Starting phenix.refine on Sun Dec 29 09:10:03 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_1821005.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Adding command-line PHIL: ------------------------- xray_data.high_resolution=3 ordered_solvent.low_resolution=4 No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 3 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_1821005.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_1821005.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== 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: 1.83, per 1000 atoms: 0.54 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: 0.53 Conformation dependent library (CDL) restraints added in 112.3 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.66 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: 527 0.91 - 1.17: 1108 1.17 - 1.42: 653 1.42 - 1.67: 828 1.67 - 1.93: 37 Bond restraints: 3153 Sorted by residual: bond pdb=" CG HIS A 138 " pdb=" CD2 HIS A 138 " ideal model delta sigma weight residual 1.354 1.582 -0.228 1.10e-02 8.26e+03 4.30e+02 bond pdb=" CA ALA A 178 " pdb=" C ALA A 178 " ideal model delta sigma weight residual 1.523 1.279 0.245 1.30e-02 5.92e+03 3.54e+02 bond pdb=" C BGLN A 80 " pdb=" O BGLN A 80 " ideal model delta sigma weight residual 1.237 1.443 -0.206 1.17e-02 7.31e+03 3.11e+02 bond pdb=" CA ALA A 6 " pdb=" C ALA A 6 " ideal model delta sigma weight residual 1.522 1.313 0.209 1.22e-02 6.72e+03 2.93e+02 bond pdb=" N ARG A 27 " pdb=" CA ARG A 27 " ideal model delta sigma weight residual 1.459 1.252 0.207 1.25e-02 6.40e+03 2.74e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.44: 3031 4.44 - 8.87: 1883 8.87 - 13.30: 696 13.30 - 17.74: 146 17.74 - 22.17: 21 Bond angle restraints: 5777 Sorted by residual: angle pdb=" NE ARG A 98 " pdb=" CZ ARG A 98 " pdb=" NH2 ARG A 98 " ideal model delta sigma weight residual 119.20 132.59 -13.39 9.00e-01 1.23e+00 2.21e+02 angle pdb=" CA ALA A 183 " pdb=" C ALA A 183 " pdb=" O ALA A 183 " ideal model delta sigma weight residual 118.63 130.80 -12.17 9.20e-01 1.18e+00 1.75e+02 angle pdb=" O MET A 26 " pdb=" C MET A 26 " pdb=" N ARG A 27 " ideal model delta sigma weight residual 122.07 109.91 12.16 1.03e+00 9.43e-01 1.39e+02 angle pdb=" CG HIS A 115 " pdb=" CD2 HIS A 115 " pdb=" NE2 HIS A 115 " ideal model delta sigma weight residual 107.20 118.86 -11.66 1.00e+00 1.00e+00 1.36e+02 angle pdb=" C PRO A 43 " pdb=" N VAL A 44 " pdb=" CA VAL A 44 " ideal model delta sigma weight residual 123.14 107.94 15.20 1.31e+00 5.83e-01 1.35e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.71: 1294 16.71 - 33.42: 128 33.42 - 50.13: 45 50.13 - 66.84: 10 66.84 - 83.55: 4 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" N ASN A 173 " pdb=" C ASN A 173 " pdb=" CA ASN A 173 " pdb=" CB ASN A 173 " ideal model delta harmonic sigma weight residual 122.80 144.47 -21.67 0 2.50e+00 1.60e-01 7.52e+01 dihedral pdb=" C THR A 160 " pdb=" N THR A 160 " pdb=" CA THR A 160 " pdb=" CB THR A 160 " ideal model delta harmonic sigma weight residual -122.00 -140.28 18.28 0 2.50e+00 1.60e-01 5.35e+01 dihedral pdb=" C ASN A 173 " pdb=" N ASN A 173 " pdb=" CA ASN A 173 " pdb=" CB ASN A 173 " ideal model delta harmonic sigma weight residual -122.60 -140.84 18.24 0 2.50e+00 1.60e-01 5.32e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.008 - 0.212: 95 0.212 - 0.416: 71 0.416 - 0.620: 51 0.620 - 0.823: 15 0.823 - 1.027: 11 Chirality restraints: 243 Sorted by residual: chirality pdb=" CG LEU A 172 " pdb=" CB LEU A 172 " pdb=" CD1 LEU A 172 " pdb=" CD2 LEU A 172 " both_signs ideal model delta sigma weight residual False -2.59 -1.56 -1.03 2.00e-01 2.50e+01 2.64e+01 chirality pdb=" CA THR A 160 " pdb=" N THR A 160 " pdb=" C THR A 160 " pdb=" CB THR A 160 " both_signs ideal model delta sigma weight residual False 2.53 1.51 1.01 2.00e-01 2.50e+01 2.56e+01 chirality pdb=" CB THR A 110 " pdb=" CA THR A 110 " pdb=" OG1 THR A 110 " pdb=" CG2 THR A 110 " both_signs ideal model delta sigma weight residual False 2.55 1.54 1.01 2.00e-01 2.50e+01 2.54e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.048 2.00e-02 2.50e+03 8.37e-02 2.10e+02 pdb=" CG PHE A 119 " -0.178 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " 0.046 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.034 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.104 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.060 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " -0.125 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.056 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.012 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " -0.067 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.075 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " 0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " -0.037 2.00e-02 2.50e+03 5.39e-02 8.72e+01 pdb=" CG TYR A 139 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " -0.062 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " -0.116 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.002 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " 0.014 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.093 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " 0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 57 " -0.046 2.00e-02 2.50e+03 8.74e-02 7.65e+01 pdb=" C SER A 57 " 0.151 2.00e-02 2.50e+03 pdb=" O SER A 57 " -0.060 2.00e-02 2.50e+03 pdb=" N LEU A 58 " -0.045 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.33: 1092 2.33 - 2.89: 8109 2.89 - 3.46: 10462 3.46 - 4.03: 15214 4.03 - 4.60: 21740 Nonbonded interactions: 56617 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.757 2.100 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.808 2.450 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.814 2.450 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.824 2.100 nonbonded pdb=" H GLY A 120 " pdb=" O HIS A 138 " model vdw 1.855 2.450 ... (remaining 56612 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_1821005_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1596 occupancy sum: 1438.50 (% of total atoms 46.85) Rotatable: count: 507 occupancy sum: 483.00 (% of total atoms 15.73) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.00 - 49.25 A, n_refl.=5182 (all), 4.86 % free)-------------| | | | r_work= 0.3620 r_free= 0.2011 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.473229 | | target function (ml) not normalized (work): 22053.018176 | | target function (ml) not normalized (free): 1150.677479 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3800 0.2218 4.8592 4.9039| | 2: 3.78 - 3.00 1.00 2430 110 0.3401 0.1660 4.0761 4.1302| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 48.91 0.83 0.13 6614.09| | 2: 3.78 - 3.00 2430 110 0.94 11.37 1.48 0.26 451.88| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 380.04 max = 12063.33 mean = 3576.74| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 89.99 mean = 30.41| |phase err.(test): min = 0.00 max = 89.97 mean = 33.51| |-----------------------------------------------------------------------------| ----------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 : 0.081 0.245 1557 Z= 5.298 Angle : 5.247 19.084 2118 Z= 3.703 Chirality : 0.399 1.027 243 Planarity : 0.032 0.090 284 Dihedral : 13.708 83.547 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 1.08 % Allowed : 3.24 % Favored : 95.68 % Rotamer: Outliers : 0.62 % Allowed : 2.48 % Favored : 96.89 % Cbeta Deviations : 35.14 % 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: -2.52 (0.47), residues: 224 helix: -2.00 (0.41), residues: 107 sheet: -1.54 (0.67), residues: 38 loop : -0.83 (0.61), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.084 0.018 ARG A 27 TYR 0.085 0.034 TYR A 141 PHE 0.170 0.041 PHE A 119 HIS 0.028 0.017 HIS A 115 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 1785 0 Protein: 8.85 115.78 16.79 3.90 1519 0 Water: 11.36 119.30 38.03 N/A 258 0 Other: 19.04 26.29 21.71 N/A 8 0 Chain A: 8.85 119.30 19.89 N/A 1785 0 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 3.00 - 49.25 A, n_refl.=5182 (all), 4.86 % free)-------------| | | | r_work= 0.3620 r_free= 0.2011 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.473229 | | target function (ml) not normalized (work): 22053.018176 | | target function (ml) not normalized (free): 1150.677479 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3572 0.3650 0.2114 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3572 0.3650 0.2114 n_refl.: 5182 remove outliers: r(all,work,free)=0.2527 0.2553 0.2114 n_refl.: 5178 overall B=-2.86 to atoms: r(all,work,free)=0.2417 0.2440 0.2071 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1569 0.1566 0.1611 n_refl.: 5178 remove outliers: r(all,work,free)=0.1564 0.1561 0.1611 n_refl.: 5176 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 98.94 88 5 0.3841 450.207 410.691 0.678 1.049 0.412 11.894-9.307 99.02 97 4 0.1876 715.189 696.852 0.958 1.047 0.399 9.237-7.194 100.00 213 7 0.2171 584.883 575.947 0.983 1.042 0.364 7.162-5.571 100.00 427 22 0.2269 438.884 425.035 0.950 1.033 0.326 5.546-4.326 100.00 867 58 0.1401 602.525 595.446 0.985 1.018 0.258 4.315-3.360 100.00 1859 96 0.1328 573.008 566.573 1.052 0.993 0.222 3.356-3.002 100.00 1373 60 0.1576 441.355 432.830 1.051 0.968 0.086 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9555 b_overall=-3.6554 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1561 r_free=0.1611 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 ASN Total number of N/Q/H flips: 2 r_work=0.1564 r_free=0.1615 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 19.121932 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.916737 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 0.1170 0.1781 0.0611 0.010 1.0 2.6 0.5 0.0 0 9.561 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.70 17.81 6.11 3.013 16.001 1.917 0.018 10.26 17.73 7.47 4.914 16.154 1.917 0.015 Individual atomic B min max mean iso aniso Overall: 2.22 111.44 17.32 5.32 1785 0 Protein: 2.22 111.22 14.64 5.31 1519 0 Water: 4.01 111.44 32.91 N/A 258 0 Other: 16.16 36.79 23.54 N/A 8 0 Chain A: 2.22 111.44 17.32 N/A 1785 0 Histogram: Values Number of atoms 2.22 - 13.14 925 13.14 - 24.07 478 24.07 - 34.99 187 34.99 - 45.91 110 45.91 - 56.83 56 56.83 - 67.75 12 67.75 - 78.68 8 78.68 - 89.60 5 89.60 - 100.52 1 100.52 - 111.44 3 =========================== Idealize ADP of riding H ========================== r_work=0.1026 r_free=0.1773 r_work=0.1022 r_free=0.1774 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1022 r_free = 0.1774 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 = 0.1020 r_free = 0.1769 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.1020 r_free= 0.1769 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ls_wunit_k1) (work): 0.014185 | | target function (ls_wunit_k1) not normalized (work): 69.844861 | | target function (ls_wunit_k1) not normalized (free): 10.430066 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1059 0.1020 0.1769 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2108 0.2108 0.2217 n_refl.: 5176 remove outliers: r(all,work,free)=0.2108 0.2108 0.2217 n_refl.: 5176 overall B=-1.00 to atoms: r(all,work,free)=0.2067 0.2065 0.2206 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.1055 0.1017 0.1753 n_refl.: 5176 remove outliers: r(all,work,free)=0.1053 0.1015 0.1753 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 0.3340 327.524 309.559 0.666 1.000 0.365 11.894-9.307 99.02 97 4 0.1512 524.717 517.024 0.997 1.002 0.361 9.237-7.194 100.00 213 7 0.1654 429.114 429.081 1.032 1.002 0.326 7.162-5.571 100.00 427 22 0.1639 321.998 317.871 0.992 1.002 0.312 5.546-4.326 100.00 867 58 0.0917 442.058 438.341 1.000 1.001 0.217 4.315-3.360 100.00 1859 96 0.0769 420.402 420.511 1.045 1.000 0.204 3.356-3.002 100.00 1373 60 0.1001 323.811 322.282 1.012 0.999 0.062 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9552 b_overall=-3.5700 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1015 r_free=0.1753 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN Total number of N/Q/H flips: 1 r_work=0.1016 r_free=0.1756 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1016 r_free=0.1756 | n_water=258 | time (s): 0.450 (total time: 0.450) Filter (dist) r_work=0.1041 r_free=0.1760 | n_water=249 | time (s): 20.590 (total time: 21.040) Filter (q & B) r_work=0.1040 r_free=0.1760 | n_water=246 | time (s): 1.320 (total time: 22.360) Compute maps r_work=0.1040 r_free=0.1760 | n_water=246 | time (s): 0.490 (total time: 22.850) Filter (map) r_work=0.1323 r_free=0.1853 | n_water=148 | time (s): 1.500 (total time: 24.350) Find peaks r_work=0.1323 r_free=0.1853 | n_water=148 | time (s): 0.440 (total time: 24.790) Add new water r_work=0.1672 r_free=0.2139 | n_water=232 | time (s): 1.320 (total time: 26.110) Refine new water occ: r_work=0.1161 r_free=0.1691 adp: r_work=0.1131 r_free=0.1704 occ: r_work=0.1128 r_free=0.1673 adp: r_work=0.1115 r_free=0.1683 occ: r_work=0.1113 r_free=0.1670 adp: r_work=0.1110 r_free=0.1675 ADP+occupancy (water only), MIN, final r_work=0.1110 r_free=0.1675 r_work=0.1110 r_free=0.1675 | n_water=232 | time (s): 4.680 (total time: 30.790) Filter (q & B) r_work=0.1110 r_free=0.1675 | n_water=232 | time (s): 1.120 (total time: 31.910) Filter (dist only) r_work=0.1117 r_free=0.1680 | n_water=230 | time (s): 18.390 (total time: 50.300) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.371140 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.685788 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 0.1020 0.1748 0.0728 0.009 1.0 4.8 0.5 0.0 0 11.186 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.20 17.48 7.28 4.671 16.644 2.686 0.014 9.52 17.73 8.21 5.400 17.037 2.686 0.013 Individual atomic B min max mean iso aniso Overall: 0.00 107.95 16.47 6.36 1757 0 Protein: 0.00 107.95 14.85 6.33 1519 0 Water: 0.00 62.72 26.83 N/A 230 0 Other: 14.23 42.12 26.84 N/A 8 0 Chain A: 0.00 107.95 15.62 N/A 1674 0 Chain S: 2.42 58.51 33.69 N/A 83 0 Histogram: Values Number of atoms 0.00 - 10.80 712 10.80 - 21.59 635 21.59 - 32.39 216 32.39 - 43.18 117 43.18 - 53.98 39 53.98 - 64.77 27 64.77 - 75.57 5 75.57 - 86.36 3 86.36 - 97.16 1 97.16 - 107.95 2 =========================== Idealize ADP of riding H ========================== r_work=0.0952 r_free=0.1773 r_work=0.0949 r_free=0.1776 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0949 r_free = 0.1776 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0945 r_free = 0.1766 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.21 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= 0.0945 r_free= 0.1766 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ls_wunit_k1) (work): 0.012273 | | target function (ls_wunit_k1) not normalized (work): 60.419775 | | target function (ls_wunit_k1) not normalized (free): 9.599984 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0986 0.0945 0.1766 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)=0.0985 0.0944 0.1775 n_refl.: 5175 remove outliers: r(all,work,free)=0.0984 0.0942 0.1775 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 0.3227 329.702 309.588 0.655 1.002 0.360 11.894-9.307 99.02 97 4 0.1543 524.717 519.696 0.977 1.005 0.325 9.237-7.194 100.00 213 7 0.1451 429.114 431.248 1.032 1.005 0.305 7.162-5.571 100.00 427 22 0.1464 321.998 319.467 1.001 1.004 0.300 5.546-4.326 100.00 867 58 0.0796 442.058 439.450 1.010 1.002 0.240 4.315-3.360 100.00 1859 96 0.0731 420.402 420.156 1.057 0.999 0.208 3.356-3.002 100.00 1373 60 0.0955 323.811 322.677 1.032 0.996 0.090 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9553 b_overall=-4.2418 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0942 r_free=0.1775 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=0.0945 r_free=0.1778 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0945 r_free=0.1778 | n_water=230 | time (s): 0.570 (total time: 0.570) Filter (dist) r_work=0.0969 r_free=0.1774 | n_water=225 | time (s): 18.150 (total time: 18.720) Filter (q & B) r_work=0.0999 r_free=0.1804 | n_water=224 | time (s): 1.330 (total time: 20.050) Compute maps r_work=0.0999 r_free=0.1804 | n_water=224 | time (s): 0.500 (total time: 20.550) Filter (map) r_work=0.1260 r_free=0.1888 | n_water=152 | time (s): 1.650 (total time: 22.200) Find peaks r_work=0.1260 r_free=0.1888 | n_water=152 | time (s): 0.590 (total time: 22.790) Add new water r_work=0.1612 r_free=0.2240 | n_water=238 | time (s): 1.500 (total time: 24.290) Refine new water occ: r_work=0.1057 r_free=0.1736 adp: r_work=0.1054 r_free=0.1744 occ: r_work=0.1044 r_free=0.1727 adp: r_work=0.1043 r_free=0.1735 occ: r_work=0.1034 r_free=0.1720 adp: r_work=0.1032 r_free=0.1729 ADP+occupancy (water only), MIN, final r_work=0.1032 r_free=0.1729 r_work=0.1032 r_free=0.1729 | n_water=238 | time (s): 11.230 (total time: 35.520) Filter (q & B) r_work=0.1034 r_free=0.1734 | n_water=237 | time (s): 1.610 (total time: 37.130) Filter (dist only) r_work=0.1043 r_free=0.1742 | n_water=236 | time (s): 19.410 (total time: 56.540) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.089921 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.237431 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 0.0940 0.1804 0.0864 0.011 1.1 5.4 0.5 0.0 0 0.545 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.40 18.04 8.64 5.331 17.597 0.237 5.148 8.99 18.05 9.06 7.196 17.641 0.237 5.050 Individual atomic B min max mean iso aniso Overall: 0.00 106.17 16.28 8.86 1763 0 Protein: 0.00 106.17 15.07 8.84 1519 0 Water: 0.00 57.72 23.68 N/A 236 0 Other: 14.48 45.77 28.00 N/A 8 0 Chain A: 0.00 106.17 15.75 N/A 1660 0 Chain S: 0.00 56.09 24.84 N/A 103 0 Histogram: Values Number of atoms 0.00 - 10.62 688 10.62 - 21.23 650 21.23 - 31.85 234 31.85 - 42.47 114 42.47 - 53.08 42 53.08 - 63.70 17 63.70 - 74.32 9 74.32 - 84.93 4 84.93 - 95.55 4 95.55 - 106.17 1 =========================== Idealize ADP of riding H ========================== r_work=0.0899 r_free=0.1805 r_work=0.0904 r_free=0.1808 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0904 r_free = 0.1808 target_work(ml) = 5.055 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0892 r_free = 0.1790 target_work(ml) = 5.045 | | occupancies: max = 1.00 min = 0.22 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= 0.0892 r_free= 0.1790 coordinate error (max.-lik. estimate): 0.27 A | | | | normalized target function (ml) (work): 5.045172 | | target function (ml) not normalized (work): 24832.338800 | | target function (ml) not normalized (free): 1827.495929 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0937 0.0892 0.1790 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2035 0.2038 0.2064 n_refl.: 5174 remove outliers: r(all,work,free)=0.2035 0.2038 0.2064 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2035 0.2038 0.2064 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0928 0.0883 0.1773 n_refl.: 5174 remove outliers: r(all,work,free)=0.0928 0.0883 0.1773 n_refl.: 5174 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 94.79 86 5 0.3671 329.702 298.132 0.586 0.988 0.324 11.894-9.307 99.02 97 4 0.1849 524.717 509.351 0.940 0.993 0.315 9.237-7.194 100.00 213 7 0.1972 429.114 422.309 1.011 0.996 0.305 7.162-5.571 100.00 427 22 0.1818 321.998 313.238 0.986 0.998 0.300 5.546-4.326 100.00 867 58 0.0930 442.058 435.744 0.999 1.000 0.230 4.315-3.360 100.00 1859 96 0.0574 420.402 419.943 1.053 1.002 0.220 3.356-3.002 100.00 1373 60 0.0585 323.811 323.313 1.029 1.005 0.080 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-6.2817 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0883 r_free=0.1773 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN Total number of N/Q/H flips: 1 r_work=0.0884 r_free=0.1771 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0884 r_free=0.1771 | n_water=236 | time (s): 0.550 (total time: 0.550) Filter (dist) r_work=0.0894 r_free=0.1784 | n_water=232 | time (s): 17.410 (total time: 17.960) Filter (q & B) r_work=0.0938 r_free=0.1800 | n_water=230 | time (s): 1.610 (total time: 19.570) Compute maps r_work=0.0938 r_free=0.1800 | n_water=230 | time (s): 0.540 (total time: 20.110) Filter (map) r_work=0.1197 r_free=0.1872 | n_water=164 | time (s): 1.830 (total time: 21.940) Find peaks r_work=0.1197 r_free=0.1872 | n_water=164 | time (s): 0.390 (total time: 22.330) Add new water r_work=0.1496 r_free=0.2134 | n_water=237 | time (s): 1.460 (total time: 23.790) Refine new water occ: r_work=0.0994 r_free=0.1743 adp: r_work=0.0990 r_free=0.1750 occ: r_work=0.0983 r_free=0.1740 adp: r_work=0.0982 r_free=0.1744 occ: r_work=0.0975 r_free=0.1735 adp: r_work=0.0975 r_free=0.1739 ADP+occupancy (water only), MIN, final r_work=0.0975 r_free=0.1739 r_work=0.0975 r_free=0.1739 | n_water=237 | time (s): 9.120 (total time: 32.910) Filter (q & B) r_work=0.0977 r_free=0.1743 | n_water=233 | time (s): 1.300 (total time: 34.210) Filter (dist only) r_work=0.0976 r_free=0.1749 | n_water=232 | time (s): 16.610 (total time: 50.820) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.046151 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.214799 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 0.0896 0.1813 0.0917 0.011 1.1 6.4 0.5 0.0 0 0.523 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 8.96 18.13 9.17 6.922 17.876 0.215 5.014 8.75 18.31 9.55 7.896 17.969 0.215 4.950 Individual atomic B min max mean iso aniso Overall: 0.00 105.03 16.55 10.26 1759 0 Protein: 0.00 105.03 15.41 10.25 1519 0 Water: 0.00 53.30 23.63 N/A 232 0 Other: 14.17 45.09 27.71 N/A 8 0 Chain A: 0.00 105.03 16.00 N/A 1651 0 Chain S: 0.00 53.30 25.04 N/A 108 0 Histogram: Values Number of atoms 0.00 - 10.50 651 10.50 - 21.01 646 21.01 - 31.51 253 31.51 - 42.01 120 42.01 - 52.52 54 52.52 - 63.02 13 63.02 - 73.52 13 73.52 - 84.02 4 84.02 - 94.53 3 94.53 - 105.03 2 =========================== Idealize ADP of riding H ========================== r_work=0.0875 r_free=0.1831 r_work=0.0879 r_free=0.1834 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0879 r_free = 0.1834 target_work(ml) = 4.954 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0871 r_free = 0.1817 target_work(ml) = 4.948 | | occupancies: max = 1.00 min = 0.22 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= 0.0871 r_free= 0.1817 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 4.947848 | | target function (ml) not normalized (work): 24353.305464 | | target function (ml) not normalized (free): 2127.654296 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0919 0.0871 0.1817 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2076 0.2076 0.2170 n_refl.: 5174 remove outliers: r(all,work,free)=0.2076 0.2076 0.2170 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2076 0.2076 0.2170 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0920 0.0872 0.1824 n_refl.: 5174 remove outliers: r(all,work,free)=0.0920 0.0872 0.1824 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 0.3827 329.702 298.314 0.592 0.987 0.330 11.894-9.307 99.02 97 4 0.2002 524.717 505.849 0.946 0.992 0.323 9.237-7.194 100.00 213 7 0.2081 429.114 419.768 1.009 0.996 0.316 7.162-5.571 100.00 427 22 0.2011 321.998 310.720 0.987 0.997 0.287 5.546-4.326 100.00 867 58 0.0969 442.058 436.869 1.010 0.999 0.230 4.315-3.360 100.00 1859 96 0.0554 420.402 420.229 1.070 1.002 0.220 3.356-3.002 100.00 1373 60 0.0429 323.811 323.786 1.049 1.004 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.0989 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0872 r_free=0.1824 After: r_work=0.0875 r_free=0.1825 ================================== NQH flips ================================== r_work=0.0875 r_free=0.1825 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN Total number of N/Q/H flips: 1 r_work=0.0875 r_free=0.1829 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0875 r_free=0.1829 | n_water=232 | time (s): 0.530 (total time: 0.530) Filter (dist) r_work=0.0884 r_free=0.1835 | n_water=229 | time (s): 19.960 (total time: 20.490) Filter (q & B) r_work=0.0957 r_free=0.1879 | n_water=227 | time (s): 1.720 (total time: 22.210) Compute maps r_work=0.0957 r_free=0.1879 | n_water=227 | time (s): 0.680 (total time: 22.890) Filter (map) r_work=0.1232 r_free=0.1965 | n_water=163 | time (s): 1.680 (total time: 24.570) Find peaks r_work=0.1232 r_free=0.1965 | n_water=163 | time (s): 0.480 (total time: 25.050) Add new water r_work=0.1513 r_free=0.2263 | n_water=231 | time (s): 1.320 (total time: 26.370) Refine new water occ: r_work=0.0974 r_free=0.1828 adp: r_work=0.0967 r_free=0.1826 occ: r_work=0.0961 r_free=0.1820 adp: r_work=0.0960 r_free=0.1824 occ: r_work=0.0955 r_free=0.1818 adp: r_work=0.0954 r_free=0.1821 ADP+occupancy (water only), MIN, final r_work=0.0954 r_free=0.1821 r_work=0.0954 r_free=0.1821 | n_water=231 | time (s): 8.720 (total time: 35.090) Filter (q & B) r_work=0.0953 r_free=0.1822 | n_water=230 | time (s): 1.500 (total time: 36.590) Filter (dist only) r_work=0.0952 r_free=0.1825 | n_water=229 | time (s): 18.360 (total time: 54.950) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.903878 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.193441 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.0902 0.1850 0.0948 0.011 1.1 8.3 0.5 0.6 0 0.452 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.02 18.50 9.48 7.853 18.178 0.193 4.985 8.90 18.68 9.78 8.618 18.268 0.193 4.938 Individual atomic B min max mean iso aniso Overall: 0.00 104.26 16.74 11.38 1756 0 Protein: 0.00 104.26 15.70 11.36 1519 0 Water: 0.00 50.60 23.32 N/A 229 0 Other: 11.35 46.07 26.69 N/A 8 0 Chain A: 0.00 104.26 16.22 N/A 1644 0 Chain S: 0.00 48.66 24.39 N/A 112 0 Histogram: Values Number of atoms 0.00 - 10.43 655 10.43 - 20.85 611 20.85 - 31.28 274 31.28 - 41.70 125 41.70 - 52.13 54 52.13 - 62.55 14 62.55 - 72.98 11 72.98 - 83.40 5 83.40 - 93.83 5 93.83 - 104.26 2 =========================== Idealize ADP of riding H ========================== r_work=0.0890 r_free=0.1868 r_work=0.0892 r_free=0.1867 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0892 r_free = 0.1867 target_work(ml) = 4.944 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0884 r_free = 0.1856 target_work(ml) = 4.938 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0884 r_free= 0.1856 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 4.937839 | | target function (ml) not normalized (work): 24304.041325 | | target function (ml) not normalized (free): 2186.399658 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.79 1.00 2492 142 0.1269 0.1879 5.5275 6.3204| | 2: 3.78 - 3.00 1.00 2430 110 0.0415 0.1818 4.3331 11.717| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.79 2492 142 0.91 12.32 1.00 0.98 13207.11| | 2: 3.78 - 3.00 2430 110 0.99 1.78 1.00 1.00 885.32| |alpha: min = 0.97 max = 1.00 mean = 0.99| |beta: min = 565.46 max = 22203.50 mean = 7123.82| |figures of merit: min = 0.00 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.83 mean = 7.11| |phase err.(test): min = 0.00 max = 89.87 mean = 7.39| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0934 0.0884 0.1856 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2119 0.2117 0.2263 n_refl.: 5174 remove outliers: r(all,work,free)=0.2119 0.2117 0.2263 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2119 0.2117 0.2263 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0932 0.0883 0.1853 n_refl.: 5174 remove outliers: r(all,work,free)=0.0932 0.0883 0.1853 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 0.3781 329.702 299.658 0.586 0.985 0.319 11.894-9.307 99.02 97 4 0.1946 524.717 506.813 0.951 0.992 0.319 9.237-7.194 100.00 213 7 0.2149 429.114 419.030 1.007 0.996 0.308 7.162-5.571 100.00 427 22 0.2056 321.998 310.475 0.991 0.998 0.300 5.546-4.326 100.00 867 58 0.1038 442.058 436.536 1.020 1.000 0.225 4.315-3.360 100.00 1859 96 0.0559 420.402 420.399 1.086 1.003 0.221 3.356-3.002 100.00 1373 60 0.0393 323.811 323.898 1.069 1.005 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.8909 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.3620 0.2011 0.081 5.247 8.8 119.3 19.9 258 0.000 1_bss: 0.1561 0.1611 0.081 5.247 6.0 116.4 17.0 258 0.000 1_settarget: 0.1561 0.1611 0.081 5.247 6.0 116.4 17.0 258 0.000 1_nqh: 0.1564 0.1615 0.081 5.247 6.0 116.4 17.0 258 0.006 1_weight: 0.1564 0.1615 0.081 5.247 6.0 116.4 17.0 258 0.006 1_xyzrec: 0.1170 0.1781 0.010 0.965 6.0 116.4 17.0 258 0.212 1_adp: 0.1026 0.1773 0.010 0.965 2.2 111.4 17.3 258 0.212 1_regHadp: 0.1022 0.1774 0.010 0.965 2.2 111.4 17.3 258 0.212 1_occ: 0.1020 0.1769 0.010 0.965 2.2 111.4 17.3 258 0.212 2_bss: 0.1015 0.1753 0.010 0.965 1.2 110.4 16.3 258 0.212 2_settarget: 0.1015 0.1753 0.010 0.965 1.2 110.4 16.3 258 0.212 2_updatecdl: 0.1015 0.1753 0.010 0.986 1.2 110.4 16.3 258 0.212 2_nqh: 0.1016 0.1756 0.010 0.986 1.2 110.4 16.3 258 0.210 2_sol: 0.1117 0.1680 0.010 0.986 1.0 110.2 15.7 230 n/a 2_weight: 0.1117 0.1680 0.010 0.986 1.0 110.2 15.7 230 n/a 2_xyzrec: 0.1020 0.1748 0.009 0.968 1.0 110.2 15.7 230 n/a 2_adp: 0.0952 0.1773 0.009 0.968 0.0 108.0 16.5 230 n/a 2_regHadp: 0.0949 0.1776 0.009 0.968 0.0 108.0 16.5 230 n/a 2_occ: 0.0945 0.1766 0.009 0.968 0.0 108.0 16.5 230 n/a 3_bss: 0.0942 0.1775 0.009 0.968 0.0 108.0 16.5 230 n/a 3_settarget: 0.0942 0.1775 0.009 0.968 0.0 108.0 16.5 230 n/a 3_updatecdl: 0.0942 0.1775 0.009 0.974 0.0 108.0 16.5 230 n/a 3_nqh: 0.0945 0.1778 0.009 0.974 0.0 108.0 16.5 230 n/a 3_sol: 0.1043 0.1742 0.009 0.974 0.0 108.0 16.2 236 n/a 3_weight: 0.1043 0.1742 0.009 0.974 0.0 108.0 16.2 236 n/a 3_xyzrec: 0.0940 0.1804 0.011 1.070 0.0 108.0 16.2 236 n/a 3_adp: 0.0899 0.1805 0.011 1.070 0.0 106.2 16.3 236 n/a 3_regHadp: 0.0904 0.1808 0.011 1.070 0.0 106.2 16.3 236 n/a 3_occ: 0.0892 0.1790 0.011 1.070 0.0 106.2 16.3 236 n/a 4_bss: 0.0883 0.1773 0.011 1.070 0.0 106.2 16.3 236 n/a 4_settarget: 0.0883 0.1773 0.011 1.070 0.0 106.2 16.3 236 n/a 4_updatecdl: 0.0883 0.1773 0.011 1.079 0.0 106.2 16.3 236 n/a 4_nqh: 0.0884 0.1771 0.011 1.079 0.0 106.2 16.3 236 n/a 4_sol: 0.0976 0.1749 0.011 1.079 0.0 106.2 16.4 232 n/a 4_weight: 0.0976 0.1749 0.011 1.079 0.0 106.2 16.4 232 n/a 4_xyzrec: 0.0896 0.1813 0.011 1.088 0.0 106.2 16.4 232 n/a 4_adp: 0.0875 0.1831 0.011 1.088 0.0 105.0 16.6 232 n/a 4_regHadp: 0.0879 0.1834 0.011 1.088 0.0 105.0 16.6 232 n/a 4_occ: 0.0871 0.1817 0.011 1.088 0.0 105.0 16.6 232 n/a 5_bss: 0.0872 0.1824 0.011 1.088 0.0 105.0 16.6 232 n/a 5_settarget: 0.0872 0.1824 0.011 1.088 0.0 105.0 16.6 232 n/a 5_updatecdl: 0.0872 0.1824 0.011 1.089 0.0 105.0 16.6 232 n/a 5_setrh: 0.0875 0.1825 0.011 1.089 0.0 105.0 16.6 232 n/a 5_nqh: 0.0875 0.1829 0.011 1.089 0.0 105.0 16.6 232 n/a 5_sol: 0.0952 0.1825 0.011 1.089 0.0 105.0 16.6 229 n/a 5_weight: 0.0952 0.1825 0.011 1.089 0.0 105.0 16.6 229 n/a 5_xyzrec: 0.0902 0.1850 0.011 1.131 0.0 105.0 16.6 229 n/a 5_adp: 0.0890 0.1868 0.011 1.131 0.0 104.3 16.7 229 n/a 5_regHadp: 0.0892 0.1867 0.011 1.131 0.0 104.3 16.7 229 n/a 5_occ: 0.0884 0.1856 0.011 1.131 0.0 104.3 16.7 229 n/a end: 0.0883 0.1853 0.011 1.131 0.0 104.3 16.7 229 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_1821005_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_1821005_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.5200 Refinement macro-cycles (run) : 484.5800 Write final files (write_after_run_outputs) : 11.5000 Total : 499.6000 Total CPU time: 8.67 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:19:01 PST -0800 (1735492741.25 s) Start R-work = 0.1561, R-free = 0.1611 Final R-work = 0.0883, R-free = 0.1853 =============================================================================== Job complete usr+sys time: 527.70 seconds wall clock time: 9 minutes 9.58 seconds (549.58 seconds total)