Starting phenix.refine on Sun Dec 29 09:10:02 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8555406.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Adding command-line PHIL: ------------------------- xray_data.high_resolution=3 ordered_solvent.low_resolution=4 No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 3 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8555406.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8555406.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 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: 1.70, per 1000 atoms: 0.50 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: 0.31 Conformation dependent library (CDL) restraints added in 106.9 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.62 - 0.90: 449 0.90 - 1.18: 1237 1.18 - 1.47: 788 1.47 - 1.75: 667 1.75 - 2.03: 12 Bond restraints: 3153 Sorted by residual: bond pdb=" C GLY A 136 " pdb=" N GLY A 137 " ideal model delta sigma weight residual 1.329 1.512 -0.183 1.00e-02 1.00e+04 3.34e+02 bond pdb=" CG HIS A 115 " pdb=" ND1 HIS A 115 " ideal model delta sigma weight residual 1.378 1.186 0.192 1.10e-02 8.26e+03 3.04e+02 bond pdb=" C LYS A 62 " pdb=" O LYS A 62 " ideal model delta sigma weight residual 1.236 1.458 -0.222 1.29e-02 6.01e+03 2.97e+02 bond pdb=" C GLU A 143 " pdb=" N ASN A 144 " ideal model delta sigma weight residual 1.329 1.562 -0.232 1.36e-02 5.41e+03 2.92e+02 bond pdb=" CZ ARG A 5 " pdb=" NH2 ARG A 5 " ideal model delta sigma weight residual 1.330 1.551 -0.221 1.30e-02 5.92e+03 2.88e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.39: 3122 4.39 - 8.78: 1743 8.78 - 13.17: 714 13.17 - 17.56: 173 17.56 - 21.95: 25 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O VAL A 50 " pdb=" C VAL A 50 " pdb=" N VAL A 51 " ideal model delta sigma weight residual 122.67 137.65 -14.98 1.09e+00 8.42e-01 1.89e+02 angle pdb=" CA ASN A 144 " pdb=" C ASN A 144 " pdb=" O ASN A 144 " ideal model delta sigma weight residual 121.47 136.75 -15.28 1.15e+00 7.56e-01 1.76e+02 angle pdb=" CA ASP A 42 " pdb=" C ASP A 42 " pdb=" O ASP A 42 " ideal model delta sigma weight residual 120.96 134.69 -13.73 1.09e+00 8.42e-01 1.59e+02 angle pdb=" CA VAL A 44 " pdb=" C VAL A 44 " pdb=" O VAL A 44 " ideal model delta sigma weight residual 120.39 133.57 -13.18 1.05e+00 9.07e-01 1.58e+02 angle pdb=" O ALYS A 132 " pdb=" C ALYS A 132 " pdb=" N MET A 133 " ideal model delta sigma weight residual 122.12 109.26 12.86 1.06e+00 8.90e-01 1.47e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.93: 1273 15.93 - 31.86: 150 31.86 - 47.79: 35 47.79 - 63.71: 20 63.71 - 79.64: 3 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C VAL A 69 " pdb=" N VAL A 69 " pdb=" CA VAL A 69 " pdb=" CB VAL A 69 " ideal model delta harmonic sigma weight residual -122.00 -140.55 18.55 0 2.50e+00 1.60e-01 5.51e+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 -141.15 18.55 0 2.50e+00 1.60e-01 5.51e+01 dihedral pdb=" N ASN A 144 " pdb=" C ASN A 144 " pdb=" CA ASN A 144 " pdb=" CB ASN A 144 " ideal model delta harmonic sigma weight residual 122.80 104.60 18.20 0 2.50e+00 1.60e-01 5.30e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.173: 85 0.173 - 0.345: 59 0.345 - 0.517: 53 0.517 - 0.688: 32 0.688 - 0.860: 14 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA BGLN A 80 " pdb=" N BGLN A 80 " pdb=" C BGLN A 80 " pdb=" CB BGLN A 80 " both_signs ideal model delta sigma weight residual False 2.51 1.65 0.86 2.00e-01 2.50e+01 1.85e+01 chirality pdb=" CB ILE A 105 " pdb=" CA ILE A 105 " pdb=" CG1 ILE A 105 " pdb=" CG2 ILE A 105 " both_signs ideal model delta sigma weight residual False 2.64 1.79 0.86 2.00e-01 2.50e+01 1.85e+01 chirality pdb=" CA PHE A 164 " pdb=" N PHE A 164 " pdb=" C PHE A 164 " pdb=" CB PHE A 164 " both_signs ideal model delta sigma weight residual False 2.51 3.36 -0.84 2.00e-01 2.50e+01 1.78e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.074 2.00e-02 2.50e+03 7.08e-02 1.50e+02 pdb=" CG PHE A 164 " 0.171 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.090 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.045 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.007 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.092 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.036 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.013 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.044 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " -0.043 2.00e-02 2.50e+03 6.56e-02 1.29e+02 pdb=" CG BTYR A 67 " -0.058 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " 0.113 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " -0.024 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " 0.111 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " -0.046 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " 0.043 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " -0.034 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " -0.005 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " 0.051 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " -0.114 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " 0.043 2.00e-02 2.50e+03 6.28e-02 1.18e+02 pdb=" CG TYR A 141 " 0.089 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " -0.034 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " -0.083 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " -0.068 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " 0.089 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " 0.067 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " -0.070 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " 0.030 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " 0.036 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " -0.065 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.28: 783 2.28 - 2.86: 7873 2.86 - 3.44: 10542 3.44 - 4.02: 15323 4.02 - 4.60: 22055 Nonbonded interactions: 56576 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.698 2.100 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.750 2.100 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.776 2.100 nonbonded pdb="HH22 ARG A 5 " pdb=" O AGLU A 64 " model vdw 1.794 2.450 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.798 2.450 ... (remaining 56571 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 6 Type Number sf(0) Gaussians S 10 15.96 2 O1- 2 8.97 2 O 551 7.97 1 N 265 6.97 1 C 957 5.97 2 H 1596 1.00 1 sf(0) = scattering factor at diffraction angle 0. =========================== Regularize ADP if needed ========================== ========================== Anomalous scatterer groups ========================= All atoms refined with f_prime=0 and f_double_prime=0. ====================== Modifying start model if requested ===================== ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 3381 n_use_u_iso = 1596 n_use_u_aniso = 1785 n_grad_site = 0 n_grad_u_iso = 0 n_grad_u_aniso = 0 n_grad_occupancy = 0 n_grad_fp = 0 n_grad_fdp = 0 total number of scatterers = 3381 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (3381 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 1596 aniso = 1785) group_adp = False (0 atoms in 0 groups) tls = False (0 atoms in 0 groups) occupancies = True (876 atoms) group_anomalous = False ============================ Non-default parameters =========================== A complete record of all parameters was written to the .eff file above. Below are only the non-defaults. #phil __ON__ refinement { electron_density_maps { map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT" mtz_label_phases = "PH2FOFCWT" fill_missing_f_obs = True } map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT_no_fill" mtz_label_phases = "PH2FOFCWT_no_fill" } map_coefficients { map_type = "mFo-DFc" mtz_label_amplitudes = "FOFCWT" mtz_label_phases = "PHFOFCWT" } map_coefficients { map_type = "anomalous" mtz_label_amplitudes = "ANOM" mtz_label_phases = "PANOM" } map { map_type = "2mFo-DFc" fill_missing_f_obs = True } map { map_type = "2mFo-DFc" } map { map_type = "mFo-DFc" } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } hydrogens { refine = individual *riding Auto } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } output { prefix = "shake_8555406_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= 0.3617 r_free= 0.2075 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.460600 | | target function (ml) not normalized (work): 21990.758374 | | target function (ml) not normalized (free): 1155.735519 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3794 0.2242 4.8538 4.9229| | 2: 3.78 - 3.00 1.00 2430 110 0.3402 0.1791 4.056 4.1516| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 48.76 0.83 0.13 6604.77| | 2: 3.78 - 3.00 2430 110 0.94 11.09 1.48 0.26 434.32| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 365.21 max = 12075.38 mean = 3563.35| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 89.99 mean = 30.20| |phase err.(test): min = 0.00 max = 89.99 mean = 33.22| |-----------------------------------------------------------------------------| ----------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 0.232 1557 Z= 5.531 Angle : 5.263 16.495 2118 Z= 3.759 Chirality : 0.374 0.860 243 Planarity : 0.033 0.105 284 Dihedral : 13.785 79.642 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % 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: -2.11 (0.48), residues: 224 helix: -2.32 (0.40), residues: 103 sheet: -0.82 (0.75), residues: 28 loop : -0.13 (0.58), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.067 0.014 ARG A 48 TYR 0.090 0.055 TYR A 141 PHE 0.147 0.050 PHE A 164 HIS 0.077 0.033 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= 0.3617 r_free= 0.2075 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.460600 | | target function (ml) not normalized (work): 21990.758374 | | target function (ml) not normalized (free): 1155.735519 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3574 0.3650 0.2162 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3574 0.3650 0.2162 n_refl.: 5182 remove outliers: r(all,work,free)=0.2524 0.2546 0.2162 n_refl.: 5178 overall B=-2.47 to atoms: r(all,work,free)=0.2427 0.2446 0.2127 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1546 0.1542 0.1640 n_refl.: 5178 remove outliers: r(all,work,free)=0.1542 0.1537 0.1640 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 0.3890 449.719 407.975 0.626 1.076 0.398 11.894-9.307 99.02 97 4 0.1843 714.415 692.648 0.900 1.073 0.382 9.237-7.194 100.00 213 7 0.2170 584.250 576.028 0.931 1.065 0.374 7.162-5.571 100.00 427 22 0.2302 438.409 424.040 0.898 1.051 0.300 5.546-4.326 100.00 867 58 0.1393 601.873 593.994 0.943 1.028 0.236 4.315-3.360 100.00 1859 96 0.1276 572.388 566.752 1.027 0.989 0.205 3.356-3.002 100.00 1373 60 0.1564 440.877 434.184 1.046 0.950 0.064 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9173 b_overall=-4.2807 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1537 r_free=0.1640 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1537 r_free=0.1640 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 19.347133 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.815850 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 0.1158 0.1751 0.0593 0.010 1.0 3.5 0.5 0.0 0 9.674 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.58 17.51 5.93 3.013 16.391 1.816 0.018 10.16 17.53 7.37 4.954 16.624 1.816 0.014 Individual atomic B min max mean iso aniso Overall: 2.61 111.83 17.86 5.32 1785 0 Protein: 2.61 111.64 15.17 5.31 1519 0 Water: 4.40 111.83 33.52 N/A 258 0 Other: 16.79 36.68 24.03 N/A 8 0 Chain A: 2.61 111.83 17.86 N/A 1785 0 Histogram: Values Number of atoms 2.61 - 13.53 908 13.53 - 24.46 490 24.46 - 35.38 191 35.38 - 46.30 105 46.30 - 57.22 57 57.22 - 68.14 17 68.14 - 79.07 8 79.07 - 89.99 5 89.99 - 100.91 1 100.91 - 111.83 3 =========================== Idealize ADP of riding H ========================== r_work=0.1016 r_free=0.1753 r_work=0.1010 r_free=0.1759 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1010 r_free = 0.1759 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 = 0.1009 r_free = 0.1760 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.19 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= 0.1009 r_free= 0.1760 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ls_wunit_k1) (work): 0.013942 | | target function (ls_wunit_k1) not normalized (work): 68.650896 | | target function (ls_wunit_k1) not normalized (free): 10.298454 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1047 0.1009 0.1760 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2111 0.2112 0.2214 n_refl.: 5176 remove outliers: r(all,work,free)=0.2111 0.2112 0.2214 n_refl.: 5176 overall B=-1.07 to atoms: r(all,work,free)=0.2065 0.2064 0.2201 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.1055 0.1017 0.1768 n_refl.: 5176 remove outliers: r(all,work,free)=0.1055 0.1017 0.1768 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 0.3265 317.961 310.061 0.707 0.999 0.381 11.894-9.307 99.02 97 4 0.1538 505.107 496.637 0.994 1.002 0.361 9.237-7.194 100.00 213 7 0.1750 413.077 412.529 1.036 1.002 0.315 7.162-5.571 100.00 427 22 0.1605 309.964 306.594 0.985 1.002 0.292 5.546-4.326 100.00 867 58 0.0914 425.537 422.378 1.000 1.001 0.212 4.315-3.360 100.00 1859 96 0.0769 404.690 404.541 1.050 0.999 0.194 3.356-3.002 100.00 1373 60 0.0999 311.710 309.903 1.021 0.998 0.051 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-3.8250 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1017 r_free=0.1768 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN Total number of N/Q/H flips: 1 r_work=0.1019 r_free=0.1768 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1019 r_free=0.1768 | n_water=258 | time (s): 0.570 (total time: 0.570) Filter (dist) r_work=0.1045 r_free=0.1772 | n_water=249 | time (s): 20.630 (total time: 21.200) Filter (q & B) r_work=0.1045 r_free=0.1774 | n_water=246 | time (s): 1.840 (total time: 23.040) Compute maps r_work=0.1045 r_free=0.1774 | n_water=246 | time (s): 0.660 (total time: 23.700) Filter (map) r_work=0.1363 r_free=0.1807 | n_water=141 | time (s): 1.670 (total time: 25.370) Find peaks r_work=0.1363 r_free=0.1807 | n_water=141 | time (s): 0.550 (total time: 25.920) Add new water r_work=0.1730 r_free=0.2100 | n_water=234 | time (s): 1.870 (total time: 27.790) Refine new water occ: r_work=0.1158 r_free=0.1700 adp: r_work=0.1131 r_free=0.1698 occ: r_work=0.1128 r_free=0.1676 adp: r_work=0.1115 r_free=0.1681 occ: r_work=0.1116 r_free=0.1673 adp: r_work=0.1113 r_free=0.1670 ADP+occupancy (water only), MIN, final r_work=0.1113 r_free=0.1670 r_work=0.1113 r_free=0.1670 | n_water=234 | time (s): 8.390 (total time: 36.180) Filter (q & B) r_work=0.1113 r_free=0.1670 | n_water=234 | time (s): 0.890 (total time: 37.070) Filter (dist only) r_work=0.1125 r_free=0.1692 | n_water=231 | time (s): 19.630 (total time: 56.700) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.336617 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.638782 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 0.1021 0.1833 0.0812 0.009 1.0 3.8 0.5 0.6 0 11.168 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.21 18.33 8.12 4.706 17.166 2.639 0.014 9.57 18.67 9.10 5.621 17.554 2.639 0.013 Individual atomic B min max mean iso aniso Overall: 0.00 106.21 16.94 6.59 1758 0 Protein: 0.00 106.21 15.35 6.57 1519 0 Water: 0.00 63.05 27.08 N/A 231 0 Other: 13.17 40.55 25.94 N/A 8 0 Chain A: 0.00 106.21 16.10 N/A 1666 0 Chain S: 3.88 58.93 32.22 N/A 92 0 Histogram: Values Number of atoms 0.00 - 10.62 624 10.62 - 21.24 703 21.24 - 31.86 224 31.86 - 42.48 116 42.48 - 53.11 49 53.11 - 63.73 28 63.73 - 74.35 7 74.35 - 84.97 2 84.97 - 95.59 3 95.59 - 106.21 2 =========================== Idealize ADP of riding H ========================== r_work=0.0957 r_free=0.1867 r_work=0.0954 r_free=0.1869 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0954 r_free = 0.1869 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0950 r_free = 0.1865 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.0950 r_free= 0.1865 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ls_wunit_k1) (work): 0.012229 | | target function (ls_wunit_k1) not normalized (work): 60.216262 | | target function (ls_wunit_k1) not normalized (free): 10.791075 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0998 0.0950 0.1865 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2150 0.2152 0.2256 n_refl.: 5176 remove outliers: r(all,work,free)=0.2150 0.2152 0.2256 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2150 0.2152 0.2256 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.1000 0.0952 0.1868 n_refl.: 5176 remove outliers: r(all,work,free)=0.0997 0.0950 0.1868 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 0.3286 315.284 300.807 0.667 1.012 0.360 11.894-9.307 99.02 97 4 0.1477 505.107 500.173 0.992 1.013 0.360 9.237-7.194 100.00 213 7 0.1550 413.077 411.824 1.034 1.012 0.300 7.162-5.571 100.00 427 22 0.1407 309.964 308.333 0.984 1.010 0.290 5.546-4.326 100.00 867 58 0.0787 425.537 422.759 1.010 1.005 0.230 4.315-3.360 100.00 1859 96 0.0742 404.690 404.047 1.068 0.998 0.200 3.356-3.002 100.00 1373 60 0.0978 311.710 310.659 1.049 0.991 0.067 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9552 b_overall=-4.6765 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0950 r_free=0.1868 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN B Total number of N/Q/H flips: 2 r_work=0.0952 r_free=0.1871 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0952 r_free=0.1871 | n_water=231 | time (s): 0.550 (total time: 0.550) Filter (dist) r_work=0.0966 r_free=0.1871 | n_water=228 | time (s): 17.730 (total time: 18.280) Filter (q & B) r_work=0.1053 r_free=0.1855 | n_water=225 | time (s): 1.920 (total time: 20.200) Compute maps r_work=0.1053 r_free=0.1855 | n_water=225 | time (s): 0.620 (total time: 20.820) Filter (map) r_work=0.1288 r_free=0.1855 | n_water=157 | time (s): 1.620 (total time: 22.440) Find peaks r_work=0.1288 r_free=0.1855 | n_water=157 | time (s): 0.390 (total time: 22.830) Add new water r_work=0.1650 r_free=0.2123 | n_water=239 | time (s): 1.320 (total time: 24.150) Refine new water occ: r_work=0.1065 r_free=0.1781 adp: r_work=0.1057 r_free=0.1794 occ: r_work=0.1046 r_free=0.1779 adp: r_work=0.1046 r_free=0.1785 occ: r_work=0.1036 r_free=0.1769 adp: r_work=0.1036 r_free=0.1775 ADP+occupancy (water only), MIN, final r_work=0.1036 r_free=0.1775 r_work=0.1036 r_free=0.1775 | n_water=239 | time (s): 9.660 (total time: 33.810) Filter (q & B) r_work=0.1036 r_free=0.1775 | n_water=239 | time (s): 1.100 (total time: 34.910) Filter (dist only) r_work=0.1036 r_free=0.1775 | n_water=239 | time (s): 17.710 (total time: 52.620) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.147478 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.236425 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 0.0927 0.1791 0.0864 0.011 1.1 4.2 0.5 0.0 0 0.574 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.27 17.91 8.64 5.499 18.178 0.236 5.105 8.87 17.80 8.93 7.147 18.179 0.236 5.008 Individual atomic B min max mean iso aniso Overall: 0.00 106.90 16.76 8.78 1766 0 Protein: 0.00 106.90 15.46 8.76 1519 0 Water: 0.00 59.44 24.68 N/A 239 0 Other: 8.17 41.77 26.05 N/A 8 0 Chain A: 0.00 106.90 16.17 N/A 1654 0 Chain S: 0.00 59.44 25.46 N/A 112 0 Histogram: Values Number of atoms 0.00 - 10.69 645 10.69 - 21.38 682 21.38 - 32.07 239 32.07 - 42.76 116 42.76 - 53.45 46 53.45 - 64.14 20 64.14 - 74.83 11 74.83 - 85.52 2 85.52 - 96.21 3 96.21 - 106.90 2 =========================== Idealize ADP of riding H ========================== r_work=0.0887 r_free=0.1780 r_work=0.0893 r_free=0.1792 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0893 r_free = 0.1792 target_work(ml) = 5.012 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0881 r_free = 0.1776 target_work(ml) = 5.003 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0881 r_free= 0.1776 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ml) (work): 5.003067 | | target function (ml) not normalized (work): 24630.096678 | | target function (ml) not normalized (free): 1880.811988 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0928 0.0881 0.1776 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2139 0.2142 0.2206 n_refl.: 5175 remove outliers: r(all,work,free)=0.2139 0.2142 0.2206 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2139 0.2142 0.2206 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0921 0.0875 0.1759 n_refl.: 5175 remove outliers: r(all,work,free)=0.0919 0.0873 0.1759 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 0.3641 317.381 288.081 0.614 0.997 0.348 11.894-9.307 99.02 97 4 0.1791 505.107 490.323 0.949 0.999 0.340 9.237-7.194 100.00 213 7 0.1945 413.077 406.882 1.002 1.001 0.290 7.162-5.571 100.00 427 22 0.1823 309.964 302.326 0.972 1.001 0.290 5.546-4.326 100.00 867 58 0.0894 425.537 421.093 0.999 1.001 0.250 4.315-3.360 100.00 1859 96 0.0577 404.690 404.114 1.055 1.001 0.210 3.356-3.002 100.00 1373 60 0.0582 311.710 311.123 1.034 1.002 0.069 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9171 b_overall=-6.3296 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0873 r_free=0.1759 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN A A 76 ASN B Total number of N/Q/H flips: 3 r_work=0.0875 r_free=0.1763 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0875 r_free=0.1763 | n_water=239 | time (s): 0.550 (total time: 0.550) Filter (dist) r_work=0.0893 r_free=0.1782 | n_water=235 | time (s): 18.570 (total time: 19.120) Filter (q & B) r_work=0.0943 r_free=0.1810 | n_water=232 | time (s): 1.400 (total time: 20.520) Compute maps r_work=0.0943 r_free=0.1810 | n_water=232 | time (s): 0.520 (total time: 21.040) Filter (map) r_work=0.1183 r_free=0.1907 | n_water=168 | time (s): 1.650 (total time: 22.690) Find peaks r_work=0.1183 r_free=0.1907 | n_water=168 | time (s): 0.390 (total time: 23.080) Add new water r_work=0.1495 r_free=0.2184 | n_water=244 | time (s): 1.380 (total time: 24.460) Refine new water occ: r_work=0.0997 r_free=0.1795 adp: r_work=0.0994 r_free=0.1810 occ: r_work=0.0983 r_free=0.1782 adp: r_work=0.0984 r_free=0.1796 occ: r_work=0.0974 r_free=0.1772 adp: r_work=0.0974 r_free=0.1786 ADP+occupancy (water only), MIN, final r_work=0.0974 r_free=0.1786 r_work=0.0974 r_free=0.1786 | n_water=244 | time (s): 10.440 (total time: 34.900) Filter (q & B) r_work=0.0974 r_free=0.1788 | n_water=242 | time (s): 1.270 (total time: 36.170) Filter (dist only) r_work=0.0978 r_free=0.1796 | n_water=240 | time (s): 18.100 (total time: 54.270) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.006031 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.275183 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 0.0902 0.1826 0.0923 0.011 1.1 3.8 0.5 0.6 0 0.503 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.02 18.26 9.23 6.882 18.342 0.275 4.980 8.76 18.43 9.67 8.052 18.434 0.275 4.913 Individual atomic B min max mean iso aniso Overall: 0.00 107.23 17.02 10.48 1767 0 Protein: 0.00 107.23 15.86 10.46 1519 0 Water: 0.00 60.86 24.04 N/A 240 0 Other: 8.01 42.87 26.31 N/A 8 0 Chain A: 0.00 107.23 16.41 N/A 1644 0 Chain S: 0.00 56.41 25.18 N/A 123 0 Histogram: Values Number of atoms 0.00 - 10.72 652 10.72 - 21.45 654 21.45 - 32.17 254 32.17 - 42.89 117 42.89 - 53.61 55 53.61 - 64.34 16 64.34 - 75.06 11 75.06 - 85.78 3 85.78 - 96.51 3 96.51 - 107.23 2 =========================== Idealize ADP of riding H ========================== r_work=0.0876 r_free=0.1843 r_work=0.0879 r_free=0.1846 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0879 r_free = 0.1846 target_work(ml) = 4.917 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0865 r_free = 0.1824 target_work(ml) = 4.908 | | 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= 0.1824 coordinate error (max.-lik. estimate): 0.31 A | | | | normalized target function (ml) (work): 4.907602 | | target function (ml) not normalized (work): 24155.217212 | | target function (ml) not normalized (free): 2278.851088 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0914 0.0865 0.1824 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2081 0.2079 0.2228 n_refl.: 5174 remove outliers: r(all,work,free)=0.2081 0.2079 0.2228 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2081 0.2079 0.2228 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0910 0.0863 0.1810 n_refl.: 5174 remove outliers: r(all,work,free)=0.0910 0.0863 0.1810 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 0.3864 317.381 287.135 0.582 0.986 0.320 11.894-9.307 99.02 97 4 0.1966 505.107 488.570 0.955 0.991 0.310 9.237-7.194 100.00 213 7 0.2096 413.077 403.717 1.011 0.994 0.301 7.162-5.571 100.00 427 22 0.2003 309.964 300.022 0.987 0.996 0.280 5.546-4.326 100.00 867 58 0.0957 425.537 419.774 1.022 0.998 0.250 4.315-3.360 100.00 1859 96 0.0537 404.690 404.185 1.082 1.002 0.210 3.356-3.002 100.00 1373 60 0.0431 311.710 311.966 1.062 1.005 0.078 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.6723 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0863 r_free=0.1810 After: r_work=0.0865 r_free=0.1808 ================================== NQH flips ================================== r_work=0.0865 r_free=0.1808 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 135 ASN Total number of N/Q/H flips: 2 r_work=0.0877 r_free=0.1816 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0877 r_free=0.1816 | n_water=240 | time (s): 0.620 (total time: 0.620) Filter (dist) r_work=0.0894 r_free=0.1824 | n_water=235 | time (s): 19.740 (total time: 20.360) Filter (q & B) r_work=0.0981 r_free=0.1861 | n_water=232 | time (s): 1.830 (total time: 22.190) Compute maps r_work=0.0981 r_free=0.1861 | n_water=232 | time (s): 0.620 (total time: 22.810) Filter (map) r_work=0.1218 r_free=0.1978 | n_water=168 | time (s): 1.750 (total time: 24.560) Find peaks r_work=0.1218 r_free=0.1978 | n_water=168 | time (s): 0.450 (total time: 25.010) Add new water r_work=0.1476 r_free=0.2176 | n_water=231 | time (s): 1.720 (total time: 26.730) Refine new water occ: r_work=0.0984 r_free=0.1849 adp: r_work=0.0977 r_free=0.1841 occ: r_work=0.0972 r_free=0.1832 adp: r_work=0.0971 r_free=0.1832 occ: r_work=0.0966 r_free=0.1824 adp: r_work=0.0966 r_free=0.1825 ADP+occupancy (water only), MIN, final r_work=0.0966 r_free=0.1825 r_work=0.0966 r_free=0.1825 | n_water=231 | time (s): 17.290 (total time: 44.020) Filter (q & B) r_work=0.0966 r_free=0.1825 | n_water=231 | time (s): 1.020 (total time: 45.040) Filter (dist only) r_work=0.0966 r_free=0.1825 | n_water=231 | time (s): 17.610 (total time: 62.650) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.937770 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.193383 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 0.0912 0.1824 0.0912 0.010 1.1 6.7 0.5 1.2 0 0.469 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.12 18.24 9.12 8.004 18.661 0.193 4.959 8.88 18.25 9.37 8.780 18.733 0.193 4.896 Individual atomic B min max mean iso aniso Overall: 0.00 104.94 17.15 11.55 1758 0 Protein: 0.00 104.94 16.16 11.53 1519 0 Water: 0.00 57.55 23.35 N/A 231 0 Other: 8.15 44.46 26.07 N/A 8 0 Chain A: 0.00 104.94 16.63 N/A 1639 0 Chain S: 0.00 57.55 24.37 N/A 119 0 Histogram: Values Number of atoms 0.00 - 10.49 616 10.49 - 20.99 633 20.99 - 31.48 291 31.48 - 41.98 130 41.98 - 52.47 43 52.47 - 62.96 21 62.96 - 73.46 10 73.46 - 83.95 9 83.95 - 94.44 3 94.44 - 104.94 2 =========================== Idealize ADP of riding H ========================== r_work=0.0888 r_free=0.1825 r_work=0.0890 r_free=0.1828 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0890 r_free = 0.1828 target_work(ml) = 4.902 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0884 r_free = 0.1820 target_work(ml) = 4.897 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0884 r_free= 0.1820 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ml) (work): 4.897468 | | target function (ml) not normalized (work): 24105.338989 | | target function (ml) not normalized (free): 2476.733297 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1273 0.1722 5.4983 6.1859| | 2: 3.78 - 3.00 1.00 2430 110 0.0410 0.1985 4.2813 14.53| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 12.30 1.00 0.94 12580.12| | 2: 3.78 - 3.00 2430 110 0.99 1.76 1.00 0.96 778.66| |alpha: min = 0.93 max = 0.96 mean = 0.95| |beta: min = 489.67 max = 21227.04 mean = 6753.72| |figures of merit: min = 0.00 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.88 mean = 7.10| |phase err.(test): min = 0.00 max = 86.57 mean = 7.14| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0932 0.0884 0.1820 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2134 0.2134 0.2240 n_refl.: 5174 remove outliers: r(all,work,free)=0.2134 0.2134 0.2240 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2134 0.2134 0.2240 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0932 0.0885 0.1818 n_refl.: 5174 remove outliers: r(all,work,free)=0.0932 0.0885 0.1818 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 0.3839 317.381 289.758 0.614 0.985 0.320 11.894-9.307 99.02 97 4 0.1934 505.107 490.585 1.000 0.992 0.310 9.237-7.194 100.00 213 7 0.2189 413.077 403.695 1.048 0.995 0.290 7.162-5.571 100.00 427 22 0.2086 309.964 299.962 1.033 0.997 0.280 5.546-4.326 100.00 867 58 0.1040 425.537 419.665 1.068 0.999 0.239 4.315-3.360 100.00 1859 96 0.0555 404.690 404.479 1.145 1.002 0.220 3.356-3.002 100.00 1373 60 0.0385 311.710 311.673 1.124 1.004 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-8.3252 ================= 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 : 0.3617 0.2075 0.082 5.263 8.8 119.3 19.9 258 0.000 1_bss: 0.1537 0.1640 0.082 5.263 6.4 116.8 17.4 258 0.000 1_settarget: 0.1537 0.1640 0.082 5.263 6.4 116.8 17.4 258 0.000 1_nqh: 0.1537 0.1640 0.082 5.263 6.4 116.8 17.4 258 0.000 1_weight: 0.1537 0.1640 0.082 5.263 6.4 116.8 17.4 258 0.000 1_xyzrec: 0.1158 0.1751 0.010 0.972 6.4 116.8 17.4 258 0.210 1_adp: 0.1016 0.1753 0.010 0.972 2.6 111.8 17.9 258 0.210 1_regHadp: 0.1010 0.1759 0.010 0.972 2.6 111.8 17.9 258 0.210 1_occ: 0.1009 0.1760 0.010 0.972 2.6 111.8 17.9 258 0.210 2_bss: 0.1017 0.1768 0.010 0.972 1.5 110.8 16.8 258 0.210 2_settarget: 0.1017 0.1768 0.010 0.972 1.5 110.8 16.8 258 0.210 2_updatecdl: 0.1017 0.1768 0.010 1.003 1.5 110.8 16.8 258 0.210 2_nqh: 0.1019 0.1768 0.010 1.003 1.5 110.8 16.8 258 0.213 2_sol: 0.1125 0.1692 0.010 1.003 1.5 110.6 16.2 231 n/a 2_weight: 0.1125 0.1692 0.010 1.003 1.5 110.6 16.2 231 n/a 2_xyzrec: 0.1021 0.1833 0.009 0.974 1.5 110.6 16.2 231 n/a 2_adp: 0.0957 0.1867 0.009 0.974 0.0 106.2 16.9 231 n/a 2_regHadp: 0.0954 0.1869 0.009 0.974 0.0 106.2 16.9 231 n/a 2_occ: 0.0950 0.1865 0.009 0.974 0.0 106.2 16.9 231 n/a 3_bss: 0.0950 0.1868 0.009 0.974 0.0 106.2 16.9 231 n/a 3_settarget: 0.0950 0.1868 0.009 0.974 0.0 106.2 16.9 231 n/a 3_updatecdl: 0.0950 0.1868 0.009 0.977 0.0 106.2 16.9 231 n/a 3_nqh: 0.0952 0.1871 0.009 0.977 0.0 106.2 16.9 231 n/a 3_sol: 0.1036 0.1775 0.009 0.977 0.0 106.2 16.8 239 n/a 3_weight: 0.1036 0.1775 0.009 0.977 0.0 106.2 16.8 239 n/a 3_xyzrec: 0.0927 0.1791 0.011 1.079 0.0 106.2 16.8 239 n/a 3_adp: 0.0887 0.1780 0.011 1.079 0.0 106.9 16.8 239 n/a 3_regHadp: 0.0893 0.1792 0.011 1.079 0.0 106.9 16.8 239 n/a 3_occ: 0.0881 0.1776 0.011 1.079 0.0 106.9 16.8 239 n/a 4_bss: 0.0873 0.1759 0.011 1.079 0.0 106.9 16.8 239 n/a 4_settarget: 0.0873 0.1759 0.011 1.079 0.0 106.9 16.8 239 n/a 4_updatecdl: 0.0873 0.1759 0.011 1.095 0.0 106.9 16.8 239 n/a 4_nqh: 0.0875 0.1763 0.011 1.095 0.0 106.9 16.8 239 n/a 4_sol: 0.0978 0.1796 0.011 1.095 0.0 106.9 16.8 240 n/a 4_weight: 0.0978 0.1796 0.011 1.095 0.0 106.9 16.8 240 n/a 4_xyzrec: 0.0902 0.1826 0.011 1.062 0.0 106.9 16.8 240 n/a 4_adp: 0.0876 0.1843 0.011 1.062 0.0 107.2 17.0 240 n/a 4_regHadp: 0.0879 0.1846 0.011 1.062 0.0 107.2 17.0 240 n/a 4_occ: 0.0865 0.1824 0.011 1.062 0.0 107.2 17.0 240 n/a 5_bss: 0.0863 0.1810 0.011 1.062 0.0 107.2 17.0 240 n/a 5_settarget: 0.0863 0.1810 0.011 1.062 0.0 107.2 17.0 240 n/a 5_updatecdl: 0.0863 0.1810 0.011 1.067 0.0 107.2 17.0 240 n/a 5_setrh: 0.0865 0.1808 0.011 1.067 0.0 107.2 17.0 240 n/a 5_nqh: 0.0877 0.1816 0.011 1.067 0.0 107.2 17.0 240 n/a 5_sol: 0.0966 0.1825 0.011 1.067 0.0 107.2 17.0 231 n/a 5_weight: 0.0966 0.1825 0.011 1.067 0.0 107.2 17.0 231 n/a 5_xyzrec: 0.0912 0.1824 0.010 1.128 0.0 107.2 17.0 231 n/a 5_adp: 0.0888 0.1825 0.010 1.128 0.0 104.9 17.1 231 n/a 5_regHadp: 0.0890 0.1828 0.010 1.128 0.0 104.9 17.1 231 n/a 5_occ: 0.0884 0.1820 0.010 1.128 0.0 104.9 17.1 231 n/a end: 0.0885 0.1818 0.010 1.128 0.0 104.9 17.1 231 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_8555406_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_8555406_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.0400 Refinement macro-cycles (run) : 491.5700 Write final files (write_after_run_outputs) : 9.9200 Total : 504.5300 Total CPU time: 8.76 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:19:07 PST -0800 (1735492747.37 s) Start R-work = 0.1537, R-free = 0.1640 Final R-work = 0.0885, R-free = 0.1818 =============================================================================== Job complete usr+sys time: 532.46 seconds wall clock time: 9 minutes 15.33 seconds (555.33 seconds total)