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_8530424.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Adding command-line PHIL: ------------------------- xray_data.high_resolution=2 ordered_solvent.low_resolution=4 No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8530424.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8530424.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 2 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.06, per 1000 atoms: 0.31 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: 0.34 Conformation dependent library (CDL) restraints added in 116.9 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.67 - 0.91: 556 0.91 - 1.16: 1074 1.16 - 1.40: 593 1.40 - 1.65: 869 1.65 - 1.89: 61 Bond restraints: 3153 Sorted by residual: bond pdb=" N LYS A 130 " pdb=" CA LYS A 130 " ideal model delta sigma weight residual 1.459 1.204 0.256 1.19e-02 7.06e+03 4.61e+02 bond pdb=" N LYS A 63 " pdb=" CA LYS A 63 " ideal model delta sigma weight residual 1.457 1.729 -0.272 1.33e-02 5.65e+03 4.18e+02 bond pdb=" CA HIS A 126 " pdb=" C HIS A 126 " ideal model delta sigma weight residual 1.528 1.729 -0.200 1.11e-02 8.12e+03 3.25e+02 bond pdb=" N THR A 154 " pdb=" CA THR A 154 " ideal model delta sigma weight residual 1.454 1.688 -0.234 1.33e-02 5.65e+03 3.09e+02 bond pdb=" CA BGLU A 90 " pdb=" C BGLU A 90 " ideal model delta sigma weight residual 1.523 1.757 -0.234 1.35e-02 5.49e+03 3.00e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.02: 2729 4.02 - 8.04: 1893 8.04 - 12.06: 872 12.06 - 16.08: 230 16.08 - 20.10: 53 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O VAL A 181 " pdb=" C VAL A 181 " pdb=" N LYS A 182 " ideal model delta sigma weight residual 121.83 138.67 -16.84 1.03e+00 9.43e-01 2.67e+02 angle pdb=" NE ARG A 28 " pdb=" CZ ARG A 28 " pdb=" NH1 ARG A 28 " ideal model delta sigma weight residual 121.50 135.63 -14.13 1.00e+00 1.00e+00 2.00e+02 angle pdb=" NE ARG A 98 " pdb=" CZ ARG A 98 " pdb=" NH1 ARG A 98 " ideal model delta sigma weight residual 121.50 134.91 -13.41 1.00e+00 1.00e+00 1.80e+02 angle pdb=" OE1 GLN A 180 " pdb=" CD GLN A 180 " pdb=" NE2 GLN A 180 " ideal model delta sigma weight residual 122.60 135.98 -13.38 1.00e+00 1.00e+00 1.79e+02 angle pdb=" CA LYS A 130 " pdb=" C LYS A 130 " pdb=" O LYS A 130 " ideal model delta sigma weight residual 120.82 134.78 -13.96 1.05e+00 9.07e-01 1.77e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.66: 1302 16.66 - 33.32: 128 33.32 - 49.98: 33 49.98 - 66.63: 14 66.63 - 83.29: 4 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C LEU A 166 " pdb=" N LEU A 166 " pdb=" CA LEU A 166 " pdb=" CB LEU A 166 " ideal model delta harmonic sigma weight residual -122.60 -144.87 22.27 0 2.50e+00 1.60e-01 7.93e+01 dihedral pdb=" N LEU A 166 " pdb=" C LEU A 166 " pdb=" CA LEU A 166 " pdb=" CB LEU A 166 " ideal model delta harmonic sigma weight residual 122.80 142.71 -19.91 0 2.50e+00 1.60e-01 6.34e+01 dihedral pdb=" C AGLU A 90 " pdb=" N AGLU A 90 " pdb=" CA AGLU A 90 " pdb=" CB AGLU A 90 " ideal model delta harmonic sigma weight residual -122.60 -140.75 18.15 0 2.50e+00 1.60e-01 5.27e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.211: 100 0.211 - 0.422: 81 0.422 - 0.633: 41 0.633 - 0.843: 16 0.843 - 1.054: 5 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA LEU A 166 " pdb=" N LEU A 166 " pdb=" C LEU A 166 " pdb=" CB LEU A 166 " both_signs ideal model delta sigma weight residual False 2.51 1.46 1.05 2.00e-01 2.50e+01 2.78e+01 chirality pdb=" CB ILE A 117 " pdb=" CA ILE A 117 " pdb=" CG1 ILE A 117 " pdb=" CG2 ILE A 117 " both_signs ideal model delta sigma weight residual False 2.64 1.62 1.03 2.00e-01 2.50e+01 2.64e+01 chirality pdb=" CA BLEU A 153 " pdb=" N BLEU A 153 " pdb=" C BLEU A 153 " pdb=" CB BLEU A 153 " both_signs ideal model delta sigma weight residual False 2.51 3.51 -1.00 2.00e-01 2.50e+01 2.48e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.067 2.00e-02 2.50e+03 6.69e-02 1.34e+02 pdb=" CG PHE A 119 " -0.095 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.067 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.079 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.100 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.011 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.104 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.009 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.062 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " -0.026 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " -0.002 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 138 " 0.048 2.00e-02 2.50e+03 6.63e-02 9.88e+01 pdb=" CG HIS A 138 " 0.001 2.00e-02 2.50e+03 pdb=" ND1 HIS A 138 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 HIS A 138 " 0.054 2.00e-02 2.50e+03 pdb=" CE1 HIS A 138 " -0.129 2.00e-02 2.50e+03 pdb=" NE2 HIS A 138 " 0.002 2.00e-02 2.50e+03 pdb=" HD1 HIS A 138 " -0.036 2.00e-02 2.50e+03 pdb=" HD2 HIS A 138 " -0.046 2.00e-02 2.50e+03 pdb=" HE1 HIS A 138 " 0.118 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " -0.031 2.00e-02 2.50e+03 5.53e-02 9.18e+01 pdb=" CG TYR A 141 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " 0.099 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " -0.082 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " 0.021 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " -0.049 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " -0.030 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " 0.056 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " -0.025 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " 0.015 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " 0.086 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.32: 1010 2.32 - 2.89: 8126 2.89 - 3.46: 10504 3.46 - 4.03: 15263 4.03 - 4.60: 21626 Nonbonded interactions: 56529 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.748 2.100 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.755 2.450 x-y,-y,-z-4/3 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.812 2.100 nonbonded pdb=" H THR A 125 " pdb=" HH TYR A 141 " model vdw 1.826 2.100 nonbonded pdb=" HD3 ARG A 5 " pdb="HH11 ARG A 5 " model vdw 1.832 2.270 ... (remaining 56524 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_8530424_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= 0.2783 r_free= 0.1868 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.423751 | | target function (ml) not normalized (work): 71854.989028 | | target function (ml) not normalized (free): 3282.366814 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3189 0.2104 7.6124 5.007| | 2: 3.63 - 2.88 1.00 2711 122 0.2622 0.1777 4.3175 4.3149| | 3: 2.88 - 2.52 1.00 2682 148 0.2563 0.1840 4.1763 4.1904| | 4: 2.52 - 2.29 1.00 2661 139 0.2541 0.1631 3.5003 3.6526| | 5: 2.29 - 2.13 1.00 2678 122 0.2650 0.1619 3.4227 3.5369| | 6: 2.13 - 2.00 1.00 2692 117 0.2759 0.1898 3.3469 3.4225| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 17.33 0.77 0.23 1270.88| | 2: 3.63 - 2.88 2711 122 0.83 23.48 1.31 0.23 1270.88| | 3: 2.88 - 2.52 2682 148 0.74 32.44 1.28 0.23 1270.88| | 4: 2.52 - 2.29 2661 139 0.93 12.08 1.30 0.26 149.81| | 5: 2.29 - 2.13 2678 122 0.91 14.45 1.32 0.26 149.81| | 6: 2.13 - 2.00 2692 117 0.89 17.20 1.34 0.26 149.81| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 149.81 max = 1270.88 mean = 716.59| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 89.98 mean = 19.49| |phase err.(test): min = 0.00 max = 89.38 mean = 19.75| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.084 0.272 1557 Z= 5.609 Angle : 5.432 16.836 2118 Z= 3.905 Chirality : 0.375 1.054 243 Planarity : 0.030 0.083 284 Dihedral : 14.044 83.291 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.24 % Favored : 96.22 % Rotamer: Outliers : 0.62 % Allowed : 3.73 % Favored : 95.65 % Cbeta Deviations : 33.51 % 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: -2.04 (0.50), residues: 224 helix: -2.30 (0.39), residues: 109 sheet: -0.50 (0.86), residues: 30 loop : 0.07 (0.66), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.130 0.031 ARG A 27 TYR 0.116 0.039 TYR A 141 PHE 0.113 0.044 PHE A 119 HIS 0.072 0.030 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= 0.2783 r_free= 0.1868 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.423751 | | target function (ml) not normalized (work): 71854.989028 | | target function (ml) not normalized (free): 3282.366814 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.3440 percent. r_work = 0.2917 r_free = 0.2032 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2864 0.2917 0.2032 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2864 0.2917 0.2032 n_refl.: 17050 remove outliers: r(all,work,free)=0.2160 0.2170 0.2032 n_refl.: 17045 overall B=-0.41 to atoms: r(all,work,free)=0.2133 0.2143 0.2015 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1624 0.1620 0.1700 n_refl.: 17045 remove outliers: r(all,work,free)=0.1622 0.1618 0.1700 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 0.3871 399.067 363.450 0.662 1.013 0.403 11.894-9.307 99.02 97 4 0.1883 633.813 615.033 0.929 1.014 0.390 9.237-7.194 100.00 213 7 0.2228 518.395 510.900 0.953 1.013 0.349 7.162-5.571 100.00 427 22 0.2366 389.056 375.837 0.927 1.012 0.279 5.546-4.326 100.00 867 58 0.1391 534.111 527.745 0.960 1.010 0.220 4.315-3.360 100.00 1859 96 0.1293 507.945 504.410 1.015 1.006 0.191 3.356-2.611 100.00 3867 181 0.1652 333.691 329.143 1.013 0.999 0.039 2.608-2.000 99.99 8818 434 0.1660 217.509 213.477 1.031 0.988 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.4483 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1618 r_free=0.1700 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=0.1618 r_free=0.1708 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.871398 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.851813 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1351 0.1633 0.0282 0.009 1.0 1.0 0.5 0.0 0 11.436 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.51 16.33 2.82 3.013 18.453 0.852 0.022 12.79 16.58 3.79 3.630 18.714 0.852 0.020 Individual atomic B min max mean iso aniso Overall: 6.15 113.89 19.97 4.09 1785 0 Protein: 6.15 112.95 17.21 4.09 1519 0 Water: 8.63 113.89 36.04 N/A 258 0 Other: 22.06 37.49 26.53 N/A 8 0 Chain A: 6.15 113.89 19.97 N/A 1785 0 Histogram: Values Number of atoms 6.15 - 16.93 1083 16.93 - 27.70 342 27.70 - 38.47 186 38.47 - 49.25 99 49.25 - 60.02 48 60.02 - 70.80 12 70.80 - 81.57 7 81.57 - 92.34 4 92.34 - 103.12 1 103.12 - 113.89 3 =========================== Idealize ADP of riding H ========================== r_work=0.1279 r_free=0.1658 r_work=0.1282 r_free=0.1666 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1282 r_free = 0.1666 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 = 0.1276 r_free = 0.1662 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.25 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= 0.1276 r_free= 0.1662 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.019917 | | target function (ls_wunit_k1) not normalized (work): 323.371729 | | target function (ls_wunit_k1) not normalized (free): 27.647839 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1294 0.1276 0.1662 n_refl.: 17043 re-set all scales: r(all,work,free)=0.1901 0.1899 0.1985 n_refl.: 17043 remove outliers: r(all,work,free)=0.1901 0.1899 0.1985 n_refl.: 17043 overall B=-0.39 to atoms: r(all,work,free)=0.1873 0.1871 0.1969 n_refl.: 17043 bulk-solvent and scaling: r(all,work,free)=0.1295 0.1277 0.1656 n_refl.: 17043 remove outliers: r(all,work,free)=0.1293 0.1275 0.1656 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 0.3452 306.650 280.879 0.627 1.010 0.368 11.894-9.307 99.02 97 4 0.1670 487.925 477.817 0.918 1.010 0.367 9.237-7.194 100.00 213 7 0.1826 399.073 396.573 0.956 1.010 0.325 7.162-5.571 100.00 427 22 0.1826 299.505 294.585 0.934 1.009 0.301 5.546-4.326 100.00 867 58 0.1046 411.172 408.691 0.957 1.007 0.200 4.315-3.360 100.00 1859 96 0.0929 391.029 390.725 1.017 1.005 0.191 3.356-2.611 100.00 3867 181 0.1302 256.884 255.631 1.015 1.000 0.091 2.608-2.000 99.99 8818 434 0.1352 167.444 165.973 1.023 0.992 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.3832 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1275 r_free=0.1656 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=0.1276 r_free=0.1654 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1276 r_free=0.1654 | n_water=258 | time (s): 0.710 (total time: 0.710) Filter (dist) r_work=0.1284 r_free=0.1642 | n_water=252 | time (s): 19.630 (total time: 20.340) Filter (q & B) r_work=0.1284 r_free=0.1641 | n_water=250 | time (s): 1.450 (total time: 21.790) Compute maps r_work=0.1284 r_free=0.1641 | n_water=250 | time (s): 0.680 (total time: 22.470) Filter (map) r_work=0.1313 r_free=0.1634 | n_water=215 | time (s): 1.530 (total time: 24.000) Find peaks r_work=0.1313 r_free=0.1634 | n_water=215 | time (s): 0.440 (total time: 24.440) Add new water r_work=0.1529 r_free=0.1876 | n_water=373 | time (s): 1.510 (total time: 25.950) Refine new water occ: r_work=0.1329 r_free=0.1578 adp: r_work=0.1274 r_free=0.1578 occ: r_work=0.1277 r_free=0.1543 adp: r_work=0.1247 r_free=0.1552 occ: r_work=0.1246 r_free=0.1545 adp: r_work=0.1236 r_free=0.1546 ADP+occupancy (water only), MIN, final r_work=0.1236 r_free=0.1546 r_work=0.1236 r_free=0.1546 | n_water=373 | time (s): 20.380 (total time: 46.330) Filter (q & B) r_work=0.1238 r_free=0.1554 | n_water=363 | time (s): 2.020 (total time: 48.350) Filter (dist only) r_work=0.1238 r_free=0.1557 | n_water=362 | time (s): 28.930 (total time: 77.280) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.765421 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.993797 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 0.1205 0.1610 0.0405 0.009 1.0 2.2 0.5 0.0 0 13.383 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.05 16.10 4.05 4.178 21.041 0.994 0.018 11.91 16.29 4.38 4.236 21.332 0.994 0.017 Individual atomic B min max mean iso aniso Overall: 6.68 107.57 21.36 4.31 1889 0 Protein: 6.68 107.57 17.79 4.30 1519 0 Water: 8.56 65.79 36.05 N/A 362 0 Other: 24.88 45.76 35.25 N/A 8 0 Chain A: 6.68 107.57 19.58 N/A 1742 0 Chain S: 18.55 64.85 42.51 N/A 147 0 Histogram: Values Number of atoms 6.68 - 16.77 1025 16.77 - 26.85 373 26.85 - 36.94 221 36.94 - 47.03 167 47.03 - 57.12 64 57.12 - 67.21 28 67.21 - 77.30 3 77.30 - 87.39 4 87.39 - 97.48 2 97.48 - 107.57 2 =========================== Idealize ADP of riding H ========================== r_work=0.1191 r_free=0.1629 r_work=0.1192 r_free=0.1629 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1192 r_free = 0.1629 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1190 r_free = 0.1627 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1190 r_free= 0.1627 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.016809 | | target function (ls_wunit_k1) not normalized (work): 272.875882 | | target function (ls_wunit_k1) not normalized (free): 25.370812 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1211 0.1190 0.1627 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1743 0.1732 0.1983 n_refl.: 17041 remove outliers: r(all,work,free)=0.1743 0.1732 0.1983 n_refl.: 17041 overall B=-0.39 to atoms: r(all,work,free)=0.1718 0.1707 0.1965 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1204 0.1183 0.1623 n_refl.: 17041 remove outliers: r(all,work,free)=0.1204 0.1183 0.1623 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 0.3239 306.650 287.009 0.602 1.005 0.350 11.894-9.307 99.02 97 4 0.1472 487.925 485.245 0.915 1.005 0.350 9.237-7.194 100.00 213 7 0.1641 399.073 400.663 0.974 1.005 0.289 7.162-5.571 100.00 427 22 0.1575 299.505 295.316 0.934 1.005 0.251 5.546-4.326 100.00 867 58 0.0874 411.172 408.652 0.960 1.004 0.205 4.315-3.360 100.00 1859 96 0.0815 391.029 390.242 1.015 1.003 0.191 3.356-2.611 100.00 3867 181 0.1194 256.884 256.035 1.013 1.001 0.131 2.608-2.000 99.99 8818 434 0.1325 167.444 166.430 1.018 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-1.3814 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1183 r_free=0.1623 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B Total number of N/Q/H flips: 1 r_work=0.1183 r_free=0.1623 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1183 r_free=0.1623 | n_water=362 | time (s): 0.610 (total time: 0.610) Filter (dist) r_work=0.1183 r_free=0.1626 | n_water=361 | time (s): 29.340 (total time: 29.950) Filter (q & B) r_work=0.1183 r_free=0.1626 | n_water=361 | time (s): 1.070 (total time: 31.020) Compute maps r_work=0.1183 r_free=0.1626 | n_water=361 | time (s): 0.860 (total time: 31.880) Filter (map) r_work=0.1259 r_free=0.1619 | n_water=269 | time (s): 2.130 (total time: 34.010) Find peaks r_work=0.1259 r_free=0.1619 | n_water=269 | time (s): 0.580 (total time: 34.590) Add new water r_work=0.1424 r_free=0.1730 | n_water=407 | time (s): 2.620 (total time: 37.210) Refine new water occ: r_work=0.1236 r_free=0.1561 adp: r_work=0.1227 r_free=0.1562 occ: r_work=0.1213 r_free=0.1548 adp: r_work=0.1202 r_free=0.1548 occ: r_work=0.1198 r_free=0.1543 adp: r_work=0.1188 r_free=0.1542 ADP+occupancy (water only), MIN, final r_work=0.1188 r_free=0.1542 r_work=0.1188 r_free=0.1542 | n_water=407 | time (s): 24.050 (total time: 61.260) Filter (q & B) r_work=0.1190 r_free=0.1544 | n_water=399 | time (s): 1.920 (total time: 63.180) Filter (dist only) r_work=0.1190 r_free=0.1547 | n_water=398 | time (s): 30.570 (total time: 93.750) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.971092 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.151456 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 0.1166 0.1565 0.0399 0.009 1.0 2.9 0.5 0.0 0 0.986 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.66 15.65 3.99 4.369 21.600 0.151 4.997 11.48 15.72 4.24 4.927 21.476 0.151 4.975 Individual atomic B min max mean iso aniso Overall: 6.41 104.83 20.90 4.68 1925 0 Protein: 6.41 104.83 17.03 4.67 1519 0 Water: 8.07 61.02 35.40 N/A 398 0 Other: 25.76 46.71 34.13 N/A 8 0 Chain A: 6.41 104.83 18.82 N/A 1738 0 Chain S: 19.82 61.02 40.23 N/A 187 0 Histogram: Values Number of atoms 6.41 - 16.25 1059 16.25 - 26.09 356 26.09 - 35.93 220 35.93 - 45.78 171 45.78 - 55.62 74 55.62 - 65.46 32 65.46 - 75.30 4 75.30 - 85.14 4 85.14 - 94.98 3 94.98 - 104.83 2 =========================== Idealize ADP of riding H ========================== r_work=0.1148 r_free=0.1572 r_work=0.1148 r_free=0.1573 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1148 r_free = 0.1573 target_work(ml) = 4.975 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1140 r_free = 0.1585 target_work(ml) = 4.973 | | occupancies: max = 1.00 min = 0.23 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= 0.1585 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.972964 | | target function (ml) not normalized (work): 80731.100609 | | target function (ml) not normalized (free): 4204.040637 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1162 0.1140 0.1585 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1664 0.1652 0.1934 n_refl.: 17041 remove outliers: r(all,work,free)=0.1664 0.1652 0.1934 n_refl.: 17041 overall B=-0.37 to atoms: r(all,work,free)=0.1638 0.1626 0.1920 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1161 0.1140 0.1585 n_refl.: 17041 remove outliers: r(all,work,free)=0.1159 0.1138 0.1585 n_refl.: 17039 ======================== 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 92.71 84 5 0.3326 299.921 284.744 0.579 1.005 0.340 11.894-9.307 99.02 97 4 0.1761 487.925 481.383 0.911 1.006 0.314 9.237-7.194 100.00 213 7 0.1801 399.073 400.083 0.983 1.006 0.245 7.162-5.571 100.00 427 22 0.1620 299.505 293.366 0.935 1.006 0.231 5.546-4.326 100.00 867 58 0.0946 411.172 407.384 0.963 1.005 0.205 4.315-3.360 100.00 1859 96 0.0885 391.029 388.928 1.012 1.004 0.191 3.356-2.611 100.00 3867 181 0.1267 256.884 254.688 1.012 1.001 0.121 2.608-2.000 99.99 8818 434 0.1084 167.444 166.115 1.017 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9552 b_overall=-1.3257 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1138 r_free=0.1585 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1138 r_free=0.1585 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1138 r_free=0.1585 | n_water=398 | time (s): 0.910 (total time: 0.910) Filter (dist) r_work=0.1138 r_free=0.1586 | n_water=397 | time (s): 34.210 (total time: 35.120) Filter (q & B) r_work=0.1138 r_free=0.1586 | n_water=397 | time (s): 0.760 (total time: 35.880) Compute maps r_work=0.1138 r_free=0.1586 | n_water=397 | time (s): 0.830 (total time: 36.710) Filter (map) r_work=0.1187 r_free=0.1582 | n_water=320 | time (s): 2.230 (total time: 38.940) Find peaks r_work=0.1187 r_free=0.1582 | n_water=320 | time (s): 0.550 (total time: 39.490) Add new water r_work=0.1320 r_free=0.1718 | n_water=462 | time (s): 1.460 (total time: 40.950) Refine new water occ: r_work=0.1156 r_free=0.1517 adp: r_work=0.1149 r_free=0.1530 occ: r_work=0.1133 r_free=0.1485 adp: r_work=0.1125 r_free=0.1499 occ: r_work=0.1117 r_free=0.1470 adp: r_work=0.1110 r_free=0.1482 ADP+occupancy (water only), MIN, final r_work=0.1110 r_free=0.1482 r_work=0.1110 r_free=0.1482 | n_water=462 | time (s): 25.370 (total time: 66.320) Filter (q & B) r_work=0.1115 r_free=0.1487 | n_water=451 | time (s): 1.840 (total time: 68.160) Filter (dist only) r_work=0.1115 r_free=0.1487 | n_water=449 | time (s): 35.960 (total time: 104.120) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.901463 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.137409 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 0.1105 0.1540 0.0435 0.010 1.0 4.8 0.5 0.0 0 0.951 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.05 15.40 4.35 4.491 21.160 0.137 4.950 10.95 15.30 4.35 4.626 21.161 0.137 4.942 Individual atomic B min max mean iso aniso Overall: 5.77 102.10 21.08 4.74 1976 0 Protein: 5.77 102.10 16.57 4.73 1519 0 Water: 8.16 60.19 36.11 N/A 449 0 Other: 25.20 45.63 32.82 N/A 8 0 Chain A: 5.77 102.10 18.30 N/A 1737 0 Chain S: 16.27 60.19 41.31 N/A 239 0 Histogram: Values Number of atoms 5.77 - 15.40 1028 15.40 - 25.04 372 25.04 - 34.67 216 34.67 - 44.30 200 44.30 - 53.94 109 53.94 - 63.57 36 63.57 - 73.20 6 73.20 - 82.84 4 82.84 - 92.47 3 92.47 - 102.10 2 =========================== Idealize ADP of riding H ========================== r_work=0.1095 r_free=0.1530 r_work=0.1095 r_free=0.1530 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1095 r_free = 0.1530 target_work(ml) = 4.942 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1086 r_free = 0.1535 target_work(ml) = 4.937 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17039 (all), 4.74 % free)------------| | | | r_work= 0.1086 r_free= 0.1535 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ml) (work): 4.937123 | | target function (ml) not normalized (work): 80139.386896 | | target function (ml) not normalized (free): 4174.345201 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1107 0.1086 0.1535 n_refl.: 17039 re-set all scales: r(all,work,free)=0.1567 0.1553 0.1871 n_refl.: 17039 remove outliers: r(all,work,free)=0.1567 0.1553 0.1871 n_refl.: 17039 overall B=-0.29 to atoms: r(all,work,free)=0.1549 0.1534 0.1861 n_refl.: 17039 bulk-solvent and scaling: r(all,work,free)=0.1107 0.1085 0.1534 n_refl.: 17039 remove outliers: r(all,work,free)=0.1107 0.1085 0.1534 n_refl.: 17039 ======================== 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 92.71 84 5 0.3434 299.921 278.942 0.559 1.002 0.328 11.894-9.307 99.02 97 4 0.1680 487.925 482.427 0.920 1.003 0.320 9.237-7.194 100.00 213 7 0.1673 399.073 400.696 0.991 1.003 0.232 7.162-5.571 100.00 427 22 0.1489 299.505 293.680 0.936 1.003 0.213 5.546-4.326 100.00 867 58 0.0918 411.172 408.226 0.965 1.003 0.191 4.315-3.360 100.00 1859 96 0.0825 391.029 388.855 1.008 1.002 0.176 3.356-2.611 100.00 3867 181 0.1204 256.884 254.742 1.005 1.001 0.131 2.608-2.000 99.99 8818 434 0.1045 167.444 166.316 1.003 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-1.0194 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1085 r_free=0.1534 After: r_work=0.1087 r_free=0.1533 ================================== NQH flips ================================== r_work=0.1087 r_free=0.1533 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1087 r_free=0.1533 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1087 r_free=0.1533 | n_water=449 | time (s): 0.720 (total time: 0.720) Filter (dist) r_work=0.1087 r_free=0.1533 | n_water=449 | time (s): 36.350 (total time: 37.070) Filter (q & B) r_work=0.1087 r_free=0.1533 | n_water=447 | time (s): 1.920 (total time: 38.990) Compute maps r_work=0.1087 r_free=0.1533 | n_water=447 | time (s): 0.810 (total time: 39.800) Filter (map) r_work=0.1169 r_free=0.1543 | n_water=342 | time (s): 2.290 (total time: 42.090) Find peaks r_work=0.1169 r_free=0.1543 | n_water=342 | time (s): 0.600 (total time: 42.690) Add new water r_work=0.1287 r_free=0.1662 | n_water=481 | time (s): 2.270 (total time: 44.960) Refine new water occ: r_work=0.1131 r_free=0.1489 adp: r_work=0.1124 r_free=0.1493 occ: r_work=0.1110 r_free=0.1466 adp: r_work=0.1102 r_free=0.1472 occ: r_work=0.1096 r_free=0.1449 adp: r_work=0.1089 r_free=0.1456 ADP+occupancy (water only), MIN, final r_work=0.1089 r_free=0.1456 r_work=0.1089 r_free=0.1456 | n_water=481 | time (s): 18.510 (total time: 63.470) Filter (q & B) r_work=0.1094 r_free=0.1460 | n_water=470 | time (s): 1.570 (total time: 65.040) Filter (dist only) r_work=0.1094 r_free=0.1461 | n_water=468 | time (s): 39.290 (total time: 104.330) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.857099 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.160531 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 0.1123 0.1500 0.0377 0.009 1.0 6.7 0.5 0.0 0 0.929 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.23 15.00 3.77 4.483 20.905 0.161 4.944 11.13 14.96 3.83 4.620 20.949 0.161 4.936 Individual atomic B min max mean iso aniso Overall: 5.47 100.90 21.06 4.95 1995 0 Protein: 5.47 100.90 16.23 4.94 1519 0 Water: 7.84 66.23 36.55 N/A 468 0 Other: 24.60 43.60 31.87 N/A 8 0 Chain A: 5.47 100.90 17.93 N/A 1737 0 Chain S: 14.48 66.23 42.10 N/A 258 0 Histogram: Values Number of atoms 5.47 - 15.01 1030 15.01 - 24.56 371 24.56 - 34.10 207 34.10 - 43.64 206 43.64 - 53.19 123 53.19 - 62.73 36 62.73 - 72.27 12 72.27 - 81.81 4 81.81 - 91.36 3 91.36 - 100.90 3 =========================== Idealize ADP of riding H ========================== r_work=0.1113 r_free=0.1496 r_work=0.1113 r_free=0.1496 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1113 r_free = 0.1496 target_work(ml) = 4.936 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1106 r_free = 0.1493 target_work(ml) = 4.933 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17039 (all), 4.74 % free)------------| | | | r_work= 0.1106 r_free= 0.1493 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ml) (work): 4.932887 | | target function (ml) not normalized (work): 80070.617394 | | target function (ml) not normalized (free): 4159.278327 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.64 1.00 2809 159 0.1104 0.1371 5.4421 5.6483| | 2: 3.63 - 2.88 1.00 2711 122 0.1082 0.1426 5.2116 5.3346| | 3: 2.88 - 2.52 1.00 2681 148 0.1355 0.1708 5.123 5.2013| | 4: 2.52 - 2.29 1.00 2661 139 0.0950 0.1474 4.6319 4.9256| | 5: 2.29 - 2.13 1.00 2678 122 0.0976 0.1503 4.5831 4.8955| | 6: 2.13 - 2.00 1.00 2692 117 0.1142 0.1738 4.577 4.7751| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2809 159 0.95 8.85 1.00 0.95 6240.87| | 2: 3.63 - 2.88 2711 122 0.92 12.75 1.01 0.95 6240.87| | 3: 2.88 - 2.52 2681 148 0.88 18.74 0.99 0.95 6240.87| | 4: 2.52 - 2.29 2661 139 0.93 12.03 1.01 0.97 2105.57| | 5: 2.29 - 2.13 2678 122 0.92 14.05 1.00 0.97 2105.57| | 6: 2.13 - 2.00 2692 117 0.89 16.81 0.99 0.97 2105.57| |alpha: min = 0.95 max = 0.97 mean = 0.96| |beta: min = 2105.57 max = 6240.87 mean = 4194.88| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.90 mean = 13.83| |phase err.(test): min = 0.00 max = 86.95 mean = 13.53| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1125 0.1106 0.1493 n_refl.: 17039 re-set all scales: r(all,work,free)=0.1562 0.1548 0.1843 n_refl.: 17039 remove outliers: r(all,work,free)=0.1562 0.1548 0.1843 n_refl.: 17039 overall B=-0.23 to atoms: r(all,work,free)=0.1549 0.1534 0.1835 n_refl.: 17039 bulk-solvent and scaling: r(all,work,free)=0.1126 0.1107 0.1497 n_refl.: 17039 remove outliers: r(all,work,free)=0.1126 0.1107 0.1497 n_refl.: 17039 ======================== 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 92.71 84 5 0.3520 299.921 278.741 0.553 1.000 0.330 11.894-9.307 99.02 97 4 0.1712 487.925 482.516 0.922 1.002 0.320 9.237-7.194 100.00 213 7 0.1698 399.073 401.434 0.990 1.003 0.220 7.162-5.571 100.00 427 22 0.1538 299.505 293.826 0.933 1.003 0.200 5.546-4.326 100.00 867 58 0.0926 411.172 408.464 0.964 1.003 0.180 4.315-3.360 100.00 1859 96 0.0862 391.029 389.011 1.005 1.002 0.181 3.356-2.611 100.00 3867 181 0.1237 256.884 254.606 1.000 1.001 0.131 2.608-2.000 99.99 8818 434 0.1051 167.444 166.092 0.990 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.7879 ================= 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 : 0.2783 0.1868 0.084 5.432 8.8 119.3 19.9 258 0.000 1_bss: 0.1618 0.1700 0.084 5.432 8.4 118.9 19.5 258 0.000 1_settarget: 0.1618 0.1700 0.084 5.432 8.4 118.9 19.5 258 0.000 1_nqh: 0.1618 0.1708 0.084 5.432 8.4 118.9 19.5 258 0.003 1_weight: 0.1618 0.1708 0.084 5.432 8.4 118.9 19.5 258 0.003 1_xyzrec: 0.1351 0.1633 0.009 0.982 8.4 118.9 19.5 258 0.151 1_adp: 0.1279 0.1658 0.009 0.982 6.2 113.9 20.0 258 0.151 1_regHadp: 0.1282 0.1666 0.009 0.982 6.2 113.9 20.0 258 0.151 1_occ: 0.1276 0.1662 0.009 0.982 6.2 113.9 20.0 258 0.151 2_bss: 0.1275 0.1656 0.009 0.982 5.8 113.5 19.6 258 0.151 2_settarget: 0.1275 0.1656 0.009 0.982 5.8 113.5 19.6 258 0.151 2_updatecdl: 0.1275 0.1656 0.009 0.990 5.8 113.5 19.6 258 0.151 2_nqh: 0.1276 0.1654 0.009 0.990 5.8 113.5 19.6 258 0.148 2_sol: 0.1238 0.1557 0.009 0.990 5.8 112.6 20.8 362 n/a 2_weight: 0.1238 0.1557 0.009 0.990 5.8 112.6 20.8 362 n/a 2_xyzrec: 0.1205 0.1610 0.009 0.967 5.8 112.6 20.8 362 n/a 2_adp: 0.1191 0.1629 0.009 0.967 6.7 107.6 21.4 362 n/a 2_regHadp: 0.1192 0.1629 0.009 0.967 6.7 107.6 21.4 362 n/a 2_occ: 0.1190 0.1627 0.009 0.967 6.7 107.6 21.4 362 n/a 3_bss: 0.1183 0.1623 0.009 0.967 6.3 107.2 21.0 362 n/a 3_settarget: 0.1183 0.1623 0.009 0.967 6.3 107.2 21.0 362 n/a 3_updatecdl: 0.1183 0.1623 0.009 0.967 6.3 107.2 21.0 362 n/a 3_nqh: 0.1183 0.1623 0.009 0.967 6.3 107.2 21.0 362 n/a 3_sol: 0.1190 0.1547 0.009 0.967 6.3 107.2 21.1 398 n/a 3_weight: 0.1190 0.1547 0.009 0.967 6.3 107.2 21.1 398 n/a 3_xyzrec: 0.1166 0.1565 0.009 0.970 6.3 107.2 21.1 398 n/a 3_adp: 0.1148 0.1572 0.009 0.970 6.4 104.8 20.9 398 n/a 3_regHadp: 0.1148 0.1573 0.009 0.970 6.4 104.8 20.9 398 n/a 3_occ: 0.1140 0.1585 0.009 0.970 6.4 104.8 20.9 398 n/a 4_bss: 0.1138 0.1585 0.009 0.970 6.0 104.5 20.5 398 n/a 4_settarget: 0.1138 0.1585 0.009 0.970 6.0 104.5 20.5 398 n/a 4_updatecdl: 0.1138 0.1585 0.009 0.971 6.0 104.5 20.5 398 n/a 4_nqh: 0.1138 0.1585 0.009 0.971 6.0 104.5 20.5 398 n/a 4_sol: 0.1115 0.1487 0.009 0.971 6.0 104.5 21.1 449 n/a 4_weight: 0.1115 0.1487 0.009 0.971 6.0 104.5 21.1 449 n/a 4_xyzrec: 0.1105 0.1540 0.010 0.981 6.0 104.5 21.1 449 n/a 4_adp: 0.1095 0.1530 0.010 0.981 5.8 102.1 21.1 449 n/a 4_regHadp: 0.1095 0.1530 0.010 0.981 5.8 102.1 21.1 449 n/a 4_occ: 0.1086 0.1535 0.010 0.981 5.8 102.1 21.1 449 n/a 5_bss: 0.1085 0.1534 0.010 0.981 5.5 101.8 20.8 449 n/a 5_settarget: 0.1085 0.1534 0.010 0.981 5.5 101.8 20.8 449 n/a 5_updatecdl: 0.1085 0.1534 0.010 0.980 5.5 101.8 20.8 449 n/a 5_setrh: 0.1087 0.1533 0.010 0.980 5.5 101.8 20.8 449 n/a 5_nqh: 0.1087 0.1533 0.010 0.980 5.5 101.8 20.8 449 n/a 5_sol: 0.1094 0.1461 0.010 0.980 5.5 101.8 21.0 468 n/a 5_weight: 0.1094 0.1461 0.010 0.980 5.5 101.8 21.0 468 n/a 5_xyzrec: 0.1123 0.1500 0.009 1.043 5.5 101.8 21.0 468 n/a 5_adp: 0.1113 0.1496 0.009 1.043 5.5 100.9 21.1 468 n/a 5_regHadp: 0.1113 0.1496 0.009 1.043 5.5 100.9 21.1 468 n/a 5_occ: 0.1106 0.1493 0.009 1.043 5.5 100.9 21.1 468 n/a end: 0.1107 0.1497 0.009 1.043 5.2 100.7 20.8 468 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_8530424_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_8530424_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.1100 Refinement macro-cycles (run) : 919.5000 Write final files (write_after_run_outputs) : 20.5700 Total : 944.1800 Total CPU time: 16.11 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:07 PST -0800 (1735494067.19 s) Start R-work = 0.1618, R-free = 0.1700 Final R-work = 0.1107, R-free = 0.1497 =============================================================================== Job complete usr+sys time: 989.40 seconds wall clock time: 16 minutes 51.89 seconds (1011.89 seconds total)