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_3657390.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 { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 3 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3657390.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3657390.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" } 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 3 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: 1.95, per 1000 atoms: 0.58 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: 0.37 Conformation dependent library (CDL) restraints added in 185.8 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.92: 550 0.92 - 1.17: 1109 1.17 - 1.43: 658 1.43 - 1.68: 799 1.68 - 1.94: 37 Bond restraints: 3153 Sorted by residual: bond pdb=" C ASP A 131 " pdb=" N BLYS A 132 " ideal model delta sigma weight residual 1.334 1.581 -0.247 1.27e-02 6.20e+03 3.77e+02 bond pdb=" CA VAL A 169 " pdb=" C VAL A 169 " ideal model delta sigma weight residual 1.524 1.766 -0.242 1.30e-02 5.92e+03 3.48e+02 bond pdb=" CA LEU A 7 " pdb=" C LEU A 7 " ideal model delta sigma weight residual 1.524 1.295 0.229 1.23e-02 6.61e+03 3.47e+02 bond pdb=" C MET A 133 " pdb=" O MET A 133 " ideal model delta sigma weight residual 1.237 1.024 0.213 1.17e-02 7.31e+03 3.31e+02 bond pdb=" C VAL A 70 " pdb=" O VAL A 70 " ideal model delta sigma weight residual 1.237 1.049 0.187 1.07e-02 8.73e+03 3.06e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.61: 3194 4.61 - 9.21: 1808 9.21 - 13.82: 668 13.82 - 18.43: 100 18.43 - 23.04: 7 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O VAL A 169 " pdb=" C VAL A 169 " pdb=" N GLU A 170 " ideal model delta sigma weight residual 121.83 139.60 -17.77 1.03e+00 9.43e-01 2.98e+02 angle pdb=" ND1 HIS A 138 " pdb=" CG HIS A 138 " pdb=" CD2 HIS A 138 " ideal model delta sigma weight residual 106.10 120.74 -14.64 1.00e+00 1.00e+00 2.14e+02 angle pdb=" CA ASP A 131 " pdb=" C ASP A 131 " pdb=" O ASP A 131 " ideal model delta sigma weight residual 120.90 135.17 -14.27 1.07e+00 8.73e-01 1.78e+02 angle pdb=" CA VAL A 181 " pdb=" C VAL A 181 " pdb=" O VAL A 181 " ideal model delta sigma weight residual 120.85 134.81 -13.96 1.06e+00 8.90e-01 1.73e+02 angle pdb=" N ILE A 21 " pdb=" CA ILE A 21 " pdb=" CB ILE A 21 " ideal model delta sigma weight residual 110.45 120.38 -9.93 7.80e-01 1.64e+00 1.62e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.79: 1286 15.79 - 31.58: 132 31.58 - 47.37: 39 47.37 - 63.16: 22 63.16 - 78.95: 2 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" N SER A 142 " pdb=" C SER A 142 " pdb=" CA SER A 142 " pdb=" CB SER A 142 " ideal model delta harmonic sigma weight residual 122.80 105.75 17.05 0 2.50e+00 1.60e-01 4.65e+01 dihedral pdb=" C LYS A 62 " pdb=" N LYS A 62 " pdb=" CA LYS A 62 " pdb=" CB LYS A 62 " ideal model delta harmonic sigma weight residual -122.60 -139.10 16.50 0 2.50e+00 1.60e-01 4.36e+01 dihedral pdb=" N APRO A 66 " pdb=" C APRO A 66 " pdb=" CA APRO A 66 " pdb=" CB APRO A 66 " ideal model delta harmonic sigma weight residual 115.10 98.77 16.33 0 2.50e+00 1.60e-01 4.27e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.005 - 0.228: 103 0.228 - 0.451: 84 0.451 - 0.674: 37 0.674 - 0.897: 14 0.897 - 1.120: 5 Chirality restraints: 243 Sorted by residual: chirality pdb=" CB ILE A 105 " pdb=" CA ILE A 105 " pdb=" CG1 ILE A 105 " pdb=" CG2 ILE A 105 " both_signs ideal model delta sigma weight residual False 2.64 1.52 1.12 2.00e-01 2.50e+01 3.14e+01 chirality pdb=" CA ASN A 144 " pdb=" N ASN A 144 " pdb=" C ASN A 144 " pdb=" CB ASN A 144 " both_signs ideal model delta sigma weight residual False 2.51 1.50 1.01 2.00e-01 2.50e+01 2.55e+01 chirality pdb=" CG LEU A 7 " pdb=" CB LEU A 7 " pdb=" CD1 LEU A 7 " pdb=" CD2 LEU A 7 " both_signs ideal model delta sigma weight residual False -2.59 -3.58 0.99 2.00e-01 2.50e+01 2.46e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " 0.003 2.00e-02 2.50e+03 6.40e-02 1.23e+02 pdb=" CG PHE A 162 " -0.128 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " 0.080 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " -0.032 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " -0.105 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " 0.039 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " -0.008 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " 0.101 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " 0.039 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " 0.028 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " 0.024 2.00e-02 2.50e+03 5.86e-02 1.03e+02 pdb=" CG ATYR A 67 " 0.047 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " 0.038 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " 0.073 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " -0.030 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " 0.055 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " -0.069 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " 0.007 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " -0.057 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " -0.136 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " 0.021 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 26 " -0.047 2.00e-02 2.50e+03 9.91e-02 9.82e+01 pdb=" N ARG A 27 " 0.170 2.00e-02 2.50e+03 pdb=" CA ARG A 27 " -0.044 2.00e-02 2.50e+03 pdb=" H ARG A 27 " -0.080 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.32: 1028 2.32 - 2.89: 8144 2.89 - 3.46: 10513 3.46 - 4.03: 15152 4.03 - 4.60: 21723 Nonbonded interactions: 56560 Sorted by model distance: nonbonded pdb=" HG SER A 47 " pdb="HH11 ARG A 48 " model vdw 1.754 2.100 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.791 2.450 nonbonded pdb=" O LEU A 7 " pdb=" H VAL A 71 " model vdw 1.806 2.450 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.830 2.450 x-y,-y,-z-4/3 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.831 2.450 ... (remaining 56555 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_3657390_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= 0.3615 r_free= 0.1997 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.462776 | | target function (ml) not normalized (work): 22001.485202 | | target function (ml) not normalized (free): 1152.201158 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3811 0.2180 4.8568 4.9021| | 2: 3.78 - 3.00 1.00 2430 110 0.3376 0.1689 4.0574 4.1464| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 48.87 0.83 0.13 6618.90| | 2: 3.78 - 3.00 2430 110 0.94 10.99 1.48 0.26 434.76| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 362.87 max = 12084.82 mean = 3570.73| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 90.00 mean = 30.20| |phase err.(test): min = 0.00 max = 89.95 mean = 32.95| |-----------------------------------------------------------------------------| ----------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 : 0.086 0.247 1557 Z= 5.709 Angle : 5.210 17.773 2118 Z= 3.742 Chirality : 0.378 1.120 243 Planarity : 0.031 0.091 284 Dihedral : 13.578 78.948 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.24 % Favored : 96.22 % Rotamer: Outliers : 1.24 % Allowed : 4.35 % Favored : 94.41 % Cbeta Deviations : 29.73 % 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: -2.50 (0.48), residues: 224 helix: -2.32 (0.41), residues: 109 sheet: -0.85 (0.73), residues: 38 loop : -0.63 (0.63), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.065 0.019 ARG A 27 TYR 0.091 0.041 TYR A 141 PHE 0.106 0.048 PHE A 162 HIS 0.043 0.022 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= 0.3615 r_free= 0.1997 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.462776 | | target function (ml) not normalized (work): 22001.485202 | | target function (ml) not normalized (free): 1152.201158 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3574 0.3651 0.2097 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3574 0.3651 0.2097 n_refl.: 5182 remove outliers: r(all,work,free)=0.2519 0.2545 0.2097 n_refl.: 5178 overall B=-2.89 to atoms: r(all,work,free)=0.2409 0.2431 0.2047 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1551 0.1549 0.1595 n_refl.: 5178 remove outliers: r(all,work,free)=0.1547 0.1544 0.1595 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 0.3799 449.543 409.467 0.668 1.055 0.398 11.894-9.307 99.02 97 4 0.1844 714.135 695.390 0.952 1.054 0.383 9.237-7.194 100.00 213 7 0.2173 584.021 575.361 0.982 1.049 0.344 7.162-5.571 100.00 427 22 0.2304 438.237 424.276 0.940 1.038 0.294 5.546-4.326 100.00 867 58 0.1377 601.637 594.459 0.985 1.021 0.226 4.315-3.360 100.00 1859 96 0.1294 572.163 566.627 1.056 0.991 0.200 3.356-3.002 100.00 1373 60 0.1580 440.704 433.674 1.059 0.961 0.086 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9555 b_overall=-3.6980 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1544 r_free=0.1595 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN Total number of N/Q/H flips: 1 r_work=0.1544 r_free=0.1593 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 19.411728 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.853919 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 0.1765 0.0602 0.010 1.0 1.9 0.5 0.0 0 9.706 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.63 17.65 6.02 3.012 15.967 1.854 0.018 10.18 17.62 7.44 5.006 16.224 1.854 0.014 Individual atomic B min max mean iso aniso Overall: 2.24 111.98 17.48 5.36 1785 0 Protein: 2.24 111.98 14.78 5.35 1519 0 Water: 3.97 111.41 33.15 N/A 258 0 Other: 16.69 35.62 23.94 N/A 8 0 Chain A: 2.24 111.98 17.48 N/A 1785 0 Histogram: Values Number of atoms 2.24 - 13.22 924 13.22 - 24.19 473 24.19 - 35.16 192 35.16 - 46.14 109 46.14 - 57.11 53 57.11 - 68.09 18 68.09 - 79.06 7 79.06 - 90.03 5 90.03 - 101.01 1 101.01 - 111.98 3 =========================== Idealize ADP of riding H ========================== r_work=0.1018 r_free=0.1762 r_work=0.1011 r_free=0.1769 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1011 r_free = 0.1769 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 = 0.1003 r_free = 0.1763 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.18 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= 0.1003 r_free= 0.1763 coordinate error (max.-lik. estimate): 0.31 A | | | | normalized target function (ls_wunit_k1) (work): 0.013721 | | target function (ls_wunit_k1) not normalized (work): 67.562494 | | target function (ls_wunit_k1) not normalized (free): 10.175749 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1042 0.1003 0.1763 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2082 0.2081 0.2217 n_refl.: 5176 remove outliers: r(all,work,free)=0.2082 0.2081 0.2217 n_refl.: 5176 overall B=-0.96 to atoms: r(all,work,free)=0.2042 0.2039 0.2205 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.1046 0.1007 0.1770 n_refl.: 5176 remove outliers: r(all,work,free)=0.1046 0.1007 0.1770 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 0.3342 330.543 314.009 0.681 1.006 0.382 11.894-9.307 99.02 97 4 0.1479 525.094 517.452 0.991 1.008 0.362 9.237-7.194 100.00 213 7 0.1654 429.423 430.639 1.024 1.008 0.310 7.162-5.571 100.00 427 22 0.1601 322.230 319.695 0.981 1.006 0.292 5.546-4.326 100.00 867 58 0.0894 442.376 439.648 0.997 1.003 0.202 4.315-3.360 100.00 1859 96 0.0766 420.704 420.459 1.043 0.998 0.193 3.356-3.002 100.00 1373 60 0.1005 324.044 322.162 1.015 0.994 0.072 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-3.4393 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1007 r_free=0.1770 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A A 180 GLN Total number of N/Q/H flips: 2 r_work=0.1010 r_free=0.1775 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1010 r_free=0.1775 | n_water=258 | time (s): 0.520 (total time: 0.520) Filter (dist) r_work=0.1042 r_free=0.1770 | n_water=248 | time (s): 21.080 (total time: 21.600) Filter (q & B) r_work=0.1042 r_free=0.1771 | n_water=245 | time (s): 1.470 (total time: 23.070) Compute maps r_work=0.1042 r_free=0.1771 | n_water=245 | time (s): 0.580 (total time: 23.650) Filter (map) r_work=0.1353 r_free=0.1830 | n_water=144 | time (s): 1.710 (total time: 25.360) Find peaks r_work=0.1353 r_free=0.1830 | n_water=144 | time (s): 0.460 (total time: 25.820) Add new water r_work=0.1702 r_free=0.1997 | n_water=232 | time (s): 1.560 (total time: 27.380) Refine new water occ: r_work=0.1143 r_free=0.1654 adp: r_work=0.1122 r_free=0.1659 occ: r_work=0.1118 r_free=0.1652 adp: r_work=0.1108 r_free=0.1660 occ: r_work=0.1107 r_free=0.1651 adp: r_work=0.1104 r_free=0.1660 ADP+occupancy (water only), MIN, final r_work=0.1104 r_free=0.1660 r_work=0.1104 r_free=0.1660 | n_water=232 | time (s): 3.730 (total time: 31.110) Filter (q & B) r_work=0.1104 r_free=0.1660 | n_water=232 | time (s): 0.720 (total time: 31.830) Filter (dist only) r_work=0.1111 r_free=0.1655 | n_water=228 | time (s): 17.500 (total time: 49.330) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.159511 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.743366 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 0.0998 0.1767 0.0769 0.009 1.0 4.5 0.5 0.6 0 11.580 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.98 17.67 7.69 4.707 16.868 2.743 0.013 9.33 17.61 8.29 5.529 17.288 2.743 0.012 Individual atomic B min max mean iso aniso Overall: 0.00 109.49 16.75 6.63 1755 0 Protein: 0.00 109.49 15.18 6.62 1519 0 Water: 0.00 62.73 27.03 N/A 228 0 Other: 12.18 32.59 21.84 N/A 8 0 Chain A: 0.00 109.49 15.90 N/A 1668 0 Chain S: 5.14 59.67 33.13 N/A 87 0 Histogram: Values Number of atoms 0.00 - 10.95 699 10.95 - 21.90 656 21.90 - 32.85 212 32.85 - 43.80 107 43.80 - 54.75 40 54.75 - 65.70 26 65.70 - 76.65 8 76.65 - 87.60 3 87.60 - 98.54 2 98.54 - 109.49 2 =========================== Idealize ADP of riding H ========================== r_work=0.0933 r_free=0.1761 r_work=0.0930 r_free=0.1764 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0930 r_free = 0.1764 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0927 r_free = 0.1751 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.25 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= 0.0927 r_free= 0.1751 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ls_wunit_k1) (work): 0.011670 | | target function (ls_wunit_k1) not normalized (work): 57.464817 | | target function (ls_wunit_k1) not normalized (free): 9.503368 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0968 0.0927 0.1751 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2109 0.2116 0.2117 n_refl.: 5176 remove outliers: r(all,work,free)=0.2109 0.2116 0.2117 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2109 0.2116 0.2117 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0971 0.0929 0.1755 n_refl.: 5176 remove outliers: r(all,work,free)=0.0967 0.0925 0.1755 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 0.3206 329.939 309.208 0.669 1.005 0.358 11.894-9.307 99.02 97 4 0.1377 525.094 522.638 0.985 1.007 0.350 9.237-7.194 100.00 213 7 0.1473 429.423 429.777 1.025 1.007 0.294 7.162-5.571 100.00 427 22 0.1337 322.230 320.499 0.992 1.006 0.280 5.546-4.326 100.00 867 58 0.0791 442.376 439.608 1.008 1.004 0.230 4.315-3.360 100.00 1859 96 0.0715 420.704 420.793 1.056 1.000 0.200 3.356-3.002 100.00 1373 60 0.0971 324.044 322.635 1.029 0.996 0.068 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9556 b_overall=-4.1452 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0925 r_free=0.1755 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B Total number of N/Q/H flips: 1 r_work=0.0926 r_free=0.1754 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0926 r_free=0.1754 | n_water=228 | time (s): 0.560 (total time: 0.560) Filter (dist) r_work=0.0947 r_free=0.1760 | n_water=222 | time (s): 17.000 (total time: 17.560) Filter (q & B) r_work=0.1032 r_free=0.1760 | n_water=219 | time (s): 1.630 (total time: 19.190) Compute maps r_work=0.1032 r_free=0.1760 | n_water=219 | time (s): 0.530 (total time: 19.720) Filter (map) r_work=0.1263 r_free=0.1803 | n_water=154 | time (s): 1.790 (total time: 21.510) Find peaks r_work=0.1263 r_free=0.1803 | n_water=154 | time (s): 0.590 (total time: 22.100) Add new water r_work=0.1626 r_free=0.2065 | n_water=235 | time (s): 1.410 (total time: 23.510) Refine new water occ: r_work=0.1032 r_free=0.1707 adp: r_work=0.1025 r_free=0.1713 occ: r_work=0.1015 r_free=0.1706 adp: r_work=0.1015 r_free=0.1708 occ: r_work=0.1007 r_free=0.1702 adp: r_work=0.1007 r_free=0.1703 ADP+occupancy (water only), MIN, final r_work=0.1007 r_free=0.1703 r_work=0.1007 r_free=0.1703 | n_water=235 | time (s): 14.240 (total time: 37.750) Filter (q & B) r_work=0.1007 r_free=0.1709 | n_water=233 | time (s): 1.250 (total time: 39.000) Filter (dist only) r_work=0.1017 r_free=0.1716 | n_water=231 | time (s): 17.720 (total time: 56.720) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.092982 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.252849 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 0.1792 0.0873 0.011 1.1 4.2 0.5 0.6 0 0.546 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.19 17.92 8.73 5.522 17.948 0.253 5.146 8.75 17.91 9.16 7.339 17.995 0.253 5.054 Individual atomic B min max mean iso aniso Overall: 0.00 109.16 16.56 9.12 1758 0 Protein: 0.00 109.16 15.39 9.13 1519 0 Water: 0.00 57.73 24.00 N/A 231 0 Other: 11.81 33.23 23.11 N/A 8 0 Chain A: 0.00 109.16 16.04 N/A 1655 0 Chain S: 0.00 55.04 24.85 N/A 103 0 Histogram: Values Number of atoms 0.00 - 10.92 699 10.92 - 21.83 639 21.83 - 32.75 242 32.75 - 43.66 112 43.66 - 54.58 30 54.58 - 65.50 19 65.50 - 76.41 9 76.41 - 87.33 3 87.33 - 98.24 3 98.24 - 109.16 2 =========================== Idealize ADP of riding H ========================== r_work=0.0875 r_free=0.1791 r_work=0.0880 r_free=0.1795 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0880 r_free = 0.1795 target_work(ml) = 5.058 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0871 r_free = 0.1786 target_work(ml) = 5.053 | | occupancies: max = 1.00 min = 0.26 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= 0.0871 r_free= 0.1786 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 5.052740 | | target function (ml) not normalized (work): 24869.585717 | | target function (ml) not normalized (free): 1816.432409 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0918 0.0871 0.1786 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2043 0.2047 0.2110 n_refl.: 5174 remove outliers: r(all,work,free)=0.2043 0.2047 0.2110 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2043 0.2047 0.2110 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0912 0.0866 0.1784 n_refl.: 5174 remove outliers: r(all,work,free)=0.0912 0.0866 0.1784 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 0.3528 329.939 303.167 0.618 0.991 0.338 11.894-9.307 99.02 97 4 0.1776 525.094 511.566 0.946 0.995 0.330 9.237-7.194 100.00 213 7 0.1865 429.423 422.497 0.997 0.997 0.280 7.162-5.571 100.00 427 22 0.1723 322.230 315.010 0.972 0.998 0.280 5.546-4.326 100.00 867 58 0.0890 442.376 437.236 0.993 1.000 0.240 4.315-3.360 100.00 1859 96 0.0582 420.704 420.084 1.045 1.002 0.210 3.356-3.002 100.00 1373 60 0.0601 324.044 323.030 1.016 1.004 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-5.7956 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0866 r_free=0.1784 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B A 80 GLN A Total number of N/Q/H flips: 2 r_work=0.0866 r_free=0.1788 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0866 r_free=0.1788 | n_water=231 | time (s): 0.670 (total time: 0.670) Filter (dist) r_work=0.0878 r_free=0.1779 | n_water=229 | time (s): 18.180 (total time: 18.850) Filter (q & B) r_work=0.0961 r_free=0.1835 | n_water=225 | time (s): 1.710 (total time: 20.560) Compute maps r_work=0.0961 r_free=0.1835 | n_water=225 | time (s): 0.630 (total time: 21.190) Filter (map) r_work=0.1219 r_free=0.1894 | n_water=159 | time (s): 1.590 (total time: 22.780) Find peaks r_work=0.1219 r_free=0.1894 | n_water=159 | time (s): 0.460 (total time: 23.240) Add new water r_work=0.1543 r_free=0.2185 | n_water=237 | time (s): 1.670 (total time: 24.910) Refine new water occ: r_work=0.1005 r_free=0.1753 adp: r_work=0.1000 r_free=0.1768 occ: r_work=0.0989 r_free=0.1738 adp: r_work=0.0988 r_free=0.1753 occ: r_work=0.0978 r_free=0.1726 adp: r_work=0.0978 r_free=0.1726 ADP+occupancy (water only), MIN, final r_work=0.0978 r_free=0.1726 r_work=0.0978 r_free=0.1726 | n_water=237 | time (s): 8.510 (total time: 33.420) Filter (q & B) r_work=0.0978 r_free=0.1730 | n_water=236 | time (s): 1.230 (total time: 34.650) Filter (dist only) r_work=0.0990 r_free=0.1747 | n_water=234 | time (s): 18.160 (total time: 52.810) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.015579 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.237699 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 0.0894 0.1777 0.0883 0.011 1.0 4.5 0.5 0.0 0 0.508 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 8.94 17.77 8.83 7.103 18.214 0.238 5.041 8.69 18.01 9.32 8.234 18.322 0.238 4.973 Individual atomic B min max mean iso aniso Overall: 0.00 106.20 16.86 10.68 1761 0 Protein: 0.00 106.20 15.78 10.68 1519 0 Water: 0.00 59.17 23.62 N/A 234 0 Other: 10.15 36.65 25.12 N/A 8 0 Chain A: 0.00 106.20 16.31 N/A 1640 0 Chain S: 0.00 59.17 24.39 N/A 121 0 Histogram: Values Number of atoms 0.00 - 10.62 650 10.62 - 21.24 639 21.24 - 31.86 280 31.86 - 42.48 97 42.48 - 53.10 56 53.10 - 63.72 17 63.72 - 74.34 9 74.34 - 84.96 7 84.96 - 95.58 3 95.58 - 106.20 3 =========================== Idealize ADP of riding H ========================== r_work=0.0869 r_free=0.1801 r_work=0.0872 r_free=0.1805 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0872 r_free = 0.1805 target_work(ml) = 4.978 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0862 r_free = 0.1795 target_work(ml) = 4.971 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0862 r_free= 0.1795 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 4.971082 | | target function (ml) not normalized (work): 24467.667547 | | target function (ml) not normalized (free): 2081.074693 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0908 0.0862 0.1795 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2073 0.2073 0.2197 n_refl.: 5174 remove outliers: r(all,work,free)=0.2073 0.2073 0.2197 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2073 0.2073 0.2197 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0906 0.0860 0.1798 n_refl.: 5174 remove outliers: r(all,work,free)=0.0906 0.0860 0.1798 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 0.3857 329.939 293.976 0.573 0.987 0.314 11.894-9.307 99.02 97 4 0.1860 525.094 517.500 0.967 0.993 0.310 9.237-7.194 100.00 213 7 0.2039 429.423 422.388 1.005 0.995 0.280 7.162-5.571 100.00 427 22 0.1862 322.230 314.702 0.995 0.997 0.280 5.546-4.326 100.00 867 58 0.0952 442.376 435.323 1.006 0.999 0.230 4.315-3.360 100.00 1859 96 0.0554 420.704 420.371 1.074 1.002 0.220 3.356-3.002 100.00 1373 60 0.0461 324.044 323.597 1.047 1.005 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.1211 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0860 r_free=0.1798 After: r_work=0.0862 r_free=0.1798 ================================== NQH flips ================================== r_work=0.0862 r_free=0.1798 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0862 r_free=0.1798 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0862 r_free=0.1798 | n_water=234 | time (s): 0.450 (total time: 0.450) Filter (dist) r_work=0.0873 r_free=0.1794 | n_water=231 | time (s): 18.820 (total time: 19.270) Filter (q & B) r_work=0.0986 r_free=0.1809 | n_water=228 | time (s): 1.700 (total time: 20.970) Compute maps r_work=0.0986 r_free=0.1809 | n_water=228 | time (s): 0.590 (total time: 21.560) Filter (map) r_work=0.1255 r_free=0.1904 | n_water=165 | time (s): 1.310 (total time: 22.870) Find peaks r_work=0.1255 r_free=0.1904 | n_water=165 | time (s): 0.560 (total time: 23.430) Add new water r_work=0.1509 r_free=0.2169 | n_water=232 | time (s): 1.720 (total time: 25.150) Refine new water occ: r_work=0.0982 r_free=0.1803 adp: r_work=0.0971 r_free=0.1815 occ: r_work=0.0966 r_free=0.1801 adp: r_work=0.0964 r_free=0.1807 occ: r_work=0.0959 r_free=0.1795 adp: r_work=0.0957 r_free=0.1802 ADP+occupancy (water only), MIN, final r_work=0.0957 r_free=0.1802 r_work=0.0957 r_free=0.1802 | n_water=232 | time (s): 16.320 (total time: 41.470) Filter (q & B) r_work=0.0957 r_free=0.1802 | n_water=231 | time (s): 1.480 (total time: 42.950) Filter (dist only) r_work=0.0960 r_free=0.1800 | n_water=230 | time (s): 17.180 (total time: 60.130) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.005465 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.235867 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 0.0903 0.1780 0.0877 0.011 1.1 7.0 0.5 0.0 0 0.503 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.03 17.80 8.77 8.134 18.590 0.236 5.019 8.83 18.09 9.26 9.280 18.737 0.236 4.958 Individual atomic B min max mean iso aniso Overall: 0.00 108.15 17.27 12.25 1757 0 Protein: 0.00 108.15 16.26 12.25 1519 0 Water: 0.00 70.17 23.63 N/A 230 0 Other: 11.96 34.97 25.00 N/A 8 0 Chain A: 0.00 108.15 16.70 N/A 1632 0 Chain S: 0.00 70.17 24.66 N/A 125 0 Histogram: Values Number of atoms 0.00 - 10.82 647 10.82 - 21.63 632 21.63 - 32.45 283 32.45 - 43.26 102 43.26 - 54.08 48 54.08 - 64.89 20 64.89 - 75.71 9 75.71 - 86.52 8 86.52 - 97.34 4 97.34 - 108.15 4 =========================== Idealize ADP of riding H ========================== r_work=0.0883 r_free=0.1809 r_work=0.0886 r_free=0.1815 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0886 r_free = 0.1815 target_work(ml) = 4.964 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0881 r_free = 0.1806 target_work(ml) = 4.959 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0881 r_free= 0.1806 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 4.959212 | | target function (ml) not normalized (work): 24409.243797 | | target function (ml) not normalized (free): 2233.218238 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1251 0.1716 5.5332 6.0882| | 2: 3.78 - 3.00 1.00 2430 110 0.0430 0.1960 4.3706 12.443| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 11.96 1.00 0.98 12846.22| | 2: 3.78 - 3.00 2430 110 0.99 1.85 1.00 1.01 930.80| |alpha: min = 0.97 max = 1.01 mean = 1.00| |beta: min = 595.67 max = 21381.32 mean = 6963.56| |figures of merit: min = 0.01 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.05 mean = 6.97| |phase err.(test): min = 0.00 max = 81.54 mean = 7.00| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0927 0.0881 0.1806 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2118 0.2118 0.2240 n_refl.: 5174 remove outliers: r(all,work,free)=0.2118 0.2118 0.2240 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2118 0.2118 0.2240 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0925 0.0880 0.1800 n_refl.: 5174 remove outliers: r(all,work,free)=0.0925 0.0880 0.1800 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 0.3919 329.939 294.927 0.586 0.984 0.318 11.894-9.307 99.02 97 4 0.1808 525.094 512.566 0.976 0.990 0.317 9.237-7.194 100.00 213 7 0.2143 429.423 419.021 1.003 0.993 0.282 7.162-5.571 100.00 427 22 0.1962 322.230 313.208 0.990 0.995 0.250 5.546-4.326 100.00 867 58 0.1024 442.376 436.713 1.019 0.998 0.234 4.315-3.360 100.00 1859 96 0.0565 420.704 420.579 1.094 1.002 0.230 3.356-3.002 100.00 1373 60 0.0416 324.044 323.963 1.066 1.006 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.9994 ================= 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 : 0.3615 0.1997 0.086 5.210 8.8 119.3 19.9 258 0.000 1_bss: 0.1544 0.1595 0.086 5.210 6.0 116.4 17.0 258 0.000 1_settarget: 0.1544 0.1595 0.086 5.210 6.0 116.4 17.0 258 0.000 1_nqh: 0.1544 0.1593 0.086 5.210 6.0 116.4 17.0 258 0.003 1_weight: 0.1544 0.1593 0.086 5.210 6.0 116.4 17.0 258 0.003 1_xyzrec: 0.1163 0.1765 0.010 0.972 6.0 116.4 17.0 258 0.196 1_adp: 0.1018 0.1762 0.010 0.972 2.2 112.0 17.5 258 0.196 1_regHadp: 0.1011 0.1769 0.010 0.972 2.2 112.0 17.5 258 0.196 1_occ: 0.1003 0.1763 0.010 0.972 2.2 112.0 17.5 258 0.196 2_bss: 0.1007 0.1770 0.010 0.972 1.3 111.0 16.5 258 0.196 2_settarget: 0.1007 0.1770 0.010 0.972 1.3 111.0 16.5 258 0.196 2_updatecdl: 0.1007 0.1770 0.010 1.005 1.3 111.0 16.5 258 0.196 2_nqh: 0.1010 0.1775 0.010 1.005 1.3 111.0 16.5 258 0.196 2_sol: 0.1111 0.1655 0.010 1.005 1.0 111.0 16.0 228 n/a 2_weight: 0.1111 0.1655 0.010 1.005 1.0 111.0 16.0 228 n/a 2_xyzrec: 0.0998 0.1767 0.009 0.979 1.0 111.0 16.0 228 n/a 2_adp: 0.0933 0.1761 0.009 0.979 0.0 109.5 16.8 228 n/a 2_regHadp: 0.0930 0.1764 0.009 0.979 0.0 109.5 16.8 228 n/a 2_occ: 0.0927 0.1751 0.009 0.979 0.0 109.5 16.8 228 n/a 3_bss: 0.0925 0.1755 0.009 0.979 0.0 109.5 16.8 228 n/a 3_settarget: 0.0925 0.1755 0.009 0.979 0.0 109.5 16.8 228 n/a 3_updatecdl: 0.0925 0.1755 0.009 0.986 0.0 109.5 16.8 228 n/a 3_nqh: 0.0926 0.1754 0.009 0.986 0.0 109.5 16.8 228 n/a 3_sol: 0.1017 0.1716 0.009 0.986 0.0 109.5 16.5 231 n/a 3_weight: 0.1017 0.1716 0.009 0.986 0.0 109.5 16.5 231 n/a 3_xyzrec: 0.0919 0.1792 0.011 1.073 0.0 109.5 16.5 231 n/a 3_adp: 0.0875 0.1791 0.011 1.073 0.0 109.2 16.6 231 n/a 3_regHadp: 0.0880 0.1795 0.011 1.073 0.0 109.2 16.6 231 n/a 3_occ: 0.0871 0.1786 0.011 1.073 0.0 109.2 16.6 231 n/a 4_bss: 0.0866 0.1784 0.011 1.073 0.0 109.2 16.6 231 n/a 4_settarget: 0.0866 0.1784 0.011 1.073 0.0 109.2 16.6 231 n/a 4_updatecdl: 0.0866 0.1784 0.011 1.077 0.0 109.2 16.6 231 n/a 4_nqh: 0.0866 0.1788 0.011 1.077 0.0 109.2 16.6 231 n/a 4_sol: 0.0990 0.1747 0.011 1.077 0.0 109.2 16.7 234 n/a 4_weight: 0.0990 0.1747 0.011 1.077 0.0 109.2 16.7 234 n/a 4_xyzrec: 0.0894 0.1777 0.011 1.034 0.0 109.2 16.7 234 n/a 4_adp: 0.0869 0.1801 0.011 1.034 0.0 106.2 16.9 234 n/a 4_regHadp: 0.0872 0.1805 0.011 1.034 0.0 106.2 16.9 234 n/a 4_occ: 0.0862 0.1795 0.011 1.034 0.0 106.2 16.9 234 n/a 5_bss: 0.0860 0.1798 0.011 1.034 0.0 106.2 16.9 234 n/a 5_settarget: 0.0860 0.1798 0.011 1.034 0.0 106.2 16.9 234 n/a 5_updatecdl: 0.0860 0.1798 0.011 1.044 0.0 106.2 16.9 234 n/a 5_setrh: 0.0862 0.1798 0.011 1.044 0.0 106.2 16.9 234 n/a 5_nqh: 0.0862 0.1798 0.011 1.044 0.0 106.2 16.9 234 n/a 5_sol: 0.0960 0.1800 0.011 1.044 0.0 106.2 17.0 230 n/a 5_weight: 0.0960 0.1800 0.011 1.044 0.0 106.2 17.0 230 n/a 5_xyzrec: 0.0903 0.1780 0.011 1.125 0.0 106.2 17.0 230 n/a 5_adp: 0.0883 0.1809 0.011 1.125 0.0 108.2 17.3 230 n/a 5_regHadp: 0.0886 0.1815 0.011 1.125 0.0 108.2 17.3 230 n/a 5_occ: 0.0881 0.1806 0.011 1.125 0.0 108.2 17.3 230 n/a end: 0.0880 0.1800 0.011 1.125 0.0 108.2 17.3 230 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_3657390_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_3657390_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.2300 Refinement macro-cycles (run) : 484.7200 Write final files (write_after_run_outputs) : 10.7500 Total : 498.7000 Total CPU time: 8.71 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:19:03 PST -0800 (1735492743.61 s) Start R-work = 0.1544, R-free = 0.1595 Final R-work = 0.0880, R-free = 0.1800 =============================================================================== Job complete usr+sys time: 529.69 seconds wall clock time: 9 minutes 11.73 seconds (551.73 seconds total)