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_2731660.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Adding command-line PHIL: ------------------------- xray_data.high_resolution=2 ordered_solvent.low_resolution=4 No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 2 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2731660.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2731660.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.19, per 1000 atoms: 0.35 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: 0.28 Conformation dependent library (CDL) restraints added in 132.0 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.64 - 0.89: 420 0.89 - 1.15: 1201 1.15 - 1.41: 598 1.41 - 1.66: 895 1.66 - 1.92: 39 Bond restraints: 3153 Sorted by residual: bond pdb=" N ATYR A 67 " pdb=" CA ATYR A 67 " ideal model delta sigma weight residual 1.455 1.217 0.238 1.21e-02 6.83e+03 3.86e+02 bond pdb=" CA GLU A 176 " pdb=" C GLU A 176 " ideal model delta sigma weight residual 1.524 1.762 -0.238 1.27e-02 6.20e+03 3.52e+02 bond pdb=" C ILE A 91 " pdb=" O ILE A 91 " ideal model delta sigma weight residual 1.237 1.032 0.205 1.14e-02 7.69e+03 3.24e+02 bond pdb=" C BGLU A 90 " pdb=" O BGLU A 90 " ideal model delta sigma weight residual 1.237 1.026 0.210 1.17e-02 7.31e+03 3.23e+02 bond pdb=" N LEU A 166 " pdb=" CA LEU A 166 " ideal model delta sigma weight residual 1.459 1.245 0.214 1.28e-02 6.10e+03 2.80e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.20: 2852 4.20 - 8.39: 1891 8.39 - 12.58: 799 12.58 - 16.78: 204 16.78 - 20.97: 31 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O HIS A 126 " pdb=" C HIS A 126 " pdb=" N PRO A 127 " ideal model delta sigma weight residual 121.30 106.14 15.16 1.03e+00 9.43e-01 2.17e+02 angle pdb=" CA ILE A 9 " pdb=" C ILE A 9 " pdb=" O ILE A 9 " ideal model delta sigma weight residual 120.53 135.60 -15.07 1.07e+00 8.73e-01 1.98e+02 angle pdb=" CA THR A 19 " pdb=" C THR A 19 " pdb=" O THR A 19 " ideal model delta sigma weight residual 120.56 137.52 -16.96 1.21e+00 6.83e-01 1.96e+02 angle pdb=" O GLU A 176 " pdb=" C GLU A 176 " pdb=" N VAL A 177 " ideal model delta sigma weight residual 122.07 136.33 -14.26 1.03e+00 9.43e-01 1.92e+02 angle pdb=" O SER A 155 " pdb=" C SER A 155 " pdb=" N ARG A 156 " ideal model delta sigma weight residual 123.26 108.99 14.27 1.05e+00 9.07e-01 1.85e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 1304 17.51 - 35.02: 128 35.02 - 52.53: 31 52.53 - 70.04: 16 70.04 - 87.55: 2 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C ILE A 105 " pdb=" N ILE A 105 " pdb=" CA ILE A 105 " pdb=" CB ILE A 105 " ideal model delta harmonic sigma weight residual -122.00 -146.95 24.95 0 2.50e+00 1.60e-01 9.96e+01 dihedral pdb=" C LEU A 151 " pdb=" N LEU A 151 " pdb=" CA LEU A 151 " pdb=" CB LEU A 151 " ideal model delta harmonic sigma weight residual -122.60 -145.52 22.92 0 2.50e+00 1.60e-01 8.41e+01 dihedral pdb=" C CYS A 106 " pdb=" N CYS A 106 " pdb=" CA CYS A 106 " pdb=" CB CYS A 106 " ideal model delta harmonic sigma weight residual -122.60 -142.53 19.93 0 2.50e+00 1.60e-01 6.36e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.217: 92 0.217 - 0.432: 85 0.432 - 0.647: 36 0.647 - 0.862: 23 0.862 - 1.077: 7 Chirality restraints: 243 Sorted by residual: chirality pdb=" CB VAL A 33 " pdb=" CA VAL A 33 " pdb=" CG1 VAL A 33 " pdb=" CG2 VAL A 33 " both_signs ideal model delta sigma weight residual False -2.63 -1.55 -1.08 2.00e-01 2.50e+01 2.90e+01 chirality pdb=" CA LEU A 151 " pdb=" N LEU A 151 " pdb=" C LEU A 151 " pdb=" CB LEU A 151 " both_signs ideal model delta sigma weight residual False 2.51 1.59 0.92 2.00e-01 2.50e+01 2.14e+01 chirality pdb=" CB VAL A 169 " pdb=" CA VAL A 169 " pdb=" CG1 VAL A 169 " pdb=" CG2 VAL A 169 " both_signs ideal model delta sigma weight residual False -2.63 -1.71 -0.92 2.00e-01 2.50e+01 2.12e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " 0.107 2.00e-02 2.50e+03 7.43e-02 1.66e+02 pdb=" CG TYR A 141 " -0.076 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " -0.052 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " 0.098 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " 0.051 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " -0.081 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " 0.133 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " -0.027 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " -0.040 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " -0.042 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " -0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 5 " -0.016 9.50e-02 1.11e+02 7.27e-02 1.18e+02 pdb=" NE ARG A 5 " -0.075 2.00e-02 2.50e+03 pdb=" CZ ARG A 5 " 0.149 2.00e-02 2.50e+03 pdb=" NH1 ARG A 5 " -0.104 2.00e-02 2.50e+03 pdb=" NH2 ARG A 5 " 0.057 2.00e-02 2.50e+03 pdb="HH11 ARG A 5 " 0.033 2.00e-02 2.50e+03 pdb="HH12 ARG A 5 " 0.016 2.00e-02 2.50e+03 pdb="HH21 ARG A 5 " -0.014 2.00e-02 2.50e+03 pdb="HH22 ARG A 5 " -0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " 0.032 2.00e-02 2.50e+03 5.88e-02 1.04e+02 pdb=" CG PHE A 162 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " -0.054 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " -0.088 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " 0.018 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " 0.017 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " -0.052 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " -0.014 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " 0.077 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " -0.008 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " -0.078 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " 0.115 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.36: 1314 2.36 - 2.92: 8268 2.92 - 3.48: 10480 3.48 - 4.04: 15127 4.04 - 4.60: 21440 Nonbonded interactions: 56629 Sorted by model distance: nonbonded pdb=" HG SER A 47 " pdb="HH11 ARG A 48 " model vdw 1.794 2.100 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.836 2.100 nonbonded pdb=" HG2 LYS A 12 " pdb=" HZ2 LYS A 12 " model vdw 1.838 2.270 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.842 2.100 nonbonded pdb=" H ALA A 104 " pdb=" O ALEU A 153 " model vdw 1.846 2.450 ... (remaining 56624 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_2731660_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1596 occupancy sum: 1438.50 (% of total atoms 46.85) Rotatable: count: 507 occupancy sum: 483.00 (% of total atoms 15.73) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2793 r_free= 0.1791 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.424091 | | target function (ml) not normalized (work): 71860.515246 | | target function (ml) not normalized (free): 3274.288099 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3186 0.2095 7.6418 5.0261| | 2: 3.63 - 2.88 1.00 2711 122 0.2649 0.1718 4.3153 4.3206| | 3: 2.88 - 2.52 1.00 2682 148 0.2567 0.1626 4.1739 4.1727| | 4: 2.52 - 2.29 1.00 2661 139 0.2576 0.1626 3.5105 3.6958| | 5: 2.29 - 2.13 1.00 2678 122 0.2673 0.1472 3.4125 3.4679| | 6: 2.13 - 2.00 1.00 2692 117 0.2738 0.1752 3.3228 3.3647| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 17.37 0.77 0.23 1271.67| | 2: 3.63 - 2.88 2711 122 0.83 23.46 1.31 0.23 1271.67| | 3: 2.88 - 2.52 2682 148 0.74 32.42 1.28 0.23 1271.67| | 4: 2.52 - 2.29 2661 139 0.93 11.62 1.30 0.26 139.16| | 5: 2.29 - 2.13 2678 122 0.92 13.81 1.32 0.26 139.16| | 6: 2.13 - 2.00 2692 117 0.90 16.50 1.33 0.26 139.16| |alpha: min = 0.23 max = 0.26 mean = 0.25| |beta: min = 139.16 max = 1271.67 mean = 711.72| |figures of merit: min = 0.00 max = 1.00 mean = 0.87| |phase err.(work): min = 0.00 max = 90.00 mean = 19.20| |phase err.(test): min = 0.00 max = 89.86 mean = 19.20| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.082 0.238 1557 Z= 5.523 Angle : 5.295 17.793 2118 Z= 3.754 Chirality : 0.405 1.077 243 Planarity : 0.033 0.101 284 Dihedral : 13.758 87.555 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.86 % Allowed : 1.86 % Favored : 96.27 % Cbeta Deviations : 38.92 % 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: -2.42 (0.47), residues: 224 helix: -2.39 (0.38), residues: 109 sheet: -0.53 (0.97), residues: 28 loop : -0.54 (0.57), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.142 0.025 ARG A 5 TYR 0.109 0.052 TYR A 141 PHE 0.088 0.033 PHE A 119 HIS 0.058 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= 0.2793 r_free= 0.1791 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.424091 | | target function (ml) not normalized (work): 71860.515246 | | target function (ml) not normalized (free): 3274.288099 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.2962 percent. r_work = 0.2923 r_free = 0.1967 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2868 0.2923 0.1967 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2868 0.2923 0.1967 n_refl.: 17050 remove outliers: r(all,work,free)=0.2157 0.2170 0.1967 n_refl.: 17045 overall B=-0.41 to atoms: r(all,work,free)=0.2130 0.2142 0.1949 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1614 0.1613 0.1635 n_refl.: 17045 remove outliers: r(all,work,free)=0.1613 0.1612 0.1635 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 0.4066 395.063 362.291 0.645 1.018 0.397 11.894-9.307 99.02 97 4 0.1817 634.088 616.364 0.927 1.019 0.380 9.237-7.194 100.00 213 7 0.2180 518.620 510.918 0.961 1.018 0.355 7.162-5.571 100.00 427 22 0.2354 389.225 375.934 0.915 1.016 0.299 5.546-4.326 100.00 867 58 0.1378 534.343 528.705 0.956 1.013 0.225 4.315-3.360 100.00 1859 96 0.1288 508.166 503.511 1.012 1.008 0.191 3.356-2.611 100.00 3867 181 0.1658 333.836 329.227 1.015 1.000 0.071 2.608-2.000 99.99 8818 434 0.1647 217.604 213.668 1.035 0.985 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.4744 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1612 r_free=0.1635 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 r_work=0.1615 r_free=0.1643 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.453490 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.878589 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 0.1350 0.1628 0.0278 0.008 1.0 1.0 0.5 0.0 0 11.227 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.50 16.28 2.78 3.013 18.446 0.879 0.023 12.76 16.50 3.74 3.662 18.722 0.879 0.020 Individual atomic B min max mean iso aniso Overall: 6.13 113.89 20.00 4.12 1785 0 Protein: 6.13 112.53 17.23 4.12 1519 0 Water: 8.85 113.89 36.10 N/A 258 0 Other: 22.05 37.46 26.42 N/A 8 0 Chain A: 6.13 113.89 20.00 N/A 1785 0 Histogram: Values Number of atoms 6.13 - 16.91 1080 16.91 - 27.68 347 27.68 - 38.46 182 38.46 - 49.23 101 49.23 - 60.01 48 60.01 - 70.78 12 70.78 - 81.56 7 81.56 - 92.33 4 92.33 - 103.11 1 103.11 - 113.89 3 =========================== Idealize ADP of riding H ========================== r_work=0.1276 r_free=0.1650 r_work=0.1280 r_free=0.1658 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1280 r_free = 0.1658 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 = 0.1275 r_free = 0.1653 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.18 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= 0.1275 r_free= 0.1653 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.019995 | | target function (ls_wunit_k1) not normalized (work): 324.660806 | | target function (ls_wunit_k1) not normalized (free): 27.100230 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1293 0.1275 0.1653 n_refl.: 17044 re-set all scales: r(all,work,free)=0.1913 0.1912 0.1990 n_refl.: 17044 remove outliers: r(all,work,free)=0.1913 0.1912 0.1990 n_refl.: 17044 overall B=-0.40 to atoms: r(all,work,free)=0.1884 0.1882 0.1974 n_refl.: 17044 bulk-solvent and scaling: r(all,work,free)=0.1295 0.1277 0.1649 n_refl.: 17044 remove outliers: r(all,work,free)=0.1293 0.1275 0.1649 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 0.3522 303.404 278.386 0.613 1.010 0.360 11.894-9.307 99.02 97 4 0.1704 487.978 477.854 0.917 1.011 0.358 9.237-7.194 100.00 213 7 0.1812 399.117 396.487 0.961 1.010 0.351 7.162-5.571 100.00 427 22 0.1836 299.537 294.425 0.931 1.009 0.301 5.546-4.326 100.00 867 58 0.1041 411.217 409.144 0.959 1.008 0.205 4.315-3.360 100.00 1859 96 0.0928 391.071 390.706 1.017 1.005 0.191 3.356-2.611 100.00 3867 181 0.1298 256.911 255.643 1.017 1.000 0.091 2.608-2.000 99.99 8818 434 0.1352 167.462 165.970 1.025 0.991 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9552 b_overall=-1.4143 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1275 r_free=0.1649 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=0.1275 r_free=0.1648 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1275 r_free=0.1648 | n_water=258 | time (s): 0.920 (total time: 0.920) Filter (dist) r_work=0.1278 r_free=0.1637 | n_water=254 | time (s): 20.330 (total time: 21.250) Filter (q & B) r_work=0.1278 r_free=0.1636 | n_water=252 | time (s): 2.070 (total time: 23.320) Compute maps r_work=0.1278 r_free=0.1636 | n_water=252 | time (s): 0.760 (total time: 24.080) Filter (map) r_work=0.1315 r_free=0.1630 | n_water=213 | time (s): 2.080 (total time: 26.160) Find peaks r_work=0.1315 r_free=0.1630 | n_water=213 | time (s): 0.530 (total time: 26.690) Add new water r_work=0.1536 r_free=0.1878 | n_water=367 | time (s): 1.640 (total time: 28.330) Refine new water occ: r_work=0.1330 r_free=0.1568 adp: r_work=0.1272 r_free=0.1563 occ: r_work=0.1278 r_free=0.1524 adp: r_work=0.1244 r_free=0.1537 occ: r_work=0.1245 r_free=0.1520 adp: r_work=0.1234 r_free=0.1526 ADP+occupancy (water only), MIN, final r_work=0.1234 r_free=0.1526 r_work=0.1234 r_free=0.1526 | n_water=367 | time (s): 10.430 (total time: 38.760) Filter (q & B) r_work=0.1236 r_free=0.1530 | n_water=358 | time (s): 1.600 (total time: 40.360) Filter (dist only) r_work=0.1236 r_free=0.1530 | n_water=358 | time (s): 26.690 (total time: 67.050) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.196440 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.998638 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 0.1211 0.1566 0.0355 0.008 0.9 2.2 0.5 0.0 0 12.098 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.11 15.66 3.55 4.192 21.042 0.999 0.018 11.93 16.01 4.08 4.272 21.319 0.999 0.017 Individual atomic B min max mean iso aniso Overall: 6.71 107.14 21.33 4.34 1885 0 Protein: 6.71 107.14 17.76 4.32 1519 0 Water: 8.79 65.77 36.14 N/A 358 0 Other: 26.13 47.37 36.80 N/A 8 0 Chain A: 6.71 107.14 19.52 N/A 1740 0 Chain S: 17.86 62.38 42.99 N/A 145 0 Histogram: Values Number of atoms 6.71 - 16.75 1021 16.75 - 26.79 384 26.79 - 36.84 208 36.84 - 46.88 164 46.88 - 56.92 72 56.92 - 66.97 24 66.97 - 77.01 4 77.01 - 87.05 5 87.05 - 97.10 1 97.10 - 107.14 2 =========================== Idealize ADP of riding H ========================== r_work=0.1193 r_free=0.1601 r_work=0.1195 r_free=0.1603 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1195 r_free = 0.1603 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1190 r_free = 0.1603 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.23 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= 0.1190 r_free= 0.1603 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.016936 | | target function (ls_wunit_k1) not normalized (work): 274.960104 | | target function (ls_wunit_k1) not normalized (free): 24.084351 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1210 0.1190 0.1603 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1749 0.1742 0.1920 n_refl.: 17042 remove outliers: r(all,work,free)=0.1749 0.1742 0.1920 n_refl.: 17042 overall B=-0.38 to atoms: r(all,work,free)=0.1724 0.1717 0.1905 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1203 0.1183 0.1596 n_refl.: 17042 remove outliers: r(all,work,free)=0.1202 0.1182 0.1596 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 0.3306 300.242 282.480 0.590 1.004 0.340 11.894-9.307 99.02 97 4 0.1553 487.978 485.416 0.912 1.005 0.334 9.237-7.194 100.00 213 7 0.1708 399.117 399.790 0.970 1.005 0.281 7.162-5.571 100.00 427 22 0.1526 299.537 295.746 0.939 1.005 0.240 5.546-4.326 100.00 867 58 0.0877 411.217 408.964 0.962 1.004 0.221 4.315-3.360 100.00 1859 96 0.0809 391.071 390.285 1.014 1.003 0.181 3.356-2.611 100.00 3867 181 0.1186 256.911 256.143 1.012 1.001 0.121 2.608-2.000 99.99 8818 434 0.1328 167.462 166.419 1.017 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.3594 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1182 r_free=0.1596 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=0.1184 r_free=0.1598 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1184 r_free=0.1598 | n_water=358 | time (s): 0.920 (total time: 0.920) Filter (dist) r_work=0.1184 r_free=0.1599 | n_water=357 | time (s): 27.760 (total time: 28.680) Filter (q & B) r_work=0.1184 r_free=0.1599 | n_water=357 | time (s): 0.970 (total time: 29.650) Compute maps r_work=0.1184 r_free=0.1599 | n_water=357 | time (s): 0.740 (total time: 30.390) Filter (map) r_work=0.1258 r_free=0.1634 | n_water=263 | time (s): 1.960 (total time: 32.350) Find peaks r_work=0.1258 r_free=0.1634 | n_water=263 | time (s): 0.450 (total time: 32.800) Add new water r_work=0.1428 r_free=0.1824 | n_water=407 | time (s): 1.750 (total time: 34.550) Refine new water occ: r_work=0.1237 r_free=0.1568 adp: r_work=0.1230 r_free=0.1579 occ: r_work=0.1214 r_free=0.1541 adp: r_work=0.1205 r_free=0.1551 occ: r_work=0.1199 r_free=0.1527 adp: r_work=0.1189 r_free=0.1532 ADP+occupancy (water only), MIN, final r_work=0.1189 r_free=0.1532 r_work=0.1189 r_free=0.1532 | n_water=407 | time (s): 38.370 (total time: 72.920) Filter (q & B) r_work=0.1193 r_free=0.1536 | n_water=397 | time (s): 1.910 (total time: 74.830) Filter (dist only) r_work=0.1193 r_free=0.1536 | n_water=397 | time (s): 31.180 (total time: 106.010) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.901115 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.121087 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 0.1170 0.1584 0.0414 0.009 1.0 3.8 0.5 0.0 0 0.951 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.70 15.84 4.14 4.373 21.489 0.121 5.000 11.53 15.88 4.35 4.872 21.364 0.121 4.976 Individual atomic B min max mean iso aniso Overall: 6.33 103.72 20.72 4.54 1924 0 Protein: 6.33 103.72 16.99 4.52 1519 0 Water: 8.63 62.28 34.71 N/A 397 0 Other: 24.94 45.36 33.27 N/A 8 0 Chain A: 6.33 103.72 18.75 N/A 1737 0 Chain S: 15.17 62.28 38.97 N/A 187 0 Histogram: Values Number of atoms 6.33 - 16.07 1061 16.07 - 25.81 351 25.81 - 35.55 230 35.55 - 45.29 171 45.29 - 55.03 70 55.03 - 64.77 28 64.77 - 74.50 4 74.50 - 84.24 4 84.24 - 93.98 3 93.98 - 103.72 2 =========================== Idealize ADP of riding H ========================== r_work=0.1153 r_free=0.1588 r_work=0.1152 r_free=0.1588 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1152 r_free = 0.1588 target_work(ml) = 4.976 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1147 r_free = 0.1594 target_work(ml) = 4.976 | | 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= 0.1147 r_free= 0.1594 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.975537 | | target function (ml) not normalized (work): 80772.859729 | | target function (ml) not normalized (free): 4199.680525 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1169 0.1147 0.1594 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1678 0.1668 0.1919 n_refl.: 17041 remove outliers: r(all,work,free)=0.1678 0.1668 0.1919 n_refl.: 17041 overall B=-0.51 to atoms: r(all,work,free)=0.1643 0.1633 0.1898 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1167 0.1145 0.1593 n_refl.: 17041 remove outliers: r(all,work,free)=0.1167 0.1145 0.1593 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 0.3541 300.242 279.207 0.566 1.006 0.334 11.894-9.307 99.02 97 4 0.1689 487.978 483.088 0.915 1.007 0.330 9.237-7.194 100.00 213 7 0.1787 399.117 400.689 0.982 1.007 0.240 7.162-5.571 100.00 427 22 0.1618 299.537 294.276 0.944 1.006 0.221 5.546-4.326 100.00 867 58 0.0921 411.217 407.339 0.964 1.005 0.206 4.315-3.360 100.00 1859 96 0.0896 391.071 388.673 1.011 1.004 0.202 3.356-2.611 100.00 3867 181 0.1270 256.911 254.721 1.010 1.001 0.162 2.608-2.000 99.99 8818 434 0.1100 167.462 166.033 1.012 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-1.1657 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1145 r_free=0.1593 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1145 r_free=0.1593 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1145 r_free=0.1593 | n_water=397 | time (s): 0.710 (total time: 0.710) Filter (dist) r_work=0.1145 r_free=0.1596 | n_water=396 | time (s): 31.470 (total time: 32.180) Filter (q & B) r_work=0.1145 r_free=0.1596 | n_water=396 | time (s): 0.980 (total time: 33.160) Compute maps r_work=0.1145 r_free=0.1596 | n_water=396 | time (s): 0.600 (total time: 33.760) Filter (map) r_work=0.1188 r_free=0.1594 | n_water=319 | time (s): 1.690 (total time: 35.450) Find peaks r_work=0.1188 r_free=0.1594 | n_water=319 | time (s): 0.510 (total time: 35.960) Add new water r_work=0.1321 r_free=0.1728 | n_water=458 | time (s): 1.700 (total time: 37.660) Refine new water occ: r_work=0.1169 r_free=0.1538 adp: r_work=0.1162 r_free=0.1546 occ: r_work=0.1149 r_free=0.1520 adp: r_work=0.1140 r_free=0.1525 occ: r_work=0.1134 r_free=0.1511 adp: r_work=0.1126 r_free=0.1514 ADP+occupancy (water only), MIN, final r_work=0.1126 r_free=0.1514 r_work=0.1126 r_free=0.1514 | n_water=458 | time (s): 31.550 (total time: 69.210) Filter (q & B) r_work=0.1129 r_free=0.1518 | n_water=449 | time (s): 2.430 (total time: 71.640) Filter (dist only) r_work=0.1133 r_free=0.1520 | n_water=448 | time (s): 35.490 (total time: 107.130) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.878639 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.178439 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 0.1130 0.1573 0.0444 0.009 1.0 3.2 0.5 0.0 0 0.939 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.30 15.73 4.44 4.405 20.924 0.178 4.966 11.15 15.63 4.47 4.581 20.999 0.178 4.954 Individual atomic B min max mean iso aniso Overall: 5.49 102.16 20.95 4.84 1975 0 Protein: 5.49 102.16 16.43 4.83 1519 0 Water: 8.25 63.09 36.02 N/A 448 0 Other: 25.61 45.00 33.98 N/A 8 0 Chain A: 5.49 102.16 18.16 N/A 1736 0 Chain S: 14.97 63.09 41.22 N/A 239 0 Histogram: Values Number of atoms 5.49 - 15.16 1030 15.16 - 24.83 377 24.83 - 34.49 212 34.49 - 44.16 195 44.16 - 53.83 106 53.83 - 63.49 41 63.49 - 73.16 5 73.16 - 82.83 4 82.83 - 92.50 2 92.50 - 102.16 3 =========================== Idealize ADP of riding H ========================== r_work=0.1115 r_free=0.1563 r_work=0.1115 r_free=0.1563 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1115 r_free = 0.1563 target_work(ml) = 4.954 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1109 r_free = 0.1558 target_work(ml) = 4.948 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1109 r_free= 0.1558 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ml) (work): 4.948377 | | target function (ml) not normalized (work): 80331.952964 | | target function (ml) not normalized (free): 4180.152527 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1130 0.1109 0.1558 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1580 0.1566 0.1878 n_refl.: 17041 remove outliers: r(all,work,free)=0.1580 0.1566 0.1878 n_refl.: 17041 overall B=-0.26 to atoms: r(all,work,free)=0.1564 0.1550 0.1868 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1129 0.1108 0.1554 n_refl.: 17041 remove outliers: r(all,work,free)=0.1129 0.1108 0.1554 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 0.3673 300.242 279.897 0.552 1.002 0.330 11.894-9.307 99.02 97 4 0.1794 487.978 484.458 0.919 1.003 0.320 9.237-7.194 100.00 213 7 0.1694 399.117 400.290 0.989 1.004 0.240 7.162-5.571 100.00 427 22 0.1522 299.537 294.299 0.945 1.003 0.209 5.546-4.326 100.00 867 58 0.0896 411.217 407.722 0.963 1.003 0.194 4.315-3.360 100.00 1859 96 0.0866 391.071 388.552 1.005 1.002 0.184 3.356-2.611 100.00 3867 181 0.1244 256.911 254.758 1.003 1.001 0.151 2.608-2.000 99.99 8818 434 0.1049 167.462 166.204 0.998 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.9144 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1108 r_free=0.1554 After: r_work=0.1110 r_free=0.1552 ================================== NQH flips ================================== r_work=0.1110 r_free=0.1552 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN Total number of N/Q/H flips: 1 r_work=0.1113 r_free=0.1553 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1113 r_free=0.1553 | n_water=448 | time (s): 0.930 (total time: 0.930) Filter (dist) r_work=0.1113 r_free=0.1553 | n_water=448 | time (s): 33.160 (total time: 34.090) Filter (q & B) r_work=0.1113 r_free=0.1553 | n_water=448 | time (s): 1.030 (total time: 35.120) Compute maps r_work=0.1113 r_free=0.1553 | n_water=448 | time (s): 0.580 (total time: 35.700) Filter (map) r_work=0.1181 r_free=0.1565 | n_water=342 | time (s): 1.490 (total time: 37.190) Find peaks r_work=0.1181 r_free=0.1565 | n_water=342 | time (s): 0.490 (total time: 37.680) Add new water r_work=0.1298 r_free=0.1675 | n_water=479 | time (s): 1.710 (total time: 39.390) Refine new water occ: r_work=0.1150 r_free=0.1503 adp: r_work=0.1142 r_free=0.1509 occ: r_work=0.1127 r_free=0.1483 adp: r_work=0.1118 r_free=0.1486 occ: r_work=0.1112 r_free=0.1470 adp: r_work=0.1103 r_free=0.1472 ADP+occupancy (water only), MIN, final r_work=0.1103 r_free=0.1472 r_work=0.1103 r_free=0.1472 | n_water=479 | time (s): 28.700 (total time: 68.090) Filter (q & B) r_work=0.1106 r_free=0.1477 | n_water=468 | time (s): 2.240 (total time: 70.330) Filter (dist only) r_work=0.1107 r_free=0.1477 | n_water=467 | time (s): 38.750 (total time: 109.080) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.920405 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.181617 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 0.1135 0.1550 0.0415 0.010 1.1 6.7 0.5 0.0 0 0.960 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.35 15.50 4.15 4.532 20.806 0.182 4.965 11.24 15.45 4.21 4.641 20.886 0.182 4.957 Individual atomic B min max mean iso aniso Overall: 5.34 101.87 21.04 5.03 1994 0 Protein: 5.34 101.87 16.19 5.01 1519 0 Water: 7.67 62.54 36.62 N/A 467 0 Other: 24.71 44.68 32.70 N/A 8 0 Chain A: 5.34 101.87 17.87 N/A 1736 0 Chain S: 18.01 62.54 42.33 N/A 258 0 Histogram: Values Number of atoms 5.34 - 14.99 1029 14.99 - 24.64 378 24.64 - 34.29 210 34.29 - 43.95 186 43.95 - 53.60 132 53.60 - 63.25 42 63.25 - 72.91 8 72.91 - 82.56 2 82.56 - 92.21 3 92.21 - 101.87 4 =========================== Idealize ADP of riding H ========================== r_work=0.1124 r_free=0.1545 r_work=0.1124 r_free=0.1545 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1124 r_free = 0.1545 target_work(ml) = 4.957 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1116 r_free = 0.1550 target_work(ml) = 4.953 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1116 r_free= 0.1550 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ml) (work): 4.953211 | | target function (ml) not normalized (work): 80410.428069 | | target function (ml) not normalized (free): 4181.047403 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.64 1.00 2811 159 0.1115 0.1441 5.4658 5.6722| | 2: 3.63 - 2.88 1.00 2711 122 0.1105 0.1419 5.2331 5.3185| | 3: 2.88 - 2.52 1.00 2681 148 0.1358 0.1817 5.1335 5.2492| | 4: 2.52 - 2.29 1.00 2661 139 0.0955 0.1594 4.654 4.9998| | 5: 2.29 - 2.13 1.00 2678 122 0.0980 0.1523 4.6067 4.8895| | 6: 2.13 - 2.00 1.00 2692 117 0.1138 0.1724 4.5971 4.8029| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2811 159 0.95 9.14 1.00 0.95 6522.11| | 2: 3.63 - 2.88 2711 122 0.92 12.95 1.01 0.95 6522.11| | 3: 2.88 - 2.52 2681 148 0.87 19.27 0.99 0.95 6522.11| | 4: 2.52 - 2.29 2661 139 0.92 12.64 1.01 0.97 2270.75| | 5: 2.29 - 2.13 2678 122 0.91 14.75 1.00 0.97 2270.75| | 6: 2.13 - 2.00 2692 117 0.89 17.49 0.99 0.97 2270.75| |alpha: min = 0.95 max = 0.97 mean = 0.96| |beta: min = 2270.75 max = 6522.11 mean = 4418.95| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.91 mean = 14.33| |phase err.(test): min = 0.00 max = 88.99 mean = 14.02| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1137 0.1116 0.1550 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1560 0.1548 0.1818 n_refl.: 17041 remove outliers: r(all,work,free)=0.1560 0.1548 0.1818 n_refl.: 17041 overall B=-0.21 to atoms: r(all,work,free)=0.1548 0.1536 0.1811 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1137 0.1116 0.1551 n_refl.: 17041 remove outliers: r(all,work,free)=0.1137 0.1116 0.1551 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 0.3668 300.242 279.857 0.552 1.001 0.330 11.894-9.307 99.02 97 4 0.1748 487.978 482.206 0.920 1.002 0.330 9.237-7.194 100.00 213 7 0.1710 399.117 400.433 0.989 1.003 0.220 7.162-5.571 100.00 427 22 0.1519 299.537 294.674 0.945 1.003 0.205 5.546-4.326 100.00 867 58 0.0924 411.217 408.366 0.962 1.003 0.200 4.315-3.360 100.00 1859 96 0.0873 391.071 388.919 1.003 1.002 0.165 3.356-2.611 100.00 3867 181 0.1257 256.911 254.537 0.998 1.001 0.151 2.608-2.000 99.99 8818 434 0.1053 167.462 166.083 0.986 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.7207 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2793 0.1791 0.082 5.295 8.8 119.3 19.9 258 0.000 1_bss: 0.1612 0.1635 0.082 5.295 8.4 118.9 19.5 258 0.000 1_settarget: 0.1612 0.1635 0.082 5.295 8.4 118.9 19.5 258 0.000 1_nqh: 0.1615 0.1643 0.082 5.295 8.4 118.9 19.5 258 0.003 1_weight: 0.1615 0.1643 0.082 5.295 8.4 118.9 19.5 258 0.003 1_xyzrec: 0.1350 0.1628 0.008 0.970 8.4 118.9 19.5 258 0.151 1_adp: 0.1276 0.1650 0.008 0.970 6.1 113.9 20.0 258 0.151 1_regHadp: 0.1280 0.1658 0.008 0.970 6.1 113.9 20.0 258 0.151 1_occ: 0.1275 0.1653 0.008 0.970 6.1 113.9 20.0 258 0.151 2_bss: 0.1275 0.1649 0.008 0.970 5.7 113.5 19.6 258 0.151 2_settarget: 0.1275 0.1649 0.008 0.970 5.7 113.5 19.6 258 0.151 2_updatecdl: 0.1275 0.1649 0.008 0.982 5.7 113.5 19.6 258 0.151 2_nqh: 0.1275 0.1648 0.008 0.982 5.7 113.5 19.6 258 0.148 2_sol: 0.1236 0.1530 0.008 0.982 5.7 112.1 20.8 358 n/a 2_weight: 0.1236 0.1530 0.008 0.982 5.7 112.1 20.8 358 n/a 2_xyzrec: 0.1211 0.1566 0.008 0.920 5.7 112.1 20.8 358 n/a 2_adp: 0.1193 0.1601 0.008 0.920 6.7 107.1 21.3 358 n/a 2_regHadp: 0.1195 0.1603 0.008 0.920 6.7 107.1 21.3 358 n/a 2_occ: 0.1190 0.1603 0.008 0.920 6.7 107.1 21.3 358 n/a 3_bss: 0.1182 0.1596 0.008 0.920 6.3 106.8 20.9 358 n/a 3_settarget: 0.1182 0.1596 0.008 0.920 6.3 106.8 20.9 358 n/a 3_updatecdl: 0.1182 0.1596 0.008 0.926 6.3 106.8 20.9 358 n/a 3_nqh: 0.1184 0.1598 0.008 0.926 6.3 106.8 20.9 358 n/a 3_sol: 0.1193 0.1536 0.008 0.926 6.3 106.8 20.9 397 n/a 3_weight: 0.1193 0.1536 0.008 0.926 6.3 106.8 20.9 397 n/a 3_xyzrec: 0.1170 0.1584 0.009 0.961 6.3 106.8 20.9 397 n/a 3_adp: 0.1153 0.1588 0.009 0.961 6.3 103.7 20.7 397 n/a 3_regHadp: 0.1152 0.1588 0.009 0.961 6.3 103.7 20.7 397 n/a 3_occ: 0.1147 0.1594 0.009 0.961 6.3 103.7 20.7 397 n/a 4_bss: 0.1145 0.1593 0.009 0.961 5.8 103.2 20.2 397 n/a 4_settarget: 0.1145 0.1593 0.009 0.961 5.8 103.2 20.2 397 n/a 4_updatecdl: 0.1145 0.1593 0.009 0.960 5.8 103.2 20.2 397 n/a 4_nqh: 0.1145 0.1593 0.009 0.960 5.8 103.2 20.2 397 n/a 4_sol: 0.1133 0.1520 0.009 0.960 5.8 103.2 20.8 448 n/a 4_weight: 0.1133 0.1520 0.009 0.960 5.8 103.2 20.8 448 n/a 4_xyzrec: 0.1130 0.1573 0.009 0.960 5.8 103.2 20.8 448 n/a 4_adp: 0.1115 0.1563 0.009 0.960 5.5 102.2 20.9 448 n/a 4_regHadp: 0.1115 0.1563 0.009 0.960 5.5 102.2 20.9 448 n/a 4_occ: 0.1109 0.1558 0.009 0.960 5.5 102.2 20.9 448 n/a 5_bss: 0.1108 0.1554 0.009 0.960 5.2 101.9 20.7 448 n/a 5_settarget: 0.1108 0.1554 0.009 0.960 5.2 101.9 20.7 448 n/a 5_updatecdl: 0.1108 0.1554 0.009 0.963 5.2 101.9 20.7 448 n/a 5_setrh: 0.1110 0.1552 0.009 0.963 5.2 101.9 20.7 448 n/a 5_nqh: 0.1113 0.1553 0.009 0.963 5.2 101.9 20.7 448 n/a 5_sol: 0.1107 0.1477 0.009 0.963 5.2 101.9 20.9 467 n/a 5_weight: 0.1107 0.1477 0.009 0.963 5.2 101.9 20.9 467 n/a 5_xyzrec: 0.1135 0.1550 0.010 1.066 5.2 101.9 20.9 467 n/a 5_adp: 0.1124 0.1545 0.010 1.066 5.3 101.9 21.0 467 n/a 5_regHadp: 0.1124 0.1545 0.010 1.066 5.3 101.9 21.0 467 n/a 5_occ: 0.1116 0.1550 0.010 1.066 5.3 101.9 21.0 467 n/a end: 0.1116 0.1551 0.010 1.066 5.1 101.7 20.8 467 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_2731660_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_2731660_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.3900 Refinement macro-cycles (run) : 910.6800 Write final files (write_after_run_outputs) : 19.5300 Total : 933.6000 Total CPU time: 15.95 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:40:58 PST -0800 (1735494058.80 s) Start R-work = 0.1612, R-free = 0.1635 Final R-work = 0.1116, R-free = 0.1551 =============================================================================== Job complete usr+sys time: 980.53 seconds wall clock time: 16 minutes 43.79 seconds (1003.79 seconds total)