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_2514713.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Adding command-line PHIL: ------------------------- xray_data.high_resolution=2 ordered_solvent.low_resolution=4 No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 2 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2514713.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2514713.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 1 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: 1.60, per 1000 atoms: 0.47 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.57 Conformation dependent library (CDL) restraints added in 206.1 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.67 - 0.92: 565 0.92 - 1.17: 1086 1.17 - 1.42: 642 1.42 - 1.67: 817 1.67 - 1.92: 43 Bond restraints: 3153 Sorted by residual: bond pdb=" N GLY A 40 " pdb=" CA GLY A 40 " ideal model delta sigma weight residual 1.444 1.695 -0.251 1.38e-02 5.25e+03 3.31e+02 bond pdb=" C GLY A 108 " pdb=" N PRO A 109 " ideal model delta sigma weight residual 1.337 1.529 -0.193 1.11e-02 8.12e+03 3.01e+02 bond pdb=" N ASP A 49 " pdb=" CA ASP A 49 " ideal model delta sigma weight residual 1.459 1.235 0.224 1.32e-02 5.74e+03 2.88e+02 bond pdb=" C THR A 125 " pdb=" O THR A 125 " ideal model delta sigma weight residual 1.233 1.043 0.190 1.17e-02 7.31e+03 2.65e+02 bond pdb=" N ALA A 178 " pdb=" CA ALA A 178 " ideal model delta sigma weight residual 1.459 1.652 -0.193 1.21e-02 6.83e+03 2.53e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.68: 3049 4.68 - 9.35: 1933 9.35 - 14.03: 681 14.03 - 18.71: 104 18.71 - 23.38: 10 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA ALA A 179 " pdb=" C ALA A 179 " pdb=" O ALA A 179 " ideal model delta sigma weight residual 120.55 138.65 -18.10 1.06e+00 8.90e-01 2.92e+02 angle pdb=" O ALA A 111 " pdb=" C ALA A 111 " pdb=" N LEU A 112 " ideal model delta sigma weight residual 122.12 136.63 -14.51 1.06e+00 8.90e-01 1.87e+02 angle pdb=" O ALA A 61 " pdb=" C ALA A 61 " pdb=" N LYS A 62 " ideal model delta sigma weight residual 122.33 140.46 -18.13 1.34e+00 5.57e-01 1.83e+02 angle pdb=" CA ALA A 179 " pdb=" C ALA A 179 " pdb=" N GLN A 180 " ideal model delta sigma weight residual 117.30 102.08 15.22 1.16e+00 7.43e-01 1.72e+02 angle pdb=" CA ALA A 178 " pdb=" C ALA A 178 " pdb=" O ALA A 178 " ideal model delta sigma weight residual 120.55 106.79 13.76 1.06e+00 8.90e-01 1.68e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.43: 1275 16.43 - 32.87: 150 32.87 - 49.30: 40 49.30 - 65.73: 13 65.73 - 82.16: 3 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C ARG A 156 " pdb=" N ARG A 156 " pdb=" CA ARG A 156 " pdb=" CB ARG A 156 " ideal model delta harmonic sigma weight residual -122.60 -144.90 22.30 0 2.50e+00 1.60e-01 7.96e+01 dihedral pdb=" N ARG A 156 " pdb=" C ARG A 156 " pdb=" CA ARG A 156 " pdb=" CB ARG A 156 " ideal model delta harmonic sigma weight residual 122.80 144.57 -21.77 0 2.50e+00 1.60e-01 7.58e+01 dihedral pdb=" N ARG A 27 " pdb=" C ARG A 27 " pdb=" CA ARG A 27 " pdb=" CB ARG A 27 " ideal model delta harmonic sigma weight residual 122.80 143.34 -20.54 0 2.50e+00 1.60e-01 6.75e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.251: 103 0.251 - 0.500: 86 0.500 - 0.750: 42 0.750 - 0.999: 9 0.999 - 1.248: 3 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA ALA A 178 " pdb=" N ALA A 178 " pdb=" C ALA A 178 " pdb=" CB ALA A 178 " both_signs ideal model delta sigma weight residual False 2.48 3.73 -1.25 2.00e-01 2.50e+01 3.90e+01 chirality pdb=" CA ARG A 156 " pdb=" N ARG A 156 " pdb=" C ARG A 156 " pdb=" CB ARG A 156 " both_signs ideal model delta sigma weight residual False 2.51 1.32 1.19 2.00e-01 2.50e+01 3.53e+01 chirality pdb=" CA BGLU A 94 " pdb=" N BGLU A 94 " pdb=" C BGLU A 94 " pdb=" CB BGLU A 94 " both_signs ideal model delta sigma weight residual False 2.51 3.51 -1.00 2.00e-01 2.50e+01 2.50e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.095 2.00e-02 2.50e+03 6.85e-02 1.41e+02 pdb=" CG PHE A 119 " -0.147 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.075 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.041 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.092 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.011 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " -0.007 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.029 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.042 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " -0.006 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.072 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " 0.001 2.00e-02 2.50e+03 5.66e-02 9.60e+01 pdb=" CG BTYR A 67 " 0.033 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " -0.041 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " 0.023 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " -0.073 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " -0.114 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " 0.080 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " 0.062 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " 0.068 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " -0.004 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " -0.044 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " -0.071 2.00e-02 2.50e+03 5.58e-02 9.33e+01 pdb=" CG PHE A 162 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " 0.082 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " -0.049 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " -0.052 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " 0.105 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " -0.035 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " 0.049 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " 0.012 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " -0.014 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " -0.063 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.28: 782 2.28 - 2.86: 7820 2.86 - 3.44: 10665 3.44 - 4.02: 15303 4.02 - 4.60: 22068 Nonbonded interactions: 56638 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.700 2.100 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.806 2.100 nonbonded pdb=" O VAL A 8 " pdb=" H ALA A 36 " model vdw 1.822 2.450 nonbonded pdb=" HG SER A 47 " pdb="HH11 ARG A 48 " model vdw 1.833 2.100 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.839 2.100 ... (remaining 56633 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_2514713_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= 0.1832 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.415537 | | target function (ml) not normalized (work): 71721.567260 | | target function (ml) not normalized (free): 3272.223749 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3191 0.2077 7.6215 5.0171| | 2: 3.63 - 2.88 1.00 2711 122 0.2641 0.1750 4.3173 4.3408| | 3: 2.88 - 2.52 1.00 2682 148 0.2590 0.1669 4.1755 4.1848| | 4: 2.52 - 2.29 1.00 2661 139 0.2539 0.1682 3.4995 3.6298| | 5: 2.29 - 2.13 1.00 2678 122 0.2669 0.1543 3.3872 3.4729| | 6: 2.13 - 2.00 1.00 2692 117 0.2744 0.1979 3.3249 3.3961| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 17.32 0.77 0.23 1280.43| | 2: 3.63 - 2.88 2711 122 0.83 23.66 1.31 0.23 1280.43| | 3: 2.88 - 2.52 2682 148 0.73 32.62 1.29 0.23 1280.43| | 4: 2.52 - 2.29 2661 139 0.93 11.51 1.30 0.26 140.47| | 5: 2.29 - 2.13 2678 122 0.92 13.86 1.32 0.26 140.47| | 6: 2.13 - 2.00 2692 117 0.90 16.41 1.34 0.26 140.47| |alpha: min = 0.23 max = 0.26 mean = 0.25| |beta: min = 140.47 max = 1280.43 mean = 716.80| |figures of merit: min = 0.00 max = 1.00 mean = 0.87| |phase err.(work): min = 0.00 max = 89.97 mean = 19.23| |phase err.(test): min = 0.00 max = 89.38 mean = 19.46| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.082 0.251 1557 Z= 5.405 Angle : 5.461 18.127 2118 Z= 3.839 Chirality : 0.407 1.248 243 Planarity : 0.033 0.095 284 Dihedral : 13.777 82.164 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 1.08 % Allowed : 2.16 % Favored : 96.76 % Rotamer: Outliers : 1.86 % Allowed : 1.86 % Favored : 96.27 % Cbeta Deviations : 37.84 % 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: -2.79 (0.46), residues: 224 helix: -2.69 (0.38), residues: 109 sheet: -1.93 (0.70), residues: 30 loop : -0.19 (0.57), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.100 0.029 ARG A 5 TYR 0.078 0.038 TYR A 139 PHE 0.145 0.050 PHE A 119 HIS 0.079 0.041 HIS A 115 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 1785 0 Protein: 8.85 115.78 16.79 3.90 1519 0 Water: 11.36 119.30 38.03 N/A 258 0 Other: 19.04 26.29 21.71 N/A 8 0 Chain A: 8.85 119.30 19.89 N/A 1785 0 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2792 r_free= 0.1832 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.415537 | | target function (ml) not normalized (work): 71721.567260 | | target function (ml) not normalized (free): 3272.223749 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.3091 percent. r_work = 0.2923 r_free = 0.1989 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2870 0.2923 0.1989 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2870 0.2923 0.1989 n_refl.: 17050 remove outliers: r(all,work,free)=0.2159 0.2170 0.1989 n_refl.: 17045 overall B=-0.41 to atoms: r(all,work,free)=0.2131 0.2142 0.1969 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1610 0.1608 0.1654 n_refl.: 17045 remove outliers: r(all,work,free)=0.1608 0.1606 0.1654 n_refl.: 17043 ======================== 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 98.94 88 5 0.3915 399.042 361.846 0.648 1.018 0.397 11.894-9.307 99.02 97 4 0.1887 633.774 616.262 0.923 1.019 0.380 9.237-7.194 100.00 213 7 0.2187 518.363 508.852 0.942 1.018 0.350 7.162-5.571 100.00 427 22 0.2331 389.032 374.908 0.916 1.016 0.284 5.546-4.326 100.00 867 58 0.1368 534.078 528.276 0.955 1.013 0.241 4.315-3.360 100.00 1859 96 0.1292 507.914 503.725 1.017 1.008 0.201 3.356-2.611 100.00 3867 181 0.1642 333.670 329.041 1.013 0.999 0.081 2.608-2.000 99.99 8818 434 0.1646 217.496 213.547 1.037 0.983 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.4540 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1606 r_free=0.1654 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN Total number of N/Q/H flips: 1 r_work=0.1609 r_free=0.1657 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.848299 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.946998 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 0.1349 0.1624 0.0275 0.009 1.0 1.0 0.5 0.0 0 11.924 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.49 16.24 2.75 3.013 18.451 0.947 0.023 12.73 16.50 3.76 3.634 18.738 0.947 0.020 Individual atomic B min max mean iso aniso Overall: 6.12 113.89 20.02 4.08 1785 0 Protein: 6.12 113.37 17.25 4.08 1519 0 Water: 8.72 113.89 36.12 N/A 258 0 Other: 22.32 36.71 26.51 N/A 8 0 Chain A: 6.12 113.89 20.02 N/A 1785 0 Histogram: Values Number of atoms 6.12 - 16.89 1080 16.89 - 27.67 343 27.67 - 38.45 189 38.45 - 49.23 98 49.23 - 60.00 48 60.00 - 70.78 12 70.78 - 81.56 7 81.56 - 92.34 4 92.34 - 103.11 1 103.11 - 113.89 3 =========================== Idealize ADP of riding H ========================== r_work=0.1273 r_free=0.1650 r_work=0.1276 r_free=0.1657 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1276 r_free = 0.1657 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1272 r_free = 0.1652 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17043 (all), 4.74 % free)------------| | | | r_work= 0.1272 r_free= 0.1652 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.019898 | | target function (ls_wunit_k1) not normalized (work): 323.066093 | | target function (ls_wunit_k1) not normalized (free): 26.954173 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1291 0.1272 0.1652 n_refl.: 17043 re-set all scales: r(all,work,free)=0.1907 0.1906 0.1995 n_refl.: 17043 remove outliers: r(all,work,free)=0.1907 0.1906 0.1995 n_refl.: 17043 overall B=-0.40 to atoms: r(all,work,free)=0.1878 0.1876 0.1980 n_refl.: 17043 bulk-solvent and scaling: r(all,work,free)=0.1292 0.1274 0.1648 n_refl.: 17043 remove outliers: r(all,work,free)=0.1291 0.1273 0.1648 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 0.3536 304.206 283.650 0.641 1.011 0.379 11.894-9.307 99.02 97 4 0.1678 487.256 476.514 0.916 1.011 0.379 9.237-7.194 100.00 213 7 0.1829 398.527 395.584 0.955 1.011 0.341 7.162-5.571 100.00 427 22 0.1860 299.095 293.808 0.929 1.010 0.301 5.546-4.326 100.00 867 58 0.1049 410.609 408.025 0.958 1.008 0.231 4.315-3.360 100.00 1859 96 0.0931 390.493 390.053 1.017 1.005 0.191 3.356-2.611 100.00 3867 181 0.1295 256.532 255.252 1.015 1.000 0.091 2.608-2.000 99.99 8818 434 0.1344 167.215 165.734 1.025 0.991 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.4163 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1273 r_free=0.1648 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1273 r_free=0.1648 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1273 r_free=0.1648 | n_water=258 | time (s): 0.820 (total time: 0.820) Filter (dist) r_work=0.1281 r_free=0.1639 | n_water=252 | time (s): 19.520 (total time: 20.340) Filter (q & B) r_work=0.1282 r_free=0.1638 | n_water=250 | time (s): 1.790 (total time: 22.130) Compute maps r_work=0.1282 r_free=0.1638 | n_water=250 | time (s): 0.690 (total time: 22.820) Filter (map) r_work=0.1318 r_free=0.1627 | n_water=211 | time (s): 1.620 (total time: 24.440) Find peaks r_work=0.1318 r_free=0.1627 | n_water=211 | time (s): 0.500 (total time: 24.940) Add new water r_work=0.1550 r_free=0.1892 | n_water=369 | time (s): 1.720 (total time: 26.660) Refine new water occ: r_work=0.1335 r_free=0.1630 adp: r_work=0.1275 r_free=0.1616 occ: r_work=0.1280 r_free=0.1590 adp: r_work=0.1246 r_free=0.1590 occ: r_work=0.1248 r_free=0.1579 adp: r_work=0.1235 r_free=0.1578 ADP+occupancy (water only), MIN, final r_work=0.1235 r_free=0.1578 r_work=0.1235 r_free=0.1578 | n_water=369 | time (s): 25.950 (total time: 52.610) Filter (q & B) r_work=0.1237 r_free=0.1582 | n_water=363 | time (s): 1.890 (total time: 54.500) Filter (dist only) r_work=0.1237 r_free=0.1584 | n_water=362 | time (s): 29.840 (total time: 84.340) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.630982 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.968218 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 0.1206 0.1611 0.0405 0.008 0.9 2.9 0.5 0.0 0 12.315 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.06 16.11 4.05 4.181 21.125 0.968 0.018 11.93 16.27 4.34 4.191 21.374 0.968 0.018 Individual atomic B min max mean iso aniso Overall: 6.61 107.97 21.37 4.23 1889 0 Protein: 6.61 107.97 17.76 4.22 1519 0 Water: 8.80 68.16 36.26 N/A 362 0 Other: 24.17 45.40 34.48 N/A 8 0 Chain A: 6.61 107.97 19.48 N/A 1738 0 Chain S: 18.72 63.56 43.14 N/A 151 0 Histogram: Values Number of atoms 6.61 - 16.75 1015 16.75 - 26.89 394 26.89 - 37.02 215 37.02 - 47.16 156 47.16 - 57.29 74 57.29 - 67.43 24 67.43 - 77.57 4 77.57 - 87.70 5 87.70 - 97.84 0 97.84 - 107.97 2 =========================== Idealize ADP of riding H ========================== r_work=0.1193 r_free=0.1627 r_work=0.1195 r_free=0.1628 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1195 r_free = 0.1628 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1194 r_free = 0.1629 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.21 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= 0.1194 r_free= 0.1629 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.016930 | | target function (ls_wunit_k1) not normalized (work): 274.866138 | | target function (ls_wunit_k1) not normalized (free): 25.841162 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1215 0.1194 0.1629 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1807 0.1802 0.1972 n_refl.: 17042 remove outliers: r(all,work,free)=0.1807 0.1802 0.1972 n_refl.: 17042 overall B=-0.37 to atoms: r(all,work,free)=0.1781 0.1775 0.1953 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1209 0.1188 0.1617 n_refl.: 17042 remove outliers: r(all,work,free)=0.1208 0.1188 0.1617 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 0.3261 306.229 283.491 0.622 1.005 0.370 11.894-9.307 99.02 97 4 0.1463 487.256 482.296 0.917 1.005 0.354 9.237-7.194 100.00 213 7 0.1617 398.527 398.697 0.968 1.005 0.310 7.162-5.571 100.00 427 22 0.1555 299.095 295.153 0.932 1.005 0.254 5.546-4.326 100.00 867 58 0.0875 410.609 407.848 0.958 1.004 0.215 4.315-3.360 100.00 1859 96 0.0828 390.493 389.679 1.015 1.003 0.201 3.356-2.611 100.00 3867 181 0.1192 256.532 255.825 1.011 1.001 0.131 2.608-2.000 99.99 8818 434 0.1334 167.215 166.182 1.016 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.3381 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1188 r_free=0.1617 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1188 r_free=0.1617 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1188 r_free=0.1617 | n_water=362 | time (s): 0.930 (total time: 0.930) Filter (dist) r_work=0.1187 r_free=0.1620 | n_water=361 | time (s): 28.670 (total time: 29.600) Filter (q & B) r_work=0.1187 r_free=0.1620 | n_water=361 | time (s): 1.000 (total time: 30.600) Compute maps r_work=0.1187 r_free=0.1620 | n_water=361 | time (s): 0.870 (total time: 31.470) Filter (map) r_work=0.1256 r_free=0.1609 | n_water=263 | time (s): 2.260 (total time: 33.730) Find peaks r_work=0.1256 r_free=0.1609 | n_water=263 | time (s): 0.590 (total time: 34.320) Add new water r_work=0.1456 r_free=0.1828 | n_water=416 | time (s): 2.260 (total time: 36.580) Refine new water occ: r_work=0.1248 r_free=0.1584 adp: r_work=0.1241 r_free=0.1591 occ: r_work=0.1217 r_free=0.1547 adp: r_work=0.1206 r_free=0.1553 occ: r_work=0.1195 r_free=0.1529 adp: r_work=0.1185 r_free=0.1532 ADP+occupancy (water only), MIN, final r_work=0.1185 r_free=0.1532 r_work=0.1185 r_free=0.1532 | n_water=416 | time (s): 31.030 (total time: 67.610) Filter (q & B) r_work=0.1187 r_free=0.1533 | n_water=410 | time (s): 2.050 (total time: 69.660) Filter (dist only) r_work=0.1188 r_free=0.1533 | n_water=409 | time (s): 33.660 (total time: 103.320) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.984369 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.144672 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 0.1164 0.1539 0.0375 0.009 1.0 3.5 0.5 0.0 0 0.992 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.64 15.39 3.75 4.313 21.647 0.145 4.986 11.43 15.52 4.09 4.843 21.529 0.145 4.965 Individual atomic B min max mean iso aniso Overall: 6.19 105.75 21.02 4.58 1936 0 Protein: 6.19 105.75 17.03 4.57 1519 0 Water: 8.78 63.91 35.63 N/A 409 0 Other: 25.33 44.42 32.93 N/A 8 0 Chain A: 6.19 105.75 18.75 N/A 1734 0 Chain S: 16.02 63.91 40.51 N/A 202 0 Histogram: Values Number of atoms 6.19 - 16.14 1052 16.14 - 26.10 371 26.10 - 36.06 218 36.06 - 46.01 175 46.01 - 55.97 77 55.97 - 65.93 31 65.93 - 75.88 4 75.88 - 85.84 5 85.84 - 95.80 1 95.80 - 105.75 2 =========================== Idealize ADP of riding H ========================== r_work=0.1143 r_free=0.1552 r_work=0.1143 r_free=0.1553 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1143 r_free = 0.1553 target_work(ml) = 4.965 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1130 r_free = 0.1551 target_work(ml) = 4.959 | | occupancies: max = 1.00 min = 0.20 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= 0.1130 r_free= 0.1551 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.958863 | | target function (ml) not normalized (work): 80502.186534 | | target function (ml) not normalized (free): 4187.914650 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1150 0.1130 0.1551 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1655 0.1648 0.1837 n_refl.: 17041 remove outliers: r(all,work,free)=0.1655 0.1648 0.1837 n_refl.: 17041 overall B=-0.37 to atoms: r(all,work,free)=0.1629 0.1622 0.1825 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1147 0.1127 0.1550 n_refl.: 17041 remove outliers: r(all,work,free)=0.1146 0.1126 0.1550 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 0.3525 302.741 278.801 0.588 1.005 0.350 11.894-9.307 99.02 97 4 0.1619 487.256 479.844 0.911 1.007 0.330 9.237-7.194 100.00 213 7 0.1712 398.527 398.976 0.983 1.007 0.290 7.162-5.571 100.00 427 22 0.1546 299.095 294.060 0.939 1.006 0.241 5.546-4.326 100.00 867 58 0.0933 410.609 407.088 0.962 1.005 0.211 4.315-3.360 100.00 1859 96 0.0870 390.493 388.238 1.010 1.004 0.211 3.356-2.611 100.00 3867 181 0.1263 256.532 254.214 1.010 1.001 0.131 2.608-2.000 99.99 8818 434 0.1077 167.215 165.953 1.017 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.3314 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1126 r_free=0.1550 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1126 r_free=0.1550 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1126 r_free=0.1550 | n_water=409 | time (s): 0.730 (total time: 0.730) Filter (dist) r_work=0.1126 r_free=0.1550 | n_water=409 | time (s): 32.010 (total time: 32.740) Filter (q & B) r_work=0.1126 r_free=0.1550 | n_water=409 | time (s): 0.970 (total time: 33.710) Compute maps r_work=0.1126 r_free=0.1550 | n_water=409 | time (s): 0.630 (total time: 34.340) Filter (map) r_work=0.1196 r_free=0.1552 | n_water=315 | time (s): 1.500 (total time: 35.840) Find peaks r_work=0.1196 r_free=0.1552 | n_water=315 | time (s): 0.550 (total time: 36.390) Add new water r_work=0.1337 r_free=0.1657 | n_water=444 | time (s): 1.970 (total time: 38.360) Refine new water occ: r_work=0.1185 r_free=0.1503 adp: r_work=0.1177 r_free=0.1504 occ: r_work=0.1159 r_free=0.1478 adp: r_work=0.1149 r_free=0.1477 occ: r_work=0.1141 r_free=0.1460 adp: r_work=0.1133 r_free=0.1460 ADP+occupancy (water only), MIN, final r_work=0.1133 r_free=0.1460 r_work=0.1133 r_free=0.1460 | n_water=444 | time (s): 30.510 (total time: 68.870) Filter (q & B) r_work=0.1135 r_free=0.1471 | n_water=437 | time (s): 1.850 (total time: 70.720) Filter (dist only) r_work=0.1137 r_free=0.1475 | n_water=436 | time (s): 34.060 (total time: 104.780) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.952007 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.154478 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1124 0.1555 0.0431 0.010 1.0 3.5 0.5 0.0 0 0.976 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.24 15.55 4.31 4.430 21.133 0.154 4.958 11.13 15.57 4.44 4.570 21.163 0.154 4.951 Individual atomic B min max mean iso aniso Overall: 5.81 103.54 21.09 4.73 1963 0 Protein: 5.81 103.54 16.60 4.73 1519 0 Water: 8.40 64.32 36.52 N/A 436 0 Other: 24.50 42.05 31.77 N/A 8 0 Chain A: 5.81 103.54 18.28 N/A 1733 0 Chain S: 14.62 64.32 42.20 N/A 230 0 Histogram: Values Number of atoms 5.81 - 15.59 1037 15.59 - 25.36 377 25.36 - 35.13 202 35.13 - 44.90 199 44.90 - 54.68 98 54.68 - 64.45 36 64.45 - 74.22 7 74.22 - 84.00 3 84.00 - 93.77 2 93.77 - 103.54 2 =========================== Idealize ADP of riding H ========================== r_work=0.1113 r_free=0.1557 r_work=0.1113 r_free=0.1558 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1113 r_free = 0.1558 target_work(ml) = 4.951 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1104 r_free = 0.1562 target_work(ml) = 4.947 | | occupancies: max = 1.00 min = 0.19 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= 0.1104 r_free= 0.1562 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.947265 | | target function (ml) not normalized (work): 80308.949156 | | target function (ml) not normalized (free): 4183.955787 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1126 0.1104 0.1562 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1599 0.1588 0.1848 n_refl.: 17040 remove outliers: r(all,work,free)=0.1599 0.1588 0.1848 n_refl.: 17040 overall B=-0.30 to atoms: r(all,work,free)=0.1579 0.1568 0.1838 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1123 0.1101 0.1559 n_refl.: 17040 remove outliers: r(all,work,free)=0.1123 0.1101 0.1559 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 0.3622 302.741 279.357 0.566 1.002 0.328 11.894-9.307 99.02 97 4 0.1781 487.256 480.241 0.920 1.004 0.320 9.237-7.194 100.00 213 7 0.1663 398.527 401.172 0.986 1.004 0.250 7.162-5.571 100.00 427 22 0.1495 299.095 294.110 0.943 1.004 0.230 5.546-4.326 100.00 867 58 0.0926 410.609 406.832 0.962 1.004 0.195 4.315-3.360 100.00 1859 96 0.0850 390.493 388.289 1.007 1.003 0.191 3.356-2.611 100.00 3867 181 0.1234 256.532 254.186 1.005 1.001 0.151 2.608-2.000 99.99 8818 434 0.1045 167.215 166.089 1.004 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-1.0481 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1101 r_free=0.1559 After: r_work=0.1103 r_free=0.1558 ================================== NQH flips ================================== r_work=0.1103 r_free=0.1558 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1103 r_free=0.1558 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1103 r_free=0.1558 | n_water=436 | time (s): 0.630 (total time: 0.630) Filter (dist) r_work=0.1103 r_free=0.1558 | n_water=436 | time (s): 33.270 (total time: 33.900) Filter (q & B) r_work=0.1103 r_free=0.1558 | n_water=436 | time (s): 1.260 (total time: 35.160) Compute maps r_work=0.1103 r_free=0.1558 | n_water=436 | time (s): 0.880 (total time: 36.040) Filter (map) r_work=0.1181 r_free=0.1578 | n_water=326 | time (s): 2.210 (total time: 38.250) Find peaks r_work=0.1181 r_free=0.1578 | n_water=326 | time (s): 0.640 (total time: 38.890) Add new water r_work=0.1312 r_free=0.1674 | n_water=467 | time (s): 2.250 (total time: 41.140) Refine new water occ: r_work=0.1145 r_free=0.1553 adp: r_work=0.1139 r_free=0.1549 occ: r_work=0.1121 r_free=0.1536 adp: r_work=0.1113 r_free=0.1530 occ: r_work=0.1104 r_free=0.1523 adp: r_work=0.1098 r_free=0.1520 ADP+occupancy (water only), MIN, final r_work=0.1098 r_free=0.1520 r_work=0.1098 r_free=0.1520 | n_water=467 | time (s): 32.220 (total time: 73.360) Filter (q & B) r_work=0.1102 r_free=0.1532 | n_water=454 | time (s): 2.210 (total time: 75.570) Filter (dist only) r_work=0.1102 r_free=0.1531 | n_water=453 | time (s): 37.500 (total time: 113.070) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.935422 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.175681 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 0.1112 0.1541 0.0429 0.011 1.1 5.1 0.5 0.0 0 0.968 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.12 15.41 4.29 4.481 20.870 0.176 4.948 11.03 15.30 4.28 4.572 20.926 0.176 4.941 Individual atomic B min max mean iso aniso Overall: 5.25 102.07 21.00 4.95 1980 0 Protein: 5.25 102.07 16.33 4.94 1519 0 Water: 7.99 65.97 36.49 N/A 453 0 Other: 23.64 40.43 30.80 N/A 8 0 Chain A: 5.25 102.07 17.97 N/A 1733 0 Chain S: 16.64 65.97 42.25 N/A 247 0 Histogram: Values Number of atoms 5.25 - 14.93 1004 14.93 - 24.61 404 24.61 - 34.29 208 34.29 - 43.98 182 43.98 - 53.66 128 53.66 - 63.34 33 63.34 - 73.02 11 73.02 - 82.70 5 82.70 - 92.38 1 92.38 - 102.07 4 =========================== Idealize ADP of riding H ========================== r_work=0.1103 r_free=0.1530 r_work=0.1103 r_free=0.1531 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1103 r_free = 0.1531 target_work(ml) = 4.941 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1098 r_free = 0.1549 target_work(ml) = 4.941 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1098 r_free= 0.1549 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.940709 | | target function (ml) not normalized (work): 80202.535918 | | target function (ml) not normalized (free): 4177.966709 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1104 0.1403 5.4441 5.6637| | 2: 3.63 - 2.88 1.00 2711 122 0.1068 0.1555 5.217 5.3828| | 3: 2.88 - 2.52 1.00 2681 148 0.1351 0.1763 5.1381 5.2205| | 4: 2.52 - 2.29 1.00 2661 139 0.0936 0.1533 4.6371 4.9538| | 5: 2.29 - 2.13 1.00 2678 122 0.0962 0.1547 4.5927 4.927| | 6: 2.13 - 2.00 1.00 2692 117 0.1127 0.1741 4.5867 4.7729| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 0.95 9.19 1.00 0.96 6601.94| | 2: 3.63 - 2.88 2711 122 0.92 13.08 1.01 0.96 6601.94| | 3: 2.88 - 2.52 2681 148 0.87 19.33 0.99 0.96 6601.94| | 4: 2.52 - 2.29 2661 139 0.92 12.50 1.01 0.97 2211.92| | 5: 2.29 - 2.13 2678 122 0.91 14.52 1.00 0.97 2211.92| | 6: 2.13 - 2.00 2692 117 0.89 17.26 0.99 0.97 2211.92| |alpha: min = 0.96 max = 0.97 mean = 0.96| |beta: min = 2211.92 max = 6601.94 mean = 4430.05| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.72 mean = 14.27| |phase err.(test): min = 0.00 max = 88.41 mean = 13.93| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1120 0.1098 0.1549 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1576 0.1564 0.1840 n_refl.: 17040 remove outliers: r(all,work,free)=0.1576 0.1564 0.1840 n_refl.: 17040 overall B=-0.24 to atoms: r(all,work,free)=0.1562 0.1550 0.1832 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1120 0.1099 0.1550 n_refl.: 17040 remove outliers: r(all,work,free)=0.1120 0.1099 0.1550 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 0.3615 302.741 279.178 0.558 1.001 0.330 11.894-9.307 99.02 97 4 0.1673 487.256 480.258 0.925 1.002 0.330 9.237-7.194 100.00 213 7 0.1673 398.527 400.950 0.986 1.003 0.240 7.162-5.571 100.00 427 22 0.1512 299.095 294.451 0.941 1.003 0.220 5.546-4.326 100.00 867 58 0.0931 410.609 407.213 0.963 1.003 0.200 4.315-3.360 100.00 1859 96 0.0855 390.493 388.089 1.005 1.002 0.191 3.356-2.611 100.00 3867 181 0.1230 256.532 254.320 1.000 1.001 0.121 2.608-2.000 99.99 8818 434 0.1038 167.215 165.874 0.992 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.8337 ================= 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 0.1832 0.082 5.461 8.8 119.3 19.9 258 0.000 1_bss: 0.1606 0.1654 0.082 5.461 8.4 118.9 19.5 258 0.000 1_settarget: 0.1606 0.1654 0.082 5.461 8.4 118.9 19.5 258 0.000 1_nqh: 0.1609 0.1657 0.082 5.461 8.4 118.9 19.5 258 0.003 1_weight: 0.1609 0.1657 0.082 5.461 8.4 118.9 19.5 258 0.003 1_xyzrec: 0.1349 0.1624 0.009 1.004 8.4 118.9 19.5 258 0.144 1_adp: 0.1273 0.1650 0.009 1.004 6.1 113.9 20.0 258 0.144 1_regHadp: 0.1276 0.1657 0.009 1.004 6.1 113.9 20.0 258 0.144 1_occ: 0.1272 0.1652 0.009 1.004 6.1 113.9 20.0 258 0.144 2_bss: 0.1273 0.1648 0.009 1.004 5.7 113.5 19.6 258 0.144 2_settarget: 0.1273 0.1648 0.009 1.004 5.7 113.5 19.6 258 0.144 2_updatecdl: 0.1273 0.1648 0.009 1.010 5.7 113.5 19.6 258 0.144 2_nqh: 0.1273 0.1648 0.009 1.010 5.7 113.5 19.6 258 0.144 2_sol: 0.1237 0.1584 0.009 1.010 5.7 113.0 20.9 362 n/a 2_weight: 0.1237 0.1584 0.009 1.010 5.7 113.0 20.9 362 n/a 2_xyzrec: 0.1206 0.1611 0.008 0.937 5.7 113.0 20.9 362 n/a 2_adp: 0.1193 0.1627 0.008 0.937 6.6 108.0 21.4 362 n/a 2_regHadp: 0.1195 0.1628 0.008 0.937 6.6 108.0 21.4 362 n/a 2_occ: 0.1194 0.1629 0.008 0.937 6.6 108.0 21.4 362 n/a 3_bss: 0.1188 0.1617 0.008 0.937 6.2 107.6 21.0 362 n/a 3_settarget: 0.1188 0.1617 0.008 0.937 6.2 107.6 21.0 362 n/a 3_updatecdl: 0.1188 0.1617 0.008 0.942 6.2 107.6 21.0 362 n/a 3_nqh: 0.1188 0.1617 0.008 0.942 6.2 107.6 21.0 362 n/a 3_sol: 0.1188 0.1533 0.008 0.942 6.2 107.6 21.2 409 n/a 3_weight: 0.1188 0.1533 0.008 0.942 6.2 107.6 21.2 409 n/a 3_xyzrec: 0.1164 0.1539 0.009 0.979 6.2 107.6 21.2 409 n/a 3_adp: 0.1143 0.1552 0.009 0.979 6.2 105.8 21.0 409 n/a 3_regHadp: 0.1143 0.1553 0.009 0.979 6.2 105.8 21.0 409 n/a 3_occ: 0.1130 0.1551 0.009 0.979 6.2 105.8 21.0 409 n/a 4_bss: 0.1126 0.1550 0.009 0.979 5.8 105.4 20.6 409 n/a 4_settarget: 0.1126 0.1550 0.009 0.979 5.8 105.4 20.6 409 n/a 4_updatecdl: 0.1126 0.1550 0.009 0.977 5.8 105.4 20.6 409 n/a 4_nqh: 0.1126 0.1550 0.009 0.977 5.8 105.4 20.6 409 n/a 4_sol: 0.1137 0.1475 0.009 0.977 5.8 105.4 21.0 436 n/a 4_weight: 0.1137 0.1475 0.009 0.977 5.8 105.4 21.0 436 n/a 4_xyzrec: 0.1124 0.1555 0.010 0.984 5.8 105.4 21.0 436 n/a 4_adp: 0.1113 0.1557 0.010 0.984 5.8 103.5 21.1 436 n/a 4_regHadp: 0.1113 0.1558 0.010 0.984 5.8 103.5 21.1 436 n/a 4_occ: 0.1104 0.1562 0.010 0.984 5.8 103.5 21.1 436 n/a 5_bss: 0.1101 0.1559 0.010 0.984 5.5 103.2 20.8 436 n/a 5_settarget: 0.1101 0.1559 0.010 0.984 5.5 103.2 20.8 436 n/a 5_updatecdl: 0.1101 0.1559 0.010 0.984 5.5 103.2 20.8 436 n/a 5_setrh: 0.1103 0.1558 0.010 0.984 5.5 103.2 20.8 436 n/a 5_nqh: 0.1103 0.1558 0.010 0.984 5.5 103.2 20.8 436 n/a 5_sol: 0.1102 0.1531 0.010 0.984 5.5 103.2 20.9 453 n/a 5_weight: 0.1102 0.1531 0.010 0.984 5.5 103.2 20.9 453 n/a 5_xyzrec: 0.1112 0.1541 0.011 1.052 5.5 103.2 20.9 453 n/a 5_adp: 0.1103 0.1530 0.011 1.052 5.2 102.1 21.0 453 n/a 5_regHadp: 0.1103 0.1531 0.011 1.052 5.2 102.1 21.0 453 n/a 5_occ: 0.1098 0.1549 0.011 1.052 5.2 102.1 21.0 453 n/a end: 0.1099 0.1550 0.011 1.052 5.0 101.8 20.8 453 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_2514713_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_2514713_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.1700 Refinement macro-cycles (run) : 940.7600 Write final files (write_after_run_outputs) : 18.4000 Total : 962.3300 Total CPU time: 16.41 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:25 PST -0800 (1735494085.76 s) Start R-work = 0.1606, R-free = 0.1654 Final R-work = 0.1099, R-free = 0.1550 =============================================================================== Job complete usr+sys time: 1004.70 seconds wall clock time: 17 minutes 7.84 seconds (1027.84 seconds total)