Starting phenix.refine on Sun Dec 29 09:24:41 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3337960.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Adding command-line PHIL: ------------------------- xray_data.high_resolution=2 ordered_solvent.low_resolution=4 No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 2 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3337960.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3337960.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 3 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: 1.50, per 1000 atoms: 0.44 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: 0.29 Conformation dependent library (CDL) restraints added in 106.0 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.64 - 0.90: 427 0.90 - 1.16: 1204 1.16 - 1.42: 637 1.42 - 1.67: 845 1.67 - 1.93: 40 Bond restraints: 3153 Sorted by residual: bond pdb=" C GLN A 95 " pdb=" O GLN A 95 " ideal model delta sigma weight residual 1.237 1.480 -0.244 1.19e-02 7.06e+03 4.19e+02 bond pdb=" CE1 HIS A 115 " pdb=" NE2 HIS A 115 " ideal model delta sigma weight residual 1.321 1.520 -0.199 1.00e-02 1.00e+04 3.95e+02 bond pdb=" CA LEU A 101 " pdb=" C LEU A 101 " ideal model delta sigma weight residual 1.523 1.289 0.234 1.23e-02 6.61e+03 3.61e+02 bond pdb=" N ALA A 183 " pdb=" CA ALA A 183 " ideal model delta sigma weight residual 1.462 1.319 0.143 7.70e-03 1.69e+04 3.43e+02 bond pdb=" C ILE A 168 " pdb=" O ILE A 168 " ideal model delta sigma weight residual 1.236 1.440 -0.204 1.11e-02 8.12e+03 3.36e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.28: 2930 4.28 - 8.55: 1862 8.55 - 12.83: 781 12.83 - 17.11: 179 17.11 - 21.39: 25 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O LYS A 89 " pdb=" C LYS A 89 " pdb=" N BGLU A 90 " ideal model delta sigma weight residual 122.09 138.18 -16.09 1.04e+00 9.25e-01 2.39e+02 angle pdb=" O LYS A 89 " pdb=" C LYS A 89 " pdb=" N AGLU A 90 " ideal model delta sigma weight residual 122.09 138.01 -15.92 1.04e+00 9.25e-01 2.34e+02 angle pdb=" C ALYS A 99 " pdb=" N GLY A 100 " pdb=" CA GLY A 100 " ideal model delta sigma weight residual 122.36 136.29 -13.93 9.70e-01 1.06e+00 2.06e+02 angle pdb=" N ILE A 21 " pdb=" CA ILE A 21 " pdb=" CB ILE A 21 " ideal model delta sigma weight residual 110.52 119.67 -9.15 6.70e-01 2.23e+00 1.86e+02 angle pdb=" O ILE A 21 " pdb=" C ILE A 21 " pdb=" N PRO A 22 " ideal model delta sigma weight residual 120.42 112.03 8.39 6.40e-01 2.44e+00 1.72e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.17: 1297 17.17 - 34.33: 131 34.33 - 51.50: 38 51.50 - 68.66: 11 68.66 - 85.82: 4 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C ARG A 48 " pdb=" N ARG A 48 " pdb=" CA ARG A 48 " pdb=" CB ARG A 48 " ideal model delta harmonic sigma weight residual -122.60 -143.44 20.84 0 2.50e+00 1.60e-01 6.95e+01 dihedral pdb=" C LEU A 38 " pdb=" N LEU A 38 " pdb=" CA LEU A 38 " pdb=" CB LEU A 38 " ideal model delta harmonic sigma weight residual -122.60 -142.59 19.99 0 2.50e+00 1.60e-01 6.40e+01 dihedral pdb=" N BASN A 97 " pdb=" C BASN A 97 " pdb=" CA BASN A 97 " pdb=" CB BASN A 97 " ideal model delta harmonic sigma weight residual 122.80 103.01 19.79 0 2.50e+00 1.60e-01 6.27e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.204: 87 0.204 - 0.407: 61 0.407 - 0.610: 55 0.610 - 0.813: 33 0.813 - 1.016: 7 Chirality restraints: 243 Sorted by residual: chirality pdb=" CG LEU A 172 " pdb=" CB LEU A 172 " pdb=" CD1 LEU A 172 " pdb=" CD2 LEU A 172 " both_signs ideal model delta sigma weight residual False -2.59 -1.57 -1.02 2.00e-01 2.50e+01 2.58e+01 chirality pdb=" CA LEU A 38 " pdb=" N LEU A 38 " pdb=" C LEU A 38 " pdb=" CB LEU A 38 " both_signs ideal model delta sigma weight residual False 2.51 1.57 0.94 2.00e-01 2.50e+01 2.22e+01 chirality pdb=" CA ARG A 48 " pdb=" N ARG A 48 " pdb=" C ARG A 48 " pdb=" CB ARG A 48 " both_signs ideal model delta sigma weight residual False 2.51 1.61 0.90 2.00e-01 2.50e+01 2.03e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 115 " -0.071 2.00e-02 2.50e+03 7.77e-02 1.36e+02 pdb=" CG HIS A 115 " 0.129 2.00e-02 2.50e+03 pdb=" ND1 HIS A 115 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 HIS A 115 " 0.044 2.00e-02 2.50e+03 pdb=" CE1 HIS A 115 " 0.060 2.00e-02 2.50e+03 pdb=" NE2 HIS A 115 " 0.037 2.00e-02 2.50e+03 pdb=" HD2 HIS A 115 " -0.102 2.00e-02 2.50e+03 pdb=" HE1 HIS A 115 " -0.122 2.00e-02 2.50e+03 pdb=" HE2 HIS A 115 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " -0.050 2.00e-02 2.50e+03 6.28e-02 1.18e+02 pdb=" CG TYR A 139 " 0.085 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " -0.052 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " 0.112 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " -0.030 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " 0.090 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.002 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " -0.000 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " -0.068 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.008 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " -0.093 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 126 " 0.046 2.00e-02 2.50e+03 6.45e-02 9.35e+01 pdb=" CG HIS A 126 " -0.156 2.00e-02 2.50e+03 pdb=" ND1 HIS A 126 " 0.060 2.00e-02 2.50e+03 pdb=" CD2 HIS A 126 " 0.060 2.00e-02 2.50e+03 pdb=" CE1 HIS A 126 " -0.004 2.00e-02 2.50e+03 pdb=" NE2 HIS A 126 " -0.054 2.00e-02 2.50e+03 pdb=" HD2 HIS A 126 " 0.016 2.00e-02 2.50e+03 pdb=" HE1 HIS A 126 " 0.013 2.00e-02 2.50e+03 pdb=" HE2 HIS A 126 " 0.018 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.37: 1380 2.37 - 2.92: 8342 2.92 - 3.48: 10421 3.48 - 4.04: 15124 4.04 - 4.60: 21393 Nonbonded interactions: 56660 Sorted by model distance: nonbonded pdb=" HG SER A 47 " pdb="HH11 ARG A 48 " model vdw 1.808 2.100 nonbonded pdb=" HE2 HIS A 126 " pdb=" O PRO A 184 " model vdw sym.op. 1.822 2.450 x-y,-y,-z-4/3 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.832 2.100 nonbonded pdb=" HD3 ARG A 5 " pdb="HH11 ARG A 5 " model vdw 1.832 2.270 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.837 2.100 ... (remaining 56655 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_3337960_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= 0.2787 r_free= 0.1805 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.416187 | | target function (ml) not normalized (work): 71732.125520 | | target function (ml) not normalized (free): 3252.993698 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2132 7.5893 5.0321| | 2: 3.63 - 2.88 1.00 2711 122 0.2619 0.1660 4.3212 4.3213| | 3: 2.88 - 2.52 1.00 2682 148 0.2550 0.1738 4.1777 4.1759| | 4: 2.52 - 2.29 1.00 2661 139 0.2599 0.1536 3.5296 3.5482| | 5: 2.29 - 2.13 1.00 2678 122 0.2670 0.1426 3.4022 3.4057| | 6: 2.13 - 2.00 1.00 2692 117 0.2736 0.1884 3.3117 3.41| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 17.47 0.77 0.23 1278.81| | 2: 3.63 - 2.88 2711 122 0.83 23.49 1.31 0.23 1278.81| | 3: 2.88 - 2.52 2682 148 0.73 32.58 1.28 0.23 1278.81| | 4: 2.52 - 2.29 2661 139 0.94 11.17 1.30 0.26 131.85| | 5: 2.29 - 2.13 2678 122 0.92 13.53 1.32 0.26 131.85| | 6: 2.13 - 2.00 2692 117 0.90 16.29 1.33 0.26 131.85| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 131.85 max = 1278.81 mean = 711.72| |figures of merit: min = 0.00 max = 1.00 mean = 0.87| |phase err.(work): min = 0.00 max = 89.83 mean = 19.09| |phase err.(test): min = 0.00 max = 89.80 mean = 19.35| |-----------------------------------------------------------------------------| ----------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 0.267 1557 Z= 5.518 Angle : 5.435 18.859 2118 Z= 3.876 Chirality : 0.419 1.016 243 Planarity : 0.033 0.105 284 Dihedral : 14.574 85.823 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.24 % Favored : 96.22 % Rotamer: Outliers : 1.24 % Allowed : 3.73 % Favored : 95.03 % Cbeta Deviations : 34.05 % 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: -2.55 (0.48), residues: 224 helix: -2.75 (0.40), residues: 103 sheet: 0.14 (1.08), residues: 28 loop : -0.72 (0.50), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.081 0.021 ARG A 27 TYR 0.063 0.022 TYR A 139 PHE 0.072 0.032 PHE A 164 HIS 0.109 0.042 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= 0.2787 r_free= 0.1805 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.416187 | | target function (ml) not normalized (work): 71732.125520 | | target function (ml) not normalized (free): 3252.993698 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.3057 percent. r_work = 0.2918 r_free = 0.1957 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2864 0.2918 0.1957 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2864 0.2918 0.1957 n_refl.: 17050 remove outliers: r(all,work,free)=0.2156 0.2169 0.1957 n_refl.: 17045 overall B=-0.41 to atoms: r(all,work,free)=0.2129 0.2141 0.1937 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1618 0.1618 0.1615 n_refl.: 17045 remove outliers: r(all,work,free)=0.1616 0.1616 0.1615 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 0.3872 398.969 360.158 0.645 1.018 0.397 11.894-9.307 99.02 97 4 0.1899 633.656 613.817 0.923 1.019 0.380 9.237-7.194 100.00 213 7 0.2193 518.267 507.544 0.959 1.018 0.364 7.162-5.571 100.00 427 22 0.2335 388.960 375.888 0.917 1.016 0.297 5.546-4.326 100.00 867 58 0.1393 533.980 528.227 0.955 1.014 0.225 4.315-3.360 100.00 1859 96 0.1278 507.820 504.574 1.013 1.008 0.201 3.356-2.611 100.00 3867 181 0.1646 333.609 329.450 1.013 0.999 0.034 2.608-2.000 99.99 8818 434 0.1668 217.456 213.324 1.036 0.984 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.4507 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1616 r_free=0.1615 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 80 GLN B Total number of N/Q/H flips: 1 r_work=0.1615 r_free=0.1616 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.334236 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.902315 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 0.1348 0.1645 0.0297 0.009 1.0 1.0 0.5 0.0 0 12.167 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.48 16.45 2.97 3.013 18.452 0.902 0.023 12.77 16.64 3.87 3.625 18.712 0.902 0.020 Individual atomic B min max mean iso aniso Overall: 6.33 113.89 19.97 4.10 1785 0 Protein: 6.33 113.21 17.21 4.11 1519 0 Water: 8.97 113.89 36.04 N/A 258 0 Other: 21.87 37.08 26.49 N/A 8 0 Chain A: 6.33 113.89 19.97 N/A 1785 0 Histogram: Values Number of atoms 6.33 - 17.08 1094 17.08 - 27.84 337 27.84 - 38.60 182 38.60 - 49.35 96 49.35 - 60.11 49 60.11 - 70.87 13 70.87 - 81.62 6 81.62 - 92.38 4 92.38 - 103.14 1 103.14 - 113.89 3 =========================== Idealize ADP of riding H ========================== r_work=0.1277 r_free=0.1664 r_work=0.1280 r_free=0.1670 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1280 r_free = 0.1670 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 = 0.1662 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.21 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= 0.1275 r_free= 0.1662 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.020003 | | target function (ls_wunit_k1) not normalized (work): 324.771534 | | target function (ls_wunit_k1) not normalized (free): 27.454385 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1293 0.1275 0.1662 n_refl.: 17043 re-set all scales: r(all,work,free)=0.1903 0.1902 0.1986 n_refl.: 17043 remove outliers: r(all,work,free)=0.1903 0.1902 0.1986 n_refl.: 17043 overall B=-0.37 to atoms: r(all,work,free)=0.1876 0.1874 0.1970 n_refl.: 17043 bulk-solvent and scaling: r(all,work,free)=0.1292 0.1274 0.1654 n_refl.: 17043 remove outliers: r(all,work,free)=0.1290 0.1272 0.1654 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 0.3427 306.681 281.014 0.631 1.006 0.370 11.894-9.307 99.02 97 4 0.1662 487.975 476.995 0.918 1.007 0.367 9.237-7.194 100.00 213 7 0.1837 399.114 395.513 0.958 1.007 0.351 7.162-5.571 100.00 427 22 0.1863 299.536 293.561 0.929 1.006 0.301 5.546-4.326 100.00 867 58 0.1048 411.214 408.589 0.958 1.005 0.221 4.315-3.360 100.00 1859 96 0.0933 391.069 390.494 1.014 1.004 0.181 3.356-2.611 100.00 3867 181 0.1295 256.910 255.631 1.011 1.001 0.091 2.608-2.000 99.99 8818 434 0.1343 167.461 166.123 1.017 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.3312 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1272 r_free=0.1654 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN B Total number of N/Q/H flips: 1 r_work=0.1272 r_free=0.1654 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1272 r_free=0.1654 | n_water=258 | time (s): 0.720 (total time: 0.720) Filter (dist) r_work=0.1277 r_free=0.1647 | n_water=253 | time (s): 20.850 (total time: 21.570) Filter (q & B) r_work=0.1277 r_free=0.1647 | n_water=251 | time (s): 1.860 (total time: 23.430) Compute maps r_work=0.1277 r_free=0.1647 | n_water=251 | time (s): 0.590 (total time: 24.020) Filter (map) r_work=0.1312 r_free=0.1650 | n_water=213 | time (s): 1.830 (total time: 25.850) Find peaks r_work=0.1312 r_free=0.1650 | n_water=213 | time (s): 0.660 (total time: 26.510) Add new water r_work=0.1528 r_free=0.1892 | n_water=376 | time (s): 2.030 (total time: 28.540) Refine new water occ: r_work=0.1327 r_free=0.1580 adp: r_work=0.1270 r_free=0.1586 occ: r_work=0.1275 r_free=0.1551 adp: r_work=0.1243 r_free=0.1561 occ: r_work=0.1245 r_free=0.1541 adp: r_work=0.1234 r_free=0.1547 ADP+occupancy (water only), MIN, final r_work=0.1234 r_free=0.1547 r_work=0.1234 r_free=0.1547 | n_water=376 | time (s): 16.730 (total time: 45.270) Filter (q & B) r_work=0.1237 r_free=0.1545 | n_water=365 | time (s): 2.240 (total time: 47.510) Filter (dist only) r_work=0.1238 r_free=0.1547 | n_water=364 | time (s): 29.400 (total time: 76.910) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.650502 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.035603 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 0.1592 0.0381 0.008 0.9 2.9 0.5 0.0 0 12.325 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.11 15.92 3.81 4.186 21.096 1.036 0.018 11.94 16.13 4.20 4.297 21.395 1.036 0.018 Individual atomic B min max mean iso aniso Overall: 7.01 107.84 21.46 4.39 1891 0 Protein: 7.01 107.84 17.78 4.38 1519 0 Water: 8.59 67.29 36.60 N/A 364 0 Other: 23.72 42.60 32.56 N/A 8 0 Chain A: 7.01 107.84 19.55 N/A 1740 0 Chain S: 19.01 67.29 43.51 N/A 151 0 Histogram: Values Number of atoms 7.01 - 17.09 1057 17.09 - 27.18 351 27.18 - 37.26 215 37.26 - 47.34 158 47.34 - 57.42 70 57.42 - 67.51 29 67.51 - 77.59 4 77.59 - 87.67 5 87.67 - 97.76 0 97.76 - 107.84 2 =========================== Idealize ADP of riding H ========================== r_work=0.1194 r_free=0.1613 r_work=0.1196 r_free=0.1615 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1196 r_free = 0.1615 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1191 r_free = 0.1610 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.19 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= 0.1191 r_free= 0.1610 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.017033 | | target function (ls_wunit_k1) not normalized (work): 276.512356 | | target function (ls_wunit_k1) not normalized (free): 24.591778 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1211 0.1191 0.1610 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1735 0.1727 0.1926 n_refl.: 17041 remove outliers: r(all,work,free)=0.1735 0.1727 0.1926 n_refl.: 17041 overall B=-0.38 to atoms: r(all,work,free)=0.1710 0.1702 0.1911 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1208 0.1188 0.1606 n_refl.: 17041 remove outliers: r(all,work,free)=0.1207 0.1186 0.1606 n_refl.: 17040 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 93.75 85 5 0.3139 303.520 289.238 0.607 1.006 0.350 11.894-9.307 99.02 97 4 0.1576 487.975 484.822 0.910 1.007 0.350 9.237-7.194 100.00 213 7 0.1687 399.114 400.155 0.968 1.007 0.297 7.162-5.571 100.00 427 22 0.1580 299.536 295.829 0.932 1.006 0.276 5.546-4.326 100.00 867 58 0.0902 411.214 408.492 0.958 1.005 0.221 4.315-3.360 100.00 1859 96 0.0817 391.069 390.206 1.014 1.004 0.201 3.356-2.611 100.00 3867 181 0.1206 256.910 255.957 1.012 1.001 0.053 2.608-2.000 99.99 8818 434 0.1314 167.461 166.424 1.018 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.3473 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1186 r_free=0.1606 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=0.1188 r_free=0.1609 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1188 r_free=0.1609 | n_water=364 | time (s): 0.680 (total time: 0.680) Filter (dist) r_work=0.1191 r_free=0.1601 | n_water=360 | time (s): 29.950 (total time: 30.630) Filter (q & B) r_work=0.1191 r_free=0.1601 | n_water=360 | time (s): 1.030 (total time: 31.660) Compute maps r_work=0.1191 r_free=0.1601 | n_water=360 | time (s): 0.690 (total time: 32.350) Filter (map) r_work=0.1255 r_free=0.1629 | n_water=260 | time (s): 1.540 (total time: 33.890) Find peaks r_work=0.1255 r_free=0.1629 | n_water=260 | time (s): 0.510 (total time: 34.400) Add new water r_work=0.1438 r_free=0.1799 | n_water=412 | time (s): 1.920 (total time: 36.320) Refine new water occ: r_work=0.1241 r_free=0.1580 adp: r_work=0.1234 r_free=0.1579 occ: r_work=0.1216 r_free=0.1561 adp: r_work=0.1206 r_free=0.1556 occ: r_work=0.1197 r_free=0.1552 adp: r_work=0.1187 r_free=0.1548 ADP+occupancy (water only), MIN, final r_work=0.1187 r_free=0.1548 r_work=0.1187 r_free=0.1548 | n_water=412 | time (s): 33.350 (total time: 69.670) Filter (q & B) r_work=0.1190 r_free=0.1559 | n_water=401 | time (s): 1.860 (total time: 71.530) Filter (dist only) r_work=0.1190 r_free=0.1560 | n_water=400 | time (s): 32.230 (total time: 103.760) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.028845 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.183719 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 0.1167 0.1558 0.0391 0.009 1.0 4.5 0.5 0.0 0 1.014 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.67 15.58 3.91 4.411 21.585 0.184 4.996 11.50 15.72 4.22 4.984 21.516 0.184 4.974 Individual atomic B min max mean iso aniso Overall: 6.35 105.32 20.95 4.84 1927 0 Protein: 6.35 105.32 17.13 4.83 1519 0 Water: 8.90 63.09 35.27 N/A 400 0 Other: 23.26 42.34 30.34 N/A 8 0 Chain A: 6.35 105.32 18.90 N/A 1738 0 Chain S: 16.49 63.09 39.79 N/A 189 0 Histogram: Values Number of atoms 6.35 - 16.25 1065 16.25 - 26.15 346 26.15 - 36.04 218 36.04 - 45.94 181 45.94 - 55.84 77 55.84 - 65.73 27 65.73 - 75.63 5 75.63 - 85.52 3 85.52 - 95.42 3 95.42 - 105.32 2 =========================== Idealize ADP of riding H ========================== r_work=0.1150 r_free=0.1572 r_work=0.1150 r_free=0.1574 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1150 r_free = 0.1574 target_work(ml) = 4.974 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1141 r_free = 0.1576 target_work(ml) = 4.969 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1141 r_free= 0.1576 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.968880 | | target function (ml) not normalized (work): 80659.821695 | | target function (ml) not normalized (free): 4193.016263 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1162 0.1141 0.1576 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1672 0.1666 0.1857 n_refl.: 17040 remove outliers: r(all,work,free)=0.1672 0.1666 0.1857 n_refl.: 17040 overall B=-0.38 to atoms: r(all,work,free)=0.1647 0.1640 0.1845 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1160 0.1139 0.1575 n_refl.: 17040 remove outliers: r(all,work,free)=0.1159 0.1138 0.1575 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 0.3389 299.952 283.888 0.583 1.003 0.344 11.894-9.307 99.02 97 4 0.1698 487.975 482.109 0.915 1.004 0.340 9.237-7.194 100.00 213 7 0.1774 399.114 400.493 0.982 1.004 0.254 7.162-5.571 100.00 427 22 0.1599 299.536 293.945 0.938 1.004 0.221 5.546-4.326 100.00 867 58 0.0938 411.214 407.350 0.964 1.004 0.211 4.315-3.360 100.00 1859 96 0.0883 391.069 388.785 1.012 1.003 0.211 3.356-2.611 100.00 3867 181 0.1266 256.910 254.650 1.012 1.002 0.121 2.608-2.000 99.99 8818 434 0.1092 167.461 166.053 1.014 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.3430 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1138 r_free=0.1575 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1138 r_free=0.1575 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1138 r_free=0.1575 | n_water=400 | time (s): 0.680 (total time: 0.680) Filter (dist) r_work=0.1138 r_free=0.1580 | n_water=399 | time (s): 31.760 (total time: 32.440) Filter (q & B) r_work=0.1138 r_free=0.1580 | n_water=399 | time (s): 0.990 (total time: 33.430) Compute maps r_work=0.1138 r_free=0.1580 | n_water=399 | time (s): 0.620 (total time: 34.050) Filter (map) r_work=0.1200 r_free=0.1586 | n_water=304 | time (s): 1.490 (total time: 35.540) Find peaks r_work=0.1200 r_free=0.1586 | n_water=304 | time (s): 0.420 (total time: 35.960) Add new water r_work=0.1358 r_free=0.1713 | n_water=448 | time (s): 1.480 (total time: 37.440) Refine new water occ: r_work=0.1184 r_free=0.1561 adp: r_work=0.1177 r_free=0.1561 occ: r_work=0.1158 r_free=0.1547 adp: r_work=0.1149 r_free=0.1543 occ: r_work=0.1140 r_free=0.1529 adp: r_work=0.1132 r_free=0.1529 ADP+occupancy (water only), MIN, final r_work=0.1132 r_free=0.1529 r_work=0.1132 r_free=0.1529 | n_water=448 | time (s): 33.290 (total time: 70.730) Filter (q & B) r_work=0.1136 r_free=0.1536 | n_water=438 | time (s): 1.460 (total time: 72.190) Filter (dist only) r_work=0.1139 r_free=0.1536 | n_water=436 | time (s): 35.980 (total time: 108.170) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.016578 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.161485 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1126 0.1585 0.0459 0.010 1.0 6.4 0.5 0.0 0 1.008 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.26 15.85 4.59 4.591 21.199 0.161 4.964 11.18 15.84 4.66 4.753 21.214 0.161 4.959 Individual atomic B min max mean iso aniso Overall: 6.04 103.01 21.06 4.90 1963 0 Protein: 6.04 103.01 16.74 4.90 1519 0 Water: 9.01 65.36 35.99 N/A 436 0 Other: 21.57 40.56 28.24 N/A 8 0 Chain A: 6.04 103.01 18.44 N/A 1737 0 Chain S: 16.32 65.36 41.24 N/A 226 0 Histogram: Values Number of atoms 6.04 - 15.74 1039 15.74 - 25.43 381 25.43 - 35.13 202 35.13 - 44.83 199 44.83 - 54.53 97 54.53 - 64.22 29 64.22 - 73.92 7 73.92 - 83.62 3 83.62 - 93.32 3 93.32 - 103.01 3 =========================== Idealize ADP of riding H ========================== r_work=0.1118 r_free=0.1584 r_work=0.1118 r_free=0.1585 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1118 r_free = 0.1585 target_work(ml) = 4.959 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1113 r_free = 0.1603 target_work(ml) = 4.960 | | occupancies: max = 1.00 min = 0.00 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= 0.1113 r_free= 0.1603 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.959682 | | target function (ml) not normalized (work): 80505.562608 | | target function (ml) not normalized (free): 4207.360204 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1137 0.1113 0.1603 n_refl.: 17039 re-set all scales: r(all,work,free)=0.1612 0.1600 0.1894 n_refl.: 17039 remove outliers: r(all,work,free)=0.1612 0.1600 0.1894 n_refl.: 17039 overall B=-0.33 to atoms: r(all,work,free)=0.1591 0.1578 0.1883 n_refl.: 17039 bulk-solvent and scaling: r(all,work,free)=0.1134 0.1110 0.1597 n_refl.: 17039 remove outliers: r(all,work,free)=0.1134 0.1110 0.1597 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 0.3525 299.952 280.177 0.561 1.002 0.340 11.894-9.307 99.02 97 4 0.1706 487.975 484.647 0.921 1.003 0.325 9.237-7.194 100.00 213 7 0.1713 399.114 399.295 0.987 1.003 0.245 7.162-5.571 100.00 427 22 0.1561 299.536 293.954 0.940 1.003 0.222 5.546-4.326 100.00 867 58 0.0936 411.214 406.895 0.965 1.003 0.214 4.315-3.360 100.00 1859 96 0.0888 391.069 388.557 1.010 1.003 0.211 3.356-2.611 100.00 3867 181 0.1248 256.910 254.619 1.007 1.001 0.151 2.608-2.000 99.99 8818 434 0.1034 167.461 166.334 1.008 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-1.1306 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1110 r_free=0.1597 After: r_work=0.1112 r_free=0.1595 ================================== NQH flips ================================== r_work=0.1112 r_free=0.1595 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1112 r_free=0.1595 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1112 r_free=0.1595 | n_water=436 | time (s): 0.740 (total time: 0.740) Filter (dist) r_work=0.1112 r_free=0.1594 | n_water=435 | time (s): 34.890 (total time: 35.630) Filter (q & B) r_work=0.1112 r_free=0.1594 | n_water=433 | time (s): 1.880 (total time: 37.510) Compute maps r_work=0.1112 r_free=0.1594 | n_water=433 | time (s): 0.580 (total time: 38.090) Filter (map) r_work=0.1186 r_free=0.1609 | n_water=329 | time (s): 1.860 (total time: 39.950) Find peaks r_work=0.1186 r_free=0.1609 | n_water=329 | time (s): 0.590 (total time: 40.540) Add new water r_work=0.1323 r_free=0.1713 | n_water=478 | time (s): 2.140 (total time: 42.680) Refine new water occ: r_work=0.1153 r_free=0.1537 adp: r_work=0.1145 r_free=0.1538 occ: r_work=0.1128 r_free=0.1524 adp: r_work=0.1119 r_free=0.1524 occ: r_work=0.1110 r_free=0.1516 adp: r_work=0.1102 r_free=0.1517 ADP+occupancy (water only), MIN, final r_work=0.1102 r_free=0.1517 r_work=0.1102 r_free=0.1517 | n_water=478 | time (s): 31.960 (total time: 74.640) Filter (q & B) r_work=0.1107 r_free=0.1528 | n_water=465 | time (s): 1.580 (total time: 76.220) Filter (dist only) r_work=0.1107 r_free=0.1528 | n_water=465 | time (s): 37.150 (total time: 113.370) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.040093 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.156317 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 0.1131 0.1558 0.0427 0.009 1.0 8.3 0.5 0.0 0 1.020 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.31 15.58 4.27 4.582 21.016 0.156 4.960 11.19 15.41 4.21 4.634 21.110 0.156 4.947 Individual atomic B min max mean iso aniso Overall: 5.66 101.37 21.24 4.95 1992 0 Protein: 5.66 101.37 16.47 4.95 1519 0 Water: 8.94 66.71 36.76 N/A 465 0 Other: 20.31 36.91 26.51 N/A 8 0 Chain A: 5.66 101.37 18.12 N/A 1737 0 Chain S: 18.77 66.71 42.52 N/A 255 0 Histogram: Values Number of atoms 5.66 - 15.23 1014 15.23 - 24.80 392 24.80 - 34.37 215 34.37 - 43.94 186 43.94 - 53.51 127 53.51 - 63.08 40 63.08 - 72.65 9 72.65 - 82.23 2 82.23 - 91.80 3 91.80 - 101.37 4 =========================== Idealize ADP of riding H ========================== r_work=0.1119 r_free=0.1541 r_work=0.1119 r_free=0.1539 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1119 r_free = 0.1539 target_work(ml) = 4.947 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1110 r_free = 0.1538 target_work(ml) = 4.941 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17039 (all), 4.74 % free)------------| | | | r_work= 0.1110 r_free= 0.1538 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.941037 | | target function (ml) not normalized (work): 80202.916607 | | target function (ml) not normalized (free): 4177.233778 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1124 0.1471 5.4636 5.7183| | 2: 3.63 - 2.88 1.00 2711 122 0.1111 0.1588 5.249 5.4027| | 3: 2.88 - 2.52 1.00 2681 148 0.1358 0.1681 5.1612 5.215| | 4: 2.52 - 2.29 1.00 2661 139 0.0937 0.1445 4.6192 4.9314| | 5: 2.29 - 2.13 1.00 2678 122 0.0948 0.1432 4.565 4.8611| | 6: 2.13 - 2.00 1.00 2692 117 0.1102 0.1713 4.5585 4.774| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 0.94 9.59 1.00 0.96 7026.51| | 2: 3.63 - 2.88 2711 122 0.92 13.58 1.01 0.96 7026.51| | 3: 2.88 - 2.52 2681 148 0.87 19.96 0.99 0.96 7026.51| | 4: 2.52 - 2.29 2661 139 0.93 11.91 1.01 0.98 2062.71| | 5: 2.29 - 2.13 2678 122 0.92 13.90 1.00 0.98 2062.71| | 6: 2.13 - 2.00 2692 117 0.90 16.64 0.99 0.98 2062.71| |alpha: min = 0.96 max = 0.98 mean = 0.97| |beta: min = 2062.71 max = 7026.51 mean = 4570.60| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.93 mean = 14.23| |phase err.(test): min = 0.00 max = 87.13 mean = 13.93| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1131 0.1110 0.1538 n_refl.: 17039 re-set all scales: r(all,work,free)=0.1592 0.1579 0.1871 n_refl.: 17039 remove outliers: r(all,work,free)=0.1592 0.1579 0.1871 n_refl.: 17039 overall B=-0.28 to atoms: r(all,work,free)=0.1574 0.1561 0.1859 n_refl.: 17039 bulk-solvent and scaling: r(all,work,free)=0.1130 0.1110 0.1538 n_refl.: 17039 remove outliers: r(all,work,free)=0.1130 0.1110 0.1538 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 0.3393 299.952 280.125 0.558 1.001 0.340 11.894-9.307 99.02 97 4 0.1669 487.975 483.805 0.923 1.002 0.330 9.237-7.194 100.00 213 7 0.1740 399.114 402.152 0.990 1.003 0.240 7.162-5.571 100.00 427 22 0.1586 299.536 293.033 0.936 1.003 0.202 5.546-4.326 100.00 867 58 0.0942 411.214 408.008 0.966 1.003 0.192 4.315-3.360 100.00 1859 96 0.0886 391.069 388.628 1.008 1.002 0.191 3.356-2.611 100.00 3867 181 0.1252 256.910 254.497 1.004 1.001 0.121 2.608-2.000 99.99 8818 434 0.1030 167.461 166.105 1.000 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.9791 ================= 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 : 0.2787 0.1805 0.082 5.435 8.8 119.3 19.9 258 0.000 1_bss: 0.1616 0.1615 0.082 5.435 8.4 118.9 19.5 258 0.000 1_settarget: 0.1616 0.1615 0.082 5.435 8.4 118.9 19.5 258 0.000 1_nqh: 0.1615 0.1616 0.082 5.435 8.4 118.9 19.5 258 0.003 1_weight: 0.1615 0.1616 0.082 5.435 8.4 118.9 19.5 258 0.003 1_xyzrec: 0.1348 0.1645 0.009 1.000 8.4 118.9 19.5 258 0.144 1_adp: 0.1277 0.1664 0.009 1.000 6.3 113.9 20.0 258 0.144 1_regHadp: 0.1280 0.1670 0.009 1.000 6.3 113.9 20.0 258 0.144 1_occ: 0.1275 0.1662 0.009 1.000 6.3 113.9 20.0 258 0.144 2_bss: 0.1272 0.1654 0.009 1.000 6.0 113.5 19.6 258 0.144 2_settarget: 0.1272 0.1654 0.009 1.000 6.0 113.5 19.6 258 0.144 2_updatecdl: 0.1272 0.1654 0.009 1.010 6.0 113.5 19.6 258 0.144 2_nqh: 0.1272 0.1654 0.009 1.010 6.0 113.5 19.6 258 0.141 2_sol: 0.1238 0.1547 0.009 1.010 6.0 112.8 20.9 364 n/a 2_weight: 0.1238 0.1547 0.009 1.010 6.0 112.8 20.9 364 n/a 2_xyzrec: 0.1211 0.1592 0.008 0.927 6.0 112.8 20.9 364 n/a 2_adp: 0.1194 0.1613 0.008 0.927 7.0 107.8 21.5 364 n/a 2_regHadp: 0.1196 0.1615 0.008 0.927 7.0 107.8 21.5 364 n/a 2_occ: 0.1191 0.1610 0.008 0.927 7.0 107.8 21.5 364 n/a 3_bss: 0.1186 0.1606 0.008 0.927 6.6 107.5 21.1 364 n/a 3_settarget: 0.1186 0.1606 0.008 0.927 6.6 107.5 21.1 364 n/a 3_updatecdl: 0.1186 0.1606 0.008 0.926 6.6 107.5 21.1 364 n/a 3_nqh: 0.1188 0.1609 0.008 0.926 6.6 107.5 21.1 364 n/a 3_sol: 0.1190 0.1560 0.008 0.926 6.6 107.5 21.1 400 n/a 3_weight: 0.1190 0.1560 0.008 0.926 6.6 107.5 21.1 400 n/a 3_xyzrec: 0.1167 0.1558 0.009 0.965 6.6 107.5 21.1 400 n/a 3_adp: 0.1150 0.1572 0.009 0.965 6.4 105.3 20.9 400 n/a 3_regHadp: 0.1150 0.1574 0.009 0.965 6.4 105.3 20.9 400 n/a 3_occ: 0.1141 0.1576 0.009 0.965 6.4 105.3 20.9 400 n/a 4_bss: 0.1138 0.1575 0.009 0.965 6.0 104.9 20.6 400 n/a 4_settarget: 0.1138 0.1575 0.009 0.965 6.0 104.9 20.6 400 n/a 4_updatecdl: 0.1138 0.1575 0.009 0.965 6.0 104.9 20.6 400 n/a 4_nqh: 0.1138 0.1575 0.009 0.965 6.0 104.9 20.6 400 n/a 4_sol: 0.1139 0.1536 0.009 0.965 6.0 104.9 21.0 436 n/a 4_weight: 0.1139 0.1536 0.009 0.965 6.0 104.9 21.0 436 n/a 4_xyzrec: 0.1126 0.1585 0.010 0.976 6.0 104.9 21.0 436 n/a 4_adp: 0.1118 0.1584 0.010 0.976 6.0 103.0 21.1 436 n/a 4_regHadp: 0.1118 0.1585 0.010 0.976 6.0 103.0 21.1 436 n/a 4_occ: 0.1113 0.1603 0.010 0.976 6.0 103.0 21.1 436 n/a 5_bss: 0.1110 0.1597 0.010 0.976 5.7 102.7 20.7 436 n/a 5_settarget: 0.1110 0.1597 0.010 0.976 5.7 102.7 20.7 436 n/a 5_updatecdl: 0.1110 0.1597 0.010 0.979 5.7 102.7 20.7 436 n/a 5_setrh: 0.1112 0.1595 0.010 0.979 5.7 102.7 20.7 436 n/a 5_nqh: 0.1112 0.1595 0.010 0.979 5.7 102.7 20.7 436 n/a 5_sol: 0.1107 0.1528 0.010 0.979 5.7 102.7 21.1 465 n/a 5_weight: 0.1107 0.1528 0.010 0.979 5.7 102.7 21.1 465 n/a 5_xyzrec: 0.1131 0.1558 0.009 1.034 5.7 102.7 21.1 465 n/a 5_adp: 0.1119 0.1541 0.009 1.034 5.7 101.4 21.2 465 n/a 5_regHadp: 0.1119 0.1539 0.009 1.034 5.7 101.4 21.2 465 n/a 5_occ: 0.1110 0.1538 0.009 1.034 5.7 101.4 21.2 465 n/a end: 0.1110 0.1538 0.009 1.034 5.4 101.1 21.0 465 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_3337960_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_3337960_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 2.9700 Refinement macro-cycles (run) : 921.8500 Write final files (write_after_run_outputs) : 22.0300 Total : 946.8500 Total CPU time: 16.12 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:08 PST -0800 (1735494068.31 s) Start R-work = 0.1616, R-free = 0.1615 Final R-work = 0.1110, R-free = 0.1538 =============================================================================== Job complete usr+sys time: 990.94 seconds wall clock time: 16 minutes 53.97 seconds (1013.97 seconds total)