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_5638674.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Adding command-line PHIL: ------------------------- xray_data.high_resolution=3 ordered_solvent.low_resolution=4 No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_5638674.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_5638674.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" 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 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: 1.39, per 1000 atoms: 0.41 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: 0.56 Conformation dependent library (CDL) restraints added in 212.0 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.67 - 0.91: 493 0.91 - 1.15: 1126 1.15 - 1.39: 584 1.39 - 1.64: 870 1.64 - 1.88: 80 Bond restraints: 3153 Sorted by residual: bond pdb=" N PHE A 162 " pdb=" CA PHE A 162 " ideal model delta sigma weight residual 1.459 1.699 -0.240 1.20e-02 6.94e+03 4.00e+02 bond pdb=" ND1 HIS A 126 " pdb=" CE1 HIS A 126 " ideal model delta sigma weight residual 1.321 1.133 0.188 1.00e-02 1.00e+04 3.53e+02 bond pdb=" C ALA A 36 " pdb=" N GLY A 37 " ideal model delta sigma weight residual 1.331 1.497 -0.167 8.90e-03 1.26e+04 3.50e+02 bond pdb=" C HIS A 138 " pdb=" O HIS A 138 " ideal model delta sigma weight residual 1.236 1.473 -0.237 1.32e-02 5.74e+03 3.24e+02 bond pdb=" CE1 HIS A 126 " pdb=" NE2 HIS A 126 " ideal model delta sigma weight residual 1.321 1.496 -0.175 1.00e-02 1.00e+04 3.07e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.87: 3176 4.87 - 9.74: 1921 9.74 - 14.61: 576 14.61 - 19.48: 98 19.48 - 24.34: 6 Bond angle restraints: 5777 Sorted by residual: angle pdb=" NE ARG A 145 " pdb=" CZ ARG A 145 " pdb=" NH2 ARG A 145 " ideal model delta sigma weight residual 119.20 132.45 -13.25 9.00e-01 1.23e+00 2.17e+02 angle pdb=" O MET A 17 " pdb=" C MET A 17 " pdb=" N GLU A 18 " ideal model delta sigma weight residual 122.09 137.38 -15.29 1.04e+00 9.25e-01 2.16e+02 angle pdb=" CA ILE A 21 " pdb=" C ILE A 21 " pdb=" O ILE A 21 " ideal model delta sigma weight residual 118.69 128.17 -9.48 6.70e-01 2.23e+00 2.00e+02 angle pdb=" CA MET A 17 " pdb=" C MET A 17 " pdb=" N GLU A 18 " ideal model delta sigma weight residual 116.97 100.54 16.43 1.20e+00 6.94e-01 1.88e+02 angle pdb=" N AASN A 76 " pdb=" CA AASN A 76 " pdb=" C AASN A 76 " ideal model delta sigma weight residual 111.33 127.20 -15.87 1.21e+00 6.83e-01 1.72e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.16: 1287 17.16 - 34.33: 135 34.33 - 51.49: 44 51.49 - 68.65: 12 68.65 - 85.81: 3 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" N GLU A 16 " pdb=" C GLU A 16 " pdb=" CA GLU A 16 " pdb=" CB GLU A 16 " ideal model delta harmonic sigma weight residual 122.80 147.04 -24.24 0 2.50e+00 1.60e-01 9.40e+01 dihedral pdb=" C GLU A 16 " pdb=" N GLU A 16 " pdb=" CA GLU A 16 " pdb=" CB GLU A 16 " ideal model delta harmonic sigma weight residual -122.60 -146.15 23.55 0 2.50e+00 1.60e-01 8.87e+01 dihedral pdb=" N VAL A 25 " pdb=" C VAL A 25 " pdb=" CA VAL A 25 " pdb=" CB VAL A 25 " ideal model delta harmonic sigma weight residual 123.40 142.41 -19.01 0 2.50e+00 1.60e-01 5.78e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.220: 92 0.220 - 0.439: 82 0.439 - 0.658: 43 0.658 - 0.877: 22 0.877 - 1.095: 4 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA GLU A 16 " pdb=" N GLU A 16 " pdb=" C GLU A 16 " pdb=" CB GLU A 16 " both_signs ideal model delta sigma weight residual False 2.51 1.42 1.10 2.00e-01 2.50e+01 3.00e+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 1.57 0.94 2.00e-01 2.50e+01 2.21e+01 chirality pdb=" CA GLU A 59 " pdb=" N GLU A 59 " pdb=" C GLU A 59 " pdb=" CB GLU A 59 " both_signs ideal model delta sigma weight residual False 2.51 3.41 -0.90 2.00e-01 2.50e+01 2.02e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 173 " 0.011 2.00e-02 2.50e+03 8.15e-02 9.95e+01 pdb=" CG ASN A 173 " -0.120 2.00e-02 2.50e+03 pdb=" OD1 ASN A 173 " 0.089 2.00e-02 2.50e+03 pdb=" ND2 ASN A 173 " -0.077 2.00e-02 2.50e+03 pdb="HD21 ASN A 173 " -0.010 2.00e-02 2.50e+03 pdb="HD22 ASN A 173 " 0.107 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 48 " -0.120 9.50e-02 1.11e+02 7.64e-02 9.66e+01 pdb=" NE ARG A 48 " 0.047 2.00e-02 2.50e+03 pdb=" CZ ARG A 48 " -0.025 2.00e-02 2.50e+03 pdb=" NH1 ARG A 48 " 0.120 2.00e-02 2.50e+03 pdb=" NH2 ARG A 48 " -0.084 2.00e-02 2.50e+03 pdb="HH11 ARG A 48 " -0.111 2.00e-02 2.50e+03 pdb="HH12 ARG A 48 " 0.026 2.00e-02 2.50e+03 pdb="HH21 ARG A 48 " 0.025 2.00e-02 2.50e+03 pdb="HH22 ARG A 48 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " 0.050 2.00e-02 2.50e+03 5.39e-02 8.71e+01 pdb=" CG PHE A 162 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " -0.099 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " 0.025 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " -0.068 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " -0.039 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " -0.022 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " -0.010 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " 0.015 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " 0.103 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " 0.014 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.33: 1076 2.33 - 2.89: 8139 2.89 - 3.46: 10488 3.46 - 4.03: 15238 4.03 - 4.60: 21760 Nonbonded interactions: 56701 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.757 2.100 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.803 2.450 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.815 2.450 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.816 2.450 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.844 2.450 x-y,-y,-z-4/3 ... (remaining 56696 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_5638674_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= 0.3619 r_free= 0.2080 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.472436 | | target function (ml) not normalized (work): 22049.110829 | | target function (ml) not normalized (free): 1153.604598 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3810 0.2302 4.851 4.9114| | 2: 3.78 - 3.00 1.00 2430 110 0.3386 0.1704 4.0829 4.1472| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 48.92 0.83 0.13 6614.29| | 2: 3.78 - 3.00 2430 110 0.93 11.42 1.48 0.26 450.81| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 381.18 max = 12066.62 mean = 3576.31| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 89.99 mean = 30.44| |phase err.(test): min = 0.00 max = 89.92 mean = 33.30| |-----------------------------------------------------------------------------| ----------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 : 0.080 0.260 1557 Z= 5.315 Angle : 5.304 19.146 2118 Z= 3.778 Chirality : 0.398 1.095 243 Planarity : 0.032 0.113 284 Dihedral : 14.211 85.809 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.70 % Favored : 96.76 % Rotamer: Outliers : 1.24 % Allowed : 3.73 % Favored : 95.03 % Cbeta Deviations : 32.43 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.45), residues: 224 helix: -2.98 (0.34), residues: 109 sheet: -0.98 (0.93), residues: 28 loop : -0.45 (0.55), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.139 0.024 ARG A 28 TYR 0.070 0.028 TYR A 139 PHE 0.074 0.039 PHE A 164 HIS 0.068 0.027 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= 0.3619 r_free= 0.2080 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.472436 | | target function (ml) not normalized (work): 22049.110829 | | target function (ml) not normalized (free): 1153.604598 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3574 0.3649 0.2187 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3574 0.3649 0.2187 n_refl.: 5182 remove outliers: r(all,work,free)=0.2530 0.2552 0.2187 n_refl.: 5178 overall B=-2.89 to atoms: r(all,work,free)=0.2422 0.2440 0.2135 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1577 0.1575 0.1624 n_refl.: 5178 remove outliers: r(all,work,free)=0.1572 0.1569 0.1624 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 0.3873 444.251 404.030 0.651 1.061 0.381 11.894-9.307 99.02 97 4 0.1832 714.660 696.981 0.945 1.058 0.383 9.237-7.194 100.00 213 7 0.2160 584.450 575.714 0.983 1.052 0.367 7.162-5.571 100.00 427 22 0.2349 438.559 424.449 0.942 1.041 0.292 5.546-4.326 100.00 867 58 0.1371 602.079 596.065 0.986 1.022 0.219 4.315-3.360 100.00 1859 96 0.1337 572.584 565.301 1.054 0.990 0.190 3.356-3.002 100.00 1373 60 0.1607 441.028 433.267 1.064 0.959 0.097 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9559 b_overall=-3.6805 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1569 r_free=0.1624 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1569 r_free=0.1624 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 19.588462 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.941171 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1159 0.1777 0.0618 0.010 1.0 2.2 0.5 0.0 0 9.794 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.59 17.77 6.18 3.013 15.966 1.941 0.018 10.18 17.79 7.60 4.871 16.136 1.941 0.015 Individual atomic B min max mean iso aniso Overall: 1.63 111.59 17.32 5.29 1785 0 Protein: 1.63 111.59 14.60 5.29 1519 0 Water: 3.97 111.41 33.07 N/A 258 0 Other: 17.88 36.89 24.33 N/A 8 0 Chain A: 1.63 111.59 17.32 N/A 1785 0 Histogram: Values Number of atoms 1.63 - 12.63 891 12.63 - 23.63 506 23.63 - 34.62 191 34.62 - 45.62 104 45.62 - 56.61 59 56.61 - 67.61 17 67.61 - 78.60 8 78.60 - 89.60 5 89.60 - 100.60 1 100.60 - 111.59 3 =========================== Idealize ADP of riding H ========================== r_work=0.1018 r_free=0.1779 r_work=0.1013 r_free=0.1786 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1013 r_free = 0.1786 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1009 r_free = 0.1769 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.22 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= 0.1009 r_free= 0.1769 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ls_wunit_k1) (work): 0.013926 | | target function (ls_wunit_k1) not normalized (work): 68.559008 | | target function (ls_wunit_k1) not normalized (free): 10.200071 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1047 0.1009 0.1769 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2000 0.1990 0.2247 n_refl.: 5175 remove outliers: r(all,work,free)=0.2000 0.1990 0.2247 n_refl.: 5175 overall B=-0.96 to atoms: r(all,work,free)=0.1963 0.1952 0.2235 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.1051 0.1012 0.1782 n_refl.: 5175 remove outliers: r(all,work,free)=0.1051 0.1012 0.1782 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 0.3284 327.349 307.216 0.662 0.999 0.360 11.894-9.307 99.02 97 4 0.1572 526.602 519.356 0.994 1.002 0.361 9.237-7.194 100.00 213 7 0.1678 430.656 430.139 1.036 1.002 0.351 7.162-5.571 100.00 427 22 0.1609 323.155 319.824 0.988 1.002 0.292 5.546-4.326 100.00 867 58 0.0914 443.646 440.438 1.001 1.001 0.202 4.315-3.360 100.00 1859 96 0.0766 421.912 421.905 1.040 1.000 0.193 3.356-3.002 100.00 1373 60 0.1001 324.974 323.070 1.010 0.998 0.092 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-3.4255 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1012 r_free=0.1782 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=0.1013 r_free=0.1781 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1013 r_free=0.1781 | n_water=258 | time (s): 0.630 (total time: 0.630) Filter (dist) r_work=0.1036 r_free=0.1767 | n_water=248 | time (s): 20.950 (total time: 21.580) Filter (q & B) r_work=0.1036 r_free=0.1768 | n_water=245 | time (s): 1.460 (total time: 23.040) Compute maps r_work=0.1036 r_free=0.1768 | n_water=245 | time (s): 0.450 (total time: 23.490) Filter (map) r_work=0.1305 r_free=0.1876 | n_water=155 | time (s): 1.370 (total time: 24.860) Find peaks r_work=0.1305 r_free=0.1876 | n_water=155 | time (s): 0.510 (total time: 25.370) Add new water r_work=0.1657 r_free=0.2116 | n_water=242 | time (s): 1.630 (total time: 27.000) Refine new water occ: r_work=0.1139 r_free=0.1636 adp: r_work=0.1114 r_free=0.1649 occ: r_work=0.1112 r_free=0.1622 adp: r_work=0.1099 r_free=0.1637 occ: r_work=0.1099 r_free=0.1623 adp: r_work=0.1099 r_free=0.1623 ADP+occupancy (water only), MIN, final r_work=0.1099 r_free=0.1623 r_work=0.1099 r_free=0.1623 | n_water=242 | time (s): 4.810 (total time: 31.810) Filter (q & B) r_work=0.1100 r_free=0.1624 | n_water=240 | time (s): 1.800 (total time: 33.610) Filter (dist only) r_work=0.1112 r_free=0.1628 | n_water=236 | time (s): 19.330 (total time: 52.940) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.299773 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.790087 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 0.1007 0.1797 0.0791 0.009 1.0 4.5 0.5 0.6 0 11.150 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.07 17.97 7.91 4.657 16.663 2.790 0.014 9.41 18.16 8.75 5.441 17.090 2.790 0.012 Individual atomic B min max mean iso aniso Overall: 0.00 108.16 16.53 6.50 1763 0 Protein: 0.00 108.16 14.92 6.47 1519 0 Water: 0.00 62.73 26.40 N/A 236 0 Other: 15.17 45.11 30.92 N/A 8 0 Chain A: 0.00 108.16 15.75 N/A 1678 0 Chain S: 8.47 60.36 32.06 N/A 85 0 Histogram: Values Number of atoms 0.00 - 10.82 691 10.82 - 21.63 662 21.63 - 32.45 218 32.45 - 43.26 116 43.26 - 54.08 36 54.08 - 64.90 24 64.90 - 75.71 9 75.71 - 86.53 3 86.53 - 97.34 2 97.34 - 108.16 2 =========================== Idealize ADP of riding H ========================== r_work=0.0941 r_free=0.1816 r_work=0.0939 r_free=0.1818 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0939 r_free = 0.1818 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0939 r_free = 0.1800 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.28 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= 0.0939 r_free= 0.1800 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ls_wunit_k1) (work): 0.011843 | | target function (ls_wunit_k1) not normalized (work): 58.304761 | | target function (ls_wunit_k1) not normalized (free): 10.119484 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0983 0.0939 0.1800 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2031 0.2027 0.2212 n_refl.: 5175 remove outliers: r(all,work,free)=0.2031 0.2027 0.2212 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2031 0.2027 0.2212 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0979 0.0936 0.1802 n_refl.: 5175 remove outliers: r(all,work,free)=0.0979 0.0936 0.1802 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 0.3266 327.349 308.662 0.664 1.004 0.350 11.894-9.307 99.02 97 4 0.1477 526.602 521.789 0.987 1.006 0.330 9.237-7.194 100.00 213 7 0.1442 430.656 433.090 1.027 1.006 0.310 7.162-5.571 100.00 427 22 0.1413 323.155 320.670 0.992 1.005 0.300 5.546-4.326 100.00 867 58 0.0807 443.646 441.131 1.007 1.003 0.225 4.315-3.360 100.00 1859 96 0.0727 421.912 421.634 1.053 0.999 0.221 3.356-3.002 100.00 1373 60 0.0948 324.974 323.979 1.028 0.995 0.110 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-4.0471 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0936 r_free=0.1802 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0936 r_free=0.1802 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0936 r_free=0.1802 | n_water=236 | time (s): 0.650 (total time: 0.650) Filter (dist) r_work=0.0949 r_free=0.1793 | n_water=232 | time (s): 20.200 (total time: 20.850) Filter (q & B) r_work=0.1009 r_free=0.1802 | n_water=230 | time (s): 1.650 (total time: 22.500) Compute maps r_work=0.1009 r_free=0.1802 | n_water=230 | time (s): 0.660 (total time: 23.160) Filter (map) r_work=0.1271 r_free=0.1931 | n_water=153 | time (s): 1.800 (total time: 24.960) Find peaks r_work=0.1271 r_free=0.1931 | n_water=153 | time (s): 0.440 (total time: 25.400) Add new water r_work=0.1672 r_free=0.2317 | n_water=243 | time (s): 1.490 (total time: 26.890) Refine new water occ: r_work=0.1081 r_free=0.1795 adp: r_work=0.1077 r_free=0.1814 occ: r_work=0.1062 r_free=0.1791 adp: r_work=0.1063 r_free=0.1802 occ: r_work=0.1049 r_free=0.1779 adp: r_work=0.1051 r_free=0.1787 ADP+occupancy (water only), MIN, final r_work=0.1051 r_free=0.1787 r_work=0.1051 r_free=0.1787 | n_water=243 | time (s): 11.220 (total time: 38.110) Filter (q & B) r_work=0.1052 r_free=0.1786 | n_water=242 | time (s): 1.910 (total time: 40.020) Filter (dist only) r_work=0.1055 r_free=0.1786 | n_water=240 | time (s): 19.210 (total time: 59.230) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.075694 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.230106 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 0.0947 0.1794 0.0847 0.011 1.1 4.5 0.5 0.0 0 0.538 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.47 17.94 8.47 5.425 17.752 0.230 5.161 9.03 17.81 8.77 7.208 17.762 0.230 5.066 Individual atomic B min max mean iso aniso Overall: 0.00 110.00 16.37 8.90 1767 0 Protein: 0.00 110.00 15.03 8.87 1519 0 Water: 0.00 60.07 24.22 N/A 240 0 Other: 18.76 50.11 34.30 N/A 8 0 Chain A: 0.00 110.00 15.80 N/A 1662 0 Chain S: 0.00 60.07 25.35 N/A 105 0 Histogram: Values Number of atoms 0.00 - 11.00 712 11.00 - 22.00 646 22.00 - 33.00 224 33.00 - 44.00 114 44.00 - 55.00 37 55.00 - 66.00 17 66.00 - 77.00 10 77.00 - 88.00 3 88.00 - 99.00 3 99.00 - 110.00 1 =========================== Idealize ADP of riding H ========================== r_work=0.0903 r_free=0.1781 r_work=0.0908 r_free=0.1790 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0908 r_free = 0.1790 target_work(ml) = 5.070 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0897 r_free = 0.1771 target_work(ml) = 5.062 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0897 r_free= 0.1771 coordinate error (max.-lik. estimate): 0.25 A | | | | normalized target function (ml) (work): 5.062472 | | target function (ml) not normalized (work): 24922.551989 | | target function (ml) not normalized (free): 1778.872670 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0941 0.0897 0.1771 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2014 0.2019 0.2077 n_refl.: 5175 remove outliers: r(all,work,free)=0.2014 0.2019 0.2077 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2014 0.2019 0.2077 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0931 0.0888 0.1760 n_refl.: 5175 remove outliers: r(all,work,free)=0.0931 0.0888 0.1760 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 0.3781 327.349 297.357 0.577 0.992 0.320 11.894-9.307 99.02 97 4 0.1937 526.602 508.677 0.949 0.995 0.320 9.237-7.194 100.00 213 7 0.1938 430.656 424.874 1.013 0.997 0.300 7.162-5.571 100.00 427 22 0.1820 323.155 314.505 0.982 0.998 0.300 5.546-4.326 100.00 867 58 0.0899 443.646 438.870 1.002 1.000 0.229 4.315-3.360 100.00 1859 96 0.0585 421.912 421.216 1.057 1.001 0.228 3.356-3.002 100.00 1373 60 0.0602 324.974 324.893 1.034 1.002 0.110 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-6.4228 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0888 r_free=0.1760 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A A 80 GLN A Total number of N/Q/H flips: 2 r_work=0.0889 r_free=0.1770 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0889 r_free=0.1770 | n_water=240 | time (s): 0.540 (total time: 0.540) Filter (dist) r_work=0.0900 r_free=0.1780 | n_water=236 | time (s): 20.340 (total time: 20.880) Filter (q & B) r_work=0.0929 r_free=0.1789 | n_water=235 | time (s): 1.950 (total time: 22.830) Compute maps r_work=0.0929 r_free=0.1789 | n_water=235 | time (s): 0.580 (total time: 23.410) Filter (map) r_work=0.1192 r_free=0.1850 | n_water=164 | time (s): 1.840 (total time: 25.250) Find peaks r_work=0.1192 r_free=0.1850 | n_water=164 | time (s): 0.580 (total time: 25.830) Add new water r_work=0.1514 r_free=0.2152 | n_water=239 | time (s): 1.750 (total time: 27.580) Refine new water occ: r_work=0.1024 r_free=0.1753 adp: r_work=0.1021 r_free=0.1762 occ: r_work=0.1011 r_free=0.1749 adp: r_work=0.1012 r_free=0.1752 occ: r_work=0.1003 r_free=0.1737 adp: r_work=0.1002 r_free=0.1741 ADP+occupancy (water only), MIN, final r_work=0.1002 r_free=0.1741 r_work=0.1002 r_free=0.1741 | n_water=239 | time (s): 9.230 (total time: 36.810) Filter (q & B) r_work=0.1002 r_free=0.1741 | n_water=239 | time (s): 0.710 (total time: 37.520) Filter (dist only) r_work=0.1018 r_free=0.1744 | n_water=237 | time (s): 17.830 (total time: 55.350) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.983208 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.241524 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 0.0921 0.1793 0.0872 0.011 1.0 3.8 0.5 0.0 0 0.492 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.21 17.93 8.72 6.934 17.852 0.242 5.048 8.92 18.04 9.11 8.058 17.951 0.242 4.981 Individual atomic B min max mean iso aniso Overall: 0.00 112.59 16.64 10.46 1764 0 Protein: 0.00 112.59 15.45 10.45 1519 0 Water: 0.00 55.00 23.68 N/A 237 0 Other: 23.91 52.16 35.43 N/A 8 0 Chain A: 0.00 112.59 16.09 N/A 1651 0 Chain S: 0.62 55.00 24.79 N/A 113 0 Histogram: Values Number of atoms 0.00 - 11.26 718 11.26 - 22.52 635 22.52 - 33.78 229 33.78 - 45.04 107 45.04 - 56.30 46 56.30 - 67.55 11 67.55 - 78.81 11 78.81 - 90.07 4 90.07 - 101.33 2 101.33 - 112.59 1 =========================== Idealize ADP of riding H ========================== r_work=0.0892 r_free=0.1804 r_work=0.0897 r_free=0.1814 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0897 r_free = 0.1814 target_work(ml) = 4.987 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0885 r_free = 0.1791 target_work(ml) = 4.979 | | occupancies: max = 1.00 min = 0.26 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= 0.0885 r_free= 0.1791 coordinate error (max.-lik. estimate): 0.25 A | | | | normalized target function (ml) (work): 4.978908 | | target function (ml) not normalized (work): 24511.161889 | | target function (ml) not normalized (free): 2070.092104 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0930 0.0885 0.1791 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2074 0.2079 0.2148 n_refl.: 5175 remove outliers: r(all,work,free)=0.2074 0.2079 0.2148 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2074 0.2079 0.2148 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0928 0.0884 0.1791 n_refl.: 5175 remove outliers: r(all,work,free)=0.0928 0.0884 0.1791 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 0.4013 327.349 296.897 0.572 0.988 0.320 11.894-9.307 99.02 97 4 0.1891 526.602 506.629 0.952 0.994 0.320 9.237-7.194 100.00 213 7 0.2108 430.656 423.570 1.010 0.997 0.300 7.162-5.571 100.00 427 22 0.2033 323.155 313.299 0.992 0.999 0.290 5.546-4.326 100.00 867 58 0.0966 443.646 438.377 1.011 1.000 0.245 4.315-3.360 100.00 1859 96 0.0564 421.912 421.730 1.076 1.002 0.240 3.356-3.002 100.00 1373 60 0.0453 324.974 324.869 1.054 1.004 0.100 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.3454 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0884 r_free=0.1791 After: r_work=0.0886 r_free=0.1789 ================================== NQH flips ================================== r_work=0.0886 r_free=0.1789 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0886 r_free=0.1789 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0886 r_free=0.1789 | n_water=237 | time (s): 0.470 (total time: 0.470) Filter (dist) r_work=0.0891 r_free=0.1804 | n_water=233 | time (s): 17.880 (total time: 18.350) Filter (q & B) r_work=0.0968 r_free=0.1815 | n_water=231 | time (s): 1.390 (total time: 19.740) Compute maps r_work=0.0968 r_free=0.1815 | n_water=231 | time (s): 0.450 (total time: 20.190) Filter (map) r_work=0.1206 r_free=0.1889 | n_water=168 | time (s): 1.450 (total time: 21.640) Find peaks r_work=0.1206 r_free=0.1889 | n_water=168 | time (s): 0.450 (total time: 22.090) Add new water r_work=0.1482 r_free=0.2167 | n_water=236 | time (s): 1.550 (total time: 23.640) Refine new water occ: r_work=0.0995 r_free=0.1797 adp: r_work=0.0985 r_free=0.1816 occ: r_work=0.0979 r_free=0.1798 adp: r_work=0.0978 r_free=0.1806 occ: r_work=0.0972 r_free=0.1784 adp: r_work=0.0972 r_free=0.1793 ADP+occupancy (water only), MIN, final r_work=0.0972 r_free=0.1793 r_work=0.0972 r_free=0.1793 | n_water=236 | time (s): 10.340 (total time: 33.980) Filter (q & B) r_work=0.0972 r_free=0.1795 | n_water=235 | time (s): 1.510 (total time: 35.490) Filter (dist only) r_work=0.0977 r_free=0.1806 | n_water=234 | time (s): 18.670 (total time: 54.160) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.991989 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.202577 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 0.0920 0.1804 0.0884 0.011 1.1 7.4 0.5 0.0 0 0.496 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.20 18.04 8.84 7.981 18.241 0.203 5.012 9.03 18.28 9.24 8.770 18.339 0.203 4.959 Individual atomic B min max mean iso aniso Overall: 0.00 113.45 16.92 11.51 1761 0 Protein: 0.00 113.45 15.80 11.51 1519 0 Water: 0.00 60.31 23.59 N/A 234 0 Other: 21.78 51.04 33.39 N/A 8 0 Chain A: 0.00 113.45 16.36 N/A 1643 0 Chain S: 0.00 60.31 24.67 N/A 118 0 Histogram: Values Number of atoms 0.00 - 11.34 695 11.34 - 22.69 648 22.69 - 34.03 242 34.03 - 45.38 107 45.38 - 56.72 34 56.72 - 68.07 17 68.07 - 79.41 10 79.41 - 90.76 4 90.76 - 102.10 2 102.10 - 113.45 2 =========================== Idealize ADP of riding H ========================== r_work=0.0903 r_free=0.1828 r_work=0.0908 r_free=0.1833 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0908 r_free = 0.1833 target_work(ml) = 4.966 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0900 r_free = 0.1811 target_work(ml) = 4.960 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0900 r_free= 0.1811 coordinate error (max.-lik. estimate): 0.25 A | | | | normalized target function (ml) (work): 4.960014 | | target function (ml) not normalized (work): 24418.150764 | | target function (ml) not normalized (free): 2124.636819 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.79 1.00 2493 142 0.1292 0.1842 5.5511 6.121| | 2: 3.78 - 3.00 1.00 2430 110 0.0422 0.1759 4.3536 11.413| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.79 2493 142 0.91 12.53 1.00 0.98 13654.48| | 2: 3.78 - 3.00 2430 110 0.99 1.82 1.00 1.00 906.20| |alpha: min = 0.97 max = 1.00 mean = 0.99| |beta: min = 569.99 max = 22777.69 mean = 7361.91| |figures of merit: min = 0.00 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.93 mean = 7.24| |phase err.(test): min = 0.00 max = 74.21 mean = 7.06| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0945 0.0900 0.1811 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2116 0.2119 0.2157 n_refl.: 5175 remove outliers: r(all,work,free)=0.2116 0.2119 0.2157 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2116 0.2119 0.2157 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0944 0.0899 0.1806 n_refl.: 5175 remove outliers: r(all,work,free)=0.0944 0.0899 0.1806 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 0.4010 327.349 296.598 0.577 0.985 0.314 11.894-9.307 99.02 97 4 0.1873 526.602 509.440 0.960 0.993 0.310 9.237-7.194 100.00 213 7 0.2198 430.656 420.521 1.004 0.997 0.292 7.162-5.571 100.00 427 22 0.2155 323.155 312.360 0.993 0.998 0.283 5.546-4.326 100.00 867 58 0.1022 443.646 438.291 1.018 1.000 0.254 4.315-3.360 100.00 1859 96 0.0571 421.912 421.733 1.091 1.002 0.240 3.356-3.002 100.00 1373 60 0.0407 324.974 324.614 1.069 1.004 0.100 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.9364 ================= 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 : 0.3619 0.2080 0.080 5.304 8.8 119.3 19.9 258 0.000 1_bss: 0.1569 0.1624 0.080 5.304 6.0 116.4 17.0 258 0.000 1_settarget: 0.1569 0.1624 0.080 5.304 6.0 116.4 17.0 258 0.000 1_nqh: 0.1569 0.1624 0.080 5.304 6.0 116.4 17.0 258 0.000 1_weight: 0.1569 0.1624 0.080 5.304 6.0 116.4 17.0 258 0.000 1_xyzrec: 0.1159 0.1777 0.010 0.976 6.0 116.4 17.0 258 0.192 1_adp: 0.1018 0.1779 0.010 0.976 1.6 111.6 17.3 258 0.192 1_regHadp: 0.1013 0.1786 0.010 0.976 1.6 111.6 17.3 258 0.192 1_occ: 0.1009 0.1769 0.010 0.976 1.6 111.6 17.3 258 0.192 2_bss: 0.1012 0.1782 0.010 0.976 0.7 110.6 16.4 258 0.192 2_settarget: 0.1012 0.1782 0.010 0.976 0.7 110.6 16.4 258 0.192 2_updatecdl: 0.1012 0.1782 0.010 1.000 0.7 110.6 16.4 258 0.192 2_nqh: 0.1013 0.1781 0.010 1.000 0.7 110.6 16.4 258 0.195 2_sol: 0.1112 0.1628 0.010 1.000 0.7 110.6 15.7 236 n/a 2_weight: 0.1112 0.1628 0.010 1.000 0.7 110.6 15.7 236 n/a 2_xyzrec: 0.1007 0.1797 0.009 0.990 0.7 110.6 15.7 236 n/a 2_adp: 0.0941 0.1816 0.009 0.990 0.0 108.2 16.5 236 n/a 2_regHadp: 0.0939 0.1818 0.009 0.990 0.0 108.2 16.5 236 n/a 2_occ: 0.0939 0.1800 0.009 0.990 0.0 108.2 16.5 236 n/a 3_bss: 0.0936 0.1802 0.009 0.990 0.0 108.2 16.5 236 n/a 3_settarget: 0.0936 0.1802 0.009 0.990 0.0 108.2 16.5 236 n/a 3_updatecdl: 0.0936 0.1802 0.009 0.997 0.0 108.2 16.5 236 n/a 3_nqh: 0.0936 0.1802 0.009 0.997 0.0 108.2 16.5 236 n/a 3_sol: 0.1055 0.1786 0.009 0.997 0.0 108.2 16.4 240 n/a 3_weight: 0.1055 0.1786 0.009 0.997 0.0 108.2 16.4 240 n/a 3_xyzrec: 0.0947 0.1794 0.011 1.073 0.0 108.2 16.4 240 n/a 3_adp: 0.0903 0.1781 0.011 1.073 0.0 110.0 16.4 240 n/a 3_regHadp: 0.0908 0.1790 0.011 1.073 0.0 110.0 16.4 240 n/a 3_occ: 0.0897 0.1771 0.011 1.073 0.0 110.0 16.4 240 n/a 4_bss: 0.0888 0.1760 0.011 1.073 0.0 110.0 16.4 240 n/a 4_settarget: 0.0888 0.1760 0.011 1.073 0.0 110.0 16.4 240 n/a 4_updatecdl: 0.0888 0.1760 0.011 1.093 0.0 110.0 16.4 240 n/a 4_nqh: 0.0889 0.1770 0.011 1.093 0.0 110.0 16.4 240 n/a 4_sol: 0.1018 0.1744 0.011 1.093 0.0 110.0 16.5 237 n/a 4_weight: 0.1018 0.1744 0.011 1.093 0.0 110.0 16.5 237 n/a 4_xyzrec: 0.0921 0.1793 0.011 1.020 0.0 110.0 16.5 237 n/a 4_adp: 0.0892 0.1804 0.011 1.020 0.0 112.6 16.6 237 n/a 4_regHadp: 0.0897 0.1814 0.011 1.020 0.0 112.6 16.6 237 n/a 4_occ: 0.0885 0.1791 0.011 1.020 0.0 112.6 16.6 237 n/a 5_bss: 0.0884 0.1791 0.011 1.020 0.0 112.6 16.6 237 n/a 5_settarget: 0.0884 0.1791 0.011 1.020 0.0 112.6 16.6 237 n/a 5_updatecdl: 0.0884 0.1791 0.011 1.026 0.0 112.6 16.6 237 n/a 5_setrh: 0.0886 0.1789 0.011 1.026 0.0 112.6 16.6 237 n/a 5_nqh: 0.0886 0.1789 0.011 1.026 0.0 112.6 16.6 237 n/a 5_sol: 0.0977 0.1806 0.011 1.026 0.0 112.6 16.7 234 n/a 5_weight: 0.0977 0.1806 0.011 1.026 0.0 112.6 16.7 234 n/a 5_xyzrec: 0.0920 0.1804 0.011 1.144 0.0 112.6 16.7 234 n/a 5_adp: 0.0903 0.1828 0.011 1.144 0.0 113.4 16.9 234 n/a 5_regHadp: 0.0908 0.1833 0.011 1.144 0.0 113.4 16.9 234 n/a 5_occ: 0.0900 0.1811 0.011 1.144 0.0 113.4 16.9 234 n/a end: 0.0899 0.1806 0.011 1.144 0.0 113.4 16.9 234 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_5638674_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_5638674_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.4900 Refinement macro-cycles (run) : 492.2600 Write final files (write_after_run_outputs) : 9.3300 Total : 505.0800 Total CPU time: 8.76 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:19:05 PST -0800 (1735492745.68 s) Start R-work = 0.1569, R-free = 0.1624 Final R-work = 0.0899, R-free = 0.1806 =============================================================================== Job complete usr+sys time: 532.65 seconds wall clock time: 9 minutes 13.77 seconds (553.77 seconds total)