Starting phenix.refine on Sun Dec 29 09:10:02 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_4872201.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 { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 3 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_4872201.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_4872201.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.31, per 1000 atoms: 0.39 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: 0.28 Conformation dependent library (CDL) restraints added in 105.4 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.65 - 0.91: 524 0.91 - 1.17: 1127 1.17 - 1.44: 671 1.44 - 1.70: 811 1.70 - 1.96: 20 Bond restraints: 3153 Sorted by residual: bond pdb=" C ARG A 5 " pdb=" O ARG A 5 " ideal model delta sigma weight residual 1.235 1.482 -0.246 1.14e-02 7.69e+03 4.67e+02 bond pdb=" N ALYS A 132 " pdb=" CA ALYS A 132 " ideal model delta sigma weight residual 1.459 1.674 -0.215 1.19e-02 7.06e+03 3.26e+02 bond pdb=" C GLY A 108 " pdb=" N PRO A 109 " ideal model delta sigma weight residual 1.337 1.524 -0.188 1.11e-02 8.12e+03 2.86e+02 bond pdb=" CA TYR A 139 " pdb=" C TYR A 139 " ideal model delta sigma weight residual 1.522 1.315 0.207 1.23e-02 6.61e+03 2.84e+02 bond pdb=" C ASP A 68 " pdb=" N VAL A 69 " ideal model delta sigma weight residual 1.332 1.135 0.197 1.20e-02 6.94e+03 2.70e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.36: 3002 4.36 - 8.72: 1849 8.72 - 13.08: 738 13.08 - 17.43: 165 17.43 - 21.79: 23 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O GLY A 78 " pdb=" C GLY A 78 " pdb=" N ALA A 79 " ideal model delta sigma weight residual 122.18 135.54 -13.36 9.60e-01 1.09e+00 1.94e+02 angle pdb=" N VAL A 88 " pdb=" CA VAL A 88 " pdb=" C VAL A 88 " ideal model delta sigma weight residual 110.62 125.63 -15.01 1.14e+00 7.69e-01 1.73e+02 angle pdb=" CA ALA A 171 " pdb=" C ALA A 171 " pdb=" N LEU A 172 " ideal model delta sigma weight residual 117.30 102.54 14.76 1.16e+00 7.43e-01 1.62e+02 angle pdb=" N ALA A 179 " pdb=" CA ALA A 179 " pdb=" C ALA A 179 " ideal model delta sigma weight residual 111.28 124.70 -13.42 1.09e+00 8.42e-01 1.52e+02 angle pdb=" CD2 HIS A 115 " pdb=" NE2 HIS A 115 " pdb=" CE1 HIS A 115 " ideal model delta sigma weight residual 109.00 121.29 -12.29 1.00e+00 1.00e+00 1.51e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.97: 1303 16.97 - 33.93: 121 33.93 - 50.89: 40 50.89 - 67.86: 14 67.86 - 84.82: 3 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C ARG A 98 " pdb=" N ARG A 98 " pdb=" CA ARG A 98 " pdb=" CB ARG A 98 " ideal model delta harmonic sigma weight residual -122.60 -146.29 23.69 0 2.50e+00 1.60e-01 8.98e+01 dihedral pdb=" N ARG A 98 " pdb=" C ARG A 98 " pdb=" CA ARG A 98 " pdb=" CB ARG A 98 " ideal model delta harmonic sigma weight residual 122.80 142.90 -20.10 0 2.50e+00 1.60e-01 6.46e+01 dihedral pdb=" C PRO A 73 " pdb=" N PRO A 73 " pdb=" CA PRO A 73 " pdb=" CB PRO A 73 " ideal model delta harmonic sigma weight residual -120.70 -102.12 -18.58 0 2.50e+00 1.60e-01 5.52e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.210: 100 0.210 - 0.420: 65 0.420 - 0.629: 47 0.629 - 0.838: 24 0.838 - 1.047: 7 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA BLEU A 153 " pdb=" N BLEU A 153 " pdb=" C BLEU A 153 " pdb=" CB BLEU A 153 " both_signs ideal model delta sigma weight residual False 2.51 3.56 -1.05 2.00e-01 2.50e+01 2.74e+01 chirality pdb=" CA PHE A 119 " pdb=" N PHE A 119 " pdb=" C PHE A 119 " pdb=" CB PHE A 119 " both_signs ideal model delta sigma weight residual False 2.51 1.53 0.98 2.00e-01 2.50e+01 2.41e+01 chirality pdb=" CA LEU A 82 " pdb=" N LEU A 82 " pdb=" C LEU A 82 " pdb=" CB LEU A 82 " both_signs ideal model delta sigma weight residual False 2.51 3.48 -0.97 2.00e-01 2.50e+01 2.37e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 28 " 0.236 9.50e-02 1.11e+02 1.05e-01 1.14e+02 pdb=" NE ARG A 28 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG A 28 " -0.050 2.00e-02 2.50e+03 pdb=" NH1 ARG A 28 " 0.070 2.00e-02 2.50e+03 pdb=" NH2 ARG A 28 " -0.133 2.00e-02 2.50e+03 pdb="HH11 ARG A 28 " -0.026 2.00e-02 2.50e+03 pdb="HH12 ARG A 28 " 0.028 2.00e-02 2.50e+03 pdb="HH21 ARG A 28 " 0.127 2.00e-02 2.50e+03 pdb="HH22 ARG A 28 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 126 " -0.006 2.00e-02 2.50e+03 7.02e-02 1.11e+02 pdb=" CG HIS A 126 " 0.071 2.00e-02 2.50e+03 pdb=" ND1 HIS A 126 " -0.046 2.00e-02 2.50e+03 pdb=" CD2 HIS A 126 " 0.034 2.00e-02 2.50e+03 pdb=" CE1 HIS A 126 " 0.100 2.00e-02 2.50e+03 pdb=" NE2 HIS A 126 " 0.059 2.00e-02 2.50e+03 pdb=" HD2 HIS A 126 " -0.108 2.00e-02 2.50e+03 pdb=" HE1 HIS A 126 " -0.104 2.00e-02 2.50e+03 pdb=" HE2 HIS A 126 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 48 " -0.074 9.50e-02 1.11e+02 7.15e-02 1.02e+02 pdb=" NE ARG A 48 " 0.073 2.00e-02 2.50e+03 pdb=" CZ ARG A 48 " -0.092 2.00e-02 2.50e+03 pdb=" NH1 ARG A 48 " 0.127 2.00e-02 2.50e+03 pdb=" NH2 ARG A 48 " -0.036 2.00e-02 2.50e+03 pdb="HH11 ARG A 48 " -0.084 2.00e-02 2.50e+03 pdb="HH12 ARG A 48 " -0.009 2.00e-02 2.50e+03 pdb="HH21 ARG A 48 " -0.021 2.00e-02 2.50e+03 pdb="HH22 ARG A 48 " 0.046 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.28: 784 2.28 - 2.86: 7835 2.86 - 3.44: 10609 3.44 - 4.02: 15298 4.02 - 4.60: 22050 Nonbonded interactions: 56576 Sorted by model distance: nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.698 2.100 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.701 2.100 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.802 2.450 x-y,-y,-z-4/3 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.808 2.100 nonbonded pdb=" O GLU A 147 " pdb=" H BTHR A 154 " model vdw 1.825 2.450 ... (remaining 56571 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_4872201_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= 0.3618 r_free= 0.2062 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.465603 | | target function (ml) not normalized (work): 22015.422628 | | target function (ml) not normalized (free): 1149.037407 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3803 0.2244 4.8545 4.8973| | 2: 3.78 - 3.00 1.00 2430 110 0.3392 0.1753 4.0655 4.1238| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 48.83 0.83 0.13 6612.33| | 2: 3.78 - 3.00 2430 110 0.94 11.09 1.48 0.26 437.84| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 365.29 max = 12072.15 mean = 3568.92| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 89.98 mean = 30.23| |phase err.(test): min = 0.00 max = 89.98 mean = 33.76| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.081 0.246 1557 Z= 5.439 Angle : 5.305 18.369 2118 Z= 3.695 Chirality : 0.396 1.047 243 Planarity : 0.032 0.102 284 Dihedral : 13.954 84.819 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.62 % Allowed : 3.11 % Favored : 96.27 % Cbeta Deviations : 35.14 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.48), residues: 224 helix: -2.10 (0.39), residues: 109 sheet: -0.17 (1.02), residues: 28 loop : -0.93 (0.58), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.109 0.023 ARG A 48 TYR 0.093 0.034 TYR A 141 PHE 0.108 0.039 PHE A 119 HIS 0.058 0.027 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= 0.3618 r_free= 0.2062 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.465603 | | target function (ml) not normalized (work): 22015.422628 | | target function (ml) not normalized (free): 1149.037407 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3576 0.3649 0.2151 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3576 0.3649 0.2151 n_refl.: 5182 remove outliers: r(all,work,free)=0.2520 0.2541 0.2151 n_refl.: 5178 overall B=-2.38 to atoms: r(all,work,free)=0.2427 0.2446 0.2114 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1562 0.1560 0.1604 n_refl.: 5178 remove outliers: r(all,work,free)=0.1558 0.1556 0.1604 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 0.3863 449.546 408.231 0.625 1.084 0.398 11.894-9.307 99.02 97 4 0.1883 714.139 694.268 0.892 1.080 0.382 9.237-7.194 100.00 213 7 0.2191 584.024 574.683 0.927 1.070 0.363 7.162-5.571 100.00 427 22 0.2323 438.239 425.971 0.889 1.055 0.292 5.546-4.326 100.00 867 58 0.1381 601.640 595.320 0.941 1.029 0.246 4.315-3.360 100.00 1859 96 0.1322 572.166 565.957 1.025 0.987 0.198 3.356-3.002 100.00 1373 60 0.1557 440.706 433.508 1.049 0.945 0.074 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9173 b_overall=-4.1349 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1556 r_free=0.1604 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=0.1556 r_free=0.1607 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 18.413723 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.727077 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 0.1160 0.1783 0.0623 0.009 1.0 2.9 0.5 0.0 0 9.207 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.60 17.83 6.23 3.013 16.474 1.727 0.018 10.25 17.77 7.51 4.734 16.635 1.727 0.015 Individual atomic B min max mean iso aniso Overall: 2.53 112.34 17.81 5.14 1785 0 Protein: 2.53 112.34 15.10 5.14 1519 0 Water: 4.48 111.91 33.58 N/A 258 0 Other: 17.24 35.42 23.62 N/A 8 0 Chain A: 2.53 112.34 17.81 N/A 1785 0 Histogram: Values Number of atoms 2.53 - 13.52 916 13.52 - 24.50 487 24.50 - 35.48 187 35.48 - 46.46 110 46.46 - 57.44 54 57.44 - 68.42 15 68.42 - 79.40 7 79.40 - 90.38 5 90.38 - 101.36 1 101.36 - 112.34 3 =========================== Idealize ADP of riding H ========================== r_work=0.1025 r_free=0.1777 r_work=0.1018 r_free=0.1782 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1018 r_free = 0.1782 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 = 0.1016 r_free = 0.1788 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.22 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= 0.1016 r_free= 0.1788 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ls_wunit_k1) (work): 0.014108 | | target function (ls_wunit_k1) not normalized (work): 69.465648 | | target function (ls_wunit_k1) not normalized (free): 10.399309 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1056 0.1016 0.1788 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2107 0.2104 0.2268 n_refl.: 5176 remove outliers: r(all,work,free)=0.2107 0.2104 0.2268 n_refl.: 5176 overall B=-0.90 to atoms: r(all,work,free)=0.2068 0.2063 0.2256 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.1058 0.1019 0.1790 n_refl.: 5176 remove outliers: r(all,work,free)=0.1056 0.1017 0.1790 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 0.3296 314.577 299.295 0.616 1.036 0.364 11.894-9.307 99.02 97 4 0.1561 503.975 495.785 0.925 1.036 0.361 9.237-7.194 100.00 213 7 0.1684 412.152 411.564 0.965 1.032 0.331 7.162-5.571 100.00 427 22 0.1672 309.270 305.003 0.931 1.025 0.292 5.546-4.326 100.00 867 58 0.0909 424.584 421.625 0.955 1.013 0.212 4.315-3.360 100.00 1859 96 0.0764 403.784 403.614 1.017 0.994 0.193 3.356-3.002 100.00 1373 60 0.1008 311.011 309.745 1.009 0.975 0.061 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9170 b_overall=-4.0394 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1017 r_free=0.1790 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1017 r_free=0.1790 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1017 r_free=0.1790 | n_water=258 | time (s): 0.730 (total time: 0.730) Filter (dist) r_work=0.1050 r_free=0.1777 | n_water=247 | time (s): 20.600 (total time: 21.330) Filter (q & B) r_work=0.1050 r_free=0.1780 | n_water=244 | time (s): 1.470 (total time: 22.800) Compute maps r_work=0.1050 r_free=0.1780 | n_water=244 | time (s): 0.450 (total time: 23.250) Filter (map) r_work=0.1351 r_free=0.1865 | n_water=139 | time (s): 1.370 (total time: 24.620) Find peaks r_work=0.1351 r_free=0.1865 | n_water=139 | time (s): 0.390 (total time: 25.010) Add new water r_work=0.1726 r_free=0.2217 | n_water=233 | time (s): 1.520 (total time: 26.530) Refine new water occ: r_work=0.1175 r_free=0.1673 adp: r_work=0.1146 r_free=0.1693 occ: r_work=0.1142 r_free=0.1656 adp: r_work=0.1129 r_free=0.1679 occ: r_work=0.1127 r_free=0.1653 adp: r_work=0.1123 r_free=0.1656 ADP+occupancy (water only), MIN, final r_work=0.1123 r_free=0.1656 r_work=0.1123 r_free=0.1656 | n_water=233 | time (s): 4.730 (total time: 31.260) Filter (q & B) r_work=0.1124 r_free=0.1664 | n_water=232 | time (s): 1.470 (total time: 32.730) Filter (dist only) r_work=0.1129 r_free=0.1663 | n_water=229 | time (s): 18.840 (total time: 51.570) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.168679 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.515131 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 0.1023 0.1767 0.0744 0.009 1.0 5.1 0.5 0.6 0 11.084 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.23 17.67 7.44 4.600 17.293 2.515 0.014 9.52 18.08 8.56 5.512 17.694 2.515 0.012 Individual atomic B min max mean iso aniso Overall: 0.00 107.16 17.12 6.49 1756 0 Protein: 0.00 107.16 15.46 6.48 1519 0 Water: 0.00 64.37 27.86 N/A 229 0 Other: 11.34 40.93 24.86 N/A 8 0 Chain A: 0.00 107.16 16.15 N/A 1663 0 Chain S: 0.00 60.75 34.50 N/A 93 0 Histogram: Values Number of atoms 0.00 - 10.72 647 10.72 - 21.43 683 21.43 - 32.15 221 32.15 - 42.86 117 42.86 - 53.58 43 53.58 - 64.30 30 64.30 - 75.01 7 75.01 - 85.73 3 85.73 - 96.44 3 96.44 - 107.16 2 =========================== Idealize ADP of riding H ========================== r_work=0.0952 r_free=0.1808 r_work=0.0949 r_free=0.1812 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0949 r_free = 0.1812 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 = 0.0946 r_free = 0.1801 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0946 r_free= 0.1801 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ls_wunit_k1) (work): 0.012170 | | target function (ls_wunit_k1) not normalized (work): 59.913334 | | target function (ls_wunit_k1) not normalized (free): 9.639657 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0989 0.0946 0.1801 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2142 0.2144 0.2228 n_refl.: 5175 remove outliers: r(all,work,free)=0.2142 0.2144 0.2228 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2142 0.2144 0.2228 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0990 0.0947 0.1817 n_refl.: 5175 remove outliers: r(all,work,free)=0.0990 0.0947 0.1817 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 0.3311 314.577 298.831 0.659 1.009 0.358 11.894-9.307 99.02 97 4 0.1517 503.975 500.064 0.976 1.010 0.330 9.237-7.194 100.00 213 7 0.1523 412.152 412.701 1.024 1.009 0.310 7.162-5.571 100.00 427 22 0.1407 309.270 307.498 1.001 1.007 0.290 5.546-4.326 100.00 867 58 0.0779 424.584 422.391 1.013 1.004 0.240 4.315-3.360 100.00 1859 96 0.0735 403.784 403.358 1.064 0.999 0.190 3.356-3.002 100.00 1373 60 0.0981 311.011 309.822 1.045 0.993 0.080 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-4.6310 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0947 r_free=0.1817 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN A Total number of N/Q/H flips: 2 r_work=0.0951 r_free=0.1821 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0951 r_free=0.1821 | n_water=229 | time (s): 0.590 (total time: 0.590) Filter (dist) r_work=0.0977 r_free=0.1834 | n_water=223 | time (s): 17.430 (total time: 18.020) Filter (q & B) r_work=0.1041 r_free=0.1837 | n_water=220 | time (s): 1.960 (total time: 19.980) Compute maps r_work=0.1041 r_free=0.1837 | n_water=220 | time (s): 0.560 (total time: 20.540) Filter (map) r_work=0.1305 r_free=0.1903 | n_water=142 | time (s): 1.500 (total time: 22.040) Find peaks r_work=0.1305 r_free=0.1903 | n_water=142 | time (s): 0.420 (total time: 22.460) Add new water r_work=0.1710 r_free=0.2332 | n_water=233 | time (s): 1.200 (total time: 23.660) Refine new water occ: r_work=0.1098 r_free=0.1792 adp: r_work=0.1094 r_free=0.1809 occ: r_work=0.1082 r_free=0.1778 adp: r_work=0.1082 r_free=0.1792 occ: r_work=0.1071 r_free=0.1760 adp: r_work=0.1070 r_free=0.1774 ADP+occupancy (water only), MIN, final r_work=0.1070 r_free=0.1774 r_work=0.1070 r_free=0.1774 | n_water=233 | time (s): 13.370 (total time: 37.030) Filter (q & B) r_work=0.1070 r_free=0.1774 | n_water=233 | time (s): 0.880 (total time: 37.910) Filter (dist only) r_work=0.1070 r_free=0.1770 | n_water=232 | time (s): 18.240 (total time: 56.150) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.153335 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.254148 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 0.0955 0.1880 0.0925 0.011 1.1 4.2 0.5 0.0 0 0.577 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.55 18.80 9.25 5.444 18.312 0.254 5.129 9.11 18.86 9.76 7.232 18.255 0.254 5.032 Individual atomic B min max mean iso aniso Overall: 0.00 106.32 16.78 8.82 1759 0 Protein: 0.00 106.32 15.47 8.81 1519 0 Water: 0.00 60.05 25.09 N/A 232 0 Other: 10.15 45.40 25.12 N/A 8 0 Chain A: 0.00 106.32 16.10 N/A 1648 0 Chain S: 0.00 60.05 26.89 N/A 111 0 Histogram: Values Number of atoms 0.00 - 10.63 633 10.63 - 21.26 688 21.26 - 31.89 230 31.89 - 42.53 124 42.53 - 53.16 48 53.16 - 63.79 18 63.79 - 74.42 10 74.42 - 85.05 3 85.05 - 95.68 4 95.68 - 106.32 1 =========================== Idealize ADP of riding H ========================== r_work=0.0911 r_free=0.1886 r_work=0.0917 r_free=0.1887 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0917 r_free = 0.1887 target_work(ml) = 5.036 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0906 r_free = 0.1876 target_work(ml) = 5.028 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0906 r_free= 0.1876 coordinate error (max.-lik. estimate): 0.26 A | | | | normalized target function (ml) (work): 5.027922 | | target function (ml) not normalized (work): 24752.460597 | | target function (ml) not normalized (free): 1825.171444 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0955 0.0906 0.1876 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2148 0.2156 0.2168 n_refl.: 5175 remove outliers: r(all,work,free)=0.2148 0.2156 0.2168 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2148 0.2156 0.2168 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0944 0.0896 0.1869 n_refl.: 5175 remove outliers: r(all,work,free)=0.0944 0.0896 0.1869 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 0.3848 314.577 285.374 0.598 0.994 0.344 11.894-9.307 99.02 97 4 0.1866 503.975 487.986 0.949 0.997 0.324 9.237-7.194 100.00 213 7 0.1912 412.152 405.803 1.009 0.999 0.294 7.162-5.571 100.00 427 22 0.1870 309.270 300.096 0.985 1.000 0.280 5.546-4.326 100.00 867 58 0.0927 424.584 419.574 1.006 1.001 0.240 4.315-3.360 100.00 1859 96 0.0580 403.784 403.105 1.066 1.003 0.202 3.356-3.002 100.00 1373 60 0.0615 311.011 310.643 1.050 1.005 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.0587 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0896 r_free=0.1869 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=0.0896 r_free=0.1866 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0896 r_free=0.1866 | n_water=232 | time (s): 0.610 (total time: 0.610) Filter (dist) r_work=0.0902 r_free=0.1868 | n_water=231 | time (s): 17.860 (total time: 18.470) Filter (q & B) r_work=0.0943 r_free=0.1884 | n_water=230 | time (s): 1.560 (total time: 20.030) Compute maps r_work=0.0943 r_free=0.1884 | n_water=230 | time (s): 0.630 (total time: 20.660) Filter (map) r_work=0.1224 r_free=0.1960 | n_water=155 | time (s): 1.940 (total time: 22.600) Find peaks r_work=0.1224 r_free=0.1960 | n_water=155 | time (s): 0.540 (total time: 23.140) Add new water r_work=0.1524 r_free=0.2217 | n_water=232 | time (s): 1.800 (total time: 24.940) Refine new water r_work=0.1524 r_free=0.2217 | n_water=232 | time (s): 0.110 (total time: 25.050) Filter (q & B) r_work=0.1224 r_free=0.1960 | n_water=155 | time (s): 1.830 (total time: 26.880) Filter (dist only) r_work=0.1260 r_free=0.1926 | n_water=146 | time (s): 12.470 (total time: 39.350) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.418069 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.262610 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 0.1118 0.1991 0.0873 0.012 1.1 3.5 0.5 0.0 0 0.709 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.18 19.91 8.73 6.897 18.031 0.263 5.308 10.57 20.33 9.75 8.336 18.076 0.263 5.225 Individual atomic B min max mean iso aniso Overall: 0.00 103.64 16.35 10.36 1673 0 Protein: 0.00 103.64 15.64 10.35 1519 0 Water: 0.00 55.90 23.21 N/A 146 0 Other: 16.92 50.47 24.74 N/A 8 0 Chain A: 0.00 103.64 16.12 N/A 1630 0 Chain S: 0.00 55.90 25.01 N/A 43 0 Histogram: Values Number of atoms 0.00 - 10.36 621 10.36 - 20.73 616 20.73 - 31.09 255 31.09 - 41.46 101 41.46 - 51.82 47 51.82 - 62.18 12 62.18 - 72.55 7 72.55 - 82.91 8 82.91 - 93.28 3 93.28 - 103.64 3 =========================== Idealize ADP of riding H ========================== r_work=0.1057 r_free=0.2033 r_work=0.1063 r_free=0.2045 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1063 r_free = 0.2045 target_work(ml) = 5.229 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1058 r_free = 0.2041 target_work(ml) = 5.227 | | occupancies: max = 1.00 min = 0.22 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= 0.1058 r_free= 0.2041 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ml) (work): 5.226643 | | target function (ml) not normalized (work): 25730.763424 | | target function (ml) not normalized (free): 1753.544619 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1108 0.1058 0.2041 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2449 0.2450 0.2593 n_refl.: 5175 remove outliers: r(all,work,free)=0.2449 0.2450 0.2593 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2449 0.2450 0.2593 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.1094 0.1044 0.2047 n_refl.: 5175 remove outliers: r(all,work,free)=0.1094 0.1044 0.2047 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 0.3881 314.577 286.068 0.668 1.002 0.370 11.894-9.307 99.02 97 4 0.1724 503.975 493.640 0.987 1.004 0.360 9.237-7.194 100.00 213 7 0.2029 412.152 404.602 1.007 1.005 0.330 7.162-5.571 100.00 427 22 0.1901 309.270 303.471 0.974 1.004 0.310 5.546-4.326 100.00 867 58 0.1092 424.584 418.996 0.992 1.003 0.290 4.315-3.360 100.00 1859 96 0.0742 403.784 402.227 1.068 1.001 0.220 3.356-3.002 100.00 1373 60 0.0805 311.011 309.454 1.068 0.999 0.065 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.2475 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1044 r_free=0.2047 After: r_work=0.1047 r_free=0.2046 ================================== NQH flips ================================== r_work=0.1047 r_free=0.2046 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1047 r_free=0.2046 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1047 r_free=0.2046 | n_water=146 | time (s): 0.580 (total time: 0.580) Filter (dist) r_work=0.1072 r_free=0.2046 | n_water=140 | time (s): 12.080 (total time: 12.660) Filter (q & B) r_work=0.1114 r_free=0.1991 | n_water=138 | time (s): 1.350 (total time: 14.010) Compute maps r_work=0.1114 r_free=0.1991 | n_water=138 | time (s): 0.460 (total time: 14.470) Filter (map) r_work=0.1146 r_free=0.1954 | n_water=130 | time (s): 1.690 (total time: 16.160) Find peaks r_work=0.1146 r_free=0.1954 | n_water=130 | time (s): 0.410 (total time: 16.570) Add new water r_work=0.1427 r_free=0.2225 | n_water=193 | time (s): 1.600 (total time: 18.170) Refine new water occ: r_work=0.1134 r_free=0.2063 adp: r_work=0.1133 r_free=0.2088 occ: r_work=0.1115 r_free=0.2065 adp: r_work=0.1117 r_free=0.2077 occ: r_work=0.1100 r_free=0.2051 adp: r_work=0.1102 r_free=0.2063 ADP+occupancy (water only), MIN, final r_work=0.1102 r_free=0.2063 r_work=0.1102 r_free=0.2063 | n_water=193 | time (s): 13.280 (total time: 31.450) Filter (q & B) r_work=0.1102 r_free=0.2060 | n_water=189 | time (s): 1.350 (total time: 32.800) Filter (dist only) r_work=0.1098 r_free=0.2056 | n_water=187 | time (s): 15.010 (total time: 47.810) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.117244 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.252861 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 0.1066 0.2108 0.1042 0.011 1.2 8.3 0.5 0.0 0 0.559 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.66 21.08 10.42 7.899 18.336 0.253 5.191 10.42 20.80 10.39 8.776 18.363 0.253 5.138 Individual atomic B min max mean iso aniso Overall: 0.00 100.69 16.96 11.33 1714 0 Protein: 0.00 100.69 15.87 11.32 1519 0 Water: 0.34 68.11 25.56 N/A 187 0 Other: 11.92 45.67 23.76 N/A 8 0 Chain A: 0.00 100.69 16.23 N/A 1620 0 Chain S: 0.34 68.11 29.61 N/A 94 0 Histogram: Values Number of atoms 0.00 - 10.07 568 10.07 - 20.14 635 20.14 - 30.21 290 30.21 - 40.27 117 40.27 - 50.34 60 50.34 - 60.41 21 60.41 - 70.48 10 70.48 - 80.55 4 80.55 - 90.62 5 90.62 - 100.69 4 =========================== Idealize ADP of riding H ========================== r_work=0.1042 r_free=0.2080 r_work=0.1046 r_free=0.2084 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1046 r_free = 0.2084 target_work(ml) = 5.144 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1007 r_free = 0.2012 target_work(ml) = 5.121 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.1007 r_free= 0.2012 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ml) (work): 5.121231 | | target function (ml) not normalized (work): 25211.820477 | | target function (ml) not normalized (free): 1849.925126 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1331 0.1975 5.5671 6.1521| | 2: 3.78 - 3.00 1.00 2430 110 0.0613 0.2075 4.6638 8.8757| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 12.77 0.99 0.95 12847.62| | 2: 3.78 - 3.00 2430 110 0.98 3.37 1.01 0.98 1589.04| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 1118.09 max = 20516.80 mean = 7290.37| |figures of merit: min = 0.01 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.02 mean = 8.13| |phase err.(test): min = 0.00 max = 84.70 mean = 8.18| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1059 0.1007 0.2012 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2411 0.2413 0.2489 n_refl.: 5175 remove outliers: r(all,work,free)=0.2411 0.2413 0.2489 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2411 0.2413 0.2489 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.1053 0.1003 0.1989 n_refl.: 5175 remove outliers: r(all,work,free)=0.1053 0.1003 0.1989 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 0.4037 314.577 283.263 0.647 0.994 0.346 11.894-9.307 99.02 97 4 0.1871 503.975 488.416 1.029 0.997 0.343 9.237-7.194 100.00 213 7 0.2164 412.152 403.641 1.062 0.999 0.317 7.162-5.571 100.00 427 22 0.2056 309.270 302.251 1.030 1.000 0.314 5.546-4.326 100.00 867 58 0.1104 424.584 418.789 1.067 1.001 0.280 4.315-3.360 100.00 1859 96 0.0691 403.784 402.960 1.153 1.003 0.230 3.356-3.002 100.00 1373 60 0.0608 311.011 309.949 1.154 1.004 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-9.1208 ================= 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 : 0.3618 0.2062 0.081 5.305 8.8 119.3 19.9 258 0.000 1_bss: 0.1556 0.1604 0.081 5.305 6.5 116.9 17.5 258 0.000 1_settarget: 0.1556 0.1604 0.081 5.305 6.5 116.9 17.5 258 0.000 1_nqh: 0.1556 0.1607 0.081 5.305 6.5 116.9 17.5 258 0.003 1_weight: 0.1556 0.1607 0.081 5.305 6.5 116.9 17.5 258 0.003 1_xyzrec: 0.1160 0.1783 0.009 0.953 6.5 116.9 17.5 258 0.217 1_adp: 0.1025 0.1777 0.009 0.953 2.5 112.3 17.8 258 0.217 1_regHadp: 0.1018 0.1782 0.009 0.953 2.5 112.3 17.8 258 0.217 1_occ: 0.1016 0.1788 0.009 0.953 2.5 112.3 17.8 258 0.217 2_bss: 0.1017 0.1790 0.009 0.953 1.6 111.4 16.9 258 0.217 2_settarget: 0.1017 0.1790 0.009 0.953 1.6 111.4 16.9 258 0.217 2_updatecdl: 0.1017 0.1790 0.009 0.976 1.6 111.4 16.9 258 0.217 2_nqh: 0.1017 0.1790 0.009 0.976 1.6 111.4 16.9 258 0.217 2_sol: 0.1129 0.1663 0.009 0.976 1.0 111.4 16.4 229 n/a 2_weight: 0.1129 0.1663 0.009 0.976 1.0 111.4 16.4 229 n/a 2_xyzrec: 0.1023 0.1767 0.009 0.958 1.0 111.4 16.4 229 n/a 2_adp: 0.0952 0.1808 0.009 0.958 0.0 107.2 17.1 229 n/a 2_regHadp: 0.0949 0.1812 0.009 0.958 0.0 107.2 17.1 229 n/a 2_occ: 0.0946 0.1801 0.009 0.958 0.0 107.2 17.1 229 n/a 3_bss: 0.0947 0.1817 0.009 0.958 0.0 107.2 17.1 229 n/a 3_settarget: 0.0947 0.1817 0.009 0.958 0.0 107.2 17.1 229 n/a 3_updatecdl: 0.0947 0.1817 0.009 0.967 0.0 107.2 17.1 229 n/a 3_nqh: 0.0951 0.1821 0.009 0.967 0.0 107.2 17.1 229 n/a 3_sol: 0.1070 0.1770 0.009 0.967 0.0 107.2 16.9 232 n/a 3_weight: 0.1070 0.1770 0.009 0.967 0.0 107.2 16.9 232 n/a 3_xyzrec: 0.0955 0.1880 0.011 1.055 0.0 107.2 16.9 232 n/a 3_adp: 0.0911 0.1886 0.011 1.055 0.0 106.3 16.8 232 n/a 3_regHadp: 0.0917 0.1887 0.011 1.055 0.0 106.3 16.8 232 n/a 3_occ: 0.0906 0.1876 0.011 1.055 0.0 106.3 16.8 232 n/a 4_bss: 0.0896 0.1869 0.011 1.055 0.0 106.3 16.8 232 n/a 4_settarget: 0.0896 0.1869 0.011 1.055 0.0 106.3 16.8 232 n/a 4_updatecdl: 0.0896 0.1869 0.011 1.063 0.0 106.3 16.8 232 n/a 4_nqh: 0.0896 0.1866 0.011 1.063 0.0 106.3 16.8 232 n/a 4_sol: 0.1260 0.1926 0.011 1.063 0.0 106.3 16.3 146 n/a 4_weight: 0.1260 0.1926 0.011 1.063 0.0 106.3 16.3 146 n/a 4_xyzrec: 0.1118 0.1991 0.012 1.100 0.0 106.3 16.3 146 n/a 4_adp: 0.1057 0.2033 0.012 1.100 0.0 103.6 16.3 146 n/a 4_regHadp: 0.1063 0.2045 0.012 1.100 0.0 103.6 16.3 146 n/a 4_occ: 0.1058 0.2041 0.012 1.100 0.0 103.6 16.3 146 n/a 5_bss: 0.1044 0.2047 0.012 1.100 0.0 103.6 16.3 146 n/a 5_settarget: 0.1044 0.2047 0.012 1.100 0.0 103.6 16.3 146 n/a 5_updatecdl: 0.1044 0.2047 0.012 1.111 0.0 103.6 16.3 146 n/a 5_setrh: 0.1047 0.2046 0.012 1.111 0.0 103.6 16.3 146 n/a 5_nqh: 0.1047 0.2046 0.012 1.111 0.0 103.6 16.3 146 n/a 5_sol: 0.1098 0.2056 0.012 1.111 0.0 103.6 16.9 187 n/a 5_weight: 0.1098 0.2056 0.012 1.111 0.0 103.6 16.9 187 n/a 5_xyzrec: 0.1066 0.2108 0.011 1.159 0.0 103.6 16.9 187 n/a 5_adp: 0.1042 0.2080 0.011 1.159 0.0 100.7 17.0 187 n/a 5_regHadp: 0.1046 0.2084 0.011 1.159 0.0 100.7 17.0 187 n/a 5_occ: 0.1007 0.2012 0.011 1.159 0.0 100.7 17.0 187 n/a end: 0.1003 0.1989 0.011 1.159 0.0 100.7 17.0 187 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_4872201_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_4872201_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.2800 Refinement macro-cycles (run) : 465.1700 Write final files (write_after_run_outputs) : 10.9000 Total : 479.3500 Total CPU time: 8.32 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:18:40 PST -0800 (1735492720.86 s) Start R-work = 0.1556, R-free = 0.1604 Final R-work = 0.1003, R-free = 0.1989 =============================================================================== Job complete usr+sys time: 508.04 seconds wall clock time: 8 minutes 50.74 seconds (530.74 seconds total)