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_2667343.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" 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_2667343.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2667343.pdb" } 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: 1.68, per 1000 atoms: 0.50 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: 0.51 Conformation dependent library (CDL) restraints added in 213.6 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.68 - 0.94: 716 0.94 - 1.20: 972 1.20 - 1.46: 762 1.46 - 1.72: 690 1.72 - 1.98: 13 Bond restraints: 3153 Sorted by residual: bond pdb=" C VAL A 123 " pdb=" O VAL A 123 " ideal model delta sigma weight residual 1.235 1.027 0.208 1.02e-02 9.61e+03 4.16e+02 bond pdb=" C VAL A 44 " pdb=" O VAL A 44 " ideal model delta sigma weight residual 1.237 1.458 -0.221 1.10e-02 8.26e+03 4.03e+02 bond pdb=" CA CYS A 46 " pdb=" C CYS A 46 " ideal model delta sigma weight residual 1.528 1.279 0.250 1.38e-02 5.25e+03 3.27e+02 bond pdb=" C SER A 161 " pdb=" O SER A 161 " ideal model delta sigma weight residual 1.237 1.444 -0.207 1.17e-02 7.31e+03 3.14e+02 bond pdb=" ND1 HIS A 115 " pdb=" CE1 HIS A 115 " ideal model delta sigma weight residual 1.321 1.148 0.173 1.00e-02 1.00e+04 2.99e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.14: 3450 5.14 - 10.28: 1734 10.28 - 15.42: 524 15.42 - 20.56: 62 20.56 - 25.70: 7 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA ASN A 135 " pdb=" CB ASN A 135 " pdb=" CG ASN A 135 " ideal model delta sigma weight residual 112.60 128.60 -16.00 1.00e+00 1.00e+00 2.56e+02 angle pdb=" NE ARG A 98 " pdb=" CZ ARG A 98 " pdb=" NH2 ARG A 98 " ideal model delta sigma weight residual 119.20 132.41 -13.21 9.00e-01 1.23e+00 2.15e+02 angle pdb=" CA ILE A 105 " pdb=" C ILE A 105 " pdb=" O ILE A 105 " ideal model delta sigma weight residual 120.39 106.39 14.00 1.05e+00 9.07e-01 1.78e+02 angle pdb=" O ALA A 36 " pdb=" C ALA A 36 " pdb=" N GLY A 37 " ideal model delta sigma weight residual 123.27 108.24 15.03 1.16e+00 7.43e-01 1.68e+02 angle pdb=" O ALA A 183 " pdb=" C ALA A 183 " pdb=" N PRO A 184 " ideal model delta sigma weight residual 121.32 136.11 -14.79 1.15e+00 7.56e-01 1.65e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 16.98: 1298 16.98 - 33.94: 130 33.94 - 50.91: 39 50.91 - 67.88: 10 67.88 - 84.85: 4 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" N ILE A 21 " pdb=" C ILE A 21 " pdb=" CA ILE A 21 " pdb=" CB ILE A 21 " ideal model delta harmonic sigma weight residual 123.40 144.88 -21.48 0 2.50e+00 1.60e-01 7.38e+01 dihedral pdb=" C GLU A 116 " pdb=" N GLU A 116 " pdb=" CA GLU A 116 " pdb=" CB GLU A 116 " ideal model delta harmonic sigma weight residual -122.60 -141.39 18.79 0 2.50e+00 1.60e-01 5.65e+01 dihedral pdb=" N GLU A 116 " pdb=" C GLU A 116 " pdb=" CA GLU A 116 " pdb=" CB GLU A 116 " ideal model delta harmonic sigma weight residual 122.80 141.40 -18.60 0 2.50e+00 1.60e-01 5.54e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.003 - 0.204: 80 0.204 - 0.406: 74 0.406 - 0.608: 53 0.608 - 0.809: 30 0.809 - 1.011: 6 Chirality restraints: 243 Sorted by residual: chirality pdb=" C2 ADTT A 201 " pdb=" C1 ADTT A 201 " pdb=" C3 ADTT A 201 " pdb=" O2 ADTT A 201 " both_signs ideal model delta sigma weight residual False -2.43 -1.42 -1.01 2.00e-01 2.50e+01 2.55e+01 chirality pdb=" CA GLU A 116 " pdb=" N GLU A 116 " pdb=" C GLU A 116 " pdb=" CB GLU A 116 " both_signs ideal model delta sigma weight residual False 2.51 1.56 0.95 2.00e-01 2.50e+01 2.27e+01 chirality pdb=" CA BTYR A 67 " pdb=" N BTYR A 67 " pdb=" C BTYR A 67 " pdb=" CB BTYR A 67 " both_signs ideal model delta sigma weight residual False 2.51 3.43 -0.92 2.00e-01 2.50e+01 2.13e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 138 " -0.053 2.00e-02 2.50e+03 7.44e-02 1.24e+02 pdb=" CG HIS A 138 " -0.010 2.00e-02 2.50e+03 pdb=" ND1 HIS A 138 " 0.100 2.00e-02 2.50e+03 pdb=" CD2 HIS A 138 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 HIS A 138 " -0.078 2.00e-02 2.50e+03 pdb=" NE2 HIS A 138 " 0.128 2.00e-02 2.50e+03 pdb=" HD1 HIS A 138 " 0.051 2.00e-02 2.50e+03 pdb=" HD2 HIS A 138 " -0.028 2.00e-02 2.50e+03 pdb=" HE1 HIS A 138 " -0.103 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 5 " -0.122 9.50e-02 1.11e+02 8.35e-02 1.21e+02 pdb=" NE ARG A 5 " 0.072 2.00e-02 2.50e+03 pdb=" CZ ARG A 5 " 0.075 2.00e-02 2.50e+03 pdb=" NH1 ARG A 5 " -0.109 2.00e-02 2.50e+03 pdb=" NH2 ARG A 5 " -0.040 2.00e-02 2.50e+03 pdb="HH11 ARG A 5 " -0.072 2.00e-02 2.50e+03 pdb="HH12 ARG A 5 " 0.109 2.00e-02 2.50e+03 pdb="HH21 ARG A 5 " -0.070 2.00e-02 2.50e+03 pdb="HH22 ARG A 5 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " -0.070 2.00e-02 2.50e+03 5.82e-02 1.02e+02 pdb=" CG PHE A 162 " 0.089 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " 0.067 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " -0.089 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " -0.105 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " 0.018 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " 0.019 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " -0.012 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " -0.006 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " 0.008 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " 0.047 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.35: 1255 2.35 - 2.91: 8223 2.91 - 3.47: 10470 3.47 - 4.04: 15282 4.04 - 4.60: 21441 Nonbonded interactions: 56671 Sorted by model distance: nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.786 2.450 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.798 2.450 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.821 2.450 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.839 2.100 nonbonded pdb=" HE2 HIS A 126 " pdb=" O PRO A 184 " model vdw sym.op. 1.862 2.450 x-y,-y,-z-4/3 ... (remaining 56666 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_2667343_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= 0.2792 r_free= 0.1830 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.397892 | | target function (ml) not normalized (work): 71434.966688 | | target function (ml) not normalized (free): 3263.545943 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3200 0.2184 7.5067 5.0415| | 2: 3.63 - 2.88 1.00 2711 122 0.2627 0.1773 4.3285 4.3309| | 3: 2.88 - 2.52 1.00 2682 148 0.2558 0.1603 4.1864 4.1863| | 4: 2.52 - 2.29 1.00 2661 139 0.2556 0.1531 3.5168 3.5624| | 5: 2.29 - 2.13 1.00 2678 122 0.2682 0.1497 3.3903 3.4449| | 6: 2.13 - 2.00 1.00 2692 117 0.2761 0.1909 3.2962 3.4064| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 17.76 0.77 0.23 1315.77| | 2: 3.63 - 2.88 2711 122 0.82 24.04 1.31 0.23 1315.77| | 3: 2.88 - 2.52 2682 148 0.73 33.04 1.28 0.23 1315.77| | 4: 2.52 - 2.29 2661 139 0.93 11.10 1.30 0.26 130.69| | 5: 2.29 - 2.13 2678 122 0.92 13.28 1.32 0.26 130.69| | 6: 2.13 - 2.00 2692 117 0.90 16.00 1.34 0.26 130.69| |alpha: min = 0.23 max = 0.26 mean = 0.25| |beta: min = 130.69 max = 1315.77 mean = 729.83| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 89.98 mean = 19.21| |phase err.(test): min = 0.00 max = 88.64 mean = 19.44| |-----------------------------------------------------------------------------| ----------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 : 0.084 0.250 1557 Z= 5.477 Angle : 5.405 17.557 2118 Z= 3.813 Chirality : 0.414 1.011 243 Planarity : 0.030 0.104 284 Dihedral : 13.616 84.852 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.70 % Favored : 96.76 % Rotamer: Outliers : 1.24 % Allowed : 3.11 % Favored : 95.65 % Cbeta Deviations : 36.22 % 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: -2.16 (0.48), residues: 224 helix: -2.44 (0.37), residues: 107 sheet: -0.79 (0.94), residues: 28 loop : 0.08 (0.59), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.088 0.022 ARG A 145 TYR 0.086 0.039 TYR A 141 PHE 0.092 0.051 PHE A 162 HIS 0.109 0.043 HIS A 138 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 1785 0 Protein: 8.85 115.78 16.79 3.90 1519 0 Water: 11.36 119.30 38.03 N/A 258 0 Other: 19.04 26.29 21.71 N/A 8 0 Chain A: 8.85 119.30 19.89 N/A 1785 0 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2792 r_free= 0.1830 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.397892 | | target function (ml) not normalized (work): 71434.966688 | | target function (ml) not normalized (free): 3263.545943 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.3117 percent. r_work = 0.2923 r_free = 0.1988 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2870 0.2923 0.1988 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2870 0.2923 0.1988 n_refl.: 17050 remove outliers: r(all,work,free)=0.2161 0.2172 0.1988 n_refl.: 17045 overall B=-0.41 to atoms: r(all,work,free)=0.2134 0.2144 0.1970 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1620 0.1618 0.1654 n_refl.: 17045 remove outliers: r(all,work,free)=0.1619 0.1617 0.1654 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 394.893 361.445 0.652 1.011 0.397 11.894-9.307 99.02 97 4 0.1892 633.815 614.969 0.929 1.013 0.377 9.237-7.194 100.00 213 7 0.2158 518.397 510.568 0.960 1.012 0.359 7.162-5.571 100.00 427 22 0.2368 389.057 376.002 0.922 1.011 0.283 5.546-4.326 100.00 867 58 0.1416 534.113 527.606 0.960 1.010 0.216 4.315-3.360 100.00 1859 96 0.1306 507.947 503.835 1.018 1.006 0.212 3.356-2.611 100.00 3867 181 0.1651 333.692 328.842 1.011 1.001 0.048 2.608-2.000 99.99 8818 434 0.1646 217.510 213.398 1.028 0.991 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.4540 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1617 r_free=0.1654 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1617 r_free=0.1654 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 21.846109 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.861109 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 0.1646 0.0295 0.008 1.0 1.3 0.5 0.0 0 10.923 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.51 16.46 2.95 3.013 18.452 0.861 0.023 12.79 16.66 3.87 3.617 18.690 0.861 0.021 Individual atomic B min max mean iso aniso Overall: 6.04 113.89 19.93 4.09 1785 0 Protein: 6.04 113.05 17.17 4.09 1519 0 Water: 8.96 113.89 36.01 N/A 258 0 Other: 21.77 36.99 26.21 N/A 8 0 Chain A: 6.04 113.89 19.93 N/A 1785 0 Histogram: Values Number of atoms 6.04 - 16.82 1072 16.82 - 27.61 354 27.61 - 38.39 184 38.39 - 49.18 97 49.18 - 59.96 51 59.96 - 70.75 12 70.75 - 81.54 7 81.54 - 92.32 4 92.32 - 103.11 1 103.11 - 113.89 3 =========================== Idealize ADP of riding H ========================== r_work=0.1279 r_free=0.1666 r_work=0.1282 r_free=0.1673 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1282 r_free = 0.1673 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 = 0.1667 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= 0.1667 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.020078 | | target function (ls_wunit_k1) not normalized (work): 326.004981 | | target function (ls_wunit_k1) not normalized (free): 27.414168 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1295 0.1277 0.1667 n_refl.: 17044 re-set all scales: r(all,work,free)=0.1908 0.1907 0.1980 n_refl.: 17044 remove outliers: r(all,work,free)=0.1908 0.1907 0.1980 n_refl.: 17044 overall B=-0.51 to atoms: r(all,work,free)=0.1871 0.1869 0.1960 n_refl.: 17044 bulk-solvent and scaling: r(all,work,free)=0.1293 0.1275 0.1657 n_refl.: 17044 remove outliers: r(all,work,free)=0.1291 0.1273 0.1657 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 0.3558 303.830 279.413 0.623 1.006 0.368 11.894-9.307 99.02 97 4 0.1702 488.663 477.313 0.918 1.007 0.367 9.237-7.194 100.00 213 7 0.1832 399.677 396.169 0.963 1.007 0.351 7.162-5.571 100.00 427 22 0.1843 299.958 294.400 0.933 1.006 0.302 5.546-4.326 100.00 867 58 0.1043 411.794 409.397 0.958 1.006 0.206 4.315-3.360 100.00 1859 96 0.0929 391.620 391.103 1.016 1.004 0.202 3.356-2.611 100.00 3867 181 0.1300 257.272 255.931 1.009 1.001 0.091 2.608-2.000 99.99 8818 434 0.1343 167.697 166.393 1.012 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9583 b_overall=-1.1630 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1273 r_free=0.1657 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1273 r_free=0.1657 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1273 r_free=0.1657 | n_water=258 | time (s): 0.730 (total time: 0.730) Filter (dist) r_work=0.1281 r_free=0.1643 | n_water=253 | time (s): 20.050 (total time: 20.780) Filter (q & B) r_work=0.1281 r_free=0.1642 | n_water=251 | time (s): 2.080 (total time: 22.860) Compute maps r_work=0.1281 r_free=0.1642 | n_water=251 | time (s): 0.640 (total time: 23.500) Filter (map) r_work=0.1315 r_free=0.1626 | n_water=212 | time (s): 1.930 (total time: 25.430) Find peaks r_work=0.1315 r_free=0.1626 | n_water=212 | time (s): 0.630 (total time: 26.060) Add new water r_work=0.1534 r_free=0.1854 | n_water=370 | time (s): 1.870 (total time: 27.930) Refine new water occ: r_work=0.1331 r_free=0.1571 adp: r_work=0.1274 r_free=0.1567 occ: r_work=0.1281 r_free=0.1541 adp: r_work=0.1248 r_free=0.1547 occ: r_work=0.1250 r_free=0.1550 adp: r_work=0.1237 r_free=0.1546 ADP+occupancy (water only), MIN, final r_work=0.1237 r_free=0.1546 r_work=0.1237 r_free=0.1546 | n_water=370 | time (s): 12.270 (total time: 40.200) Filter (q & B) r_work=0.1238 r_free=0.1553 | n_water=361 | time (s): 1.530 (total time: 41.730) Filter (dist only) r_work=0.1238 r_free=0.1554 | n_water=360 | time (s): 27.650 (total time: 69.380) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.948794 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.948614 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 0.1589 0.0377 0.008 0.9 2.6 0.5 0.0 0 11.974 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.12 15.89 3.77 4.175 20.863 0.949 0.018 11.98 16.14 4.15 4.202 21.097 0.949 0.018 Individual atomic B min max mean iso aniso Overall: 6.42 107.53 21.06 4.17 1887 0 Protein: 6.42 107.53 17.48 4.17 1519 0 Water: 8.68 65.66 35.91 N/A 360 0 Other: 23.92 44.00 34.42 N/A 8 0 Chain A: 6.42 107.53 19.24 N/A 1739 0 Chain S: 17.38 63.78 42.53 N/A 148 0 Histogram: Values Number of atoms 6.42 - 16.53 1024 16.53 - 26.64 384 26.64 - 36.75 223 36.75 - 46.87 151 46.87 - 56.98 70 56.98 - 67.09 25 67.09 - 77.20 3 77.20 - 87.31 5 87.31 - 97.42 0 97.42 - 107.53 2 =========================== Idealize ADP of riding H ========================== r_work=0.1198 r_free=0.1614 r_work=0.1200 r_free=0.1615 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1615 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 = 0.1197 r_free = 0.1621 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.28 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= 0.1197 r_free= 0.1621 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.017191 | | target function (ls_wunit_k1) not normalized (work): 279.088893 | | target function (ls_wunit_k1) not normalized (free): 25.022634 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1218 0.1197 0.1621 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1745 0.1735 0.1970 n_refl.: 17042 remove outliers: r(all,work,free)=0.1745 0.1735 0.1970 n_refl.: 17042 overall B=-0.38 to atoms: r(all,work,free)=0.1722 0.1711 0.1954 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1214 0.1193 0.1616 n_refl.: 17042 remove outliers: r(all,work,free)=0.1213 0.1192 0.1616 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 0.3271 300.664 284.408 0.604 1.007 0.350 11.894-9.307 99.02 97 4 0.1478 488.663 486.790 0.917 1.008 0.350 9.237-7.194 100.00 213 7 0.1713 399.677 400.322 0.976 1.007 0.310 7.162-5.571 100.00 427 22 0.1551 299.958 296.688 0.936 1.007 0.271 5.546-4.326 100.00 867 58 0.0874 411.794 409.381 0.961 1.005 0.211 4.315-3.360 100.00 1859 96 0.0834 391.620 390.879 1.013 1.004 0.201 3.356-2.611 100.00 3867 181 0.1209 257.272 256.519 1.010 1.000 0.058 2.608-2.000 99.99 8818 434 0.1328 167.697 166.590 1.013 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-1.1650 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1192 r_free=0.1616 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1192 r_free=0.1616 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1192 r_free=0.1616 | n_water=360 | time (s): 0.860 (total time: 0.860) Filter (dist) r_work=0.1192 r_free=0.1618 | n_water=359 | time (s): 29.030 (total time: 29.890) Filter (q & B) r_work=0.1192 r_free=0.1618 | n_water=359 | time (s): 0.890 (total time: 30.780) Compute maps r_work=0.1192 r_free=0.1618 | n_water=359 | time (s): 0.680 (total time: 31.460) Filter (map) r_work=0.1254 r_free=0.1637 | n_water=263 | time (s): 1.770 (total time: 33.230) Find peaks r_work=0.1254 r_free=0.1637 | n_water=263 | time (s): 0.520 (total time: 33.750) Add new water r_work=0.1437 r_free=0.1838 | n_water=412 | time (s): 1.520 (total time: 35.270) Refine new water occ: r_work=0.1246 r_free=0.1597 adp: r_work=0.1238 r_free=0.1602 occ: r_work=0.1220 r_free=0.1565 adp: r_work=0.1210 r_free=0.1569 occ: r_work=0.1203 r_free=0.1548 adp: r_work=0.1193 r_free=0.1549 ADP+occupancy (water only), MIN, final r_work=0.1193 r_free=0.1549 r_work=0.1193 r_free=0.1549 | n_water=412 | time (s): 31.690 (total time: 66.960) Filter (q & B) r_work=0.1197 r_free=0.1559 | n_water=400 | time (s): 2.370 (total time: 69.330) Filter (dist only) r_work=0.1197 r_free=0.1559 | n_water=400 | time (s): 30.720 (total time: 100.050) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.880601 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.158489 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 0.1173 0.1572 0.0400 0.009 1.0 3.5 0.5 0.0 0 0.940 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.73 15.72 4.00 4.256 21.233 0.158 4.999 11.52 15.85 4.32 4.789 21.153 0.158 4.980 Individual atomic B min max mean iso aniso Overall: 6.08 105.65 20.63 4.63 1927 0 Protein: 6.08 105.65 16.78 4.62 1519 0 Water: 8.80 62.42 34.93 N/A 400 0 Other: 26.93 47.37 35.75 N/A 8 0 Chain A: 6.08 105.65 18.53 N/A 1735 0 Chain S: 15.41 62.42 39.55 N/A 192 0 Histogram: Values Number of atoms 6.08 - 16.04 1057 16.04 - 25.99 354 25.99 - 35.95 236 35.95 - 45.91 170 45.91 - 55.86 75 55.86 - 65.82 23 65.82 - 75.78 5 75.78 - 85.73 3 85.73 - 95.69 2 95.69 - 105.65 2 =========================== Idealize ADP of riding H ========================== r_work=0.1152 r_free=0.1585 r_work=0.1152 r_free=0.1586 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1152 r_free = 0.1586 target_work(ml) = 4.980 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1145 r_free = 0.1591 target_work(ml) = 4.975 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1145 r_free= 0.1591 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.974522 | | target function (ml) not normalized (work): 80756.395143 | | target function (ml) not normalized (free): 4198.573178 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1166 0.1145 0.1591 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1671 0.1660 0.1914 n_refl.: 17041 remove outliers: r(all,work,free)=0.1671 0.1660 0.1914 n_refl.: 17041 overall B=-0.38 to atoms: r(all,work,free)=0.1645 0.1633 0.1903 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1164 0.1142 0.1588 n_refl.: 17041 remove outliers: r(all,work,free)=0.1164 0.1142 0.1588 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 0.3487 300.664 276.634 0.572 1.007 0.340 11.894-9.307 99.02 97 4 0.1731 488.663 482.646 0.909 1.008 0.340 9.237-7.194 100.00 213 7 0.1782 399.677 399.024 0.990 1.007 0.275 7.162-5.571 100.00 427 22 0.1646 299.958 294.277 0.939 1.007 0.238 5.546-4.326 100.00 867 58 0.0947 411.794 408.592 0.967 1.006 0.226 4.315-3.360 100.00 1859 96 0.0897 391.620 389.390 1.011 1.004 0.211 3.356-2.611 100.00 3867 181 0.1282 257.272 254.992 1.010 1.001 0.111 2.608-2.000 99.99 8818 434 0.1074 167.697 166.348 1.014 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-1.1885 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1142 r_free=0.1588 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1142 r_free=0.1588 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1142 r_free=0.1588 | n_water=400 | time (s): 0.760 (total time: 0.760) Filter (dist) r_work=0.1142 r_free=0.1588 | n_water=400 | time (s): 28.810 (total time: 29.570) Filter (q & B) r_work=0.1142 r_free=0.1588 | n_water=400 | time (s): 1.140 (total time: 30.710) Compute maps r_work=0.1142 r_free=0.1588 | n_water=400 | time (s): 0.820 (total time: 31.530) Filter (map) r_work=0.1195 r_free=0.1631 | n_water=317 | time (s): 1.800 (total time: 33.330) Find peaks r_work=0.1195 r_free=0.1631 | n_water=317 | time (s): 0.570 (total time: 33.900) Add new water r_work=0.1345 r_free=0.1755 | n_water=459 | time (s): 2.090 (total time: 35.990) Refine new water occ: r_work=0.1181 r_free=0.1552 adp: r_work=0.1172 r_free=0.1559 occ: r_work=0.1157 r_free=0.1533 adp: r_work=0.1147 r_free=0.1537 occ: r_work=0.1140 r_free=0.1526 adp: r_work=0.1131 r_free=0.1526 ADP+occupancy (water only), MIN, final r_work=0.1131 r_free=0.1526 r_work=0.1131 r_free=0.1526 | n_water=459 | time (s): 33.610 (total time: 69.600) Filter (q & B) r_work=0.1134 r_free=0.1535 | n_water=452 | time (s): 2.270 (total time: 71.870) Filter (dist only) r_work=0.1134 r_free=0.1535 | n_water=452 | time (s): 33.360 (total time: 105.230) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.131944 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.138804 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 0.1113 0.1581 0.0468 0.010 1.0 5.8 0.5 0.0 0 1.066 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.13 15.81 4.68 4.441 20.947 0.139 4.961 11.02 15.77 4.75 4.554 20.978 0.139 4.952 Individual atomic B min max mean iso aniso Overall: 5.98 101.83 20.95 4.63 1979 0 Protein: 5.98 101.83 16.40 4.63 1519 0 Water: 8.74 62.46 36.01 N/A 452 0 Other: 26.42 44.47 34.22 N/A 8 0 Chain A: 5.98 101.83 18.09 N/A 1734 0 Chain S: 16.26 62.46 41.20 N/A 245 0 Histogram: Values Number of atoms 5.98 - 15.57 1040 15.57 - 25.15 367 25.15 - 34.74 229 34.74 - 44.32 183 44.32 - 53.91 98 53.91 - 63.49 48 63.49 - 73.08 6 73.08 - 82.66 3 82.66 - 92.25 3 92.25 - 101.83 2 =========================== Idealize ADP of riding H ========================== r_work=0.1102 r_free=0.1577 r_work=0.1102 r_free=0.1578 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1102 r_free = 0.1578 target_work(ml) = 4.952 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1093 r_free = 0.1582 target_work(ml) = 4.949 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1093 r_free= 0.1582 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.948991 | | target function (ml) not normalized (work): 80341.917697 | | target function (ml) not normalized (free): 4193.346318 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1116 0.1093 0.1582 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1588 0.1574 0.1883 n_refl.: 17041 remove outliers: r(all,work,free)=0.1588 0.1574 0.1883 n_refl.: 17041 overall B=-0.27 to atoms: r(all,work,free)=0.1571 0.1556 0.1874 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1114 0.1091 0.1579 n_refl.: 17041 remove outliers: r(all,work,free)=0.1113 0.1090 0.1579 n_refl.: 17040 ======================== 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 93.75 85 5 0.3569 297.094 276.622 0.556 1.001 0.340 11.894-9.307 99.02 97 4 0.1725 488.663 482.941 0.916 1.002 0.330 9.237-7.194 100.00 213 7 0.1668 399.677 400.707 0.994 1.002 0.240 7.162-5.571 100.00 427 22 0.1544 299.958 294.859 0.944 1.002 0.220 5.546-4.326 100.00 867 58 0.0878 411.794 409.062 0.967 1.002 0.205 4.315-3.360 100.00 1859 96 0.0846 391.620 389.852 1.007 1.002 0.201 3.356-2.611 100.00 3867 181 0.1229 257.272 254.878 1.002 1.001 0.141 2.608-2.000 99.99 8818 434 0.1032 167.697 166.483 0.997 1.000 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-0.9344 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1090 r_free=0.1579 After: r_work=0.1092 r_free=0.1577 ================================== NQH flips ================================== r_work=0.1092 r_free=0.1577 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1092 r_free=0.1577 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1092 r_free=0.1577 | n_water=452 | time (s): 0.680 (total time: 0.680) Filter (dist) r_work=0.1098 r_free=0.1572 | n_water=450 | time (s): 35.850 (total time: 36.530) Filter (q & B) r_work=0.1098 r_free=0.1571 | n_water=447 | time (s): 2.170 (total time: 38.700) Compute maps r_work=0.1098 r_free=0.1571 | n_water=447 | time (s): 0.750 (total time: 39.450) Filter (map) r_work=0.1172 r_free=0.1567 | n_water=339 | time (s): 1.600 (total time: 41.050) Find peaks r_work=0.1172 r_free=0.1567 | n_water=339 | time (s): 0.440 (total time: 41.490) Add new water r_work=0.1300 r_free=0.1676 | n_water=470 | time (s): 1.630 (total time: 43.120) Refine new water occ: r_work=0.1143 r_free=0.1530 adp: r_work=0.1134 r_free=0.1535 occ: r_work=0.1122 r_free=0.1518 adp: r_work=0.1112 r_free=0.1522 occ: r_work=0.1106 r_free=0.1511 adp: r_work=0.1099 r_free=0.1515 ADP+occupancy (water only), MIN, final r_work=0.1099 r_free=0.1515 r_work=0.1099 r_free=0.1515 | n_water=470 | time (s): 23.300 (total time: 66.420) Filter (q & B) r_work=0.1101 r_free=0.1521 | n_water=462 | time (s): 1.670 (total time: 68.090) Filter (dist only) r_work=0.1101 r_free=0.1521 | n_water=462 | time (s): 34.780 (total time: 102.870) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.988075 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.150310 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 0.1117 0.1540 0.0422 0.010 1.1 4.5 0.5 0.0 0 0.994 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.17 15.40 4.22 4.406 20.731 0.150 4.945 11.08 15.33 4.25 4.519 20.796 0.150 4.936 Individual atomic B min max mean iso aniso Overall: 5.23 99.09 20.91 4.82 1989 0 Protein: 5.23 99.09 16.17 4.81 1519 0 Water: 8.43 64.19 36.30 N/A 462 0 Other: 25.85 43.30 33.33 N/A 8 0 Chain A: 5.23 99.09 17.82 N/A 1733 0 Chain S: 19.43 64.19 41.83 N/A 256 0 Histogram: Values Number of atoms 5.23 - 14.62 985 14.62 - 24.01 401 24.01 - 33.39 217 33.39 - 42.78 189 42.78 - 52.16 132 52.16 - 61.55 42 61.55 - 70.94 14 70.94 - 80.32 2 80.32 - 89.71 3 89.71 - 99.09 4 =========================== Idealize ADP of riding H ========================== r_work=0.1108 r_free=0.1533 r_work=0.1108 r_free=0.1533 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1108 r_free = 0.1533 target_work(ml) = 4.936 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1102 r_free = 0.1530 target_work(ml) = 4.933 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1102 r_free= 0.1530 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 4.933319 | | target function (ml) not normalized (work): 80082.567303 | | target function (ml) not normalized (free): 4168.768507 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.64 1.00 2810 159 0.1116 0.1459 5.453 5.6649| | 2: 3.63 - 2.88 1.00 2711 122 0.1088 0.1578 5.2284 5.394| | 3: 2.88 - 2.52 1.00 2681 148 0.1365 0.1597 5.1402 5.1906| | 4: 2.52 - 2.29 1.00 2661 139 0.0920 0.1490 4.6152 4.9438| | 5: 2.29 - 2.13 1.00 2678 122 0.0944 0.1480 4.5675 4.8968| | 6: 2.13 - 2.00 1.00 2692 117 0.1112 0.1709 4.566 4.7621| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2810 159 0.94 9.33 1.00 0.96 6589.16| | 2: 3.63 - 2.88 2711 122 0.92 13.04 1.01 0.96 6589.16| | 3: 2.88 - 2.52 2681 148 0.87 19.31 0.99 0.96 6589.16| | 4: 2.52 - 2.29 2661 139 0.93 11.85 1.01 0.98 2074.96| | 5: 2.29 - 2.13 2678 122 0.92 13.91 1.00 0.98 2074.96| | 6: 2.13 - 2.00 2692 117 0.90 16.56 0.99 0.98 2074.96| |alpha: min = 0.96 max = 0.98 mean = 0.97| |beta: min = 2074.96 max = 6589.16 mean = 4355.84| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.92 mean = 13.97| |phase err.(test): min = 0.00 max = 88.71 mean = 13.48| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1123 0.1102 0.1530 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1573 0.1560 0.1852 n_refl.: 17040 remove outliers: r(all,work,free)=0.1573 0.1560 0.1852 n_refl.: 17040 overall B=-0.24 to atoms: r(all,work,free)=0.1559 0.1546 0.1843 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1123 0.1102 0.1528 n_refl.: 17040 remove outliers: r(all,work,free)=0.1123 0.1102 0.1528 n_refl.: 17040 ======================== 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 93.75 85 5 0.3612 297.094 274.682 0.538 1.005 0.324 11.894-9.307 99.02 97 4 0.1804 488.663 481.893 0.914 1.006 0.320 9.237-7.194 100.00 213 7 0.1726 399.677 400.183 0.992 1.006 0.240 7.162-5.571 100.00 427 22 0.1512 299.958 294.544 0.937 1.005 0.214 5.546-4.326 100.00 867 58 0.0920 411.794 408.698 0.965 1.004 0.208 4.315-3.360 100.00 1859 96 0.0879 391.620 389.701 1.003 1.003 0.191 3.356-2.611 100.00 3867 181 0.1237 257.272 254.933 1.000 1.000 0.141 2.608-2.000 99.99 8818 434 0.1028 167.697 166.397 0.995 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.8237 ================= 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 : 0.2792 0.1830 0.084 5.405 8.8 119.3 19.9 258 0.000 1_bss: 0.1617 0.1654 0.084 5.405 8.4 118.9 19.5 258 0.000 1_settarget: 0.1617 0.1654 0.084 5.405 8.4 118.9 19.5 258 0.000 1_nqh: 0.1617 0.1654 0.084 5.405 8.4 118.9 19.5 258 0.000 1_weight: 0.1617 0.1654 0.084 5.405 8.4 118.9 19.5 258 0.000 1_xyzrec: 0.1351 0.1646 0.008 0.963 8.4 118.9 19.5 258 0.148 1_adp: 0.1279 0.1666 0.008 0.963 6.0 113.9 19.9 258 0.148 1_regHadp: 0.1282 0.1673 0.008 0.963 6.0 113.9 19.9 258 0.148 1_occ: 0.1277 0.1667 0.008 0.963 6.0 113.9 19.9 258 0.148 2_bss: 0.1273 0.1657 0.008 0.963 5.5 113.4 19.4 258 0.148 2_settarget: 0.1273 0.1657 0.008 0.963 5.5 113.4 19.4 258 0.148 2_updatecdl: 0.1273 0.1657 0.008 0.976 5.5 113.4 19.4 258 0.148 2_nqh: 0.1273 0.1657 0.008 0.976 5.5 113.4 19.4 258 0.148 2_sol: 0.1238 0.1554 0.008 0.976 5.5 112.5 20.6 360 n/a 2_weight: 0.1238 0.1554 0.008 0.976 5.5 112.5 20.6 360 n/a 2_xyzrec: 0.1212 0.1589 0.008 0.914 5.5 112.5 20.6 360 n/a 2_adp: 0.1198 0.1614 0.008 0.914 6.4 107.5 21.1 360 n/a 2_regHadp: 0.1200 0.1615 0.008 0.914 6.4 107.5 21.1 360 n/a 2_occ: 0.1197 0.1621 0.008 0.914 6.4 107.5 21.1 360 n/a 3_bss: 0.1192 0.1616 0.008 0.914 6.0 107.2 20.7 360 n/a 3_settarget: 0.1192 0.1616 0.008 0.914 6.0 107.2 20.7 360 n/a 3_updatecdl: 0.1192 0.1616 0.008 0.911 6.0 107.2 20.7 360 n/a 3_nqh: 0.1192 0.1616 0.008 0.911 6.0 107.2 20.7 360 n/a 3_sol: 0.1197 0.1559 0.008 0.911 6.0 107.2 20.8 400 n/a 3_weight: 0.1197 0.1559 0.008 0.911 6.0 107.2 20.8 400 n/a 3_xyzrec: 0.1173 0.1572 0.009 0.968 6.0 107.2 20.8 400 n/a 3_adp: 0.1152 0.1585 0.009 0.968 6.1 105.6 20.6 400 n/a 3_regHadp: 0.1152 0.1586 0.009 0.968 6.1 105.6 20.6 400 n/a 3_occ: 0.1145 0.1591 0.009 0.968 6.1 105.6 20.6 400 n/a 4_bss: 0.1142 0.1588 0.009 0.968 5.7 105.3 20.2 400 n/a 4_settarget: 0.1142 0.1588 0.009 0.968 5.7 105.3 20.2 400 n/a 4_updatecdl: 0.1142 0.1588 0.009 0.969 5.7 105.3 20.2 400 n/a 4_nqh: 0.1142 0.1588 0.009 0.969 5.7 105.3 20.2 400 n/a 4_sol: 0.1134 0.1535 0.009 0.969 5.7 105.3 20.9 452 n/a 4_weight: 0.1134 0.1535 0.009 0.969 5.7 105.3 20.9 452 n/a 4_xyzrec: 0.1113 0.1581 0.010 1.002 5.7 105.3 20.9 452 n/a 4_adp: 0.1102 0.1577 0.010 1.002 6.0 101.8 21.0 452 n/a 4_regHadp: 0.1102 0.1578 0.010 1.002 6.0 101.8 21.0 452 n/a 4_occ: 0.1093 0.1582 0.010 1.002 6.0 101.8 21.0 452 n/a 5_bss: 0.1090 0.1579 0.010 1.002 5.7 101.6 20.7 452 n/a 5_settarget: 0.1090 0.1579 0.010 1.002 5.7 101.6 20.7 452 n/a 5_updatecdl: 0.1090 0.1579 0.010 1.002 5.7 101.6 20.7 452 n/a 5_setrh: 0.1092 0.1577 0.010 1.002 5.7 101.6 20.7 452 n/a 5_nqh: 0.1092 0.1577 0.010 1.002 5.7 101.6 20.7 452 n/a 5_sol: 0.1101 0.1521 0.010 1.002 5.7 101.6 20.8 462 n/a 5_weight: 0.1101 0.1521 0.010 1.002 5.7 101.6 20.8 462 n/a 5_xyzrec: 0.1117 0.1540 0.010 1.101 5.7 101.6 20.8 462 n/a 5_adp: 0.1108 0.1533 0.010 1.101 5.2 99.1 20.9 462 n/a 5_regHadp: 0.1108 0.1533 0.010 1.101 5.2 99.1 20.9 462 n/a 5_occ: 0.1102 0.1530 0.010 1.101 5.2 99.1 20.9 462 n/a end: 0.1102 0.1528 0.010 1.101 5.0 98.9 20.7 462 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_2667343_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_2667343_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.3200 Refinement macro-cycles (run) : 901.2400 Write final files (write_after_run_outputs) : 20.2800 Total : 924.8400 Total CPU time: 15.78 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:40:47 PST -0800 (1735494047.37 s) Start R-work = 0.1617, R-free = 0.1654 Final R-work = 0.1102, R-free = 0.1528 =============================================================================== Job complete usr+sys time: 970.09 seconds wall clock time: 16 minutes 32.54 seconds (992.54 seconds total)