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_7509253.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_7509253.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7509253.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 3 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" 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" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.71, per 1000 atoms: 0.51 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: 0.33 Conformation dependent library (CDL) restraints added in 118.9 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.62 - 0.91: 515 0.91 - 1.20: 1164 1.20 - 1.48: 846 1.48 - 1.77: 619 1.77 - 2.05: 9 Bond restraints: 3153 Sorted by residual: bond pdb=" NE ARG A 27 " pdb=" CZ ARG A 27 " ideal model delta sigma weight residual 1.326 1.556 -0.230 1.10e-02 8.26e+03 4.37e+02 bond pdb=" C GLU A 163 " pdb=" N PHE A 164 " ideal model delta sigma weight residual 1.334 1.554 -0.220 1.20e-02 6.94e+03 3.36e+02 bond pdb=" C ALYS A 132 " pdb=" O ALYS A 132 " ideal model delta sigma weight residual 1.236 1.024 0.212 1.16e-02 7.43e+03 3.34e+02 bond pdb=" C SER A 142 " pdb=" O SER A 142 " ideal model delta sigma weight residual 1.234 1.456 -0.222 1.26e-02 6.30e+03 3.10e+02 bond pdb=" CA ALA A 79 " pdb=" C ALA A 79 " ideal model delta sigma weight residual 1.523 1.288 0.235 1.35e-02 5.49e+03 3.04e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.85: 3238 4.85 - 9.70: 1869 9.70 - 14.54: 583 14.54 - 19.39: 79 19.39 - 24.24: 8 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA ALYS A 132 " pdb=" C ALYS A 132 " pdb=" N MET A 133 " ideal model delta sigma weight residual 116.79 99.92 16.87 1.28e+00 6.10e-01 1.74e+02 angle pdb=" CA THR A 140 " pdb=" C THR A 140 " pdb=" O THR A 140 " ideal model delta sigma weight residual 120.36 134.46 -14.10 1.08e+00 8.57e-01 1.70e+02 angle pdb=" CA GLY A 174 " pdb=" C GLY A 174 " pdb=" O GLY A 174 " ideal model delta sigma weight residual 122.43 132.88 -10.45 8.10e-01 1.52e+00 1.66e+02 angle pdb=" O AGLU A 90 " pdb=" C AGLU A 90 " pdb=" N ILE A 91 " ideal model delta sigma weight residual 122.07 108.94 13.13 1.03e+00 9.43e-01 1.63e+02 angle pdb=" CG HIS A 126 " pdb=" CD2 HIS A 126 " pdb=" NE2 HIS A 126 " ideal model delta sigma weight residual 107.20 95.14 12.06 1.00e+00 1.00e+00 1.45e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.53: 1280 15.53 - 31.06: 134 31.06 - 46.59: 37 46.59 - 62.12: 24 62.12 - 77.65: 6 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" N VAL A 23 " pdb=" C VAL A 23 " pdb=" CA VAL A 23 " pdb=" CB VAL A 23 " ideal model delta harmonic sigma weight residual 123.40 106.53 16.87 0 2.50e+00 1.60e-01 4.55e+01 dihedral pdb=" C CYS A 46 " pdb=" N CYS A 46 " pdb=" CA CYS A 46 " pdb=" CB CYS A 46 " ideal model delta harmonic sigma weight residual -122.60 -138.47 15.87 0 2.50e+00 1.60e-01 4.03e+01 dihedral pdb=" C VAL A 123 " pdb=" N VAL A 123 " pdb=" CA VAL A 123 " pdb=" CB VAL A 123 " ideal model delta harmonic sigma weight residual -122.00 -137.47 15.47 0 2.50e+00 1.60e-01 3.83e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.003 - 0.198: 92 0.198 - 0.392: 83 0.392 - 0.587: 41 0.587 - 0.782: 19 0.782 - 0.977: 8 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA SER A 161 " pdb=" N SER A 161 " pdb=" C SER A 161 " pdb=" CB SER A 161 " both_signs ideal model delta sigma weight residual False 2.51 1.53 0.98 2.00e-01 2.50e+01 2.38e+01 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 -1.65 -0.94 2.00e-01 2.50e+01 2.21e+01 chirality pdb=" CB VAL A 23 " pdb=" CA VAL A 23 " pdb=" CG1 VAL A 23 " pdb=" CG2 VAL A 23 " both_signs ideal model delta sigma weight residual False -2.63 -3.51 0.88 2.00e-01 2.50e+01 1.95e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 5 " 0.084 9.50e-02 1.11e+02 7.51e-02 1.10e+02 pdb=" NE ARG A 5 " -0.079 2.00e-02 2.50e+03 pdb=" CZ ARG A 5 " 0.021 2.00e-02 2.50e+03 pdb=" NH1 ARG A 5 " 0.029 2.00e-02 2.50e+03 pdb=" NH2 ARG A 5 " 0.128 2.00e-02 2.50e+03 pdb="HH11 ARG A 5 " 0.070 2.00e-02 2.50e+03 pdb="HH12 ARG A 5 " -0.115 2.00e-02 2.50e+03 pdb="HH21 ARG A 5 " -0.032 2.00e-02 2.50e+03 pdb="HH22 ARG A 5 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB AASN A 97 " -0.069 2.00e-02 2.50e+03 8.55e-02 1.10e+02 pdb=" CG AASN A 97 " 0.109 2.00e-02 2.50e+03 pdb=" OD1AASN A 97 " -0.038 2.00e-02 2.50e+03 pdb=" ND2AASN A 97 " 0.126 2.00e-02 2.50e+03 pdb="HD21AASN A 97 " -0.092 2.00e-02 2.50e+03 pdb="HD22AASN A 97 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 115 " -0.055 2.00e-02 2.50e+03 6.88e-02 1.06e+02 pdb=" CG HIS A 115 " 0.020 2.00e-02 2.50e+03 pdb=" ND1 HIS A 115 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 HIS A 115 " 0.051 2.00e-02 2.50e+03 pdb=" CE1 HIS A 115 " -0.104 2.00e-02 2.50e+03 pdb=" NE2 HIS A 115 " -0.031 2.00e-02 2.50e+03 pdb=" HD2 HIS A 115 " 0.065 2.00e-02 2.50e+03 pdb=" HE1 HIS A 115 " 0.119 2.00e-02 2.50e+03 pdb=" HE2 HIS A 115 " -0.078 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.37: 1340 2.37 - 2.92: 8350 2.92 - 3.48: 10476 3.48 - 4.04: 15047 4.04 - 4.60: 21459 Nonbonded interactions: 56672 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.807 2.100 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.814 2.450 x-y,-y,-z-4/3 nonbonded pdb=" O ALA A 14 " pdb=" H SER A 47 " model vdw 1.827 2.450 nonbonded pdb=" H GLY A 120 " pdb=" O HIS A 138 " model vdw 1.838 2.450 nonbonded pdb=" H VAL A 35 " pdb=" OD2 ASP A 55 " model vdw 1.862 2.450 ... (remaining 56667 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_7509253_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= 0.1978 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.467047 | | target function (ml) not normalized (work): 22022.542737 | | target function (ml) not normalized (free): 1145.356857 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3803 0.2197 4.8479 4.8967| | 2: 3.78 - 3.00 1.00 2430 110 0.3397 0.1607 4.0752 4.0911| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 49.25 - 3.79 2500 142 0.50 48.89 0.83 0.13 6606.82| | 2: 3.78 - 3.00 2430 110 0.94 11.30 1.48 0.26 445.92| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 377.25 max = 12071.00 mean = 3570.11| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 89.97 mean = 30.36| |phase err.(test): min = 0.00 max = 89.96 mean = 33.23| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.082 0.249 1557 Z= 5.469 Angle : 5.342 18.550 2118 Z= 3.795 Chirality : 0.368 0.977 243 Planarity : 0.032 0.115 284 Dihedral : 13.964 77.646 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.16 % Favored : 97.30 % Rotamer: Outliers : 1.86 % Allowed : 3.11 % Favored : 95.03 % Cbeta Deviations : 31.35 % 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: -2.44 (0.49), residues: 224 helix: -2.44 (0.39), residues: 103 sheet: -0.73 (0.80), residues: 38 loop : -0.56 (0.66), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.085 0.021 ARG A 98 TYR 0.108 0.046 TYR A 139 PHE 0.094 0.039 PHE A 164 HIS 0.035 0.016 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= 0.1978 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.467047 | | target function (ml) not normalized (work): 22022.542737 | | target function (ml) not normalized (free): 1145.356857 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3575 0.3654 0.2078 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3575 0.3654 0.2078 n_refl.: 5182 remove outliers: r(all,work,free)=0.2525 0.2552 0.2078 n_refl.: 5178 overall B=-2.90 to atoms: r(all,work,free)=0.2413 0.2436 0.2036 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1559 0.1560 0.1538 n_refl.: 5178 remove outliers: r(all,work,free)=0.1555 0.1556 0.1538 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 0.3801 449.739 410.158 0.663 1.058 0.392 11.894-9.307 99.02 97 4 0.1856 714.446 695.021 0.951 1.057 0.373 9.237-7.194 100.00 213 7 0.2192 584.275 576.736 0.977 1.051 0.374 7.162-5.571 100.00 427 22 0.2343 438.427 424.843 0.940 1.040 0.326 5.546-4.326 100.00 867 58 0.1364 601.899 595.517 0.982 1.022 0.216 4.315-3.360 100.00 1859 96 0.1326 572.412 565.785 1.058 0.991 0.211 3.356-3.002 100.00 1373 60 0.1567 440.896 433.091 1.060 0.960 0.065 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9556 b_overall=-3.7066 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1556 r_free=0.1538 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1556 r_free=0.1538 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 19.811444 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.124776 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 0.1163 0.1760 0.0596 0.010 1.0 3.2 0.5 0.0 0 9.906 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.63 17.60 5.96 3.013 15.959 2.125 0.018 10.22 17.52 7.30 5.051 16.123 2.125 0.014 Individual atomic B min max mean iso aniso Overall: 1.62 111.40 17.30 5.45 1785 0 Protein: 1.62 111.32 14.59 5.44 1519 0 Water: 3.97 111.40 33.02 N/A 258 0 Other: 15.66 38.64 24.06 N/A 8 0 Chain A: 1.62 111.40 17.30 N/A 1785 0 Histogram: Values Number of atoms 1.62 - 12.60 880 12.60 - 23.58 506 23.58 - 34.56 196 34.56 - 45.53 115 45.53 - 56.51 55 56.51 - 67.49 16 67.49 - 78.47 8 78.47 - 89.44 5 89.44 - 100.42 1 100.42 - 111.40 3 =========================== Idealize ADP of riding H ========================== r_work=0.1022 r_free=0.1752 r_work=0.1017 r_free=0.1759 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1017 r_free = 0.1759 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1014 r_free = 0.1746 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.10 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= 0.1014 r_free= 0.1746 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ls_wunit_k1) (work): 0.014090 | | target function (ls_wunit_k1) not normalized (work): 69.380215 | | target function (ls_wunit_k1) not normalized (free): 10.095166 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1052 0.1014 0.1746 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2083 0.2082 0.2221 n_refl.: 5176 remove outliers: r(all,work,free)=0.2083 0.2082 0.2221 n_refl.: 5176 overall B=-0.94 to atoms: r(all,work,free)=0.2044 0.2041 0.2210 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.1057 0.1019 0.1750 n_refl.: 5176 remove outliers: r(all,work,free)=0.1057 0.1019 0.1750 n_refl.: 5176 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 96.88 88 5 0.3259 331.740 324.088 0.705 0.998 0.376 11.894-9.307 99.02 97 4 0.1612 526.995 518.658 0.990 1.001 0.351 9.237-7.194 100.00 213 7 0.1664 430.977 430.827 1.029 1.002 0.341 7.162-5.571 100.00 427 22 0.1630 323.396 318.914 0.983 1.001 0.312 5.546-4.326 100.00 867 58 0.0904 443.977 440.481 0.996 1.001 0.207 4.315-3.360 100.00 1859 96 0.0777 422.227 422.130 1.042 1.000 0.203 3.356-3.002 100.00 1373 60 0.1004 325.217 323.775 1.007 0.999 0.051 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-3.3672 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1019 r_free=0.1750 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1019 r_free=0.1750 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1019 r_free=0.1750 | n_water=258 | time (s): 0.600 (total time: 0.600) Filter (dist) r_work=0.1044 r_free=0.1753 | n_water=247 | time (s): 22.130 (total time: 22.730) Filter (q & B) r_work=0.1044 r_free=0.1757 | n_water=244 | time (s): 1.290 (total time: 24.020) Compute maps r_work=0.1044 r_free=0.1757 | n_water=244 | time (s): 0.570 (total time: 24.590) Filter (map) r_work=0.1363 r_free=0.1857 | n_water=143 | time (s): 1.520 (total time: 26.110) Find peaks r_work=0.1363 r_free=0.1857 | n_water=143 | time (s): 0.400 (total time: 26.510) Add new water r_work=0.1747 r_free=0.2161 | n_water=237 | time (s): 1.330 (total time: 27.840) Refine new water occ: r_work=0.1168 r_free=0.1675 adp: r_work=0.1140 r_free=0.1675 occ: r_work=0.1134 r_free=0.1655 adp: r_work=0.1122 r_free=0.1658 occ: r_work=0.1121 r_free=0.1644 adp: r_work=0.1121 r_free=0.1644 ADP+occupancy (water only), MIN, final r_work=0.1121 r_free=0.1644 r_work=0.1121 r_free=0.1644 | n_water=237 | time (s): 5.550 (total time: 33.390) Filter (q & B) r_work=0.1121 r_free=0.1644 | n_water=237 | time (s): 1.170 (total time: 34.560) Filter (dist only) r_work=0.1130 r_free=0.1622 | n_water=234 | time (s): 18.570 (total time: 53.130) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.538210 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.859958 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 0.1005 0.1803 0.0799 0.009 1.0 3.5 0.5 0.6 0 11.269 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.05 18.03 7.99 4.753 16.673 2.860 0.013 9.40 18.19 8.80 5.569 17.110 2.860 0.012 Individual atomic B min max mean iso aniso Overall: 0.00 106.42 16.54 6.58 1761 0 Protein: 0.00 106.42 14.94 6.53 1519 0 Water: 0.00 62.74 26.34 N/A 234 0 Other: 20.85 51.03 32.39 N/A 8 0 Chain A: 0.00 106.42 15.71 N/A 1667 0 Chain S: 5.29 58.03 31.18 N/A 94 0 Histogram: Values Number of atoms 0.00 - 10.64 682 10.64 - 21.28 663 21.28 - 31.93 213 31.93 - 42.57 122 42.57 - 53.21 43 53.21 - 63.85 24 63.85 - 74.50 7 74.50 - 85.14 3 85.14 - 95.78 2 95.78 - 106.42 2 =========================== Idealize ADP of riding H ========================== r_work=0.0940 r_free=0.1819 r_work=0.0939 r_free=0.1819 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0939 r_free = 0.1819 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0936 r_free = 0.1815 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.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.0936 r_free= 0.1815 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ls_wunit_k1) (work): 0.011772 | | target function (ls_wunit_k1) not normalized (work): 57.965740 | | target function (ls_wunit_k1) not normalized (free): 10.095669 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0981 0.0936 0.1815 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2123 0.2128 0.2190 n_refl.: 5176 remove outliers: r(all,work,free)=0.2123 0.2128 0.2190 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2123 0.2128 0.2190 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0981 0.0937 0.1810 n_refl.: 5176 remove outliers: r(all,work,free)=0.0977 0.0932 0.1810 n_refl.: 5174 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 94.79 86 5 0.3034 331.134 313.772 0.668 1.013 0.360 11.894-9.307 99.02 97 4 0.1423 526.995 521.643 0.982 1.014 0.350 9.237-7.194 100.00 213 7 0.1437 430.977 431.783 1.013 1.013 0.329 7.162-5.571 100.00 427 22 0.1370 323.396 320.586 0.988 1.010 0.300 5.546-4.326 100.00 867 58 0.0800 443.977 441.221 1.000 1.006 0.240 4.315-3.360 100.00 1859 96 0.0716 422.227 422.028 1.057 0.999 0.210 3.356-3.002 100.00 1373 60 0.0995 325.217 324.217 1.029 0.991 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9556 b_overall=-3.9946 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0932 r_free=0.1810 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A Total number of N/Q/H flips: 1 r_work=0.0933 r_free=0.1810 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0933 r_free=0.1810 | n_water=234 | time (s): 0.580 (total time: 0.580) Filter (dist) r_work=0.0937 r_free=0.1800 | n_water=232 | time (s): 17.670 (total time: 18.250) Filter (q & B) r_work=0.1018 r_free=0.1799 | n_water=229 | time (s): 1.580 (total time: 19.830) Compute maps r_work=0.1018 r_free=0.1799 | n_water=229 | time (s): 0.500 (total time: 20.330) Filter (map) r_work=0.1278 r_free=0.1837 | n_water=156 | time (s): 1.300 (total time: 21.630) Find peaks r_work=0.1278 r_free=0.1837 | n_water=156 | time (s): 0.430 (total time: 22.060) Add new water r_work=0.1642 r_free=0.2225 | n_water=239 | time (s): 1.280 (total time: 23.340) Refine new water occ: r_work=0.1059 r_free=0.1729 adp: r_work=0.1054 r_free=0.1745 occ: r_work=0.1042 r_free=0.1724 adp: r_work=0.1044 r_free=0.1735 occ: r_work=0.1033 r_free=0.1710 adp: r_work=0.1034 r_free=0.1721 ADP+occupancy (water only), MIN, final r_work=0.1034 r_free=0.1721 r_work=0.1034 r_free=0.1721 | n_water=239 | time (s): 12.540 (total time: 35.880) Filter (q & B) r_work=0.1035 r_free=0.1729 | n_water=237 | time (s): 1.800 (total time: 37.680) Filter (dist only) r_work=0.1038 r_free=0.1721 | n_water=234 | time (s): 19.660 (total time: 57.340) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.101833 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.227410 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 0.0923 0.1776 0.0853 0.011 1.0 3.5 0.5 0.0 0 0.551 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.23 17.76 8.53 5.466 17.753 0.227 5.152 8.76 17.64 8.88 7.319 17.805 0.227 5.056 Individual atomic B min max mean iso aniso Overall: 0.00 107.89 16.45 9.04 1761 0 Protein: 0.00 107.89 15.19 9.01 1519 0 Water: 0.44 59.99 24.19 N/A 234 0 Other: 15.85 46.91 29.62 N/A 8 0 Chain A: 0.00 107.89 15.87 N/A 1655 0 Chain S: 1.84 59.99 25.51 N/A 106 0 Histogram: Values Number of atoms 0.00 - 10.79 672 10.79 - 21.58 664 21.58 - 32.37 234 32.37 - 43.16 117 43.16 - 53.95 39 53.95 - 64.73 16 64.73 - 75.52 10 75.52 - 86.31 6 86.31 - 97.10 2 97.10 - 107.89 1 =========================== Idealize ADP of riding H ========================== r_work=0.0876 r_free=0.1764 r_work=0.0883 r_free=0.1775 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0883 r_free = 0.1775 target_work(ml) = 5.061 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0873 r_free = 0.1754 target_work(ml) = 5.054 | | occupancies: max = 1.00 min = 0.27 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= 0.0873 r_free= 0.1754 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 5.053653 | | target function (ml) not normalized (work): 24874.082186 | | target function (ml) not normalized (free): 1784.617085 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0918 0.0873 0.1754 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2024 0.2029 0.2074 n_refl.: 5174 remove outliers: r(all,work,free)=0.2024 0.2029 0.2074 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2024 0.2029 0.2074 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0911 0.0867 0.1749 n_refl.: 5174 remove outliers: r(all,work,free)=0.0911 0.0867 0.1749 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 0.3649 331.134 307.167 0.612 0.994 0.340 11.894-9.307 99.02 97 4 0.1693 526.995 515.225 0.956 0.997 0.340 9.237-7.194 100.00 213 7 0.1808 430.977 425.855 0.992 0.999 0.310 7.162-5.571 100.00 427 22 0.1772 323.396 315.567 0.975 1.000 0.300 5.546-4.326 100.00 867 58 0.0892 443.977 438.980 0.989 1.001 0.230 4.315-3.360 100.00 1859 96 0.0582 422.227 422.149 1.046 1.003 0.220 3.356-3.002 100.00 1373 60 0.0603 325.217 324.806 1.018 1.004 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-5.8413 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0867 r_free=0.1749 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0867 r_free=0.1749 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0867 r_free=0.1749 | n_water=234 | time (s): 0.650 (total time: 0.650) Filter (dist) r_work=0.0880 r_free=0.1751 | n_water=232 | time (s): 18.220 (total time: 18.870) Filter (q & B) r_work=0.0912 r_free=0.1755 | n_water=231 | time (s): 1.230 (total time: 20.100) Compute maps r_work=0.0912 r_free=0.1755 | n_water=231 | time (s): 0.420 (total time: 20.520) Filter (map) r_work=0.1188 r_free=0.1859 | n_water=165 | time (s): 1.340 (total time: 21.860) Find peaks r_work=0.1188 r_free=0.1859 | n_water=165 | time (s): 0.460 (total time: 22.320) Add new water r_work=0.1498 r_free=0.2151 | n_water=237 | time (s): 1.690 (total time: 24.010) Refine new water occ: r_work=0.0994 r_free=0.1791 adp: r_work=0.0992 r_free=0.1789 occ: r_work=0.0982 r_free=0.1779 adp: r_work=0.0982 r_free=0.1779 occ: r_work=0.0972 r_free=0.1768 adp: r_work=0.0972 r_free=0.1768 ADP+occupancy (water only), MIN, final r_work=0.0972 r_free=0.1768 r_work=0.0972 r_free=0.1768 | n_water=237 | time (s): 14.300 (total time: 38.310) Filter (q & B) r_work=0.0972 r_free=0.1771 | n_water=236 | time (s): 1.450 (total time: 39.760) Filter (dist only) r_work=0.0972 r_free=0.1771 | n_water=236 | time (s): 17.300 (total time: 57.060) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.977565 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.242711 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 0.0893 0.1818 0.0925 0.010 1.0 4.2 0.5 0.6 0 0.489 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 8.93 18.18 9.25 7.032 18.063 0.243 5.024 8.73 18.40 9.67 8.343 18.139 0.243 4.961 Individual atomic B min max mean iso aniso Overall: 0.00 110.11 16.77 10.89 1763 0 Protein: 0.00 110.11 15.54 10.87 1519 0 Water: 0.00 61.19 24.31 N/A 236 0 Other: 15.69 45.53 28.95 N/A 8 0 Chain A: 0.00 110.11 16.15 N/A 1646 0 Chain S: 0.00 60.60 25.54 N/A 117 0 Histogram: Values Number of atoms 0.00 - 11.01 686 11.01 - 22.02 648 22.02 - 33.03 238 33.03 - 44.04 111 44.04 - 55.06 46 55.06 - 66.07 17 66.07 - 77.08 9 77.08 - 88.09 5 88.09 - 99.10 1 99.10 - 110.11 2 =========================== Idealize ADP of riding H ========================== r_work=0.0873 r_free=0.1840 r_work=0.0878 r_free=0.1847 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0878 r_free = 0.1847 target_work(ml) = 4.968 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0869 r_free = 0.1832 target_work(ml) = 4.961 | | occupancies: max = 1.00 min = 0.28 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= 0.0869 r_free= 0.1832 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 4.960825 | | target function (ml) not normalized (work): 24417.182499 | | target function (ml) not normalized (free): 2117.322499 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0918 0.0869 0.1832 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2069 0.2073 0.2131 n_refl.: 5174 remove outliers: r(all,work,free)=0.2069 0.2073 0.2131 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2069 0.2073 0.2131 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0915 0.0867 0.1828 n_refl.: 5174 remove outliers: r(all,work,free)=0.0915 0.0867 0.1828 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 0.3894 331.134 300.837 0.572 0.989 0.317 11.894-9.307 99.02 97 4 0.1937 526.995 510.315 0.955 0.993 0.316 9.237-7.194 100.00 213 7 0.2052 430.977 424.347 1.005 0.996 0.305 7.162-5.571 100.00 427 22 0.1969 323.396 314.582 0.994 0.997 0.300 5.546-4.326 100.00 867 58 0.0966 443.977 437.977 1.011 0.999 0.230 4.315-3.360 100.00 1859 96 0.0554 422.227 422.106 1.078 1.002 0.220 3.356-3.002 100.00 1373 60 0.0435 325.217 325.518 1.052 1.004 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.3371 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0867 r_free=0.1828 After: r_work=0.0870 r_free=0.1827 ================================== NQH flips ================================== r_work=0.0870 r_free=0.1827 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0870 r_free=0.1827 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0870 r_free=0.1827 | n_water=236 | time (s): 0.720 (total time: 0.720) Filter (dist) r_work=0.0870 r_free=0.1827 | n_water=236 | time (s): 17.200 (total time: 17.920) Filter (q & B) r_work=0.1010 r_free=0.1911 | n_water=231 | time (s): 1.660 (total time: 19.580) Compute maps r_work=0.1010 r_free=0.1911 | n_water=231 | time (s): 0.660 (total time: 20.240) Filter (map) r_work=0.1251 r_free=0.1945 | n_water=163 | time (s): 1.940 (total time: 22.180) Find peaks r_work=0.1251 r_free=0.1945 | n_water=163 | time (s): 0.490 (total time: 22.670) Add new water r_work=0.1529 r_free=0.2183 | n_water=232 | time (s): 1.330 (total time: 24.000) Refine new water occ: r_work=0.0980 r_free=0.1797 adp: r_work=0.0974 r_free=0.1795 occ: r_work=0.0965 r_free=0.1781 adp: r_work=0.0966 r_free=0.1787 occ: r_work=0.0958 r_free=0.1774 adp: r_work=0.0959 r_free=0.1780 ADP+occupancy (water only), MIN, final r_work=0.0959 r_free=0.1780 r_work=0.0959 r_free=0.1780 | n_water=232 | time (s): 13.550 (total time: 37.550) Filter (q & B) r_work=0.0959 r_free=0.1786 | n_water=228 | time (s): 1.730 (total time: 39.280) Filter (dist only) r_work=0.0971 r_free=0.1788 | n_water=226 | time (s): 16.830 (total time: 56.110) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.940237 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.228584 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.0919 0.1826 0.0907 0.010 1.1 8.0 0.5 0.0 0 0.470 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.19 18.26 9.07 8.260 18.352 0.229 5.026 8.97 18.25 9.28 9.093 18.463 0.229 4.974 Individual atomic B min max mean iso aniso Overall: 0.00 108.03 16.99 11.98 1753 0 Protein: 0.00 108.03 15.89 11.96 1519 0 Water: 0.00 59.53 23.89 N/A 226 0 Other: 16.73 46.12 30.99 N/A 8 0 Chain A: 0.00 108.03 16.44 N/A 1637 0 Chain S: 1.50 59.53 24.77 N/A 116 0 Histogram: Values Number of atoms 0.00 - 10.80 656 10.80 - 21.61 636 21.61 - 32.41 256 32.41 - 43.21 123 43.21 - 54.01 46 54.01 - 64.82 13 64.82 - 75.62 13 75.62 - 86.42 5 86.42 - 97.22 3 97.22 - 108.03 2 =========================== Idealize ADP of riding H ========================== r_work=0.0897 r_free=0.1825 r_work=0.0900 r_free=0.1827 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0900 r_free = 0.1827 target_work(ml) = 4.979 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0895 r_free = 0.1816 target_work(ml) = 4.976 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0895 r_free= 0.1816 coordinate error (max.-lik. estimate): 0.26 A | | | | normalized target function (ml) (work): 4.975643 | | target function (ml) not normalized (work): 24490.112827 | | target function (ml) not normalized (free): 2098.214274 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.79 1.00 2492 142 0.1273 0.1829 5.5455 6.1389| | 2: 3.78 - 3.00 1.00 2430 110 0.0435 0.1793 4.3913 11.15| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 0.92 12.18 1.00 0.98 13368.25| | 2: 3.78 - 3.00 2430 110 0.99 1.93 1.00 1.00 969.56| |alpha: min = 0.97 max = 1.01 mean = 0.99| |beta: min = 622.42 max = 22314.47 mean = 7246.99| |figures of merit: min = 0.01 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.02 mean = 7.12| |phase err.(test): min = 0.00 max = 89.14 mean = 7.12| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0942 0.0895 0.1816 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2137 0.2140 0.2214 n_refl.: 5174 remove outliers: r(all,work,free)=0.2137 0.2140 0.2214 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2137 0.2140 0.2214 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0950 0.0904 0.1823 n_refl.: 5174 remove outliers: r(all,work,free)=0.0950 0.0904 0.1823 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 0.3799 331.134 302.224 0.594 0.985 0.320 11.894-9.307 99.02 97 4 0.2029 526.995 509.109 0.968 0.991 0.320 9.237-7.194 100.00 213 7 0.2086 430.977 422.008 1.006 0.994 0.300 7.162-5.571 100.00 427 22 0.2057 323.396 314.275 0.993 0.996 0.290 5.546-4.326 100.00 867 58 0.1041 443.977 437.178 1.017 0.998 0.208 4.315-3.360 100.00 1859 96 0.0591 422.227 422.174 1.095 1.001 0.171 3.356-3.002 100.00 1373 60 0.0427 325.217 325.470 1.073 1.004 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-8.0480 ================= 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 0.1978 0.082 5.342 8.8 119.3 19.9 258 0.000 1_bss: 0.1556 0.1538 0.082 5.342 5.9 116.4 17.0 258 0.000 1_settarget: 0.1556 0.1538 0.082 5.342 5.9 116.4 17.0 258 0.000 1_nqh: 0.1556 0.1538 0.082 5.342 5.9 116.4 17.0 258 0.000 1_weight: 0.1556 0.1538 0.082 5.342 5.9 116.4 17.0 258 0.000 1_xyzrec: 0.1163 0.1760 0.010 0.999 5.9 116.4 17.0 258 0.203 1_adp: 0.1022 0.1752 0.010 0.999 1.6 111.4 17.3 258 0.203 1_regHadp: 0.1017 0.1759 0.010 0.999 1.6 111.4 17.3 258 0.203 1_occ: 0.1014 0.1746 0.010 0.999 1.6 111.4 17.3 258 0.203 2_bss: 0.1019 0.1750 0.010 0.999 0.7 110.5 16.4 258 0.203 2_settarget: 0.1019 0.1750 0.010 0.999 0.7 110.5 16.4 258 0.203 2_updatecdl: 0.1019 0.1750 0.010 1.021 0.7 110.5 16.4 258 0.203 2_nqh: 0.1019 0.1750 0.010 1.021 0.7 110.5 16.4 258 0.203 2_sol: 0.1130 0.1622 0.010 1.021 0.7 110.4 15.7 234 n/a 2_weight: 0.1130 0.1622 0.010 1.021 0.7 110.4 15.7 234 n/a 2_xyzrec: 0.1005 0.1803 0.009 0.966 0.7 110.4 15.7 234 n/a 2_adp: 0.0940 0.1819 0.009 0.966 0.0 106.4 16.5 234 n/a 2_regHadp: 0.0939 0.1819 0.009 0.966 0.0 106.4 16.5 234 n/a 2_occ: 0.0936 0.1815 0.009 0.966 0.0 106.4 16.5 234 n/a 3_bss: 0.0932 0.1810 0.009 0.966 0.0 106.4 16.5 234 n/a 3_settarget: 0.0932 0.1810 0.009 0.966 0.0 106.4 16.5 234 n/a 3_updatecdl: 0.0932 0.1810 0.009 0.972 0.0 106.4 16.5 234 n/a 3_nqh: 0.0933 0.1810 0.009 0.972 0.0 106.4 16.5 234 n/a 3_sol: 0.1038 0.1721 0.009 0.972 0.0 106.4 16.4 234 n/a 3_weight: 0.1038 0.1721 0.009 0.972 0.0 106.4 16.4 234 n/a 3_xyzrec: 0.0923 0.1776 0.011 1.041 0.0 106.4 16.4 234 n/a 3_adp: 0.0876 0.1764 0.011 1.041 0.0 107.9 16.5 234 n/a 3_regHadp: 0.0883 0.1775 0.011 1.041 0.0 107.9 16.5 234 n/a 3_occ: 0.0873 0.1754 0.011 1.041 0.0 107.9 16.5 234 n/a 4_bss: 0.0867 0.1749 0.011 1.041 0.0 107.9 16.5 234 n/a 4_settarget: 0.0867 0.1749 0.011 1.041 0.0 107.9 16.5 234 n/a 4_updatecdl: 0.0867 0.1749 0.011 1.064 0.0 107.9 16.5 234 n/a 4_nqh: 0.0867 0.1749 0.011 1.064 0.0 107.9 16.5 234 n/a 4_sol: 0.0972 0.1771 0.011 1.064 0.0 107.9 16.6 236 n/a 4_weight: 0.0972 0.1771 0.011 1.064 0.0 107.9 16.6 236 n/a 4_xyzrec: 0.0893 0.1818 0.010 1.042 0.0 107.9 16.6 236 n/a 4_adp: 0.0873 0.1840 0.010 1.042 0.0 110.1 16.8 236 n/a 4_regHadp: 0.0878 0.1847 0.010 1.042 0.0 110.1 16.8 236 n/a 4_occ: 0.0869 0.1832 0.010 1.042 0.0 110.1 16.8 236 n/a 5_bss: 0.0867 0.1828 0.010 1.042 0.0 110.1 16.8 236 n/a 5_settarget: 0.0867 0.1828 0.010 1.042 0.0 110.1 16.8 236 n/a 5_updatecdl: 0.0867 0.1828 0.010 1.046 0.0 110.1 16.8 236 n/a 5_setrh: 0.0870 0.1827 0.010 1.046 0.0 110.1 16.8 236 n/a 5_nqh: 0.0870 0.1827 0.010 1.046 0.0 110.1 16.8 236 n/a 5_sol: 0.0971 0.1788 0.010 1.046 0.0 110.1 16.8 226 n/a 5_weight: 0.0971 0.1788 0.010 1.046 0.0 110.1 16.8 226 n/a 5_xyzrec: 0.0919 0.1826 0.010 1.122 0.0 110.1 16.8 226 n/a 5_adp: 0.0897 0.1825 0.010 1.122 0.0 108.0 17.0 226 n/a 5_regHadp: 0.0900 0.1827 0.010 1.122 0.0 108.0 17.0 226 n/a 5_occ: 0.0895 0.1816 0.010 1.122 0.0 108.0 17.0 226 n/a end: 0.0904 0.1823 0.010 1.122 0.0 108.0 17.0 226 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_7509253_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_7509253_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.1100 Refinement macro-cycles (run) : 496.2400 Write final files (write_after_run_outputs) : 9.8600 Total : 509.2100 Total CPU time: 8.87 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:19:13 PST -0800 (1735492753.17 s) Start R-work = 0.1556, R-free = 0.1538 Final R-work = 0.0904, R-free = 0.1823 =============================================================================== Job complete usr+sys time: 539.44 seconds wall clock time: 9 minutes 21.00 seconds (561.00 seconds total)