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_2731660.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" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2731660.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2731660.pdb" 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 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: 2.06, per 1000 atoms: 0.61 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: 0.30 Conformation dependent library (CDL) restraints added in 107.6 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: 0.64 - 0.89: 420 0.89 - 1.15: 1201 1.15 - 1.41: 598 1.41 - 1.66: 895 1.66 - 1.92: 39 Bond restraints: 3153 Sorted by residual: bond pdb=" N ATYR A 67 " pdb=" CA ATYR A 67 " ideal model delta sigma weight residual 1.455 1.217 0.238 1.21e-02 6.83e+03 3.86e+02 bond pdb=" CA GLU A 176 " pdb=" C GLU A 176 " ideal model delta sigma weight residual 1.524 1.762 -0.238 1.27e-02 6.20e+03 3.52e+02 bond pdb=" C ILE A 91 " pdb=" O ILE A 91 " ideal model delta sigma weight residual 1.237 1.032 0.205 1.14e-02 7.69e+03 3.24e+02 bond pdb=" C BGLU A 90 " pdb=" O BGLU A 90 " ideal model delta sigma weight residual 1.237 1.026 0.210 1.17e-02 7.31e+03 3.23e+02 bond pdb=" N LEU A 166 " pdb=" CA LEU A 166 " ideal model delta sigma weight residual 1.459 1.245 0.214 1.28e-02 6.10e+03 2.80e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.20: 2852 4.20 - 8.39: 1891 8.39 - 12.58: 799 12.58 - 16.78: 204 16.78 - 20.97: 31 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O HIS A 126 " pdb=" C HIS A 126 " pdb=" N PRO A 127 " ideal model delta sigma weight residual 121.30 106.14 15.16 1.03e+00 9.43e-01 2.17e+02 angle pdb=" CA ILE A 9 " pdb=" C ILE A 9 " pdb=" O ILE A 9 " ideal model delta sigma weight residual 120.53 135.60 -15.07 1.07e+00 8.73e-01 1.98e+02 angle pdb=" CA THR A 19 " pdb=" C THR A 19 " pdb=" O THR A 19 " ideal model delta sigma weight residual 120.56 137.52 -16.96 1.21e+00 6.83e-01 1.96e+02 angle pdb=" O GLU A 176 " pdb=" C GLU A 176 " pdb=" N VAL A 177 " ideal model delta sigma weight residual 122.07 136.33 -14.26 1.03e+00 9.43e-01 1.92e+02 angle pdb=" O SER A 155 " pdb=" C SER A 155 " pdb=" N ARG A 156 " ideal model delta sigma weight residual 123.26 108.99 14.27 1.05e+00 9.07e-01 1.85e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 1304 17.51 - 35.02: 128 35.02 - 52.53: 31 52.53 - 70.04: 16 70.04 - 87.55: 2 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C ILE A 105 " pdb=" N ILE A 105 " pdb=" CA ILE A 105 " pdb=" CB ILE A 105 " ideal model delta harmonic sigma weight residual -122.00 -146.95 24.95 0 2.50e+00 1.60e-01 9.96e+01 dihedral pdb=" C LEU A 151 " pdb=" N LEU A 151 " pdb=" CA LEU A 151 " pdb=" CB LEU A 151 " ideal model delta harmonic sigma weight residual -122.60 -145.52 22.92 0 2.50e+00 1.60e-01 8.41e+01 dihedral pdb=" C CYS A 106 " pdb=" N CYS A 106 " pdb=" CA CYS A 106 " pdb=" CB CYS A 106 " ideal model delta harmonic sigma weight residual -122.60 -142.53 19.93 0 2.50e+00 1.60e-01 6.36e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.217: 92 0.217 - 0.432: 85 0.432 - 0.647: 36 0.647 - 0.862: 23 0.862 - 1.077: 7 Chirality restraints: 243 Sorted by residual: chirality pdb=" CB VAL A 33 " pdb=" CA VAL A 33 " pdb=" CG1 VAL A 33 " pdb=" CG2 VAL A 33 " both_signs ideal model delta sigma weight residual False -2.63 -1.55 -1.08 2.00e-01 2.50e+01 2.90e+01 chirality pdb=" CA LEU A 151 " pdb=" N LEU A 151 " pdb=" C LEU A 151 " pdb=" CB LEU A 151 " both_signs ideal model delta sigma weight residual False 2.51 1.59 0.92 2.00e-01 2.50e+01 2.14e+01 chirality pdb=" CB VAL A 169 " pdb=" CA VAL A 169 " pdb=" CG1 VAL A 169 " pdb=" CG2 VAL A 169 " both_signs ideal model delta sigma weight residual False -2.63 -1.71 -0.92 2.00e-01 2.50e+01 2.12e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " 0.107 2.00e-02 2.50e+03 7.43e-02 1.66e+02 pdb=" CG TYR A 141 " -0.076 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " -0.052 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " 0.098 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " 0.051 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " -0.081 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " 0.133 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " -0.027 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " -0.040 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " -0.042 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " -0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 5 " -0.016 9.50e-02 1.11e+02 7.27e-02 1.18e+02 pdb=" NE ARG A 5 " -0.075 2.00e-02 2.50e+03 pdb=" CZ ARG A 5 " 0.149 2.00e-02 2.50e+03 pdb=" NH1 ARG A 5 " -0.104 2.00e-02 2.50e+03 pdb=" NH2 ARG A 5 " 0.057 2.00e-02 2.50e+03 pdb="HH11 ARG A 5 " 0.033 2.00e-02 2.50e+03 pdb="HH12 ARG A 5 " 0.016 2.00e-02 2.50e+03 pdb="HH21 ARG A 5 " -0.014 2.00e-02 2.50e+03 pdb="HH22 ARG A 5 " -0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " 0.032 2.00e-02 2.50e+03 5.88e-02 1.04e+02 pdb=" CG PHE A 162 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " -0.054 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " -0.088 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " 0.018 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " 0.017 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " -0.052 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " -0.014 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " 0.077 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " -0.008 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " -0.078 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " 0.115 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.36: 1314 2.36 - 2.92: 8268 2.92 - 3.48: 10480 3.48 - 4.04: 15127 4.04 - 4.60: 21440 Nonbonded interactions: 56629 Sorted by model distance: nonbonded pdb=" HG SER A 47 " pdb="HH11 ARG A 48 " model vdw 1.794 2.100 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.836 2.100 nonbonded pdb=" HG2 LYS A 12 " pdb=" HZ2 LYS A 12 " model vdw 1.838 2.270 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.842 2.100 nonbonded pdb=" H ALA A 104 " pdb=" O ALEU A 153 " model vdw 1.846 2.450 ... (remaining 56624 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_2731660_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= 0.3620 r_free= 0.1991 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.463002 | | target function (ml) not normalized (work): 22002.600110 | | target function (ml) not normalized (free): 1147.732197 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3798 0.2202 4.8445 4.9205| | 2: 3.78 - 3.00 1.00 2430 110 0.3404 0.1634 4.0705 4.082| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 48.81 0.83 0.13 6601.36| | 2: 3.78 - 3.00 2430 110 0.94 11.22 1.48 0.26 444.57| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 380.04 max = 12073.79 mean = 3566.67| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 89.98 mean = 30.28| |phase err.(test): min = 0.00 max = 90.00 mean = 32.97| |-----------------------------------------------------------------------------| ----------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 : 0.082 0.238 1557 Z= 5.523 Angle : 5.295 17.793 2118 Z= 3.754 Chirality : 0.405 1.077 243 Planarity : 0.033 0.101 284 Dihedral : 13.758 87.555 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.86 % Allowed : 1.86 % Favored : 96.27 % Cbeta Deviations : 38.92 % 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: -2.42 (0.47), residues: 224 helix: -2.39 (0.38), residues: 109 sheet: -0.53 (0.97), residues: 28 loop : -0.54 (0.57), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.142 0.025 ARG A 5 TYR 0.109 0.052 TYR A 141 PHE 0.088 0.033 PHE A 119 HIS 0.058 0.025 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= 0.3620 r_free= 0.1991 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.463002 | | target function (ml) not normalized (work): 22002.600110 | | target function (ml) not normalized (free): 1147.732197 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3574 0.3653 0.2106 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3574 0.3653 0.2106 n_refl.: 5182 remove outliers: r(all,work,free)=0.2528 0.2554 0.2106 n_refl.: 5178 overall B=-2.96 to atoms: r(all,work,free)=0.2414 0.2437 0.2061 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1565 0.1564 0.1596 n_refl.: 5178 remove outliers: r(all,work,free)=0.1561 0.1559 0.1596 n_refl.: 5176 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 98.94 88 5 0.3878 450.025 408.489 0.663 1.065 0.398 11.894-9.307 99.02 97 4 0.1807 714.900 697.143 0.949 1.061 0.383 9.237-7.194 100.00 213 7 0.2181 584.646 577.935 0.986 1.054 0.359 7.162-5.571 100.00 427 22 0.2358 438.706 424.287 0.938 1.043 0.304 5.546-4.326 100.00 867 58 0.1367 602.281 595.163 0.984 1.023 0.226 4.315-3.360 100.00 1859 96 0.1299 572.776 566.034 1.053 0.991 0.190 3.356-3.002 100.00 1373 60 0.1624 441.176 433.755 1.069 0.959 0.065 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9556 b_overall=-3.7850 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1559 r_free=0.1596 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 r_work=0.1563 r_free=0.1605 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 18.719159 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.915102 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 0.1159 0.1792 0.0633 0.009 1.0 2.9 0.5 0.0 0 9.360 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.59 17.92 6.33 3.013 15.900 1.915 0.018 10.19 17.81 7.62 4.973 16.110 1.915 0.014 Individual atomic B min max mean iso aniso Overall: 2.03 111.34 17.33 5.35 1785 0 Protein: 2.03 110.86 14.61 5.34 1519 0 Water: 3.91 111.34 33.09 N/A 258 0 Other: 17.39 35.79 23.82 N/A 8 0 Chain A: 2.03 111.34 17.33 N/A 1785 0 Histogram: Values Number of atoms 2.03 - 12.96 912 12.96 - 23.89 483 23.89 - 34.82 189 34.82 - 45.75 112 45.75 - 56.68 56 56.68 - 67.61 16 67.61 - 78.55 8 78.55 - 89.48 5 89.48 - 100.41 1 100.41 - 111.34 3 =========================== Idealize ADP of riding H ========================== r_work=0.1019 r_free=0.1781 r_work=0.1013 r_free=0.1786 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1013 r_free = 0.1786 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1006 r_free = 0.1791 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.1006 r_free= 0.1791 coordinate error (max.-lik. estimate): 0.33 A | | | | normalized target function (ls_wunit_k1) (work): 0.013861 | | target function (ls_wunit_k1) not normalized (work): 68.249705 | | target function (ls_wunit_k1) not normalized (free): 10.789554 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1046 0.1006 0.1791 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2084 0.2082 0.2230 n_refl.: 5176 remove outliers: r(all,work,free)=0.2084 0.2082 0.2230 n_refl.: 5176 overall B=-0.99 to atoms: r(all,work,free)=0.2043 0.2039 0.2219 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.1047 0.1008 0.1786 n_refl.: 5176 remove outliers: r(all,work,free)=0.1047 0.1008 0.1786 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 0.3339 331.363 314.564 0.678 1.012 0.383 11.894-9.307 99.02 97 4 0.1506 526.397 518.234 0.988 1.013 0.352 9.237-7.194 100.00 213 7 0.1679 430.488 430.715 1.020 1.012 0.315 7.162-5.571 100.00 427 22 0.1619 323.029 318.936 0.981 1.009 0.292 5.546-4.326 100.00 867 58 0.0899 443.473 440.389 0.996 1.005 0.201 4.315-3.360 100.00 1859 96 0.0762 421.748 421.487 1.043 0.998 0.192 3.356-3.002 100.00 1373 60 0.0997 324.848 323.568 1.023 0.991 0.062 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-3.5392 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1008 r_free=0.1786 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1008 r_free=0.1786 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1008 r_free=0.1786 | n_water=258 | time (s): 0.480 (total time: 0.480) Filter (dist) r_work=0.1032 r_free=0.1780 | n_water=250 | time (s): 20.210 (total time: 20.690) Filter (q & B) r_work=0.1032 r_free=0.1779 | n_water=247 | time (s): 1.340 (total time: 22.030) Compute maps r_work=0.1032 r_free=0.1779 | n_water=247 | time (s): 0.530 (total time: 22.560) Filter (map) r_work=0.1359 r_free=0.1863 | n_water=146 | time (s): 1.500 (total time: 24.060) Find peaks r_work=0.1359 r_free=0.1863 | n_water=146 | time (s): 0.460 (total time: 24.520) Add new water r_work=0.1721 r_free=0.2129 | n_water=233 | time (s): 1.510 (total time: 26.030) Refine new water occ: r_work=0.1148 r_free=0.1678 adp: r_work=0.1125 r_free=0.1685 occ: r_work=0.1123 r_free=0.1660 adp: r_work=0.1111 r_free=0.1673 occ: r_work=0.1110 r_free=0.1658 adp: r_work=0.1110 r_free=0.1658 ADP+occupancy (water only), MIN, final r_work=0.1110 r_free=0.1658 r_work=0.1110 r_free=0.1658 | n_water=233 | time (s): 4.670 (total time: 30.700) Filter (q & B) r_work=0.1110 r_free=0.1658 | n_water=233 | time (s): 1.010 (total time: 31.710) Filter (dist only) r_work=0.1112 r_free=0.1660 | n_water=232 | time (s): 16.780 (total time: 48.490) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.550909 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.740046 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 0.0998 0.1739 0.0741 0.009 1.0 3.8 0.5 0.6 0 11.275 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.98 17.39 7.41 4.690 16.620 2.740 0.014 9.32 17.72 8.40 5.305 16.977 2.740 0.012 Individual atomic B min max mean iso aniso Overall: 0.00 108.66 16.34 6.32 1759 0 Protein: 0.00 108.66 14.75 6.31 1519 0 Water: 0.00 63.24 26.51 N/A 232 0 Other: 11.41 35.47 22.76 N/A 8 0 Chain A: 0.00 108.66 15.62 N/A 1673 0 Chain S: 2.72 55.00 30.23 N/A 86 0 Histogram: Values Number of atoms 0.00 - 10.87 726 10.87 - 21.73 629 21.73 - 32.60 221 32.60 - 43.46 108 43.46 - 54.33 43 54.33 - 65.20 20 65.20 - 76.06 6 76.06 - 86.93 3 86.93 - 97.79 1 97.79 - 108.66 2 =========================== Idealize ADP of riding H ========================== r_work=0.0932 r_free=0.1772 r_work=0.0929 r_free=0.1774 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0929 r_free = 0.1774 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 = 0.0928 r_free = 0.1774 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.0928 r_free= 0.1774 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ls_wunit_k1) (work): 0.011869 | | target function (ls_wunit_k1) not normalized (work): 58.443047 | | target function (ls_wunit_k1) not normalized (free): 9.678727 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0970 0.0928 0.1774 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2095 0.2100 0.2142 n_refl.: 5176 remove outliers: r(all,work,free)=0.2095 0.2100 0.2142 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2095 0.2100 0.2142 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0972 0.0930 0.1773 n_refl.: 5176 remove outliers: r(all,work,free)=0.0968 0.0925 0.1773 n_refl.: 5174 ======================== 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 94.79 86 5 0.3138 330.758 312.767 0.648 1.012 0.360 11.894-9.307 99.02 97 4 0.1494 526.397 522.068 0.982 1.014 0.340 9.237-7.194 100.00 213 7 0.1475 430.488 432.656 1.023 1.014 0.304 7.162-5.571 100.00 427 22 0.1401 323.029 320.677 0.995 1.011 0.290 5.546-4.326 100.00 867 58 0.0785 443.473 441.009 1.006 1.007 0.220 4.315-3.360 100.00 1859 96 0.0713 421.748 421.621 1.056 0.999 0.202 3.356-3.002 100.00 1373 60 0.0952 324.848 324.333 1.039 0.991 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9557 b_overall=-4.2219 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0925 r_free=0.1773 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=0.0930 r_free=0.1777 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0930 r_free=0.1777 | n_water=232 | time (s): 0.690 (total time: 0.690) Filter (dist) r_work=0.0946 r_free=0.1784 | n_water=228 | time (s): 17.700 (total time: 18.390) Filter (q & B) r_work=0.1028 r_free=0.1771 | n_water=225 | time (s): 1.810 (total time: 20.200) Compute maps r_work=0.1028 r_free=0.1771 | n_water=225 | time (s): 0.630 (total time: 20.830) Filter (map) r_work=0.1301 r_free=0.1846 | n_water=155 | time (s): 1.760 (total time: 22.590) Find peaks r_work=0.1301 r_free=0.1846 | n_water=155 | time (s): 0.600 (total time: 23.190) Add new water r_work=0.1680 r_free=0.2271 | n_water=246 | time (s): 1.820 (total time: 25.010) Refine new water occ: r_work=0.1068 r_free=0.1747 adp: r_work=0.1059 r_free=0.1768 occ: r_work=0.1048 r_free=0.1741 adp: r_work=0.1047 r_free=0.1751 occ: r_work=0.1037 r_free=0.1725 adp: r_work=0.1036 r_free=0.1735 ADP+occupancy (water only), MIN, final r_work=0.1036 r_free=0.1735 r_work=0.1036 r_free=0.1735 | n_water=246 | time (s): 12.670 (total time: 37.680) Filter (q & B) r_work=0.1038 r_free=0.1732 | n_water=244 | time (s): 1.500 (total time: 39.180) Filter (dist only) r_work=0.1038 r_free=0.1732 | n_water=244 | time (s): 16.620 (total time: 55.800) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.070491 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.220616 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 0.0930 0.1776 0.0846 0.010 1.1 4.2 0.5 0.6 0 0.535 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.30 17.76 8.46 5.291 17.585 0.221 5.149 8.83 18.00 9.17 7.164 17.620 0.221 5.049 Individual atomic B min max mean iso aniso Overall: 0.00 108.72 16.39 8.84 1771 0 Protein: 0.00 108.72 14.96 8.82 1519 0 Water: 0.00 58.35 25.11 N/A 244 0 Other: 7.34 39.83 23.48 N/A 8 0 Chain A: 0.00 108.72 15.73 N/A 1657 0 Chain S: 0.00 58.35 26.06 N/A 114 0 Histogram: Values Number of atoms 0.00 - 10.87 710 10.87 - 21.74 640 21.74 - 32.61 225 32.61 - 43.49 124 43.49 - 54.36 38 54.36 - 65.23 19 65.23 - 76.10 8 76.10 - 86.97 2 86.97 - 97.84 4 97.84 - 108.72 1 =========================== Idealize ADP of riding H ========================== r_work=0.0883 r_free=0.1800 r_work=0.0888 r_free=0.1808 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0888 r_free = 0.1808 target_work(ml) = 5.054 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0876 r_free = 0.1795 target_work(ml) = 5.045 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0876 r_free= 0.1795 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ml) (work): 5.045466 | | target function (ml) not normalized (work): 24833.781654 | | target function (ml) not normalized (free): 1818.557916 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0922 0.0876 0.1795 n_refl.: 5174 re-set all scales: r(all,work,free)=0.1982 0.1984 0.2092 n_refl.: 5174 remove outliers: r(all,work,free)=0.1982 0.1984 0.2092 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.1982 0.1984 0.2092 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0915 0.0869 0.1779 n_refl.: 5174 remove outliers: r(all,work,free)=0.0915 0.0869 0.1779 n_refl.: 5174 ======================== 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 94.79 86 5 0.3617 330.758 302.667 0.590 0.990 0.324 11.894-9.307 99.02 97 4 0.1836 526.397 516.164 0.957 0.994 0.320 9.237-7.194 100.00 213 7 0.1885 430.488 426.336 1.012 0.996 0.290 7.162-5.571 100.00 427 22 0.1790 323.029 313.749 0.983 0.998 0.290 5.546-4.326 100.00 867 58 0.0887 443.473 438.200 0.996 1.000 0.220 4.315-3.360 100.00 1859 96 0.0579 421.748 421.208 1.050 1.003 0.210 3.356-3.002 100.00 1373 60 0.0585 324.848 324.502 1.028 1.005 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-6.2232 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0869 r_free=0.1779 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=0.0871 r_free=0.1775 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0871 r_free=0.1775 | n_water=244 | time (s): 0.510 (total time: 0.510) Filter (dist) r_work=0.0882 r_free=0.1782 | n_water=241 | time (s): 19.520 (total time: 20.030) Filter (q & B) r_work=0.0964 r_free=0.1816 | n_water=238 | time (s): 1.340 (total time: 21.370) Compute maps r_work=0.0964 r_free=0.1816 | n_water=238 | time (s): 0.520 (total time: 21.890) Filter (map) r_work=0.1244 r_free=0.1884 | n_water=165 | time (s): 1.440 (total time: 23.330) Find peaks r_work=0.1244 r_free=0.1884 | n_water=165 | time (s): 0.540 (total time: 23.870) Add new water r_work=0.1560 r_free=0.2144 | n_water=246 | time (s): 1.840 (total time: 25.710) Refine new water occ: r_work=0.0983 r_free=0.1764 adp: r_work=0.0976 r_free=0.1775 occ: r_work=0.0968 r_free=0.1751 adp: r_work=0.0967 r_free=0.1764 occ: r_work=0.0960 r_free=0.1744 adp: r_work=0.0958 r_free=0.1756 ADP+occupancy (water only), MIN, final r_work=0.0958 r_free=0.1756 r_work=0.0958 r_free=0.1756 | n_water=246 | time (s): 10.800 (total time: 36.510) Filter (q & B) r_work=0.0958 r_free=0.1756 | n_water=244 | time (s): 1.230 (total time: 37.740) Filter (dist only) r_work=0.0981 r_free=0.1736 | n_water=241 | time (s): 18.380 (total time: 56.120) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.006768 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.225906 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 0.0897 0.1808 0.0911 0.011 1.1 4.8 0.5 0.0 0 0.503 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 8.97 18.08 9.11 6.889 17.805 0.226 5.023 8.69 18.37 9.68 8.139 17.925 0.226 4.948 Individual atomic B min max mean iso aniso Overall: 0.00 108.47 16.67 10.57 1768 0 Protein: 0.00 108.47 15.38 10.56 1519 0 Water: 0.00 63.97 24.50 N/A 241 0 Other: 11.51 41.74 23.80 N/A 8 0 Chain A: 0.00 108.47 16.02 N/A 1645 0 Chain S: 0.00 63.97 25.30 N/A 123 0 Histogram: Values Number of atoms 0.00 - 10.85 672 10.85 - 21.69 647 21.69 - 32.54 255 32.54 - 43.39 115 43.39 - 54.23 45 54.23 - 65.08 16 65.08 - 75.93 8 75.93 - 86.77 5 86.77 - 97.62 4 97.62 - 108.47 1 =========================== Idealize ADP of riding H ========================== r_work=0.0869 r_free=0.1837 r_work=0.0872 r_free=0.1843 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0872 r_free = 0.1843 target_work(ml) = 4.955 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0865 r_free = 0.1836 target_work(ml) = 4.947 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0865 r_free= 0.1836 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ml) (work): 4.947180 | | target function (ml) not normalized (work): 24350.020704 | | target function (ml) not normalized (free): 2121.889021 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0914 0.0865 0.1836 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2046 0.2043 0.2213 n_refl.: 5174 remove outliers: r(all,work,free)=0.2046 0.2043 0.2213 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2046 0.2043 0.2213 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0914 0.0864 0.1843 n_refl.: 5174 remove outliers: r(all,work,free)=0.0914 0.0864 0.1843 n_refl.: 5174 ======================== 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 94.79 86 5 0.3823 330.758 294.686 0.587 0.986 0.328 11.894-9.307 99.02 97 4 0.1905 526.397 516.680 0.962 0.992 0.327 9.237-7.194 100.00 213 7 0.2127 430.488 422.639 1.011 0.995 0.295 7.162-5.571 100.00 427 22 0.2053 323.029 311.976 0.987 0.997 0.290 5.546-4.326 100.00 867 58 0.0951 443.473 437.529 1.010 0.999 0.220 4.315-3.360 100.00 1859 96 0.0536 421.748 421.404 1.073 1.002 0.210 3.356-3.002 100.00 1373 60 0.0432 324.848 324.221 1.052 1.005 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.2221 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0864 r_free=0.1843 After: r_work=0.0867 r_free=0.1841 ================================== NQH flips ================================== r_work=0.0867 r_free=0.1841 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=0.0868 r_free=0.1844 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0868 r_free=0.1844 | n_water=241 | time (s): 0.510 (total time: 0.510) Filter (dist) r_work=0.0882 r_free=0.1862 | n_water=238 | time (s): 18.350 (total time: 18.860) Filter (q & B) r_work=0.0966 r_free=0.1830 | n_water=236 | time (s): 1.440 (total time: 20.300) Compute maps r_work=0.0966 r_free=0.1830 | n_water=236 | time (s): 0.470 (total time: 20.770) Filter (map) r_work=0.1223 r_free=0.1938 | n_water=171 | time (s): 1.630 (total time: 22.400) Find peaks r_work=0.1223 r_free=0.1938 | n_water=171 | time (s): 0.400 (total time: 22.800) Add new water r_work=0.1510 r_free=0.2164 | n_water=240 | time (s): 1.160 (total time: 23.960) Refine new water occ: r_work=0.0980 r_free=0.1840 adp: r_work=0.0972 r_free=0.1857 occ: r_work=0.0967 r_free=0.1843 adp: r_work=0.0966 r_free=0.1849 occ: r_work=0.0961 r_free=0.1837 adp: r_work=0.0959 r_free=0.1843 ADP+occupancy (water only), MIN, final r_work=0.0959 r_free=0.1843 r_work=0.0959 r_free=0.1843 | n_water=240 | time (s): 8.390 (total time: 32.350) Filter (q & B) r_work=0.0960 r_free=0.1844 | n_water=239 | time (s): 1.770 (total time: 34.120) Filter (dist only) r_work=0.0960 r_free=0.1844 | n_water=239 | time (s): 16.410 (total time: 50.530) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.917332 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.234960 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 0.0906 0.1864 0.0958 0.010 1.1 5.1 0.5 0.0 0 0.459 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.06 18.64 9.58 8.042 18.207 0.235 4.994 8.86 18.68 9.82 9.129 18.346 0.235 4.932 Individual atomic B min max mean iso aniso Overall: 0.00 109.91 17.00 12.12 1766 0 Protein: 0.00 109.91 15.87 12.11 1519 0 Water: 0.00 61.01 23.95 N/A 239 0 Other: 10.32 36.74 23.51 N/A 8 0 Chain A: 0.00 109.91 16.42 N/A 1641 0 Chain S: 0.00 61.01 24.61 N/A 125 0 Histogram: Values Number of atoms 0.00 - 10.99 682 10.99 - 21.98 629 21.98 - 32.97 257 32.97 - 43.97 120 43.97 - 54.96 41 54.96 - 65.95 18 65.95 - 76.94 9 76.94 - 87.93 5 87.93 - 98.92 3 98.92 - 109.91 2 =========================== Idealize ADP of riding H ========================== r_work=0.0886 r_free=0.1868 r_work=0.0889 r_free=0.1869 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0889 r_free = 0.1869 target_work(ml) = 4.938 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0882 r_free = 0.1866 target_work(ml) = 4.932 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0882 r_free= 0.1866 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ml) (work): 4.932330 | | target function (ml) not normalized (work): 24276.926441 | | target function (ml) not normalized (free): 2267.897115 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.79 1.00 2492 142 0.1275 0.1865 5.5377 6.2794| | 2: 3.78 - 3.00 1.00 2430 110 0.0403 0.1867 4.3115 12.511| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2492 142 0.91 12.50 1.00 0.98 13946.98| | 2: 3.78 - 3.00 2430 110 0.99 1.72 1.00 1.00 845.72| |alpha: min = 0.96 max = 1.00 mean = 0.99| |beta: min = 535.97 max = 23705.10 mean = 7478.86| |figures of merit: min = 0.00 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.73 mean = 7.18| |phase err.(test): min = 0.00 max = 79.59 mean = 7.22| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0932 0.0882 0.1866 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2087 0.2082 0.2255 n_refl.: 5174 remove outliers: r(all,work,free)=0.2087 0.2082 0.2255 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2087 0.2082 0.2255 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0930 0.0880 0.1865 n_refl.: 5174 remove outliers: r(all,work,free)=0.0930 0.0880 0.1865 n_refl.: 5174 ======================== 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 94.79 86 5 0.4005 330.758 298.411 0.600 0.983 0.324 11.894-9.307 99.02 97 4 0.1920 526.397 513.741 0.972 0.991 0.320 9.237-7.194 100.00 213 7 0.2250 430.488 418.341 1.005 0.995 0.304 7.162-5.571 100.00 427 22 0.2065 323.029 312.652 0.982 0.997 0.280 5.546-4.326 100.00 867 58 0.1015 443.473 437.312 1.021 0.999 0.220 4.315-3.360 100.00 1859 96 0.0545 421.748 421.204 1.092 1.002 0.210 3.356-3.002 100.00 1373 60 0.0391 324.848 324.689 1.073 1.005 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-8.0559 ================= 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 : 0.3620 0.1991 0.082 5.295 8.8 119.3 19.9 258 0.000 1_bss: 0.1559 0.1596 0.082 5.295 5.9 116.3 16.9 258 0.000 1_settarget: 0.1559 0.1596 0.082 5.295 5.9 116.3 16.9 258 0.000 1_nqh: 0.1563 0.1605 0.082 5.295 5.9 116.3 16.9 258 0.003 1_weight: 0.1563 0.1605 0.082 5.295 5.9 116.3 16.9 258 0.003 1_xyzrec: 0.1159 0.1792 0.009 0.966 5.9 116.3 16.9 258 0.212 1_adp: 0.1019 0.1781 0.009 0.966 2.0 111.3 17.3 258 0.212 1_regHadp: 0.1013 0.1786 0.009 0.966 2.0 111.3 17.3 258 0.212 1_occ: 0.1006 0.1791 0.009 0.966 2.0 111.3 17.3 258 0.212 2_bss: 0.1008 0.1786 0.009 0.966 1.0 110.4 16.3 258 0.212 2_settarget: 0.1008 0.1786 0.009 0.966 1.0 110.4 16.3 258 0.212 2_updatecdl: 0.1008 0.1786 0.009 0.986 1.0 110.4 16.3 258 0.212 2_nqh: 0.1008 0.1786 0.009 0.986 1.0 110.4 16.3 258 0.212 2_sol: 0.1112 0.1660 0.009 0.986 1.0 109.9 15.7 232 n/a 2_weight: 0.1112 0.1660 0.009 0.986 1.0 109.9 15.7 232 n/a 2_xyzrec: 0.0998 0.1739 0.009 0.967 1.0 109.9 15.7 232 n/a 2_adp: 0.0932 0.1772 0.009 0.967 0.0 108.7 16.3 232 n/a 2_regHadp: 0.0929 0.1774 0.009 0.967 0.0 108.7 16.3 232 n/a 2_occ: 0.0928 0.1774 0.009 0.967 0.0 108.7 16.3 232 n/a 3_bss: 0.0925 0.1773 0.009 0.967 0.0 108.7 16.3 232 n/a 3_settarget: 0.0925 0.1773 0.009 0.967 0.0 108.7 16.3 232 n/a 3_updatecdl: 0.0925 0.1773 0.009 0.976 0.0 108.7 16.3 232 n/a 3_nqh: 0.0930 0.1777 0.009 0.976 0.0 108.7 16.3 232 n/a 3_sol: 0.1038 0.1732 0.009 0.976 0.0 108.7 16.3 244 n/a 3_weight: 0.1038 0.1732 0.009 0.976 0.0 108.7 16.3 244 n/a 3_xyzrec: 0.0930 0.1776 0.010 1.065 0.0 108.7 16.3 244 n/a 3_adp: 0.0883 0.1800 0.010 1.065 0.0 108.7 16.4 244 n/a 3_regHadp: 0.0888 0.1808 0.010 1.065 0.0 108.7 16.4 244 n/a 3_occ: 0.0876 0.1795 0.010 1.065 0.0 108.7 16.4 244 n/a 4_bss: 0.0869 0.1779 0.010 1.065 0.0 108.7 16.4 244 n/a 4_settarget: 0.0869 0.1779 0.010 1.065 0.0 108.7 16.4 244 n/a 4_updatecdl: 0.0869 0.1779 0.010 1.082 0.0 108.7 16.4 244 n/a 4_nqh: 0.0871 0.1775 0.010 1.082 0.0 108.7 16.4 244 n/a 4_sol: 0.0981 0.1736 0.010 1.082 0.0 108.7 16.4 241 n/a 4_weight: 0.0981 0.1736 0.010 1.082 0.0 108.7 16.4 241 n/a 4_xyzrec: 0.0897 0.1808 0.011 1.068 0.0 108.7 16.4 241 n/a 4_adp: 0.0869 0.1837 0.011 1.068 0.0 108.5 16.7 241 n/a 4_regHadp: 0.0872 0.1843 0.011 1.068 0.0 108.5 16.7 241 n/a 4_occ: 0.0865 0.1836 0.011 1.068 0.0 108.5 16.7 241 n/a 5_bss: 0.0864 0.1843 0.011 1.068 0.0 108.5 16.7 241 n/a 5_settarget: 0.0864 0.1843 0.011 1.068 0.0 108.5 16.7 241 n/a 5_updatecdl: 0.0864 0.1843 0.011 1.068 0.0 108.5 16.7 241 n/a 5_setrh: 0.0867 0.1841 0.011 1.068 0.0 108.5 16.7 241 n/a 5_nqh: 0.0868 0.1844 0.011 1.068 0.0 108.5 16.7 241 n/a 5_sol: 0.0960 0.1844 0.011 1.068 0.0 108.5 16.7 239 n/a 5_weight: 0.0960 0.1844 0.011 1.068 0.0 108.5 16.7 239 n/a 5_xyzrec: 0.0906 0.1864 0.010 1.125 0.0 108.5 16.7 239 n/a 5_adp: 0.0886 0.1868 0.010 1.125 0.0 109.9 17.0 239 n/a 5_regHadp: 0.0889 0.1869 0.010 1.125 0.0 109.9 17.0 239 n/a 5_occ: 0.0882 0.1866 0.010 1.125 0.0 109.9 17.0 239 n/a end: 0.0880 0.1865 0.010 1.125 0.0 109.9 17.0 239 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_2731660_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_2731660_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 2.8300 Refinement macro-cycles (run) : 479.9600 Write final files (write_after_run_outputs) : 10.9600 Total : 493.7500 Total CPU time: 8.61 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:18:59 PST -0800 (1735492739.05 s) Start R-work = 0.1559, R-free = 0.1596 Final R-work = 0.0880, R-free = 0.1865 =============================================================================== Job complete usr+sys time: 524.79 seconds wall clock time: 9 minutes 7.95 seconds (547.95 seconds total)