Starting phenix.refine on Sun Dec 29 09:24:41 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8315495.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=2 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 = 2 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8315495.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8315495.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 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: 1.24, per 1000 atoms: 0.37 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: 0.29 Conformation dependent library (CDL) restraints added in 105.0 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.65 - 0.91: 547 0.91 - 1.17: 1097 1.17 - 1.42: 632 1.42 - 1.68: 839 1.68 - 1.94: 38 Bond restraints: 3153 Sorted by residual: bond pdb=" N SER A 3 " pdb=" CA SER A 3 " ideal model delta sigma weight residual 1.454 1.725 -0.271 1.18e-02 7.18e+03 5.28e+02 bond pdb=" CA GLU A 147 " pdb=" C GLU A 147 " ideal model delta sigma weight residual 1.522 1.277 0.246 1.19e-02 7.06e+03 4.27e+02 bond pdb=" NE ARG A 145 " pdb=" CZ ARG A 145 " ideal model delta sigma weight residual 1.326 1.545 -0.219 1.10e-02 8.26e+03 3.97e+02 bond pdb=" C GLY A 40 " pdb=" O GLY A 40 " ideal model delta sigma weight residual 1.236 1.056 0.181 1.02e-02 9.61e+03 3.14e+02 bond pdb=" C SER A 57 " pdb=" O SER A 57 " ideal model delta sigma weight residual 1.234 1.447 -0.213 1.23e-02 6.61e+03 2.99e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.85: 3263 4.85 - 9.70: 1816 9.70 - 14.55: 612 14.55 - 19.40: 79 19.40 - 24.25: 7 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O ILE A 21 " pdb=" C ILE A 21 " pdb=" N PRO A 22 " ideal model delta sigma weight residual 120.42 130.32 -9.90 6.40e-01 2.44e+00 2.39e+02 angle pdb=" O ALA A 183 " pdb=" C ALA A 183 " pdb=" N PRO A 184 " ideal model delta sigma weight residual 120.55 105.90 14.65 9.50e-01 1.11e+00 2.38e+02 angle pdb=" O GLU A 16 " pdb=" C GLU A 16 " pdb=" N MET A 17 " ideal model delta sigma weight residual 122.12 107.07 15.05 1.06e+00 8.90e-01 2.02e+02 angle pdb=" O GLY A 108 " pdb=" C GLY A 108 " pdb=" N PRO A 109 " ideal model delta sigma weight residual 121.77 135.47 -13.70 1.00e+00 1.00e+00 1.88e+02 angle pdb=" O GLY A 157 " pdb=" C GLY A 157 " pdb=" N PRO A 158 " ideal model delta sigma weight residual 121.77 108.48 13.29 1.00e+00 1.00e+00 1.77e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 1315 17.65 - 35.30: 112 35.30 - 52.95: 40 52.95 - 70.61: 12 70.61 - 88.26: 2 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C AGLU A 90 " pdb=" N AGLU A 90 " pdb=" CA AGLU A 90 " pdb=" CB AGLU A 90 " ideal model delta harmonic sigma weight residual -122.60 -142.47 19.87 0 2.50e+00 1.60e-01 6.32e+01 dihedral pdb=" C ALYS A 99 " pdb=" N ALYS A 99 " pdb=" CA ALYS A 99 " pdb=" CB ALYS A 99 " ideal model delta harmonic sigma weight residual -122.60 -142.17 19.57 0 2.50e+00 1.60e-01 6.13e+01 dihedral pdb=" N AGLU A 90 " pdb=" C AGLU A 90 " pdb=" CA AGLU A 90 " pdb=" CB AGLU A 90 " ideal model delta harmonic sigma weight residual 122.80 141.69 -18.89 0 2.50e+00 1.60e-01 5.71e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.216: 105 0.216 - 0.431: 72 0.431 - 0.646: 41 0.646 - 0.862: 22 0.862 - 1.077: 3 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA ASP A 60 " pdb=" N ASP A 60 " pdb=" C ASP A 60 " pdb=" CB ASP A 60 " both_signs ideal model delta sigma weight residual False 2.51 1.43 1.08 2.00e-01 2.50e+01 2.90e+01 chirality pdb=" CA AGLU A 64 " pdb=" N AGLU A 64 " pdb=" C AGLU A 64 " pdb=" CB AGLU A 64 " both_signs ideal model delta sigma weight residual False 2.51 3.39 -0.88 2.00e-01 2.50e+01 1.94e+01 chirality pdb=" CA VAL A 50 " pdb=" N VAL A 50 " pdb=" C VAL A 50 " pdb=" CB VAL A 50 " both_signs ideal model delta sigma weight residual False 2.44 3.32 -0.88 2.00e-01 2.50e+01 1.94e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " -0.100 2.00e-02 2.50e+03 6.38e-02 1.22e+02 pdb=" CG BTYR A 67 " 0.023 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " -0.014 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " 0.027 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " 0.069 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " 0.067 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " -0.071 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " -0.096 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " -0.030 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " 0.066 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " 0.089 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.023 2.00e-02 2.50e+03 6.25e-02 1.17e+02 pdb=" CG PHE A 119 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.088 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.028 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.125 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.028 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " -0.002 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.085 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.052 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.078 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " -0.009 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 28 " 0.011 9.50e-02 1.11e+02 6.69e-02 1.00e+02 pdb=" NE ARG A 28 " -0.106 2.00e-02 2.50e+03 pdb=" CZ ARG A 28 " 0.091 2.00e-02 2.50e+03 pdb=" NH1 ARG A 28 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 28 " -0.031 2.00e-02 2.50e+03 pdb="HH11 ARG A 28 " 0.082 2.00e-02 2.50e+03 pdb="HH12 ARG A 28 " -0.071 2.00e-02 2.50e+03 pdb="HH21 ARG A 28 " 0.078 2.00e-02 2.50e+03 pdb="HH22 ARG A 28 " -0.040 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.31: 1025 2.31 - 2.88: 8054 2.88 - 3.46: 10574 3.46 - 4.03: 15124 4.03 - 4.60: 21875 Nonbonded interactions: 56652 Sorted by model distance: nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.741 2.100 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.743 2.450 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.770 2.100 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.787 2.450 nonbonded pdb=" HG SER A 47 " pdb="HH11 ARG A 48 " model vdw 1.788 2.100 ... (remaining 56647 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 2 N 265 6.97 2 C 957 5.97 2 H 1596 1.00 2 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_8315495_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: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2789 r_free= 0.1821 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.433148 | | target function (ml) not normalized (work): 72007.615990 | | target function (ml) not normalized (free): 3270.957610 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 49.25 - 3.64 1.00 2819 159 0.3196 0.2161 7.6862 5.0431| | 2: 3.63 - 2.88 1.00 2711 122 0.2653 0.1614 4.3145 4.2821| | 3: 2.88 - 2.52 1.00 2682 148 0.2551 0.1695 4.1704 4.1651| | 4: 2.52 - 2.29 1.00 2661 139 0.2534 0.1605 3.5128 3.6226| | 5: 2.29 - 2.13 1.00 2678 122 0.2670 0.1448 3.4185 3.4479| | 6: 2.13 - 2.00 1.00 2692 117 0.2737 0.2009 3.327 3.4706| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 - 3.64 2819 159 0.88 17.13 0.77 0.23 1252.10| | 2: 3.63 - 2.88 2711 122 0.83 23.37 1.32 0.23 1252.10| | 3: 2.88 - 2.52 2682 148 0.74 32.10 1.28 0.23 1252.10| | 4: 2.52 - 2.29 2661 139 0.93 11.84 1.29 0.26 142.79| | 5: 2.29 - 2.13 2678 122 0.92 13.99 1.32 0.26 142.79| | 6: 2.13 - 2.00 2692 117 0.89 16.85 1.33 0.26 142.79| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 142.79 max = 1252.10 mean = 703.62| |figures of merit: min = 0.00 max = 1.00 mean = 0.87| |phase err.(work): min = 0.00 max = 89.99 mean = 19.21| |phase err.(test): min = 0.00 max = 89.45 mean = 19.53| |-----------------------------------------------------------------------------| ----------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 0.271 1557 Z= 5.557 Angle : 5.380 22.608 2118 Z= 3.810 Chirality : 0.381 1.077 243 Planarity : 0.033 0.126 284 Dihedral : 13.949 88.257 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.54 % Allowed : 1.62 % Favored : 97.84 % Rotamer: Outliers : 1.24 % Allowed : 3.73 % Favored : 95.03 % Cbeta Deviations : 24.86 % 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: -1.85 (0.47), residues: 224 helix: -2.24 (0.40), residues: 102 sheet: -0.68 (0.82), residues: 28 loop : 0.15 (0.55), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.102 0.018 ARG A 28 TYR 0.116 0.041 TYR A 141 PHE 0.113 0.040 PHE A 119 HIS 0.067 0.033 HIS A 126 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: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2789 r_free= 0.1821 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.433148 | | target function (ml) not normalized (work): 72007.615990 | | target function (ml) not normalized (free): 3270.957610 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.3285 percent. r_work = 0.2921 r_free = 0.1979 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2868 0.2921 0.1979 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2868 0.2921 0.1979 n_refl.: 17050 remove outliers: r(all,work,free)=0.2163 0.2175 0.1979 n_refl.: 17045 overall B=-0.38 to atoms: r(all,work,free)=0.2138 0.2150 0.1963 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1625 0.1624 0.1635 n_refl.: 17045 remove outliers: r(all,work,free)=0.1624 0.1623 0.1635 n_refl.: 17044 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 100.00 89 5 0.4060 395.053 362.311 0.646 1.011 0.393 11.894-9.307 99.02 97 4 0.1871 634.072 616.911 0.924 1.013 0.375 9.237-7.194 100.00 213 7 0.2172 518.607 511.679 0.961 1.013 0.355 7.162-5.571 100.00 427 22 0.2328 389.215 378.252 0.921 1.012 0.341 5.546-4.326 100.00 867 58 0.1397 534.330 528.652 0.958 1.010 0.257 4.315-3.360 100.00 1859 96 0.1294 508.153 503.994 1.013 1.006 0.191 3.356-2.611 100.00 3867 181 0.1656 333.828 329.658 1.013 1.000 0.101 2.608-2.000 99.99 8818 434 0.1673 217.598 213.453 1.025 0.989 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.3683 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1623 r_free=0.1635 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1623 r_free=0.1635 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.870930 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.959742 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 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 0.1352 0.1629 0.0277 0.009 1.0 1.3 0.5 0.0 0 11.935 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.52 16.29 2.77 3.013 18.476 0.960 0.023 12.79 16.47 3.67 3.598 18.672 0.960 0.021 Individual atomic B min max mean iso aniso Overall: 6.01 113.92 19.87 4.10 1785 0 Protein: 6.01 113.41 17.10 4.11 1519 0 Water: 8.39 113.92 36.04 N/A 258 0 Other: 21.60 37.26 26.04 N/A 8 0 Chain A: 6.01 113.92 19.87 N/A 1785 0 Histogram: Values Number of atoms 6.01 - 16.80 1084 16.80 - 27.59 341 27.59 - 38.38 185 38.38 - 49.17 96 49.17 - 59.96 52 59.96 - 70.75 12 70.75 - 81.55 7 81.55 - 92.34 4 92.34 - 103.13 1 103.13 - 113.92 3 =========================== Idealize ADP of riding H ========================== r_work=0.1279 r_free=0.1647 r_work=0.1282 r_free=0.1654 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1282 r_free = 0.1654 target_work(ls_wunit_k1) = 0.021 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1278 r_free = 0.1648 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17044 (all), 4.73 % free)------------| | | | r_work= 0.1278 r_free= 0.1648 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.020209 | | target function (ls_wunit_k1) not normalized (work): 328.138082 | | target function (ls_wunit_k1) not normalized (free): 26.975390 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1296 0.1278 0.1648 n_refl.: 17044 re-set all scales: r(all,work,free)=0.1912 0.1912 0.1972 n_refl.: 17044 remove outliers: r(all,work,free)=0.1912 0.1912 0.1972 n_refl.: 17044 overall B=-0.50 to atoms: r(all,work,free)=0.1876 0.1875 0.1953 n_refl.: 17044 bulk-solvent and scaling: r(all,work,free)=0.1293 0.1276 0.1638 n_refl.: 17044 remove outliers: r(all,work,free)=0.1292 0.1274 0.1638 n_refl.: 17042 ======================== 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 0.3510 303.413 279.322 0.626 1.006 0.366 11.894-9.307 99.02 97 4 0.1698 487.992 477.244 0.920 1.007 0.364 9.237-7.194 100.00 213 7 0.1848 399.128 396.081 0.961 1.007 0.341 7.162-5.571 100.00 427 22 0.1862 299.546 293.636 0.928 1.006 0.274 5.546-4.326 100.00 867 58 0.1059 411.228 408.538 0.959 1.006 0.241 4.315-3.360 100.00 1859 96 0.0938 391.082 390.387 1.015 1.004 0.192 3.356-2.611 100.00 3867 181 0.1292 256.919 255.527 1.010 1.001 0.112 2.608-2.000 99.99 8818 434 0.1342 167.467 166.179 1.010 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9583 b_overall=-1.1309 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1274 r_free=0.1638 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1274 r_free=0.1638 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1274 r_free=0.1638 | n_water=258 | time (s): 0.880 (total time: 0.880) Filter (dist) r_work=0.1282 r_free=0.1627 | n_water=253 | time (s): 21.680 (total time: 22.560) Filter (q & B) r_work=0.1281 r_free=0.1626 | n_water=251 | time (s): 1.690 (total time: 24.250) Compute maps r_work=0.1281 r_free=0.1626 | n_water=251 | time (s): 0.570 (total time: 24.820) Filter (map) r_work=0.1321 r_free=0.1613 | n_water=209 | time (s): 1.410 (total time: 26.230) Find peaks r_work=0.1321 r_free=0.1613 | n_water=209 | time (s): 0.420 (total time: 26.650) Add new water r_work=0.1547 r_free=0.1890 | n_water=376 | time (s): 1.440 (total time: 28.090) Refine new water occ: r_work=0.1337 r_free=0.1606 adp: r_work=0.1275 r_free=0.1601 occ: r_work=0.1283 r_free=0.1575 adp: r_work=0.1249 r_free=0.1579 occ: r_work=0.1250 r_free=0.1571 adp: r_work=0.1238 r_free=0.1570 ADP+occupancy (water only), MIN, final r_work=0.1238 r_free=0.1570 r_work=0.1238 r_free=0.1570 | n_water=376 | time (s): 19.840 (total time: 47.930) Filter (q & B) r_work=0.1241 r_free=0.1579 | n_water=365 | time (s): 1.550 (total time: 49.480) Filter (dist only) r_work=0.1242 r_free=0.1581 | n_water=364 | time (s): 28.260 (total time: 77.740) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.454592 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.975157 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 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 0.1212 0.1605 0.0393 0.008 0.9 1.9 0.5 0.0 0 12.227 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.12 16.05 3.93 4.178 20.868 0.975 0.018 11.98 16.22 4.24 4.235 21.184 0.975 0.018 Individual atomic B min max mean iso aniso Overall: 6.37 107.91 21.29 4.35 1891 0 Protein: 6.37 107.91 17.66 4.34 1519 0 Water: 8.15 68.10 36.19 N/A 364 0 Other: 23.60 44.55 33.62 N/A 8 0 Chain A: 6.37 107.91 19.37 N/A 1736 0 Chain S: 17.20 63.83 42.84 N/A 155 0 Histogram: Values Number of atoms 6.37 - 16.52 1013 16.52 - 26.67 391 26.67 - 36.83 222 36.83 - 46.98 158 46.98 - 57.14 66 57.14 - 67.29 30 67.29 - 77.45 4 77.45 - 87.60 5 87.60 - 97.75 0 97.75 - 107.91 2 =========================== Idealize ADP of riding H ========================== r_work=0.1198 r_free=0.1622 r_work=0.1200 r_free=0.1622 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1622 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1198 r_free = 0.1637 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17042 (all), 4.74 % free)------------| | | | r_work= 0.1198 r_free= 0.1637 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.017028 | | target function (ls_wunit_k1) not normalized (work): 276.446911 | | target function (ls_wunit_k1) not normalized (free): 25.806717 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1219 0.1198 0.1637 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1757 0.1749 0.1953 n_refl.: 17042 remove outliers: r(all,work,free)=0.1757 0.1749 0.1953 n_refl.: 17042 overall B=-0.42 to atoms: r(all,work,free)=0.1731 0.1722 0.1934 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1215 0.1195 0.1622 n_refl.: 17042 remove outliers: r(all,work,free)=0.1215 0.1195 0.1622 n_refl.: 17042 ======================== 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 0.3289 303.413 284.843 0.601 1.006 0.340 11.894-9.307 99.02 97 4 0.1515 487.992 484.608 0.915 1.007 0.334 9.237-7.194 100.00 213 7 0.1660 399.128 398.814 0.977 1.006 0.311 7.162-5.571 100.00 427 22 0.1542 299.546 295.715 0.935 1.006 0.271 5.546-4.326 100.00 867 58 0.0895 411.228 408.574 0.959 1.005 0.211 4.315-3.360 100.00 1859 96 0.0834 391.082 390.141 1.016 1.003 0.202 3.356-2.611 100.00 3867 181 0.1202 256.919 256.182 1.010 1.001 0.132 2.608-2.000 99.99 8818 434 0.1335 167.467 166.465 1.012 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-1.1653 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1195 r_free=0.1622 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 97 ASN B Total number of N/Q/H flips: 2 r_work=0.1196 r_free=0.1624 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1624 | n_water=364 | time (s): 0.730 (total time: 0.730) Filter (dist) r_work=0.1197 r_free=0.1623 | n_water=363 | time (s): 29.460 (total time: 30.190) Filter (q & B) r_work=0.1197 r_free=0.1623 | n_water=363 | time (s): 0.780 (total time: 30.970) Compute maps r_work=0.1197 r_free=0.1623 | n_water=363 | time (s): 0.610 (total time: 31.580) Filter (map) r_work=0.1264 r_free=0.1613 | n_water=262 | time (s): 1.660 (total time: 33.240) Find peaks r_work=0.1264 r_free=0.1613 | n_water=262 | time (s): 0.430 (total time: 33.670) Add new water r_work=0.1441 r_free=0.1779 | n_water=408 | time (s): 1.330 (total time: 35.000) Refine new water occ: r_work=0.1244 r_free=0.1559 adp: r_work=0.1238 r_free=0.1563 occ: r_work=0.1218 r_free=0.1533 adp: r_work=0.1209 r_free=0.1531 occ: r_work=0.1200 r_free=0.1523 adp: r_work=0.1193 r_free=0.1522 ADP+occupancy (water only), MIN, final r_work=0.1193 r_free=0.1522 r_work=0.1193 r_free=0.1522 | n_water=408 | time (s): 37.660 (total time: 72.660) Filter (q & B) r_work=0.1194 r_free=0.1526 | n_water=398 | time (s): 1.540 (total time: 74.200) Filter (dist only) r_work=0.1194 r_free=0.1525 | n_water=397 | time (s): 30.630 (total time: 104.830) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.026445 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.183542 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 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 0.1167 0.1547 0.0380 0.009 1.0 3.5 0.5 0.0 0 1.013 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.67 15.47 3.80 4.371 21.364 0.184 4.994 11.45 15.61 4.16 4.969 21.242 0.184 4.972 Individual atomic B min max mean iso aniso Overall: 6.01 107.19 20.62 4.78 1924 0 Protein: 6.01 107.19 16.80 4.78 1519 0 Water: 8.18 62.98 35.00 N/A 397 0 Other: 24.35 43.51 32.00 N/A 8 0 Chain A: 6.01 107.19 18.57 N/A 1734 0 Chain S: 16.78 62.98 39.37 N/A 190 0 Histogram: Values Number of atoms 6.01 - 16.13 1076 16.13 - 26.25 345 26.25 - 36.37 224 36.37 - 46.48 174 46.48 - 56.60 67 56.60 - 66.72 26 66.72 - 76.84 4 76.84 - 86.96 5 86.96 - 97.07 1 97.07 - 107.19 2 =========================== Idealize ADP of riding H ========================== r_work=0.1145 r_free=0.1561 r_work=0.1145 r_free=0.1563 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1145 r_free = 0.1563 target_work(ml) = 4.973 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1138 r_free = 0.1556 target_work(ml) = 4.968 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17042 (all), 4.74 % free)------------| | | | r_work= 0.1138 r_free= 0.1556 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ml) (work): 4.968254 | | target function (ml) not normalized (work): 80659.596250 | | target function (ml) not normalized (free): 4194.332706 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1158 0.1138 0.1556 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1663 0.1654 0.1887 n_refl.: 17042 remove outliers: r(all,work,free)=0.1663 0.1654 0.1887 n_refl.: 17042 overall B=-0.33 to atoms: r(all,work,free)=0.1641 0.1632 0.1878 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1157 0.1137 0.1556 n_refl.: 17042 remove outliers: r(all,work,free)=0.1156 0.1136 0.1556 n_refl.: 17041 ======================== 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 0.3549 299.922 282.730 0.576 1.006 0.340 11.894-9.307 99.02 97 4 0.1723 487.992 481.790 0.912 1.007 0.321 9.237-7.194 100.00 213 7 0.1771 399.128 399.536 0.986 1.007 0.270 7.162-5.571 100.00 427 22 0.1657 299.546 292.836 0.938 1.006 0.230 5.546-4.326 100.00 867 58 0.0923 411.228 407.938 0.965 1.006 0.221 4.315-3.360 100.00 1859 96 0.0881 391.082 388.725 1.011 1.004 0.201 3.356-2.611 100.00 3867 181 0.1260 256.919 254.774 1.010 1.001 0.131 2.608-2.000 99.99 8818 434 0.1086 167.467 166.101 1.011 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-1.1355 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1136 r_free=0.1556 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1136 r_free=0.1556 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1136 r_free=0.1556 | n_water=397 | time (s): 0.620 (total time: 0.620) Filter (dist) r_work=0.1136 r_free=0.1556 | n_water=397 | time (s): 27.520 (total time: 28.140) Filter (q & B) r_work=0.1136 r_free=0.1556 | n_water=397 | time (s): 0.780 (total time: 28.920) Compute maps r_work=0.1136 r_free=0.1556 | n_water=397 | time (s): 0.560 (total time: 29.480) Filter (map) r_work=0.1197 r_free=0.1595 | n_water=316 | time (s): 1.630 (total time: 31.110) Find peaks r_work=0.1197 r_free=0.1595 | n_water=316 | time (s): 0.610 (total time: 31.720) Add new water r_work=0.1341 r_free=0.1689 | n_water=463 | time (s): 2.150 (total time: 33.870) Refine new water occ: r_work=0.1172 r_free=0.1539 adp: r_work=0.1164 r_free=0.1541 occ: r_work=0.1149 r_free=0.1523 adp: r_work=0.1139 r_free=0.1523 occ: r_work=0.1133 r_free=0.1520 adp: r_work=0.1125 r_free=0.1519 ADP+occupancy (water only), MIN, final r_work=0.1125 r_free=0.1519 r_work=0.1125 r_free=0.1519 | n_water=463 | time (s): 30.170 (total time: 64.040) Filter (q & B) r_work=0.1130 r_free=0.1527 | n_water=449 | time (s): 1.490 (total time: 65.530) Filter (dist only) r_work=0.1133 r_free=0.1530 | n_water=447 | time (s): 35.490 (total time: 101.020) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.903089 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.170002 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 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 0.1124 0.1616 0.0492 0.009 1.0 4.5 0.5 0.0 0 0.952 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.24 16.16 4.92 4.532 20.981 0.170 4.971 11.14 16.10 4.96 4.658 21.006 0.170 4.962 Individual atomic B min max mean iso aniso Overall: 5.79 105.73 20.96 4.83 1974 0 Protein: 5.79 105.73 16.40 4.83 1519 0 Water: 8.18 62.13 36.31 N/A 447 0 Other: 21.87 40.08 28.39 N/A 8 0 Chain A: 5.79 105.73 18.10 N/A 1733 0 Chain S: 17.04 62.13 41.45 N/A 241 0 Histogram: Values Number of atoms 5.79 - 15.78 1078 15.78 - 25.78 354 25.78 - 35.77 209 35.77 - 45.77 196 45.77 - 55.76 93 55.76 - 65.75 30 65.75 - 75.75 6 75.75 - 85.74 4 85.74 - 95.74 2 95.74 - 105.73 2 =========================== Idealize ADP of riding H ========================== r_work=0.1114 r_free=0.1610 r_work=0.1114 r_free=0.1612 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1114 r_free = 0.1612 target_work(ml) = 4.963 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1111 r_free = 0.1632 target_work(ml) = 4.964 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1111 r_free= 0.1632 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ml) (work): 4.963697 | | target function (ml) not normalized (work): 80580.664552 | | target function (ml) not normalized (free): 4206.915942 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1136 0.1111 0.1632 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1597 0.1581 0.1941 n_refl.: 17041 remove outliers: r(all,work,free)=0.1597 0.1581 0.1941 n_refl.: 17041 overall B=-0.26 to atoms: r(all,work,free)=0.1581 0.1565 0.1932 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1134 0.1108 0.1630 n_refl.: 17041 remove outliers: r(all,work,free)=0.1134 0.1108 0.1630 n_refl.: 17041 ======================== 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 0.3670 299.922 280.464 0.564 1.001 0.330 11.894-9.307 99.02 97 4 0.1673 487.992 480.078 0.923 1.002 0.330 9.237-7.194 100.00 213 7 0.1673 399.128 399.968 0.990 1.002 0.250 7.162-5.571 100.00 427 22 0.1543 299.546 292.944 0.942 1.002 0.230 5.546-4.326 100.00 867 58 0.0928 411.228 407.607 0.966 1.002 0.205 4.315-3.360 100.00 1859 96 0.0856 391.082 388.587 1.006 1.002 0.191 3.356-2.611 100.00 3867 181 0.1256 256.919 254.613 1.000 1.001 0.121 2.608-2.000 99.99 8818 434 0.1044 167.467 166.229 0.994 1.000 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.8947 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1108 r_free=0.1630 After: r_work=0.1110 r_free=0.1629 ================================== NQH flips ================================== r_work=0.1110 r_free=0.1629 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1110 r_free=0.1629 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1110 r_free=0.1629 | n_water=447 | time (s): 0.670 (total time: 0.670) Filter (dist) r_work=0.1110 r_free=0.1621 | n_water=446 | time (s): 39.000 (total time: 39.670) Filter (q & B) r_work=0.1110 r_free=0.1621 | n_water=446 | time (s): 0.850 (total time: 40.520) Compute maps r_work=0.1110 r_free=0.1621 | n_water=446 | time (s): 0.660 (total time: 41.180) Filter (map) r_work=0.1190 r_free=0.1608 | n_water=328 | time (s): 2.090 (total time: 43.270) Find peaks r_work=0.1190 r_free=0.1608 | n_water=328 | time (s): 0.620 (total time: 43.890) Add new water r_work=0.1320 r_free=0.1703 | n_water=473 | time (s): 2.090 (total time: 45.980) Refine new water occ: r_work=0.1148 r_free=0.1532 adp: r_work=0.1141 r_free=0.1539 occ: r_work=0.1124 r_free=0.1509 adp: r_work=0.1116 r_free=0.1517 occ: r_work=0.1107 r_free=0.1504 adp: r_work=0.1100 r_free=0.1508 ADP+occupancy (water only), MIN, final r_work=0.1100 r_free=0.1508 r_work=0.1100 r_free=0.1508 | n_water=473 | time (s): 26.310 (total time: 72.290) Filter (q & B) r_work=0.1103 r_free=0.1524 | n_water=462 | time (s): 1.920 (total time: 74.210) Filter (dist only) r_work=0.1103 r_free=0.1525 | n_water=461 | time (s): 36.650 (total time: 110.860) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.051370 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.155143 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 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 0.1121 0.1566 0.0444 0.010 1.0 7.4 0.5 0.0 0 1.026 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.21 15.66 4.44 4.528 20.731 0.155 4.957 11.12 15.43 4.32 4.585 20.772 0.155 4.946 Individual atomic B min max mean iso aniso Overall: 5.70 104.44 20.86 4.84 1988 0 Protein: 5.70 104.44 16.15 4.84 1519 0 Water: 8.08 60.96 36.27 N/A 461 0 Other: 21.15 36.83 27.43 N/A 8 0 Chain A: 5.70 104.44 17.81 N/A 1733 0 Chain S: 20.25 60.96 41.58 N/A 255 0 Histogram: Values Number of atoms 5.70 - 15.58 1086 15.58 - 25.45 342 25.45 - 35.32 209 35.32 - 45.20 192 45.20 - 55.07 113 55.07 - 64.95 33 64.95 - 74.82 5 74.82 - 84.69 3 84.69 - 94.57 3 94.57 - 104.44 2 =========================== Idealize ADP of riding H ========================== r_work=0.1112 r_free=0.1543 r_work=0.1112 r_free=0.1543 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1112 r_free = 0.1543 target_work(ml) = 4.946 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1103 r_free = 0.1537 target_work(ml) = 4.940 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1103 r_free= 0.1537 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.939617 | | target function (ml) not normalized (work): 80189.742207 | | target function (ml) not normalized (free): 4180.532325 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.64 1.00 2811 159 0.1114 0.1401 5.4474 5.6746| | 2: 3.63 - 2.88 1.00 2711 122 0.1083 0.1582 5.2249 5.4043| | 3: 2.88 - 2.52 1.00 2681 148 0.1373 0.1677 5.1454 5.21| | 4: 2.52 - 2.29 1.00 2661 139 0.0914 0.1572 4.626 4.9846| | 5: 2.29 - 2.13 1.00 2678 122 0.0961 0.1469 4.585 4.8861| | 6: 2.13 - 2.00 1.00 2692 117 0.1119 0.1743 4.5798 4.7769| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 - 3.64 2811 159 0.94 9.30 1.00 0.96 6691.51| | 2: 3.63 - 2.88 2711 122 0.92 13.28 1.01 0.96 6691.51| | 3: 2.88 - 2.52 2681 148 0.87 19.47 0.99 0.96 6691.51| | 4: 2.52 - 2.29 2661 139 0.92 12.42 1.01 0.97 2165.68| | 5: 2.29 - 2.13 2678 122 0.91 14.36 1.00 0.97 2165.68| | 6: 2.13 - 2.00 2692 117 0.89 17.03 0.99 0.97 2165.68| |alpha: min = 0.96 max = 0.97 mean = 0.97| |beta: min = 2165.68 max = 6691.51 mean = 4452.57| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.94 mean = 14.27| |phase err.(test): min = 0.00 max = 85.84 mean = 13.88| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1124 0.1103 0.1537 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1581 0.1568 0.1860 n_refl.: 17041 remove outliers: r(all,work,free)=0.1581 0.1568 0.1860 n_refl.: 17041 overall B=-0.21 to atoms: r(all,work,free)=0.1569 0.1556 0.1852 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1126 0.1105 0.1537 n_refl.: 17041 remove outliers: r(all,work,free)=0.1126 0.1105 0.1537 n_refl.: 17041 ======================== 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 0.3678 299.922 280.378 0.560 1.001 0.330 11.894-9.307 99.02 97 4 0.1782 487.992 478.714 0.921 1.003 0.300 9.237-7.194 100.00 213 7 0.1688 399.128 399.971 0.987 1.003 0.230 7.162-5.571 100.00 427 22 0.1544 299.546 293.974 0.939 1.003 0.230 5.546-4.326 100.00 867 58 0.0934 411.228 407.978 0.964 1.003 0.200 4.315-3.360 100.00 1859 96 0.0868 391.082 388.437 1.004 1.002 0.191 3.356-2.611 100.00 3867 181 0.1244 256.919 254.605 0.996 1.001 0.131 2.608-2.000 99.99 8818 434 0.1030 167.467 166.134 0.986 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.7147 ================= 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 : 0.2789 0.1821 0.082 5.380 8.8 119.3 19.9 258 0.000 1_bss: 0.1623 0.1635 0.082 5.380 8.5 118.9 19.5 258 0.000 1_settarget: 0.1623 0.1635 0.082 5.380 8.5 118.9 19.5 258 0.000 1_nqh: 0.1623 0.1635 0.082 5.380 8.5 118.9 19.5 258 0.000 1_weight: 0.1623 0.1635 0.082 5.380 8.5 118.9 19.5 258 0.000 1_xyzrec: 0.1352 0.1629 0.009 0.988 8.5 118.9 19.5 258 0.137 1_adp: 0.1279 0.1647 0.009 0.988 6.0 113.9 19.9 258 0.137 1_regHadp: 0.1282 0.1654 0.009 0.988 6.0 113.9 19.9 258 0.137 1_occ: 0.1278 0.1648 0.009 0.988 6.0 113.9 19.9 258 0.137 2_bss: 0.1274 0.1638 0.009 0.988 5.5 113.4 19.4 258 0.137 2_settarget: 0.1274 0.1638 0.009 0.988 5.5 113.4 19.4 258 0.137 2_updatecdl: 0.1274 0.1638 0.009 1.002 5.5 113.4 19.4 258 0.137 2_nqh: 0.1274 0.1638 0.009 1.002 5.5 113.4 19.4 258 0.137 2_sol: 0.1242 0.1581 0.009 1.002 5.5 112.9 20.7 364 n/a 2_weight: 0.1242 0.1581 0.009 1.002 5.5 112.9 20.7 364 n/a 2_xyzrec: 0.1212 0.1605 0.008 0.921 5.5 112.9 20.7 364 n/a 2_adp: 0.1198 0.1622 0.008 0.921 6.4 107.9 21.3 364 n/a 2_regHadp: 0.1200 0.1622 0.008 0.921 6.4 107.9 21.3 364 n/a 2_occ: 0.1198 0.1637 0.008 0.921 6.4 107.9 21.3 364 n/a 3_bss: 0.1195 0.1622 0.008 0.921 5.9 107.5 20.9 364 n/a 3_settarget: 0.1195 0.1622 0.008 0.921 5.9 107.5 20.9 364 n/a 3_updatecdl: 0.1195 0.1622 0.008 0.922 5.9 107.5 20.9 364 n/a 3_nqh: 0.1196 0.1624 0.008 0.922 5.9 107.5 20.9 364 n/a 3_sol: 0.1194 0.1525 0.008 0.922 5.9 107.5 20.8 397 n/a 3_weight: 0.1194 0.1525 0.008 0.922 5.9 107.5 20.8 397 n/a 3_xyzrec: 0.1167 0.1547 0.009 0.981 5.9 107.5 20.8 397 n/a 3_adp: 0.1145 0.1561 0.009 0.981 6.0 107.2 20.6 397 n/a 3_regHadp: 0.1145 0.1563 0.009 0.981 6.0 107.2 20.6 397 n/a 3_occ: 0.1138 0.1556 0.009 0.981 6.0 107.2 20.6 397 n/a 4_bss: 0.1136 0.1556 0.009 0.981 5.7 106.9 20.3 397 n/a 4_settarget: 0.1136 0.1556 0.009 0.981 5.7 106.9 20.3 397 n/a 4_updatecdl: 0.1136 0.1556 0.009 0.981 5.7 106.9 20.3 397 n/a 4_nqh: 0.1136 0.1556 0.009 0.981 5.7 106.9 20.3 397 n/a 4_sol: 0.1133 0.1530 0.009 0.981 5.7 106.9 20.9 447 n/a 4_weight: 0.1133 0.1530 0.009 0.981 5.7 106.9 20.9 447 n/a 4_xyzrec: 0.1124 0.1616 0.009 0.955 5.7 106.9 20.9 447 n/a 4_adp: 0.1114 0.1610 0.009 0.955 5.8 105.7 21.0 447 n/a 4_regHadp: 0.1114 0.1612 0.009 0.955 5.8 105.7 21.0 447 n/a 4_occ: 0.1111 0.1632 0.009 0.955 5.8 105.7 21.0 447 n/a 5_bss: 0.1108 0.1630 0.009 0.955 5.5 105.5 20.7 447 n/a 5_settarget: 0.1108 0.1630 0.009 0.955 5.5 105.5 20.7 447 n/a 5_updatecdl: 0.1108 0.1630 0.009 0.957 5.5 105.5 20.7 447 n/a 5_setrh: 0.1110 0.1629 0.009 0.957 5.5 105.5 20.7 447 n/a 5_nqh: 0.1110 0.1629 0.009 0.957 5.5 105.5 20.7 447 n/a 5_sol: 0.1103 0.1525 0.009 0.957 5.5 105.5 20.8 461 n/a 5_weight: 0.1103 0.1525 0.009 0.957 5.5 105.5 20.8 461 n/a 5_xyzrec: 0.1121 0.1566 0.010 1.048 5.5 105.5 20.8 461 n/a 5_adp: 0.1112 0.1543 0.010 1.048 5.7 104.4 20.9 461 n/a 5_regHadp: 0.1112 0.1543 0.010 1.048 5.7 104.4 20.9 461 n/a 5_occ: 0.1103 0.1537 0.010 1.048 5.7 104.4 20.9 461 n/a end: 0.1105 0.1537 0.010 1.048 5.5 104.2 20.7 461 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_8315495_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_8315495_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.4200 Refinement macro-cycles (run) : 921.7100 Write final files (write_after_run_outputs) : 19.5700 Total : 944.7000 Total CPU time: 16.09 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:07 PST -0800 (1735494067.06 s) Start R-work = 0.1623, R-free = 0.1635 Final R-work = 0.1105, R-free = 0.1537 =============================================================================== Job complete usr+sys time: 987.52 seconds wall clock time: 16 minutes 50.77 seconds (1010.77 seconds total)