380 1.010 1.001 0.240 4.315-3.360 100.00 1859 96 0.0729 419.810 420.006 1.055 1.000 0.200 3.356-3.002 100.00 1373 60 0.0964 323.356 323.752 1.032 0.999 0.079 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-4.2938 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0931 r_free=0.1791 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A A 80 GLN A Total number of N/Q/H flips: 2 r_work=0.0932 r_free=0.1797 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0932 r_free=0.1797 | n_water=233 | time (s): 0.470 (total time: 0.470) Filter (dist) r_work=0.0954 r_free=0.1798 | n_water=228 | time (s): 19.720 (total time: 20.190) Filter (q & B) r_work=0.1019 r_free=0.1825 | n_water=225 | time (s): 1.260 (total time: 21.450) Compute maps r_work=0.1019 r_free=0.1825 | n_water=225 | time (s): 0.550 (total time: 22.000) Filter (map) r_work=0.1278 r_free=0.1902 | n_water=150 | time (s): 1.640 (total time: 23.640) Find peaks r_work=0.1278 r_free=0.1902 | n_water=150 | time (s): 0.400 (total time: 24.040) Add new water r_work=0.1649 r_free=0.2221 | n_water=233 | time (s): 1.350 (total time: 25.390) Refine new water r_work=0.1649 r_free=0.2221 | n_water=233 | time (s): 0.060 (total time: 25.450) Filter (q & B) r_work=0.1278 r_free=0.1902 | n_water=150 | time (s): 1.570 (total time: 27.020) Filter (dist only) r_work=0.1295 r_free=0.1871 | n_water=142 | time (s): 13.020 (total time: 40.040) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.409399 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.289139 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 0.1153 0.1950 0.0797 0.012 1.1 4.8 0.5 0.6 0 0.705 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.53 19.50 7.97 5.388 17.747 0.289 5.416 10.74 19.59 8.85 7.401 17.709 0.289 5.318 Individual atomic B min max mean iso aniso Overall: 0.00 106.07 15.88 8.81 1669 0 Protein: 0.00 106.07 15.11 8.82 1519 0 Water: 1.35 57.86 23.69 N/A 142 0 Other: 15.09 34.41 23.23 N/A 8 0 Chain A: 0.00 106.07 15.79 N/A 1653 0 Chain S: 8.65 44.91 25.06 N/A 16 0 Histogram: Values Number of atoms 0.00 - 10.61 663 10.61 - 21.21 632 21.21 - 31.82 210 31.82 - 42.43 93 42.43 - 53.03 36 53.03 - 63.64 17 63.64 - 74.25 10 74.25 - 84.85 3 84.85 - 95.46 3 95.46 - 106.07 2 =========================== Idealize ADP of riding H ========================== r_work=0.1074 r_free=0.1959 r_work=0.1080 r_free=0.1964 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1080 r_free = 0.1964 target_work(ml) = 5.320 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1078 r_free = 0.1964 target_work(ml) = 5.319 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.1078 r_free= 0.1964 coordinate error (max.-lik. estimate): 0.33 A | | | | normalized target function (ml) (work): 5.318688 | | target function (ml) not normalized (work): 26189.221253 | | target function (ml) not normalized (free): 1677.544352 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1126 0.1078 0.1964 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2404 0.2412 0.2430 n_refl.: 5176 remove outliers: r(all,work,free)=0.2404 0.2412 0.2430 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2404 0.2412 0.2430 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.1111 0.1063 0.1966 n_refl.: 5176 remove outliers: r(all,work,free)=0.1109 0.1061 0.1966 n_refl.: 5175 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3415 327.063 308.919 0.696 1.004 0.374 11.894-9.307 99.02 97 4 0.1685 523.979 514.961 0.970 1.008 0.360 9.237-7.194 100.00 213 7 0.1798 428.511 422.634 0.985 1.008 0.350 7.162-5.571 100.00 427 22 0.1784 321.545 315.789 0.966 1.007 0.330 5.546-4.326 100.00 867 58 0.1074 441.436 435.732 0.977 1.004 0.254 4.315-3.360 100.00 1859 96 0.0789 419.810 417.905 1.051 0.999 0.240 3.356-3.002 100.00 1373 60 0.0929 323.356 320.993 1.045 0.993 0.084 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9170 b_overall=-6.1598 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1061 r_free=0.1966 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=0.1071 r_free=0.1971 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1071 r_free=0.1971 | n_water=142 | time (s): 0.620 (total time: 0.620) Filter (dist) r_work=0.1092 r_free=0.1955 | n_water=137 | time (s): 11.460 (total time: 12.080) Filter (q & B) r_work=0.1092 r_free=0.1955 | n_water=137 | time (s): 1.000 (total time: 13.080) Compute maps r_work=0.1092 r_free=0.1955 | n_water=137 | time (s): 0.490 (total time: 13.570) Filter (map) r_work=0.1162 r_free=0.1972 | n_water=124 | time (s): 1.420 (total time: 14.990) Find peaks r_work=0.1162 r_free=0.1972 | n_water=124 | time (s): 0.500 (total time: 15.490) Add new water r_work=0.1426 r_free=0.2333 | n_water=180 | time (s): 1.660 (total time: 17.150) Refine new water occ: r_work=0.1142 r_free=0.2016 adp: r_work=0.1143 r_free=0.2031 occ: r_work=0.1130 r_free=0.2000 adp: r_work=0.1131 r_free=0.2014 occ: r_work=0.1119 r_free=0.1982 adp: r_work=0.1119 r_free=0.1998 ADP+occupancy (water only), MIN, final r_work=0.1119 r_free=0.1998 r_work=0.1119 r_free=0.1998 | n_water=180 | time (s): 14.400 (total time: 31.550) Filter (q & B) r_work=0.1119 r_free=0.1998 | n_water=180 | time (s): 1.030 (total time: 32.580) Filter (dist only) r_work=0.1119 r_free=0.1992 | n_water=178 | time (s): 14.250 (total time: 46.830) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.228112 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.233423 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 0.2058 0.1017 0.011 1.1 4.5 0.5 1.2 0 0.614 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.41 20.58 10.17 6.876 17.863 0.233 5.226 10.06 20.65 10.59 8.147 17.896 0.233 5.160 Individual atomic B min max mean iso aniso Overall: 0.00 104.38 16.42 10.37 1705 0 Protein: 0.00 104.38 15.39 10.38 1519 0 Water: 1.65 55.01 24.91 N/A 178 0 Other: 17.97 31.62 23.32 N/A 8 0 Chain A: 0.00 104.38 15.90 N/A 1639 0 Chain S: 8.05 55.01 29.38 N/A 66 0 Histogram: Values Number of atoms 0.00 - 10.44 643 10.44 - 20.88 617 20.88 - 31.31 249 31.31 - 41.75 114 41.75 - 52.19 43 52.19 - 62.63 18 62.63 - 73.07 10 73.07 - 83.50 5 83.50 - 93.94 4 93.94 - 104.38 2 =========================== Idealize ADP of riding H ========================== r_work=0.1006 r_free=0.2065 r_work=0.1010 r_free=0.2068 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1010 r_free = 0.2068 target_work(ml) = 5.165 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0979 r_free = 0.2021 target_work(ml) = 5.146 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0979 r_free= 0.2021 coordinate error (max.-lik. estimate): 0.31 A | | | | normalized target function (ml) (work): 5.145880 | | target function (ml) not normalized (work): 25333.166780 | | target function (ml) not normalized (free): 1831.607249 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1032 0.0979 0.2021 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2372 0.2379 0.2393 n_refl.: 5175 remove outliers: r(all,work,free)=0.2372 0.2379 0.2393 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2372 0.2379 0.2393 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.1027 0.0974 0.2020 n_refl.: 5175 remove outliers: r(all,work,free)=0.1027 0.0974 0.2020 n_refl.: 5175 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3590 327.063 304.485 0.670 0.994 0.360 11.894-9.307 99.02 97 4 0.1857 523.979 513.858 0.965 1.000 0.360 9.237-7.194 100.00 213 7 0.1995 428.511 419.385 0.998 1.002 0.360 7.162-5.571 100.00 427 22 0.2027 321.545 311.668 0.979 1.002 0.340 5.546-4.326 100.00 867 58 0.1060 441.436 436.039 0.997 1.002 0.254 4.315-3.360 100.00 1859 96 0.0671 419.810 418.461 1.076 1.002 0.240 3.356-3.002 100.00 1373 60 0.0631 323.356 322.037 1.068 1.001 0.083 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.4517 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0974 r_free=0.2020 After: r_work=0.0977 r_free=0.2020 ================================== NQH flips ================================== r_work=0.0977 r_free=0.2020 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 B Total number of N/Q/H flips: 1 r_work=0.0977 r_free=0.2020 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0977 r_free=0.2020 | n_water=178 | time (s): 0.460 (total time: 0.460) Filter (dist) r_work=0.0977 r_free=0.2020 | n_water=178 | time (s): 14.020 (total time: 14.480) Filter (q & B) r_work=0.0977 r_free=0.2020 | n_water=178 | time (s): 0.850 (total time: 15.330) Compute maps r_work=0.0977 r_free=0.2020 | n_water=178 | time (s): 0.520 (total time: 15.850) Filter (map) r_work=0.1157 r_free=0.1892 | n_water=129 | time (s): 1.410 (total time: 17.260) Find peaks r_work=0.1157 r_free=0.1892 | n_water=129 | time (s): 0.520 (total time: 17.780) Add new water r_work=0.1400 r_free=0.2103 | n_water=180 | time (s): 1.410 (total time: 19.190) Refine new water occ: r_work=0.1046 r_free=0.1973 adp: r_work=0.1046 r_free=0.1985 occ: r_work=0.1036 r_free=0.1969 adp: r_work=0.1037 r_free=0.1977 occ: r_work=0.1028 r_free=0.1962 adp: r_work=0.1028 r_free=0.1969 ADP+occupancy (water only), MIN, final r_work=0.1028 r_free=0.1969 r_work=0.1028 r_free=0.1969 | n_water=180 | time (s): 10.260 (total time: 29.450) Filter (q & B) r_work=0.1028 r_free=0.1972 | n_water=179 | time (s): 1.700 (total time: 31.150) Filter (dist only) r_work=0.1025 r_free=0.1979 | n_water=178 | time (s): 13.850 (total time: 45.000) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.068363 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.240643 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 0.0998 0.1977 0.0979 0.012 1.2 5.8 0.5 1.2 0 0.534 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.98 19.77 9.79 7.900 18.046 0.241 5.139 9.83 19.83 9.99 8.822 18.111 0.241 5.094 Individual atomic B min max mean iso aniso Overall: 0.00 103.44 16.54 11.59 1705 0 Protein: 0.00 103.44 15.70 11.59 1519 0 Water: 0.37 57.97 23.45 N/A 178 0 Other: 17.19 33.38 23.56 N/A 8 0 Chain A: 0.00 103.44 16.08 N/A 1630 0 Chain S: 4.67 57.97 26.55 N/A 75 0 Histogram: Values Number of atoms 0.00 - 10.34 622 10.34 - 20.69 600 20.69 - 31.03 292 31.03 - 41.38 112 41.38 - 51.72 42 51.72 - 62.06 13 62.06 - 72.41 12 72.41 - 82.75 5 82.75 - 93.09 5 93.09 - 103.44 2 =========================== Idealize ADP of riding H ========================== r_work=0.0983 r_free=0.1983 r_work=0.0988 r_free=0.1987 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0988 r_free = 0.1987 target_work(ml) = 5.098 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0975 r_free = 0.1963 target_work(ml) = 5.092 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0975 r_free= 0.1963 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ml) (work): 5.091569 | | target function (ml) not normalized (work): 25065.793159 | | target function (ml) not normalized (free): 1990.035316 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.79 1.00 2493 142 0.1334 0.1961 5.5982 6.1762| | 2: 3.78 - 3.00 1.00 2430 110 0.0536 0.1968 4.5718 10.118| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.79 2493 142 0.91 12.46 1.00 0.99 13334.48| | 2: 3.78 - 3.00 2430 110 0.98 2.78 1.00 1.01 1377.39| |alpha: min = 0.98 max = 1.01 mean = 1.00| |beta: min = 912.13 max = 21257.22 mean = 7432.44| |figures of merit: min = 0.01 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.48 mean = 7.68| |phase err.(test): min = 0.00 max = 79.63 mean = 7.47| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1025 0.0975 0.1963 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2425 0.2427 0.2514 n_refl.: 5175 remove outliers: r(all,work,free)=0.2425 0.2427 0.2514 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2425 0.2427 0.2514 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.1023 0.0973 0.1972 n_refl.: 5175 remove outliers: r(all,work,free)=0.1023 0.0973 0.1972 n_refl.: 5175 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3705 327.063 302.572 0.672 0.991 0.359 11.894-9.307 99.02 97 4 0.1850 523.979 514.167 0.973 0.998 0.356 9.237-7.194 100.00 213 7 0.2073 428.511 418.859 0.998 1.000 0.336 7.162-5.571 100.00 427 22 0.2110 321.545 311.833 0.986 1.001 0.320 5.546-4.326 100.00 867 58 0.1126 441.436 435.676 1.006 1.002 0.260 4.315-3.360 100.00 1859 96 0.0675 419.810 418.562 1.093 1.001 0.243 3.356-3.002 100.00 1373 60 0.0513 323.356 322.423 1.090 1.001 0.087 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-8.2897 ================= 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 0.2097 0.082 5.342 8.8 119.3 19.9 258 0.000 1_bss: 0.1555 0.1606 0.082 5.342 6.1 116.5 17.1 258 0.000 1_settarget: 0.1555 0.1606 0.082 5.342 6.1 116.5 17.1 258 0.000 1_nqh: 0.1555 0.1606 0.082 5.342 6.1 116.5 17.1 258 0.000 1_weight: 0.1555 0.1606 0.082 5.342 6.1 116.5 17.1 258 0.000 1_xyzrec: 0.1163 0.1820 0.010 0.970 6.1 116.5 17.1 258 0.213 1_adp: 0.1024 0.1802 0.010 0.970 1.9 111.5 17.4 258 0.213 1_regHadp: 0.1018 0.1810 0.010 0.970 1.9 111.5 17.4 258 0.213 1_occ: 0.1013 0.1814 0.010 0.970 1.9 111.5 17.4 258 0.213 2_bss: 0.1012 0.1802 0.010 0.970 1.0 110.6 16.5 258 0.213 2_settarget: 0.1012 0.1802 0.010 0.970 1.0 110.6 16.5 258 0.213 2_updatecdl: 0.1012 0.1802 0.010 0.992 1.0 110.6 16.5 258 0.213 2_nqh: 0.1012 0.1800 0.010 0.992 1.0 110.6 16.5 258 0.215 2_sol: 0.1111 0.1675 0.010 0.992 1.0 110.4 16.0 233 n/a 2_weight: 0.1111 0.1675 0.010 0.992 1.0 110.4 16.0 233 n/a 2_xyzrec: 0.0998 0.1765 0.009 0.987 1.0 110.4 16.0 233 n/a 2_adp: 0.0934 0.1774 0.009 0.987 0.0 107.7 16.8 233 n/a 2_regHadp: 0.0932 0.1777 0.009 0.987 0.0 107.7 16.8 233 n/a 2_occ: 0.0929 0.1773 0.009 0.987 0.0 107.7 16.8 233 n/a 3_bss: 0.0931 0.1791 0.009 0.987 0.0 107.7 16.8 233 n/a 3_settarget: 0.0931 0.1791 0.009 0.987 0.0 107.7 16.8 233 n/a 3_updatecdl: 0.0931 0.1791 0.009 0.989 0.0 107.7 16.8 233 n/a 3_nqh: 0.0932 0.1797 0.009 0.989 0.0 107.7 16.8 233 n/a 3_sol: 0.1295 0.1871 0.009 0.989 0.0 107.7 16.0 142 n/a 3_weight: 0.1295 0.1871 0.009 0.989 0.0 107.7 16.0 142 n/a 3_xyzrec: 0.1153 0.1950 0.012 1.109 0.0 107.7 16.0 142 n/a 3_adp: 0.1074 0.1959 0.012 1.109 0.0 106.1 15.9 142 n/a 3_regHadp: 0.1080 0.1964 0.012 1.109 0.0 106.1 15.9 142 n/a 3_occ: 0.1078 0.1964 0.012 1.109 0.0 106.1 15.9 142 n/a 4_bss: 0.1061 0.1966 0.012 1.109 0.0 106.1 15.9 142 n/a 4_settarget: 0.1061 0.1966 0.012 1.109 0.0 106.1 15.9 142 n/a 4_updatecdl: 0.1061 0.1966 0.012 1.120 0.0 106.1 15.9 142 n/a 4_nqh: 0.1071 0.1971 0.012 1.120 0.0 106.1 15.9 142 n/a 4_sol: 0.1119 0.1992 0.012 1.120 0.0 106.1 16.4 178 n/a 4_weight: 0.1119 0.1992 0.012 1.120 0.0 106.1 16.4 178 n/a 4_xyzrec: 0.1041 0.2058 0.011 1.121 0.0 106.1 16.4 178 n/a 4_adp: 0.1006 0.2065 0.011 1.121 0.0 104.4 16.4 178 n/a 4_regHadp: 0.1010 0.2068 0.011 1.121 0.0 104.4 16.4 178 n/a 4_occ: 0.0979 0.2021 0.011 1.121 0.0 104.4 16.4 178 n/a 5_bss: 0.0974 0.2020 0.011 1.121 0.0 104.4 16.4 178 n/a 5_settarget: 0.0974 0.2020 0.011 1.121 0.0 104.4 16.4 178 n/a 5_updatecdl: 0.0974 0.2020 0.012 1.123 0.0 104.4 16.4 178 n/a 5_setrh: 0.0977 0.2020 0.012 1.123 0.0 104.4 16.4 178 n/a 5_nqh: 0.0977 0.2020 0.012 1.123 0.0 104.4 16.4 178 n/a 5_sol: 0.1025 0.1979 0.012 1.123 0.0 104.4 16.4 178 n/a 5_weight: 0.1025 0.1979 0.012 1.123 0.0 104.4 16.4 178 n/a 5_xyzrec: 0.0998 0.1977 0.012 1.204 0.0 104.4 16.4 178 n/a 5_adp: 0.0983 0.1983 0.012 1.204 0.0 103.4 16.5 178 n/a 5_regHadp: 0.0988 0.1987 0.012 1.204 0.0 103.4 16.5 178 n/a 5_occ: 0.0975 0.1963 0.012 1.204 0.0 103.4 16.5 178 n/a end: 0.0973 0.1972 0.012 1.204 0.0 103.4 16.5 178 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_8960824_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_8960824_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.0700 Refinement macro-cycles (run) : 452.9700 Write final files (write_after_run_outputs) : 10.6100 Total : 466.6500 Total CPU time: 8.14 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:18:30 PST -0800 (1735492710.22 s) Start R-work = 0.1555, R-free = 0.1606 Final R-work = 0.0973, R-free = 0.1972 =============================================================================== Job complete usr+sys time: 498.20 seconds wall clock time: 8 minutes 40.45 seconds (520.45 seconds total)