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_1617309.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" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_1617309.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_1617309.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 3 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.65, per 1000 atoms: 0.49 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: 0.57 Conformation dependent library (CDL) restraints added in 213.2 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.91: 550 0.91 - 1.17: 1095 1.17 - 1.42: 641 1.42 - 1.67: 828 1.67 - 1.93: 39 Bond restraints: 3153 Sorted by residual: bond pdb=" CA ILE A 21 " pdb=" CB ILE A 21 " ideal model delta sigma weight residual 1.537 1.400 0.137 5.00e-03 4.00e+04 7.49e+02 bond pdb=" CA TYR A 141 " pdb=" C TYR A 141 " ideal model delta sigma weight residual 1.524 1.275 0.249 1.31e-02 5.83e+03 3.61e+02 bond pdb=" C BGLN A 80 " pdb=" O BGLN A 80 " ideal model delta sigma weight residual 1.236 1.020 0.216 1.15e-02 7.56e+03 3.53e+02 bond pdb=" C GLN A 180 " pdb=" N VAL A 181 " ideal model delta sigma weight residual 1.334 1.563 -0.229 1.25e-02 6.40e+03 3.35e+02 bond pdb=" N ILE A 31 " pdb=" CA ILE A 31 " ideal model delta sigma weight residual 1.458 1.671 -0.213 1.17e-02 7.31e+03 3.32e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.34: 3470 5.34 - 10.68: 1850 10.68 - 16.02: 409 16.02 - 21.36: 45 21.36 - 26.71: 3 Bond angle restraints: 5777 Sorted by residual: angle pdb=" NE ARG A 27 " pdb=" CZ ARG A 27 " pdb=" NH2 ARG A 27 " ideal model delta sigma weight residual 119.20 104.35 14.85 9.00e-01 1.23e+00 2.72e+02 angle pdb=" O ILE A 52 " pdb=" C ILE A 52 " pdb=" N ACYS A 53 " ideal model delta sigma weight residual 123.18 138.56 -15.38 1.05e+00 9.07e-01 2.15e+02 angle pdb=" CA GLU A 170 " pdb=" C GLU A 170 " pdb=" O GLU A 170 " ideal model delta sigma weight residual 120.63 134.55 -13.92 1.08e+00 8.57e-01 1.66e+02 angle pdb=" OE1AGLN A 80 " pdb=" CD AGLN A 80 " pdb=" NE2AGLN A 80 " ideal model delta sigma weight residual 122.60 109.84 12.76 1.00e+00 1.00e+00 1.63e+02 angle pdb=" O ILE A 21 " pdb=" C ILE A 21 " pdb=" N PRO A 22 " ideal model delta sigma weight residual 120.42 128.37 -7.95 6.40e-01 2.44e+00 1.54e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.45: 1299 17.45 - 34.89: 126 34.89 - 52.33: 39 52.33 - 69.78: 15 69.78 - 87.22: 2 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: 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 -145.87 23.27 0 2.50e+00 1.60e-01 8.66e+01 dihedral pdb=" C ARG A 48 " pdb=" N ARG A 48 " pdb=" CA ARG A 48 " pdb=" CB ARG A 48 " ideal model delta harmonic sigma weight residual -122.60 -143.97 21.37 0 2.50e+00 1.60e-01 7.31e+01 dihedral pdb=" N ARG A 48 " pdb=" C ARG A 48 " pdb=" CA ARG A 48 " pdb=" CB ARG A 48 " ideal model delta harmonic sigma weight residual 122.80 143.75 -20.95 0 2.50e+00 1.60e-01 7.02e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.211: 98 0.211 - 0.419: 75 0.419 - 0.628: 53 0.628 - 0.837: 12 0.837 - 1.046: 5 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA ARG A 48 " pdb=" N ARG A 48 " pdb=" C ARG A 48 " pdb=" CB ARG A 48 " both_signs ideal model delta sigma weight residual False 2.51 1.46 1.05 2.00e-01 2.50e+01 2.73e+01 chirality pdb=" CA ALYS A 99 " pdb=" N ALYS A 99 " pdb=" C ALYS A 99 " pdb=" CB ALYS A 99 " both_signs ideal model delta sigma weight residual False 2.51 1.48 1.03 2.00e-01 2.50e+01 2.65e+01 chirality pdb=" CA BTYR A 67 " pdb=" N BTYR A 67 " pdb=" C BTYR A 67 " pdb=" CB BTYR A 67 " both_signs ideal model delta sigma weight residual False 2.51 3.44 -0.93 2.00e-01 2.50e+01 2.15e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.102 2.00e-02 2.50e+03 7.42e-02 1.65e+02 pdb=" CG PHE A 164 " 0.119 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " -0.040 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.092 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.101 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.094 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.040 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.087 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.023 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.006 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " 0.048 2.00e-02 2.50e+03 6.66e-02 1.33e+02 pdb=" CG PHE A 162 " -0.103 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " -0.086 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " 0.091 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " -0.057 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " 0.080 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " -0.064 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " 0.069 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " -0.032 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " 0.047 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " -0.034 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " 0.070 2.00e-02 2.50e+03 6.43e-02 1.24e+02 pdb=" CG BTYR A 67 " -0.051 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " -0.073 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " -0.048 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " 0.090 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " -0.059 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " -0.016 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " 0.044 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " -0.059 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " 0.109 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " 0.048 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " -0.055 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.34: 1240 2.34 - 2.91: 8270 2.91 - 3.47: 10441 3.47 - 4.04: 15154 4.04 - 4.60: 21532 Nonbonded interactions: 56637 Sorted by model distance: nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.781 2.450 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.810 2.450 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.811 2.450 nonbonded pdb=" O GLN A 95 " pdb=" H BGLY A 100 " model vdw 1.826 2.450 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.840 2.450 ... (remaining 56632 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_1617309_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= 0.3625 r_free= 0.1989 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.475525 | | target function (ml) not normalized (work): 22064.338914 | | target function (ml) not normalized (free): 1147.520425 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3805 0.2148 4.8494 4.8975| | 2: 3.78 - 3.00 1.00 2430 110 0.3406 0.1720 4.0908 4.1098| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 49.25 - 3.79 2500 142 0.50 48.81 0.83 0.13 6601.57| | 2: 3.78 - 3.00 2430 110 0.93 11.56 1.48 0.26 463.93| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 399.91 max = 12062.27 mean = 3576.33| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 90.00 mean = 30.45| |phase err.(test): min = 0.00 max = 89.95 mean = 33.70| |-----------------------------------------------------------------------------| ----------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 0.249 1557 Z= 5.572 Angle : 5.349 20.777 2118 Z= 3.757 Chirality : 0.370 1.046 243 Planarity : 0.033 0.089 284 Dihedral : 13.847 87.219 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.86 % Allowed : 2.48 % Favored : 95.65 % 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: -1.93 (0.51), residues: 224 helix: -2.69 (0.40), residues: 101 sheet: 0.90 (0.96), residues: 28 loop : -0.02 (0.61), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.065 0.021 ARG A 27 TYR 0.102 0.046 TYR A 139 PHE 0.115 0.051 PHE A 164 HIS 0.086 0.045 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= 0.3625 r_free= 0.1989 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.475525 | | target function (ml) not normalized (work): 22064.338914 | | target function (ml) not normalized (free): 1147.520425 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3580 0.3657 0.2097 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3580 0.3657 0.2097 n_refl.: 5182 remove outliers: r(all,work,free)=0.2530 0.2556 0.2097 n_refl.: 5178 overall B=-2.60 to atoms: r(all,work,free)=0.2432 0.2455 0.2051 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1568 0.1566 0.1593 n_refl.: 5178 remove outliers: r(all,work,free)=0.1562 0.1560 0.1593 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 97.87 87 5 0.3761 453.376 403.215 0.643 1.062 0.408 11.894-9.307 99.02 97 4 0.1894 714.179 686.739 0.906 1.059 0.380 9.237-7.194 100.00 213 7 0.2137 584.056 570.710 0.941 1.052 0.364 7.162-5.571 100.00 427 22 0.2277 438.263 421.162 0.909 1.041 0.289 5.546-4.326 100.00 867 58 0.1387 601.673 593.262 0.949 1.022 0.225 4.315-3.360 100.00 1859 96 0.1319 572.198 565.955 1.028 0.991 0.189 3.356-3.002 100.00 1373 60 0.1611 440.731 436.406 1.040 0.961 0.096 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9176 b_overall=-4.4961 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1560 r_free=0.1593 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN A Total number of N/Q/H flips: 2 r_work=0.1567 r_free=0.1594 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 19.836641 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.717627 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 0.1156 0.1766 0.0610 0.010 1.0 2.6 0.5 0.0 0 9.918 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.56 17.66 6.10 3.013 16.260 1.718 0.018 10.18 17.56 7.38 4.720 16.475 1.718 0.014 Individual atomic B min max mean iso aniso Overall: 2.48 112.79 17.69 5.15 1785 0 Protein: 2.48 112.79 14.97 5.14 1519 0 Water: 4.55 111.70 33.56 N/A 258 0 Other: 16.80 34.72 23.93 N/A 8 0 Chain A: 2.48 112.79 17.69 N/A 1785 0 Histogram: Values Number of atoms 2.48 - 13.51 925 13.51 - 24.54 485 24.54 - 35.58 184 35.58 - 46.61 104 46.61 - 57.64 58 57.64 - 68.67 14 68.67 - 79.70 6 79.70 - 90.73 5 90.73 - 101.76 1 101.76 - 112.79 3 =========================== Idealize ADP of riding H ========================== r_work=0.1018 r_free=0.1756 r_work=0.1012 r_free=0.1763 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1012 r_free = 0.1763 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 = 0.1008 r_free = 0.1746 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.1008 r_free= 0.1746 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ls_wunit_k1) (work): 0.013829 | | target function (ls_wunit_k1) not normalized (work): 68.079119 | | target function (ls_wunit_k1) not normalized (free): 10.137026 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1046 0.1008 0.1746 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2103 0.2102 0.2223 n_refl.: 5175 remove outliers: r(all,work,free)=0.2103 0.2102 0.2223 n_refl.: 5175 overall B=-1.07 to atoms: r(all,work,free)=0.2057 0.2054 0.2210 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.1049 0.1012 0.1743 n_refl.: 5175 remove outliers: r(all,work,free)=0.1049 0.1012 0.1743 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 0.3202 322.385 305.382 0.676 1.023 0.384 11.894-9.307 99.02 97 4 0.1532 507.835 500.226 0.971 1.022 0.366 9.237-7.194 100.00 213 7 0.1669 415.308 414.584 1.013 1.020 0.341 7.162-5.571 100.00 427 22 0.1595 311.638 309.015 0.977 1.016 0.292 5.546-4.326 100.00 867 58 0.0926 427.835 425.050 0.993 1.008 0.207 4.315-3.360 100.00 1859 96 0.0767 406.876 407.019 1.054 0.995 0.194 3.356-3.002 100.00 1373 60 0.0999 313.393 311.610 1.037 0.983 0.072 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-3.8327 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1012 r_free=0.1743 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A Total number of N/Q/H flips: 1 r_work=0.1012 r_free=0.1742 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1012 r_free=0.1742 | n_water=258 | time (s): 0.670 (total time: 0.670) Filter (dist) r_work=0.1042 r_free=0.1762 | n_water=246 | time (s): 20.910 (total time: 21.580) Filter (q & B) r_work=0.1043 r_free=0.1759 | n_water=243 | time (s): 1.660 (total time: 23.240) Compute maps r_work=0.1043 r_free=0.1759 | n_water=243 | time (s): 0.490 (total time: 23.730) Filter (map) r_work=0.1344 r_free=0.1831 | n_water=143 | time (s): 1.320 (total time: 25.050) Find peaks r_work=0.1344 r_free=0.1831 | n_water=143 | time (s): 0.390 (total time: 25.440) Add new water r_work=0.1688 r_free=0.2110 | n_water=233 | time (s): 1.320 (total time: 26.760) Refine new water occ: r_work=0.1162 r_free=0.1643 adp: r_work=0.1142 r_free=0.1648 occ: r_work=0.1140 r_free=0.1625 adp: r_work=0.1129 r_free=0.1633 occ: r_work=0.1129 r_free=0.1619 adp: r_work=0.1129 r_free=0.1619 ADP+occupancy (water only), MIN, final r_work=0.1129 r_free=0.1619 r_work=0.1129 r_free=0.1619 | n_water=233 | time (s): 9.550 (total time: 36.310) Filter (q & B) r_work=0.1131 r_free=0.1631 | n_water=231 | time (s): 1.560 (total time: 37.870) Filter (dist only) r_work=0.1134 r_free=0.1632 | n_water=229 | time (s): 17.780 (total time: 55.650) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.410210 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.974364 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 0.1022 0.1799 0.0777 0.009 1.0 4.8 0.5 0.0 0 11.205 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.22 17.99 7.77 4.592 16.867 2.974 0.014 9.47 18.54 9.08 5.854 17.419 2.974 0.012 Individual atomic B min max mean iso aniso Overall: 0.00 109.26 16.92 6.97 1756 0 Protein: 0.00 109.26 15.48 6.95 1519 0 Water: 0.00 64.00 26.15 N/A 229 0 Other: 12.45 40.40 27.07 N/A 8 0 Chain A: 0.00 109.26 16.20 N/A 1668 0 Chain S: 0.00 64.00 30.70 N/A 88 0 Histogram: Values Number of atoms 0.00 - 10.93 659 10.93 - 21.85 680 21.85 - 32.78 225 32.78 - 43.70 116 43.70 - 54.63 38 54.63 - 65.55 23 65.55 - 76.48 7 76.48 - 87.41 5 87.41 - 98.33 2 98.33 - 109.26 1 =========================== Idealize ADP of riding H ========================== r_work=0.0947 r_free=0.1854 r_work=0.0943 r_free=0.1857 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0943 r_free = 0.1857 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0944 r_free = 0.1843 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.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0944 r_free= 0.1843 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ls_wunit_k1) (work): 0.012072 | | target function (ls_wunit_k1) not normalized (work): 59.431438 | | target function (ls_wunit_k1) not normalized (free): 10.356606 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0990 0.0944 0.1843 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2159 0.2162 0.2273 n_refl.: 5175 remove outliers: r(all,work,free)=0.2159 0.2162 0.2273 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2159 0.2162 0.2273 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0990 0.0944 0.1848 n_refl.: 5175 remove outliers: r(all,work,free)=0.0989 0.0942 0.1848 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 0.3114 319.693 303.501 0.684 1.013 0.377 11.894-9.307 99.02 97 4 0.1435 507.835 500.633 0.974 1.014 0.350 9.237-7.194 100.00 213 7 0.1456 415.308 415.013 1.012 1.014 0.340 7.162-5.571 100.00 427 22 0.1430 311.638 308.291 0.995 1.011 0.290 5.546-4.326 100.00 867 58 0.0802 427.835 424.813 1.008 1.006 0.240 4.315-3.360 100.00 1859 96 0.0745 406.876 406.972 1.069 0.998 0.210 3.356-3.002 100.00 1373 60 0.0958 313.393 313.402 1.052 0.990 0.090 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9552 b_overall=-4.7589 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0942 r_free=0.1848 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 80 GLN A Total number of N/Q/H flips: 2 r_work=0.0946 r_free=0.1838 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0946 r_free=0.1838 | n_water=229 | time (s): 0.630 (total time: 0.630) Filter (dist) r_work=0.0956 r_free=0.1826 | n_water=225 | time (s): 18.100 (total time: 18.730) Filter (q & B) r_work=0.1020 r_free=0.1839 | n_water=222 | time (s): 1.470 (total time: 20.200) Compute maps r_work=0.1020 r_free=0.1839 | n_water=222 | time (s): 0.440 (total time: 20.640) Filter (map) r_work=0.1275 r_free=0.1864 | n_water=143 | time (s): 1.370 (total time: 22.010) Find peaks r_work=0.1275 r_free=0.1864 | n_water=143 | time (s): 0.400 (total time: 22.410) Add new water r_work=0.1679 r_free=0.2242 | n_water=236 | time (s): 1.380 (total time: 23.790) Refine new water occ: r_work=0.1066 r_free=0.1836 adp: r_work=0.1059 r_free=0.1854 occ: r_work=0.1049 r_free=0.1831 adp: r_work=0.1049 r_free=0.1841 occ: r_work=0.1039 r_free=0.1820 adp: r_work=0.1039 r_free=0.1828 ADP+occupancy (water only), MIN, final r_work=0.1039 r_free=0.1828 r_work=0.1039 r_free=0.1828 | n_water=236 | time (s): 10.270 (total time: 34.060) Filter (q & B) r_work=0.1040 r_free=0.1828 | n_water=235 | time (s): 1.370 (total time: 35.430) Filter (dist only) r_work=0.1047 r_free=0.1837 | n_water=233 | time (s): 17.630 (total time: 53.060) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.141623 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.254760 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 0.0937 0.1884 0.0947 0.011 1.1 4.2 0.5 0.6 0 0.571 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.37 18.84 9.47 5.749 18.290 0.255 5.125 8.98 18.68 9.70 7.774 18.378 0.255 5.031 Individual atomic B min max mean iso aniso Overall: 0.00 108.25 16.87 9.59 1760 0 Protein: 0.00 108.25 15.77 9.58 1519 0 Water: 0.00 57.91 23.66 N/A 233 0 Other: 12.78 42.66 28.36 N/A 8 0 Chain A: 0.00 108.25 16.39 N/A 1653 0 Chain S: 0.00 55.47 24.23 N/A 107 0 Histogram: Values Number of atoms 0.00 - 10.82 639 10.82 - 21.65 684 21.65 - 32.47 253 32.47 - 43.30 109 43.30 - 54.12 37 54.12 - 64.95 19 64.95 - 75.77 11 75.77 - 86.60 3 86.60 - 97.42 4 97.42 - 108.25 1 =========================== Idealize ADP of riding H ========================== r_work=0.0898 r_free=0.1868 r_work=0.0906 r_free=0.1875 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0906 r_free = 0.1875 target_work(ml) = 5.037 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0893 r_free = 0.1868 target_work(ml) = 5.030 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0893 r_free= 0.1868 coordinate error (max.-lik. estimate): 0.27 A | | | | normalized target function (ml) (work): 5.030266 | | target function (ml) not normalized (work): 24758.967004 | | target function (ml) not normalized (free): 1856.854504 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0942 0.0893 0.1868 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2167 0.2174 0.2187 n_refl.: 5174 remove outliers: r(all,work,free)=0.2167 0.2174 0.2187 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2167 0.2174 0.2187 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0936 0.0888 0.1857 n_refl.: 5174 remove outliers: r(all,work,free)=0.0936 0.0888 0.1857 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 0.3700 319.693 292.670 0.630 0.998 0.360 11.894-9.307 99.02 97 4 0.1782 507.835 494.808 0.952 1.001 0.360 9.237-7.194 100.00 213 7 0.1884 415.308 410.301 0.981 1.002 0.304 7.162-5.571 100.00 427 22 0.1797 311.638 303.286 0.978 1.002 0.280 5.546-4.326 100.00 867 58 0.0919 427.835 423.094 0.992 1.002 0.230 4.315-3.360 100.00 1859 96 0.0597 406.876 406.357 1.058 1.002 0.220 3.356-3.002 100.00 1373 60 0.0607 313.393 312.882 1.034 1.002 0.087 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-6.3774 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0888 r_free=0.1857 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=0.0891 r_free=0.1859 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0891 r_free=0.1859 | n_water=233 | time (s): 0.510 (total time: 0.510) Filter (dist) r_work=0.0907 r_free=0.1869 | n_water=229 | time (s): 18.600 (total time: 19.110) Filter (q & B) r_work=0.0976 r_free=0.1891 | n_water=226 | time (s): 1.490 (total time: 20.600) Compute maps r_work=0.0976 r_free=0.1891 | n_water=226 | time (s): 0.480 (total time: 21.080) Filter (map) r_work=0.1225 r_free=0.1873 | n_water=155 | time (s): 1.270 (total time: 22.350) Find peaks r_work=0.1225 r_free=0.1873 | n_water=155 | time (s): 0.450 (total time: 22.800) Add new water r_work=0.1529 r_free=0.2229 | n_water=227 | time (s): 1.430 (total time: 24.230) Refine new water occ: r_work=0.1017 r_free=0.1875 adp: r_work=0.1012 r_free=0.1885 occ: r_work=0.1003 r_free=0.1861 adp: r_work=0.1003 r_free=0.1870 occ: r_work=0.0995 r_free=0.1845 adp: r_work=0.0995 r_free=0.1855 ADP+occupancy (water only), MIN, final r_work=0.0995 r_free=0.1855 r_work=0.0995 r_free=0.1855 | n_water=227 | time (s): 12.610 (total time: 36.840) Filter (q & B) r_work=0.0995 r_free=0.1860 | n_water=226 | time (s): 1.280 (total time: 38.120) Filter (dist only) r_work=0.0996 r_free=0.1850 | n_water=224 | time (s): 16.710 (total time: 54.830) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.056298 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.210396 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 0.0901 0.1892 0.0991 0.011 1.0 4.2 0.5 0.6 0 0.528 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.01 18.92 9.91 7.422 18.565 0.210 5.022 8.77 19.21 10.44 8.379 18.638 0.210 4.958 Individual atomic B min max mean iso aniso Overall: 0.00 105.25 17.09 10.79 1751 0 Protein: 0.00 105.25 16.10 10.78 1519 0 Water: 0.00 61.12 23.41 N/A 224 0 Other: 13.47 44.10 28.59 N/A 8 0 Chain A: 0.00 105.25 16.64 N/A 1642 0 Chain S: 0.00 55.04 23.97 N/A 109 0 Histogram: Values Number of atoms 0.00 - 10.52 610 10.52 - 21.05 655 21.05 - 31.57 285 31.57 - 42.10 113 42.10 - 52.62 49 52.62 - 63.15 16 63.15 - 73.67 11 73.67 - 84.20 7 84.20 - 94.72 3 94.72 - 105.25 2 =========================== Idealize ADP of riding H ========================== r_work=0.0877 r_free=0.1921 r_work=0.0880 r_free=0.1926 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0880 r_free = 0.1926 target_work(ml) = 4.964 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0870 r_free = 0.1906 target_work(ml) = 4.956 | | 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= 0.0870 r_free= 0.1906 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ml) (work): 4.956107 | | target function (ml) not normalized (work): 24393.956906 | | target function (ml) not normalized (free): 2201.527831 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0922 0.0870 0.1906 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2223 0.2228 0.2265 n_refl.: 5174 remove outliers: r(all,work,free)=0.2223 0.2228 0.2265 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2223 0.2228 0.2265 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0919 0.0868 0.1898 n_refl.: 5174 remove outliers: r(all,work,free)=0.0917 0.0866 0.1898 n_refl.: 5173 ======================== 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 93.75 85 5 0.3547 321.854 288.146 0.614 0.993 0.348 11.894-9.307 99.02 97 4 0.1848 507.835 494.627 0.950 0.997 0.333 9.237-7.194 100.00 213 7 0.2056 415.308 407.429 0.989 0.999 0.320 7.162-5.571 100.00 427 22 0.1919 311.638 303.761 0.987 1.000 0.281 5.546-4.326 100.00 867 58 0.0944 427.835 422.496 1.009 1.001 0.231 4.315-3.360 100.00 1859 96 0.0566 406.876 406.628 1.080 1.002 0.223 3.356-3.002 100.00 1373 60 0.0474 313.393 312.944 1.058 1.003 0.090 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9171 b_overall=-7.4160 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0866 r_free=0.1898 After: r_work=0.0869 r_free=0.1896 ================================== NQH flips ================================== r_work=0.0869 r_free=0.1896 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN A Total number of N/Q/H flips: 2 r_work=0.0870 r_free=0.1891 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0870 r_free=0.1891 | n_water=224 | time (s): 0.620 (total time: 0.620) Filter (dist) r_work=0.0872 r_free=0.1879 | n_water=223 | time (s): 17.210 (total time: 17.830) Filter (q & B) r_work=0.0973 r_free=0.1914 | n_water=220 | time (s): 1.290 (total time: 19.120) Compute maps r_work=0.0973 r_free=0.1914 | n_water=220 | time (s): 0.420 (total time: 19.540) Filter (map) r_work=0.1230 r_free=0.1928 | n_water=157 | time (s): 1.490 (total time: 21.030) Find peaks r_work=0.1230 r_free=0.1928 | n_water=157 | time (s): 0.470 (total time: 21.500) Add new water r_work=0.1505 r_free=0.2171 | n_water=221 | time (s): 1.340 (total time: 22.840) Refine new water occ: r_work=0.0978 r_free=0.1856 adp: r_work=0.0971 r_free=0.1858 occ: r_work=0.0966 r_free=0.1848 adp: r_work=0.0964 r_free=0.1852 occ: r_work=0.0960 r_free=0.1841 adp: r_work=0.0958 r_free=0.1844 ADP+occupancy (water only), MIN, final r_work=0.0958 r_free=0.1844 r_work=0.0958 r_free=0.1844 | n_water=221 | time (s): 10.610 (total time: 33.450) Filter (q & B) r_work=0.0958 r_free=0.1840 | n_water=220 | time (s): 1.470 (total time: 34.920) Filter (dist only) r_work=0.0958 r_free=0.1840 | n_water=220 | time (s): 17.210 (total time: 52.130) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.956366 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.207007 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 0.0905 0.1853 0.0949 0.010 1.1 6.1 0.5 0.6 0 0.478 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.05 18.53 9.49 8.212 18.818 0.207 4.985 8.89 18.58 9.69 8.956 18.902 0.207 4.932 Individual atomic B min max mean iso aniso Overall: 0.00 102.54 17.28 11.80 1747 0 Protein: 0.00 102.54 16.43 11.79 1519 0 Water: 0.00 62.34 22.73 N/A 220 0 Other: 10.99 44.43 27.92 N/A 8 0 Chain A: 0.00 102.54 16.85 N/A 1631 0 Chain S: 0.00 50.43 23.35 N/A 116 0 Histogram: Values Number of atoms 0.00 - 10.25 578 10.25 - 20.51 648 20.51 - 30.76 306 30.76 - 41.02 115 41.02 - 51.27 55 51.27 - 61.53 20 61.53 - 71.78 12 71.78 - 82.03 4 82.03 - 92.29 5 92.29 - 102.54 4 =========================== Idealize ADP of riding H ========================== r_work=0.0889 r_free=0.1858 r_work=0.0891 r_free=0.1861 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0891 r_free = 0.1861 target_work(ml) = 4.936 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0885 r_free = 0.1851 target_work(ml) = 4.932 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5173 (all), 4.87 % free)-------------| | | | r_work= 0.0885 r_free= 0.1851 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ml) (work): 4.931784 | | target function (ml) not normalized (work): 24269.308950 | | target function (ml) not normalized (free): 2312.285935 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.79 1.00 2491 142 0.1253 0.1809 5.5025 6.2081| | 2: 3.78 - 3.00 1.00 2430 110 0.0436 0.1922 4.3467 13.007| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2491 142 0.92 11.99 1.00 0.96 11998.52| | 2: 3.78 - 3.00 2430 110 0.99 1.90 1.00 0.98 877.80| |alpha: min = 0.95 max = 0.98 mean = 0.97| |beta: min = 558.96 max = 19878.21 mean = 6507.09| |figures of merit: min = 0.00 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.94 mean = 7.01| |phase err.(test): min = 0.00 max = 88.15 mean = 7.47| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0934 0.0885 0.1851 n_refl.: 5173 re-set all scales: r(all,work,free)=0.2189 0.2192 0.2280 n_refl.: 5173 remove outliers: r(all,work,free)=0.2189 0.2192 0.2280 n_refl.: 5173 overall B=-0.00 to atoms: r(all,work,free)=0.2189 0.2192 0.2280 n_refl.: 5173 bulk-solvent and scaling: r(all,work,free)=0.0933 0.0884 0.1852 n_refl.: 5173 remove outliers: r(all,work,free)=0.0933 0.0884 0.1852 n_refl.: 5173 ======================== 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 93.75 85 5 0.3665 321.854 292.679 0.616 0.983 0.335 11.894-9.307 99.02 97 4 0.1883 507.835 492.884 0.965 0.989 0.331 9.237-7.194 100.00 213 7 0.2100 415.308 405.893 0.996 0.993 0.310 7.162-5.571 100.00 427 22 0.2075 311.638 302.057 0.992 0.995 0.280 5.546-4.326 100.00 867 58 0.1009 427.835 421.668 1.020 0.998 0.233 4.315-3.360 100.00 1859 96 0.0576 406.876 406.821 1.096 1.003 0.226 3.356-3.002 100.00 1373 60 0.0411 313.393 313.662 1.073 1.007 0.080 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-8.1958 ================= 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 : 0.3625 0.1989 0.082 5.349 8.8 119.3 19.9 258 0.000 1_bss: 0.1560 0.1593 0.082 5.349 6.2 116.7 17.3 258 0.000 1_settarget: 0.1560 0.1593 0.082 5.349 6.2 116.7 17.3 258 0.000 1_nqh: 0.1567 0.1594 0.082 5.349 6.2 116.7 17.3 258 0.006 1_weight: 0.1567 0.1594 0.082 5.349 6.2 116.7 17.3 258 0.006 1_xyzrec: 0.1156 0.1766 0.010 0.998 6.2 116.7 17.3 258 0.197 1_adp: 0.1018 0.1756 0.010 0.998 2.5 112.8 17.7 258 0.197 1_regHadp: 0.1012 0.1763 0.010 0.998 2.5 112.8 17.7 258 0.197 1_occ: 0.1008 0.1746 0.010 0.998 2.5 112.8 17.7 258 0.197 2_bss: 0.1012 0.1743 0.010 0.998 1.4 111.7 16.6 258 0.197 2_settarget: 0.1012 0.1743 0.010 0.998 1.4 111.7 16.6 258 0.197 2_updatecdl: 0.1012 0.1743 0.010 1.013 1.4 111.7 16.6 258 0.197 2_nqh: 0.1012 0.1742 0.010 1.013 1.4 111.7 16.6 258 0.199 2_sol: 0.1134 0.1632 0.010 1.013 1.0 111.7 15.9 229 n/a 2_weight: 0.1134 0.1632 0.010 1.013 1.0 111.7 15.9 229 n/a 2_xyzrec: 0.1022 0.1799 0.009 0.967 1.0 111.7 15.9 229 n/a 2_adp: 0.0947 0.1854 0.009 0.967 0.0 109.3 16.9 229 n/a 2_regHadp: 0.0943 0.1857 0.009 0.967 0.0 109.3 16.9 229 n/a 2_occ: 0.0944 0.1843 0.009 0.967 0.0 109.3 16.9 229 n/a 3_bss: 0.0942 0.1848 0.009 0.967 0.0 109.3 16.9 229 n/a 3_settarget: 0.0942 0.1848 0.009 0.967 0.0 109.3 16.9 229 n/a 3_updatecdl: 0.0942 0.1848 0.009 0.976 0.0 109.3 16.9 229 n/a 3_nqh: 0.0946 0.1838 0.009 0.976 0.0 109.3 16.9 229 n/a 3_sol: 0.1047 0.1837 0.009 0.976 0.0 109.3 16.7 233 n/a 3_weight: 0.1047 0.1837 0.009 0.976 0.0 109.3 16.7 233 n/a 3_xyzrec: 0.0937 0.1884 0.011 1.063 0.0 109.3 16.7 233 n/a 3_adp: 0.0898 0.1868 0.011 1.063 0.0 108.2 16.9 233 n/a 3_regHadp: 0.0906 0.1875 0.011 1.063 0.0 108.2 16.9 233 n/a 3_occ: 0.0893 0.1868 0.011 1.063 0.0 108.2 16.9 233 n/a 4_bss: 0.0888 0.1857 0.011 1.063 0.0 108.2 16.9 233 n/a 4_settarget: 0.0888 0.1857 0.011 1.063 0.0 108.2 16.9 233 n/a 4_updatecdl: 0.0888 0.1857 0.011 1.067 0.0 108.2 16.9 233 n/a 4_nqh: 0.0891 0.1859 0.011 1.067 0.0 108.2 16.9 233 n/a 4_sol: 0.0996 0.1850 0.011 1.067 0.0 108.2 17.0 224 n/a 4_weight: 0.0996 0.1850 0.011 1.067 0.0 108.2 17.0 224 n/a 4_xyzrec: 0.0901 0.1892 0.011 1.043 0.0 108.2 17.0 224 n/a 4_adp: 0.0877 0.1921 0.011 1.043 0.0 105.2 17.1 224 n/a 4_regHadp: 0.0880 0.1926 0.011 1.043 0.0 105.2 17.1 224 n/a 4_occ: 0.0870 0.1906 0.011 1.043 0.0 105.2 17.1 224 n/a 5_bss: 0.0866 0.1898 0.011 1.043 0.0 105.2 17.1 224 n/a 5_settarget: 0.0866 0.1898 0.011 1.043 0.0 105.2 17.1 224 n/a 5_updatecdl: 0.0866 0.1898 0.011 1.044 0.0 105.2 17.1 224 n/a 5_setrh: 0.0869 0.1896 0.011 1.044 0.0 105.2 17.1 224 n/a 5_nqh: 0.0870 0.1891 0.011 1.044 0.0 105.2 17.1 224 n/a 5_sol: 0.0958 0.1840 0.011 1.044 0.0 105.2 17.1 220 n/a 5_weight: 0.0958 0.1840 0.011 1.044 0.0 105.2 17.1 220 n/a 5_xyzrec: 0.0905 0.1853 0.010 1.119 0.0 105.2 17.1 220 n/a 5_adp: 0.0889 0.1858 0.010 1.119 0.0 102.5 17.3 220 n/a 5_regHadp: 0.0891 0.1861 0.010 1.119 0.0 102.5 17.3 220 n/a 5_occ: 0.0885 0.1851 0.010 1.119 0.0 102.5 17.3 220 n/a end: 0.0884 0.1852 0.010 1.119 0.0 102.5 17.3 220 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_1617309_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_1617309_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.2600 Refinement macro-cycles (run) : 488.1800 Write final files (write_after_run_outputs) : 10.6200 Total : 502.0600 Total CPU time: 8.71 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:19:04 PST -0800 (1735492744.49 s) Start R-work = 0.1560, R-free = 0.1593 Final R-work = 0.0884, R-free = 0.1852 =============================================================================== Job complete usr+sys time: 530.16 seconds wall clock time: 9 minutes 12.68 seconds (552.68 seconds total)