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_3031784.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 { 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" 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_3031784.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3031784.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: 1.31, per 1000 atoms: 0.39 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.28 Conformation dependent library (CDL) restraints added in 124.9 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.63 - 0.89: 395 0.89 - 1.15: 1224 1.15 - 1.41: 630 1.41 - 1.67: 858 1.67 - 1.93: 46 Bond restraints: 3153 Sorted by residual: bond pdb=" N ALA A 183 " pdb=" CA ALA A 183 " ideal model delta sigma weight residual 1.462 1.608 -0.146 7.70e-03 1.69e+04 3.58e+02 bond pdb=" CG HIS A 138 " pdb=" ND1 HIS A 138 " ideal model delta sigma weight residual 1.378 1.172 0.206 1.10e-02 8.26e+03 3.52e+02 bond pdb=" C ILE A 52 " pdb=" O ILE A 52 " ideal model delta sigma weight residual 1.237 1.034 0.204 1.10e-02 8.26e+03 3.42e+02 bond pdb=" C VAL A 123 " pdb=" O VAL A 123 " ideal model delta sigma weight residual 1.233 1.040 0.193 1.08e-02 8.57e+03 3.18e+02 bond pdb=" CA ASP A 60 " pdb=" C ASP A 60 " ideal model delta sigma weight residual 1.524 1.745 -0.221 1.26e-02 6.30e+03 3.08e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.46: 3113 4.46 - 8.92: 1829 8.92 - 13.38: 687 13.38 - 17.84: 133 17.84 - 22.30: 15 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA ARG A 98 " pdb=" C ARG A 98 " pdb=" O ARG A 98 " ideal model delta sigma weight residual 119.43 137.78 -18.35 1.21e+00 6.83e-01 2.30e+02 angle pdb=" OE1AGLN A 80 " pdb=" CD AGLN A 80 " pdb=" NE2AGLN A 80 " ideal model delta sigma weight residual 122.60 136.28 -13.68 1.00e+00 1.00e+00 1.87e+02 angle pdb=" O AGLU A 90 " pdb=" C AGLU A 90 " pdb=" N ILE A 91 " ideal model delta sigma weight residual 122.07 135.83 -13.76 1.03e+00 9.43e-01 1.78e+02 angle pdb=" N VAL A 23 " pdb=" CA VAL A 23 " pdb=" CB VAL A 23 " ideal model delta sigma weight residual 110.62 124.46 -13.84 1.05e+00 9.07e-01 1.74e+02 angle pdb=" CA LEU A 92 " pdb=" C LEU A 92 " pdb=" O LEU A 92 " ideal model delta sigma weight residual 120.19 134.73 -14.54 1.15e+00 7.56e-01 1.60e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.65: 1281 16.65 - 33.30: 143 33.30 - 49.95: 36 49.95 - 66.59: 19 66.59 - 83.24: 2 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C BLYS A 99 " pdb=" N BLYS A 99 " pdb=" CA BLYS A 99 " pdb=" CB BLYS A 99 " ideal model delta harmonic sigma weight residual -122.60 -148.83 26.23 0 2.50e+00 1.60e-01 1.10e+02 dihedral pdb=" N BLYS A 99 " pdb=" C BLYS A 99 " pdb=" CA BLYS A 99 " pdb=" CB BLYS A 99 " ideal model delta harmonic sigma weight residual 122.80 146.02 -23.22 0 2.50e+00 1.60e-01 8.63e+01 dihedral pdb=" N AASN A 76 " pdb=" C AASN A 76 " pdb=" CA AASN A 76 " pdb=" CB AASN A 76 " ideal model delta harmonic sigma weight residual 122.80 100.77 22.03 0 2.50e+00 1.60e-01 7.76e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.213: 98 0.213 - 0.427: 68 0.427 - 0.640: 44 0.640 - 0.853: 27 0.853 - 1.066: 6 Chirality restraints: 243 Sorted by residual: chirality pdb=" CB THR A 110 " pdb=" CA THR A 110 " pdb=" OG1 THR A 110 " pdb=" CG2 THR A 110 " both_signs ideal model delta sigma weight residual False 2.55 1.49 1.07 2.00e-01 2.50e+01 2.84e+01 chirality pdb=" CA BLYS A 99 " pdb=" N BLYS A 99 " pdb=" C BLYS A 99 " pdb=" CB BLYS A 99 " both_signs ideal model delta sigma weight residual False 2.51 1.52 0.99 2.00e-01 2.50e+01 2.46e+01 chirality pdb=" CA ASP A 68 " pdb=" N ASP A 68 " pdb=" C ASP A 68 " pdb=" CB ASP A 68 " both_signs ideal model delta sigma weight residual False 2.51 1.55 0.96 2.00e-01 2.50e+01 2.32e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " 0.089 2.00e-02 2.50e+03 5.87e-02 1.04e+02 pdb=" CG PHE A 164 " 0.070 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " -0.050 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " -0.098 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.000 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.072 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.053 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.053 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.006 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 126 " 0.015 2.00e-02 2.50e+03 6.29e-02 8.91e+01 pdb=" CG HIS A 126 " -0.119 2.00e-02 2.50e+03 pdb=" ND1 HIS A 126 " 0.061 2.00e-02 2.50e+03 pdb=" CD2 HIS A 126 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 HIS A 126 " 0.094 2.00e-02 2.50e+03 pdb=" NE2 HIS A 126 " 0.031 2.00e-02 2.50e+03 pdb=" HD2 HIS A 126 " 0.041 2.00e-02 2.50e+03 pdb=" HE1 HIS A 126 " -0.066 2.00e-02 2.50e+03 pdb=" HE2 HIS A 126 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 5 " 0.060 9.50e-02 1.11e+02 6.44e-02 8.46e+01 pdb=" NE ARG A 5 " -0.090 2.00e-02 2.50e+03 pdb=" CZ ARG A 5 " 0.032 2.00e-02 2.50e+03 pdb=" NH1 ARG A 5 " 0.054 2.00e-02 2.50e+03 pdb=" NH2 ARG A 5 " -0.063 2.00e-02 2.50e+03 pdb="HH11 ARG A 5 " 0.050 2.00e-02 2.50e+03 pdb="HH12 ARG A 5 " -0.064 2.00e-02 2.50e+03 pdb="HH21 ARG A 5 " 0.102 2.00e-02 2.50e+03 pdb="HH22 ARG A 5 " -0.025 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.33: 1120 2.33 - 2.90: 8110 2.90 - 3.47: 10544 3.47 - 4.03: 15209 4.03 - 4.60: 21683 Nonbonded interactions: 56666 Sorted by model distance: nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.763 2.100 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.823 2.100 nonbonded pdb=" O ILE A 102 " pdb=" H ALEU A 153 " model vdw 1.838 2.450 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.838 2.450 nonbonded pdb=" H LEU A 10 " pdb=" O ALA A 36 " model vdw 1.842 2.450 ... (remaining 56661 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_3031784_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= 0.1995 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.475168 | | target function (ml) not normalized (work): 22062.579445 | | target function (ml) not normalized (free): 1155.256787 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3808 0.2138 4.8539 4.9076| | 2: 3.78 - 3.00 1.00 2430 110 0.3390 0.1753 4.0855 4.1671| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 48.89 0.83 0.13 6619.57| | 2: 3.78 - 3.00 2430 110 0.93 11.51 1.48 0.26 459.63| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 390.13 max = 12074.72 mean = 3583.33| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 89.99 mean = 30.47| |phase err.(test): min = 0.00 max = 89.98 mean = 33.50| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.083 0.232 1557 Z= 5.599 Angle : 5.167 19.341 2118 Z= 3.645 Chirality : 0.398 1.066 243 Planarity : 0.030 0.086 284 Dihedral : 14.193 83.240 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.24 % Favored : 96.22 % Rotamer: Outliers : 3.73 % Allowed : 1.86 % Favored : 94.41 % Cbeta Deviations : 31.89 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.53), residues: 224 helix: -2.16 (0.45), residues: 102 sheet: -1.71 (0.83), residues: 30 loop : 0.61 (0.65), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.063 0.016 ARG A 27 TYR 0.089 0.035 TYR A 141 PHE 0.108 0.037 PHE A 162 HIS 0.084 0.030 HIS A 115 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 1785 0 Protein: 8.85 115.78 16.79 3.90 1519 0 Water: 11.36 119.30 38.03 N/A 258 0 Other: 19.04 26.29 21.71 N/A 8 0 Chain A: 8.85 119.30 19.89 N/A 1785 0 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 3.00 - 49.25 A, n_refl.=5182 (all), 4.86 % free)-------------| | | | r_work= 0.3620 r_free= 0.1995 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.475168 | | target function (ml) not normalized (work): 22062.579445 | | target function (ml) not normalized (free): 1155.256787 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3577 0.3653 0.2084 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3577 0.3653 0.2084 n_refl.: 5182 remove outliers: r(all,work,free)=0.2526 0.2553 0.2084 n_refl.: 5178 overall B=-2.67 to atoms: r(all,work,free)=0.2426 0.2449 0.2042 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1574 0.1573 0.1605 n_refl.: 5178 remove outliers: r(all,work,free)=0.1570 0.1568 0.1605 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 0.3848 449.683 402.252 0.669 1.010 0.398 11.894-9.307 99.02 97 4 0.1860 714.357 688.434 0.953 1.011 0.377 9.237-7.194 100.00 213 7 0.2182 584.203 572.618 0.988 1.010 0.357 7.162-5.571 100.00 427 22 0.2371 438.373 419.650 0.940 1.008 0.343 5.546-4.326 100.00 867 58 0.1357 601.824 592.133 0.970 1.005 0.257 4.315-3.360 100.00 1859 96 0.1325 572.341 567.763 1.021 0.999 0.199 3.356-3.002 100.00 1373 60 0.1621 440.841 435.766 1.007 0.993 0.043 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9173 b_overall=-4.6341 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1568 r_free=0.1605 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A Total number of N/Q/H flips: 1 r_work=0.1571 r_free=0.1615 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 19.634842 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.962288 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1164 0.1791 0.0628 0.010 1.0 2.6 0.5 0.0 0 9.817 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.64 17.91 6.28 3.013 16.189 1.962 0.018 10.22 17.73 7.51 4.935 16.418 1.962 0.014 Individual atomic B min max mean iso aniso Overall: 2.37 111.63 17.65 5.32 1785 0 Protein: 2.37 110.98 14.94 5.31 1519 0 Water: 4.22 111.63 33.39 N/A 258 0 Other: 16.19 37.81 24.39 N/A 8 0 Chain A: 2.37 111.63 17.65 N/A 1785 0 Histogram: Values Number of atoms 2.37 - 13.30 912 13.30 - 24.22 482 24.22 - 35.15 192 35.15 - 46.08 113 46.08 - 57.00 57 57.00 - 67.93 12 67.93 - 78.85 8 78.85 - 89.78 5 89.78 - 100.70 1 100.70 - 111.63 3 =========================== Idealize ADP of riding H ========================== r_work=0.1022 r_free=0.1773 r_work=0.1016 r_free=0.1779 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1016 r_free = 0.1779 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 = 0.1017 r_free = 0.1783 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.1017 r_free= 0.1783 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ls_wunit_k1) (work): 0.014124 | | target function (ls_wunit_k1) not normalized (work): 69.544426 | | target function (ls_wunit_k1) not normalized (free): 10.493498 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1056 0.1017 0.1783 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2124 0.2126 0.2207 n_refl.: 5176 remove outliers: r(all,work,free)=0.2124 0.2126 0.2207 n_refl.: 5176 overall B=-0.95 to atoms: r(all,work,free)=0.2083 0.2083 0.2195 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.1053 0.1015 0.1773 n_refl.: 5176 remove outliers: r(all,work,free)=0.1053 0.1015 0.1773 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 0.3350 320.373 303.285 0.651 1.003 0.381 11.894-9.307 99.02 97 4 0.1540 508.939 500.211 0.953 1.005 0.361 9.237-7.194 100.00 213 7 0.1655 416.211 416.601 0.992 1.005 0.332 7.162-5.571 100.00 427 22 0.1640 312.316 308.916 0.953 1.004 0.322 5.546-4.326 100.00 867 58 0.0917 428.765 425.367 0.965 1.002 0.215 4.315-3.360 100.00 1859 96 0.0765 407.760 407.751 1.016 0.999 0.200 3.356-3.002 100.00 1373 60 0.0999 314.074 312.874 0.992 0.996 0.047 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-4.2619 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1015 r_free=0.1773 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1015 r_free=0.1773 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1015 r_free=0.1773 | n_water=258 | time (s): 0.470 (total time: 0.470) Filter (dist) r_work=0.1043 r_free=0.1785 | n_water=247 | time (s): 20.700 (total time: 21.170) Filter (q & B) r_work=0.1043 r_free=0.1788 | n_water=244 | time (s): 1.420 (total time: 22.590) Compute maps r_work=0.1043 r_free=0.1788 | n_water=244 | time (s): 0.500 (total time: 23.090) Filter (map) r_work=0.1379 r_free=0.1807 | n_water=138 | time (s): 1.860 (total time: 24.950) Find peaks r_work=0.1379 r_free=0.1807 | n_water=138 | time (s): 0.590 (total time: 25.540) Add new water r_work=0.1730 r_free=0.2112 | n_water=222 | time (s): 1.440 (total time: 26.980) Refine new water occ: r_work=0.1179 r_free=0.1660 adp: r_work=0.1157 r_free=0.1670 occ: r_work=0.1155 r_free=0.1634 adp: r_work=0.1144 r_free=0.1645 occ: r_work=0.1144 r_free=0.1618 adp: r_work=0.1141 r_free=0.1627 ADP+occupancy (water only), MIN, final r_work=0.1141 r_free=0.1627 r_work=0.1141 r_free=0.1627 | n_water=222 | time (s): 4.920 (total time: 31.900) Filter (q & B) r_work=0.1141 r_free=0.1627 | n_water=222 | time (s): 0.690 (total time: 32.590) Filter (dist only) r_work=0.1148 r_free=0.1622 | n_water=218 | time (s): 16.480 (total time: 49.070) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.829963 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.662990 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 0.1026 0.1760 0.0735 0.009 1.0 3.5 0.5 0.6 0 11.415 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.26 17.60 7.35 4.694 17.023 2.663 0.014 9.62 17.71 8.09 5.343 17.456 2.663 0.013 Individual atomic B min max mean iso aniso Overall: 0.00 105.57 16.83 6.27 1745 0 Protein: 0.00 105.57 15.33 6.26 1519 0 Water: 0.00 63.25 27.13 N/A 218 0 Other: 11.22 33.04 20.82 N/A 8 0 Chain A: 0.00 105.57 16.04 N/A 1662 0 Chain S: 4.24 63.11 32.67 N/A 83 0 Histogram: Values Number of atoms 0.00 - 10.56 621 10.56 - 21.11 707 21.11 - 31.67 208 31.67 - 42.23 124 42.23 - 52.79 44 52.79 - 63.34 24 63.34 - 73.90 9 73.90 - 84.46 3 84.46 - 95.02 3 95.02 - 105.57 2 =========================== Idealize ADP of riding H ========================== r_work=0.0962 r_free=0.1771 r_work=0.0960 r_free=0.1769 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0960 r_free = 0.1769 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0957 r_free = 0.1752 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= 0.0957 r_free= 0.1752 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ls_wunit_k1) (work): 0.012233 | | target function (ls_wunit_k1) not normalized (work): 60.234722 | | target function (ls_wunit_k1) not normalized (free): 9.583151 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0998 0.0957 0.1752 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2201 0.2212 0.2144 n_refl.: 5176 remove outliers: r(all,work,free)=0.2201 0.2212 0.2144 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2201 0.2212 0.2144 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0998 0.0956 0.1776 n_refl.: 5176 remove outliers: r(all,work,free)=0.0998 0.0956 0.1776 n_refl.: 5176 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 96.88 88 5 0.3099 320.373 308.471 0.710 1.026 0.393 11.894-9.307 99.02 97 4 0.1449 508.939 503.600 0.967 1.026 0.355 9.237-7.194 100.00 213 7 0.1428 416.211 416.345 0.998 1.024 0.325 7.162-5.571 100.00 427 22 0.1441 312.316 309.432 0.979 1.019 0.320 5.546-4.326 100.00 867 58 0.0825 428.765 426.451 0.997 1.010 0.250 4.315-3.360 100.00 1859 96 0.0741 407.760 407.753 1.061 0.996 0.200 3.356-3.002 100.00 1373 60 0.0999 314.074 313.002 1.052 0.981 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-4.3209 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0956 r_free=0.1776 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=0.0956 r_free=0.1775 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0956 r_free=0.1775 | n_water=218 | time (s): 0.470 (total time: 0.470) Filter (dist) r_work=0.0973 r_free=0.1768 | n_water=213 | time (s): 18.550 (total time: 19.020) Filter (q & B) r_work=0.1030 r_free=0.1784 | n_water=211 | time (s): 1.460 (total time: 20.480) Compute maps r_work=0.1030 r_free=0.1784 | n_water=211 | time (s): 0.650 (total time: 21.130) Filter (map) r_work=0.1275 r_free=0.1841 | n_water=139 | time (s): 1.770 (total time: 22.900) Find peaks r_work=0.1275 r_free=0.1841 | n_water=139 | time (s): 0.470 (total time: 23.370) Add new water r_work=0.1680 r_free=0.2166 | n_water=226 | time (s): 1.380 (total time: 24.750) Refine new water occ: r_work=0.1073 r_free=0.1728 adp: r_work=0.1068 r_free=0.1739 occ: r_work=0.1055 r_free=0.1727 adp: r_work=0.1055 r_free=0.1732 occ: r_work=0.1044 r_free=0.1722 adp: r_work=0.1043 r_free=0.1726 ADP+occupancy (water only), MIN, final r_work=0.1043 r_free=0.1726 r_work=0.1043 r_free=0.1726 | n_water=226 | time (s): 12.160 (total time: 36.910) Filter (q & B) r_work=0.1045 r_free=0.1731 | n_water=223 | time (s): 1.220 (total time: 38.130) Filter (dist only) r_work=0.1040 r_free=0.1730 | n_water=221 | time (s): 17.790 (total time: 55.920) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.134391 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.215822 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 0.0948 0.1803 0.0855 0.011 1.1 4.8 0.5 1.2 0 0.567 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.48 18.03 8.55 5.305 18.106 0.216 5.139 9.06 18.01 8.94 7.167 18.085 0.216 5.051 Individual atomic B min max mean iso aniso Overall: 0.00 104.98 16.58 8.73 1748 0 Protein: 0.00 104.98 15.40 8.72 1519 0 Water: 0.00 58.25 24.49 N/A 221 0 Other: 13.44 38.82 23.73 N/A 8 0 Chain A: 0.00 104.98 16.09 N/A 1652 0 Chain S: 0.00 55.91 25.14 N/A 96 0 Histogram: Values Number of atoms 0.00 - 10.50 611 10.50 - 21.00 710 21.00 - 31.49 234 31.49 - 41.99 119 41.99 - 52.49 40 52.49 - 62.99 14 62.99 - 73.48 10 73.48 - 83.98 4 83.98 - 94.48 4 94.48 - 104.98 2 =========================== Idealize ADP of riding H ========================== r_work=0.0906 r_free=0.1801 r_work=0.0911 r_free=0.1807 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0911 r_free = 0.1807 target_work(ml) = 5.055 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0899 r_free = 0.1806 target_work(ml) = 5.049 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.0899 r_free= 0.1806 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 5.048858 | | target function (ml) not normalized (work): 24860.578354 | | target function (ml) not normalized (free): 1767.907221 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0945 0.0899 0.1806 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2213 0.2228 0.2107 n_refl.: 5176 remove outliers: r(all,work,free)=0.2213 0.2228 0.2107 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2213 0.2228 0.2107 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0942 0.0897 0.1800 n_refl.: 5176 remove outliers: r(all,work,free)=0.0940 0.0895 0.1800 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 0.3473 317.675 296.153 0.686 0.992 0.365 11.894-9.307 99.02 97 4 0.1828 508.939 492.907 0.989 0.996 0.325 9.237-7.194 100.00 213 7 0.1902 416.211 409.413 1.042 0.997 0.310 7.162-5.571 100.00 427 22 0.1822 312.316 303.067 1.020 0.999 0.310 5.546-4.326 100.00 867 58 0.0922 428.765 423.879 1.035 1.000 0.250 4.315-3.360 100.00 1859 96 0.0589 407.760 407.722 1.100 1.002 0.210 3.356-3.002 100.00 1373 60 0.0644 314.074 313.783 1.082 1.004 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9552 b_overall=-6.5037 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0895 r_free=0.1800 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 ASN Total number of N/Q/H flips: 1 r_work=0.0898 r_free=0.1799 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0898 r_free=0.1799 | n_water=221 | time (s): 0.600 (total time: 0.600) Filter (dist) r_work=0.0909 r_free=0.1816 | n_water=217 | time (s): 18.330 (total time: 18.930) Filter (q & B) r_work=0.0943 r_free=0.1816 | n_water=215 | time (s): 1.240 (total time: 20.170) Compute maps r_work=0.0943 r_free=0.1816 | n_water=215 | time (s): 0.450 (total time: 20.620) Filter (map) r_work=0.1199 r_free=0.1903 | n_water=149 | time (s): 1.290 (total time: 21.910) Find peaks r_work=0.1199 r_free=0.1903 | n_water=149 | time (s): 0.390 (total time: 22.300) Add new water r_work=0.1548 r_free=0.2209 | n_water=225 | time (s): 1.170 (total time: 23.470) Refine new water occ: r_work=0.1007 r_free=0.1859 adp: r_work=0.1005 r_free=0.1866 occ: r_work=0.0994 r_free=0.1850 adp: r_work=0.0994 r_free=0.1856 occ: r_work=0.0983 r_free=0.1840 adp: r_work=0.0983 r_free=0.1846 ADP+occupancy (water only), MIN, final r_work=0.0983 r_free=0.1846 r_work=0.0983 r_free=0.1846 | n_water=225 | time (s): 9.860 (total time: 33.330) Filter (q & B) r_work=0.0984 r_free=0.1846 | n_water=224 | time (s): 1.860 (total time: 35.190) Filter (dist only) r_work=0.0996 r_free=0.1850 | n_water=219 | time (s): 17.970 (total time: 53.160) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.024876 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.216997 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 0.0919 0.1926 0.1008 0.011 1.1 4.8 0.5 2.5 0 0.512 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.19 19.26 10.08 6.837 18.145 0.217 5.027 8.95 19.60 10.65 8.173 18.270 0.217 4.964 Individual atomic B min max mean iso aniso Overall: 0.00 104.46 16.85 10.66 1746 0 Protein: 0.00 104.46 15.81 10.65 1519 0 Water: 0.00 55.09 23.74 N/A 219 0 Other: 13.51 38.38 25.30 N/A 8 0 Chain A: 0.00 104.46 16.35 N/A 1642 0 Chain S: 1.20 55.09 24.85 N/A 104 0 Histogram: Values Number of atoms 0.00 - 10.45 606 10.45 - 20.89 683 20.89 - 31.34 259 31.34 - 41.78 107 41.78 - 52.23 52 52.23 - 62.67 18 62.67 - 73.12 8 73.12 - 83.57 7 83.57 - 94.01 5 94.01 - 104.46 1 =========================== Idealize ADP of riding H ========================== r_work=0.0895 r_free=0.1960 r_work=0.0900 r_free=0.1967 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0900 r_free = 0.1967 target_work(ml) = 4.968 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0892 r_free = 0.1959 target_work(ml) = 4.962 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0892 r_free= 0.1959 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ml) (work): 4.961787 | | target function (ml) not normalized (work): 24426.879797 | | target function (ml) not normalized (free): 2108.364026 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0946 0.0892 0.1959 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2257 0.2267 0.2227 n_refl.: 5175 remove outliers: r(all,work,free)=0.2257 0.2267 0.2227 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2257 0.2267 0.2227 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0945 0.0891 0.1953 n_refl.: 5175 remove outliers: r(all,work,free)=0.0943 0.0889 0.1953 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 0.3611 319.788 289.109 0.602 0.992 0.328 11.894-9.307 99.02 97 4 0.1981 508.939 492.239 0.956 0.996 0.316 9.237-7.194 100.00 213 7 0.2116 416.211 407.238 1.006 0.999 0.312 7.162-5.571 100.00 427 22 0.2049 312.316 302.875 0.989 1.000 0.310 5.546-4.326 100.00 867 58 0.0976 428.765 423.784 1.015 1.001 0.260 4.315-3.360 100.00 1859 96 0.0566 407.760 407.742 1.086 1.003 0.219 3.356-3.002 100.00 1373 60 0.0472 314.074 313.974 1.070 1.004 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9171 b_overall=-7.8747 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0889 r_free=0.1953 After: r_work=0.0892 r_free=0.1950 ================================== NQH flips ================================== r_work=0.0892 r_free=0.1950 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B A 135 ASN Total number of N/Q/H flips: 2 r_work=0.0893 r_free=0.1954 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0893 r_free=0.1954 | n_water=219 | time (s): 0.440 (total time: 0.440) Filter (dist) r_work=0.0899 r_free=0.1954 | n_water=217 | time (s): 17.500 (total time: 17.940) Filter (q & B) r_work=0.0973 r_free=0.1946 | n_water=215 | time (s): 1.480 (total time: 19.420) Compute maps r_work=0.0973 r_free=0.1946 | n_water=215 | time (s): 0.460 (total time: 19.880) Filter (map) r_work=0.1224 r_free=0.2016 | n_water=150 | time (s): 1.200 (total time: 21.080) Find peaks r_work=0.1224 r_free=0.2016 | n_water=150 | time (s): 0.420 (total time: 21.500) Add new water r_work=0.1523 r_free=0.2255 | n_water=215 | time (s): 1.410 (total time: 22.910) Refine new water occ: r_work=0.1009 r_free=0.1936 adp: r_work=0.1003 r_free=0.1953 occ: r_work=0.0996 r_free=0.1935 adp: r_work=0.0996 r_free=0.1944 occ: r_work=0.0989 r_free=0.1926 adp: r_work=0.0989 r_free=0.1936 ADP+occupancy (water only), MIN, final r_work=0.0989 r_free=0.1936 r_work=0.0989 r_free=0.1936 | n_water=215 | time (s): 11.170 (total time: 34.080) Filter (q & B) r_work=0.0990 r_free=0.1942 | n_water=213 | time (s): 1.520 (total time: 35.600) Filter (dist only) r_work=0.0986 r_free=0.1934 | n_water=211 | time (s): 17.820 (total time: 53.420) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.985529 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.224036 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 0.0932 0.1916 0.0984 0.011 1.1 6.1 0.5 1.9 0 0.493 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.32 19.16 9.84 8.114 18.537 0.224 5.009 9.10 19.00 9.90 9.138 18.659 0.224 4.953 Individual atomic B min max mean iso aniso Overall: 0.00 104.28 17.12 12.12 1738 0 Protein: 0.00 104.28 16.20 12.13 1519 0 Water: 0.00 51.44 23.43 N/A 211 0 Other: 14.37 39.38 26.08 N/A 8 0 Chain A: 0.00 104.28 16.65 N/A 1633 0 Chain S: 0.00 51.44 24.36 N/A 105 0 Histogram: Values Number of atoms 0.00 - 10.43 590 10.43 - 20.86 656 20.86 - 31.28 279 31.28 - 41.71 124 41.71 - 52.14 51 52.14 - 62.57 15 62.57 - 73.00 7 73.00 - 83.43 8 83.43 - 93.85 5 93.85 - 104.28 3 =========================== Idealize ADP of riding H ========================== r_work=0.0910 r_free=0.1900 r_work=0.0913 r_free=0.1905 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0913 r_free = 0.1905 target_work(ml) = 4.958 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0905 r_free = 0.1904 target_work(ml) = 4.953 | | 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= 0.0905 r_free= 0.1904 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 4.953205 | | target function (ml) not normalized (work): 24379.676329 | | target function (ml) not normalized (free): 2109.445090 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1892 5.5136 6.2367| | 2: 3.78 - 3.00 1.00 2430 110 0.0456 0.1924 4.3785 11.126| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 12.43 1.00 0.95 12759.10| | 2: 3.78 - 3.00 2430 110 0.99 2.10 1.00 0.97 947.80| |alpha: min = 0.94 max = 0.97 mean = 0.96| |beta: min = 613.57 max = 21303.82 mean = 6927.84| |figures of merit: min = 0.00 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.76 mean = 7.33| |phase err.(test): min = 0.00 max = 71.97 mean = 7.03| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0955 0.0905 0.1904 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2225 0.2232 0.2233 n_refl.: 5174 remove outliers: r(all,work,free)=0.2225 0.2232 0.2233 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2225 0.2232 0.2233 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0954 0.0904 0.1907 n_refl.: 5174 remove outliers: r(all,work,free)=0.0954 0.0904 0.1907 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 0.3734 319.788 293.636 0.638 0.987 0.328 11.894-9.307 99.02 97 4 0.2020 508.939 490.218 1.001 0.994 0.320 9.237-7.194 100.00 213 7 0.2158 416.211 406.323 1.047 0.997 0.320 7.162-5.571 100.00 427 22 0.2062 312.316 302.835 1.033 0.999 0.320 5.546-4.326 100.00 867 58 0.1030 428.765 423.247 1.064 1.001 0.260 4.315-3.360 100.00 1859 96 0.0583 407.760 407.429 1.148 1.003 0.220 3.356-3.002 100.00 1373 60 0.0439 314.074 314.006 1.135 1.005 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-8.6322 ================= 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 0.1995 0.083 5.167 8.8 119.3 19.9 258 0.000 1_bss: 0.1568 0.1605 0.083 5.167 6.2 116.6 17.2 258 0.000 1_settarget: 0.1568 0.1605 0.083 5.167 6.2 116.6 17.2 258 0.000 1_nqh: 0.1571 0.1615 0.083 5.167 6.2 116.6 17.2 258 0.003 1_weight: 0.1571 0.1615 0.083 5.167 6.2 116.6 17.2 258 0.003 1_xyzrec: 0.1164 0.1791 0.010 0.991 6.2 116.6 17.2 258 0.202 1_adp: 0.1022 0.1773 0.010 0.991 2.4 111.6 17.7 258 0.202 1_regHadp: 0.1016 0.1779 0.010 0.991 2.4 111.6 17.7 258 0.202 1_occ: 0.1017 0.1783 0.010 0.991 2.4 111.6 17.7 258 0.202 2_bss: 0.1015 0.1773 0.010 0.991 1.4 110.7 16.7 258 0.202 2_settarget: 0.1015 0.1773 0.010 0.991 1.4 110.7 16.7 258 0.202 2_updatecdl: 0.1015 0.1773 0.010 1.006 1.4 110.7 16.7 258 0.202 2_nqh: 0.1015 0.1773 0.010 1.006 1.4 110.7 16.7 258 0.202 2_sol: 0.1148 0.1622 0.010 1.006 1.0 110.0 16.0 218 n/a 2_weight: 0.1148 0.1622 0.010 1.006 1.0 110.0 16.0 218 n/a 2_xyzrec: 0.1026 0.1760 0.009 0.980 1.0 110.0 16.0 218 n/a 2_adp: 0.0962 0.1771 0.009 0.980 0.0 105.6 16.8 218 n/a 2_regHadp: 0.0960 0.1769 0.009 0.980 0.0 105.6 16.8 218 n/a 2_occ: 0.0957 0.1752 0.009 0.980 0.0 105.6 16.8 218 n/a 3_bss: 0.0956 0.1776 0.009 0.980 0.0 105.6 16.8 218 n/a 3_settarget: 0.0956 0.1776 0.009 0.980 0.0 105.6 16.8 218 n/a 3_updatecdl: 0.0956 0.1776 0.009 0.985 0.0 105.6 16.8 218 n/a 3_nqh: 0.0956 0.1775 0.009 0.985 0.0 105.6 16.8 218 n/a 3_sol: 0.1040 0.1730 0.009 0.985 0.0 105.6 16.6 221 n/a 3_weight: 0.1040 0.1730 0.009 0.985 0.0 105.6 16.6 221 n/a 3_xyzrec: 0.0948 0.1803 0.011 1.095 0.0 105.6 16.6 221 n/a 3_adp: 0.0906 0.1801 0.011 1.095 0.0 105.0 16.6 221 n/a 3_regHadp: 0.0911 0.1807 0.011 1.095 0.0 105.0 16.6 221 n/a 3_occ: 0.0899 0.1806 0.011 1.095 0.0 105.0 16.6 221 n/a 4_bss: 0.0895 0.1800 0.011 1.095 0.0 105.0 16.6 221 n/a 4_settarget: 0.0895 0.1800 0.011 1.095 0.0 105.0 16.6 221 n/a 4_updatecdl: 0.0895 0.1800 0.011 1.092 0.0 105.0 16.6 221 n/a 4_nqh: 0.0898 0.1799 0.011 1.092 0.0 105.0 16.6 221 n/a 4_sol: 0.0996 0.1850 0.011 1.092 0.0 105.0 16.6 219 n/a 4_weight: 0.0996 0.1850 0.011 1.092 0.0 105.0 16.6 219 n/a 4_xyzrec: 0.0919 0.1926 0.011 1.057 0.0 105.0 16.6 219 n/a 4_adp: 0.0895 0.1960 0.011 1.057 0.0 104.5 16.9 219 n/a 4_regHadp: 0.0900 0.1967 0.011 1.057 0.0 104.5 16.9 219 n/a 4_occ: 0.0892 0.1959 0.011 1.057 0.0 104.5 16.9 219 n/a 5_bss: 0.0889 0.1953 0.011 1.057 0.0 104.5 16.9 219 n/a 5_settarget: 0.0889 0.1953 0.011 1.057 0.0 104.5 16.9 219 n/a 5_updatecdl: 0.0889 0.1953 0.011 1.064 0.0 104.5 16.9 219 n/a 5_setrh: 0.0892 0.1950 0.011 1.064 0.0 104.5 16.9 219 n/a 5_nqh: 0.0893 0.1954 0.011 1.064 0.0 104.5 16.9 219 n/a 5_sol: 0.0986 0.1934 0.011 1.064 0.0 104.5 16.9 211 n/a 5_weight: 0.0986 0.1934 0.011 1.064 0.0 104.5 16.9 211 n/a 5_xyzrec: 0.0932 0.1916 0.011 1.136 0.0 104.5 16.9 211 n/a 5_adp: 0.0910 0.1900 0.011 1.136 0.0 104.3 17.1 211 n/a 5_regHadp: 0.0913 0.1905 0.011 1.136 0.0 104.3 17.1 211 n/a 5_occ: 0.0905 0.1904 0.011 1.136 0.0 104.3 17.1 211 n/a end: 0.0904 0.1907 0.011 1.136 0.0 104.3 17.1 211 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_3031784_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_3031784_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 2.9500 Refinement macro-cycles (run) : 482.7400 Write final files (write_after_run_outputs) : 11.1400 Total : 496.8300 Total CPU time: 8.62 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:18:58 PST -0800 (1735492738.42 s) Start R-work = 0.1568, R-free = 0.1605 Final R-work = 0.0904, R-free = 0.1907 =============================================================================== Job complete usr+sys time: 525.59 seconds wall clock time: 9 minutes 7.25 seconds (547.25 seconds total)