Starting phenix.refine on Sun Dec 29 09:10:02 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_1664580.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_1664580.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_1664580.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 3 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== 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: 1.58, per 1000 atoms: 0.47 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: 0.30 Conformation dependent library (CDL) restraints added in 112.0 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.63 - 0.88: 403 0.88 - 1.14: 1201 1.14 - 1.40: 589 1.40 - 1.66: 906 1.66 - 1.92: 54 Bond restraints: 3153 Sorted by residual: bond pdb=" N VAL A 33 " pdb=" CA VAL A 33 " ideal model delta sigma weight residual 1.459 1.238 0.221 1.20e-02 6.94e+03 3.38e+02 bond pdb=" N ILE A 52 " pdb=" CA ILE A 52 " ideal model delta sigma weight residual 1.459 1.673 -0.215 1.20e-02 6.94e+03 3.20e+02 bond pdb=" C GLY A 159 " pdb=" O GLY A 159 " ideal model delta sigma weight residual 1.236 1.057 0.179 1.08e-02 8.57e+03 2.76e+02 bond pdb=" C VAL A 51 " pdb=" O VAL A 51 " ideal model delta sigma weight residual 1.236 1.053 0.183 1.12e-02 7.97e+03 2.67e+02 bond pdb=" CA VAL A 44 " pdb=" CB VAL A 44 " ideal model delta sigma weight residual 1.540 1.739 -0.199 1.23e-02 6.61e+03 2.62e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.64: 3071 4.64 - 9.27: 1907 9.27 - 13.91: 663 13.91 - 18.54: 124 18.54 - 23.18: 12 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O ALA A 165 " pdb=" C ALA A 165 " pdb=" N LEU A 166 " ideal model delta sigma weight residual 122.07 107.39 14.68 1.03e+00 9.43e-01 2.03e+02 angle pdb=" O GLY A 157 " pdb=" C GLY A 157 " pdb=" N PRO A 158 " ideal model delta sigma weight residual 121.77 107.84 13.93 1.00e+00 1.00e+00 1.94e+02 angle pdb=" CA VAL A 186 " pdb=" C VAL A 186 " pdb=" O VAL A 186 " ideal model delta sigma weight residual 120.78 137.07 -16.29 1.25e+00 6.40e-01 1.70e+02 angle pdb=" O BCYS A 53 " pdb=" C BCYS A 53 " pdb=" N PRO A 54 " ideal model delta sigma weight residual 121.23 131.37 -10.14 8.10e-01 1.52e+00 1.57e+02 angle pdb=" CA GLY A 136 " pdb=" C GLY A 136 " pdb=" O GLY A 136 " ideal model delta sigma weight residual 119.27 132.58 -13.31 1.07e+00 8.73e-01 1.55e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 16.66: 1304 16.66 - 33.31: 119 33.31 - 49.96: 39 49.96 - 66.61: 16 66.61 - 83.26: 3 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C GLU A 143 " pdb=" N GLU A 143 " pdb=" CA GLU A 143 " pdb=" CB GLU A 143 " ideal model delta harmonic sigma weight residual -122.60 -145.66 23.06 0 2.50e+00 1.60e-01 8.50e+01 dihedral pdb=" C ARG A 48 " pdb=" N ARG A 48 " pdb=" CA ARG A 48 " pdb=" CB ARG A 48 " ideal model delta harmonic sigma weight residual -122.60 -145.42 22.82 0 2.50e+00 1.60e-01 8.33e+01 dihedral pdb=" N ARG A 48 " pdb=" C ARG A 48 " pdb=" CA ARG A 48 " pdb=" CB ARG A 48 " ideal model delta harmonic sigma weight residual 122.80 144.94 -22.14 0 2.50e+00 1.60e-01 7.84e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.267: 117 0.267 - 0.532: 88 0.532 - 0.798: 24 0.798 - 1.064: 11 1.064 - 1.330: 3 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA GLU A 143 " pdb=" N GLU A 143 " pdb=" C GLU A 143 " pdb=" CB GLU A 143 " both_signs ideal model delta sigma weight residual False 2.51 1.18 1.33 2.00e-01 2.50e+01 4.42e+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 -1.33 -1.26 2.00e-01 2.50e+01 3.96e+01 chirality pdb=" CA ARG A 48 " pdb=" N ARG A 48 " pdb=" C ARG A 48 " pdb=" CB ARG A 48 " both_signs ideal model delta sigma weight residual False 2.51 1.33 1.18 2.00e-01 2.50e+01 3.45e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 145 " -0.095 9.50e-02 1.11e+02 7.29e-02 9.78e+01 pdb=" NE ARG A 145 " -0.070 2.00e-02 2.50e+03 pdb=" CZ ARG A 145 " 0.073 2.00e-02 2.50e+03 pdb=" NH1 ARG A 145 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 145 " -0.090 2.00e-02 2.50e+03 pdb="HH11 ARG A 145 " 0.083 2.00e-02 2.50e+03 pdb="HH12 ARG A 145 " -0.091 2.00e-02 2.50e+03 pdb="HH21 ARG A 145 " 0.065 2.00e-02 2.50e+03 pdb="HH22 ARG A 145 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.101 2.00e-02 2.50e+03 5.43e-02 8.84e+01 pdb=" CG PHE A 164 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.074 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.078 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " -0.014 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.045 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.014 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.038 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.039 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.014 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG BGLN A 80 " 0.059 2.00e-02 2.50e+03 7.62e-02 8.71e+01 pdb=" CD BGLN A 80 " -0.100 2.00e-02 2.50e+03 pdb=" OE1BGLN A 80 " -0.007 2.00e-02 2.50e+03 pdb=" NE2BGLN A 80 " 0.106 2.00e-02 2.50e+03 pdb="HE21BGLN A 80 " -0.094 2.00e-02 2.50e+03 pdb="HE22BGLN A 80 " 0.035 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.28: 784 2.28 - 2.86: 7812 2.86 - 3.44: 10667 3.44 - 4.02: 15259 4.02 - 4.60: 22099 Nonbonded interactions: 56621 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.697 2.100 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.813 2.450 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.821 2.450 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.836 2.100 nonbonded pdb=" H VAL A 44 " pdb=" O ILE A 52 " model vdw 1.840 2.450 ... (remaining 56616 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_1664580_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= 0.3626 r_free= 0.2030 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.468963 | | target function (ml) not normalized (work): 22031.989592 | | target function (ml) not normalized (free): 1149.913886 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3822 0.2222 4.8483 4.9026| | 2: 3.78 - 3.00 1.00 2430 110 0.3386 0.1706 4.0787 4.1249| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 48.62 0.83 0.13 6591.93| | 2: 3.78 - 3.00 2430 110 0.94 11.28 1.48 0.26 448.50| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 381.58 max = 12042.70 mean = 3563.83| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 90.00 mean = 30.21| |phase err.(test): min = 0.00 max = 89.89 mean = 33.25| |-----------------------------------------------------------------------------| ----------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 0.259 1557 Z= 5.326 Angle : 5.330 17.017 2118 Z= 3.694 Chirality : 0.404 1.330 243 Planarity : 0.032 0.104 284 Dihedral : 13.685 83.258 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.54 % Allowed : 1.62 % Favored : 97.84 % Rotamer: Outliers : 1.24 % Allowed : 3.11 % Favored : 95.65 % Cbeta Deviations : 31.89 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.47), residues: 224 helix: -3.06 (0.33), residues: 103 sheet: -0.23 (0.89), residues: 28 loop : -0.69 (0.59), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.093 0.025 ARG A 145 TYR 0.066 0.031 TYR A 141 PHE 0.082 0.042 PHE A 162 HIS 0.044 0.016 HIS A 138 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= 0.3626 r_free= 0.2030 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.468963 | | target function (ml) not normalized (work): 22031.989592 | | target function (ml) not normalized (free): 1149.913886 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3581 0.3659 0.2149 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3581 0.3659 0.2149 n_refl.: 5182 remove outliers: r(all,work,free)=0.2533 0.2557 0.2149 n_refl.: 5178 overall B=-2.39 to atoms: r(all,work,free)=0.2440 0.2461 0.2111 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1565 0.1562 0.1642 n_refl.: 5178 remove outliers: r(all,work,free)=0.1563 0.1559 0.1642 n_refl.: 5177 ======================== 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 32.574-12.150 100.00 89 5 0.4058 444.986 405.525 0.611 1.104 0.394 11.894-9.307 99.02 97 4 0.1907 714.371 692.229 0.871 1.098 0.382 9.237-7.194 100.00 213 7 0.2206 584.213 575.095 0.898 1.087 0.363 7.162-5.571 100.00 427 22 0.2317 438.381 424.360 0.878 1.068 0.308 5.546-4.326 100.00 867 58 0.1387 601.835 594.475 0.939 1.037 0.230 4.315-3.360 100.00 1859 96 0.1309 572.352 566.216 1.029 0.984 0.198 3.356-3.002 100.00 1373 60 0.1575 440.849 433.484 1.061 0.932 0.074 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9170 b_overall=-4.1558 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1559 r_free=0.1642 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN B Total number of N/Q/H flips: 1 r_work=0.1562 r_free=0.1644 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 18.540214 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.738755 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 0.1154 0.1786 0.0633 0.010 1.0 3.5 0.5 0.0 0 9.270 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.54 17.86 6.33 3.013 16.473 1.739 0.018 10.20 17.89 7.69 4.797 16.660 1.739 0.015 Individual atomic B min max mean iso aniso Overall: 2.52 111.91 17.85 5.19 1785 0 Protein: 2.52 111.89 15.14 5.18 1519 0 Water: 4.48 111.91 33.64 N/A 258 0 Other: 16.96 38.60 24.17 N/A 8 0 Chain A: 2.52 111.91 17.85 N/A 1785 0 Histogram: Values Number of atoms 2.52 - 13.46 913 13.46 - 24.40 487 24.40 - 35.34 187 35.34 - 46.28 112 46.28 - 57.21 55 57.21 - 68.15 13 68.15 - 79.09 8 79.09 - 90.03 6 90.03 - 100.97 1 100.97 - 111.91 3 =========================== Idealize ADP of riding H ========================== r_work=0.1020 r_free=0.1789 r_work=0.1014 r_free=0.1793 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1014 r_free = 0.1793 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1017 r_free = 0.1799 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5177 (all), 4.87 % free)-------------| | | | r_work= 0.1017 r_free= 0.1799 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ls_wunit_k1) (work): 0.014157 | | target function (ls_wunit_k1) not normalized (work): 69.725680 | | target function (ls_wunit_k1) not normalized (free): 10.326589 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1056 0.1017 0.1799 n_refl.: 5177 re-set all scales: r(all,work,free)=0.2129 0.2128 0.2262 n_refl.: 5177 remove outliers: r(all,work,free)=0.2129 0.2128 0.2262 n_refl.: 5177 overall B=-0.91 to atoms: r(all,work,free)=0.2089 0.2087 0.2251 n_refl.: 5177 bulk-solvent and scaling: r(all,work,free)=0.1058 0.1019 0.1804 n_refl.: 5177 remove outliers: r(all,work,free)=0.1056 0.1017 0.1804 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 0.3404 311.255 297.163 0.609 1.046 0.370 11.894-9.307 99.02 97 4 0.1522 503.982 496.482 0.910 1.045 0.351 9.237-7.194 100.00 213 7 0.1683 412.158 412.497 0.949 1.040 0.316 7.162-5.571 100.00 427 22 0.1631 309.274 306.122 0.924 1.031 0.302 5.546-4.326 100.00 867 58 0.0914 424.589 421.906 0.955 1.017 0.207 4.315-3.360 100.00 1859 96 0.0768 403.789 403.795 1.022 0.992 0.203 3.356-3.002 100.00 1373 60 0.1003 311.015 309.575 1.016 0.968 0.059 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9170 b_overall=-4.0841 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1017 r_free=0.1804 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN B Total number of N/Q/H flips: 1 r_work=0.1017 r_free=0.1805 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1017 r_free=0.1805 | n_water=258 | time (s): 0.670 (total time: 0.670) Filter (dist) r_work=0.1049 r_free=0.1801 | n_water=247 | time (s): 21.610 (total time: 22.280) Filter (q & B) r_work=0.1049 r_free=0.1792 | n_water=243 | time (s): 1.450 (total time: 23.730) Compute maps r_work=0.1049 r_free=0.1792 | n_water=243 | time (s): 0.440 (total time: 24.170) Filter (map) r_work=0.1358 r_free=0.1913 | n_water=146 | time (s): 1.560 (total time: 25.730) Find peaks r_work=0.1358 r_free=0.1913 | n_water=146 | time (s): 0.440 (total time: 26.170) Add new water r_work=0.1691 r_free=0.2229 | n_water=229 | time (s): 1.370 (total time: 27.540) Refine new water occ: r_work=0.1172 r_free=0.1736 adp: r_work=0.1150 r_free=0.1742 occ: r_work=0.1147 r_free=0.1715 adp: r_work=0.1135 r_free=0.1727 occ: r_work=0.1135 r_free=0.1705 adp: r_work=0.1131 r_free=0.1710 ADP+occupancy (water only), MIN, final r_work=0.1131 r_free=0.1710 r_work=0.1131 r_free=0.1710 | n_water=229 | time (s): 3.570 (total time: 31.110) Filter (q & B) r_work=0.1131 r_free=0.1710 | n_water=229 | time (s): 0.720 (total time: 31.830) Filter (dist only) r_work=0.1131 r_free=0.1704 | n_water=228 | time (s): 18.450 (total time: 50.280) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.300608 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.516345 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 0.1014 0.1796 0.0782 0.009 1.0 6.4 0.5 0.6 0 12.150 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.14 17.96 7.82 4.635 17.297 2.516 0.014 9.49 18.26 8.77 5.497 17.726 2.516 0.012 Individual atomic B min max mean iso aniso Overall: 0.00 109.08 17.12 6.45 1755 0 Protein: 0.00 109.08 15.57 6.45 1519 0 Water: 0.00 63.90 27.28 N/A 228 0 Other: 13.17 32.69 21.54 N/A 8 0 Chain A: 0.00 109.08 16.30 N/A 1672 0 Chain S: 0.50 59.29 33.58 N/A 83 0 Histogram: Values Number of atoms 0.00 - 10.91 646 10.91 - 21.82 700 21.82 - 32.72 215 32.72 - 43.63 111 43.63 - 54.54 40 54.54 - 65.45 29 65.45 - 76.35 8 76.35 - 87.26 2 87.26 - 98.17 2 98.17 - 109.08 2 =========================== Idealize ADP of riding H ========================== r_work=0.0949 r_free=0.1826 r_work=0.0945 r_free=0.1827 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0945 r_free = 0.1827 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0946 r_free = 0.1813 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.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.0946 r_free= 0.1813 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ls_wunit_k1) (work): 0.012099 | | target function (ls_wunit_k1) not normalized (work): 59.575546 | | target function (ls_wunit_k1) not normalized (free): 9.759911 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0990 0.0946 0.1813 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2174 0.2180 0.2219 n_refl.: 5176 remove outliers: r(all,work,free)=0.2174 0.2180 0.2219 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2174 0.2180 0.2219 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0991 0.0947 0.1828 n_refl.: 5176 remove outliers: r(all,work,free)=0.0991 0.0947 0.1828 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 0.3345 311.255 298.707 0.649 1.024 0.358 11.894-9.307 99.02 97 4 0.1480 503.982 498.945 0.967 1.025 0.335 9.237-7.194 100.00 213 7 0.1469 412.158 414.541 1.009 1.023 0.304 7.162-5.571 100.00 427 22 0.1442 309.274 306.947 0.983 1.018 0.290 5.546-4.326 100.00 867 58 0.0800 424.589 422.401 1.011 1.010 0.220 4.315-3.360 100.00 1859 96 0.0730 403.789 403.446 1.074 0.996 0.210 3.356-3.002 100.00 1373 60 0.0975 311.015 309.387 1.060 0.982 0.082 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-4.8365 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0947 r_free=0.1828 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=0.0947 r_free=0.1829 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0947 r_free=0.1829 | n_water=228 | time (s): 0.550 (total time: 0.550) Filter (dist) r_work=0.0980 r_free=0.1832 | n_water=221 | time (s): 19.900 (total time: 20.450) Filter (q & B) r_work=0.1041 r_free=0.1849 | n_water=218 | time (s): 1.540 (total time: 21.990) Compute maps r_work=0.1041 r_free=0.1849 | n_water=218 | time (s): 0.670 (total time: 22.660) Filter (map) r_work=0.1320 r_free=0.1885 | n_water=144 | time (s): 1.950 (total time: 24.610) Find peaks r_work=0.1320 r_free=0.1885 | n_water=144 | time (s): 0.520 (total time: 25.130) Add new water r_work=0.1720 r_free=0.2200 | n_water=236 | time (s): 1.700 (total time: 26.830) Refine new water occ: r_work=0.1089 r_free=0.1772 adp: r_work=0.1084 r_free=0.1781 occ: r_work=0.1071 r_free=0.1759 adp: r_work=0.1071 r_free=0.1768 occ: r_work=0.1060 r_free=0.1747 adp: r_work=0.1059 r_free=0.1758 ADP+occupancy (water only), MIN, final r_work=0.1059 r_free=0.1758 r_work=0.1059 r_free=0.1758 | n_water=236 | time (s): 10.370 (total time: 37.200) Filter (q & B) r_work=0.1059 r_free=0.1763 | n_water=235 | time (s): 1.670 (total time: 38.870) Filter (dist only) r_work=0.1070 r_free=0.1767 | n_water=232 | time (s): 18.250 (total time: 57.120) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.160032 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.259212 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 0.0973 0.1827 0.0854 0.011 1.1 4.8 0.5 0.6 0 0.580 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.73 18.27 8.54 5.430 18.392 0.259 5.154 9.29 18.15 8.87 7.511 18.411 0.259 5.054 Individual atomic B min max mean iso aniso Overall: 0.00 108.96 16.98 9.25 1759 0 Protein: 0.00 108.96 15.71 9.26 1519 0 Water: 0.00 58.28 25.04 N/A 232 0 Other: 14.06 39.31 23.60 N/A 8 0 Chain A: 0.00 108.96 16.41 N/A 1655 0 Chain S: 0.00 57.31 26.05 N/A 104 0 Histogram: Values Number of atoms 0.00 - 10.90 640 10.90 - 21.79 689 21.79 - 32.69 241 32.69 - 43.59 112 43.59 - 54.48 41 54.48 - 65.38 20 65.38 - 76.27 8 76.27 - 87.17 3 87.17 - 98.07 4 98.07 - 108.96 1 =========================== Idealize ADP of riding H ========================== r_work=0.0929 r_free=0.1815 r_work=0.0934 r_free=0.1818 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0934 r_free = 0.1818 target_work(ml) = 5.059 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0918 r_free = 0.1797 target_work(ml) = 5.048 | | 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.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.0918 r_free= 0.1797 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 5.047554 | | target function (ml) not normalized (work): 24854.156655 | | target function (ml) not normalized (free): 1792.734936 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0962 0.0918 0.1797 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2201 0.2210 0.2173 n_refl.: 5176 remove outliers: r(all,work,free)=0.2201 0.2210 0.2173 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2201 0.2210 0.2173 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0953 0.0909 0.1787 n_refl.: 5176 remove outliers: r(all,work,free)=0.0951 0.0907 0.1787 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 0.3697 313.288 277.881 0.573 0.994 0.324 11.894-9.307 99.02 97 4 0.1826 503.982 489.231 0.947 0.998 0.320 9.237-7.194 100.00 213 7 0.1854 412.158 407.084 1.013 0.999 0.295 7.162-5.571 100.00 427 22 0.1886 309.274 300.807 0.983 1.000 0.290 5.546-4.326 100.00 867 58 0.0938 424.589 419.402 1.017 1.001 0.220 4.315-3.360 100.00 1859 96 0.0602 403.789 403.570 1.082 1.002 0.220 3.356-3.002 100.00 1373 60 0.0635 311.015 310.390 1.059 1.003 0.080 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9172 b_overall=-7.5202 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0907 r_free=0.1787 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0907 r_free=0.1787 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0907 r_free=0.1787 | n_water=232 | time (s): 0.530 (total time: 0.530) Filter (dist) r_work=0.0920 r_free=0.1806 | n_water=228 | time (s): 17.680 (total time: 18.210) Filter (q & B) r_work=0.0948 r_free=0.1828 | n_water=227 | time (s): 1.810 (total time: 20.020) Compute maps r_work=0.0948 r_free=0.1828 | n_water=227 | time (s): 0.540 (total time: 20.560) Filter (map) r_work=0.1237 r_free=0.1891 | n_water=154 | time (s): 1.820 (total time: 22.380) Find peaks r_work=0.1237 r_free=0.1891 | n_water=154 | time (s): 0.590 (total time: 22.970) Add new water r_work=0.1531 r_free=0.2138 | n_water=225 | time (s): 1.540 (total time: 24.510) Refine new water occ: r_work=0.1023 r_free=0.1844 adp: r_work=0.1020 r_free=0.1850 occ: r_work=0.1013 r_free=0.1836 adp: r_work=0.1013 r_free=0.1842 occ: r_work=0.1007 r_free=0.1828 adp: r_work=0.1007 r_free=0.1828 ADP+occupancy (water only), MIN, final r_work=0.1007 r_free=0.1828 r_work=0.1007 r_free=0.1828 | n_water=225 | time (s): 5.990 (total time: 30.500) Filter (q & B) r_work=0.1007 r_free=0.1828 | n_water=224 | time (s): 1.300 (total time: 31.800) Filter (dist only) r_work=0.1006 r_free=0.1831 | n_water=223 | time (s): 16.150 (total time: 47.950) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.999359 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.235092 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 0.0912 0.1855 0.0943 0.011 1.1 6.4 0.5 0.6 0 0.500 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.12 18.55 9.43 7.200 18.501 0.235 5.006 8.89 18.88 9.99 8.429 18.623 0.235 4.943 Individual atomic B min max mean iso aniso Overall: 0.00 110.54 17.06 10.97 1750 0 Protein: 0.00 110.54 16.12 10.98 1519 0 Water: 0.00 57.02 23.23 N/A 223 0 Other: 15.53 39.05 24.46 N/A 8 0 Chain A: 0.00 110.54 16.65 N/A 1644 0 Chain S: 0.00 57.02 23.50 N/A 106 0 Histogram: Values Number of atoms 0.00 - 11.05 644 11.05 - 22.11 668 22.11 - 33.16 262 33.16 - 44.22 104 44.22 - 55.27 39 55.27 - 66.32 13 66.32 - 77.38 11 77.38 - 88.43 3 88.43 - 99.49 4 99.49 - 110.54 2 =========================== Idealize ADP of riding H ========================== r_work=0.0889 r_free=0.1888 r_work=0.0893 r_free=0.1889 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0893 r_free = 0.1889 target_work(ml) = 4.948 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0886 r_free = 0.1874 target_work(ml) = 4.943 | | 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.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0886 r_free= 0.1874 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ml) (work): 4.942671 | | target function (ml) not normalized (work): 24332.768856 | | target function (ml) not normalized (free): 2046.081084 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0936 0.0886 0.1874 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2171 0.2169 0.2302 n_refl.: 5175 remove outliers: r(all,work,free)=0.2171 0.2169 0.2302 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2171 0.2169 0.2302 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0934 0.0884 0.1881 n_refl.: 5175 remove outliers: r(all,work,free)=0.0934 0.0884 0.1881 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 0.3989 313.288 282.432 0.603 0.987 0.317 11.894-9.307 99.02 97 4 0.1923 503.982 486.293 0.985 0.992 0.316 9.237-7.194 100.00 213 7 0.2099 412.158 403.867 1.053 0.995 0.300 7.162-5.571 100.00 427 22 0.2040 309.274 299.636 1.033 0.997 0.300 5.546-4.326 100.00 867 58 0.0972 424.589 419.192 1.070 0.999 0.243 4.315-3.360 100.00 1859 96 0.0555 403.789 403.584 1.144 1.002 0.236 3.356-3.002 100.00 1373 60 0.0465 311.015 311.051 1.119 1.004 0.088 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-8.2501 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0884 r_free=0.1881 After: r_work=0.0887 r_free=0.1879 ================================== NQH flips ================================== r_work=0.0887 r_free=0.1879 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0887 r_free=0.1879 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0887 r_free=0.1879 | n_water=223 | time (s): 0.470 (total time: 0.470) Filter (dist) r_work=0.0900 r_free=0.1853 | n_water=220 | time (s): 17.260 (total time: 17.730) Filter (q & B) r_work=0.1002 r_free=0.1899 | n_water=217 | time (s): 1.440 (total time: 19.170) Compute maps r_work=0.1002 r_free=0.1899 | n_water=217 | time (s): 0.480 (total time: 19.650) Filter (map) r_work=0.1279 r_free=0.2006 | n_water=156 | time (s): 1.480 (total time: 21.130) Find peaks r_work=0.1279 r_free=0.2006 | n_water=156 | time (s): 0.460 (total time: 21.590) Add new water r_work=0.1555 r_free=0.2222 | n_water=221 | time (s): 1.270 (total time: 22.860) Refine new water occ: r_work=0.0995 r_free=0.1881 adp: r_work=0.0987 r_free=0.1889 occ: r_work=0.0983 r_free=0.1875 adp: r_work=0.0982 r_free=0.1884 occ: r_work=0.0978 r_free=0.1872 adp: r_work=0.0977 r_free=0.1879 ADP+occupancy (water only), MIN, final r_work=0.0977 r_free=0.1879 r_work=0.0977 r_free=0.1879 | n_water=221 | time (s): 12.820 (total time: 35.680) Filter (q & B) r_work=0.0977 r_free=0.1879 | n_water=221 | time (s): 0.730 (total time: 36.410) Filter (dist only) r_work=0.0992 r_free=0.1889 | n_water=218 | time (s): 18.150 (total time: 54.560) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.031328 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.220439 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 0.0926 0.1875 0.0949 0.011 1.1 8.0 0.5 0.6 0 0.516 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.26 18.75 9.49 8.340 18.874 0.220 5.005 9.07 19.05 9.98 9.292 18.984 0.220 4.950 Individual atomic B min max mean iso aniso Overall: 0.00 112.02 17.39 12.26 1745 0 Protein: 0.00 112.02 16.51 12.28 1519 0 Water: 0.00 58.42 23.27 N/A 218 0 Other: 13.49 38.55 23.77 N/A 8 0 Chain A: 0.00 112.02 16.89 N/A 1631 0 Chain S: 0.00 58.42 24.52 N/A 114 0 Histogram: Values Number of atoms 0.00 - 11.20 648 11.20 - 22.40 665 22.40 - 33.61 239 33.61 - 44.81 121 44.81 - 56.01 36 56.01 - 67.21 17 67.21 - 78.42 9 78.42 - 89.62 3 89.62 - 100.82 5 100.82 - 112.02 2 =========================== Idealize ADP of riding H ========================== r_work=0.0907 r_free=0.1905 r_work=0.0912 r_free=0.1909 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0912 r_free = 0.1909 target_work(ml) = 4.954 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0905 r_free = 0.1901 target_work(ml) = 4.949 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0905 r_free= 0.1901 coordinate error (max.-lik. estimate): 0.27 A | | | | normalized target function (ml) (work): 4.949488 | | target function (ml) not normalized (work): 24366.330663 | | target function (ml) not normalized (free): 2109.665891 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.79 1.00 2493 142 0.1272 0.1879 5.509 6.2003| | 2: 3.78 - 3.00 1.00 2430 110 0.0457 0.1938 4.3755 11.175| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.79 2493 142 0.91 12.40 1.00 0.90 12439.03| | 2: 3.78 - 3.00 2430 110 0.99 2.04 1.00 0.92 942.28| |alpha: min = 0.89 max = 0.92 mean = 0.91| |beta: min = 611.21 max = 20725.67 mean = 6764.22| |figures of merit: min = 0.00 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.80 mean = 7.29| |phase err.(test): min = 0.00 max = 79.40 mean = 7.52| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0955 0.0905 0.1901 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2236 0.2234 0.2368 n_refl.: 5175 remove outliers: r(all,work,free)=0.2236 0.2234 0.2368 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2236 0.2234 0.2368 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0953 0.0904 0.1896 n_refl.: 5175 remove outliers: r(all,work,free)=0.0953 0.0904 0.1896 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 0.4019 313.288 276.387 0.603 0.986 0.318 11.894-9.307 99.02 97 4 0.1829 503.982 492.754 1.012 0.992 0.308 9.237-7.194 100.00 213 7 0.2126 412.158 405.343 1.062 0.995 0.300 7.162-5.571 100.00 427 22 0.2068 309.274 300.532 1.030 0.997 0.300 5.546-4.326 100.00 867 58 0.1025 424.589 418.005 1.071 0.999 0.250 4.315-3.360 100.00 1859 96 0.0587 403.789 403.879 1.160 1.003 0.250 3.356-3.002 100.00 1373 60 0.0442 311.015 310.791 1.136 1.005 0.080 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-8.9163 ================= 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 : 0.3626 0.2030 0.081 5.330 8.8 119.3 19.9 258 0.000 1_bss: 0.1559 0.1642 0.081 5.330 6.5 116.9 17.5 258 0.000 1_settarget: 0.1559 0.1642 0.081 5.330 6.5 116.9 17.5 258 0.000 1_nqh: 0.1562 0.1644 0.081 5.330 6.5 116.9 17.5 258 0.003 1_weight: 0.1562 0.1644 0.081 5.330 6.5 116.9 17.5 258 0.003 1_xyzrec: 0.1154 0.1786 0.010 0.975 6.5 116.9 17.5 258 0.217 1_adp: 0.1020 0.1789 0.010 0.975 2.5 111.9 17.9 258 0.217 1_regHadp: 0.1014 0.1793 0.010 0.975 2.5 111.9 17.9 258 0.217 1_occ: 0.1017 0.1799 0.010 0.975 2.5 111.9 17.9 258 0.217 2_bss: 0.1017 0.1804 0.010 0.975 1.6 111.0 16.9 258 0.217 2_settarget: 0.1017 0.1804 0.010 0.975 1.6 111.0 16.9 258 0.217 2_updatecdl: 0.1017 0.1804 0.010 0.991 1.6 111.0 16.9 258 0.217 2_nqh: 0.1017 0.1805 0.010 0.991 1.6 111.0 16.9 258 0.215 2_sol: 0.1131 0.1704 0.010 0.991 1.0 111.0 16.3 228 n/a 2_weight: 0.1131 0.1704 0.010 0.991 1.0 111.0 16.3 228 n/a 2_xyzrec: 0.1014 0.1796 0.009 1.000 1.0 111.0 16.3 228 n/a 2_adp: 0.0949 0.1826 0.009 1.000 0.0 109.1 17.1 228 n/a 2_regHadp: 0.0945 0.1827 0.009 1.000 0.0 109.1 17.1 228 n/a 2_occ: 0.0946 0.1813 0.009 1.000 0.0 109.1 17.1 228 n/a 3_bss: 0.0947 0.1828 0.009 1.000 0.0 109.1 17.1 228 n/a 3_settarget: 0.0947 0.1828 0.009 1.000 0.0 109.1 17.1 228 n/a 3_updatecdl: 0.0947 0.1828 0.009 1.006 0.0 109.1 17.1 228 n/a 3_nqh: 0.0947 0.1829 0.009 1.006 0.0 109.1 17.1 228 n/a 3_sol: 0.1070 0.1767 0.009 1.006 0.0 109.1 16.9 232 n/a 3_weight: 0.1070 0.1767 0.009 1.006 0.0 109.1 16.9 232 n/a 3_xyzrec: 0.0973 0.1827 0.011 1.101 0.0 109.1 16.9 232 n/a 3_adp: 0.0929 0.1815 0.011 1.101 0.0 109.0 17.0 232 n/a 3_regHadp: 0.0934 0.1818 0.011 1.101 0.0 109.0 17.0 232 n/a 3_occ: 0.0918 0.1797 0.011 1.101 0.0 109.0 17.0 232 n/a 4_bss: 0.0907 0.1787 0.011 1.101 0.0 109.0 17.0 232 n/a 4_settarget: 0.0907 0.1787 0.011 1.101 0.0 109.0 17.0 232 n/a 4_updatecdl: 0.0907 0.1787 0.011 1.108 0.0 109.0 17.0 232 n/a 4_nqh: 0.0907 0.1787 0.011 1.108 0.0 109.0 17.0 232 n/a 4_sol: 0.1006 0.1831 0.011 1.108 0.0 109.0 16.8 223 n/a 4_weight: 0.1006 0.1831 0.011 1.108 0.0 109.0 16.8 223 n/a 4_xyzrec: 0.0912 0.1855 0.011 1.071 0.0 109.0 16.8 223 n/a 4_adp: 0.0889 0.1888 0.011 1.071 0.0 110.5 17.1 223 n/a 4_regHadp: 0.0893 0.1889 0.011 1.071 0.0 110.5 17.1 223 n/a 4_occ: 0.0886 0.1874 0.011 1.071 0.0 110.5 17.1 223 n/a 5_bss: 0.0884 0.1881 0.011 1.071 0.0 110.5 17.1 223 n/a 5_settarget: 0.0884 0.1881 0.011 1.071 0.0 110.5 17.1 223 n/a 5_updatecdl: 0.0884 0.1881 0.011 1.086 0.0 110.5 17.1 223 n/a 5_setrh: 0.0887 0.1879 0.011 1.086 0.0 110.5 17.1 223 n/a 5_nqh: 0.0887 0.1879 0.011 1.086 0.0 110.5 17.1 223 n/a 5_sol: 0.0992 0.1889 0.011 1.086 0.0 110.5 17.2 218 n/a 5_weight: 0.0992 0.1889 0.011 1.086 0.0 110.5 17.2 218 n/a 5_xyzrec: 0.0926 0.1875 0.011 1.143 0.0 110.5 17.2 218 n/a 5_adp: 0.0907 0.1905 0.011 1.143 0.0 112.0 17.4 218 n/a 5_regHadp: 0.0912 0.1909 0.011 1.143 0.0 112.0 17.4 218 n/a 5_occ: 0.0905 0.1901 0.011 1.143 0.0 112.0 17.4 218 n/a end: 0.0904 0.1896 0.011 1.143 0.0 112.0 17.4 218 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_1664580_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_1664580_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.2900 Refinement macro-cycles (run) : 480.8000 Write final files (write_after_run_outputs) : 11.4900 Total : 495.5800 Total CPU time: 8.58 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:18:56 PST -0800 (1735492736.51 s) Start R-work = 0.1559, R-free = 0.1642 Final R-work = 0.0904, R-free = 0.1896 =============================================================================== Job complete usr+sys time: 522.60 seconds wall clock time: 9 minutes 4.95 seconds (544.95 seconds total)