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_2655235.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Adding command-line PHIL: ------------------------- xray_data.high_resolution=2 ordered_solvent.low_resolution=4 No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 2 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2655235.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2655235.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 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: 1.23, per 1000 atoms: 0.36 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: 0.30 Conformation dependent library (CDL) restraints added in 186.7 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.90: 478 0.90 - 1.15: 1138 1.15 - 1.40: 568 1.40 - 1.64: 894 1.64 - 1.89: 75 Bond restraints: 3153 Sorted by residual: bond pdb=" CA ILE A 91 " pdb=" CB ILE A 91 " ideal model delta sigma weight residual 1.540 1.301 0.239 1.11e-02 8.12e+03 4.63e+02 bond pdb=" NE ARG A 27 " pdb=" CZ ARG A 27 " ideal model delta sigma weight residual 1.326 1.093 0.233 1.10e-02 8.26e+03 4.47e+02 bond pdb=" ND1 HIS A 126 " pdb=" CE1 HIS A 126 " ideal model delta sigma weight residual 1.321 1.111 0.210 1.00e-02 1.00e+04 4.40e+02 bond pdb=" CA ALA A 167 " pdb=" C ALA A 167 " ideal model delta sigma weight residual 1.523 1.260 0.263 1.30e-02 5.92e+03 4.11e+02 bond pdb=" C ILE A 52 " pdb=" O ILE A 52 " ideal model delta sigma weight residual 1.237 1.422 -0.186 1.07e-02 8.73e+03 3.01e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.17: 2865 4.17 - 8.34: 1869 8.34 - 12.51: 804 12.51 - 16.68: 215 16.68 - 20.85: 24 Bond angle restraints: 5777 Sorted by residual: angle pdb=" OE1AGLN A 80 " pdb=" CD AGLN A 80 " pdb=" NE2AGLN A 80 " ideal model delta sigma weight residual 122.60 139.16 -16.56 1.00e+00 1.00e+00 2.74e+02 angle pdb=" O GLY A 40 " pdb=" C GLY A 40 " pdb=" N BLYS A 41 " ideal model delta sigma weight residual 123.06 109.64 13.42 9.50e-01 1.11e+00 1.99e+02 angle pdb=" O LYS A 182 " pdb=" C LYS A 182 " pdb=" N ALA A 183 " ideal model delta sigma weight residual 122.15 106.60 15.55 1.14e+00 7.69e-01 1.86e+02 angle pdb=" O VAL A 35 " pdb=" C VAL A 35 " pdb=" N ALA A 36 " ideal model delta sigma weight residual 122.62 107.57 15.05 1.17e+00 7.31e-01 1.66e+02 angle pdb=" O SER A 142 " pdb=" C SER A 142 " pdb=" N GLU A 143 " ideal model delta sigma weight residual 123.27 138.96 -15.69 1.22e+00 6.72e-01 1.65e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.02 - 17.91: 1322 17.91 - 35.80: 109 35.80 - 53.69: 34 53.69 - 71.58: 14 71.58 - 89.48: 2 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C ILE A 21 " pdb=" N ILE A 21 " pdb=" CA ILE A 21 " pdb=" CB ILE A 21 " ideal model delta harmonic sigma weight residual -122.00 -142.55 20.55 0 2.50e+00 1.60e-01 6.76e+01 dihedral pdb=" C BLYS A 99 " pdb=" N BLYS A 99 " pdb=" CA BLYS A 99 " pdb=" CB BLYS A 99 " ideal model delta harmonic sigma weight residual -122.60 -142.64 20.04 0 2.50e+00 1.60e-01 6.43e+01 dihedral pdb=" N ILE A 21 " pdb=" C ILE A 21 " pdb=" CA ILE A 21 " pdb=" CB ILE A 21 " ideal model delta harmonic sigma weight residual 123.40 141.68 -18.28 0 2.50e+00 1.60e-01 5.35e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.004 - 0.188: 91 0.188 - 0.373: 75 0.373 - 0.558: 47 0.558 - 0.742: 20 0.742 - 0.927: 10 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA BLYS A 99 " pdb=" N BLYS A 99 " pdb=" C BLYS A 99 " pdb=" CB BLYS A 99 " both_signs ideal model delta sigma weight residual False 2.51 1.58 0.93 2.00e-01 2.50e+01 2.15e+01 chirality pdb=" CA THR A 140 " pdb=" N THR A 140 " pdb=" C THR A 140 " pdb=" CB THR A 140 " both_signs ideal model delta sigma weight residual False 2.53 1.62 0.91 2.00e-01 2.50e+01 2.05e+01 chirality pdb=" CA LYS A 62 " pdb=" N LYS A 62 " pdb=" C LYS A 62 " pdb=" CB LYS A 62 " both_signs ideal model delta sigma weight residual False 2.51 1.61 0.90 2.00e-01 2.50e+01 2.04e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.093 2.00e-02 2.50e+03 6.35e-02 1.21e+02 pdb=" CG PHE A 164 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.091 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.019 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.084 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.002 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.047 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.069 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.010 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.018 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.122 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " 0.019 2.00e-02 2.50e+03 5.90e-02 1.04e+02 pdb=" CG BTYR A 67 " 0.013 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " 0.026 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " -0.071 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " 0.096 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " -0.062 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " -0.092 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " -0.010 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " -0.052 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " 0.017 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " 0.014 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " 0.103 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BASN A 97 " -0.003 2.00e-02 2.50e+03 8.06e-02 9.74e+01 pdb=" CG BASN A 97 " 0.098 2.00e-02 2.50e+03 pdb=" OD1BASN A 97 " -0.037 2.00e-02 2.50e+03 pdb=" ND2BASN A 97 " -0.151 2.00e-02 2.50e+03 pdb="HD21BASN A 97 " 0.066 2.00e-02 2.50e+03 pdb="HD22BASN A 97 " 0.028 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.37: 1400 2.37 - 2.93: 8341 2.93 - 3.48: 10427 3.48 - 4.04: 15040 4.04 - 4.60: 21376 Nonbonded interactions: 56584 Sorted by model distance: nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.810 2.450 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.823 2.450 nonbonded pdb=" HE2 HIS A 126 " pdb=" O PRO A 184 " model vdw sym.op. 1.847 2.450 x-y,-y,-z-4/3 nonbonded pdb=" O PHE A 162 " pdb=" H LEU A 166 " model vdw 1.848 2.450 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.856 2.100 ... (remaining 56579 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_2655235_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= 0.2785 r_free= 0.1848 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.404215 | | target function (ml) not normalized (work): 71537.663976 | | target function (ml) not normalized (free): 3255.981497 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3212 0.2166 7.5627 5.0334| | 2: 3.63 - 2.88 1.00 2711 122 0.2629 0.1759 4.3197 4.3243| | 3: 2.88 - 2.52 1.00 2682 148 0.2555 0.1774 4.1836 4.1856| | 4: 2.52 - 2.29 1.00 2661 139 0.2523 0.1585 3.4921 3.5873| | 5: 2.29 - 2.13 1.00 2678 122 0.2638 0.1388 3.3898 3.3383| | 6: 2.13 - 2.00 1.00 2692 117 0.2754 0.1960 3.3124 3.4422| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 17.55 0.77 0.23 1293.35| | 2: 3.63 - 2.88 2711 122 0.83 23.83 1.32 0.23 1293.35| | 3: 2.88 - 2.52 2682 148 0.73 32.58 1.28 0.23 1293.35| | 4: 2.52 - 2.29 2661 139 0.93 11.23 1.29 0.26 132.50| | 5: 2.29 - 2.13 2678 122 0.92 13.38 1.32 0.26 132.50| | 6: 2.13 - 2.00 2692 117 0.90 16.07 1.33 0.26 132.50| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 132.50 max = 1293.35 mean = 719.39| |figures of merit: min = 0.00 max = 1.00 mean = 0.87| |phase err.(work): min = 0.00 max = 89.91 mean = 19.11| |phase err.(test): min = 0.00 max = 88.87 mean = 19.11| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.083 0.263 1557 Z= 5.670 Angle : 5.286 17.753 2118 Z= 3.726 Chirality : 0.365 0.927 243 Planarity : 0.033 0.083 284 Dihedral : 14.241 89.475 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.16 % Favored : 97.30 % Rotamer: Outliers : 1.24 % Allowed : 3.11 % Favored : 95.65 % Cbeta Deviations : 32.97 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.49 % 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: -2.84 (0.47), residues: 224 helix: -2.55 (0.37), residues: 107 sheet: -0.26 (0.83), residues: 38 loop : -1.38 (0.58), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.085 0.022 ARG A 5 TYR 0.058 0.025 TYR A 139 PHE 0.058 0.025 PHE A 164 HIS 0.053 0.025 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= 0.2785 r_free= 0.1848 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.404215 | | target function (ml) not normalized (work): 71537.663976 | | target function (ml) not normalized (free): 3255.981497 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.2974 percent. r_work = 0.2915 r_free = 0.2000 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2861 0.2915 0.2000 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2861 0.2915 0.2000 n_refl.: 17050 remove outliers: r(all,work,free)=0.2156 0.2167 0.2000 n_refl.: 17045 overall B=-0.39 to atoms: r(all,work,free)=0.2130 0.2140 0.1981 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1609 0.1607 0.1661 n_refl.: 17045 remove outliers: r(all,work,free)=0.1608 0.1606 0.1661 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 0.4152 394.847 359.612 0.660 1.011 0.404 11.894-9.307 99.02 97 4 0.1912 633.741 615.600 0.932 1.012 0.399 9.237-7.194 100.00 213 7 0.2176 518.337 509.102 0.965 1.012 0.365 7.162-5.571 100.00 427 22 0.2321 389.012 375.713 0.919 1.011 0.303 5.546-4.326 100.00 867 58 0.1372 534.051 528.244 0.957 1.009 0.230 4.315-3.360 100.00 1859 96 0.1310 507.888 502.884 1.019 1.006 0.211 3.356-2.611 100.00 3867 181 0.1626 333.653 329.290 1.011 1.000 0.061 2.608-2.000 99.99 8818 434 0.1642 217.485 213.571 1.027 0.990 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.4021 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1606 r_free=0.1661 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1606 r_free=0.1661 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.704422 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.893427 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 0.1639 0.0286 0.009 1.0 1.3 0.5 0.0 0 11.352 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.52 16.39 2.86 3.013 18.466 0.893 0.023 12.79 16.62 3.83 3.598 18.680 0.893 0.021 Individual atomic B min max mean iso aniso Overall: 5.58 113.91 19.90 4.09 1785 0 Protein: 5.58 113.04 17.13 4.09 1519 0 Water: 8.81 113.91 36.02 N/A 258 0 Other: 21.57 37.18 26.28 N/A 8 0 Chain A: 5.58 113.91 19.90 N/A 1785 0 Histogram: Values Number of atoms 5.58 - 16.41 1050 16.41 - 27.24 369 27.24 - 38.08 187 38.08 - 48.91 99 48.91 - 59.74 53 59.74 - 70.58 11 70.58 - 81.41 8 81.41 - 92.24 4 92.24 - 103.07 1 103.07 - 113.91 3 =========================== Idealize ADP of riding H ========================== r_work=0.1279 r_free=0.1662 r_work=0.1282 r_free=0.1669 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1282 r_free = 0.1669 target_work(ls_wunit_k1) = 0.021 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1278 r_free = 0.1661 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17044 (all), 4.73 % free)------------| | | | r_work= 0.1278 r_free= 0.1661 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.020091 | | target function (ls_wunit_k1) not normalized (work): 326.211380 | | target function (ls_wunit_k1) not normalized (free): 27.706068 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1296 0.1278 0.1661 n_refl.: 17044 re-set all scales: r(all,work,free)=0.1911 0.1910 0.1974 n_refl.: 17044 remove outliers: r(all,work,free)=0.1911 0.1910 0.1974 n_refl.: 17044 overall B=-0.51 to atoms: r(all,work,free)=0.1874 0.1873 0.1953 n_refl.: 17044 bulk-solvent and scaling: r(all,work,free)=0.1293 0.1275 0.1647 n_refl.: 17044 remove outliers: r(all,work,free)=0.1291 0.1274 0.1647 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 0.3544 303.418 278.413 0.627 1.006 0.369 11.894-9.307 99.02 97 4 0.1708 487.999 476.606 0.919 1.007 0.368 9.237-7.194 100.00 213 7 0.1829 399.134 395.897 0.963 1.007 0.351 7.162-5.571 100.00 427 22 0.1838 299.551 294.123 0.933 1.006 0.311 5.546-4.326 100.00 867 58 0.1040 411.235 408.807 0.958 1.005 0.210 4.315-3.360 100.00 1859 96 0.0929 391.089 390.596 1.016 1.004 0.192 3.356-2.611 100.00 3867 181 0.1298 256.923 255.531 1.009 1.001 0.091 2.608-2.000 99.99 8818 434 0.1348 167.470 166.176 1.011 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9583 b_overall=-1.1563 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1274 r_free=0.1647 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1274 r_free=0.1647 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1274 r_free=0.1647 | n_water=258 | time (s): 0.810 (total time: 0.810) Filter (dist) r_work=0.1282 r_free=0.1635 | n_water=253 | time (s): 20.960 (total time: 21.770) Filter (q & B) r_work=0.1282 r_free=0.1635 | n_water=251 | time (s): 1.760 (total time: 23.530) Compute maps r_work=0.1282 r_free=0.1635 | n_water=251 | time (s): 0.580 (total time: 24.110) Filter (map) r_work=0.1322 r_free=0.1621 | n_water=211 | time (s): 2.120 (total time: 26.230) Find peaks r_work=0.1322 r_free=0.1621 | n_water=211 | time (s): 0.670 (total time: 26.900) Add new water r_work=0.1538 r_free=0.1840 | n_water=368 | time (s): 1.780 (total time: 28.680) Refine new water occ: r_work=0.1329 r_free=0.1564 adp: r_work=0.1271 r_free=0.1564 occ: r_work=0.1275 r_free=0.1533 adp: r_work=0.1242 r_free=0.1542 occ: r_work=0.1244 r_free=0.1528 adp: r_work=0.1232 r_free=0.1535 ADP+occupancy (water only), MIN, final r_work=0.1232 r_free=0.1535 r_work=0.1232 r_free=0.1535 | n_water=368 | time (s): 19.100 (total time: 47.780) Filter (q & B) r_work=0.1235 r_free=0.1543 | n_water=359 | time (s): 1.630 (total time: 49.410) Filter (dist only) r_work=0.1236 r_free=0.1544 | n_water=358 | time (s): 28.520 (total time: 77.930) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.360525 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.967062 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 0.1210 0.1594 0.0383 0.008 0.9 1.9 0.5 0.0 0 12.180 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.10 15.94 3.83 4.170 20.841 0.967 0.018 11.96 16.25 4.29 4.197 21.165 0.967 0.018 Individual atomic B min max mean iso aniso Overall: 6.58 107.53 21.24 4.29 1885 0 Protein: 6.58 107.53 17.67 4.28 1519 0 Water: 8.12 65.68 36.05 N/A 358 0 Other: 25.29 47.05 36.21 N/A 8 0 Chain A: 6.58 107.53 19.41 N/A 1738 0 Chain S: 16.60 61.72 42.84 N/A 147 0 Histogram: Values Number of atoms 6.58 - 16.67 1025 16.67 - 26.77 377 26.77 - 36.86 214 36.86 - 46.96 170 46.96 - 57.05 67 57.05 - 67.15 22 67.15 - 77.24 3 77.24 - 87.34 4 87.34 - 97.43 1 97.43 - 107.53 2 =========================== Idealize ADP of riding H ========================== r_work=0.1196 r_free=0.1625 r_work=0.1197 r_free=0.1625 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1197 r_free = 0.1625 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 = 0.1196 r_free = 0.1628 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.26 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= 0.1196 r_free= 0.1628 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.016958 | | target function (ls_wunit_k1) not normalized (work): 275.313484 | | target function (ls_wunit_k1) not normalized (free): 25.082036 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1216 0.1196 0.1628 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1757 0.1749 0.1949 n_refl.: 17042 remove outliers: r(all,work,free)=0.1757 0.1749 0.1949 n_refl.: 17042 overall B=-0.42 to atoms: r(all,work,free)=0.1730 0.1722 0.1933 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1212 0.1192 0.1618 n_refl.: 17042 remove outliers: r(all,work,free)=0.1211 0.1191 0.1618 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 0.3262 300.255 282.508 0.605 1.007 0.350 11.894-9.307 99.02 97 4 0.1469 487.999 487.944 0.919 1.007 0.336 9.237-7.194 100.00 213 7 0.1642 399.134 401.481 0.974 1.007 0.285 7.162-5.571 100.00 427 22 0.1554 299.551 296.063 0.937 1.006 0.271 5.546-4.326 100.00 867 58 0.0880 411.235 408.962 0.961 1.005 0.211 4.315-3.360 100.00 1859 96 0.0831 391.089 390.563 1.015 1.003 0.202 3.356-2.611 100.00 3867 181 0.1201 256.923 256.147 1.009 1.001 0.111 2.608-2.000 99.99 8818 434 0.1333 167.470 166.367 1.012 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-1.1633 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1191 r_free=0.1618 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=0.1622 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1192 r_free=0.1622 | n_water=358 | time (s): 0.890 (total time: 0.890) Filter (dist) r_work=0.1192 r_free=0.1623 | n_water=357 | time (s): 29.810 (total time: 30.700) Filter (q & B) r_work=0.1192 r_free=0.1623 | n_water=357 | time (s): 1.340 (total time: 32.040) Compute maps r_work=0.1192 r_free=0.1623 | n_water=357 | time (s): 0.620 (total time: 32.660) Filter (map) r_work=0.1254 r_free=0.1628 | n_water=266 | time (s): 1.670 (total time: 34.330) Find peaks r_work=0.1254 r_free=0.1628 | n_water=266 | time (s): 0.630 (total time: 34.960) Add new water r_work=0.1445 r_free=0.1775 | n_water=419 | time (s): 2.180 (total time: 37.140) Refine new water occ: r_work=0.1242 r_free=0.1588 adp: r_work=0.1233 r_free=0.1580 occ: r_work=0.1215 r_free=0.1574 adp: r_work=0.1203 r_free=0.1562 occ: r_work=0.1195 r_free=0.1566 adp: r_work=0.1185 r_free=0.1556 ADP+occupancy (water only), MIN, final r_work=0.1185 r_free=0.1556 r_work=0.1185 r_free=0.1556 | n_water=419 | time (s): 29.270 (total time: 66.410) Filter (q & B) r_work=0.1189 r_free=0.1554 | n_water=408 | time (s): 2.290 (total time: 68.700) Filter (dist only) r_work=0.1189 r_free=0.1554 | n_water=408 | time (s): 30.540 (total time: 99.240) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.881849 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.120180 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 0.1168 0.1556 0.0388 0.009 1.0 3.5 0.5 0.0 0 0.941 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.68 15.56 3.88 4.343 21.469 0.120 4.991 11.48 15.58 4.11 4.814 21.354 0.120 4.967 Individual atomic B min max mean iso aniso Overall: 6.08 103.94 20.79 4.48 1935 0 Protein: 6.08 103.94 16.84 4.48 1519 0 Water: 8.51 62.08 35.20 N/A 408 0 Other: 28.54 47.45 36.28 N/A 8 0 Chain A: 6.08 103.94 18.57 N/A 1734 0 Chain S: 15.96 62.08 39.97 N/A 201 0 Histogram: Values Number of atoms 6.08 - 15.86 1052 15.86 - 25.65 352 25.65 - 35.44 230 35.44 - 45.22 182 45.22 - 55.01 78 55.01 - 64.80 29 64.80 - 74.58 4 74.58 - 84.37 4 84.37 - 94.16 2 94.16 - 103.94 2 =========================== Idealize ADP of riding H ========================== r_work=0.1148 r_free=0.1558 r_work=0.1148 r_free=0.1560 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1148 r_free = 0.1560 target_work(ml) = 4.968 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1140 r_free = 0.1569 target_work(ml) = 4.965 | | occupancies: max = 1.00 min = 0.21 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= 0.1140 r_free= 0.1569 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.964821 | | target function (ml) not normalized (work): 80598.904264 | | target function (ml) not normalized (free): 4189.785395 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1161 0.1140 0.1569 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1659 0.1651 0.1871 n_refl.: 17041 remove outliers: r(all,work,free)=0.1659 0.1651 0.1871 n_refl.: 17041 overall B=-0.37 to atoms: r(all,work,free)=0.1634 0.1626 0.1861 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1160 0.1139 0.1572 n_refl.: 17041 remove outliers: r(all,work,free)=0.1159 0.1138 0.1572 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 0.3437 296.690 276.672 0.568 1.003 0.340 11.894-9.307 99.02 97 4 0.1713 487.999 481.761 0.920 1.004 0.340 9.237-7.194 100.00 213 7 0.1729 399.134 400.999 0.990 1.004 0.265 7.162-5.571 100.00 427 22 0.1608 299.551 294.789 0.944 1.004 0.251 5.546-4.326 100.00 867 58 0.0937 411.235 408.065 0.968 1.004 0.210 4.315-3.360 100.00 1859 96 0.0872 391.089 388.795 1.013 1.003 0.201 3.356-2.611 100.00 3867 181 0.1270 256.923 254.645 1.009 1.001 0.142 2.608-2.000 99.99 8818 434 0.1096 167.470 166.021 1.008 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-1.1554 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1138 r_free=0.1572 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=0.1139 r_free=0.1568 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1139 r_free=0.1568 | n_water=408 | time (s): 0.920 (total time: 0.920) Filter (dist) r_work=0.1139 r_free=0.1575 | n_water=407 | time (s): 32.620 (total time: 33.540) Filter (q & B) r_work=0.1139 r_free=0.1575 | n_water=407 | time (s): 0.900 (total time: 34.440) Compute maps r_work=0.1139 r_free=0.1575 | n_water=407 | time (s): 0.600 (total time: 35.040) Filter (map) r_work=0.1190 r_free=0.1578 | n_water=321 | time (s): 1.550 (total time: 36.590) Find peaks r_work=0.1190 r_free=0.1578 | n_water=321 | time (s): 0.490 (total time: 37.080) Add new water r_work=0.1338 r_free=0.1688 | n_water=464 | time (s): 1.730 (total time: 38.810) Refine new water occ: r_work=0.1176 r_free=0.1538 adp: r_work=0.1169 r_free=0.1538 occ: r_work=0.1151 r_free=0.1521 adp: r_work=0.1143 r_free=0.1522 occ: r_work=0.1134 r_free=0.1507 adp: r_work=0.1127 r_free=0.1508 ADP+occupancy (water only), MIN, final r_work=0.1127 r_free=0.1508 r_work=0.1127 r_free=0.1508 | n_water=464 | time (s): 23.930 (total time: 62.740) Filter (q & B) r_work=0.1131 r_free=0.1517 | n_water=455 | time (s): 2.310 (total time: 65.050) Filter (dist only) r_work=0.1131 r_free=0.1514 | n_water=453 | time (s): 37.510 (total time: 102.560) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.017652 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.168737 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 0.1126 0.1576 0.0450 0.010 1.0 4.5 0.5 0.0 0 1.009 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.26 15.76 4.50 4.373 20.984 0.169 4.966 11.12 15.70 4.58 4.595 21.031 0.169 4.955 Individual atomic B min max mean iso aniso Overall: 5.79 101.33 20.97 4.81 1980 0 Protein: 5.79 101.33 16.37 4.80 1519 0 Water: 8.31 63.84 36.14 N/A 453 0 Other: 27.65 48.43 35.50 N/A 8 0 Chain A: 5.79 101.33 18.04 N/A 1732 0 Chain S: 18.21 63.84 41.46 N/A 248 0 Histogram: Values Number of atoms 5.79 - 15.34 1045 15.34 - 24.90 355 24.90 - 34.45 219 34.45 - 44.00 196 44.00 - 53.56 98 53.56 - 63.11 50 63.11 - 72.67 8 72.67 - 82.22 4 82.22 - 91.78 2 91.78 - 101.33 3 =========================== Idealize ADP of riding H ========================== r_work=0.1112 r_free=0.1570 r_work=0.1112 r_free=0.1570 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1112 r_free = 0.1570 target_work(ml) = 4.955 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1104 r_free = 0.1577 target_work(ml) = 4.953 | | 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= 0.1577 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ml) (work): 4.952693 | | target function (ml) not normalized (work): 80397.061798 | | target function (ml) not normalized (free): 4192.063671 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1127 0.1104 0.1577 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1575 0.1563 0.1849 n_refl.: 17040 remove outliers: r(all,work,free)=0.1575 0.1563 0.1849 n_refl.: 17040 overall B=-0.26 to atoms: r(all,work,free)=0.1560 0.1547 0.1842 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1125 0.1102 0.1573 n_refl.: 17040 remove outliers: r(all,work,free)=0.1125 0.1102 0.1573 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 0.3645 296.690 278.801 0.543 1.000 0.313 11.894-9.307 99.02 97 4 0.1798 487.999 482.243 0.918 1.001 0.300 9.237-7.194 100.00 213 7 0.1718 399.134 400.052 0.989 1.002 0.230 7.162-5.571 100.00 427 22 0.1547 299.551 293.593 0.942 1.002 0.210 5.546-4.326 100.00 867 58 0.0917 411.235 407.865 0.966 1.002 0.201 4.315-3.360 100.00 1859 96 0.0853 391.089 388.426 1.006 1.002 0.201 3.356-2.611 100.00 3867 181 0.1233 256.923 254.691 1.002 1.001 0.121 2.608-2.000 99.99 8818 434 0.1042 167.470 166.330 0.993 1.000 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.8862 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1102 r_free=0.1573 After: r_work=0.1105 r_free=0.1571 ================================== NQH flips ================================== r_work=0.1105 r_free=0.1571 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1105 r_free=0.1571 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1105 r_free=0.1571 | n_water=453 | time (s): 0.670 (total time: 0.670) Filter (dist) r_work=0.1105 r_free=0.1571 | n_water=453 | time (s): 35.550 (total time: 36.220) Filter (q & B) r_work=0.1105 r_free=0.1571 | n_water=452 | time (s): 1.710 (total time: 37.930) Compute maps r_work=0.1105 r_free=0.1571 | n_water=452 | time (s): 0.680 (total time: 38.610) Filter (map) r_work=0.1181 r_free=0.1562 | n_water=334 | time (s): 2.310 (total time: 40.920) Find peaks r_work=0.1181 r_free=0.1562 | n_water=334 | time (s): 0.590 (total time: 41.510) Add new water r_work=0.1309 r_free=0.1668 | n_water=474 | time (s): 1.750 (total time: 43.260) Refine new water occ: r_work=0.1146 r_free=0.1522 adp: r_work=0.1139 r_free=0.1527 occ: r_work=0.1125 r_free=0.1507 adp: r_work=0.1118 r_free=0.1510 occ: r_work=0.1110 r_free=0.1495 adp: r_work=0.1104 r_free=0.1500 ADP+occupancy (water only), MIN, final r_work=0.1104 r_free=0.1500 r_work=0.1104 r_free=0.1500 | n_water=474 | time (s): 32.710 (total time: 75.970) Filter (q & B) r_work=0.1109 r_free=0.1510 | n_water=462 | time (s): 1.810 (total time: 77.780) Filter (dist only) r_work=0.1118 r_free=0.1508 | n_water=458 | time (s): 36.650 (total time: 114.430) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.946397 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.146332 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 0.1136 0.1543 0.0407 0.010 1.1 5.1 0.5 0.0 0 0.973 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.36 15.43 4.07 4.522 20.706 0.146 4.958 11.25 15.37 4.12 4.593 20.725 0.146 4.949 Individual atomic B min max mean iso aniso Overall: 5.45 99.24 20.73 4.88 1985 0 Protein: 5.45 99.24 16.08 4.86 1519 0 Water: 7.79 63.80 35.90 N/A 458 0 Other: 26.46 44.97 34.53 N/A 8 0 Chain A: 5.45 99.24 17.69 N/A 1729 0 Chain S: 17.62 63.80 41.26 N/A 256 0 Histogram: Values Number of atoms 5.45 - 14.83 1021 14.83 - 24.21 367 24.21 - 33.59 221 33.59 - 42.97 195 42.97 - 52.34 122 52.34 - 61.72 38 61.72 - 71.10 11 71.10 - 80.48 2 80.48 - 89.86 4 89.86 - 99.24 4 =========================== Idealize ADP of riding H ========================== r_work=0.1125 r_free=0.1537 r_work=0.1125 r_free=0.1537 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1125 r_free = 0.1537 target_work(ml) = 4.949 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1120 r_free = 0.1540 target_work(ml) = 4.948 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1120 r_free= 0.1540 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ml) (work): 4.947575 | | target function (ml) not normalized (work): 80313.981965 | | target function (ml) not normalized (free): 4177.431938 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1132 0.1460 5.4633 5.6758| | 2: 3.63 - 2.88 1.00 2711 122 0.1099 0.1482 5.2276 5.3569| | 3: 2.88 - 2.52 1.00 2681 148 0.1359 0.1678 5.1393 5.2197| | 4: 2.52 - 2.29 1.00 2661 139 0.0952 0.1619 4.6445 4.9952| | 5: 2.29 - 2.13 1.00 2678 122 0.0982 0.1424 4.5956 4.8672| | 6: 2.13 - 2.00 1.00 2692 117 0.1142 0.1753 4.5862 4.7929| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 9.22 1.00 0.96 6532.53| | 2: 3.63 - 2.88 2711 122 0.92 12.98 1.01 0.96 6532.53| | 3: 2.88 - 2.52 2681 148 0.87 19.20 0.99 0.96 6532.53| | 4: 2.52 - 2.29 2661 139 0.93 12.39 1.01 0.97 2188.95| | 5: 2.29 - 2.13 2678 122 0.91 14.43 1.00 0.97 2188.95| | 6: 2.13 - 2.00 2692 117 0.89 17.20 0.99 0.97 2188.95| |alpha: min = 0.96 max = 0.97 mean = 0.96| |beta: min = 2188.95 max = 6532.53 mean = 4383.62| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.92 mean = 14.20| |phase err.(test): min = 0.00 max = 86.88 mean = 13.75| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1140 0.1120 0.1540 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1570 0.1559 0.1815 n_refl.: 17040 remove outliers: r(all,work,free)=0.1570 0.1559 0.1815 n_refl.: 17040 overall B=-0.20 to atoms: r(all,work,free)=0.1560 0.1548 0.1809 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1140 0.1120 0.1537 n_refl.: 17040 remove outliers: r(all,work,free)=0.1140 0.1120 0.1537 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 0.3704 296.690 274.465 0.539 1.002 0.330 11.894-9.307 99.02 97 4 0.1744 487.999 482.162 0.918 1.002 0.330 9.237-7.194 100.00 213 7 0.1761 399.134 401.004 0.985 1.003 0.225 7.162-5.571 100.00 427 22 0.1600 299.551 293.458 0.936 1.002 0.207 5.546-4.326 100.00 867 58 0.0925 411.235 407.813 0.964 1.002 0.188 4.315-3.360 100.00 1859 96 0.0890 391.089 389.050 1.004 1.002 0.174 3.356-2.611 100.00 3867 181 0.1243 256.923 254.616 0.999 1.001 0.121 2.608-2.000 99.99 8818 434 0.1055 167.470 166.098 0.984 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.6767 ================= 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 : 0.2785 0.1848 0.083 5.286 8.8 119.3 19.9 258 0.000 1_bss: 0.1606 0.1661 0.083 5.286 8.5 118.9 19.5 258 0.000 1_settarget: 0.1606 0.1661 0.083 5.286 8.5 118.9 19.5 258 0.000 1_nqh: 0.1606 0.1661 0.083 5.286 8.5 118.9 19.5 258 0.000 1_weight: 0.1606 0.1661 0.083 5.286 8.5 118.9 19.5 258 0.000 1_xyzrec: 0.1352 0.1639 0.009 0.960 8.5 118.9 19.5 258 0.147 1_adp: 0.1279 0.1662 0.009 0.960 5.6 113.9 19.9 258 0.147 1_regHadp: 0.1282 0.1669 0.009 0.960 5.6 113.9 19.9 258 0.147 1_occ: 0.1278 0.1661 0.009 0.960 5.6 113.9 19.9 258 0.147 2_bss: 0.1274 0.1647 0.009 0.960 5.1 113.4 19.4 258 0.147 2_settarget: 0.1274 0.1647 0.009 0.960 5.1 113.4 19.4 258 0.147 2_updatecdl: 0.1274 0.1647 0.009 0.974 5.1 113.4 19.4 258 0.147 2_nqh: 0.1274 0.1647 0.009 0.974 5.1 113.4 19.4 258 0.147 2_sol: 0.1236 0.1544 0.009 0.974 5.1 112.5 20.6 358 n/a 2_weight: 0.1236 0.1544 0.009 0.974 5.1 112.5 20.6 358 n/a 2_xyzrec: 0.1210 0.1594 0.008 0.925 5.1 112.5 20.6 358 n/a 2_adp: 0.1196 0.1625 0.008 0.925 6.6 107.5 21.2 358 n/a 2_regHadp: 0.1197 0.1625 0.008 0.925 6.6 107.5 21.2 358 n/a 2_occ: 0.1196 0.1628 0.008 0.925 6.6 107.5 21.2 358 n/a 3_bss: 0.1191 0.1618 0.008 0.925 6.2 107.1 20.8 358 n/a 3_settarget: 0.1191 0.1618 0.008 0.925 6.2 107.1 20.8 358 n/a 3_updatecdl: 0.1191 0.1618 0.008 0.929 6.2 107.1 20.8 358 n/a 3_nqh: 0.1192 0.1622 0.008 0.929 6.2 107.1 20.8 358 n/a 3_sol: 0.1189 0.1554 0.008 0.929 6.2 107.1 21.0 408 n/a 3_weight: 0.1189 0.1554 0.008 0.929 6.2 107.1 21.0 408 n/a 3_xyzrec: 0.1168 0.1556 0.009 0.962 6.2 107.1 21.0 408 n/a 3_adp: 0.1148 0.1558 0.009 0.962 6.1 103.9 20.8 408 n/a 3_regHadp: 0.1148 0.1560 0.009 0.962 6.1 103.9 20.8 408 n/a 3_occ: 0.1140 0.1569 0.009 0.962 6.1 103.9 20.8 408 n/a 4_bss: 0.1138 0.1572 0.009 0.962 5.7 103.6 20.4 408 n/a 4_settarget: 0.1138 0.1572 0.009 0.962 5.7 103.6 20.4 408 n/a 4_updatecdl: 0.1138 0.1572 0.009 0.960 5.7 103.6 20.4 408 n/a 4_nqh: 0.1139 0.1568 0.009 0.960 5.7 103.6 20.4 408 n/a 4_sol: 0.1131 0.1514 0.009 0.960 5.7 103.6 20.9 453 n/a 4_weight: 0.1131 0.1514 0.009 0.960 5.7 103.6 20.9 453 n/a 4_xyzrec: 0.1126 0.1576 0.010 0.990 5.7 103.6 20.9 453 n/a 4_adp: 0.1112 0.1570 0.010 0.990 5.8 101.3 21.0 453 n/a 4_regHadp: 0.1112 0.1570 0.010 0.990 5.8 101.3 21.0 453 n/a 4_occ: 0.1104 0.1577 0.010 0.990 5.8 101.3 21.0 453 n/a 5_bss: 0.1102 0.1573 0.010 0.990 5.5 101.1 20.7 453 n/a 5_settarget: 0.1102 0.1573 0.010 0.990 5.5 101.1 20.7 453 n/a 5_updatecdl: 0.1102 0.1573 0.010 0.991 5.5 101.1 20.7 453 n/a 5_setrh: 0.1105 0.1571 0.010 0.991 5.5 101.1 20.7 453 n/a 5_nqh: 0.1105 0.1571 0.010 0.991 5.5 101.1 20.7 453 n/a 5_sol: 0.1118 0.1508 0.010 0.991 5.5 101.1 20.7 458 n/a 5_weight: 0.1118 0.1508 0.010 0.991 5.5 101.1 20.7 458 n/a 5_xyzrec: 0.1136 0.1543 0.010 1.098 5.5 101.1 20.7 458 n/a 5_adp: 0.1125 0.1537 0.010 1.098 5.5 99.2 20.7 458 n/a 5_regHadp: 0.1125 0.1537 0.010 1.098 5.5 99.2 20.7 458 n/a 5_occ: 0.1120 0.1540 0.010 1.098 5.5 99.2 20.7 458 n/a end: 0.1120 0.1537 0.010 1.098 5.3 99.0 20.5 458 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_2655235_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_2655235_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.0300 Refinement macro-cycles (run) : 928.2400 Write final files (write_after_run_outputs) : 20.6000 Total : 951.8700 Total CPU time: 16.23 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:17 PST -0800 (1735494077.19 s) Start R-work = 0.1606, R-free = 0.1661 Final R-work = 0.1120, R-free = 0.1537 =============================================================================== Job complete usr+sys time: 995.87 seconds wall clock time: 17 minutes 0.50 seconds (1020.50 seconds total)