Starting phenix.refine on Sun Dec 29 09:24:42 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8569971.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 { 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" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8569971.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8569971.pdb" 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" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.78, per 1000 atoms: 0.53 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: 0.46 Conformation dependent library (CDL) restraints added in 135.5 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.64 - 0.91: 530 0.91 - 1.19: 1154 1.19 - 1.47: 771 1.47 - 1.74: 684 1.74 - 2.02: 14 Bond restraints: 3153 Sorted by residual: bond pdb=" C ALA A 36 " pdb=" N GLY A 37 " ideal model delta sigma weight residual 1.332 1.512 -0.180 6.60e-03 2.30e+04 7.43e+02 bond pdb=" C GLN A 180 " pdb=" N VAL A 181 " ideal model delta sigma weight residual 1.335 1.581 -0.246 1.20e-02 6.94e+03 4.22e+02 bond pdb=" C GLY A 174 " pdb=" O GLY A 174 " ideal model delta sigma weight residual 1.230 0.984 0.246 1.22e-02 6.72e+03 4.07e+02 bond pdb=" C GLY A 37 " pdb=" O GLY A 37 " ideal model delta sigma weight residual 1.234 1.027 0.207 1.05e-02 9.07e+03 3.88e+02 bond pdb=" C BGLN A 80 " pdb=" O BGLN A 80 " ideal model delta sigma weight residual 1.236 1.025 0.212 1.15e-02 7.56e+03 3.40e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.98: 3327 4.98 - 9.97: 1831 9.97 - 14.95: 525 14.95 - 19.94: 86 19.94 - 24.92: 8 Bond angle restraints: 5777 Sorted by residual: angle pdb=" NE ARG A 98 " pdb=" CZ ARG A 98 " pdb=" NH1 ARG A 98 " ideal model delta sigma weight residual 121.50 136.19 -14.69 1.00e+00 1.00e+00 2.16e+02 angle pdb=" CA ALYS A 132 " pdb=" C ALYS A 132 " pdb=" O ALYS A 132 " ideal model delta sigma weight residual 120.70 135.34 -14.64 1.03e+00 9.43e-01 2.02e+02 angle pdb=" CA GLY A 37 " pdb=" C GLY A 37 " pdb=" O GLY A 37 " ideal model delta sigma weight residual 120.76 132.10 -11.34 8.10e-01 1.52e+00 1.96e+02 angle pdb=" CA GLY A 37 " pdb=" C GLY A 37 " pdb=" N LEU A 38 " ideal model delta sigma weight residual 115.86 100.57 15.29 1.13e+00 7.83e-01 1.83e+02 angle pdb=" CA PHE A 164 " pdb=" C PHE A 164 " pdb=" O PHE A 164 " ideal model delta sigma weight residual 120.42 107.20 13.22 1.06e+00 8.90e-01 1.56e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.75: 1286 16.75 - 33.49: 138 33.49 - 50.24: 40 50.24 - 66.99: 16 66.99 - 83.73: 1 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C CYS A 106 " pdb=" N CYS A 106 " pdb=" CA CYS A 106 " pdb=" CB CYS A 106 " ideal model delta harmonic sigma weight residual -122.60 -143.53 20.93 0 2.50e+00 1.60e-01 7.01e+01 dihedral pdb=" C BLYS A 99 " pdb=" N BLYS A 99 " pdb=" CA BLYS A 99 " pdb=" CB BLYS A 99 " ideal model delta harmonic sigma weight residual -122.60 -142.19 19.59 0 2.50e+00 1.60e-01 6.14e+01 dihedral pdb=" N BLYS A 99 " pdb=" C BLYS A 99 " pdb=" CA BLYS A 99 " pdb=" CB BLYS A 99 " ideal model delta harmonic sigma weight residual 122.80 140.60 -17.80 0 2.50e+00 1.60e-01 5.07e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.004 - 0.207: 93 0.207 - 0.411: 73 0.411 - 0.615: 46 0.615 - 0.818: 24 0.818 - 1.022: 7 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA PHE A 164 " pdb=" N PHE A 164 " pdb=" C PHE A 164 " pdb=" CB PHE A 164 " both_signs ideal model delta sigma weight residual False 2.51 3.53 -1.02 2.00e-01 2.50e+01 2.61e+01 chirality pdb=" CA GLN A 180 " pdb=" N GLN A 180 " pdb=" C GLN A 180 " pdb=" CB GLN A 180 " both_signs ideal model delta sigma weight residual False 2.51 3.48 -0.97 2.00e-01 2.50e+01 2.36e+01 chirality pdb=" CB VAL A 8 " pdb=" CA VAL A 8 " pdb=" CG1 VAL A 8 " pdb=" CG2 VAL A 8 " both_signs ideal model delta sigma weight residual False -2.63 -1.69 -0.94 2.00e-01 2.50e+01 2.20e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " -0.000 2.00e-02 2.50e+03 6.53e-02 1.28e+02 pdb=" CG PHE A 119 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.090 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " -0.042 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.128 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.080 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.004 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " -0.026 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.080 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.104 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 145 " 0.040 9.50e-02 1.11e+02 6.74e-02 9.83e+01 pdb=" NE ARG A 145 " 0.039 2.00e-02 2.50e+03 pdb=" CZ ARG A 145 " -0.047 2.00e-02 2.50e+03 pdb=" NH1 ARG A 145 " -0.065 2.00e-02 2.50e+03 pdb=" NH2 ARG A 145 " 0.147 2.00e-02 2.50e+03 pdb="HH11 ARG A 145 " -0.003 2.00e-02 2.50e+03 pdb="HH12 ARG A 145 " 0.044 2.00e-02 2.50e+03 pdb="HH21 ARG A 145 " -0.081 2.00e-02 2.50e+03 pdb="HH22 ARG A 145 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " -0.043 2.00e-02 2.50e+03 5.45e-02 8.90e+01 pdb=" CG TYR A 139 " 0.086 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " 0.106 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " 0.048 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.004 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " -0.063 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " -0.062 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " -0.059 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " -0.035 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.31: 951 2.31 - 2.88: 8124 2.88 - 3.46: 10582 3.46 - 4.03: 15177 4.03 - 4.60: 21855 Nonbonded interactions: 56689 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.742 2.100 nonbonded pdb=" HG2 LYS A 12 " pdb=" HZ2 LYS A 12 " model vdw 1.807 2.270 nonbonded pdb="HE21 GLN A 45 " pdb=" OD1 ASP A 49 " model vdw 1.809 2.450 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.820 2.450 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.844 2.100 ... (remaining 56684 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_8569971_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= 0.2787 r_free= 0.1797 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.416886 | | target function (ml) not normalized (work): 71743.473680 | | target function (ml) not normalized (free): 3270.018625 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3185 0.2097 7.5784 5.0277| | 2: 3.63 - 2.88 1.00 2711 122 0.2640 0.1744 4.3223 4.3315| | 3: 2.88 - 2.52 1.00 2682 148 0.2565 0.1590 4.1769 4.1868| | 4: 2.52 - 2.29 1.00 2661 139 0.2591 0.1612 3.507 3.6196| | 5: 2.29 - 2.13 1.00 2678 122 0.2626 0.1484 3.4085 3.4531| | 6: 2.13 - 2.00 1.00 2692 117 0.2735 0.1830 3.3431 3.4028| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 17.44 0.77 0.23 1282.03| | 2: 3.63 - 2.88 2711 122 0.83 23.69 1.32 0.23 1282.03| | 3: 2.88 - 2.52 2682 148 0.73 32.66 1.29 0.23 1282.03| | 4: 2.52 - 2.29 2661 139 0.93 11.87 1.30 0.26 143.93| | 5: 2.29 - 2.13 2678 122 0.91 14.11 1.31 0.26 143.93| | 6: 2.13 - 2.00 2692 117 0.90 16.69 1.33 0.26 143.93| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 143.93 max = 1282.03 mean = 719.32| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 89.95 mean = 19.41| |phase err.(test): min = 0.00 max = 89.99 mean = 19.49| |-----------------------------------------------------------------------------| ----------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 : 0.083 0.266 1557 Z= 5.641 Angle : 5.182 20.690 2118 Z= 3.682 Chirality : 0.386 1.022 243 Planarity : 0.032 0.094 284 Dihedral : 14.037 83.732 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.54 % Allowed : 0.54 % Favored : 98.92 % Rotamer: Outliers : 1.24 % Allowed : 3.73 % Favored : 95.03 % Cbeta Deviations : 30.27 % 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: -2.63 (0.45), residues: 224 helix: -2.81 (0.33), residues: 109 sheet: -0.30 (0.68), residues: 38 loop : -0.38 (0.63), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.087 0.025 ARG A 28 TYR 0.080 0.032 TYR A 141 PHE 0.098 0.039 PHE A 119 HIS 0.026 0.012 HIS A 115 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 1785 0 Protein: 8.85 115.78 16.79 3.90 1519 0 Water: 11.36 119.30 38.03 N/A 258 0 Other: 19.04 26.29 21.71 N/A 8 0 Chain A: 8.85 119.30 19.89 N/A 1785 0 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2787 r_free= 0.1797 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.416886 | | target function (ml) not normalized (work): 71743.473680 | | target function (ml) not normalized (free): 3270.018625 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.3295 percent. r_work = 0.2920 r_free = 0.1954 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2865 0.2920 0.1954 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2865 0.2920 0.1954 n_refl.: 17050 remove outliers: r(all,work,free)=0.2159 0.2172 0.1954 n_refl.: 17045 overall B=-0.40 to atoms: r(all,work,free)=0.2133 0.2145 0.1940 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1616 0.1615 0.1627 n_refl.: 17045 remove outliers: r(all,work,free)=0.1615 0.1614 0.1627 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 0.4063 394.877 360.009 0.651 1.012 0.393 11.894-9.307 99.02 97 4 0.1894 633.790 614.274 0.925 1.012 0.370 9.237-7.194 100.00 213 7 0.2187 518.376 509.600 0.964 1.012 0.350 7.162-5.571 100.00 427 22 0.2322 389.042 376.733 0.925 1.011 0.299 5.546-4.326 100.00 867 58 0.1399 534.092 528.215 0.959 1.009 0.235 4.315-3.360 100.00 1859 96 0.1284 507.927 503.489 1.015 1.006 0.212 3.356-2.611 100.00 3867 181 0.1633 333.679 329.409 1.013 1.000 0.101 2.608-2.000 99.99 8818 434 0.1667 217.501 213.410 1.027 0.990 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.4163 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1614 r_free=0.1627 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=0.1616 r_free=0.1622 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.923178 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.867588 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 0.1351 0.1627 0.0276 0.009 1.0 1.0 0.5 0.0 0 11.462 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.51 16.27 2.76 3.013 18.462 0.868 0.023 12.77 16.47 3.71 3.539 18.684 0.868 0.021 Individual atomic B min max mean iso aniso Overall: 6.14 113.90 19.91 4.03 1785 0 Protein: 6.14 113.00 17.15 4.04 1519 0 Water: 8.80 113.90 35.98 N/A 258 0 Other: 21.66 36.72 25.99 N/A 8 0 Chain A: 6.14 113.90 19.91 N/A 1785 0 Histogram: Values Number of atoms 6.14 - 16.92 1089 16.92 - 27.70 339 27.70 - 38.47 184 38.47 - 49.25 97 49.25 - 60.02 49 60.02 - 70.80 12 70.80 - 81.57 7 81.57 - 92.35 4 92.35 - 103.13 1 103.13 - 113.90 3 =========================== Idealize ADP of riding H ========================== r_work=0.1277 r_free=0.1647 r_work=0.1280 r_free=0.1654 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1280 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 = 0.1277 r_free = 0.1645 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.21 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= 0.1277 r_free= 0.1645 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.020185 | | target function (ls_wunit_k1) not normalized (work): 327.740265 | | target function (ls_wunit_k1) not normalized (free): 26.746649 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1295 0.1277 0.1645 n_refl.: 17044 re-set all scales: r(all,work,free)=0.1910 0.1910 0.1969 n_refl.: 17044 remove outliers: r(all,work,free)=0.1910 0.1910 0.1969 n_refl.: 17044 overall B=-0.39 to atoms: r(all,work,free)=0.1882 0.1881 0.1952 n_refl.: 17044 bulk-solvent and scaling: r(all,work,free)=0.1295 0.1278 0.1635 n_refl.: 17044 remove outliers: r(all,work,free)=0.1293 0.1276 0.1635 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 0.3508 303.206 280.177 0.617 1.010 0.366 11.894-9.307 99.02 97 4 0.1695 487.659 476.683 0.912 1.010 0.364 9.237-7.194 100.00 213 7 0.1851 398.856 396.138 0.960 1.010 0.341 7.162-5.571 100.00 427 22 0.1871 299.342 293.664 0.933 1.009 0.301 5.546-4.326 100.00 867 58 0.1055 410.948 408.530 0.957 1.007 0.215 4.315-3.360 100.00 1859 96 0.0931 390.816 390.386 1.018 1.005 0.201 3.356-2.611 100.00 3867 181 0.1302 256.744 255.421 1.016 1.000 0.091 2.608-2.000 99.99 8818 434 0.1343 167.353 165.904 1.022 0.992 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9552 b_overall=-1.3839 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1276 r_free=0.1635 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1276 r_free=0.1635 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1276 r_free=0.1635 | n_water=258 | time (s): 0.780 (total time: 0.780) Filter (dist) r_work=0.1287 r_free=0.1621 | n_water=250 | time (s): 21.140 (total time: 21.920) Filter (q & B) r_work=0.1286 r_free=0.1619 | n_water=248 | time (s): 2.220 (total time: 24.140) Compute maps r_work=0.1286 r_free=0.1619 | n_water=248 | time (s): 0.720 (total time: 24.860) Filter (map) r_work=0.1320 r_free=0.1609 | n_water=211 | time (s): 1.650 (total time: 26.510) Find peaks r_work=0.1320 r_free=0.1609 | n_water=211 | time (s): 0.510 (total time: 27.020) Add new water r_work=0.1543 r_free=0.1846 | n_water=374 | time (s): 1.620 (total time: 28.640) Refine new water occ: r_work=0.1339 r_free=0.1552 adp: r_work=0.1275 r_free=0.1546 occ: r_work=0.1281 r_free=0.1518 adp: r_work=0.1246 r_free=0.1531 occ: r_work=0.1248 r_free=0.1515 adp: r_work=0.1234 r_free=0.1526 ADP+occupancy (water only), MIN, final r_work=0.1234 r_free=0.1526 r_work=0.1234 r_free=0.1526 | n_water=374 | time (s): 19.270 (total time: 47.910) Filter (q & B) r_work=0.1238 r_free=0.1531 | n_water=363 | time (s): 1.930 (total time: 49.840) Filter (dist only) r_work=0.1239 r_free=0.1533 | n_water=362 | time (s): 26.940 (total time: 76.780) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.743884 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.981205 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 0.1217 0.1582 0.0365 0.008 0.9 1.9 0.5 0.0 0 12.372 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.17 15.82 3.65 4.144 21.049 0.981 0.018 12.05 16.01 3.96 4.198 21.390 0.981 0.018 Individual atomic B min max mean iso aniso Overall: 6.80 107.61 21.53 4.27 1889 0 Protein: 6.80 107.61 17.88 4.26 1519 0 Water: 8.53 68.30 36.67 N/A 362 0 Other: 22.89 38.68 29.59 N/A 8 0 Chain A: 6.80 107.61 19.58 N/A 1738 0 Chain S: 19.73 64.36 44.05 N/A 151 0 Histogram: Values Number of atoms 6.80 - 16.88 1023 16.88 - 26.96 381 26.96 - 37.04 212 37.04 - 47.12 160 47.12 - 57.20 68 57.20 - 67.28 34 67.28 - 77.37 4 77.37 - 87.45 5 87.45 - 97.53 0 97.53 - 107.61 2 =========================== Idealize ADP of riding H ========================== r_work=0.1205 r_free=0.1601 r_work=0.1208 r_free=0.1602 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1208 r_free = 0.1602 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 = 0.1201 r_free = 0.1599 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.20 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= 0.1201 r_free= 0.1599 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.016996 | | target function (ls_wunit_k1) not normalized (work): 275.932289 | | target function (ls_wunit_k1) not normalized (free): 24.246400 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1220 0.1201 0.1599 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1767 0.1760 0.1935 n_refl.: 17042 remove outliers: r(all,work,free)=0.1767 0.1760 0.1935 n_refl.: 17042 overall B=-0.38 to atoms: r(all,work,free)=0.1742 0.1734 0.1919 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1213 0.1194 0.1590 n_refl.: 17042 remove outliers: r(all,work,free)=0.1213 0.1194 0.1590 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 0.3328 303.206 284.037 0.604 1.004 0.350 11.894-9.307 99.02 97 4 0.1518 487.659 485.674 0.910 1.005 0.338 9.237-7.194 100.00 213 7 0.1602 398.856 399.982 0.972 1.005 0.290 7.162-5.571 100.00 427 22 0.1553 299.342 295.629 0.938 1.005 0.271 5.546-4.326 100.00 867 58 0.0867 410.948 408.999 0.958 1.004 0.221 4.315-3.360 100.00 1859 96 0.0835 390.816 389.947 1.015 1.003 0.201 3.356-2.611 100.00 3867 181 0.1214 256.744 255.887 1.012 1.001 0.063 2.608-2.000 99.99 8818 434 0.1332 167.353 166.314 1.018 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-1.3671 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1194 r_free=0.1590 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1194 r_free=0.1590 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1194 r_free=0.1590 | n_water=362 | time (s): 0.760 (total time: 0.760) Filter (dist) r_work=0.1193 r_free=0.1592 | n_water=361 | time (s): 29.080 (total time: 29.840) Filter (q & B) r_work=0.1193 r_free=0.1592 | n_water=361 | time (s): 0.800 (total time: 30.640) Compute maps r_work=0.1193 r_free=0.1592 | n_water=361 | time (s): 0.610 (total time: 31.250) Filter (map) r_work=0.1265 r_free=0.1622 | n_water=261 | time (s): 1.780 (total time: 33.030) Find peaks r_work=0.1265 r_free=0.1622 | n_water=261 | time (s): 0.660 (total time: 33.690) Add new water r_work=0.1451 r_free=0.1773 | n_water=404 | time (s): 2.050 (total time: 35.740) Refine new water occ: r_work=0.1251 r_free=0.1551 adp: r_work=0.1244 r_free=0.1550 occ: r_work=0.1226 r_free=0.1535 adp: r_work=0.1216 r_free=0.1533 occ: r_work=0.1207 r_free=0.1523 adp: r_work=0.1199 r_free=0.1521 ADP+occupancy (water only), MIN, final r_work=0.1199 r_free=0.1521 r_work=0.1199 r_free=0.1521 | n_water=404 | time (s): 34.740 (total time: 70.480) Filter (q & B) r_work=0.1202 r_free=0.1532 | n_water=395 | time (s): 1.690 (total time: 72.170) Filter (dist only) r_work=0.1205 r_free=0.1539 | n_water=394 | time (s): 31.340 (total time: 103.510) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.855415 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.144250 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 0.1189 0.1564 0.0375 0.009 0.9 3.8 0.5 0.0 0 0.928 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.89 15.64 3.75 4.345 21.585 0.144 5.004 11.70 15.66 3.97 4.897 21.497 0.144 4.979 Individual atomic B min max mean iso aniso Overall: 6.44 105.34 20.88 4.63 1921 0 Protein: 6.44 105.34 17.12 4.62 1519 0 Water: 9.03 60.58 35.22 N/A 394 0 Other: 21.61 39.74 27.83 N/A 8 0 Chain A: 6.44 105.34 18.79 N/A 1732 0 Chain S: 18.18 60.58 40.00 N/A 189 0 Histogram: Values Number of atoms 6.44 - 16.33 1070 16.33 - 26.22 352 26.22 - 36.11 215 36.11 - 46.00 165 46.00 - 55.89 84 55.89 - 65.78 22 65.78 - 75.67 5 75.67 - 85.56 4 85.56 - 95.45 2 95.45 - 105.34 2 =========================== Idealize ADP of riding H ========================== r_work=0.1170 r_free=0.1566 r_work=0.1170 r_free=0.1567 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1170 r_free = 0.1567 target_work(ml) = 4.979 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1163 r_free = 0.1557 target_work(ml) = 4.973 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17042 (all), 4.74 % free)------------| | | | r_work= 0.1163 r_free= 0.1557 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 4.972984 | | target function (ml) not normalized (work): 80736.396911 | | target function (ml) not normalized (free): 4192.509833 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1182 0.1163 0.1557 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1690 0.1684 0.1853 n_refl.: 17042 remove outliers: r(all,work,free)=0.1690 0.1684 0.1853 n_refl.: 17042 overall B=-0.40 to atoms: r(all,work,free)=0.1662 0.1656 0.1836 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1179 0.1160 0.1550 n_refl.: 17042 remove outliers: r(all,work,free)=0.1178 0.1159 0.1550 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 0.3610 299.717 279.739 0.563 1.005 0.330 11.894-9.307 99.02 97 4 0.1773 487.659 480.447 0.910 1.006 0.309 9.237-7.194 100.00 213 7 0.1838 398.856 399.659 0.979 1.006 0.258 7.162-5.571 100.00 427 22 0.1703 299.342 292.337 0.938 1.006 0.256 5.546-4.326 100.00 867 58 0.0948 410.948 407.533 0.962 1.005 0.211 4.315-3.360 100.00 1859 96 0.0910 390.816 388.853 1.012 1.004 0.191 3.356-2.611 100.00 3867 181 0.1298 256.744 254.402 1.016 1.001 0.132 2.608-2.000 99.99 8818 434 0.1090 167.353 165.961 1.021 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.4170 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1159 r_free=0.1550 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN Total number of N/Q/H flips: 1 r_work=0.1159 r_free=0.1545 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1159 r_free=0.1545 | n_water=394 | time (s): 0.640 (total time: 0.640) Filter (dist) r_work=0.1159 r_free=0.1540 | n_water=393 | time (s): 33.090 (total time: 33.730) Filter (q & B) r_work=0.1160 r_free=0.1541 | n_water=392 | time (s): 1.600 (total time: 35.330) Compute maps r_work=0.1160 r_free=0.1541 | n_water=392 | time (s): 0.850 (total time: 36.180) Filter (map) r_work=0.1212 r_free=0.1555 | n_water=308 | time (s): 1.950 (total time: 38.130) Find peaks r_work=0.1212 r_free=0.1555 | n_water=308 | time (s): 0.520 (total time: 38.650) Add new water r_work=0.1359 r_free=0.1716 | n_water=459 | time (s): 1.900 (total time: 40.550) Refine new water occ: r_work=0.1184 r_free=0.1533 adp: r_work=0.1178 r_free=0.1534 occ: r_work=0.1161 r_free=0.1511 adp: r_work=0.1153 r_free=0.1512 occ: r_work=0.1144 r_free=0.1499 adp: r_work=0.1138 r_free=0.1499 ADP+occupancy (water only), MIN, final r_work=0.1138 r_free=0.1499 r_work=0.1138 r_free=0.1499 | n_water=459 | time (s): 33.770 (total time: 74.320) Filter (q & B) r_work=0.1142 r_free=0.1509 | n_water=449 | time (s): 1.650 (total time: 75.970) Filter (dist only) r_work=0.1142 r_free=0.1509 | n_water=449 | time (s): 33.300 (total time: 109.270) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.934187 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.179018 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 0.1127 0.1576 0.0449 0.010 1.0 3.5 0.5 0.0 0 0.967 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.27 15.76 4.49 4.472 21.208 0.179 4.966 11.15 15.79 4.64 4.651 21.251 0.179 4.958 Individual atomic B min max mean iso aniso Overall: 5.75 102.79 21.17 4.87 1976 0 Protein: 5.75 102.79 16.69 4.87 1519 0 Water: 8.80 65.75 36.20 N/A 449 0 Other: 21.52 40.33 27.88 N/A 8 0 Chain A: 5.75 102.79 18.31 N/A 1731 0 Chain S: 15.17 65.75 41.36 N/A 245 0 Histogram: Values Number of atoms 5.75 - 15.45 1024 15.45 - 25.16 388 25.16 - 34.86 219 34.86 - 44.57 181 44.57 - 54.27 109 54.27 - 63.97 36 63.97 - 73.68 11 73.68 - 83.38 4 83.38 - 93.09 2 93.09 - 102.79 2 =========================== Idealize ADP of riding H ========================== r_work=0.1115 r_free=0.1579 r_work=0.1115 r_free=0.1581 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1115 r_free = 0.1581 target_work(ml) = 4.959 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1106 r_free = 0.1584 target_work(ml) = 4.958 | | occupancies: max = 1.00 min = 0.23 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= 0.1106 r_free= 0.1584 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.958082 | | target function (ml) not normalized (work): 80489.497944 | | target function (ml) not normalized (free): 4199.337633 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1129 0.1106 0.1584 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1604 0.1592 0.1872 n_refl.: 17041 remove outliers: r(all,work,free)=0.1604 0.1592 0.1872 n_refl.: 17041 overall B=-0.32 to atoms: r(all,work,free)=0.1583 0.1571 0.1861 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1127 0.1104 0.1581 n_refl.: 17041 remove outliers: r(all,work,free)=0.1127 0.1104 0.1581 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 0.3692 299.717 279.007 0.551 1.002 0.324 11.894-9.307 99.02 97 4 0.1807 487.659 478.148 0.918 1.004 0.320 9.237-7.194 100.00 213 7 0.1672 398.856 400.451 0.990 1.004 0.230 7.162-5.571 100.00 427 22 0.1512 299.342 293.453 0.937 1.004 0.230 5.546-4.326 100.00 867 58 0.0924 410.948 407.550 0.965 1.003 0.211 4.315-3.360 100.00 1859 96 0.0860 390.816 388.508 1.009 1.002 0.171 3.356-2.611 100.00 3867 181 0.1250 256.744 254.278 1.009 1.001 0.162 2.608-2.000 99.99 8818 434 0.1033 167.353 166.184 1.008 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-1.1219 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1104 r_free=0.1581 After: r_work=0.1106 r_free=0.1581 ================================== NQH flips ================================== r_work=0.1106 r_free=0.1581 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1106 r_free=0.1581 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1106 r_free=0.1581 | n_water=449 | time (s): 0.620 (total time: 0.620) Filter (dist) r_work=0.1106 r_free=0.1572 | n_water=448 | time (s): 37.480 (total time: 38.100) Filter (q & B) r_work=0.1106 r_free=0.1572 | n_water=448 | time (s): 0.970 (total time: 39.070) Compute maps r_work=0.1106 r_free=0.1572 | n_water=448 | time (s): 0.790 (total time: 39.860) Filter (map) r_work=0.1184 r_free=0.1550 | n_water=329 | time (s): 1.720 (total time: 41.580) Find peaks r_work=0.1184 r_free=0.1550 | n_water=329 | time (s): 0.500 (total time: 42.080) Add new water r_work=0.1320 r_free=0.1667 | n_water=479 | time (s): 2.110 (total time: 44.190) Refine new water occ: r_work=0.1145 r_free=0.1520 adp: r_work=0.1136 r_free=0.1524 occ: r_work=0.1121 r_free=0.1501 adp: r_work=0.1112 r_free=0.1504 occ: r_work=0.1105 r_free=0.1498 adp: r_work=0.1098 r_free=0.1495 ADP+occupancy (water only), MIN, final r_work=0.1098 r_free=0.1495 r_work=0.1098 r_free=0.1495 | n_water=479 | time (s): 30.760 (total time: 74.950) Filter (q & B) r_work=0.1101 r_free=0.1508 | n_water=467 | time (s): 1.500 (total time: 76.450) Filter (dist only) r_work=0.1101 r_free=0.1510 | n_water=466 | time (s): 38.020 (total time: 114.470) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.957790 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.201495 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 0.1125 0.1524 0.0399 0.010 1.1 6.1 0.5 0.0 0 0.979 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.25 15.24 3.99 4.575 20.950 0.201 4.952 11.11 15.18 4.07 4.674 21.041 0.201 4.941 Individual atomic B min max mean iso aniso Overall: 5.41 102.58 21.11 5.12 1993 0 Protein: 5.41 102.58 16.41 5.11 1519 0 Water: 8.30 68.61 36.32 N/A 466 0 Other: 21.46 38.65 27.57 N/A 8 0 Chain A: 5.41 102.58 17.99 N/A 1731 0 Chain S: 16.56 68.61 41.71 N/A 262 0 Histogram: Values Number of atoms 5.41 - 15.13 1031 15.13 - 24.85 380 24.85 - 34.56 213 34.56 - 44.28 189 44.28 - 54.00 128 54.00 - 63.71 31 63.71 - 73.43 12 73.43 - 83.15 3 83.15 - 92.86 3 92.86 - 102.58 3 =========================== Idealize ADP of riding H ========================== r_work=0.1111 r_free=0.1518 r_work=0.1111 r_free=0.1517 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1111 r_free = 0.1517 target_work(ml) = 4.941 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1103 r_free = 0.1513 target_work(ml) = 4.936 | | occupancies: max = 1.00 min = 0.24 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= 0.1513 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.935910 | | target function (ml) not normalized (work): 80129.555525 | | target function (ml) not normalized (free): 4166.198947 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1115 0.1441 5.4519 5.6767| | 2: 3.63 - 2.88 1.00 2711 122 0.1079 0.1467 5.2153 5.3518| | 3: 2.88 - 2.52 1.00 2681 148 0.1352 0.1655 5.1276 5.1869| | 4: 2.52 - 2.29 1.00 2661 139 0.0932 0.1532 4.6285 4.9775| | 5: 2.29 - 2.13 1.00 2678 122 0.0963 0.1459 4.5828 4.8597| | 6: 2.13 - 2.00 1.00 2692 117 0.1129 0.1668 4.58 4.7715| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 0.95 8.94 1.00 0.95 6366.94| | 2: 3.63 - 2.88 2711 122 0.92 12.87 1.01 0.95 6366.94| | 3: 2.88 - 2.52 2681 148 0.87 18.96 0.99 0.95 6366.94| | 4: 2.52 - 2.29 2661 139 0.93 12.20 1.01 0.97 2139.93| | 5: 2.29 - 2.13 2678 122 0.91 14.29 1.00 0.97 2139.93| | 6: 2.13 - 2.00 2692 117 0.89 16.95 0.99 0.97 2139.93| |alpha: min = 0.95 max = 0.97 mean = 0.96| |beta: min = 2139.93 max = 6366.94 mean = 4275.83| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.78 mean = 14.00| |phase err.(test): min = 0.00 max = 88.41 mean = 13.53| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1123 0.1103 0.1513 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1576 0.1566 0.1805 n_refl.: 17041 remove outliers: r(all,work,free)=0.1576 0.1566 0.1805 n_refl.: 17041 overall B=-0.25 to atoms: r(all,work,free)=0.1561 0.1550 0.1795 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1123 0.1103 0.1512 n_refl.: 17041 remove outliers: r(all,work,free)=0.1123 0.1103 0.1512 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 0.3636 299.717 280.733 0.546 1.004 0.324 11.894-9.307 99.02 97 4 0.1750 487.659 479.992 0.917 1.005 0.319 9.237-7.194 100.00 213 7 0.1718 398.856 400.462 0.988 1.006 0.220 7.162-5.571 100.00 427 22 0.1501 299.342 294.341 0.933 1.005 0.200 5.546-4.326 100.00 867 58 0.0937 410.948 407.287 0.962 1.005 0.201 4.315-3.360 100.00 1859 96 0.0865 390.816 388.716 1.005 1.003 0.181 3.356-2.611 100.00 3867 181 0.1230 256.744 254.460 1.003 1.001 0.063 2.608-2.000 99.99 8818 434 0.1040 167.353 165.999 0.998 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.8832 ================= 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 : 0.2787 0.1797 0.083 5.182 8.8 119.3 19.9 258 0.000 1_bss: 0.1614 0.1627 0.083 5.182 8.4 118.9 19.5 258 0.000 1_settarget: 0.1614 0.1627 0.083 5.182 8.4 118.9 19.5 258 0.000 1_nqh: 0.1616 0.1622 0.083 5.182 8.4 118.9 19.5 258 0.003 1_weight: 0.1616 0.1622 0.083 5.182 8.4 118.9 19.5 258 0.003 1_xyzrec: 0.1351 0.1627 0.009 0.980 8.4 118.9 19.5 258 0.147 1_adp: 0.1277 0.1647 0.009 0.980 6.1 113.9 19.9 258 0.147 1_regHadp: 0.1280 0.1654 0.009 0.980 6.1 113.9 19.9 258 0.147 1_occ: 0.1277 0.1645 0.009 0.980 6.1 113.9 19.9 258 0.147 2_bss: 0.1276 0.1635 0.009 0.980 5.8 113.5 19.5 258 0.147 2_settarget: 0.1276 0.1635 0.009 0.980 5.8 113.5 19.5 258 0.147 2_updatecdl: 0.1276 0.1635 0.009 0.995 5.8 113.5 19.5 258 0.147 2_nqh: 0.1276 0.1635 0.009 0.995 5.8 113.5 19.5 258 0.147 2_sol: 0.1239 0.1533 0.009 0.995 5.8 112.6 20.9 362 n/a 2_weight: 0.1239 0.1533 0.009 0.995 5.8 112.6 20.9 362 n/a 2_xyzrec: 0.1217 0.1582 0.008 0.932 5.8 112.6 20.9 362 n/a 2_adp: 0.1205 0.1601 0.008 0.932 6.8 107.6 21.5 362 n/a 2_regHadp: 0.1208 0.1602 0.008 0.932 6.8 107.6 21.5 362 n/a 2_occ: 0.1201 0.1599 0.008 0.932 6.8 107.6 21.5 362 n/a 3_bss: 0.1194 0.1590 0.008 0.932 6.4 107.2 21.2 362 n/a 3_settarget: 0.1194 0.1590 0.008 0.932 6.4 107.2 21.2 362 n/a 3_updatecdl: 0.1194 0.1590 0.008 0.937 6.4 107.2 21.2 362 n/a 3_nqh: 0.1194 0.1590 0.008 0.937 6.4 107.2 21.2 362 n/a 3_sol: 0.1205 0.1539 0.008 0.937 6.4 107.2 21.0 394 n/a 3_weight: 0.1205 0.1539 0.008 0.937 6.4 107.2 21.0 394 n/a 3_xyzrec: 0.1189 0.1564 0.009 0.949 6.4 107.2 21.0 394 n/a 3_adp: 0.1170 0.1566 0.009 0.949 6.4 105.3 20.9 394 n/a 3_regHadp: 0.1170 0.1567 0.009 0.949 6.4 105.3 20.9 394 n/a 3_occ: 0.1163 0.1557 0.009 0.949 6.4 105.3 20.9 394 n/a 4_bss: 0.1159 0.1550 0.009 0.949 6.0 104.9 20.5 394 n/a 4_settarget: 0.1159 0.1550 0.009 0.949 6.0 104.9 20.5 394 n/a 4_updatecdl: 0.1159 0.1550 0.009 0.946 6.0 104.9 20.5 394 n/a 4_nqh: 0.1159 0.1545 0.009 0.946 6.0 104.9 20.5 394 n/a 4_sol: 0.1142 0.1509 0.009 0.946 6.0 104.9 21.1 449 n/a 4_weight: 0.1142 0.1509 0.009 0.946 6.0 104.9 21.1 449 n/a 4_xyzrec: 0.1127 0.1576 0.010 0.980 6.0 104.9 21.1 449 n/a 4_adp: 0.1115 0.1579 0.010 0.980 5.7 102.8 21.2 449 n/a 4_regHadp: 0.1115 0.1581 0.010 0.980 5.7 102.8 21.2 449 n/a 4_occ: 0.1106 0.1584 0.010 0.980 5.7 102.8 21.2 449 n/a 5_bss: 0.1104 0.1581 0.010 0.980 5.4 102.5 20.8 449 n/a 5_settarget: 0.1104 0.1581 0.010 0.980 5.4 102.5 20.8 449 n/a 5_updatecdl: 0.1104 0.1581 0.010 0.979 5.4 102.5 20.8 449 n/a 5_setrh: 0.1106 0.1581 0.010 0.979 5.4 102.5 20.8 449 n/a 5_nqh: 0.1106 0.1581 0.010 0.979 5.4 102.5 20.8 449 n/a 5_sol: 0.1101 0.1510 0.010 0.979 5.4 102.5 20.9 466 n/a 5_weight: 0.1101 0.1510 0.010 0.979 5.4 102.5 20.9 466 n/a 5_xyzrec: 0.1125 0.1524 0.010 1.065 5.4 102.5 20.9 466 n/a 5_adp: 0.1111 0.1518 0.010 1.065 5.4 102.6 21.1 466 n/a 5_regHadp: 0.1111 0.1517 0.010 1.065 5.4 102.6 21.1 466 n/a 5_occ: 0.1103 0.1513 0.010 1.065 5.4 102.6 21.1 466 n/a end: 0.1103 0.1512 0.010 1.065 5.2 102.3 20.9 466 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_8569971_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_8569971_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.4100 Refinement macro-cycles (run) : 932.5600 Write final files (write_after_run_outputs) : 20.1700 Total : 956.1400 Total CPU time: 16.33 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:22 PST -0800 (1735494082.66 s) Start R-work = 0.1614, R-free = 0.1627 Final R-work = 0.1103, R-free = 0.1512 =============================================================================== Job complete usr+sys time: 1000.33 seconds wall clock time: 17 minutes 4.49 seconds (1024.49 seconds total)