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_6113322.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_6113322.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6113322.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 1 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: 1.34, per 1000 atoms: 0.40 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 122.8 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.69 - 0.96: 898 0.96 - 1.24: 861 1.24 - 1.52: 928 1.52 - 1.79: 458 1.79 - 2.07: 8 Bond restraints: 3153 Sorted by residual: bond pdb=" C ILE A 102 " pdb=" O ILE A 102 " ideal model delta sigma weight residual 1.237 1.020 0.217 1.09e-02 8.42e+03 3.96e+02 bond pdb=" N ALA A 114 " pdb=" CA ALA A 114 " ideal model delta sigma weight residual 1.458 1.233 0.226 1.23e-02 6.61e+03 3.37e+02 bond pdb=" N VAL A 33 " pdb=" CA VAL A 33 " ideal model delta sigma weight residual 1.459 1.226 0.233 1.27e-02 6.20e+03 3.36e+02 bond pdb=" C VAL A 25 " pdb=" O VAL A 25 " ideal model delta sigma weight residual 1.237 1.050 0.187 1.13e-02 7.83e+03 2.73e+02 bond pdb=" CA VAL A 33 " pdb=" CB VAL A 33 " ideal model delta sigma weight residual 1.539 1.728 -0.190 1.19e-02 7.06e+03 2.54e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.69: 3219 4.69 - 9.39: 1812 9.39 - 14.08: 621 14.08 - 18.77: 114 18.77 - 23.46: 11 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA VAL A 70 " pdb=" C VAL A 70 " pdb=" O VAL A 70 " ideal model delta sigma weight residual 120.57 103.80 16.77 1.07e+00 8.73e-01 2.46e+02 angle pdb=" OE1 GLN A 180 " pdb=" CD GLN A 180 " pdb=" NE2 GLN A 180 " ideal model delta sigma weight residual 122.60 108.26 14.34 1.00e+00 1.00e+00 2.06e+02 angle pdb=" NE ARG A 5 " pdb=" CZ ARG A 5 " pdb=" NH2 ARG A 5 " ideal model delta sigma weight residual 119.20 131.65 -12.45 9.00e-01 1.23e+00 1.91e+02 angle pdb=" CA ILE A 102 " pdb=" C ILE A 102 " pdb=" N ALA A 103 " ideal model delta sigma weight residual 116.51 101.93 14.58 1.07e+00 8.73e-01 1.86e+02 angle pdb=" CA VAL A 177 " pdb=" C VAL A 177 " pdb=" O VAL A 177 " ideal model delta sigma weight residual 120.85 106.64 14.21 1.06e+00 8.90e-01 1.80e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.39: 1275 15.39 - 30.78: 138 30.78 - 46.17: 45 46.17 - 61.56: 17 61.56 - 76.95: 6 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" N ASP A 49 " pdb=" C ASP A 49 " pdb=" CA ASP A 49 " pdb=" CB ASP A 49 " ideal model delta harmonic sigma weight residual 122.80 141.57 -18.77 0 2.50e+00 1.60e-01 5.64e+01 dihedral pdb=" C ASP A 49 " pdb=" N ASP A 49 " pdb=" CA ASP A 49 " pdb=" CB ASP A 49 " ideal model delta harmonic sigma weight residual -122.60 -140.93 18.33 0 2.50e+00 1.60e-01 5.38e+01 dihedral pdb=" C VAL A 70 " pdb=" N VAL A 70 " pdb=" CA VAL A 70 " pdb=" CB VAL A 70 " ideal model delta harmonic sigma weight residual -122.00 -139.39 17.39 0 2.50e+00 1.60e-01 4.84e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.214: 99 0.214 - 0.428: 78 0.428 - 0.642: 38 0.642 - 0.856: 20 0.856 - 1.070: 8 Chirality restraints: 243 Sorted by residual: chirality pdb=" CB ILE A 117 " pdb=" CA ILE A 117 " pdb=" CG1 ILE A 117 " pdb=" CG2 ILE A 117 " both_signs ideal model delta sigma weight residual False 2.64 1.57 1.07 2.00e-01 2.50e+01 2.86e+01 chirality pdb=" CB VAL A 8 " pdb=" CA VAL A 8 " pdb=" CG1 VAL A 8 " pdb=" CG2 VAL A 8 " both_signs ideal model delta sigma weight residual False -2.63 -3.63 1.00 2.00e-01 2.50e+01 2.52e+01 chirality pdb=" CG LEU A 172 " pdb=" CB LEU A 172 " pdb=" CD1 LEU A 172 " pdb=" CD2 LEU A 172 " both_signs ideal model delta sigma weight residual False -2.59 -1.63 -0.96 2.00e-01 2.50e+01 2.30e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.111 2.00e-02 2.50e+03 9.57e-02 2.75e+02 pdb=" CG PHE A 164 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.148 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " -0.023 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.046 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.126 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.173 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.054 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.000 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.009 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.103 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.100 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.160 2.00e-02 2.50e+03 7.58e-02 1.72e+02 pdb=" CG PHE A 119 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.034 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.053 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.159 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.050 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.041 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " -0.078 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 48 " -0.108 9.50e-02 1.11e+02 8.40e-02 1.31e+02 pdb=" NE ARG A 48 " 0.077 2.00e-02 2.50e+03 pdb=" CZ ARG A 48 " 0.081 2.00e-02 2.50e+03 pdb=" NH1 ARG A 48 " -0.023 2.00e-02 2.50e+03 pdb=" NH2 ARG A 48 " -0.073 2.00e-02 2.50e+03 pdb="HH11 ARG A 48 " -0.076 2.00e-02 2.50e+03 pdb="HH12 ARG A 48 " 0.012 2.00e-02 2.50e+03 pdb="HH21 ARG A 48 " -0.114 2.00e-02 2.50e+03 pdb="HH22 ARG A 48 " 0.120 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.28: 811 2.28 - 2.86: 7922 2.86 - 3.44: 10498 3.44 - 4.02: 15339 4.02 - 4.60: 22072 Nonbonded interactions: 56642 Sorted by model distance: nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.705 2.450 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.829 2.100 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.843 2.450 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.845 2.450 x-y,-y,-z-4/3 nonbonded pdb="HH21 ARG A 145 " pdb=" OE2 GLU A 163 " model vdw 1.846 2.450 ... (remaining 56637 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_6113322_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= 0.3623 r_free= 0.2063 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.473579 | | target function (ml) not normalized (work): 22054.742258 | | target function (ml) not normalized (free): 1151.518054 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3810 0.2277 4.8614 4.9192| | 2: 3.78 - 3.00 1.00 2430 110 0.3395 0.1702 4.0746 4.1181| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 48.87 0.83 0.13 6612.15| | 2: 3.78 - 3.00 2430 110 0.94 11.41 1.48 0.26 456.46| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 387.26 max = 12068.55 mean = 3578.01| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 89.99 mean = 30.41| |phase err.(test): min = 0.00 max = 89.99 mean = 33.41| |-----------------------------------------------------------------------------| ----------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 : 0.084 0.276 1557 Z= 5.511 Angle : 5.139 16.891 2118 Z= 3.679 Chirality : 0.395 1.070 243 Planarity : 0.032 0.119 284 Dihedral : 13.647 76.946 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.70 % Favored : 96.76 % Rotamer: Outliers : 2.48 % Allowed : 3.11 % Favored : 94.41 % Cbeta Deviations : 25.95 % 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: -2.37 (0.49), residues: 224 helix: -2.22 (0.41), residues: 109 sheet: -0.66 (0.85), residues: 38 loop : -0.61 (0.59), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.102 0.026 ARG A 98 TYR 0.083 0.041 TYR A 139 PHE 0.190 0.055 PHE A 164 HIS 0.069 0.042 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= 0.3623 r_free= 0.2063 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.473579 | | target function (ml) not normalized (work): 22054.742258 | | target function (ml) not normalized (free): 1151.518054 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3578 0.3656 0.2139 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3578 0.3656 0.2139 n_refl.: 5182 remove outliers: r(all,work,free)=0.2527 0.2551 0.2139 n_refl.: 5178 overall B=-2.47 to atoms: r(all,work,free)=0.2432 0.2454 0.2101 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1580 0.1580 0.1585 n_refl.: 5178 remove outliers: r(all,work,free)=0.1578 0.1577 0.1585 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 0.4127 444.899 402.818 0.632 1.059 0.388 11.894-9.307 99.02 97 4 0.1867 714.231 695.945 0.911 1.057 0.372 9.237-7.194 100.00 213 7 0.2161 584.099 576.163 0.939 1.051 0.353 7.162-5.571 100.00 427 22 0.2321 438.295 424.085 0.910 1.040 0.335 5.546-4.326 100.00 867 58 0.1375 601.717 595.103 0.953 1.022 0.247 4.315-3.360 100.00 1859 96 0.1339 572.240 565.489 1.023 0.991 0.167 3.356-3.002 100.00 1373 60 0.1620 440.763 433.163 1.034 0.960 0.064 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9170 b_overall=-4.3008 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1577 r_free=0.1585 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN Total number of N/Q/H flips: 1 r_work=0.1577 r_free=0.1583 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 18.384529 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.812923 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1163 0.1802 0.0639 0.009 1.0 2.9 0.5 0.0 0 9.192 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.63 18.02 6.39 3.013 16.390 1.813 0.018 10.29 17.95 7.67 4.791 16.569 1.813 0.015 Individual atomic B min max mean iso aniso Overall: 2.49 111.83 17.76 5.21 1785 0 Protein: 2.49 111.58 15.04 5.20 1519 0 Water: 4.40 111.83 33.54 N/A 258 0 Other: 18.11 38.67 24.20 N/A 8 0 Chain A: 2.49 111.83 17.76 N/A 1785 0 Histogram: Values Number of atoms 2.49 - 13.43 911 13.43 - 24.36 492 24.36 - 35.29 182 35.29 - 46.23 111 46.23 - 57.16 57 57.16 - 68.10 15 68.10 - 79.03 8 79.03 - 89.96 5 89.96 - 100.90 1 100.90 - 111.83 3 =========================== Idealize ADP of riding H ========================== r_work=0.1029 r_free=0.1795 r_work=0.1023 r_free=0.1799 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1023 r_free = 0.1799 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1019 r_free = 0.1805 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5177 (all), 4.87 % free)-------------| | | | r_work= 0.1019 r_free= 0.1805 coordinate error (max.-lik. estimate): 0.31 A | | | | normalized target function (ls_wunit_k1) (work): 0.014286 | | target function (ls_wunit_k1) not normalized (work): 70.357292 | | target function (ls_wunit_k1) not normalized (free): 10.211025 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1058 0.1019 0.1805 n_refl.: 5177 re-set all scales: r(all,work,free)=0.2123 0.2124 0.2231 n_refl.: 5177 remove outliers: r(all,work,free)=0.2123 0.2124 0.2231 n_refl.: 5177 overall B=-0.93 to atoms: r(all,work,free)=0.2083 0.2081 0.2219 n_refl.: 5177 bulk-solvent and scaling: r(all,work,free)=0.1058 0.1019 0.1796 n_refl.: 5177 remove outliers: r(all,work,free)=0.1054 0.1015 0.1796 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 0.3285 314.520 293.491 0.619 1.017 0.360 11.894-9.307 99.02 97 4 0.1530 505.964 498.836 0.944 1.019 0.361 9.237-7.194 100.00 213 7 0.1668 413.778 413.171 0.980 1.017 0.321 7.162-5.571 100.00 427 22 0.1656 310.490 306.640 0.946 1.013 0.312 5.546-4.326 100.00 867 58 0.0920 426.259 422.797 0.963 1.007 0.212 4.315-3.360 100.00 1859 96 0.0761 405.377 405.104 1.016 0.997 0.176 3.356-3.002 100.00 1373 60 0.1007 312.238 311.069 0.999 0.987 0.051 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9174 b_overall=-4.1571 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1015 r_free=0.1796 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 144 ASN Total number of N/Q/H flips: 2 r_work=0.1018 r_free=0.1802 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1018 r_free=0.1802 | n_water=258 | time (s): 0.470 (total time: 0.470) Filter (dist) r_work=0.1042 r_free=0.1786 | n_water=249 | time (s): 21.320 (total time: 21.790) Filter (q & B) r_work=0.1042 r_free=0.1788 | n_water=246 | time (s): 1.700 (total time: 23.490) Compute maps r_work=0.1042 r_free=0.1788 | n_water=246 | time (s): 0.540 (total time: 24.030) Filter (map) r_work=0.1333 r_free=0.1898 | n_water=151 | time (s): 1.480 (total time: 25.510) Find peaks r_work=0.1333 r_free=0.1898 | n_water=151 | time (s): 0.420 (total time: 25.930) Add new water r_work=0.1704 r_free=0.2194 | n_water=247 | time (s): 1.700 (total time: 27.630) Refine new water occ: r_work=0.1164 r_free=0.1768 adp: r_work=0.1131 r_free=0.1759 occ: r_work=0.1129 r_free=0.1734 adp: r_work=0.1112 r_free=0.1738 occ: r_work=0.1112 r_free=0.1720 adp: r_work=0.1107 r_free=0.1720 ADP+occupancy (water only), MIN, final r_work=0.1107 r_free=0.1720 r_work=0.1107 r_free=0.1720 | n_water=247 | time (s): 8.550 (total time: 36.180) Filter (q & B) r_work=0.1107 r_free=0.1720 | n_water=247 | time (s): 0.980 (total time: 37.160) Filter (dist only) r_work=0.1113 r_free=0.1711 | n_water=243 | time (s): 19.150 (total time: 56.310) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.365899 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.417107 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 0.1010 0.1782 0.0772 0.009 1.0 4.5 0.5 0.6 0 11.183 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.10 17.82 7.72 4.633 17.307 2.417 0.014 9.39 18.14 8.75 5.431 17.649 2.417 0.012 Individual atomic B min max mean iso aniso Overall: 0.00 106.63 17.12 6.28 1770 0 Protein: 0.00 106.63 15.26 6.26 1519 0 Water: 0.00 63.84 28.46 N/A 243 0 Other: 13.95 38.80 24.64 N/A 8 0 Chain A: 0.00 106.63 16.07 N/A 1676 0 Chain S: 3.41 58.46 35.84 N/A 94 0 Histogram: Values Number of atoms 0.00 - 10.66 654 10.66 - 21.33 674 21.33 - 31.99 223 31.99 - 42.65 124 42.65 - 53.31 43 53.31 - 63.98 36 63.98 - 74.64 9 74.64 - 85.30 4 85.30 - 95.97 1 95.97 - 106.63 2 =========================== Idealize ADP of riding H ========================== r_work=0.0939 r_free=0.1814 r_work=0.0936 r_free=0.1813 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0936 r_free = 0.1813 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0933 r_free = 0.1800 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0933 r_free= 0.1800 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ls_wunit_k1) (work): 0.012055 | | target function (ls_wunit_k1) not normalized (work): 59.344923 | | target function (ls_wunit_k1) not normalized (free): 9.600692 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0976 0.0933 0.1800 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2039 0.2038 0.2152 n_refl.: 5175 remove outliers: r(all,work,free)=0.2039 0.2038 0.2152 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2039 0.2038 0.2152 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0974 0.0930 0.1803 n_refl.: 5175 remove outliers: r(all,work,free)=0.0974 0.0930 0.1803 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 0.3368 314.520 298.210 0.620 1.002 0.350 11.894-9.307 99.02 97 4 0.1504 505.964 499.095 0.945 1.005 0.350 9.237-7.194 100.00 213 7 0.1481 413.778 414.625 0.990 1.005 0.310 7.162-5.571 100.00 427 22 0.1450 310.490 307.992 0.965 1.004 0.300 5.546-4.326 100.00 867 58 0.0783 426.259 423.453 0.977 1.003 0.229 4.315-3.360 100.00 1859 96 0.0707 405.377 405.136 1.026 1.000 0.180 3.356-3.002 100.00 1373 60 0.0953 312.238 311.199 1.005 0.996 0.090 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-4.8611 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0930 r_free=0.1803 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=0.0932 r_free=0.1808 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0932 r_free=0.1808 | n_water=243 | time (s): 0.490 (total time: 0.490) Filter (dist) r_work=0.0951 r_free=0.1803 | n_water=239 | time (s): 19.330 (total time: 19.820) Filter (q & B) r_work=0.1010 r_free=0.1799 | n_water=237 | time (s): 1.310 (total time: 21.130) Compute maps r_work=0.1010 r_free=0.1799 | n_water=237 | time (s): 0.470 (total time: 21.600) Filter (map) r_work=0.1304 r_free=0.1884 | n_water=157 | time (s): 1.570 (total time: 23.170) Find peaks r_work=0.1304 r_free=0.1884 | n_water=157 | time (s): 0.590 (total time: 23.760) Add new water r_work=0.1662 r_free=0.2260 | n_water=246 | time (s): 1.340 (total time: 25.100) Refine new water occ: r_work=0.1046 r_free=0.1761 adp: r_work=0.1042 r_free=0.1776 occ: r_work=0.1028 r_free=0.1755 adp: r_work=0.1028 r_free=0.1762 occ: r_work=0.1015 r_free=0.1745 adp: r_work=0.1015 r_free=0.1749 ADP+occupancy (water only), MIN, final r_work=0.1015 r_free=0.1749 r_work=0.1015 r_free=0.1749 | n_water=246 | time (s): 9.840 (total time: 34.940) Filter (q & B) r_work=0.1015 r_free=0.1749 | n_water=246 | time (s): 0.910 (total time: 35.850) Filter (dist only) r_work=0.1014 r_free=0.1745 | n_water=245 | time (s): 18.970 (total time: 54.820) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.090324 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.208131 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 0.0917 0.1762 0.0844 0.011 1.1 4.8 0.5 0.0 0 0.545 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.17 17.62 8.44 5.298 18.106 0.208 5.102 8.72 17.64 8.92 7.219 18.126 0.208 5.004 Individual atomic B min max mean iso aniso Overall: 0.00 105.40 16.83 8.91 1772 0 Protein: 0.00 105.40 15.41 8.90 1519 0 Water: 0.00 59.95 25.32 N/A 245 0 Other: 11.76 42.95 26.56 N/A 8 0 Chain A: 0.00 105.40 16.17 N/A 1662 0 Chain S: 0.00 55.67 26.88 N/A 110 0 Histogram: Values Number of atoms 0.00 - 10.54 644 10.54 - 21.08 672 21.08 - 31.62 238 31.62 - 42.16 127 42.16 - 52.70 49 52.70 - 63.24 21 63.24 - 73.78 12 73.78 - 84.32 5 84.32 - 94.86 3 94.86 - 105.40 1 =========================== Idealize ADP of riding H ========================== r_work=0.0872 r_free=0.1764 r_work=0.0878 r_free=0.1776 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0878 r_free = 0.1776 target_work(ml) = 5.009 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0868 r_free = 0.1760 target_work(ml) = 5.002 | | 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= 0.0868 r_free= 0.1760 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 5.002165 | | target function (ml) not normalized (work): 24625.660255 | | target function (ml) not normalized (free): 1799.489481 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0913 0.0868 0.1760 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2031 0.2037 0.2037 n_refl.: 5175 remove outliers: r(all,work,free)=0.2031 0.2037 0.2037 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2031 0.2037 0.2037 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0905 0.0861 0.1752 n_refl.: 5175 remove outliers: r(all,work,free)=0.0905 0.0861 0.1752 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 0.3661 314.520 289.035 0.582 0.990 0.320 11.894-9.307 99.02 97 4 0.1834 505.964 492.184 0.949 0.995 0.320 9.237-7.194 100.00 213 7 0.1826 413.778 409.680 1.012 0.998 0.295 7.162-5.571 100.00 427 22 0.1772 310.490 302.910 0.987 0.999 0.290 5.546-4.326 100.00 867 58 0.0875 426.259 421.255 1.007 1.000 0.230 4.315-3.360 100.00 1859 96 0.0567 405.377 404.798 1.063 1.002 0.190 3.356-3.002 100.00 1373 60 0.0597 312.238 311.915 1.045 1.004 0.085 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-6.8510 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0861 r_free=0.1752 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0861 r_free=0.1752 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0861 r_free=0.1752 | n_water=245 | time (s): 0.520 (total time: 0.520) Filter (dist) r_work=0.0869 r_free=0.1751 | n_water=243 | time (s): 20.170 (total time: 20.690) Filter (q & B) r_work=0.0948 r_free=0.1788 | n_water=240 | time (s): 1.840 (total time: 22.530) Compute maps r_work=0.0948 r_free=0.1788 | n_water=240 | time (s): 0.680 (total time: 23.210) Filter (map) r_work=0.1263 r_free=0.1939 | n_water=158 | time (s): 1.780 (total time: 24.990) Find peaks r_work=0.1263 r_free=0.1939 | n_water=158 | time (s): 0.570 (total time: 25.560) Add new water r_work=0.1588 r_free=0.2303 | n_water=239 | time (s): 1.910 (total time: 27.470) Refine new water occ: r_work=0.0983 r_free=0.1786 adp: r_work=0.0978 r_free=0.1799 occ: r_work=0.0969 r_free=0.1769 adp: r_work=0.0968 r_free=0.1786 occ: r_work=0.0960 r_free=0.1758 adp: r_work=0.0960 r_free=0.1774 ADP+occupancy (water only), MIN, final r_work=0.0960 r_free=0.1774 r_work=0.0960 r_free=0.1774 | n_water=239 | time (s): 7.870 (total time: 35.340) Filter (q & B) r_work=0.0960 r_free=0.1778 | n_water=238 | time (s): 1.470 (total time: 36.810) Filter (dist only) r_work=0.0976 r_free=0.1785 | n_water=236 | time (s): 19.410 (total time: 56.220) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.019471 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.209156 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 0.0877 0.1816 0.0939 0.011 1.1 4.8 0.5 0.6 0 0.510 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 8.77 18.16 9.39 6.952 18.199 0.209 4.976 8.57 18.60 10.03 8.133 18.332 0.209 4.913 Individual atomic B min max mean iso aniso Overall: 0.00 105.76 17.03 10.65 1763 0 Protein: 0.00 105.76 15.86 10.65 1519 0 Water: 0.00 58.27 24.21 N/A 236 0 Other: 14.31 45.64 27.49 N/A 8 0 Chain A: 0.00 105.76 16.51 N/A 1651 0 Chain S: 0.00 53.06 24.67 N/A 112 0 Histogram: Values Number of atoms 0.00 - 10.58 634 10.58 - 21.15 654 21.15 - 31.73 261 31.73 - 42.30 121 42.30 - 52.88 54 52.88 - 63.46 15 63.46 - 74.03 13 74.03 - 84.61 6 84.61 - 95.18 3 95.18 - 105.76 2 =========================== Idealize ADP of riding H ========================== r_work=0.0857 r_free=0.1860 r_work=0.0861 r_free=0.1865 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0861 r_free = 0.1865 target_work(ml) = 4.918 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0854 r_free = 0.1849 target_work(ml) = 4.913 | | 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= 0.0854 r_free= 0.1849 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ml) (work): 4.912540 | | target function (ml) not normalized (work): 24184.433580 | | target function (ml) not normalized (free): 2203.164393 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0904 0.0854 0.1849 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2084 0.2086 0.2159 n_refl.: 5175 remove outliers: r(all,work,free)=0.2084 0.2086 0.2159 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2084 0.2086 0.2159 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0903 0.0854 0.1851 n_refl.: 5175 remove outliers: r(all,work,free)=0.0903 0.0854 0.1851 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 0.3872 314.520 278.551 0.563 0.983 0.319 11.894-9.307 99.02 97 4 0.1783 505.964 498.059 0.971 0.990 0.318 9.237-7.194 100.00 213 7 0.2006 413.778 408.217 1.017 0.994 0.295 7.162-5.571 100.00 427 22 0.1951 310.490 302.227 1.002 0.996 0.290 5.546-4.326 100.00 867 58 0.0946 426.259 419.749 1.018 0.998 0.224 4.315-3.360 100.00 1859 96 0.0545 405.377 405.533 1.084 1.002 0.210 3.356-3.002 100.00 1373 60 0.0441 312.238 312.053 1.067 1.005 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.7901 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0854 r_free=0.1851 After: r_work=0.0856 r_free=0.1851 ================================== NQH flips ================================== r_work=0.0856 r_free=0.1851 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A Total number of N/Q/H flips: 1 r_work=0.0857 r_free=0.1849 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0857 r_free=0.1849 | n_water=236 | time (s): 0.690 (total time: 0.690) Filter (dist) r_work=0.0872 r_free=0.1866 | n_water=231 | time (s): 19.530 (total time: 20.220) Filter (q & B) r_work=0.0911 r_free=0.1869 | n_water=230 | time (s): 1.430 (total time: 21.650) Compute maps r_work=0.0911 r_free=0.1869 | n_water=230 | time (s): 0.600 (total time: 22.250) Filter (map) r_work=0.1229 r_free=0.1975 | n_water=162 | time (s): 1.480 (total time: 23.730) Find peaks r_work=0.1229 r_free=0.1975 | n_water=162 | time (s): 0.400 (total time: 24.130) Add new water r_work=0.1515 r_free=0.2279 | n_water=233 | time (s): 1.350 (total time: 25.480) Refine new water occ: r_work=0.0977 r_free=0.1867 adp: r_work=0.0973 r_free=0.1875 occ: r_work=0.0964 r_free=0.1858 adp: r_work=0.0965 r_free=0.1868 occ: r_work=0.0956 r_free=0.1853 adp: r_work=0.0956 r_free=0.1862 ADP+occupancy (water only), MIN, final r_work=0.0956 r_free=0.1862 r_work=0.0956 r_free=0.1862 | n_water=233 | time (s): 10.420 (total time: 35.900) Filter (q & B) r_work=0.0956 r_free=0.1871 | n_water=230 | time (s): 1.390 (total time: 37.290) Filter (dist only) r_work=0.0956 r_free=0.1871 | n_water=230 | time (s): 17.050 (total time: 54.340) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.034960 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.206386 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 0.0898 0.1891 0.0993 0.010 1.2 7.4 0.5 0.6 0 0.517 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 8.98 18.91 9.93 8.117 18.606 0.206 4.959 8.81 19.12 10.31 8.915 18.718 0.206 4.907 Individual atomic B min max mean iso aniso Overall: 0.00 110.39 17.30 11.83 1757 0 Protein: 0.00 110.39 16.23 11.81 1519 0 Water: 0.00 55.69 24.00 N/A 230 0 Other: 10.15 45.91 26.40 N/A 8 0 Chain A: 0.00 110.39 16.77 N/A 1645 0 Chain S: 0.00 55.69 25.05 N/A 112 0 Histogram: Values Number of atoms 0.00 - 11.04 650 11.04 - 22.08 653 22.08 - 33.12 254 33.12 - 44.16 121 44.16 - 55.19 41 55.19 - 66.23 13 66.23 - 77.27 14 77.27 - 88.31 7 88.31 - 99.35 2 99.35 - 110.39 2 =========================== Idealize ADP of riding H ========================== r_work=0.0881 r_free=0.1912 r_work=0.0883 r_free=0.1913 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0883 r_free = 0.1913 target_work(ml) = 4.912 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0875 r_free = 0.1899 target_work(ml) = 4.906 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0875 r_free= 0.1899 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ml) (work): 4.906409 | | target function (ml) not normalized (work): 24154.249099 | | target function (ml) not normalized (free): 2409.224300 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1249 0.1823 5.4886 6.2449| | 2: 3.78 - 3.00 1.00 2430 110 0.0419 0.2027 4.3091 13.84| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 12.04 1.00 0.94 12110.46| | 2: 3.78 - 3.00 2430 110 0.99 1.88 1.00 0.96 830.05| |alpha: min = 0.92 max = 0.97 mean = 0.95| |beta: min = 530.10 max = 20326.36 mean = 6542.43| |figures of merit: min = 0.01 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.33 mean = 7.03| |phase err.(test): min = 0.00 max = 76.13 mean = 6.95| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0926 0.0875 0.1899 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2154 0.2157 0.2225 n_refl.: 5175 remove outliers: r(all,work,free)=0.2154 0.2157 0.2225 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2154 0.2157 0.2225 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0927 0.0875 0.1912 n_refl.: 5175 remove outliers: r(all,work,free)=0.0927 0.0875 0.1912 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 0.3961 314.520 286.462 0.593 0.984 0.310 11.894-9.307 99.02 97 4 0.1749 505.964 492.390 1.004 0.992 0.324 9.237-7.194 100.00 213 7 0.2145 413.778 406.486 1.047 0.995 0.303 7.162-5.571 100.00 427 22 0.2072 310.490 302.324 1.044 0.997 0.283 5.546-4.326 100.00 867 58 0.0984 426.259 420.589 1.070 0.999 0.240 4.315-3.360 100.00 1859 96 0.0563 405.377 405.549 1.148 1.001 0.220 3.356-3.002 100.00 1373 60 0.0408 312.238 311.895 1.129 1.003 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-8.4987 ================= 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 : 0.3623 0.2063 0.084 5.139 8.8 119.3 19.9 258 0.000 1_bss: 0.1577 0.1585 0.084 5.139 6.4 116.8 17.4 258 0.000 1_settarget: 0.1577 0.1585 0.084 5.139 6.4 116.8 17.4 258 0.000 1_nqh: 0.1577 0.1583 0.084 5.139 6.4 116.8 17.4 258 0.003 1_weight: 0.1577 0.1583 0.084 5.139 6.4 116.8 17.4 258 0.003 1_xyzrec: 0.1163 0.1802 0.009 0.966 6.4 116.8 17.4 258 0.215 1_adp: 0.1029 0.1795 0.009 0.966 2.5 111.8 17.8 258 0.215 1_regHadp: 0.1023 0.1799 0.009 0.966 2.5 111.8 17.8 258 0.215 1_occ: 0.1019 0.1805 0.009 0.966 2.5 111.8 17.8 258 0.215 2_bss: 0.1015 0.1796 0.009 0.966 1.6 110.9 16.8 258 0.215 2_settarget: 0.1015 0.1796 0.009 0.966 1.6 110.9 16.8 258 0.215 2_updatecdl: 0.1015 0.1796 0.009 0.980 1.6 110.9 16.8 258 0.215 2_nqh: 0.1018 0.1802 0.009 0.980 1.6 110.9 16.8 258 0.215 2_sol: 0.1113 0.1711 0.009 0.980 1.0 110.7 16.5 243 n/a 2_weight: 0.1113 0.1711 0.009 0.980 1.0 110.7 16.5 243 n/a 2_xyzrec: 0.1010 0.1782 0.009 0.972 1.0 110.7 16.5 243 n/a 2_adp: 0.0939 0.1814 0.009 0.972 0.0 106.6 17.1 243 n/a 2_regHadp: 0.0936 0.1813 0.009 0.972 0.0 106.6 17.1 243 n/a 2_occ: 0.0933 0.1800 0.009 0.972 0.0 106.6 17.1 243 n/a 3_bss: 0.0930 0.1803 0.009 0.972 0.0 106.6 17.1 243 n/a 3_settarget: 0.0930 0.1803 0.009 0.972 0.0 106.6 17.1 243 n/a 3_updatecdl: 0.0930 0.1803 0.009 0.976 0.0 106.6 17.1 243 n/a 3_nqh: 0.0932 0.1808 0.009 0.976 0.0 106.6 17.1 243 n/a 3_sol: 0.1014 0.1745 0.009 0.976 0.0 106.6 16.8 245 n/a 3_weight: 0.1014 0.1745 0.009 0.976 0.0 106.6 16.8 245 n/a 3_xyzrec: 0.0917 0.1762 0.011 1.062 0.0 106.6 16.8 245 n/a 3_adp: 0.0872 0.1764 0.011 1.062 0.0 105.4 16.8 245 n/a 3_regHadp: 0.0878 0.1776 0.011 1.062 0.0 105.4 16.8 245 n/a 3_occ: 0.0868 0.1760 0.011 1.062 0.0 105.4 16.8 245 n/a 4_bss: 0.0861 0.1752 0.011 1.062 0.0 105.4 16.8 245 n/a 4_settarget: 0.0861 0.1752 0.011 1.062 0.0 105.4 16.8 245 n/a 4_updatecdl: 0.0861 0.1752 0.011 1.077 0.0 105.4 16.8 245 n/a 4_nqh: 0.0861 0.1752 0.011 1.077 0.0 105.4 16.8 245 n/a 4_sol: 0.0976 0.1785 0.011 1.077 0.0 105.4 16.8 236 n/a 4_weight: 0.0976 0.1785 0.011 1.077 0.0 105.4 16.8 236 n/a 4_xyzrec: 0.0877 0.1816 0.011 1.056 0.0 105.4 16.8 236 n/a 4_adp: 0.0857 0.1860 0.011 1.056 0.0 105.8 17.0 236 n/a 4_regHadp: 0.0861 0.1865 0.011 1.056 0.0 105.8 17.0 236 n/a 4_occ: 0.0854 0.1849 0.011 1.056 0.0 105.8 17.0 236 n/a 5_bss: 0.0854 0.1851 0.011 1.056 0.0 105.8 17.0 236 n/a 5_settarget: 0.0854 0.1851 0.011 1.056 0.0 105.8 17.0 236 n/a 5_updatecdl: 0.0854 0.1851 0.011 1.061 0.0 105.8 17.0 236 n/a 5_setrh: 0.0856 0.1851 0.011 1.061 0.0 105.8 17.0 236 n/a 5_nqh: 0.0857 0.1849 0.011 1.061 0.0 105.8 17.0 236 n/a 5_sol: 0.0956 0.1871 0.011 1.061 0.0 105.8 17.1 230 n/a 5_weight: 0.0956 0.1871 0.011 1.061 0.0 105.8 17.1 230 n/a 5_xyzrec: 0.0898 0.1891 0.010 1.182 0.0 105.8 17.1 230 n/a 5_adp: 0.0881 0.1912 0.010 1.182 0.0 110.4 17.3 230 n/a 5_regHadp: 0.0883 0.1913 0.010 1.182 0.0 110.4 17.3 230 n/a 5_occ: 0.0875 0.1899 0.010 1.182 0.0 110.4 17.3 230 n/a end: 0.0875 0.1912 0.010 1.182 0.0 110.4 17.3 230 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_6113322_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_6113322_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.1500 Refinement macro-cycles (run) : 497.4800 Write final files (write_after_run_outputs) : 9.3600 Total : 509.9900 Total CPU time: 8.84 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:19:12 PST -0800 (1735492752.63 s) Start R-work = 0.1577, R-free = 0.1585 Final R-work = 0.0875, R-free = 0.1912 =============================================================================== Job complete usr+sys time: 537.55 seconds wall clock time: 9 minutes 20.42 seconds (560.42 seconds total)