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_7783516.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_7783516.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7783516.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: 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: 0.52 Conformation dependent library (CDL) restraints added in 205.3 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.64 - 0.90: 457 0.90 - 1.16: 1171 1.16 - 1.42: 639 1.42 - 1.68: 854 1.68 - 1.94: 32 Bond restraints: 3153 Sorted by residual: bond pdb=" CA ILE A 21 " pdb=" CB ILE A 21 " ideal model delta sigma weight residual 1.539 1.409 0.130 5.40e-03 3.43e+04 5.79e+02 bond pdb=" C AGLU A 90 " pdb=" O AGLU A 90 " ideal model delta sigma weight residual 1.236 1.032 0.205 1.15e-02 7.56e+03 3.17e+02 bond pdb=" CA ALA A 183 " pdb=" C ALA A 183 " ideal model delta sigma weight residual 1.520 1.729 -0.209 1.23e-02 6.61e+03 2.88e+02 bond pdb=" C ALEU A 153 " pdb=" N THR A 154 " ideal model delta sigma weight residual 1.331 1.545 -0.214 1.30e-02 5.92e+03 2.71e+02 bond pdb=" C LEU A 72 " pdb=" O LEU A 72 " ideal model delta sigma weight residual 1.244 1.083 0.161 1.00e-02 1.00e+04 2.59e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.36: 3022 4.36 - 8.71: 1846 8.71 - 13.07: 726 13.07 - 17.42: 159 17.42 - 21.78: 24 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA HIS A 126 " pdb=" C HIS A 126 " pdb=" O HIS A 126 " ideal model delta sigma weight residual 120.70 138.95 -18.25 1.09e+00 8.42e-01 2.80e+02 angle pdb=" O GLY A 30 " pdb=" C GLY A 30 " pdb=" N ILE A 31 " ideal model delta sigma weight residual 122.30 140.94 -18.64 1.19e+00 7.06e-01 2.45e+02 angle pdb=" CA ALYS A 41 " pdb=" C ALYS A 41 " pdb=" O ALYS A 41 " ideal model delta sigma weight residual 119.49 138.25 -18.76 1.21e+00 6.83e-01 2.40e+02 angle pdb=" O ALYS A 41 " pdb=" C ALYS A 41 " pdb=" N ASP A 42 " ideal model delta sigma weight residual 122.39 102.59 19.80 1.30e+00 5.92e-01 2.32e+02 angle pdb=" O MET A 133 " pdb=" C MET A 133 " pdb=" N MET A 134 " ideal model delta sigma weight residual 122.15 105.06 17.09 1.14e+00 7.69e-01 2.25e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 1325 18.00 - 35.99: 107 35.99 - 53.98: 38 53.98 - 71.97: 8 71.97 - 89.96: 3 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" N PRO A 43 " pdb=" C PRO A 43 " pdb=" CA PRO A 43 " pdb=" CB PRO A 43 " ideal model delta harmonic sigma weight residual 115.10 136.12 -21.02 0 2.50e+00 1.60e-01 7.07e+01 dihedral pdb=" N GLU A 59 " pdb=" C GLU A 59 " pdb=" CA GLU A 59 " pdb=" CB GLU A 59 " ideal model delta harmonic sigma weight residual 122.80 141.87 -19.07 0 2.50e+00 1.60e-01 5.82e+01 dihedral pdb=" C LEU A 151 " pdb=" N LEU A 151 " pdb=" CA LEU A 151 " pdb=" CB LEU A 151 " ideal model delta harmonic sigma weight residual -122.60 -140.83 18.23 0 2.50e+00 1.60e-01 5.32e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.208: 101 0.208 - 0.416: 70 0.416 - 0.623: 48 0.623 - 0.831: 14 0.831 - 1.039: 10 Chirality restraints: 243 Sorted by residual: chirality pdb=" CB VAL A 69 " pdb=" CA VAL A 69 " pdb=" CG1 VAL A 69 " pdb=" CG2 VAL A 69 " both_signs ideal model delta sigma weight residual False -2.63 -1.59 -1.04 2.00e-01 2.50e+01 2.70e+01 chirality pdb=" CB ILE A 105 " pdb=" CA ILE A 105 " pdb=" CG1 ILE A 105 " pdb=" CG2 ILE A 105 " both_signs ideal model delta sigma weight residual False 2.64 1.64 1.00 2.00e-01 2.50e+01 2.52e+01 chirality pdb=" CA ASP A 68 " pdb=" N ASP A 68 " pdb=" C ASP A 68 " pdb=" CB ASP A 68 " both_signs ideal model delta sigma weight residual False 2.51 1.51 1.00 2.00e-01 2.50e+01 2.48e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 145 " -0.093 9.50e-02 1.11e+02 7.14e-02 9.42e+01 pdb=" NE ARG A 145 " -0.006 2.00e-02 2.50e+03 pdb=" CZ ARG A 145 " -0.023 2.00e-02 2.50e+03 pdb=" NH1 ARG A 145 " -0.047 2.00e-02 2.50e+03 pdb=" NH2 ARG A 145 " 0.159 2.00e-02 2.50e+03 pdb="HH11 ARG A 145 " 0.051 2.00e-02 2.50e+03 pdb="HH12 ARG A 145 " -0.024 2.00e-02 2.50e+03 pdb="HH21 ARG A 145 " -0.068 2.00e-02 2.50e+03 pdb="HH22 ARG A 145 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " -0.079 2.00e-02 2.50e+03 5.47e-02 8.99e+01 pdb=" CG PHE A 162 " 0.006 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " 0.027 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " 0.016 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " 0.031 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " 0.006 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " 0.125 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " -0.036 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " -0.089 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " 0.039 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 126 " 0.085 2.00e-02 2.50e+03 6.08e-02 8.32e+01 pdb=" CG HIS A 126 " -0.091 2.00e-02 2.50e+03 pdb=" ND1 HIS A 126 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 HIS A 126 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 HIS A 126 " 0.018 2.00e-02 2.50e+03 pdb=" NE2 HIS A 126 " 0.072 2.00e-02 2.50e+03 pdb=" HD2 HIS A 126 " -0.083 2.00e-02 2.50e+03 pdb=" HE1 HIS A 126 " -0.055 2.00e-02 2.50e+03 pdb=" HE2 HIS A 126 " 0.043 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.39: 1582 2.39 - 2.94: 8410 2.94 - 3.49: 10392 3.49 - 4.05: 15052 4.05 - 4.60: 21167 Nonbonded interactions: 56603 Sorted by model distance: nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.832 2.450 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.862 2.450 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.862 2.450 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.865 2.450 nonbonded pdb=" O ALA A 79 " pdb=" H SER A 83 " model vdw 1.878 2.450 ... (remaining 56598 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_7783516_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= 0.3611 r_free= 0.1992 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.461345 | | target function (ml) not normalized (work): 21994.432091 | | target function (ml) not normalized (free): 1146.400632 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3796 0.2171 4.8514 4.912| | 2: 3.78 - 3.00 1.00 2430 110 0.3384 0.1690 4.06 4.0809| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 48.79 0.83 0.13 6604.26| | 2: 3.78 - 3.00 2430 110 0.94 11.27 1.48 0.26 441.11| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 374.71 max = 12081.56 mean = 3566.44| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 89.99 mean = 30.29| |phase err.(test): min = 0.00 max = 89.95 mean = 32.75| |-----------------------------------------------------------------------------| ----------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 0.217 1557 Z= 5.585 Angle : 5.378 19.804 2118 Z= 3.831 Chirality : 0.387 1.039 243 Planarity : 0.031 0.081 284 Dihedral : 14.039 89.962 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 1.28 Ramachandran Plot: Outliers : 1.62 % Allowed : 2.16 % Favored : 96.22 % Rotamer: Outliers : 0.62 % Allowed : 4.35 % Favored : 95.03 % Cbeta Deviations : 31.35 % 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: -3.09 (0.48), residues: 224 helix: -3.07 (0.36), residues: 109 sheet: 0.22 (0.97), residues: 28 loop : -1.10 (0.57), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.062 0.021 ARG A 27 TYR 0.104 0.032 TYR A 139 PHE 0.055 0.027 PHE A 119 HIS 0.037 0.021 HIS A 115 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 1785 0 Protein: 8.85 115.78 16.79 3.90 1519 0 Water: 11.36 119.30 38.03 N/A 258 0 Other: 19.04 26.29 21.71 N/A 8 0 Chain A: 8.85 119.30 19.89 N/A 1785 0 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 3.00 - 49.25 A, n_refl.=5182 (all), 4.86 % free)-------------| | | | r_work= 0.3611 r_free= 0.1992 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.461345 | | target function (ml) not normalized (work): 21994.432091 | | target function (ml) not normalized (free): 1146.400632 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3564 0.3640 0.2087 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3564 0.3640 0.2087 n_refl.: 5182 remove outliers: r(all,work,free)=0.2509 0.2534 0.2087 n_refl.: 5178 overall B=-2.78 to atoms: r(all,work,free)=0.2402 0.2424 0.2037 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1569 0.1567 0.1602 n_refl.: 5178 remove outliers: r(all,work,free)=0.1567 0.1565 0.1602 n_refl.: 5177 ======================== 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 32.574-12.150 100.00 89 5 0.4006 445.511 406.472 0.673 1.014 0.398 11.894-9.307 99.02 97 4 0.1867 715.213 689.495 0.954 1.015 0.382 9.237-7.194 100.00 213 7 0.2200 584.903 571.610 0.980 1.014 0.384 7.162-5.571 100.00 427 22 0.2331 438.898 422.287 0.941 1.011 0.293 5.546-4.326 100.00 867 58 0.1384 602.545 592.224 0.970 1.005 0.258 4.315-3.360 100.00 1859 96 0.1311 573.027 568.350 1.029 0.994 0.189 3.356-3.002 100.00 1373 60 0.1607 441.369 435.972 1.024 0.984 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9170 b_overall=-4.8551 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1565 r_free=0.1602 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=0.1566 r_free=0.1604 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 19.313785 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.809736 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 0.1167 0.1804 0.0637 0.010 1.0 3.2 0.5 0.0 0 9.657 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.67 18.04 6.37 3.013 16.074 1.810 0.018 10.23 17.95 7.72 4.968 16.379 1.810 0.015 Individual atomic B min max mean iso aniso Overall: 2.18 111.51 17.68 5.28 1785 0 Protein: 2.18 111.37 14.97 5.28 1519 0 Water: 4.42 111.51 33.41 N/A 258 0 Other: 17.68 36.14 24.87 N/A 8 0 Chain A: 2.18 111.51 17.68 N/A 1785 0 Histogram: Values Number of atoms 2.18 - 13.12 894 13.12 - 24.05 500 24.05 - 34.98 190 34.98 - 45.91 113 45.91 - 56.85 55 56.85 - 67.78 16 67.78 - 78.71 8 78.71 - 89.65 5 89.65 - 100.58 1 100.58 - 111.51 3 =========================== Idealize ADP of riding H ========================== r_work=0.1023 r_free=0.1795 r_work=0.1015 r_free=0.1804 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1015 r_free = 0.1804 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 = 0.1020 r_free = 0.1813 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5177 (all), 4.87 % free)-------------| | | | r_work= 0.1020 r_free= 0.1813 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ls_wunit_k1) (work): 0.014219 | | target function (ls_wunit_k1) not normalized (work): 70.028531 | | target function (ls_wunit_k1) not normalized (free): 10.912052 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1060 0.1020 0.1813 n_refl.: 5177 re-set all scales: r(all,work,free)=0.2139 0.2140 0.2228 n_refl.: 5177 remove outliers: r(all,work,free)=0.2139 0.2140 0.2228 n_refl.: 5177 overall B=-1.01 to atoms: r(all,work,free)=0.2095 0.2094 0.2218 n_refl.: 5177 bulk-solvent and scaling: r(all,work,free)=0.1060 0.1019 0.1811 n_refl.: 5177 remove outliers: r(all,work,free)=0.1058 0.1017 0.1811 n_refl.: 5176 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 96.88 88 5 0.3415 314.915 299.594 0.634 1.005 0.368 11.894-9.307 99.02 97 4 0.1533 509.909 500.854 0.954 1.007 0.363 9.237-7.194 100.00 213 7 0.1677 417.004 416.832 0.992 1.008 0.325 7.162-5.571 100.00 427 22 0.1634 312.911 309.137 0.955 1.006 0.292 5.546-4.326 100.00 867 58 0.0928 429.582 426.384 0.969 1.004 0.243 4.315-3.360 100.00 1859 96 0.0762 408.537 408.662 1.020 0.999 0.194 3.356-3.002 100.00 1373 60 0.1002 314.673 313.519 1.000 0.994 0.021 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9170 b_overall=-4.5054 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1017 r_free=0.1811 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1017 r_free=0.1811 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1017 r_free=0.1811 | n_water=258 | time (s): 0.660 (total time: 0.660) Filter (dist) r_work=0.1043 r_free=0.1803 | n_water=247 | time (s): 21.010 (total time: 21.670) Filter (q & B) r_work=0.1044 r_free=0.1808 | n_water=244 | time (s): 1.310 (total time: 22.980) Compute maps r_work=0.1044 r_free=0.1808 | n_water=244 | time (s): 0.460 (total time: 23.440) Filter (map) r_work=0.1343 r_free=0.1909 | n_water=146 | time (s): 1.570 (total time: 25.010) Find peaks r_work=0.1343 r_free=0.1909 | n_water=146 | time (s): 0.590 (total time: 25.600) Add new water r_work=0.1708 r_free=0.2195 | n_water=239 | time (s): 1.780 (total time: 27.380) Refine new water occ: r_work=0.1169 r_free=0.1739 adp: r_work=0.1142 r_free=0.1734 occ: r_work=0.1138 r_free=0.1722 adp: r_work=0.1123 r_free=0.1716 occ: r_work=0.1123 r_free=0.1703 adp: r_work=0.1118 r_free=0.1699 ADP+occupancy (water only), MIN, final r_work=0.1118 r_free=0.1699 r_work=0.1118 r_free=0.1699 | n_water=239 | time (s): 3.840 (total time: 31.220) Filter (q & B) r_work=0.1118 r_free=0.1700 | n_water=238 | time (s): 1.450 (total time: 32.670) Filter (dist only) r_work=0.1123 r_free=0.1695 | n_water=237 | time (s): 17.950 (total time: 50.620) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 21.781003 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.594097 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 0.1012 0.1867 0.0856 0.009 1.0 3.5 0.5 0.6 0 10.891 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.12 18.67 8.56 4.679 17.126 2.594 0.014 9.46 18.79 9.33 5.392 17.546 2.594 0.012 Individual atomic B min max mean iso aniso Overall: 0.00 106.98 17.05 6.38 1764 0 Protein: 0.00 106.98 15.32 6.37 1519 0 Water: 0.00 62.79 28.06 N/A 237 0 Other: 11.67 30.14 19.53 N/A 8 0 Chain A: 0.00 106.98 16.09 N/A 1672 0 Chain S: 3.64 59.32 34.47 N/A 92 0 Histogram: Values Number of atoms 0.00 - 10.70 644 10.70 - 21.40 687 21.40 - 32.09 227 32.09 - 42.79 113 42.79 - 53.49 52 53.49 - 64.19 29 64.19 - 74.89 5 74.89 - 85.58 2 85.58 - 96.28 3 96.28 - 106.98 2 =========================== Idealize ADP of riding H ========================== r_work=0.0946 r_free=0.1879 r_work=0.0944 r_free=0.1880 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0944 r_free = 0.1880 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0942 r_free = 0.1849 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.0942 r_free= 0.1849 coordinate error (max.-lik. estimate): 0.31 A | | | | normalized target function (ls_wunit_k1) (work): 0.012002 | | target function (ls_wunit_k1) not normalized (work): 59.099805 | | target function (ls_wunit_k1) not normalized (free): 10.649160 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0989 0.0942 0.1849 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2155 0.2156 0.2263 n_refl.: 5176 remove outliers: r(all,work,free)=0.2155 0.2156 0.2263 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2155 0.2156 0.2263 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0989 0.0942 0.1848 n_refl.: 5176 remove outliers: r(all,work,free)=0.0987 0.0940 0.1848 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 0.3231 316.972 299.209 0.620 1.013 0.352 11.894-9.307 99.02 97 4 0.1455 509.909 506.197 0.944 1.014 0.347 9.237-7.194 100.00 213 7 0.1485 417.004 416.490 0.984 1.014 0.320 7.162-5.571 100.00 427 22 0.1400 312.911 310.515 0.958 1.011 0.290 5.546-4.326 100.00 867 58 0.0802 429.582 426.932 0.974 1.006 0.250 4.315-3.360 100.00 1859 96 0.0725 408.537 408.422 1.028 0.998 0.200 3.356-3.002 100.00 1373 60 0.0978 314.673 313.410 1.014 0.990 0.040 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9171 b_overall=-4.9258 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0940 r_free=0.1848 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0940 r_free=0.1848 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0940 r_free=0.1848 | n_water=237 | time (s): 0.570 (total time: 0.570) Filter (dist) r_work=0.0951 r_free=0.1840 | n_water=234 | time (s): 17.490 (total time: 18.060) Filter (q & B) r_work=0.1009 r_free=0.1843 | n_water=232 | time (s): 1.370 (total time: 19.430) Compute maps r_work=0.1009 r_free=0.1843 | n_water=232 | time (s): 0.500 (total time: 19.930) Filter (map) r_work=0.1269 r_free=0.1891 | n_water=153 | time (s): 1.620 (total time: 21.550) Find peaks r_work=0.1269 r_free=0.1891 | n_water=153 | time (s): 0.590 (total time: 22.140) Add new water r_work=0.1616 r_free=0.2207 | n_water=231 | time (s): 1.610 (total time: 23.750) Refine new water occ: r_work=0.1044 r_free=0.1819 adp: r_work=0.1036 r_free=0.1820 occ: r_work=0.1027 r_free=0.1809 adp: r_work=0.1027 r_free=0.1811 occ: r_work=0.1018 r_free=0.1800 adp: r_work=0.1017 r_free=0.1802 ADP+occupancy (water only), MIN, final r_work=0.1017 r_free=0.1802 r_work=0.1017 r_free=0.1802 | n_water=231 | time (s): 7.380 (total time: 31.130) Filter (q & B) r_work=0.1017 r_free=0.1805 | n_water=230 | time (s): 1.510 (total time: 32.640) Filter (dist only) r_work=0.1030 r_free=0.1824 | n_water=226 | time (s): 17.590 (total time: 50.230) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.096346 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.211915 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 0.0922 0.1886 0.0964 0.011 1.1 4.8 0.5 0.0 0 0.548 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.22 18.86 9.64 5.361 18.107 0.212 5.120 8.78 18.68 9.90 7.201 18.120 0.212 5.026 Individual atomic B min max mean iso aniso Overall: 0.00 104.98 16.66 8.88 1753 0 Protein: 0.00 104.98 15.47 8.88 1519 0 Water: 0.00 57.79 24.66 N/A 226 0 Other: 7.94 29.09 17.19 N/A 8 0 Chain A: 0.00 104.98 16.15 N/A 1661 0 Chain S: 0.00 54.86 25.98 N/A 92 0 Histogram: Values Number of atoms 0.00 - 10.50 608 10.50 - 21.00 711 21.00 - 31.49 240 31.49 - 41.99 114 41.99 - 52.49 40 52.49 - 62.99 21 62.99 - 73.48 10 73.48 - 83.98 4 83.98 - 94.48 3 94.48 - 104.98 2 =========================== Idealize ADP of riding H ========================== r_work=0.0878 r_free=0.1868 r_work=0.0883 r_free=0.1876 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0883 r_free = 0.1876 target_work(ml) = 5.030 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0877 r_free = 0.1866 target_work(ml) = 5.025 | | occupancies: max = 1.00 min = 0.27 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= 0.0877 r_free= 0.1866 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ml) (work): 5.025435 | | target function (ml) not normalized (work): 24740.214480 | | target function (ml) not normalized (free): 1902.502685 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0927 0.0877 0.1866 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2092 0.2093 0.2198 n_refl.: 5175 remove outliers: r(all,work,free)=0.2092 0.2093 0.2198 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2092 0.2093 0.2198 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0921 0.0872 0.1863 n_refl.: 5175 remove outliers: r(all,work,free)=0.0921 0.0872 0.1863 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 0.3758 316.972 294.055 0.600 0.991 0.330 11.894-9.307 99.02 97 4 0.1699 509.909 495.739 0.961 0.994 0.340 9.237-7.194 100.00 213 7 0.1808 417.004 410.583 1.007 0.997 0.340 7.162-5.571 100.00 427 22 0.1757 312.911 304.782 0.987 0.998 0.300 5.546-4.326 100.00 867 58 0.0904 429.582 424.041 1.000 1.000 0.234 4.315-3.360 100.00 1859 96 0.0583 408.537 408.107 1.058 1.002 0.220 3.356-3.002 100.00 1373 60 0.0609 314.673 314.308 1.041 1.003 0.040 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-6.6073 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0872 r_free=0.1863 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0872 r_free=0.1863 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0872 r_free=0.1863 | n_water=226 | time (s): 0.610 (total time: 0.610) Filter (dist) r_work=0.0879 r_free=0.1869 | n_water=224 | time (s): 18.410 (total time: 19.020) Filter (q & B) r_work=0.0944 r_free=0.1898 | n_water=222 | time (s): 1.550 (total time: 20.570) Compute maps r_work=0.0944 r_free=0.1898 | n_water=222 | time (s): 0.650 (total time: 21.220) Filter (map) r_work=0.1255 r_free=0.1950 | n_water=151 | time (s): 1.850 (total time: 23.070) Find peaks r_work=0.1255 r_free=0.1950 | n_water=151 | time (s): 0.490 (total time: 23.560) Add new water r_work=0.1593 r_free=0.2273 | n_water=231 | time (s): 1.410 (total time: 24.970) Refine new water occ: r_work=0.1001 r_free=0.1853 adp: r_work=0.0997 r_free=0.1859 occ: r_work=0.0988 r_free=0.1839 adp: r_work=0.0988 r_free=0.1846 occ: r_work=0.0980 r_free=0.1824 adp: r_work=0.0979 r_free=0.1833 ADP+occupancy (water only), MIN, final r_work=0.0979 r_free=0.1833 r_work=0.0979 r_free=0.1833 | n_water=231 | time (s): 15.790 (total time: 40.760) Filter (q & B) r_work=0.0979 r_free=0.1834 | n_water=230 | time (s): 1.220 (total time: 41.980) Filter (dist only) r_work=0.0999 r_free=0.1829 | n_water=227 | time (s): 16.890 (total time: 58.870) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.987305 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.216868 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 0.0911 0.1903 0.0992 0.011 1.0 4.2 0.5 0.6 0 0.494 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.11 19.03 9.92 6.935 18.254 0.217 5.030 8.86 19.45 10.59 8.150 18.357 0.217 4.960 Individual atomic B min max mean iso aniso Overall: 0.00 103.65 16.94 10.55 1754 0 Protein: 0.00 103.65 15.86 10.56 1519 0 Water: 0.00 52.79 24.21 N/A 227 0 Other: 9.68 27.65 16.19 N/A 8 0 Chain A: 0.00 103.65 16.40 N/A 1642 0 Chain S: 0.00 50.32 24.79 N/A 112 0 Histogram: Values Number of atoms 0.00 - 10.37 608 10.37 - 20.73 658 20.73 - 31.10 270 31.10 - 41.46 124 41.46 - 51.83 54 51.83 - 62.19 18 62.19 - 72.56 11 72.56 - 82.92 5 82.92 - 93.29 4 93.29 - 103.65 2 =========================== Idealize ADP of riding H ========================== r_work=0.0886 r_free=0.1945 r_work=0.0889 r_free=0.1954 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0889 r_free = 0.1954 target_work(ml) = 4.964 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0878 r_free = 0.1935 target_work(ml) = 4.957 | | occupancies: max = 1.00 min = 0.28 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= 0.0878 r_free= 0.1935 coordinate error (max.-lik. estimate): 0.31 A | | | | normalized target function (ml) (work): 4.956702 | | target function (ml) not normalized (work): 24401.844220 | | target function (ml) not normalized (free): 2252.766400 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0932 0.0878 0.1935 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2144 0.2145 0.2255 n_refl.: 5175 remove outliers: r(all,work,free)=0.2144 0.2145 0.2255 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2144 0.2145 0.2255 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0930 0.0877 0.1926 n_refl.: 5175 remove outliers: r(all,work,free)=0.0930 0.0877 0.1926 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 0.3730 316.972 285.077 0.583 0.987 0.320 11.894-9.307 99.02 97 4 0.1931 509.909 498.524 0.963 0.992 0.320 9.237-7.194 100.00 213 7 0.2085 417.004 409.218 1.013 0.995 0.304 7.162-5.571 100.00 427 22 0.1958 312.911 304.630 0.998 0.997 0.290 5.546-4.326 100.00 867 58 0.0968 429.582 422.865 1.017 0.999 0.230 4.315-3.360 100.00 1859 96 0.0562 408.537 408.275 1.088 1.002 0.220 3.356-3.002 100.00 1373 60 0.0468 314.673 314.304 1.072 1.004 0.040 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.9644 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0877 r_free=0.1926 After: r_work=0.0880 r_free=0.1925 ================================== NQH flips ================================== r_work=0.0880 r_free=0.1925 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0880 r_free=0.1925 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0880 r_free=0.1925 | n_water=227 | time (s): 0.660 (total time: 0.660) Filter (dist) r_work=0.0893 r_free=0.1927 | n_water=224 | time (s): 16.650 (total time: 17.310) Filter (q & B) r_work=0.0965 r_free=0.1915 | n_water=222 | time (s): 1.540 (total time: 18.850) Compute maps r_work=0.0965 r_free=0.1915 | n_water=222 | time (s): 0.580 (total time: 19.430) Filter (map) r_work=0.1266 r_free=0.1929 | n_water=156 | time (s): 1.500 (total time: 20.930) Find peaks r_work=0.1266 r_free=0.1929 | n_water=156 | time (s): 0.390 (total time: 21.320) Add new water r_work=0.1513 r_free=0.2159 | n_water=221 | time (s): 1.240 (total time: 22.560) Refine new water occ: r_work=0.0989 r_free=0.1916 adp: r_work=0.0982 r_free=0.1923 occ: r_work=0.0979 r_free=0.1911 adp: r_work=0.0978 r_free=0.1913 occ: r_work=0.0976 r_free=0.1904 adp: r_work=0.0975 r_free=0.1906 ADP+occupancy (water only), MIN, final r_work=0.0975 r_free=0.1906 r_work=0.0975 r_free=0.1906 | n_water=221 | time (s): 12.640 (total time: 35.200) Filter (q & B) r_work=0.0975 r_free=0.1907 | n_water=218 | time (s): 1.610 (total time: 36.810) Filter (dist only) r_work=0.0975 r_free=0.1907 | n_water=218 | time (s): 15.490 (total time: 52.300) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.941546 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.248992 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 0.0911 0.1907 0.0996 0.011 1.1 7.4 0.5 0.0 0 0.471 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.11 19.07 9.96 8.038 18.569 0.249 5.004 8.95 19.47 10.51 9.054 18.715 0.249 4.957 Individual atomic B min max mean iso aniso Overall: 0.00 106.06 17.22 12.01 1745 0 Protein: 0.00 106.06 16.30 12.02 1519 0 Water: 0.00 60.58 23.78 N/A 218 0 Other: 6.47 24.70 14.30 N/A 8 0 Chain A: 0.00 106.06 16.79 N/A 1636 0 Chain S: 0.00 57.29 23.77 N/A 109 0 Histogram: Values Number of atoms 0.00 - 10.61 615 10.61 - 21.21 636 21.21 - 31.82 297 31.82 - 42.43 106 42.43 - 53.03 51 53.03 - 63.64 17 63.64 - 74.24 13 74.24 - 84.85 2 84.85 - 95.46 6 95.46 - 106.06 2 =========================== Idealize ADP of riding H ========================== r_work=0.0895 r_free=0.1947 r_work=0.0898 r_free=0.1954 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0898 r_free = 0.1954 target_work(ml) = 4.961 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0894 r_free = 0.1945 target_work(ml) = 4.957 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0894 r_free= 0.1945 coordinate error (max.-lik. estimate): 0.31 A | | | | normalized target function (ml) (work): 4.957391 | | target function (ml) not normalized (work): 24405.234791 | | target function (ml) not normalized (free): 2251.335487 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1252 0.1876 5.4996 6.2346| | 2: 3.78 - 3.00 1.00 2430 110 0.0459 0.2061 4.4011 12.418| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 0.92 11.99 1.00 0.95 12061.28| | 2: 3.78 - 3.00 2430 110 0.99 2.00 1.00 0.97 978.78| |alpha: min = 0.94 max = 0.97 mean = 0.96| |beta: min = 644.36 max = 20027.66 mean = 6590.94| |figures of merit: min = 0.00 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.96 mean = 7.06| |phase err.(test): min = 0.00 max = 82.50 mean = 7.67| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0947 0.0894 0.1945 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2194 0.2197 0.2296 n_refl.: 5175 remove outliers: r(all,work,free)=0.2194 0.2197 0.2296 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2194 0.2197 0.2296 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0946 0.0893 0.1956 n_refl.: 5175 remove outliers: r(all,work,free)=0.0946 0.0893 0.1956 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 0.3723 316.972 293.699 0.643 0.985 0.329 11.894-9.307 99.02 97 4 0.1862 509.909 493.478 1.005 0.992 0.329 9.237-7.194 100.00 213 7 0.2136 417.004 406.762 1.051 0.995 0.310 7.162-5.571 100.00 427 22 0.1994 312.911 303.418 1.040 0.997 0.300 5.546-4.326 100.00 867 58 0.1027 429.582 423.232 1.061 0.999 0.230 4.315-3.360 100.00 1859 96 0.0581 408.537 408.430 1.147 1.002 0.220 3.356-3.002 100.00 1373 60 0.0442 314.673 314.866 1.135 1.004 0.040 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-8.5737 ================= 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 : 0.3611 0.1992 0.083 5.378 8.8 119.3 19.9 258 0.000 1_bss: 0.1565 0.1602 0.083 5.378 6.1 116.5 17.1 258 0.000 1_settarget: 0.1565 0.1602 0.083 5.378 6.1 116.5 17.1 258 0.000 1_nqh: 0.1566 0.1604 0.083 5.378 6.1 116.5 17.1 258 0.003 1_weight: 0.1566 0.1604 0.083 5.378 6.1 116.5 17.1 258 0.003 1_xyzrec: 0.1167 0.1804 0.010 0.973 6.1 116.5 17.1 258 0.204 1_adp: 0.1023 0.1795 0.010 0.973 2.2 111.5 17.7 258 0.204 1_regHadp: 0.1015 0.1804 0.010 0.973 2.2 111.5 17.7 258 0.204 1_occ: 0.1020 0.1813 0.010 0.973 2.2 111.5 17.7 258 0.204 2_bss: 0.1017 0.1811 0.010 0.973 1.2 110.5 16.7 258 0.204 2_settarget: 0.1017 0.1811 0.010 0.973 1.2 110.5 16.7 258 0.204 2_updatecdl: 0.1017 0.1811 0.010 1.002 1.2 110.5 16.7 258 0.204 2_nqh: 0.1017 0.1811 0.010 1.002 1.2 110.5 16.7 258 0.204 2_sol: 0.1123 0.1695 0.010 1.002 1.0 110.4 16.3 237 n/a 2_weight: 0.1123 0.1695 0.010 1.002 1.0 110.4 16.3 237 n/a 2_xyzrec: 0.1012 0.1867 0.009 0.969 1.0 110.4 16.3 237 n/a 2_adp: 0.0946 0.1879 0.009 0.969 0.0 107.0 17.1 237 n/a 2_regHadp: 0.0944 0.1880 0.009 0.969 0.0 107.0 17.1 237 n/a 2_occ: 0.0942 0.1849 0.009 0.969 0.0 107.0 17.1 237 n/a 3_bss: 0.0940 0.1848 0.009 0.969 0.0 107.0 17.1 237 n/a 3_settarget: 0.0940 0.1848 0.009 0.969 0.0 107.0 17.1 237 n/a 3_updatecdl: 0.0940 0.1848 0.009 0.974 0.0 107.0 17.1 237 n/a 3_nqh: 0.0940 0.1848 0.009 0.974 0.0 107.0 17.1 237 n/a 3_sol: 0.1030 0.1824 0.009 0.974 0.0 107.0 16.6 226 n/a 3_weight: 0.1030 0.1824 0.009 0.974 0.0 107.0 16.6 226 n/a 3_xyzrec: 0.0922 0.1886 0.011 1.069 0.0 107.0 16.6 226 n/a 3_adp: 0.0878 0.1868 0.011 1.069 0.0 105.0 16.7 226 n/a 3_regHadp: 0.0883 0.1876 0.011 1.069 0.0 105.0 16.7 226 n/a 3_occ: 0.0877 0.1866 0.011 1.069 0.0 105.0 16.7 226 n/a 4_bss: 0.0872 0.1863 0.011 1.069 0.0 105.0 16.7 226 n/a 4_settarget: 0.0872 0.1863 0.011 1.069 0.0 105.0 16.7 226 n/a 4_updatecdl: 0.0872 0.1863 0.011 1.074 0.0 105.0 16.7 226 n/a 4_nqh: 0.0872 0.1863 0.011 1.074 0.0 105.0 16.7 226 n/a 4_sol: 0.0999 0.1829 0.011 1.074 0.0 105.0 16.7 227 n/a 4_weight: 0.0999 0.1829 0.011 1.074 0.0 105.0 16.7 227 n/a 4_xyzrec: 0.0911 0.1903 0.011 1.017 0.0 105.0 16.7 227 n/a 4_adp: 0.0886 0.1945 0.011 1.017 0.0 103.7 16.9 227 n/a 4_regHadp: 0.0889 0.1954 0.011 1.017 0.0 103.7 16.9 227 n/a 4_occ: 0.0878 0.1935 0.011 1.017 0.0 103.7 16.9 227 n/a 5_bss: 0.0877 0.1926 0.011 1.017 0.0 103.7 16.9 227 n/a 5_settarget: 0.0877 0.1926 0.011 1.017 0.0 103.7 16.9 227 n/a 5_updatecdl: 0.0877 0.1926 0.011 1.026 0.0 103.7 16.9 227 n/a 5_setrh: 0.0880 0.1925 0.011 1.026 0.0 103.7 16.9 227 n/a 5_nqh: 0.0880 0.1925 0.011 1.026 0.0 103.7 16.9 227 n/a 5_sol: 0.0975 0.1907 0.011 1.026 0.0 103.7 16.9 218 n/a 5_weight: 0.0975 0.1907 0.011 1.026 0.0 103.7 16.9 218 n/a 5_xyzrec: 0.0911 0.1907 0.011 1.097 0.0 103.7 16.9 218 n/a 5_adp: 0.0895 0.1947 0.011 1.097 0.0 106.1 17.2 218 n/a 5_regHadp: 0.0898 0.1954 0.011 1.097 0.0 106.1 17.2 218 n/a 5_occ: 0.0894 0.1945 0.011 1.097 0.0 106.1 17.2 218 n/a end: 0.0893 0.1956 0.011 1.097 0.0 106.1 17.2 218 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_7783516_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_7783516_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.8200 Refinement macro-cycles (run) : 473.3800 Write final files (write_after_run_outputs) : 11.8900 Total : 489.0900 Total CPU time: 8.53 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:18:53 PST -0800 (1735492733.84 s) Start R-work = 0.1565, R-free = 0.1602 Final R-work = 0.0893, R-free = 0.1956 =============================================================================== Job complete usr+sys time: 521.22 seconds wall clock time: 9 minutes 3.52 seconds (543.52 seconds total)