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_4735076.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 { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_4735076.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_4735076.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 3 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" 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" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.20, per 1000 atoms: 0.35 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: 0.32 Conformation dependent library (CDL) restraints added in 189.7 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.63 - 0.89: 390 0.89 - 1.15: 1214 1.15 - 1.40: 614 1.40 - 1.66: 889 1.66 - 1.92: 46 Bond restraints: 3153 Sorted by residual: bond pdb=" N ALA A 36 " pdb=" CA ALA A 36 " ideal model delta sigma weight residual 1.456 1.690 -0.233 1.23e-02 6.61e+03 3.60e+02 bond pdb=" C GLN A 180 " pdb=" O GLN A 180 " ideal model delta sigma weight residual 1.236 0.997 0.239 1.29e-02 6.01e+03 3.42e+02 bond pdb=" C GLY A 78 " pdb=" O GLY A 78 " ideal model delta sigma weight residual 1.234 1.455 -0.222 1.21e-02 6.83e+03 3.36e+02 bond pdb=" C LYS A 12 " pdb=" O LYS A 12 " ideal model delta sigma weight residual 1.234 1.016 0.219 1.20e-02 6.94e+03 3.33e+02 bond pdb=" C GLY A 157 " pdb=" O GLY A 157 " ideal model delta sigma weight residual 1.235 1.479 -0.244 1.35e-02 5.49e+03 3.26e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.47: 3088 4.47 - 8.94: 1853 8.94 - 13.41: 670 13.41 - 17.88: 152 17.88 - 22.35: 14 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA ILE A 21 " pdb=" C ILE A 21 " pdb=" N PRO A 22 " ideal model delta sigma weight residual 120.83 109.48 11.35 5.90e-01 2.87e+00 3.70e+02 angle pdb=" O ILE A 21 " pdb=" C ILE A 21 " pdb=" N PRO A 22 " ideal model delta sigma weight residual 120.42 130.43 -10.01 6.40e-01 2.44e+00 2.45e+02 angle pdb=" CA GLU A 116 " pdb=" C GLU A 116 " pdb=" O GLU A 116 " ideal model delta sigma weight residual 120.98 104.33 16.65 1.24e+00 6.50e-01 1.80e+02 angle pdb=" O ALEU A 153 " pdb=" C ALEU A 153 " pdb=" N THR A 154 " ideal model delta sigma weight residual 123.12 140.58 -17.46 1.32e+00 5.74e-01 1.75e+02 angle pdb=" CG HIS A 115 " pdb=" CD2 HIS A 115 " pdb=" NE2 HIS A 115 " ideal model delta sigma weight residual 107.20 94.55 12.65 1.00e+00 1.00e+00 1.60e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.87: 1300 16.87 - 33.74: 126 33.74 - 50.61: 35 50.61 - 67.47: 17 67.47 - 84.34: 3 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" N BLYS A 99 " pdb=" C BLYS A 99 " pdb=" CA BLYS A 99 " pdb=" CB BLYS A 99 " ideal model delta harmonic sigma weight residual 122.80 143.36 -20.56 0 2.50e+00 1.60e-01 6.76e+01 dihedral pdb=" C VAL A 20 " pdb=" N VAL A 20 " pdb=" CA VAL A 20 " pdb=" CB VAL A 20 " ideal model delta harmonic sigma weight residual -122.00 -142.42 20.42 0 2.50e+00 1.60e-01 6.67e+01 dihedral pdb=" C ALYS A 99 " pdb=" N ALYS A 99 " pdb=" CA ALYS A 99 " pdb=" CB ALYS A 99 " ideal model delta harmonic sigma weight residual -122.60 -142.20 19.60 0 2.50e+00 1.60e-01 6.14e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.003 - 0.198: 89 0.198 - 0.393: 77 0.393 - 0.588: 43 0.588 - 0.783: 25 0.783 - 0.978: 9 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA LEU A 58 " pdb=" N LEU A 58 " pdb=" C LEU A 58 " pdb=" CB LEU A 58 " both_signs ideal model delta sigma weight residual False 2.51 1.53 0.98 2.00e-01 2.50e+01 2.39e+01 chirality pdb=" CA ALA A 183 " pdb=" N ALA A 183 " pdb=" C ALA A 183 " pdb=" CB ALA A 183 " both_signs ideal model delta sigma weight residual False 2.48 1.52 0.97 2.00e-01 2.50e+01 2.34e+01 chirality pdb=" CA BLYS A 99 " pdb=" N BLYS A 99 " pdb=" C BLYS A 99 " pdb=" CB BLYS A 99 " both_signs ideal model delta sigma weight residual False 2.51 1.55 0.96 2.00e-01 2.50e+01 2.29e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.018 2.00e-02 2.50e+03 6.78e-02 1.38e+02 pdb=" CG PHE A 119 " -0.170 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " 0.038 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " -0.102 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.066 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.083 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.035 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.007 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " -0.013 2.00e-02 2.50e+03 6.68e-02 1.34e+02 pdb=" CG TYR A 139 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " 0.083 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " 0.084 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " -0.080 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.071 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " -0.065 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.015 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " -0.099 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " -0.020 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.108 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 5 " 0.035 9.50e-02 1.11e+02 7.54e-02 1.25e+02 pdb=" NE ARG A 5 " -0.063 2.00e-02 2.50e+03 pdb=" CZ ARG A 5 " -0.022 2.00e-02 2.50e+03 pdb=" NH1 ARG A 5 " -0.063 2.00e-02 2.50e+03 pdb=" NH2 ARG A 5 " -0.072 2.00e-02 2.50e+03 pdb="HH11 ARG A 5 " 0.096 2.00e-02 2.50e+03 pdb="HH12 ARG A 5 " 0.021 2.00e-02 2.50e+03 pdb="HH21 ARG A 5 " 0.154 2.00e-02 2.50e+03 pdb="HH22 ARG A 5 " -0.053 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.28: 759 2.28 - 2.86: 7804 2.86 - 3.44: 10629 3.44 - 4.02: 15316 4.02 - 4.60: 22095 Nonbonded interactions: 56603 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.695 2.100 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.721 2.100 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.781 2.450 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.801 2.100 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.835 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_4735076_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= 0.3626 r_free= 0.2020 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.467394 | | target function (ml) not normalized (work): 22024.250451 | | target function (ml) not normalized (free): 1148.890317 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3811 0.2175 4.8499 4.89| | 2: 3.78 - 3.00 1.00 2430 110 0.3400 0.1756 4.0739 4.1319| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 48.84 0.83 0.13 6607.32| | 2: 3.78 - 3.00 2430 110 0.93 11.41 1.48 0.26 450.69| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 383.36 max = 12070.61 mean = 3572.71| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 89.99 mean = 30.39| |phase err.(test): min = 0.00 max = 89.98 mean = 33.29| |-----------------------------------------------------------------------------| ----------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 0.244 1557 Z= 5.545 Angle : 5.417 18.814 2118 Z= 3.858 Chirality : 0.388 0.978 243 Planarity : 0.031 0.133 284 Dihedral : 14.032 84.343 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.86 % Allowed : 1.86 % Favored : 96.27 % Cbeta Deviations : 34.05 % 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: -1.98 (0.49), residues: 224 helix: -2.23 (0.41), residues: 109 sheet: 0.06 (0.95), residues: 28 loop : -0.17 (0.55), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.066 0.020 ARG A 48 TYR 0.077 0.042 TYR A 139 PHE 0.142 0.046 PHE A 119 HIS 0.057 0.028 HIS A 126 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 1785 0 Protein: 8.85 115.78 16.79 3.90 1519 0 Water: 11.36 119.30 38.03 N/A 258 0 Other: 19.04 26.29 21.71 N/A 8 0 Chain A: 8.85 119.30 19.89 N/A 1785 0 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 3.00 - 49.25 A, n_refl.=5182 (all), 4.86 % free)-------------| | | | r_work= 0.3626 r_free= 0.2020 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.467394 | | target function (ml) not normalized (work): 22024.250451 | | target function (ml) not normalized (free): 1148.890317 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3580 0.3658 0.2094 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3580 0.3658 0.2094 n_refl.: 5182 remove outliers: r(all,work,free)=0.2528 0.2552 0.2094 n_refl.: 5178 overall B=-2.79 to atoms: r(all,work,free)=0.2422 0.2443 0.2054 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1572 0.1572 0.1583 n_refl.: 5178 remove outliers: r(all,work,free)=0.1570 0.1570 0.1583 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 0.4060 444.706 408.674 0.650 1.088 0.402 11.894-9.307 99.02 97 4 0.1868 713.921 693.070 0.917 1.083 0.396 9.237-7.194 100.00 213 7 0.2209 583.846 573.111 0.954 1.074 0.365 7.162-5.571 100.00 427 22 0.2318 438.105 424.121 0.930 1.057 0.356 5.546-4.326 100.00 867 58 0.1406 601.456 593.587 0.971 1.031 0.230 4.315-3.360 100.00 1859 96 0.1316 571.992 566.095 1.058 0.986 0.200 3.356-3.002 100.00 1373 60 0.1596 440.572 432.964 1.080 0.941 0.053 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9552 b_overall=-3.5829 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1570 r_free=0.1583 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN Total number of N/Q/H flips: 1 r_work=0.1572 r_free=0.1589 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 19.245533 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.600423 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 0.1164 0.1745 0.0581 0.010 1.0 2.6 0.5 0.0 0 9.623 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.64 17.45 5.81 3.012 16.071 1.600 0.018 10.36 17.74 7.38 4.450 16.186 1.600 0.015 Individual atomic B min max mean iso aniso Overall: 2.63 111.51 17.32 4.91 1785 0 Protein: 2.63 110.82 14.61 4.91 1519 0 Water: 4.08 111.51 33.09 N/A 258 0 Other: 17.39 34.70 23.04 N/A 8 0 Chain A: 2.63 111.51 17.32 N/A 1785 0 Histogram: Values Number of atoms 2.63 - 13.52 966 13.52 - 24.41 454 24.41 - 35.29 177 35.29 - 46.18 106 46.18 - 57.07 53 57.07 - 67.96 13 67.96 - 78.85 7 78.85 - 89.73 5 89.73 - 100.62 1 100.62 - 111.51 3 =========================== Idealize ADP of riding H ========================== r_work=0.1036 r_free=0.1774 r_work=0.1028 r_free=0.1779 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1028 r_free = 0.1779 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 = 0.1029 r_free = 0.1771 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.23 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= 0.1029 r_free= 0.1771 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ls_wunit_k1) (work): 0.014448 | | target function (ls_wunit_k1) not normalized (work): 71.157255 | | target function (ls_wunit_k1) not normalized (free): 10.179193 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1067 0.1029 0.1771 n_refl.: 5177 re-set all scales: r(all,work,free)=0.2129 0.2130 0.2216 n_refl.: 5177 remove outliers: r(all,work,free)=0.2129 0.2130 0.2216 n_refl.: 5177 overall B=-0.97 to atoms: r(all,work,free)=0.2089 0.2088 0.2206 n_refl.: 5177 bulk-solvent and scaling: r(all,work,free)=0.1072 0.1035 0.1776 n_refl.: 5177 remove outliers: r(all,work,free)=0.1070 0.1033 0.1776 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 0.3383 323.512 306.281 0.662 1.002 0.370 11.894-9.307 99.02 97 4 0.1527 523.828 517.188 0.994 1.004 0.371 9.237-7.194 100.00 213 7 0.1674 428.388 429.009 1.036 1.004 0.336 7.162-5.571 100.00 427 22 0.1654 321.453 318.176 0.989 1.003 0.322 5.546-4.326 100.00 867 58 0.0927 441.309 438.287 0.998 1.002 0.217 4.315-3.360 100.00 1859 96 0.0783 419.690 419.792 1.044 1.000 0.204 3.356-3.002 100.00 1373 60 0.1032 323.263 321.348 1.010 0.997 0.061 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9553 b_overall=-3.4627 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1033 r_free=0.1776 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A A 180 GLN Total number of N/Q/H flips: 2 r_work=0.1035 r_free=0.1778 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1035 r_free=0.1778 | n_water=258 | time (s): 0.560 (total time: 0.560) Filter (dist) r_work=0.1056 r_free=0.1783 | n_water=249 | time (s): 18.790 (total time: 19.350) Filter (q & B) r_work=0.1056 r_free=0.1791 | n_water=246 | time (s): 1.540 (total time: 20.890) Compute maps r_work=0.1056 r_free=0.1791 | n_water=246 | time (s): 0.640 (total time: 21.530) Filter (map) r_work=0.1308 r_free=0.1895 | n_water=151 | time (s): 1.590 (total time: 23.120) Find peaks r_work=0.1308 r_free=0.1895 | n_water=151 | time (s): 0.560 (total time: 23.680) Add new water r_work=0.1630 r_free=0.2125 | n_water=230 | time (s): 1.290 (total time: 24.970) Refine new water occ: r_work=0.1164 r_free=0.1685 adp: r_work=0.1143 r_free=0.1687 occ: r_work=0.1139 r_free=0.1671 adp: r_work=0.1131 r_free=0.1678 occ: r_work=0.1130 r_free=0.1665 adp: r_work=0.1128 r_free=0.1670 ADP+occupancy (water only), MIN, final r_work=0.1128 r_free=0.1670 r_work=0.1128 r_free=0.1670 | n_water=230 | time (s): 2.950 (total time: 27.920) Filter (q & B) r_work=0.1128 r_free=0.1670 | n_water=230 | time (s): 0.740 (total time: 28.660) Filter (dist only) r_work=0.1135 r_free=0.1666 | n_water=226 | time (s): 15.910 (total time: 44.570) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.211482 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.926199 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 0.1036 0.1775 0.0739 0.009 1.0 4.2 0.5 0.0 0 11.606 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.36 17.75 7.39 4.423 16.553 2.926 0.014 9.58 17.80 8.22 5.689 16.967 2.926 0.013 Individual atomic B min max mean iso aniso Overall: 0.00 106.00 16.39 6.73 1753 0 Protein: 0.00 106.00 14.94 6.73 1519 0 Water: 0.00 63.30 25.99 N/A 226 0 Other: 11.42 31.64 20.84 N/A 8 0 Chain A: 0.00 106.00 15.68 N/A 1675 0 Chain S: 1.05 55.00 31.69 N/A 78 0 Histogram: Values Number of atoms 0.00 - 10.60 678 10.60 - 21.20 656 21.20 - 31.80 220 31.80 - 42.40 120 42.40 - 53.00 43 53.00 - 63.60 20 63.60 - 74.20 9 74.20 - 84.80 2 84.80 - 95.40 3 95.40 - 106.00 2 =========================== Idealize ADP of riding H ========================== r_work=0.0958 r_free=0.1780 r_work=0.0955 r_free=0.1784 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0955 r_free = 0.1784 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0948 r_free = 0.1747 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= 0.0948 r_free= 0.1747 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ls_wunit_k1) (work): 0.012231 | | target function (ls_wunit_k1) not normalized (work): 60.223593 | | target function (ls_wunit_k1) not normalized (free): 9.400624 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0989 0.0948 0.1747 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2156 0.2161 0.2202 n_refl.: 5176 remove outliers: r(all,work,free)=0.2156 0.2161 0.2202 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2156 0.2161 0.2202 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0988 0.0947 0.1758 n_refl.: 5176 remove outliers: r(all,work,free)=0.0988 0.0947 0.1758 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 0.3343 323.512 309.509 0.682 1.005 0.370 11.894-9.307 99.02 97 4 0.1455 523.828 518.561 0.991 1.006 0.370 9.237-7.194 100.00 213 7 0.1506 428.388 427.364 1.023 1.006 0.310 7.162-5.571 100.00 427 22 0.1437 321.453 319.112 0.990 1.005 0.310 5.546-4.326 100.00 867 58 0.0801 441.309 438.625 1.001 1.003 0.240 4.315-3.360 100.00 1859 96 0.0729 419.690 419.472 1.049 1.000 0.210 3.356-3.002 100.00 1373 60 0.0972 323.263 321.791 1.020 0.996 0.090 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-3.8065 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0947 r_free=0.1758 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=0.0948 r_free=0.1763 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0948 r_free=0.1763 | n_water=226 | time (s): 0.600 (total time: 0.600) Filter (dist) r_work=0.0962 r_free=0.1761 | n_water=222 | time (s): 17.700 (total time: 18.300) Filter (q & B) r_work=0.1023 r_free=0.1803 | n_water=220 | time (s): 1.780 (total time: 20.080) Compute maps r_work=0.1023 r_free=0.1803 | n_water=220 | time (s): 0.570 (total time: 20.650) Filter (map) r_work=0.1256 r_free=0.1853 | n_water=152 | time (s): 1.360 (total time: 22.010) Find peaks r_work=0.1256 r_free=0.1853 | n_water=152 | time (s): 0.460 (total time: 22.470) Add new water r_work=0.1641 r_free=0.2181 | n_water=233 | time (s): 1.360 (total time: 23.830) Refine new water occ: r_work=0.1052 r_free=0.1749 adp: r_work=0.1046 r_free=0.1755 occ: r_work=0.1035 r_free=0.1736 adp: r_work=0.1036 r_free=0.1743 occ: r_work=0.1026 r_free=0.1725 adp: r_work=0.1026 r_free=0.1731 ADP+occupancy (water only), MIN, final r_work=0.1026 r_free=0.1731 r_work=0.1026 r_free=0.1731 | n_water=233 | time (s): 7.620 (total time: 31.450) Filter (q & B) r_work=0.1026 r_free=0.1731 | n_water=233 | time (s): 0.750 (total time: 32.200) Filter (dist only) r_work=0.1039 r_free=0.1729 | n_water=231 | time (s): 16.050 (total time: 48.250) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.120154 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.196426 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 0.0945 0.1812 0.0867 0.011 1.1 3.5 0.5 1.2 0 0.560 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.45 18.12 8.67 5.553 17.671 0.196 5.161 9.08 18.17 9.10 7.259 17.693 0.196 5.073 Individual atomic B min max mean iso aniso Overall: 0.00 106.38 16.28 8.95 1758 0 Protein: 0.00 106.38 15.09 8.96 1519 0 Water: 0.00 58.30 23.96 N/A 231 0 Other: 7.31 31.79 20.54 N/A 8 0 Chain A: 0.00 106.38 15.76 N/A 1663 0 Chain S: 0.00 50.00 25.52 N/A 95 0 Histogram: Values Number of atoms 0.00 - 10.64 671 10.64 - 21.28 671 21.28 - 31.91 227 31.91 - 42.55 112 42.55 - 53.19 41 53.19 - 63.83 18 63.83 - 74.47 8 74.47 - 85.11 5 85.11 - 95.74 4 95.74 - 106.38 1 =========================== Idealize ADP of riding H ========================== r_work=0.0908 r_free=0.1817 r_work=0.0912 r_free=0.1823 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0912 r_free = 0.1823 target_work(ml) = 5.078 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0900 r_free = 0.1798 target_work(ml) = 5.070 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.0900 r_free= 0.1798 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 5.069955 | | target function (ml) not normalized (work): 24964.459234 | | target function (ml) not normalized (free): 1795.311937 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0946 0.0900 0.1798 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2139 0.2148 0.2122 n_refl.: 5176 remove outliers: r(all,work,free)=0.2139 0.2148 0.2122 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2139 0.2148 0.2122 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0939 0.0894 0.1794 n_refl.: 5176 remove outliers: r(all,work,free)=0.0939 0.0894 0.1794 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 0.3868 323.512 296.693 0.619 0.996 0.356 11.894-9.307 99.02 97 4 0.1778 523.828 509.116 0.957 0.998 0.353 9.237-7.194 100.00 213 7 0.1858 428.388 423.544 0.992 1.000 0.309 7.162-5.571 100.00 427 22 0.1848 321.453 312.425 0.971 1.001 0.290 5.546-4.326 100.00 867 58 0.0933 441.309 436.202 0.989 1.001 0.250 4.315-3.360 100.00 1859 96 0.0578 419.690 419.047 1.043 1.002 0.220 3.356-3.002 100.00 1373 60 0.0633 323.263 322.413 1.015 1.003 0.080 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-5.6801 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0894 r_free=0.1794 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0894 r_free=0.1794 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0894 r_free=0.1794 | n_water=231 | time (s): 0.530 (total time: 0.530) Filter (dist) r_work=0.0921 r_free=0.1792 | n_water=225 | time (s): 17.620 (total time: 18.150) Filter (q & B) r_work=0.0991 r_free=0.1807 | n_water=222 | time (s): 1.260 (total time: 19.410) Compute maps r_work=0.0991 r_free=0.1807 | n_water=222 | time (s): 0.630 (total time: 20.040) Filter (map) r_work=0.1261 r_free=0.1875 | n_water=152 | time (s): 1.500 (total time: 21.540) Find peaks r_work=0.1261 r_free=0.1875 | n_water=152 | time (s): 0.420 (total time: 21.960) Add new water r_work=0.1653 r_free=0.2185 | n_water=240 | time (s): 1.330 (total time: 23.290) Refine new water occ: r_work=0.1030 r_free=0.1769 adp: r_work=0.1022 r_free=0.1777 occ: r_work=0.1011 r_free=0.1751 adp: r_work=0.1010 r_free=0.1761 occ: r_work=0.1000 r_free=0.1734 adp: r_work=0.0999 r_free=0.1742 ADP+occupancy (water only), MIN, final r_work=0.0999 r_free=0.1742 r_work=0.0999 r_free=0.1742 | n_water=240 | time (s): 9.910 (total time: 33.200) Filter (q & B) r_work=0.0999 r_free=0.1742 | n_water=240 | time (s): 0.770 (total time: 33.970) Filter (dist only) r_work=0.0999 r_free=0.1742 | n_water=240 | time (s): 16.630 (total time: 50.600) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.006238 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.232297 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 0.0918 0.1799 0.0881 0.011 1.0 4.5 0.5 0.6 0 0.503 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.18 17.99 8.81 6.963 17.903 0.232 5.042 8.97 18.54 9.57 8.158 17.979 0.232 4.982 Individual atomic B min max mean iso aniso Overall: 0.00 105.65 16.65 10.63 1767 0 Protein: 0.00 105.65 15.39 10.63 1519 0 Water: 0.41 61.26 24.38 N/A 240 0 Other: 9.51 37.70 22.56 N/A 8 0 Chain A: 0.00 105.65 15.96 N/A 1650 0 Chain S: 0.41 57.32 26.37 N/A 117 0 Histogram: Values Number of atoms 0.00 - 10.56 678 10.56 - 21.13 629 21.13 - 31.69 258 31.69 - 42.26 110 42.26 - 52.82 51 52.82 - 63.39 21 63.39 - 73.95 8 73.95 - 84.52 8 84.52 - 95.08 2 95.08 - 105.65 2 =========================== Idealize ADP of riding H ========================== r_work=0.0897 r_free=0.1854 r_work=0.0901 r_free=0.1859 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0901 r_free = 0.1859 target_work(ml) = 4.987 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0888 r_free = 0.1842 target_work(ml) = 4.980 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.0888 r_free= 0.1842 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 4.979648 | | target function (ml) not normalized (work): 24519.786676 | | target function (ml) not normalized (free): 2102.092460 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0936 0.0888 0.1842 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2165 0.2175 0.2150 n_refl.: 5176 remove outliers: r(all,work,free)=0.2165 0.2175 0.2150 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2165 0.2175 0.2150 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0932 0.0884 0.1839 n_refl.: 5176 remove outliers: r(all,work,free)=0.0929 0.0881 0.1839 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 0.3773 325.625 287.443 0.582 0.995 0.340 11.894-9.307 99.02 97 4 0.1893 523.828 506.029 0.960 0.998 0.340 9.237-7.194 100.00 213 7 0.2126 428.388 419.722 1.000 1.000 0.284 7.162-5.571 100.00 427 22 0.2050 321.453 310.638 0.984 1.000 0.270 5.546-4.326 100.00 867 58 0.0984 441.309 435.712 1.011 1.001 0.250 4.315-3.360 100.00 1859 96 0.0542 419.690 419.323 1.077 1.003 0.220 3.356-3.002 100.00 1373 60 0.0472 323.263 322.808 1.052 1.004 0.080 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9171 b_overall=-7.2864 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0881 r_free=0.1839 After: r_work=0.0885 r_free=0.1836 ================================== NQH flips ================================== r_work=0.0885 r_free=0.1836 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B Total number of N/Q/H flips: 1 r_work=0.0887 r_free=0.1834 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0887 r_free=0.1834 | n_water=240 | time (s): 0.590 (total time: 0.590) Filter (dist) r_work=0.0911 r_free=0.1827 | n_water=232 | time (s): 18.890 (total time: 19.480) Filter (q & B) r_work=0.0945 r_free=0.1830 | n_water=230 | time (s): 1.450 (total time: 20.930) Compute maps r_work=0.0945 r_free=0.1830 | n_water=230 | time (s): 0.490 (total time: 21.420) Filter (map) r_work=0.1251 r_free=0.1963 | n_water=149 | time (s): 1.300 (total time: 22.720) Find peaks r_work=0.1251 r_free=0.1963 | n_water=149 | time (s): 0.410 (total time: 23.130) Add new water r_work=0.1547 r_free=0.2170 | n_water=217 | time (s): 1.540 (total time: 24.670) Refine new water occ: r_work=0.1015 r_free=0.1886 adp: r_work=0.1012 r_free=0.1890 occ: r_work=0.1007 r_free=0.1881 adp: r_work=0.1006 r_free=0.1884 occ: r_work=0.1002 r_free=0.1875 adp: r_work=0.1000 r_free=0.1878 ADP+occupancy (water only), MIN, final r_work=0.1000 r_free=0.1878 r_work=0.1000 r_free=0.1878 | n_water=217 | time (s): 13.370 (total time: 38.040) Filter (q & B) r_work=0.1001 r_free=0.1880 | n_water=216 | time (s): 1.710 (total time: 39.750) Filter (dist only) r_work=0.1001 r_free=0.1880 | n_water=216 | time (s): 14.670 (total time: 54.420) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.961287 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.220257 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 0.0936 0.1903 0.0967 0.010 1.1 7.0 0.5 0.6 0 0.481 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.36 19.03 9.67 8.078 18.042 0.220 5.066 9.12 18.73 9.61 8.908 18.222 0.220 5.008 Individual atomic B min max mean iso aniso Overall: 0.00 106.10 16.82 11.76 1743 0 Protein: 0.00 106.10 15.93 11.76 1519 0 Water: 0.00 56.26 22.84 N/A 216 0 Other: 12.63 37.65 24.11 N/A 8 0 Chain A: 0.00 106.10 16.39 N/A 1642 0 Chain S: 0.00 50.00 23.78 N/A 101 0 Histogram: Values Number of atoms 0.00 - 10.61 656 10.61 - 21.22 628 21.22 - 31.83 263 31.83 - 42.44 110 42.44 - 53.05 45 53.05 - 63.66 18 63.66 - 74.27 8 74.27 - 84.88 8 84.88 - 95.49 5 95.49 - 106.10 2 =========================== Idealize ADP of riding H ========================== r_work=0.0912 r_free=0.1873 r_work=0.0915 r_free=0.1871 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0915 r_free = 0.1871 target_work(ml) = 5.012 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0909 r_free = 0.1859 target_work(ml) = 5.009 | | 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= 0.0909 r_free= 0.1859 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 5.008574 | | target function (ml) not normalized (work): 24657.212249 | | target function (ml) not normalized (free): 2073.929303 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1261 0.1812 5.5312 6.162| | 2: 3.78 - 3.00 1.00 2430 110 0.0479 0.1938 4.4724 10.899| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 11.95 1.00 0.99 12598.57| | 2: 3.78 - 3.00 2430 110 0.99 2.30 1.00 1.00 1120.77| |alpha: min = 0.98 max = 1.00 mean = 0.99| |beta: min = 745.47 max = 20726.83 mean = 6933.11| |figures of merit: min = 0.01 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 88.99 mean = 7.19| |phase err.(test): min = 0.00 max = 78.30 mean = 7.20| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0956 0.0909 0.1859 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2172 0.2177 0.2231 n_refl.: 5175 remove outliers: r(all,work,free)=0.2172 0.2177 0.2231 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2172 0.2177 0.2231 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0955 0.0907 0.1861 n_refl.: 5175 remove outliers: r(all,work,free)=0.0955 0.0907 0.1861 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 0.3804 325.625 288.083 0.587 0.989 0.330 11.894-9.307 99.02 97 4 0.1865 523.828 514.200 0.979 0.993 0.330 9.237-7.194 100.00 213 7 0.2089 428.388 421.552 1.010 0.996 0.305 7.162-5.571 100.00 427 22 0.2014 321.453 312.814 0.993 0.998 0.300 5.546-4.326 100.00 867 58 0.1034 441.309 434.008 1.004 1.000 0.250 4.315-3.360 100.00 1859 96 0.0594 419.690 419.841 1.081 1.003 0.230 3.356-3.002 100.00 1373 60 0.0468 323.263 322.783 1.056 1.006 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.4875 ================= 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 : 0.3626 0.2020 0.083 5.417 8.8 119.3 19.9 258 0.000 1_bss: 0.1570 0.1583 0.083 5.417 6.1 116.5 17.1 258 0.000 1_settarget: 0.1570 0.1583 0.083 5.417 6.1 116.5 17.1 258 0.000 1_nqh: 0.1572 0.1589 0.083 5.417 6.1 116.5 17.1 258 0.003 1_weight: 0.1572 0.1589 0.083 5.417 6.1 116.5 17.1 258 0.003 1_xyzrec: 0.1164 0.1745 0.010 0.997 6.1 116.5 17.1 258 0.196 1_adp: 0.1036 0.1774 0.010 0.997 2.6 111.5 17.3 258 0.196 1_regHadp: 0.1028 0.1779 0.010 0.997 2.6 111.5 17.3 258 0.196 1_occ: 0.1029 0.1771 0.010 0.997 2.6 111.5 17.3 258 0.196 2_bss: 0.1033 0.1776 0.010 0.997 1.7 110.5 16.3 258 0.196 2_settarget: 0.1033 0.1776 0.010 0.997 1.7 110.5 16.3 258 0.196 2_updatecdl: 0.1033 0.1776 0.010 1.008 1.7 110.5 16.3 258 0.196 2_nqh: 0.1035 0.1778 0.010 1.008 1.7 110.5 16.3 258 0.196 2_sol: 0.1135 0.1666 0.010 1.008 1.7 109.9 15.6 226 n/a 2_weight: 0.1135 0.1666 0.010 1.008 1.7 109.9 15.6 226 n/a 2_xyzrec: 0.1036 0.1775 0.009 0.979 1.7 109.9 15.6 226 n/a 2_adp: 0.0958 0.1780 0.009 0.979 0.0 106.0 16.4 226 n/a 2_regHadp: 0.0955 0.1784 0.009 0.979 0.0 106.0 16.4 226 n/a 2_occ: 0.0948 0.1747 0.009 0.979 0.0 106.0 16.4 226 n/a 3_bss: 0.0947 0.1758 0.009 0.979 0.0 106.0 16.4 226 n/a 3_settarget: 0.0947 0.1758 0.009 0.979 0.0 106.0 16.4 226 n/a 3_updatecdl: 0.0947 0.1758 0.009 0.984 0.0 106.0 16.4 226 n/a 3_nqh: 0.0948 0.1763 0.009 0.984 0.0 106.0 16.4 226 n/a 3_sol: 0.1039 0.1729 0.009 0.984 0.0 106.0 16.2 231 n/a 3_weight: 0.1039 0.1729 0.009 0.984 0.0 106.0 16.2 231 n/a 3_xyzrec: 0.0945 0.1812 0.011 1.059 0.0 106.0 16.2 231 n/a 3_adp: 0.0908 0.1817 0.011 1.059 0.0 106.4 16.3 231 n/a 3_regHadp: 0.0912 0.1823 0.011 1.059 0.0 106.4 16.3 231 n/a 3_occ: 0.0900 0.1798 0.011 1.059 0.0 106.4 16.3 231 n/a 4_bss: 0.0894 0.1794 0.011 1.059 0.0 106.4 16.3 231 n/a 4_settarget: 0.0894 0.1794 0.011 1.059 0.0 106.4 16.3 231 n/a 4_updatecdl: 0.0894 0.1794 0.011 1.076 0.0 106.4 16.3 231 n/a 4_nqh: 0.0894 0.1794 0.011 1.076 0.0 106.4 16.3 231 n/a 4_sol: 0.0999 0.1742 0.011 1.076 0.0 106.4 16.5 240 n/a 4_weight: 0.0999 0.1742 0.011 1.076 0.0 106.4 16.5 240 n/a 4_xyzrec: 0.0918 0.1799 0.011 1.034 0.0 106.4 16.5 240 n/a 4_adp: 0.0897 0.1854 0.011 1.034 0.0 105.6 16.6 240 n/a 4_regHadp: 0.0901 0.1859 0.011 1.034 0.0 105.6 16.6 240 n/a 4_occ: 0.0888 0.1842 0.011 1.034 0.0 105.6 16.6 240 n/a 5_bss: 0.0881 0.1839 0.011 1.034 0.0 105.6 16.6 240 n/a 5_settarget: 0.0881 0.1839 0.011 1.034 0.0 105.6 16.6 240 n/a 5_updatecdl: 0.0881 0.1839 0.011 1.034 0.0 105.6 16.6 240 n/a 5_setrh: 0.0885 0.1836 0.011 1.034 0.0 105.6 16.6 240 n/a 5_nqh: 0.0887 0.1834 0.011 1.034 0.0 105.6 16.6 240 n/a 5_sol: 0.1001 0.1880 0.011 1.034 0.0 105.6 16.5 216 n/a 5_weight: 0.1001 0.1880 0.011 1.034 0.0 105.6 16.5 216 n/a 5_xyzrec: 0.0936 0.1903 0.010 1.110 0.0 105.6 16.5 216 n/a 5_adp: 0.0912 0.1873 0.010 1.110 0.0 106.1 16.8 216 n/a 5_regHadp: 0.0915 0.1871 0.010 1.110 0.0 106.1 16.8 216 n/a 5_occ: 0.0909 0.1859 0.010 1.110 0.0 106.1 16.8 216 n/a end: 0.0907 0.1861 0.010 1.110 0.0 106.1 16.8 216 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_4735076_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_4735076_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.2500 Refinement macro-cycles (run) : 472.3300 Write final files (write_after_run_outputs) : 11.5200 Total : 487.1000 Total CPU time: 8.52 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:18:54 PST -0800 (1735492734.03 s) Start R-work = 0.1570, R-free = 0.1583 Final R-work = 0.0907, R-free = 0.1861 =============================================================================== Job complete usr+sys time: 520.71 seconds wall clock time: 9 minutes 4.36 seconds (544.36 seconds total)