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_3975290.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" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 2 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3975290.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3975290.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 =============================================================================== 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: 1.16, per 1000 atoms: 0.34 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: 0.38 Conformation dependent library (CDL) restraints added in 130.2 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.51 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: 703 0.94 - 1.20: 1000 1.20 - 1.46: 743 1.46 - 1.73: 696 1.73 - 1.99: 11 Bond restraints: 3153 Sorted by residual: bond pdb=" N LYS A 89 " pdb=" CA LYS A 89 " ideal model delta sigma weight residual 1.459 1.700 -0.241 1.23e-02 6.61e+03 3.83e+02 bond pdb=" CA BLYS A 132 " pdb=" C BLYS A 132 " ideal model delta sigma weight residual 1.524 1.753 -0.229 1.26e-02 6.30e+03 3.30e+02 bond pdb=" N BGLU A 64 " pdb=" CA BGLU A 64 " ideal model delta sigma weight residual 1.456 1.669 -0.213 1.18e-02 7.18e+03 3.26e+02 bond pdb=" N ARG A 28 " pdb=" CA ARG A 28 " ideal model delta sigma weight residual 1.458 1.224 0.233 1.30e-02 5.92e+03 3.22e+02 bond pdb=" C ILE A 168 " pdb=" O ILE A 168 " ideal model delta sigma weight residual 1.237 1.437 -0.201 1.13e-02 7.83e+03 3.15e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.84: 3221 4.84 - 9.68: 1828 9.68 - 14.52: 613 14.52 - 19.36: 100 19.36 - 24.20: 15 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O ALA A 103 " pdb=" C ALA A 103 " pdb=" N ALA A 104 " ideal model delta sigma weight residual 123.27 144.05 -20.78 1.16e+00 7.43e-01 3.21e+02 angle pdb=" O GLU A 59 " pdb=" C GLU A 59 " pdb=" N ASP A 60 " ideal model delta sigma weight residual 122.12 140.18 -18.06 1.06e+00 8.90e-01 2.90e+02 angle pdb=" C GLY A 40 " pdb=" N ALYS A 41 " pdb=" CA ALYS A 41 " ideal model delta sigma weight residual 120.31 140.41 -20.10 1.52e+00 4.33e-01 1.75e+02 angle pdb=" O GLY A 75 " pdb=" C GLY A 75 " pdb=" N AASN A 76 " ideal model delta sigma weight residual 122.70 105.88 16.82 1.30e+00 5.92e-01 1.67e+02 angle pdb=" O GLY A 157 " pdb=" C GLY A 157 " pdb=" N PRO A 158 " ideal model delta sigma weight residual 121.77 109.05 12.72 1.00e+00 1.00e+00 1.62e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 15.68: 1278 15.68 - 31.35: 133 31.35 - 47.02: 44 47.02 - 62.69: 22 62.69 - 78.37: 4 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C ARG A 98 " pdb=" N ARG A 98 " pdb=" CA ARG A 98 " pdb=" CB ARG A 98 " ideal model delta harmonic sigma weight residual -122.60 -141.12 18.52 0 2.50e+00 1.60e-01 5.49e+01 dihedral pdb=" C ILE A 105 " pdb=" N ILE A 105 " pdb=" CA ILE A 105 " pdb=" CB ILE A 105 " ideal model delta harmonic sigma weight residual -122.00 -140.49 18.49 0 2.50e+00 1.60e-01 5.47e+01 dihedral pdb=" N BLEU A 153 " pdb=" C BLEU A 153 " pdb=" CA BLEU A 153 " pdb=" CB BLEU A 153 " ideal model delta harmonic sigma weight residual 122.80 105.45 17.35 0 2.50e+00 1.60e-01 4.82e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.240: 116 0.240 - 0.479: 67 0.479 - 0.718: 46 0.718 - 0.956: 13 0.956 - 1.195: 1 Chirality restraints: 243 Sorted by residual: chirality pdb=" CB VAL A 20 " pdb=" CA VAL A 20 " pdb=" CG1 VAL A 20 " pdb=" CG2 VAL A 20 " both_signs ideal model delta sigma weight residual False -2.63 -1.43 -1.20 2.00e-01 2.50e+01 3.57e+01 chirality pdb=" CA LYS A 89 " pdb=" N LYS A 89 " pdb=" C LYS A 89 " pdb=" CB LYS A 89 " both_signs ideal model delta sigma weight residual False 2.51 3.46 -0.95 2.00e-01 2.50e+01 2.25e+01 chirality pdb=" CA PRO A 127 " pdb=" N PRO A 127 " pdb=" C PRO A 127 " pdb=" CB PRO A 127 " both_signs ideal model delta sigma weight residual False 2.72 1.82 0.90 2.00e-01 2.50e+01 2.03e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 5 " -0.026 9.50e-02 1.11e+02 6.31e-02 8.80e+01 pdb=" NE ARG A 5 " -0.064 2.00e-02 2.50e+03 pdb=" CZ ARG A 5 " 0.023 2.00e-02 2.50e+03 pdb=" NH1 ARG A 5 " -0.033 2.00e-02 2.50e+03 pdb=" NH2 ARG A 5 " 0.132 2.00e-02 2.50e+03 pdb="HH11 ARG A 5 " 0.076 2.00e-02 2.50e+03 pdb="HH12 ARG A 5 " -0.057 2.00e-02 2.50e+03 pdb="HH21 ARG A 5 " -0.030 2.00e-02 2.50e+03 pdb="HH22 ARG A 5 " -0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " 0.043 2.00e-02 2.50e+03 5.24e-02 8.23e+01 pdb=" CG BTYR A 67 " -0.038 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " -0.091 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " -0.028 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " 0.086 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " 0.052 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " 0.077 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " -0.057 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " 0.015 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " -0.012 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " -0.026 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 156 " -0.148 9.50e-02 1.11e+02 7.69e-02 8.11e+01 pdb=" NE ARG A 156 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG A 156 " -0.088 2.00e-02 2.50e+03 pdb=" NH1 ARG A 156 " -0.033 2.00e-02 2.50e+03 pdb=" NH2 ARG A 156 " -0.045 2.00e-02 2.50e+03 pdb="HH11 ARG A 156 " 0.033 2.00e-02 2.50e+03 pdb="HH12 ARG A 156 " 0.071 2.00e-02 2.50e+03 pdb="HH21 ARG A 156 " 0.109 2.00e-02 2.50e+03 pdb="HH22 ARG A 156 " -0.050 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.32: 1049 2.32 - 2.89: 8078 2.89 - 3.46: 10513 3.46 - 4.03: 15254 4.03 - 4.60: 21801 Nonbonded interactions: 56695 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.750 2.100 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.762 2.450 nonbonded pdb="HH21 ARG A 145 " pdb=" OE2 GLU A 163 " model vdw 1.782 2.450 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.784 2.450 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.819 2.450 ... (remaining 56690 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_3975290_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= 0.2793 r_free= 0.1861 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.405705 | | target function (ml) not normalized (work): 71561.863074 | | target function (ml) not normalized (free): 3279.622229 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3181 0.2161 7.5236 5.0382| | 2: 3.63 - 2.88 1.00 2711 122 0.2642 0.1615 4.3289 4.3101| | 3: 2.88 - 2.52 1.00 2682 148 0.2559 0.1772 4.1798 4.1963| | 4: 2.52 - 2.29 1.00 2661 139 0.2577 0.1640 3.5227 3.5829| | 5: 2.29 - 2.13 1.00 2678 122 0.2673 0.1595 3.3973 3.4901| | 6: 2.13 - 2.00 1.00 2692 117 0.2777 0.2091 3.3192 3.4859| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 17.49 0.77 0.23 1296.07| | 2: 3.63 - 2.88 2711 122 0.83 23.84 1.31 0.23 1296.07| | 3: 2.88 - 2.52 2682 148 0.73 32.94 1.28 0.23 1296.07| | 4: 2.52 - 2.29 2661 139 0.93 11.67 1.30 0.26 142.41| | 5: 2.29 - 2.13 2678 122 0.91 14.15 1.32 0.26 142.41| | 6: 2.13 - 2.00 2692 117 0.90 16.77 1.34 0.26 142.41| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 142.41 max = 1296.07 mean = 725.67| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 89.94 mean = 19.48| |phase err.(test): min = 0.00 max = 88.28 mean = 19.52| |-----------------------------------------------------------------------------| ----------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= 5.583 Angle : 5.396 20.784 2118 Z= 3.828 Chirality : 0.384 1.195 243 Planarity : 0.030 0.116 284 Dihedral : 13.889 78.366 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 1.08 % Allowed : 1.08 % Favored : 97.84 % Rotamer: Outliers : 2.48 % Allowed : 1.24 % Favored : 96.27 % 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: -2.76 (0.44), residues: 224 helix: -2.90 (0.32), residues: 102 sheet: -2.04 (0.75), residues: 30 loop : -0.04 (0.55), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.067 0.016 ARG A 145 TYR 0.082 0.035 TYR A 139 PHE 0.087 0.030 PHE A 164 HIS 0.050 0.028 HIS A 126 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 1785 0 Protein: 8.85 115.78 16.79 3.90 1519 0 Water: 11.36 119.30 38.03 N/A 258 0 Other: 19.04 26.29 21.71 N/A 8 0 Chain A: 8.85 119.30 19.89 N/A 1785 0 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2793 r_free= 0.1861 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.405705 | | target function (ml) not normalized (work): 71561.863074 | | target function (ml) not normalized (free): 3279.622229 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.2772 percent. r_work = 0.2921 r_free = 0.2024 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2869 0.2921 0.2024 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2869 0.2921 0.2024 n_refl.: 17050 remove outliers: r(all,work,free)=0.2164 0.2174 0.2024 n_refl.: 17045 overall B=-0.44 to atoms: r(all,work,free)=0.2135 0.2144 0.2004 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1620 0.1616 0.1700 n_refl.: 17045 remove outliers: r(all,work,free)=0.1619 0.1615 0.1700 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 0.4039 395.171 373.579 0.678 1.005 0.397 11.894-9.307 99.02 97 4 0.1857 634.262 616.649 0.937 1.006 0.380 9.237-7.194 100.00 213 7 0.2184 518.762 510.047 0.968 1.006 0.361 7.162-5.571 100.00 427 22 0.2344 389.332 375.109 0.930 1.006 0.321 5.546-4.326 100.00 867 58 0.1355 534.490 530.321 0.967 1.005 0.210 4.315-3.360 100.00 1859 96 0.1311 508.305 504.148 1.019 1.004 0.192 3.356-2.611 100.00 3867 181 0.1635 333.927 329.030 1.015 1.001 0.071 2.608-2.000 99.99 8818 434 0.1667 217.663 213.713 1.029 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.5719 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1615 r_free=0.1700 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1615 r_free=0.1700 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.324664 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.915989 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1352 0.1630 0.0278 0.009 1.0 1.6 0.5 0.0 0 11.662 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.52 16.30 2.78 3.013 18.419 0.916 0.023 12.78 16.49 3.71 3.665 18.724 0.916 0.021 Individual atomic B min max mean iso aniso Overall: 6.38 113.86 20.02 4.09 1785 0 Protein: 6.38 112.89 17.27 4.09 1519 0 Water: 8.92 113.86 36.03 N/A 258 0 Other: 21.81 36.85 26.50 N/A 8 0 Chain A: 6.38 113.86 20.02 N/A 1785 0 Histogram: Values Number of atoms 6.38 - 17.13 1093 17.13 - 27.87 334 27.87 - 38.62 185 38.62 - 49.37 98 49.37 - 60.12 48 60.12 - 70.87 13 70.87 - 81.61 6 81.61 - 92.36 4 92.36 - 103.11 1 103.11 - 113.86 3 =========================== Idealize ADP of riding H ========================== r_work=0.1278 r_free=0.1649 r_work=0.1281 r_free=0.1656 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1281 r_free = 0.1656 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 = 0.1646 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.26 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= 0.1646 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.020080 | | target function (ls_wunit_k1) not normalized (work): 326.045080 | | target function (ls_wunit_k1) not normalized (free): 26.802669 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1294 0.1277 0.1646 n_refl.: 17044 re-set all scales: r(all,work,free)=0.1918 0.1917 0.1988 n_refl.: 17044 remove outliers: r(all,work,free)=0.1918 0.1917 0.1988 n_refl.: 17044 overall B=-0.41 to atoms: r(all,work,free)=0.1888 0.1886 0.1971 n_refl.: 17044 bulk-solvent and scaling: r(all,work,free)=0.1293 0.1276 0.1638 n_refl.: 17044 remove outliers: r(all,work,free)=0.1292 0.1275 0.1638 n_refl.: 17042 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3520 303.892 280.673 0.630 1.009 0.370 11.894-9.307 99.02 97 4 0.1691 488.762 478.096 0.917 1.010 0.364 9.237-7.194 100.00 213 7 0.1809 399.758 397.510 0.962 1.009 0.341 7.162-5.571 100.00 427 22 0.1847 300.019 294.954 0.931 1.008 0.301 5.546-4.326 100.00 867 58 0.1043 411.878 409.553 0.959 1.007 0.205 4.315-3.360 100.00 1859 96 0.0933 391.700 391.173 1.018 1.004 0.191 3.356-2.611 100.00 3867 181 0.1292 257.324 256.087 1.017 1.000 0.091 2.608-2.000 99.99 8818 434 0.1352 167.731 166.274 1.026 0.992 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.4520 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1275 r_free=0.1638 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1275 r_free=0.1638 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1275 r_free=0.1638 | n_water=258 | time (s): 0.750 (total time: 0.750) Filter (dist) r_work=0.1283 r_free=0.1632 | n_water=252 | time (s): 20.570 (total time: 21.320) Filter (q & B) r_work=0.1283 r_free=0.1632 | n_water=250 | time (s): 1.470 (total time: 22.790) Compute maps r_work=0.1283 r_free=0.1632 | n_water=250 | time (s): 0.700 (total time: 23.490) Filter (map) r_work=0.1321 r_free=0.1616 | n_water=210 | time (s): 2.140 (total time: 25.630) Find peaks r_work=0.1321 r_free=0.1616 | n_water=210 | time (s): 0.620 (total time: 26.250) Add new water r_work=0.1531 r_free=0.1851 | n_water=363 | time (s): 1.830 (total time: 28.080) Refine new water occ: r_work=0.1334 r_free=0.1560 adp: r_work=0.1275 r_free=0.1569 occ: r_work=0.1281 r_free=0.1531 adp: r_work=0.1249 r_free=0.1545 occ: r_work=0.1251 r_free=0.1528 adp: r_work=0.1240 r_free=0.1531 ADP+occupancy (water only), MIN, final r_work=0.1240 r_free=0.1531 r_work=0.1240 r_free=0.1531 | n_water=363 | time (s): 16.500 (total time: 44.580) Filter (q & B) r_work=0.1242 r_free=0.1534 | n_water=355 | time (s): 1.440 (total time: 46.020) Filter (dist only) r_work=0.1242 r_free=0.1537 | n_water=354 | time (s): 27.830 (total time: 73.850) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.262720 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.034406 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 0.1216 0.1596 0.0380 0.009 0.9 1.9 0.5 0.0 0 12.631 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.16 15.96 3.80 4.184 21.047 1.034 0.018 11.99 16.12 4.13 4.187 21.283 1.034 0.018 Individual atomic B min max mean iso aniso Overall: 6.55 107.49 21.20 4.23 1881 0 Protein: 6.55 107.49 17.68 4.22 1519 0 Water: 8.77 65.73 36.02 N/A 354 0 Other: 24.80 43.58 33.21 N/A 8 0 Chain A: 6.55 107.49 19.39 N/A 1737 0 Chain S: 19.91 64.38 42.98 N/A 144 0 Histogram: Values Number of atoms 6.55 - 16.64 1017 16.64 - 26.74 377 26.74 - 36.83 223 36.83 - 46.92 159 46.92 - 57.02 68 57.02 - 67.11 27 67.11 - 77.21 3 77.21 - 87.30 5 87.30 - 97.39 0 97.39 - 107.49 2 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1612 r_work=0.1200 r_free=0.1610 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1610 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 = 0.1613 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.24 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= 0.1613 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.017161 | | target function (ls_wunit_k1) not normalized (work): 278.616888 | | target function (ls_wunit_k1) not normalized (free): 24.410457 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1217 0.1197 0.1613 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1766 0.1760 0.1932 n_refl.: 17042 remove outliers: r(all,work,free)=0.1766 0.1760 0.1932 n_refl.: 17042 overall B=-0.40 to atoms: r(all,work,free)=0.1741 0.1734 0.1916 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1212 0.1192 0.1609 n_refl.: 17042 remove outliers: r(all,work,free)=0.1211 0.1191 0.1609 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 0.3274 300.725 282.201 0.606 1.002 0.350 11.894-9.307 99.02 97 4 0.1497 488.762 486.047 0.919 1.003 0.344 9.237-7.194 100.00 213 7 0.1714 399.758 398.290 0.973 1.003 0.320 7.162-5.571 100.00 427 22 0.1559 300.019 295.630 0.935 1.003 0.244 5.546-4.326 100.00 867 58 0.0894 411.878 408.179 0.961 1.003 0.221 4.315-3.360 100.00 1859 96 0.0827 391.700 390.425 1.018 1.003 0.201 3.356-2.611 100.00 3867 181 0.1201 257.324 256.470 1.013 1.002 0.121 2.608-2.000 99.99 8818 434 0.1327 167.731 167.126 1.017 1.000 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.4217 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1191 r_free=0.1609 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 97 ASN B Total number of N/Q/H flips: 2 r_work=0.1192 r_free=0.1614 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1192 r_free=0.1614 | n_water=354 | time (s): 0.680 (total time: 0.680) Filter (dist) r_work=0.1193 r_free=0.1616 | n_water=353 | time (s): 28.510 (total time: 29.190) Filter (q & B) r_work=0.1193 r_free=0.1616 | n_water=353 | time (s): 0.940 (total time: 30.130) Compute maps r_work=0.1193 r_free=0.1616 | n_water=353 | time (s): 0.540 (total time: 30.670) Filter (map) r_work=0.1248 r_free=0.1626 | n_water=266 | time (s): 1.400 (total time: 32.070) Find peaks r_work=0.1248 r_free=0.1626 | n_water=266 | time (s): 0.550 (total time: 32.620) Add new water r_work=0.1423 r_free=0.1804 | n_water=407 | time (s): 1.560 (total time: 34.180) Refine new water occ: r_work=0.1238 r_free=0.1576 adp: r_work=0.1230 r_free=0.1581 occ: r_work=0.1215 r_free=0.1547 adp: r_work=0.1204 r_free=0.1554 occ: r_work=0.1199 r_free=0.1528 adp: r_work=0.1190 r_free=0.1532 ADP+occupancy (water only), MIN, final r_work=0.1190 r_free=0.1532 r_work=0.1190 r_free=0.1532 | n_water=407 | time (s): 34.810 (total time: 68.990) Filter (q & B) r_work=0.1193 r_free=0.1537 | n_water=398 | time (s): 1.970 (total time: 70.960) Filter (dist only) r_work=0.1193 r_free=0.1535 | n_water=397 | time (s): 32.030 (total time: 102.990) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.834469 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.173459 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 0.1171 0.1555 0.0384 0.009 1.0 3.8 0.5 0.0 0 0.917 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.71 15.55 3.84 4.304 21.389 0.173 4.998 11.52 15.67 4.15 4.890 21.338 0.173 4.978 Individual atomic B min max mean iso aniso Overall: 6.13 104.82 20.78 4.75 1924 0 Protein: 6.13 104.82 16.96 4.74 1519 0 Water: 8.88 64.69 35.14 N/A 397 0 Other: 26.10 45.93 33.67 N/A 8 0 Chain A: 6.13 104.82 18.76 N/A 1737 0 Chain S: 14.88 64.69 39.55 N/A 187 0 Histogram: Values Number of atoms 6.13 - 16.00 1056 16.00 - 25.87 354 25.87 - 35.74 217 35.74 - 45.61 178 45.61 - 55.48 79 55.48 - 65.34 27 65.34 - 75.21 5 75.21 - 85.08 3 85.08 - 94.95 3 94.95 - 104.82 2 =========================== Idealize ADP of riding H ========================== r_work=0.1152 r_free=0.1567 r_work=0.1153 r_free=0.1571 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1153 r_free = 0.1571 target_work(ml) = 4.979 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1152 r_free = 0.1578 target_work(ml) = 4.977 | | occupancies: max = 1.00 min = 0.24 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= 0.1152 r_free= 0.1578 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.977069 | | target function (ml) not normalized (work): 80797.744029 | | target function (ml) not normalized (free): 4201.363443 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1173 0.1152 0.1578 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1680 0.1672 0.1878 n_refl.: 17041 remove outliers: r(all,work,free)=0.1680 0.1672 0.1878 n_refl.: 17041 overall B=-0.37 to atoms: r(all,work,free)=0.1655 0.1646 0.1864 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1172 0.1151 0.1575 n_refl.: 17041 remove outliers: r(all,work,free)=0.1171 0.1150 0.1575 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 0.3586 297.154 277.083 0.562 1.005 0.340 11.894-9.307 99.02 97 4 0.1786 488.762 482.763 0.910 1.006 0.337 9.237-7.194 100.00 213 7 0.1801 399.758 398.450 0.976 1.006 0.310 7.162-5.571 100.00 427 22 0.1630 300.019 295.286 0.940 1.006 0.241 5.546-4.326 100.00 867 58 0.0935 411.878 407.966 0.962 1.005 0.209 4.315-3.360 100.00 1859 96 0.0902 391.700 389.301 1.011 1.003 0.195 3.356-2.611 100.00 3867 181 0.1286 257.324 254.938 1.013 1.000 0.152 2.608-2.000 99.99 8818 434 0.1092 167.731 166.271 1.016 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.3114 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1150 r_free=0.1575 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1150 r_free=0.1575 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1150 r_free=0.1575 | n_water=397 | time (s): 0.700 (total time: 0.700) Filter (dist) r_work=0.1150 r_free=0.1577 | n_water=396 | time (s): 33.870 (total time: 34.570) Filter (q & B) r_work=0.1150 r_free=0.1577 | n_water=396 | time (s): 1.060 (total time: 35.630) Compute maps r_work=0.1150 r_free=0.1577 | n_water=396 | time (s): 0.620 (total time: 36.250) Filter (map) r_work=0.1197 r_free=0.1577 | n_water=319 | time (s): 1.610 (total time: 37.860) Find peaks r_work=0.1197 r_free=0.1577 | n_water=319 | time (s): 0.450 (total time: 38.310) Add new water r_work=0.1338 r_free=0.1700 | n_water=454 | time (s): 1.640 (total time: 39.950) Refine new water occ: r_work=0.1177 r_free=0.1545 adp: r_work=0.1171 r_free=0.1547 occ: r_work=0.1154 r_free=0.1533 adp: r_work=0.1146 r_free=0.1533 occ: r_work=0.1140 r_free=0.1526 adp: r_work=0.1132 r_free=0.1528 ADP+occupancy (water only), MIN, final r_work=0.1132 r_free=0.1528 r_work=0.1132 r_free=0.1528 | n_water=454 | time (s): 21.690 (total time: 61.640) Filter (q & B) r_work=0.1136 r_free=0.1536 | n_water=444 | time (s): 1.880 (total time: 63.520) Filter (dist only) r_work=0.1139 r_free=0.1536 | n_water=443 | time (s): 35.480 (total time: 99.000) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.918931 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.165507 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 0.1581 0.0454 0.009 1.0 4.5 0.5 0.0 0 0.959 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.27 15.81 4.54 4.526 21.098 0.166 4.966 11.17 15.86 4.69 4.662 21.100 0.166 4.962 Individual atomic B min max mean iso aniso Overall: 5.40 102.51 20.98 4.83 1970 0 Protein: 5.40 102.51 16.53 4.82 1519 0 Water: 7.10 65.81 36.06 N/A 443 0 Other: 23.71 44.38 31.06 N/A 8 0 Chain A: 5.40 102.51 18.26 N/A 1736 0 Chain S: 13.15 65.81 41.15 N/A 234 0 Histogram: Values Number of atoms 5.40 - 15.12 998 15.12 - 24.83 401 24.83 - 34.54 217 34.54 - 44.25 200 44.25 - 53.96 99 53.96 - 63.67 40 63.67 - 73.38 7 73.38 - 83.09 3 83.09 - 92.80 3 92.80 - 102.51 2 =========================== Idealize ADP of riding H ========================== r_work=0.1117 r_free=0.1586 r_work=0.1117 r_free=0.1586 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1117 r_free = 0.1586 target_work(ml) = 4.963 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1111 r_free = 0.1587 target_work(ml) = 4.962 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1111 r_free= 0.1587 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ml) (work): 4.961601 | | target function (ml) not normalized (work): 80541.663141 | | target function (ml) not normalized (free): 4201.984809 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1134 0.1111 0.1587 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1602 0.1589 0.1883 n_refl.: 17040 remove outliers: r(all,work,free)=0.1602 0.1589 0.1883 n_refl.: 17040 overall B=-0.30 to atoms: r(all,work,free)=0.1582 0.1570 0.1873 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1132 0.1109 0.1585 n_refl.: 17040 remove outliers: r(all,work,free)=0.1132 0.1109 0.1585 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 0.3717 297.154 275.712 0.546 1.000 0.316 11.894-9.307 99.02 97 4 0.1791 488.762 480.139 0.919 1.002 0.307 9.237-7.194 100.00 213 7 0.1723 399.758 401.564 0.986 1.002 0.250 7.162-5.571 100.00 427 22 0.1537 300.019 294.035 0.946 1.002 0.240 5.546-4.326 100.00 867 58 0.0928 411.878 408.264 0.966 1.002 0.211 4.315-3.360 100.00 1859 96 0.0876 391.700 389.255 1.009 1.002 0.211 3.356-2.611 100.00 3867 181 0.1253 257.324 255.012 1.005 1.002 0.141 2.608-2.000 99.99 8818 434 0.1031 167.731 166.549 1.001 1.000 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-1.0388 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1109 r_free=0.1585 After: r_work=0.1111 r_free=0.1585 ================================== NQH flips ================================== r_work=0.1111 r_free=0.1585 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1111 r_free=0.1585 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1111 r_free=0.1585 | n_water=443 | time (s): 0.770 (total time: 0.770) Filter (dist) r_work=0.1111 r_free=0.1585 | n_water=443 | time (s): 34.830 (total time: 35.600) Filter (q & B) r_work=0.1111 r_free=0.1585 | n_water=443 | time (s): 1.010 (total time: 36.610) Compute maps r_work=0.1111 r_free=0.1585 | n_water=443 | time (s): 0.830 (total time: 37.440) Filter (map) r_work=0.1185 r_free=0.1572 | n_water=338 | time (s): 2.220 (total time: 39.660) Find peaks r_work=0.1185 r_free=0.1572 | n_water=338 | time (s): 0.440 (total time: 40.100) Add new water r_work=0.1316 r_free=0.1685 | n_water=471 | time (s): 1.700 (total time: 41.800) Refine new water occ: r_work=0.1155 r_free=0.1554 adp: r_work=0.1148 r_free=0.1561 occ: r_work=0.1133 r_free=0.1539 adp: r_work=0.1125 r_free=0.1543 occ: r_work=0.1118 r_free=0.1526 adp: r_work=0.1112 r_free=0.1531 ADP+occupancy (water only), MIN, final r_work=0.1112 r_free=0.1531 r_work=0.1112 r_free=0.1531 | n_water=471 | time (s): 25.640 (total time: 67.440) Filter (q & B) r_work=0.1114 r_free=0.1530 | n_water=464 | time (s): 2.170 (total time: 69.610) Filter (dist only) r_work=0.1114 r_free=0.1530 | n_water=464 | time (s): 36.630 (total time: 106.240) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.005509 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.154365 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 0.1133 0.1567 0.0434 0.010 1.1 6.1 0.5 0.0 0 1.003 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.33 15.67 4.34 4.533 20.801 0.154 4.965 11.22 15.49 4.27 4.603 20.847 0.154 4.952 Individual atomic B min max mean iso aniso Overall: 5.03 100.84 20.89 4.88 1991 0 Protein: 5.03 100.84 16.21 4.87 1519 0 Water: 6.29 66.07 36.07 N/A 464 0 Other: 22.37 39.28 28.84 N/A 8 0 Chain A: 5.03 100.84 17.89 N/A 1735 0 Chain S: 13.80 66.07 41.22 N/A 256 0 Histogram: Values Number of atoms 5.03 - 14.61 981 14.61 - 24.19 412 24.19 - 33.78 213 33.78 - 43.36 208 43.36 - 52.94 118 52.94 - 62.52 41 62.52 - 72.10 9 72.10 - 81.68 2 81.68 - 91.26 4 91.26 - 100.84 3 =========================== Idealize ADP of riding H ========================== r_work=0.1122 r_free=0.1549 r_work=0.1122 r_free=0.1548 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1122 r_free = 0.1548 target_work(ml) = 4.951 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1117 r_free = 0.1551 target_work(ml) = 4.949 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1117 r_free= 0.1551 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.948513 | | target function (ml) not normalized (work): 80329.209541 | | target function (ml) not normalized (free): 4179.185386 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1130 0.1466 5.4626 5.6793| | 2: 3.63 - 2.88 1.00 2711 122 0.1112 0.1522 5.2402 5.371| | 3: 2.88 - 2.52 1.00 2681 148 0.1369 0.1762 5.1525 5.2468| | 4: 2.52 - 2.29 1.00 2661 139 0.0930 0.1492 4.634 4.9579| | 5: 2.29 - 2.13 1.00 2678 122 0.0965 0.1504 4.5899 4.8951| | 6: 2.13 - 2.00 1.00 2692 117 0.1128 0.1710 4.5825 4.7696| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 9.38 1.00 0.96 6801.39| | 2: 3.63 - 2.88 2711 122 0.92 13.30 1.01 0.96 6801.39| | 3: 2.88 - 2.52 2681 148 0.87 19.54 0.99 0.96 6801.39| | 4: 2.52 - 2.29 2661 139 0.93 12.33 1.01 0.97 2182.26| | 5: 2.29 - 2.13 2678 122 0.91 14.39 1.00 0.97 2182.26| | 6: 2.13 - 2.00 2692 117 0.89 17.12 0.99 0.97 2182.26| |alpha: min = 0.96 max = 0.97 mean = 0.96| |beta: min = 2182.26 max = 6801.39 mean = 4516.16| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.96 mean = 14.31| |phase err.(test): min = 0.00 max = 87.37 mean = 14.04| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1138 0.1117 0.1551 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1589 0.1578 0.1843 n_refl.: 17040 remove outliers: r(all,work,free)=0.1589 0.1578 0.1843 n_refl.: 17040 overall B=-0.23 to atoms: r(all,work,free)=0.1575 0.1564 0.1835 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1139 0.1118 0.1551 n_refl.: 17040 remove outliers: r(all,work,free)=0.1139 0.1118 0.1551 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 0.3545 297.154 278.769 0.539 1.004 0.314 11.894-9.307 99.02 97 4 0.1793 488.762 481.551 0.916 1.005 0.303 9.237-7.194 100.00 213 7 0.1745 399.758 402.770 0.984 1.005 0.240 7.162-5.571 100.00 427 22 0.1555 300.019 294.570 0.936 1.005 0.222 5.546-4.326 100.00 867 58 0.0952 411.878 408.192 0.963 1.004 0.198 4.315-3.360 100.00 1859 96 0.0888 391.700 389.705 1.002 1.003 0.184 3.356-2.611 100.00 3867 181 0.1255 257.324 254.908 1.002 1.001 0.141 2.608-2.000 99.99 8818 434 0.1041 167.731 166.385 0.993 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.8056 ================= 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 : 0.2793 0.1861 0.084 5.396 8.8 119.3 19.9 258 0.000 1_bss: 0.1615 0.1700 0.084 5.396 8.4 118.9 19.4 258 0.000 1_settarget: 0.1615 0.1700 0.084 5.396 8.4 118.9 19.4 258 0.000 1_nqh: 0.1615 0.1700 0.084 5.396 8.4 118.9 19.4 258 0.000 1_weight: 0.1615 0.1700 0.084 5.396 8.4 118.9 19.4 258 0.000 1_xyzrec: 0.1352 0.1630 0.009 0.978 8.4 118.9 19.4 258 0.145 1_adp: 0.1278 0.1649 0.009 0.978 6.4 113.9 20.0 258 0.145 1_regHadp: 0.1281 0.1656 0.009 0.978 6.4 113.9 20.0 258 0.145 1_occ: 0.1277 0.1646 0.009 0.978 6.4 113.9 20.0 258 0.145 2_bss: 0.1275 0.1638 0.009 0.978 6.0 113.5 19.6 258 0.145 2_settarget: 0.1275 0.1638 0.009 0.978 6.0 113.5 19.6 258 0.145 2_updatecdl: 0.1275 0.1638 0.009 0.993 6.0 113.5 19.6 258 0.145 2_nqh: 0.1275 0.1638 0.009 0.993 6.0 113.5 19.6 258 0.145 2_sol: 0.1242 0.1537 0.009 0.993 6.0 112.5 20.8 354 n/a 2_weight: 0.1242 0.1537 0.009 0.993 6.0 112.5 20.8 354 n/a 2_xyzrec: 0.1216 0.1596 0.009 0.948 6.0 112.5 20.8 354 n/a 2_adp: 0.1199 0.1612 0.009 0.948 6.5 107.5 21.2 354 n/a 2_regHadp: 0.1200 0.1610 0.009 0.948 6.5 107.5 21.2 354 n/a 2_occ: 0.1197 0.1613 0.009 0.948 6.5 107.5 21.2 354 n/a 3_bss: 0.1191 0.1609 0.009 0.948 6.2 107.1 20.8 354 n/a 3_settarget: 0.1191 0.1609 0.009 0.948 6.2 107.1 20.8 354 n/a 3_updatecdl: 0.1191 0.1609 0.009 0.947 6.2 107.1 20.8 354 n/a 3_nqh: 0.1192 0.1614 0.009 0.947 6.2 107.1 20.8 354 n/a 3_sol: 0.1193 0.1535 0.009 0.947 6.2 107.1 20.9 397 n/a 3_weight: 0.1193 0.1535 0.009 0.947 6.2 107.1 20.9 397 n/a 3_xyzrec: 0.1171 0.1555 0.009 0.958 6.2 107.1 20.9 397 n/a 3_adp: 0.1152 0.1567 0.009 0.958 6.1 104.8 20.8 397 n/a 3_regHadp: 0.1153 0.1571 0.009 0.958 6.1 104.8 20.8 397 n/a 3_occ: 0.1152 0.1578 0.009 0.958 6.1 104.8 20.8 397 n/a 4_bss: 0.1150 0.1575 0.009 0.958 5.8 104.5 20.4 397 n/a 4_settarget: 0.1150 0.1575 0.009 0.958 5.8 104.5 20.4 397 n/a 4_updatecdl: 0.1150 0.1575 0.009 0.957 5.8 104.5 20.4 397 n/a 4_nqh: 0.1150 0.1575 0.009 0.957 5.8 104.5 20.4 397 n/a 4_sol: 0.1139 0.1536 0.009 0.957 5.8 104.5 21.0 443 n/a 4_weight: 0.1139 0.1536 0.009 0.957 5.8 104.5 21.0 443 n/a 4_xyzrec: 0.1127 0.1581 0.009 0.961 5.8 104.5 21.0 443 n/a 4_adp: 0.1117 0.1586 0.009 0.961 5.4 102.5 21.0 443 n/a 4_regHadp: 0.1117 0.1586 0.009 0.961 5.4 102.5 21.0 443 n/a 4_occ: 0.1111 0.1587 0.009 0.961 5.4 102.5 21.0 443 n/a 5_bss: 0.1109 0.1585 0.009 0.961 5.1 102.2 20.7 443 n/a 5_settarget: 0.1109 0.1585 0.009 0.961 5.1 102.2 20.7 443 n/a 5_updatecdl: 0.1109 0.1585 0.009 0.962 5.1 102.2 20.7 443 n/a 5_setrh: 0.1111 0.1585 0.009 0.962 5.1 102.2 20.7 443 n/a 5_nqh: 0.1111 0.1585 0.009 0.962 5.1 102.2 20.7 443 n/a 5_sol: 0.1114 0.1530 0.009 0.962 5.1 102.2 20.8 464 n/a 5_weight: 0.1114 0.1530 0.009 0.962 5.1 102.2 20.8 464 n/a 5_xyzrec: 0.1133 0.1567 0.010 1.064 5.1 102.2 20.8 464 n/a 5_adp: 0.1122 0.1549 0.010 1.064 5.0 100.8 20.9 464 n/a 5_regHadp: 0.1122 0.1548 0.010 1.064 5.0 100.8 20.9 464 n/a 5_occ: 0.1117 0.1551 0.010 1.064 5.0 100.8 20.9 464 n/a end: 0.1118 0.1551 0.010 1.064 4.8 100.6 20.7 464 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_3975290_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_3975290_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.2900 Refinement macro-cycles (run) : 901.4000 Write final files (write_after_run_outputs) : 19.2600 Total : 923.9500 Total CPU time: 15.78 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:40:47 PST -0800 (1735494047.54 s) Start R-work = 0.1615, R-free = 0.1700 Final R-work = 0.1118, R-free = 0.1551 =============================================================================== Job complete usr+sys time: 971.27 seconds wall clock time: 16 minutes 33.64 seconds (993.64 seconds total)