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_6470396.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Adding command-line PHIL: ------------------------- xray_data.high_resolution=3 ordered_solvent.low_resolution=4 No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6470396.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6470396.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 3 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 2 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: 2.02, per 1000 atoms: 0.60 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: 0.34 Conformation dependent library (CDL) restraints added in 105.0 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.91: 498 0.91 - 1.15: 1124 1.15 - 1.40: 600 1.40 - 1.65: 853 1.65 - 1.90: 78 Bond restraints: 3153 Sorted by residual: bond pdb=" C BGLU A 94 " pdb=" O BGLU A 94 " ideal model delta sigma weight residual 1.237 1.448 -0.211 1.19e-02 7.06e+03 3.15e+02 bond pdb=" ND1 HIS A 126 " pdb=" CE1 HIS A 126 " ideal model delta sigma weight residual 1.321 1.150 0.171 1.00e-02 1.00e+04 2.93e+02 bond pdb=" CA ALA A 114 " pdb=" C ALA A 114 " ideal model delta sigma weight residual 1.523 1.739 -0.216 1.30e-02 5.92e+03 2.76e+02 bond pdb=" C LYS A 63 " pdb=" O LYS A 63 " ideal model delta sigma weight residual 1.236 1.444 -0.209 1.29e-02 6.01e+03 2.61e+02 bond pdb=" CA ALA A 14 " pdb=" C ALA A 14 " ideal model delta sigma weight residual 1.525 1.731 -0.207 1.28e-02 6.10e+03 2.61e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.01: 3319 5.01 - 10.01: 1843 10.01 - 15.02: 551 15.02 - 20.03: 59 20.03 - 25.03: 5 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O AGLU A 96 " pdb=" C AGLU A 96 " pdb=" N AASN A 97 " ideal model delta sigma weight residual 122.07 106.39 15.68 1.03e+00 9.43e-01 2.32e+02 angle pdb=" O BCYS A 53 " pdb=" C BCYS A 53 " pdb=" N PRO A 54 " ideal model delta sigma weight residual 121.19 135.28 -14.09 9.40e-01 1.13e+00 2.25e+02 angle pdb=" NE ARG A 28 " pdb=" CZ ARG A 28 " pdb=" NH1 ARG A 28 " ideal model delta sigma weight residual 121.50 106.70 14.80 1.00e+00 1.00e+00 2.19e+02 angle pdb=" O ALA A 111 " pdb=" C ALA A 111 " pdb=" N LEU A 112 " ideal model delta sigma weight residual 122.12 136.28 -14.16 1.06e+00 8.90e-01 1.78e+02 angle pdb=" N ILE A 9 " pdb=" CA ILE A 9 " pdb=" CB ILE A 9 " ideal model delta sigma weight residual 111.21 126.44 -15.23 1.17e+00 7.31e-01 1.69e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.02 - 16.51: 1284 16.51 - 33.00: 135 33.00 - 49.49: 43 49.49 - 65.98: 16 65.98 - 82.47: 3 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C LYS A 182 " pdb=" N LYS A 182 " pdb=" CA LYS A 182 " pdb=" CB LYS A 182 " ideal model delta harmonic sigma weight residual -122.60 -104.13 -18.47 0 2.50e+00 1.60e-01 5.46e+01 dihedral pdb=" C BGLU A 96 " pdb=" N BGLU A 96 " pdb=" CA BGLU A 96 " pdb=" CB BGLU A 96 " ideal model delta harmonic sigma weight residual -122.60 -140.42 17.82 0 2.50e+00 1.60e-01 5.08e+01 dihedral pdb=" C VAL A 123 " pdb=" N VAL A 123 " pdb=" CA VAL A 123 " pdb=" CB VAL A 123 " ideal model delta harmonic sigma weight residual -122.00 -104.99 -17.01 0 2.50e+00 1.60e-01 4.63e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.003 - 0.290: 124 0.290 - 0.576: 87 0.576 - 0.862: 28 0.862 - 1.148: 3 1.148 - 1.434: 1 Chirality restraints: 243 Sorted by residual: chirality pdb=" CG LEU A 172 " pdb=" CB LEU A 172 " pdb=" CD1 LEU A 172 " pdb=" CD2 LEU A 172 " both_signs ideal model delta sigma weight residual False -2.59 -1.16 -1.43 2.00e-01 2.50e+01 5.14e+01 chirality pdb=" CB VAL A 44 " pdb=" CA VAL A 44 " pdb=" CG1 VAL A 44 " pdb=" CG2 VAL A 44 " both_signs ideal model delta sigma weight residual False -2.63 -3.64 1.01 2.00e-01 2.50e+01 2.54e+01 chirality pdb=" CA BGLU A 96 " pdb=" N BGLU A 96 " pdb=" C BGLU A 96 " pdb=" CB BGLU A 96 " both_signs ideal model delta sigma weight residual False 2.51 1.59 0.92 2.00e-01 2.50e+01 2.11e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " -0.074 2.00e-02 2.50e+03 5.88e-02 1.04e+02 pdb=" CG ATYR A 67 " -0.079 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " 0.115 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " 0.013 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " -0.074 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " 0.029 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " -0.006 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " -0.067 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " 0.053 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " 0.028 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " 0.020 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 115 " -0.035 2.00e-02 2.50e+03 6.75e-02 1.03e+02 pdb=" CG HIS A 115 " -0.006 2.00e-02 2.50e+03 pdb=" ND1 HIS A 115 " 0.115 2.00e-02 2.50e+03 pdb=" CD2 HIS A 115 " -0.055 2.00e-02 2.50e+03 pdb=" CE1 HIS A 115 " -0.029 2.00e-02 2.50e+03 pdb=" NE2 HIS A 115 " -0.113 2.00e-02 2.50e+03 pdb=" HD2 HIS A 115 " 0.073 2.00e-02 2.50e+03 pdb=" HE1 HIS A 115 " -0.016 2.00e-02 2.50e+03 pdb=" HE2 HIS A 115 " 0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " 0.036 2.00e-02 2.50e+03 5.67e-02 9.65e+01 pdb=" CG TYR A 141 " -0.078 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " 0.051 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " -0.022 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " 0.038 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " 0.078 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " 0.009 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " 0.067 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " -0.086 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " -0.093 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.34: 1194 2.34 - 2.91: 8234 2.91 - 3.47: 10532 3.47 - 4.04: 15142 4.04 - 4.60: 21506 Nonbonded interactions: 56608 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.780 2.100 nonbonded pdb=" HG SER A 47 " pdb="HH11 ARG A 48 " model vdw 1.791 2.100 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.801 2.450 x-y,-y,-z-4/3 nonbonded pdb=" H LYS A 122 " pdb=" OD2 ASP A 149 " model vdw 1.825 2.450 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.834 2.450 ... (remaining 56603 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_6470396_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= 0.3625 r_free= 0.1967 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.474780 | | target function (ml) not normalized (work): 22060.664033 | | target function (ml) not normalized (free): 1140.077083 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3813 0.2172 4.847 4.8856| | 2: 3.78 - 3.00 1.00 2430 110 0.3396 0.1621 4.0918 4.0575| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 48.82 0.83 0.13 6606.11| | 2: 3.78 - 3.00 2430 110 0.94 11.30 1.48 0.26 455.64| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 389.65 max = 12070.13 mean = 3574.54| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 90.00 mean = 30.32| |phase err.(test): min = 0.00 max = 89.97 mean = 33.47| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.083 0.236 1557 Z= 5.511 Angle : 5.297 17.365 2118 Z= 3.728 Chirality : 0.379 1.434 243 Planarity : 0.033 0.094 284 Dihedral : 14.260 82.471 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.24 % Allowed : 3.11 % Favored : 95.65 % Cbeta Deviations : 27.03 % 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: -3.02 (0.45), residues: 224 helix: -2.90 (0.39), residues: 103 sheet: -0.84 (0.85), residues: 28 loop : -1.00 (0.52), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.075 0.021 ARG A 156 TYR 0.078 0.030 TYR A 139 PHE 0.110 0.041 PHE A 162 HIS 0.075 0.030 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= 0.3625 r_free= 0.1967 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.474780 | | target function (ml) not normalized (work): 22060.664033 | | target function (ml) not normalized (free): 1140.077083 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3584 0.3660 0.2084 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3584 0.3660 0.2084 n_refl.: 5182 remove outliers: r(all,work,free)=0.2525 0.2550 0.2084 n_refl.: 5178 overall B=-2.87 to atoms: r(all,work,free)=0.2415 0.2436 0.2034 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1563 0.1564 0.1554 n_refl.: 5178 remove outliers: r(all,work,free)=0.1557 0.1558 0.1554 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 97.87 87 5 0.3774 453.464 404.934 0.674 1.047 0.398 11.894-9.307 99.02 97 4 0.1847 714.317 695.079 0.949 1.045 0.383 9.237-7.194 100.00 213 7 0.2210 584.169 575.925 0.989 1.040 0.364 7.162-5.571 100.00 427 22 0.2312 438.348 424.961 0.953 1.031 0.303 5.546-4.326 100.00 867 58 0.1356 601.790 595.131 0.987 1.017 0.215 4.315-3.360 100.00 1859 96 0.1310 572.308 567.166 1.054 0.992 0.179 3.356-3.002 100.00 1373 60 0.1615 440.816 432.577 1.051 0.968 0.087 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9559 b_overall=-3.6526 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1558 r_free=0.1554 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 r_work=0.1560 r_free=0.1553 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 19.201115 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.875403 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 0.1769 0.0616 0.010 1.0 2.2 0.5 0.0 0 9.601 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.53 17.69 6.16 3.013 15.990 1.875 0.018 10.10 17.70 7.60 4.964 16.223 1.875 0.014 Individual atomic B min max mean iso aniso Overall: 2.26 111.43 17.46 5.31 1785 0 Protein: 2.26 111.40 14.77 5.30 1519 0 Water: 4.00 111.43 33.10 N/A 258 0 Other: 15.38 37.04 23.69 N/A 8 0 Chain A: 2.26 111.43 17.46 N/A 1785 0 Histogram: Values Number of atoms 2.26 - 13.17 912 13.17 - 24.09 485 24.09 - 35.01 194 35.01 - 45.93 107 45.93 - 56.84 51 56.84 - 67.76 19 67.76 - 78.68 8 78.68 - 89.60 5 89.60 - 100.51 1 100.51 - 111.43 3 =========================== Idealize ADP of riding H ========================== r_work=0.1010 r_free=0.1770 r_work=0.1003 r_free=0.1779 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1003 r_free = 0.1779 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 = 0.1003 r_free = 0.1760 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.1003 r_free= 0.1760 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ls_wunit_k1) (work): 0.013725 | | target function (ls_wunit_k1) not normalized (work): 67.568995 | | target function (ls_wunit_k1) not normalized (free): 10.287300 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1043 0.1003 0.1760 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2080 0.2078 0.2220 n_refl.: 5175 remove outliers: r(all,work,free)=0.2080 0.2078 0.2220 n_refl.: 5175 overall B=-0.95 to atoms: r(all,work,free)=0.2041 0.2036 0.2210 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.1046 0.1007 0.1774 n_refl.: 5175 remove outliers: r(all,work,free)=0.1046 0.1007 0.1774 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 0.3212 332.967 314.692 0.684 1.004 0.381 11.894-9.307 99.02 97 4 0.1508 524.505 515.968 0.983 1.006 0.351 9.237-7.194 100.00 213 7 0.1660 428.941 429.000 1.024 1.006 0.324 7.162-5.571 100.00 427 22 0.1614 321.868 318.905 0.987 1.004 0.309 5.546-4.326 100.00 867 58 0.0912 441.879 439.017 0.996 1.002 0.196 4.315-3.360 100.00 1859 96 0.0760 420.232 420.195 1.043 0.999 0.183 3.356-3.002 100.00 1373 60 0.1001 323.680 322.307 1.012 0.995 0.092 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-3.4116 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1007 r_free=0.1774 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN Total number of N/Q/H flips: 1 r_work=0.1007 r_free=0.1774 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1007 r_free=0.1774 | n_water=258 | time (s): 0.580 (total time: 0.580) Filter (dist) r_work=0.1034 r_free=0.1759 | n_water=247 | time (s): 21.340 (total time: 21.920) Filter (q & B) r_work=0.1035 r_free=0.1762 | n_water=245 | time (s): 1.760 (total time: 23.680) Compute maps r_work=0.1035 r_free=0.1762 | n_water=245 | time (s): 0.620 (total time: 24.300) Filter (map) r_work=0.1360 r_free=0.1822 | n_water=141 | time (s): 2.000 (total time: 26.300) Find peaks r_work=0.1360 r_free=0.1822 | n_water=141 | time (s): 0.400 (total time: 26.700) Add new water r_work=0.1709 r_free=0.2075 | n_water=235 | time (s): 1.670 (total time: 28.370) Refine new water occ: r_work=0.1154 r_free=0.1660 adp: r_work=0.1129 r_free=0.1660 occ: r_work=0.1126 r_free=0.1643 adp: r_work=0.1116 r_free=0.1650 occ: r_work=0.1114 r_free=0.1643 adp: r_work=0.1114 r_free=0.1643 ADP+occupancy (water only), MIN, final r_work=0.1114 r_free=0.1643 r_work=0.1114 r_free=0.1643 | n_water=235 | time (s): 4.680 (total time: 33.050) Filter (q & B) r_work=0.1114 r_free=0.1643 | n_water=235 | time (s): 0.790 (total time: 33.840) Filter (dist only) r_work=0.1115 r_free=0.1639 | n_water=233 | time (s): 19.090 (total time: 52.930) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 21.660815 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.763924 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 0.1009 0.1775 0.0766 0.009 1.0 4.2 0.5 0.6 0 10.830 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.09 17.75 7.66 4.678 16.826 2.764 0.014 9.39 17.75 8.37 5.528 17.209 2.764 0.012 Individual atomic B min max mean iso aniso Overall: 0.00 107.44 16.57 6.55 1760 0 Protein: 0.00 107.44 15.03 6.52 1519 0 Water: 0.00 62.76 26.27 N/A 233 0 Other: 10.09 39.78 24.96 N/A 8 0 Chain A: 0.00 107.44 15.82 N/A 1668 0 Chain S: 2.32 62.28 30.14 N/A 92 0 Histogram: Values Number of atoms 0.00 - 10.74 679 10.74 - 21.49 671 21.49 - 32.23 212 32.23 - 42.98 120 42.98 - 53.72 43 53.72 - 64.47 20 64.47 - 75.21 7 75.21 - 85.95 3 85.95 - 96.70 4 96.70 - 107.44 1 =========================== Idealize ADP of riding H ========================== r_work=0.0939 r_free=0.1775 r_work=0.0935 r_free=0.1768 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0935 r_free = 0.1768 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0933 r_free = 0.1750 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.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0933 r_free= 0.1750 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ls_wunit_k1) (work): 0.011830 | | target function (ls_wunit_k1) not normalized (work): 58.241094 | | target function (ls_wunit_k1) not normalized (free): 9.445421 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0974 0.0933 0.1750 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2097 0.2105 0.2109 n_refl.: 5175 remove outliers: r(all,work,free)=0.2097 0.2105 0.2109 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2097 0.2105 0.2109 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0973 0.0931 0.1762 n_refl.: 5175 remove outliers: r(all,work,free)=0.0969 0.0927 0.1762 n_refl.: 5173 ======================== 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 93.75 85 5 0.3105 332.419 311.786 0.658 1.006 0.360 11.894-9.307 99.02 97 4 0.1432 524.505 522.104 0.982 1.008 0.344 9.237-7.194 100.00 213 7 0.1446 428.941 429.650 1.020 1.008 0.305 7.162-5.571 100.00 427 22 0.1342 321.868 319.935 0.997 1.007 0.300 5.546-4.326 100.00 867 58 0.0775 441.879 439.329 1.007 1.005 0.240 4.315-3.360 100.00 1859 96 0.0726 420.232 419.678 1.055 1.001 0.207 3.356-3.002 100.00 1373 60 0.0976 323.680 322.796 1.028 0.997 0.090 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9557 b_overall=-4.1206 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0927 r_free=0.1762 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A Total number of N/Q/H flips: 1 r_work=0.0928 r_free=0.1764 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0928 r_free=0.1764 | n_water=233 | time (s): 0.560 (total time: 0.560) Filter (dist) r_work=0.0937 r_free=0.1756 | n_water=230 | time (s): 18.590 (total time: 19.150) Filter (q & B) r_work=0.0997 r_free=0.1767 | n_water=228 | time (s): 1.610 (total time: 20.760) Compute maps r_work=0.0997 r_free=0.1767 | n_water=228 | time (s): 0.510 (total time: 21.270) Filter (map) r_work=0.1262 r_free=0.1827 | n_water=153 | time (s): 1.370 (total time: 22.640) Find peaks r_work=0.1262 r_free=0.1827 | n_water=153 | time (s): 0.400 (total time: 23.040) Add new water r_work=0.1660 r_free=0.2164 | n_water=246 | time (s): 1.220 (total time: 24.260) Refine new water occ: r_work=0.1053 r_free=0.1758 adp: r_work=0.1047 r_free=0.1769 occ: r_work=0.1034 r_free=0.1760 adp: r_work=0.1035 r_free=0.1765 occ: r_work=0.1024 r_free=0.1756 adp: r_work=0.1024 r_free=0.1761 ADP+occupancy (water only), MIN, final r_work=0.1024 r_free=0.1761 r_work=0.1024 r_free=0.1761 | n_water=246 | time (s): 12.140 (total time: 36.400) Filter (q & B) r_work=0.1024 r_free=0.1766 | n_water=244 | time (s): 1.430 (total time: 37.830) Filter (dist only) r_work=0.1033 r_free=0.1780 | n_water=242 | time (s): 19.020 (total time: 56.850) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.075607 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.233309 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 0.0935 0.1811 0.0876 0.011 1.0 4.2 0.5 0.6 0 0.538 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.35 18.11 8.76 5.458 17.856 0.233 5.158 8.95 18.10 9.15 7.141 17.842 0.233 5.068 Individual atomic B min max mean iso aniso Overall: 0.00 105.94 16.43 8.75 1769 0 Protein: 0.00 105.94 15.14 8.73 1519 0 Water: 0.00 57.76 24.24 N/A 242 0 Other: 10.26 42.08 24.42 N/A 8 0 Chain A: 0.00 105.94 15.79 N/A 1651 0 Chain S: 0.00 54.26 25.37 N/A 118 0 Histogram: Values Number of atoms 0.00 - 10.59 669 10.59 - 21.19 659 21.19 - 31.78 241 31.78 - 42.38 124 42.38 - 52.97 40 52.97 - 63.56 17 63.56 - 74.16 9 74.16 - 84.75 4 84.75 - 95.35 5 95.35 - 105.94 1 =========================== Idealize ADP of riding H ========================== r_work=0.0895 r_free=0.1810 r_work=0.0901 r_free=0.1817 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0901 r_free = 0.1817 target_work(ml) = 5.073 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0889 r_free = 0.1809 target_work(ml) = 5.065 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5173 (all), 4.87 % free)-------------| | | | r_work= 0.0889 r_free= 0.1809 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 5.064637 | | target function (ml) not normalized (work): 24923.080840 | | target function (ml) not normalized (free): 1828.957569 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0935 0.0889 0.1809 n_refl.: 5173 re-set all scales: r(all,work,free)=0.2022 0.2025 0.2126 n_refl.: 5173 remove outliers: r(all,work,free)=0.2022 0.2025 0.2126 n_refl.: 5173 overall B=-0.00 to atoms: r(all,work,free)=0.2022 0.2025 0.2126 n_refl.: 5173 bulk-solvent and scaling: r(all,work,free)=0.0926 0.0880 0.1802 n_refl.: 5173 remove outliers: r(all,work,free)=0.0926 0.0880 0.1802 n_refl.: 5173 ======================== 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 93.75 85 5 0.3508 332.419 304.980 0.597 0.990 0.328 11.894-9.307 99.02 97 4 0.1749 524.505 512.674 0.947 0.995 0.327 9.237-7.194 100.00 213 7 0.1911 428.941 420.060 1.002 0.998 0.300 7.162-5.571 100.00 427 22 0.1786 321.868 312.920 0.983 0.999 0.269 5.546-4.326 100.00 867 58 0.0888 441.879 436.260 0.997 1.000 0.234 4.315-3.360 100.00 1859 96 0.0597 420.232 419.441 1.054 1.003 0.218 3.356-3.002 100.00 1373 60 0.0613 323.680 323.535 1.029 1.005 0.080 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-6.3082 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0880 r_free=0.1802 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A A 76 ASN B Total number of N/Q/H flips: 2 r_work=0.0881 r_free=0.1802 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0881 r_free=0.1802 | n_water=242 | time (s): 0.580 (total time: 0.580) Filter (dist) r_work=0.0898 r_free=0.1807 | n_water=240 | time (s): 20.720 (total time: 21.300) Filter (q & B) r_work=0.0985 r_free=0.1818 | n_water=235 | time (s): 1.440 (total time: 22.740) Compute maps r_work=0.0985 r_free=0.1818 | n_water=235 | time (s): 0.460 (total time: 23.200) Filter (map) r_work=0.1262 r_free=0.1880 | n_water=159 | time (s): 1.350 (total time: 24.550) Find peaks r_work=0.1262 r_free=0.1880 | n_water=159 | time (s): 0.400 (total time: 24.950) Add new water r_work=0.1578 r_free=0.2109 | n_water=233 | time (s): 1.280 (total time: 26.230) Refine new water occ: r_work=0.0994 r_free=0.1785 adp: r_work=0.0985 r_free=0.1795 occ: r_work=0.0978 r_free=0.1789 adp: r_work=0.0977 r_free=0.1794 occ: r_work=0.0971 r_free=0.1788 adp: r_work=0.0970 r_free=0.1793 ADP+occupancy (water only), MIN, final r_work=0.0970 r_free=0.1793 r_work=0.0970 r_free=0.1793 | n_water=233 | time (s): 11.830 (total time: 38.060) Filter (q & B) r_work=0.0970 r_free=0.1795 | n_water=232 | time (s): 1.310 (total time: 39.370) Filter (dist only) r_work=0.0976 r_free=0.1804 | n_water=231 | time (s): 17.230 (total time: 56.600) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.947057 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.246576 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 0.0891 0.1802 0.0911 0.010 1.0 5.8 0.5 1.2 0 0.474 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 8.91 18.02 9.11 6.836 17.876 0.247 5.038 8.65 18.06 9.40 8.180 17.976 0.247 4.969 Individual atomic B min max mean iso aniso Overall: 0.00 104.57 16.62 10.67 1758 0 Protein: 0.00 104.57 15.50 10.65 1519 0 Water: 0.00 55.62 23.69 N/A 231 0 Other: 8.97 41.33 24.45 N/A 8 0 Chain A: 0.00 104.57 16.04 N/A 1640 0 Chain S: 0.00 49.26 24.72 N/A 118 0 Histogram: Values Number of atoms 0.00 - 10.46 640 10.46 - 20.91 663 20.91 - 31.37 252 31.37 - 41.83 110 41.83 - 52.28 54 52.28 - 62.74 17 62.74 - 73.20 11 73.20 - 83.65 5 83.65 - 94.11 2 94.11 - 104.57 4 =========================== Idealize ADP of riding H ========================== r_work=0.0865 r_free=0.1806 r_work=0.0869 r_free=0.1808 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0869 r_free = 0.1808 target_work(ml) = 4.973 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0862 r_free = 0.1799 target_work(ml) = 4.968 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5173 (all), 4.87 % free)-------------| | | | r_work= 0.0862 r_free= 0.1799 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 4.968345 | | target function (ml) not normalized (work): 24449.227110 | | target function (ml) not normalized (free): 2105.607850 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0909 0.0862 0.1799 n_refl.: 5173 re-set all scales: r(all,work,free)=0.2051 0.2053 0.2159 n_refl.: 5173 remove outliers: r(all,work,free)=0.2051 0.2053 0.2159 n_refl.: 5173 overall B=-0.00 to atoms: r(all,work,free)=0.2051 0.2053 0.2159 n_refl.: 5173 bulk-solvent and scaling: r(all,work,free)=0.0908 0.0861 0.1804 n_refl.: 5173 remove outliers: r(all,work,free)=0.0908 0.0861 0.1804 n_refl.: 5173 ======================== 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 93.75 85 5 0.3634 332.419 300.243 0.590 0.987 0.320 11.894-9.307 99.02 97 4 0.1825 524.505 510.699 0.953 0.993 0.320 9.237-7.194 100.00 213 7 0.2120 428.941 418.171 1.001 0.996 0.280 7.162-5.571 100.00 427 22 0.1956 321.868 312.124 0.992 0.997 0.270 5.546-4.326 100.00 867 58 0.0932 441.879 436.167 1.009 0.999 0.226 4.315-3.360 100.00 1859 96 0.0555 420.232 420.025 1.070 1.002 0.223 3.356-3.002 100.00 1373 60 0.0456 323.680 323.889 1.050 1.005 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.1321 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0861 r_free=0.1804 After: r_work=0.0864 r_free=0.1802 ================================== NQH flips ================================== r_work=0.0864 r_free=0.1802 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN B Total number of N/Q/H flips: 1 r_work=0.0864 r_free=0.1801 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0864 r_free=0.1801 | n_water=231 | time (s): 0.620 (total time: 0.620) Filter (dist) r_work=0.0872 r_free=0.1802 | n_water=229 | time (s): 17.230 (total time: 17.850) Filter (q & B) r_work=0.0980 r_free=0.1804 | n_water=226 | time (s): 1.260 (total time: 19.110) Compute maps r_work=0.0980 r_free=0.1804 | n_water=226 | time (s): 0.470 (total time: 19.580) Filter (map) r_work=0.1209 r_free=0.1901 | n_water=171 | time (s): 1.440 (total time: 21.020) Find peaks r_work=0.1209 r_free=0.1901 | n_water=171 | time (s): 0.390 (total time: 21.410) Add new water r_work=0.1462 r_free=0.2119 | n_water=232 | time (s): 1.240 (total time: 22.650) Refine new water occ: r_work=0.0956 r_free=0.1834 adp: r_work=0.0945 r_free=0.1849 occ: r_work=0.0940 r_free=0.1837 adp: r_work=0.0939 r_free=0.1843 occ: r_work=0.0935 r_free=0.1833 adp: r_work=0.0934 r_free=0.1839 ADP+occupancy (water only), MIN, final r_work=0.0934 r_free=0.1839 r_work=0.0934 r_free=0.1839 | n_water=232 | time (s): 10.400 (total time: 33.050) Filter (q & B) r_work=0.0934 r_free=0.1838 | n_water=231 | time (s): 1.320 (total time: 34.370) Filter (dist only) r_work=0.0934 r_free=0.1839 | n_water=230 | time (s): 18.530 (total time: 52.900) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.934492 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.222859 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 0.0888 0.1831 0.0943 0.011 1.2 9.0 0.5 1.2 0 0.467 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 8.88 18.31 9.43 8.108 18.175 0.223 4.972 8.69 18.31 9.62 8.987 18.247 0.223 4.920 Individual atomic B min max mean iso aniso Overall: 0.00 103.19 16.79 11.94 1757 0 Protein: 0.00 103.19 15.83 11.92 1519 0 Water: 0.00 54.38 22.80 N/A 230 0 Other: 8.72 40.89 25.33 N/A 8 0 Chain A: 0.00 103.19 16.27 N/A 1634 0 Chain S: 0.00 47.46 23.64 N/A 123 0 Histogram: Values Number of atoms 0.00 - 10.32 640 10.32 - 20.64 624 20.64 - 30.96 275 30.96 - 41.28 123 41.28 - 51.60 53 51.60 - 61.91 19 61.91 - 72.23 7 72.23 - 82.55 8 82.55 - 92.87 4 92.87 - 103.19 4 =========================== Idealize ADP of riding H ========================== r_work=0.0869 r_free=0.1831 r_work=0.0870 r_free=0.1833 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0870 r_free = 0.1833 target_work(ml) = 4.923 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0867 r_free = 0.1827 target_work(ml) = 4.921 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5173 (all), 4.87 % free)-------------| | | | r_work= 0.0867 r_free= 0.1827 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 4.920649 | | target function (ml) not normalized (work): 24214.514539 | | target function (ml) not normalized (free): 2260.844652 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.79 1.00 2491 142 0.1249 0.1818 5.5247 6.1828| | 2: 3.78 - 3.00 1.00 2430 110 0.0401 0.1843 4.3014 12.572| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2491 142 0.92 11.92 1.00 0.98 12847.38| | 2: 3.78 - 3.00 2430 110 0.99 1.71 1.00 1.00 830.85| |alpha: min = 0.97 max = 1.00 mean = 0.99| |beta: min = 524.54 max = 21580.54 mean = 6913.59| |figures of merit: min = 0.01 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.14 mean = 6.88| |phase err.(test): min = 0.00 max = 81.21 mean = 6.89| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0916 0.0867 0.1827 n_refl.: 5173 re-set all scales: r(all,work,free)=0.2092 0.2095 0.2161 n_refl.: 5173 remove outliers: r(all,work,free)=0.2092 0.2095 0.2161 n_refl.: 5173 overall B=-0.00 to atoms: r(all,work,free)=0.2092 0.2095 0.2161 n_refl.: 5173 bulk-solvent and scaling: r(all,work,free)=0.0914 0.0866 0.1825 n_refl.: 5173 remove outliers: r(all,work,free)=0.0914 0.0866 0.1825 n_refl.: 5173 ======================== 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 93.75 85 5 0.3677 332.419 301.179 0.596 0.984 0.320 11.894-9.307 99.02 97 4 0.1883 524.505 510.789 0.961 0.991 0.320 9.237-7.194 100.00 213 7 0.2190 428.941 417.479 0.999 0.994 0.291 7.162-5.571 100.00 427 22 0.2028 321.868 311.392 0.993 0.996 0.272 5.546-4.326 100.00 867 58 0.0995 441.879 435.825 1.019 0.999 0.235 4.315-3.360 100.00 1859 96 0.0554 420.232 420.104 1.087 1.003 0.230 3.356-3.002 100.00 1373 60 0.0379 323.680 324.042 1.068 1.006 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.8895 ================= 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 : 0.3625 0.1967 0.083 5.297 8.8 119.3 19.9 258 0.000 1_bss: 0.1558 0.1554 0.083 5.297 6.0 116.4 17.0 258 0.000 1_settarget: 0.1558 0.1554 0.083 5.297 6.0 116.4 17.0 258 0.000 1_nqh: 0.1560 0.1553 0.083 5.297 6.0 116.4 17.0 258 0.003 1_weight: 0.1560 0.1553 0.083 5.297 6.0 116.4 17.0 258 0.003 1_xyzrec: 0.1153 0.1769 0.010 0.981 6.0 116.4 17.0 258 0.206 1_adp: 0.1010 0.1770 0.010 0.981 2.3 111.4 17.5 258 0.206 1_regHadp: 0.1003 0.1779 0.010 0.981 2.3 111.4 17.5 258 0.206 1_occ: 0.1003 0.1760 0.010 0.981 2.3 111.4 17.5 258 0.206 2_bss: 0.1007 0.1774 0.010 0.981 1.3 110.5 16.5 258 0.206 2_settarget: 0.1007 0.1774 0.010 0.981 1.3 110.5 16.5 258 0.206 2_updatecdl: 0.1007 0.1774 0.010 1.000 1.3 110.5 16.5 258 0.206 2_nqh: 0.1007 0.1774 0.010 1.000 1.3 110.5 16.5 258 0.204 2_sol: 0.1115 0.1639 0.010 1.000 1.0 110.4 15.8 233 n/a 2_weight: 0.1115 0.1639 0.010 1.000 1.0 110.4 15.8 233 n/a 2_xyzrec: 0.1009 0.1775 0.009 0.956 1.0 110.4 15.8 233 n/a 2_adp: 0.0939 0.1775 0.009 0.956 0.0 107.4 16.6 233 n/a 2_regHadp: 0.0935 0.1768 0.009 0.956 0.0 107.4 16.6 233 n/a 2_occ: 0.0933 0.1750 0.009 0.956 0.0 107.4 16.6 233 n/a 3_bss: 0.0927 0.1762 0.009 0.956 0.0 107.4 16.6 233 n/a 3_settarget: 0.0927 0.1762 0.009 0.956 0.0 107.4 16.6 233 n/a 3_updatecdl: 0.0927 0.1762 0.009 0.962 0.0 107.4 16.6 233 n/a 3_nqh: 0.0928 0.1764 0.009 0.962 0.0 107.4 16.6 233 n/a 3_sol: 0.1033 0.1780 0.009 0.962 0.0 107.4 16.5 242 n/a 3_weight: 0.1033 0.1780 0.009 0.962 0.0 107.4 16.5 242 n/a 3_xyzrec: 0.0935 0.1811 0.011 1.047 0.0 107.4 16.5 242 n/a 3_adp: 0.0895 0.1810 0.011 1.047 0.0 105.9 16.4 242 n/a 3_regHadp: 0.0901 0.1817 0.011 1.047 0.0 105.9 16.4 242 n/a 3_occ: 0.0889 0.1809 0.011 1.047 0.0 105.9 16.4 242 n/a 4_bss: 0.0880 0.1802 0.011 1.047 0.0 105.9 16.4 242 n/a 4_settarget: 0.0880 0.1802 0.011 1.047 0.0 105.9 16.4 242 n/a 4_updatecdl: 0.0880 0.1802 0.011 1.047 0.0 105.9 16.4 242 n/a 4_nqh: 0.0881 0.1802 0.011 1.047 0.0 105.9 16.4 242 n/a 4_sol: 0.0976 0.1804 0.011 1.047 0.0 105.9 16.4 231 n/a 4_weight: 0.0976 0.1804 0.011 1.047 0.0 105.9 16.4 231 n/a 4_xyzrec: 0.0891 0.1802 0.010 1.013 0.0 105.9 16.4 231 n/a 4_adp: 0.0865 0.1806 0.010 1.013 0.0 104.6 16.6 231 n/a 4_regHadp: 0.0869 0.1808 0.010 1.013 0.0 104.6 16.6 231 n/a 4_occ: 0.0862 0.1799 0.010 1.013 0.0 104.6 16.6 231 n/a 5_bss: 0.0861 0.1804 0.010 1.013 0.0 104.6 16.6 231 n/a 5_settarget: 0.0861 0.1804 0.010 1.013 0.0 104.6 16.6 231 n/a 5_updatecdl: 0.0861 0.1804 0.010 1.025 0.0 104.6 16.6 231 n/a 5_setrh: 0.0864 0.1802 0.010 1.025 0.0 104.6 16.6 231 n/a 5_nqh: 0.0864 0.1801 0.010 1.025 0.0 104.6 16.6 231 n/a 5_sol: 0.0934 0.1839 0.010 1.025 0.0 104.6 16.6 230 n/a 5_weight: 0.0934 0.1839 0.010 1.025 0.0 104.6 16.6 230 n/a 5_xyzrec: 0.0888 0.1831 0.011 1.159 0.0 104.6 16.6 230 n/a 5_adp: 0.0869 0.1831 0.011 1.159 0.0 103.2 16.8 230 n/a 5_regHadp: 0.0870 0.1833 0.011 1.159 0.0 103.2 16.8 230 n/a 5_occ: 0.0867 0.1827 0.011 1.159 0.0 103.2 16.8 230 n/a end: 0.0866 0.1825 0.011 1.159 0.0 103.2 16.8 230 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_6470396_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_6470396_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.1000 Refinement macro-cycles (run) : 490.7600 Write final files (write_after_run_outputs) : 9.8500 Total : 503.7100 Total CPU time: 8.75 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:19:07 PST -0800 (1735492747.30 s) Start R-work = 0.1558, R-free = 0.1554 Final R-work = 0.0866, R-free = 0.1825 =============================================================================== Job complete usr+sys time: 532.30 seconds wall clock time: 9 minutes 15.29 seconds (555.29 seconds total)