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_7766834.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_7766834.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7766834.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 3 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.59, 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: 0.32 Conformation dependent library (CDL) restraints added in 137.4 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.63 - 0.90: 429 0.90 - 1.17: 1199 1.17 - 1.43: 682 1.43 - 1.70: 820 1.70 - 1.97: 23 Bond restraints: 3153 Sorted by residual: bond pdb=" N THR A 125 " pdb=" CA THR A 125 " ideal model delta sigma weight residual 1.456 1.671 -0.215 1.16e-02 7.43e+03 3.43e+02 bond pdb=" N VAL A 181 " pdb=" CA VAL A 181 " ideal model delta sigma weight residual 1.460 1.675 -0.216 1.21e-02 6.83e+03 3.18e+02 bond pdb=" N VAL A 33 " pdb=" CA VAL A 33 " ideal model delta sigma weight residual 1.459 1.252 0.207 1.20e-02 6.94e+03 2.98e+02 bond pdb=" CE1 HIS A 126 " pdb=" NE2 HIS A 126 " ideal model delta sigma weight residual 1.321 1.490 -0.169 1.00e-02 1.00e+04 2.85e+02 bond pdb=" C VAL A 25 " pdb=" O VAL A 25 " ideal model delta sigma weight residual 1.237 1.422 -0.185 1.12e-02 7.97e+03 2.74e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.38: 2988 4.38 - 8.76: 1875 8.76 - 13.14: 725 13.14 - 17.52: 160 17.52 - 21.91: 29 Bond angle restraints: 5777 Sorted by residual: angle pdb=" NE ARG A 48 " pdb=" CZ ARG A 48 " pdb=" NH2 ARG A 48 " ideal model delta sigma weight residual 119.20 133.45 -14.25 9.00e-01 1.23e+00 2.51e+02 angle pdb=" O ACYS A 53 " pdb=" C ACYS A 53 " pdb=" N PRO A 54 " ideal model delta sigma weight residual 121.23 133.77 -12.54 8.10e-01 1.52e+00 2.40e+02 angle pdb=" O VAL A 177 " pdb=" C VAL A 177 " pdb=" N ALA A 178 " ideal model delta sigma weight residual 121.94 136.04 -14.10 1.00e+00 1.00e+00 1.99e+02 angle pdb=" NE ARG A 145 " pdb=" CZ ARG A 145 " pdb=" NH2 ARG A 145 " ideal model delta sigma weight residual 119.20 106.74 12.46 9.00e-01 1.23e+00 1.92e+02 angle pdb=" CA BCYS A 53 " pdb=" C BCYS A 53 " pdb=" O BCYS A 53 " ideal model delta sigma weight residual 119.29 110.61 8.68 6.50e-01 2.37e+00 1.78e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.66: 1323 17.66 - 35.30: 105 35.30 - 52.95: 38 52.95 - 70.60: 11 70.60 - 88.25: 4 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" N SER A 47 " pdb=" C SER A 47 " pdb=" CA SER A 47 " pdb=" CB SER A 47 " ideal model delta harmonic sigma weight residual 122.80 140.21 -17.41 0 2.50e+00 1.60e-01 4.85e+01 dihedral pdb=" C SER A 47 " pdb=" N SER A 47 " pdb=" CA SER A 47 " pdb=" CB SER A 47 " ideal model delta harmonic sigma weight residual -122.60 -139.63 17.03 0 2.50e+00 1.60e-01 4.64e+01 dihedral pdb=" C ILE A 21 " pdb=" N ILE A 21 " pdb=" CA ILE A 21 " pdb=" CB ILE A 21 " ideal model delta harmonic sigma weight residual -122.00 -138.83 16.83 0 2.50e+00 1.60e-01 4.53e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.182: 85 0.182 - 0.363: 73 0.363 - 0.544: 45 0.544 - 0.726: 33 0.726 - 0.907: 7 Chirality restraints: 243 Sorted by residual: chirality pdb=" CG LEU A 92 " pdb=" CB LEU A 92 " pdb=" CD1 LEU A 92 " pdb=" CD2 LEU A 92 " both_signs ideal model delta sigma weight residual False -2.59 -3.50 0.91 2.00e-01 2.50e+01 2.06e+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 -1.69 -0.90 2.00e-01 2.50e+01 2.01e+01 chirality pdb=" CA SER A 47 " pdb=" N SER A 47 " pdb=" C SER A 47 " pdb=" CB SER A 47 " both_signs ideal model delta sigma weight residual False 2.51 1.64 0.87 2.00e-01 2.50e+01 1.87e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.118 2.00e-02 2.50e+03 7.88e-02 1.86e+02 pdb=" CG PHE A 119 " -0.125 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.094 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.091 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.049 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.048 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.005 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.124 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.072 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " -0.032 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.138 2.00e-02 2.50e+03 7.86e-02 1.85e+02 pdb=" CG PHE A 164 " 0.165 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " -0.042 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.089 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " -0.029 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " 0.066 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.003 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.024 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.029 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.103 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 123 " -0.040 2.00e-02 2.50e+03 9.05e-02 8.19e+01 pdb=" C VAL A 123 " 0.156 2.00e-02 2.50e+03 pdb=" O VAL A 123 " -0.064 2.00e-02 2.50e+03 pdb=" N THR A 124 " -0.052 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.26: 700 2.26 - 2.85: 7720 2.85 - 3.43: 10601 3.43 - 4.02: 15338 4.02 - 4.60: 22374 Nonbonded interactions: 56733 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.677 2.100 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.827 2.450 x-y,-y,-z-4/3 nonbonded pdb=" HA3BGLY A 65 " pdb=" HA BPRO A 66 " model vdw 1.830 2.440 nonbonded pdb=" H LYS A 122 " pdb=" OD2 ASP A 149 " model vdw 1.832 2.450 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.849 2.100 ... (remaining 56728 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_7766834_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= 0.3630 r_free= 0.1993 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.469494 | | target function (ml) not normalized (work): 22034.604287 | | target function (ml) not normalized (free): 1153.315086 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3820 0.2167 4.8523 4.9127| | 2: 3.78 - 3.00 1.00 2430 110 0.3399 0.1699 4.0757 4.1428| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 48.80 0.83 0.13 6607.51| | 2: 3.78 - 3.00 2430 110 0.93 11.45 1.48 0.26 451.69| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 383.76 max = 12067.92 mean = 3573.30| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 90.00 mean = 30.39| |phase err.(test): min = 0.00 max = 89.92 mean = 33.32| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.082 0.241 1557 Z= 5.449 Angle : 5.364 17.071 2118 Z= 3.752 Chirality : 0.368 0.907 243 Planarity : 0.031 0.104 284 Dihedral : 14.050 88.249 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.24 % Allowed : 2.48 % Favored : 96.27 % Cbeta Deviations : 34.05 % 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: -2.21 (0.50), residues: 224 helix: -2.64 (0.36), residues: 109 sheet: -0.60 (0.93), residues: 28 loop : 0.28 (0.65), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.070 0.016 ARG A 28 TYR 0.074 0.023 TYR A 139 PHE 0.168 0.053 PHE A 164 HIS 0.084 0.036 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= 0.3630 r_free= 0.1993 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.469494 | | target function (ml) not normalized (work): 22034.604287 | | target function (ml) not normalized (free): 1153.315086 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3585 0.3663 0.2107 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3585 0.3663 0.2107 n_refl.: 5182 remove outliers: r(all,work,free)=0.2530 0.2554 0.2107 n_refl.: 5178 overall B=-2.88 to atoms: r(all,work,free)=0.2419 0.2440 0.2056 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1578 0.1575 0.1619 n_refl.: 5178 remove outliers: r(all,work,free)=0.1572 0.1570 0.1619 n_refl.: 5175 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 97.87 87 5 0.3946 443.886 402.929 0.650 1.062 0.381 11.894-9.307 99.02 97 4 0.1825 714.073 694.397 0.946 1.059 0.380 9.237-7.194 100.00 213 7 0.2200 583.970 575.706 0.973 1.053 0.375 7.162-5.571 100.00 427 22 0.2335 438.199 425.709 0.943 1.041 0.294 5.546-4.326 100.00 867 58 0.1382 601.585 593.555 0.987 1.022 0.257 4.315-3.360 100.00 1859 96 0.1326 572.113 566.171 1.054 0.990 0.190 3.356-3.002 100.00 1373 60 0.1609 440.666 432.256 1.063 0.958 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9559 b_overall=-3.6641 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1570 r_free=0.1619 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 r_work=0.1572 r_free=0.1618 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 19.139657 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.830370 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 0.1155 0.1810 0.0654 0.010 1.0 2.6 0.5 0.0 0 9.570 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.55 18.10 6.54 3.013 15.978 1.830 0.018 10.20 18.08 7.88 4.747 16.143 1.830 0.014 Individual atomic B min max mean iso aniso Overall: 2.26 111.42 17.32 5.18 1785 0 Protein: 2.26 111.32 14.60 5.18 1519 0 Water: 3.98 111.42 33.14 N/A 258 0 Other: 17.07 34.83 23.23 N/A 8 0 Chain A: 2.26 111.42 17.32 N/A 1785 0 Histogram: Values Number of atoms 2.26 - 13.18 946 13.18 - 24.09 459 24.09 - 35.01 183 35.01 - 45.92 110 45.92 - 56.84 56 56.84 - 67.75 14 67.75 - 78.67 8 78.67 - 89.59 5 89.59 - 100.50 1 100.50 - 111.42 3 =========================== Idealize ADP of riding H ========================== r_work=0.1020 r_free=0.1808 r_work=0.1014 r_free=0.1810 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1014 r_free = 0.1810 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 = 0.1007 r_free = 0.1804 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.1007 r_free= 0.1804 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ls_wunit_k1) (work): 0.013904 | | target function (ls_wunit_k1) not normalized (work): 68.451219 | | target function (ls_wunit_k1) not normalized (free): 10.389368 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1047 0.1007 0.1804 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2005 0.1995 0.2258 n_refl.: 5175 remove outliers: r(all,work,free)=0.2005 0.1995 0.2258 n_refl.: 5175 overall B=-0.97 to atoms: r(all,work,free)=0.1966 0.1955 0.2248 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.1043 0.1003 0.1798 n_refl.: 5175 remove outliers: r(all,work,free)=0.1043 0.1003 0.1798 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 0.3278 326.388 309.953 0.654 1.012 0.360 11.894-9.307 99.02 97 4 0.1531 525.055 516.700 0.981 1.014 0.361 9.237-7.194 100.00 213 7 0.1644 429.391 427.563 1.019 1.013 0.331 7.162-5.571 100.00 427 22 0.1634 322.206 318.479 0.980 1.010 0.255 5.546-4.326 100.00 867 58 0.0902 442.343 439.068 0.998 1.005 0.222 4.315-3.360 100.00 1859 96 0.0756 420.673 420.479 1.044 0.998 0.193 3.356-3.002 100.00 1373 60 0.0992 324.020 323.103 1.020 0.990 0.062 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-3.4747 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1003 r_free=0.1798 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1003 r_free=0.1798 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1003 r_free=0.1798 | n_water=258 | time (s): 0.520 (total time: 0.520) Filter (dist) r_work=0.1035 r_free=0.1783 | n_water=247 | time (s): 21.130 (total time: 21.650) Filter (q & B) r_work=0.1037 r_free=0.1783 | n_water=244 | time (s): 1.880 (total time: 23.530) Compute maps r_work=0.1037 r_free=0.1783 | n_water=244 | time (s): 0.630 (total time: 24.160) Filter (map) r_work=0.1328 r_free=0.1882 | n_water=147 | time (s): 1.760 (total time: 25.920) Find peaks r_work=0.1328 r_free=0.1882 | n_water=147 | time (s): 0.450 (total time: 26.370) Add new water r_work=0.1682 r_free=0.2141 | n_water=234 | time (s): 1.250 (total time: 27.620) Refine new water occ: r_work=0.1152 r_free=0.1685 adp: r_work=0.1126 r_free=0.1704 occ: r_work=0.1123 r_free=0.1675 adp: r_work=0.1111 r_free=0.1691 occ: r_work=0.1111 r_free=0.1676 adp: r_work=0.1111 r_free=0.1676 ADP+occupancy (water only), MIN, final r_work=0.1111 r_free=0.1676 r_work=0.1111 r_free=0.1676 | n_water=234 | time (s): 7.780 (total time: 35.400) Filter (q & B) r_work=0.1111 r_free=0.1676 | n_water=234 | time (s): 0.790 (total time: 36.190) Filter (dist only) r_work=0.1115 r_free=0.1664 | n_water=231 | time (s): 18.370 (total time: 54.560) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.241320 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.581656 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 0.1008 0.1784 0.0776 0.009 1.0 4.8 0.5 0.0 0 11.621 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.08 17.84 7.76 4.583 16.586 2.582 0.014 9.40 18.13 8.73 5.386 17.001 2.582 0.012 Individual atomic B min max mean iso aniso Overall: 0.00 107.05 16.44 6.36 1758 0 Protein: 0.00 107.05 14.88 6.34 1519 0 Water: 0.00 64.38 26.35 N/A 231 0 Other: 14.64 41.84 27.10 N/A 8 0 Chain A: 0.00 107.05 15.63 N/A 1672 0 Chain S: 4.24 60.64 32.29 N/A 86 0 Histogram: Values Number of atoms 0.00 - 10.71 691 10.71 - 21.41 666 21.41 - 32.12 209 32.12 - 42.82 116 42.82 - 53.53 33 53.53 - 64.23 29 64.23 - 74.94 7 74.94 - 85.64 2 85.64 - 96.35 3 96.35 - 107.05 2 =========================== Idealize ADP of riding H ========================== r_work=0.0940 r_free=0.1813 r_work=0.0938 r_free=0.1814 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0938 r_free = 0.1814 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0934 r_free = 0.1811 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0934 r_free= 0.1811 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ls_wunit_k1) (work): 0.011757 | | target function (ls_wunit_k1) not normalized (work): 57.881637 | | target function (ls_wunit_k1) not normalized (free): 10.365194 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0979 0.0934 0.1811 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2036 0.2031 0.2233 n_refl.: 5175 remove outliers: r(all,work,free)=0.2036 0.2031 0.2233 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2036 0.2031 0.2233 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0977 0.0933 0.1824 n_refl.: 5175 remove outliers: r(all,work,free)=0.0977 0.0933 0.1824 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 0.3225 326.388 312.573 0.659 1.010 0.354 11.894-9.307 99.02 97 4 0.1472 525.055 518.655 0.970 1.012 0.340 9.237-7.194 100.00 213 7 0.1436 429.391 430.399 1.017 1.012 0.330 7.162-5.571 100.00 427 22 0.1371 322.206 320.091 0.992 1.009 0.280 5.546-4.326 100.00 867 58 0.0803 442.343 439.684 1.005 1.005 0.240 4.315-3.360 100.00 1859 96 0.0730 420.673 420.327 1.054 0.998 0.207 3.356-3.002 100.00 1373 60 0.0950 324.020 323.512 1.032 0.991 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-4.0487 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0933 r_free=0.1824 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN A Total number of N/Q/H flips: 2 r_work=0.0938 r_free=0.1829 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0938 r_free=0.1829 | n_water=231 | time (s): 0.520 (total time: 0.520) Filter (dist) r_work=0.0971 r_free=0.1852 | n_water=225 | time (s): 18.800 (total time: 19.320) Filter (q & B) r_work=0.1077 r_free=0.1866 | n_water=221 | time (s): 1.260 (total time: 20.580) Compute maps r_work=0.1077 r_free=0.1866 | n_water=221 | time (s): 0.470 (total time: 21.050) Filter (map) r_work=0.1306 r_free=0.1918 | n_water=147 | time (s): 1.650 (total time: 22.700) Find peaks r_work=0.1306 r_free=0.1918 | n_water=147 | time (s): 0.440 (total time: 23.140) Add new water r_work=0.1725 r_free=0.2327 | n_water=244 | time (s): 1.220 (total time: 24.360) Refine new water occ: r_work=0.1073 r_free=0.1800 adp: r_work=0.1065 r_free=0.1822 occ: r_work=0.1050 r_free=0.1784 adp: r_work=0.1050 r_free=0.1801 occ: r_work=0.1036 r_free=0.1760 adp: r_work=0.1036 r_free=0.1775 ADP+occupancy (water only), MIN, final r_work=0.1036 r_free=0.1775 r_work=0.1036 r_free=0.1775 | n_water=244 | time (s): 11.980 (total time: 36.340) Filter (q & B) r_work=0.1036 r_free=0.1775 | n_water=244 | time (s): 0.750 (total time: 37.090) Filter (dist only) r_work=0.1045 r_free=0.1766 | n_water=241 | time (s): 20.640 (total time: 57.730) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.076552 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.227498 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.0940 0.1778 0.0838 0.011 1.1 4.8 0.5 0.0 0 0.538 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.40 17.78 8.38 5.325 17.722 0.227 5.155 8.96 17.79 8.83 7.040 17.687 0.227 5.060 Individual atomic B min max mean iso aniso Overall: 0.00 106.89 16.33 8.63 1768 0 Protein: 0.00 106.89 14.96 8.62 1519 0 Water: 0.00 57.87 24.59 N/A 241 0 Other: 14.34 45.79 28.37 N/A 8 0 Chain A: 0.00 106.89 15.66 N/A 1658 0 Chain S: 0.00 57.87 26.53 N/A 110 0 Histogram: Values Number of atoms 0.00 - 10.69 675 10.69 - 21.38 663 21.38 - 32.07 240 32.07 - 42.76 118 42.76 - 53.45 37 53.45 - 64.14 16 64.14 - 74.83 11 74.83 - 85.52 3 85.52 - 96.20 3 96.20 - 106.89 2 =========================== Idealize ADP of riding H ========================== r_work=0.0896 r_free=0.1779 r_work=0.0902 r_free=0.1786 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0902 r_free = 0.1786 target_work(ml) = 5.065 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0890 r_free = 0.1759 target_work(ml) = 5.058 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0890 r_free= 0.1759 coordinate error (max.-lik. estimate): 0.27 A | | | | normalized target function (ml) (work): 5.057674 | | target function (ml) not normalized (work): 24898.929852 | | target function (ml) not normalized (free): 1778.134103 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0934 0.0890 0.1759 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2040 0.2047 0.2032 n_refl.: 5175 remove outliers: r(all,work,free)=0.2040 0.2047 0.2032 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2040 0.2047 0.2032 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0925 0.0882 0.1754 n_refl.: 5175 remove outliers: r(all,work,free)=0.0925 0.0882 0.1754 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 0.3676 326.388 299.177 0.579 0.991 0.320 11.894-9.307 99.02 97 4 0.1825 525.055 512.077 0.954 0.996 0.320 9.237-7.194 100.00 213 7 0.1873 429.391 423.762 1.006 0.998 0.299 7.162-5.571 100.00 427 22 0.1794 322.206 313.852 0.985 0.999 0.280 5.546-4.326 100.00 867 58 0.0899 442.343 436.700 1.004 1.000 0.225 4.315-3.360 100.00 1859 96 0.0587 420.673 420.100 1.061 1.002 0.210 3.356-3.002 100.00 1373 60 0.0616 324.020 324.087 1.039 1.003 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-6.6570 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0882 r_free=0.1754 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0882 r_free=0.1754 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0882 r_free=0.1754 | n_water=241 | time (s): 0.530 (total time: 0.530) Filter (dist) r_work=0.0893 r_free=0.1762 | n_water=238 | time (s): 19.390 (total time: 19.920) Filter (q & B) r_work=0.0967 r_free=0.1808 | n_water=235 | time (s): 1.300 (total time: 21.220) Compute maps r_work=0.0967 r_free=0.1808 | n_water=235 | time (s): 0.570 (total time: 21.790) Filter (map) r_work=0.1276 r_free=0.1857 | n_water=155 | time (s): 1.590 (total time: 23.380) Find peaks r_work=0.1276 r_free=0.1857 | n_water=155 | time (s): 0.580 (total time: 23.960) Add new water r_work=0.1616 r_free=0.2188 | n_water=241 | time (s): 1.540 (total time: 25.500) Refine new water r_work=0.1616 r_free=0.2188 | n_water=241 | time (s): 0.070 (total time: 25.570) Filter (q & B) r_work=0.1276 r_free=0.1857 | n_water=155 | time (s): 1.250 (total time: 26.820) Filter (dist only) r_work=0.1281 r_free=0.1850 | n_water=153 | time (s): 11.590 (total time: 38.410) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.389531 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.326286 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 0.1123 0.1958 0.0835 0.011 1.1 4.5 0.5 0.6 0 0.695 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.23 19.58 8.35 6.752 17.564 0.326 5.360 10.59 19.97 9.38 8.257 17.632 0.326 5.269 Individual atomic B min max mean iso aniso Overall: 0.00 104.14 15.96 10.34 1680 0 Protein: 0.00 104.14 15.13 10.33 1519 0 Water: 1.10 52.73 23.54 N/A 153 0 Other: 16.25 49.59 29.17 N/A 8 0 Chain A: 0.00 104.14 15.76 N/A 1646 0 Chain S: 1.10 52.58 25.62 N/A 34 0 Histogram: Values Number of atoms 0.00 - 10.41 650 10.41 - 20.83 606 20.83 - 31.24 248 31.24 - 41.66 95 41.66 - 52.07 46 52.07 - 62.49 13 62.49 - 72.90 13 72.90 - 83.31 4 83.31 - 93.73 2 93.73 - 104.14 3 =========================== Idealize ADP of riding H ========================== r_work=0.1059 r_free=0.1997 r_work=0.1063 r_free=0.2010 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1063 r_free = 0.2010 target_work(ml) = 5.272 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1060 r_free = 0.1998 target_work(ml) = 5.270 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.1060 r_free= 0.1998 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ml) (work): 5.269832 | | target function (ml) not normalized (work): 25943.385268 | | target function (ml) not normalized (free): 1753.398918 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1107 0.1060 0.1998 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2340 0.2340 0.2437 n_refl.: 5175 remove outliers: r(all,work,free)=0.2340 0.2340 0.2437 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2340 0.2340 0.2437 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.1095 0.1047 0.2005 n_refl.: 5175 remove outliers: r(all,work,free)=0.1095 0.1047 0.2005 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 0.3755 326.388 298.980 0.630 0.992 0.332 11.894-9.307 99.02 97 4 0.1687 525.055 512.000 0.983 0.997 0.334 9.237-7.194 100.00 213 7 0.1987 429.391 421.450 1.017 0.999 0.334 7.162-5.571 100.00 427 22 0.1909 322.206 315.415 0.976 1.000 0.310 5.546-4.326 100.00 867 58 0.1098 442.343 436.422 0.999 1.000 0.259 4.315-3.360 100.00 1859 96 0.0755 420.673 418.980 1.075 1.000 0.240 3.356-3.002 100.00 1373 60 0.0809 324.020 323.042 1.060 1.000 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.2575 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1047 r_free=0.2005 After: r_work=0.1050 r_free=0.2004 ================================== NQH flips ================================== r_work=0.1050 r_free=0.2004 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1050 r_free=0.2004 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1050 r_free=0.2004 | n_water=153 | time (s): 0.600 (total time: 0.600) Filter (dist) r_work=0.1076 r_free=0.1993 | n_water=147 | time (s): 12.540 (total time: 13.140) Filter (q & B) r_work=0.1076 r_free=0.1993 | n_water=147 | time (s): 0.860 (total time: 14.000) Compute maps r_work=0.1076 r_free=0.1993 | n_water=147 | time (s): 0.610 (total time: 14.610) Filter (map) r_work=0.1128 r_free=0.1979 | n_water=134 | time (s): 1.830 (total time: 16.440) Find peaks r_work=0.1128 r_free=0.1979 | n_water=134 | time (s): 0.430 (total time: 16.870) Add new water r_work=0.1455 r_free=0.2281 | n_water=204 | time (s): 1.510 (total time: 18.380) Refine new water occ: r_work=0.1112 r_free=0.2000 adp: r_work=0.1114 r_free=0.2015 occ: r_work=0.1098 r_free=0.1987 adp: r_work=0.1101 r_free=0.2004 occ: r_work=0.1085 r_free=0.1975 adp: r_work=0.1087 r_free=0.1992 ADP+occupancy (water only), MIN, final r_work=0.1087 r_free=0.1992 r_work=0.1087 r_free=0.1992 | n_water=204 | time (s): 11.320 (total time: 29.700) Filter (q & B) r_work=0.1089 r_free=0.1983 | n_water=201 | time (s): 1.720 (total time: 31.420) Filter (dist only) r_work=0.1089 r_free=0.1983 | n_water=201 | time (s): 14.690 (total time: 46.110) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.230022 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.228692 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 0.1041 0.1981 0.0939 0.012 1.2 7.4 0.5 0.6 0 0.615 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.41 19.81 9.39 7.865 17.853 0.229 5.183 10.21 19.78 9.57 8.795 17.930 0.229 5.128 Individual atomic B min max mean iso aniso Overall: 0.00 104.06 16.66 11.46 1728 0 Protein: 0.00 104.06 15.51 11.44 1519 0 Water: 0.00 54.09 24.93 N/A 201 0 Other: 16.89 53.09 28.61 N/A 8 0 Chain A: 0.00 104.06 15.99 N/A 1635 0 Chain S: 0.00 54.09 28.55 N/A 93 0 Histogram: Values Number of atoms 0.00 - 10.41 636 10.41 - 20.81 599 20.81 - 31.22 286 31.22 - 41.62 125 41.62 - 52.03 45 52.03 - 62.44 12 62.44 - 72.84 12 72.84 - 83.25 9 83.25 - 93.65 1 93.65 - 104.06 3 =========================== Idealize ADP of riding H ========================== r_work=0.1021 r_free=0.1978 r_work=0.1026 r_free=0.1979 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1026 r_free = 0.1979 target_work(ml) = 5.135 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0996 r_free = 0.1935 target_work(ml) = 5.112 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0996 r_free= 0.1935 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ml) (work): 5.111603 | | target function (ml) not normalized (work): 25164.423873 | | target function (ml) not normalized (free): 1873.464084 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1357 0.1882 5.6103 6.124| | 2: 3.78 - 3.00 1.00 2430 110 0.0555 0.2027 4.6 9.1259| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 13.08 0.99 0.97 14322.35| | 2: 3.78 - 3.00 2430 110 0.98 3.01 1.01 1.01 1449.13| |alpha: min = 0.95 max = 1.01 mean = 0.99| |beta: min = 975.68 max = 23188.34 mean = 7968.11| |figures of merit: min = 0.00 max = 1.00 mean = 0.94| |phase err.(work): min = 0.00 max = 89.95 mean = 8.11| |phase err.(test): min = 0.00 max = 87.78 mean = 8.03| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1043 0.0996 0.1935 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2283 0.2287 0.2329 n_refl.: 5175 remove outliers: r(all,work,free)=0.2283 0.2287 0.2329 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2283 0.2287 0.2329 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.1038 0.0991 0.1911 n_refl.: 5175 remove outliers: r(all,work,free)=0.1038 0.0991 0.1911 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 0.3998 326.388 290.342 0.615 0.983 0.310 11.894-9.307 99.02 97 4 0.1947 525.055 509.112 1.026 0.989 0.310 9.237-7.194 100.00 213 7 0.2258 429.391 419.313 1.074 0.993 0.305 7.162-5.571 100.00 427 22 0.2090 322.206 314.952 1.032 0.995 0.300 5.546-4.326 100.00 867 58 0.1133 442.343 435.791 1.075 0.998 0.245 4.315-3.360 100.00 1859 96 0.0663 420.673 419.597 1.163 1.003 0.240 3.356-3.002 100.00 1373 60 0.0547 324.020 323.558 1.147 1.007 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-9.2531 ================= 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 : 0.3630 0.1993 0.082 5.364 8.8 119.3 19.9 258 0.000 1_bss: 0.1570 0.1619 0.082 5.364 6.0 116.4 17.0 258 0.000 1_settarget: 0.1570 0.1619 0.082 5.364 6.0 116.4 17.0 258 0.000 1_nqh: 0.1572 0.1618 0.082 5.364 6.0 116.4 17.0 258 0.003 1_weight: 0.1572 0.1618 0.082 5.364 6.0 116.4 17.0 258 0.003 1_xyzrec: 0.1155 0.1810 0.010 0.978 6.0 116.4 17.0 258 0.220 1_adp: 0.1020 0.1808 0.010 0.978 2.3 111.4 17.3 258 0.220 1_regHadp: 0.1014 0.1810 0.010 0.978 2.3 111.4 17.3 258 0.220 1_occ: 0.1007 0.1804 0.010 0.978 2.3 111.4 17.3 258 0.220 2_bss: 0.1003 0.1798 0.010 0.978 1.3 110.4 16.3 258 0.220 2_settarget: 0.1003 0.1798 0.010 0.978 1.3 110.4 16.3 258 0.220 2_updatecdl: 0.1003 0.1798 0.010 1.012 1.3 110.4 16.3 258 0.220 2_nqh: 0.1003 0.1798 0.010 1.012 1.3 110.4 16.3 258 0.220 2_sol: 0.1115 0.1664 0.010 1.012 1.3 110.3 15.6 231 n/a 2_weight: 0.1115 0.1664 0.010 1.012 1.3 110.3 15.6 231 n/a 2_xyzrec: 0.1008 0.1784 0.009 0.976 1.3 110.3 15.6 231 n/a 2_adp: 0.0940 0.1813 0.009 0.976 0.0 107.1 16.4 231 n/a 2_regHadp: 0.0938 0.1814 0.009 0.976 0.0 107.1 16.4 231 n/a 2_occ: 0.0934 0.1811 0.009 0.976 0.0 107.1 16.4 231 n/a 3_bss: 0.0933 0.1824 0.009 0.976 0.0 107.1 16.4 231 n/a 3_settarget: 0.0933 0.1824 0.009 0.976 0.0 107.1 16.4 231 n/a 3_updatecdl: 0.0933 0.1824 0.009 0.980 0.0 107.1 16.4 231 n/a 3_nqh: 0.0938 0.1829 0.009 0.980 0.0 107.1 16.4 231 n/a 3_sol: 0.1045 0.1766 0.009 0.980 0.0 107.1 16.4 241 n/a 3_weight: 0.1045 0.1766 0.009 0.980 0.0 107.1 16.4 241 n/a 3_xyzrec: 0.0940 0.1778 0.011 1.052 0.0 107.1 16.4 241 n/a 3_adp: 0.0896 0.1779 0.011 1.052 0.0 106.9 16.3 241 n/a 3_regHadp: 0.0902 0.1786 0.011 1.052 0.0 106.9 16.3 241 n/a 3_occ: 0.0890 0.1759 0.011 1.052 0.0 106.9 16.3 241 n/a 4_bss: 0.0882 0.1754 0.011 1.052 0.0 106.9 16.3 241 n/a 4_settarget: 0.0882 0.1754 0.011 1.052 0.0 106.9 16.3 241 n/a 4_updatecdl: 0.0882 0.1754 0.011 1.071 0.0 106.9 16.3 241 n/a 4_nqh: 0.0882 0.1754 0.011 1.071 0.0 106.9 16.3 241 n/a 4_sol: 0.1281 0.1850 0.011 1.071 0.0 106.9 15.8 153 n/a 4_weight: 0.1281 0.1850 0.011 1.071 0.0 106.9 15.8 153 n/a 4_xyzrec: 0.1123 0.1958 0.011 1.121 0.0 106.9 15.8 153 n/a 4_adp: 0.1059 0.1997 0.011 1.121 0.0 104.1 16.0 153 n/a 4_regHadp: 0.1063 0.2010 0.011 1.121 0.0 104.1 16.0 153 n/a 4_occ: 0.1060 0.1998 0.011 1.121 0.0 104.1 16.0 153 n/a 5_bss: 0.1047 0.2005 0.011 1.121 0.0 104.1 16.0 153 n/a 5_settarget: 0.1047 0.2005 0.011 1.121 0.0 104.1 16.0 153 n/a 5_updatecdl: 0.1047 0.2005 0.011 1.128 0.0 104.1 16.0 153 n/a 5_setrh: 0.1050 0.2004 0.011 1.128 0.0 104.1 16.0 153 n/a 5_nqh: 0.1050 0.2004 0.011 1.128 0.0 104.1 16.0 153 n/a 5_sol: 0.1089 0.1983 0.011 1.128 0.0 104.1 16.5 201 n/a 5_weight: 0.1089 0.1983 0.011 1.128 0.0 104.1 16.5 201 n/a 5_xyzrec: 0.1041 0.1981 0.012 1.223 0.0 104.1 16.5 201 n/a 5_adp: 0.1021 0.1978 0.012 1.223 0.0 104.1 16.7 201 n/a 5_regHadp: 0.1026 0.1979 0.012 1.223 0.0 104.1 16.7 201 n/a 5_occ: 0.0996 0.1935 0.012 1.223 0.0 104.1 16.7 201 n/a end: 0.0991 0.1912 0.012 1.223 0.0 104.1 16.7 201 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_7766834_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_7766834_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.6800 Refinement macro-cycles (run) : 465.2200 Write final files (write_after_run_outputs) : 12.0900 Total : 480.9900 Total CPU time: 8.37 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:18:43 PST -0800 (1735492723.86 s) Start R-work = 0.1570, R-free = 0.1619 Final R-work = 0.0991, R-free = 0.1912 =============================================================================== Job complete usr+sys time: 510.65 seconds wall clock time: 8 minutes 53.19 seconds (533.19 seconds total)