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_6369642.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_6369642.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6369642.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 2 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: 1.43, per 1000 atoms: 0.42 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: 0.58 Conformation dependent library (CDL) restraints added in 199.2 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.65 - 0.91: 537 0.91 - 1.18: 1122 1.18 - 1.44: 687 1.44 - 1.71: 785 1.71 - 1.97: 22 Bond restraints: 3153 Sorted by residual: bond pdb=" CG HIS A 126 " pdb=" CD2 HIS A 126 " ideal model delta sigma weight residual 1.354 1.113 0.241 1.10e-02 8.26e+03 4.82e+02 bond pdb=" C LEU A 92 " pdb=" O LEU A 92 " ideal model delta sigma weight residual 1.237 0.992 0.244 1.17e-02 7.31e+03 4.37e+02 bond pdb=" N ILE A 52 " pdb=" CA ILE A 52 " ideal model delta sigma weight residual 1.459 1.223 0.236 1.24e-02 6.50e+03 3.62e+02 bond pdb=" N ALA A 114 " pdb=" CA ALA A 114 " ideal model delta sigma weight residual 1.459 1.683 -0.224 1.20e-02 6.94e+03 3.49e+02 bond pdb=" N ALA A 36 " pdb=" CA ALA A 36 " ideal model delta sigma weight residual 1.456 1.233 0.223 1.23e-02 6.61e+03 3.29e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.63: 3164 4.63 - 9.26: 1869 9.26 - 13.89: 611 13.89 - 18.52: 118 18.52 - 23.15: 15 Bond angle restraints: 5777 Sorted by residual: angle pdb=" ND1 HIS A 126 " pdb=" CG HIS A 126 " pdb=" CD2 HIS A 126 " ideal model delta sigma weight residual 106.10 122.14 -16.04 1.00e+00 1.00e+00 2.57e+02 angle pdb=" CA SER A 3 " pdb=" C SER A 3 " pdb=" O SER A 3 " ideal model delta sigma weight residual 121.56 140.37 -18.81 1.21e+00 6.83e-01 2.42e+02 angle pdb=" O GLU A 116 " pdb=" C GLU A 116 " pdb=" N ILE A 117 " ideal model delta sigma weight residual 122.55 140.44 -17.89 1.24e+00 6.50e-01 2.08e+02 angle pdb=" O GLY A 174 " pdb=" C GLY A 174 " pdb=" N ALYS A 175 " ideal model delta sigma weight residual 122.87 137.51 -14.64 1.04e+00 9.25e-01 1.98e+02 angle pdb=" O ALA A 79 " pdb=" C ALA A 79 " pdb=" N AGLN A 80 " ideal model delta sigma weight residual 122.22 138.07 -15.85 1.17e+00 7.31e-01 1.83e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.81: 1300 16.81 - 33.61: 123 33.61 - 50.41: 37 50.41 - 67.21: 18 67.21 - 84.02: 3 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" N ASP A 60 " pdb=" C ASP A 60 " pdb=" CA ASP A 60 " pdb=" CB ASP A 60 " ideal model delta harmonic sigma weight residual 122.80 143.97 -21.17 0 2.50e+00 1.60e-01 7.17e+01 dihedral pdb=" C ASP A 60 " pdb=" N ASP A 60 " pdb=" CA ASP A 60 " pdb=" CB ASP A 60 " ideal model delta harmonic sigma weight residual -122.60 -142.39 19.79 0 2.50e+00 1.60e-01 6.27e+01 dihedral pdb=" C BLYS A 99 " pdb=" N BLYS A 99 " pdb=" CA BLYS A 99 " pdb=" CB BLYS A 99 " ideal model delta harmonic sigma weight residual -122.60 -140.23 17.63 0 2.50e+00 1.60e-01 4.97e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.005 - 0.226: 118 0.226 - 0.447: 65 0.447 - 0.668: 37 0.668 - 0.889: 17 0.889 - 1.110: 6 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA ASP A 60 " pdb=" N ASP A 60 " pdb=" C ASP A 60 " pdb=" CB ASP A 60 " both_signs ideal model delta sigma weight residual False 2.51 1.40 1.11 2.00e-01 2.50e+01 3.08e+01 chirality pdb=" CB ILE A 117 " pdb=" CA ILE A 117 " pdb=" CG1 ILE A 117 " pdb=" CG2 ILE A 117 " both_signs ideal model delta sigma weight residual False 2.64 1.57 1.07 2.00e-01 2.50e+01 2.86e+01 chirality pdb=" CA BGLU A 64 " pdb=" N BGLU A 64 " pdb=" C BGLU A 64 " pdb=" CB BGLU A 64 " both_signs ideal model delta sigma weight residual False 2.51 3.54 -1.03 2.00e-01 2.50e+01 2.66e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.048 2.00e-02 2.50e+03 6.79e-02 1.38e+02 pdb=" CG PHE A 119 " -0.134 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " 0.111 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.066 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " -0.090 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.084 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.029 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.017 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.003 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.020 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.019 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " -0.086 2.00e-02 2.50e+03 6.35e-02 1.21e+02 pdb=" CG TYR A 141 " 0.103 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " 0.079 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " 0.086 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " -0.066 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " -0.033 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " -0.044 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " 0.007 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " 0.001 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " -0.081 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " -0.016 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " 0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 138 " 0.076 2.00e-02 2.50e+03 6.67e-02 1.00e+02 pdb=" CG HIS A 138 " 0.062 2.00e-02 2.50e+03 pdb=" ND1 HIS A 138 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 HIS A 138 " -0.071 2.00e-02 2.50e+03 pdb=" CE1 HIS A 138 " 0.065 2.00e-02 2.50e+03 pdb=" NE2 HIS A 138 " 0.059 2.00e-02 2.50e+03 pdb=" HD1 HIS A 138 " -0.109 2.00e-02 2.50e+03 pdb=" HD2 HIS A 138 " -0.068 2.00e-02 2.50e+03 pdb=" HE1 HIS A 138 " 0.016 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.36: 1365 2.36 - 2.92: 8328 2.92 - 3.48: 10431 3.48 - 4.04: 15189 4.04 - 4.60: 21318 Nonbonded interactions: 56631 Sorted by model distance: nonbonded pdb=" O ALA A 14 " pdb=" H SER A 47 " model vdw 1.802 2.450 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.805 2.450 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.835 2.100 nonbonded pdb=" H ALA A 6 " pdb=" O LYS A 32 " model vdw 1.844 2.450 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.849 2.100 ... (remaining 56626 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_6369642_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= 0.1860 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.410034 | | target function (ml) not normalized (work): 71632.183588 | | target function (ml) not normalized (free): 3274.007840 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2096 7.5264 5.0233| | 2: 3.63 - 2.88 1.00 2711 122 0.2669 0.1771 4.3352 4.3184| | 3: 2.88 - 2.52 1.00 2682 148 0.2554 0.1799 4.1851 4.1968| | 4: 2.52 - 2.29 1.00 2661 139 0.2511 0.1729 3.5081 3.67| | 5: 2.29 - 2.13 1.00 2678 122 0.2659 0.1517 3.4104 3.4396| | 6: 2.13 - 2.00 1.00 2692 117 0.2742 0.1908 3.332 3.3979| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 17.63 0.77 0.23 1300.34| | 2: 3.63 - 2.88 2711 122 0.83 23.92 1.32 0.23 1300.34| | 3: 2.88 - 2.52 2682 148 0.73 32.80 1.28 0.23 1300.34| | 4: 2.52 - 2.29 2661 139 0.93 11.48 1.29 0.26 138.66| | 5: 2.29 - 2.13 2678 122 0.92 13.60 1.32 0.26 138.66| | 6: 2.13 - 2.00 2692 117 0.90 16.40 1.33 0.26 138.66| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 138.66 max = 1300.34 mean = 725.97| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 89.99 mean = 19.31| |phase err.(test): min = 0.00 max = 89.99 mean = 19.56| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.084 0.244 1557 Z= 5.707 Angle : 5.299 18.810 2118 Z= 3.727 Chirality : 0.381 1.110 243 Planarity : 0.029 0.139 284 Dihedral : 14.119 84.017 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.54 % Allowed : 1.08 % Favored : 98.38 % Rotamer: Outliers : 1.86 % Allowed : 3.11 % Favored : 95.03 % Cbeta Deviations : 29.73 % 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: -2.05 (0.47), residues: 224 helix: -2.31 (0.38), residues: 102 sheet: -0.68 (0.86), residues: 28 loop : -0.12 (0.56), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.108 0.030 ARG A 28 TYR 0.108 0.055 TYR A 141 PHE 0.140 0.044 PHE A 119 HIS 0.068 0.038 HIS A 138 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= 0.1860 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.410034 | | target function (ml) not normalized (work): 71632.183588 | | target function (ml) not normalized (free): 3274.007840 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.3128 percent. r_work = 0.2918 r_free = 0.2013 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2866 0.2918 0.2013 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2866 0.2918 0.2013 n_refl.: 17050 remove outliers: r(all,work,free)=0.2158 0.2168 0.2013 n_refl.: 17045 overall B=-0.39 to atoms: r(all,work,free)=0.2133 0.2142 0.1994 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1624 0.1620 0.1699 n_refl.: 17045 remove outliers: r(all,work,free)=0.1622 0.1618 0.1699 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 0.3893 398.925 360.406 0.650 1.015 0.403 11.894-9.307 99.02 97 4 0.1853 633.588 613.079 0.922 1.016 0.390 9.237-7.194 100.00 213 7 0.2204 518.211 509.684 0.949 1.016 0.355 7.162-5.571 100.00 427 22 0.2279 388.918 376.391 0.919 1.014 0.289 5.546-4.326 100.00 867 58 0.1368 533.922 528.236 0.956 1.012 0.220 4.315-3.360 100.00 1859 96 0.1317 507.765 502.816 1.012 1.007 0.139 3.356-2.611 100.00 3867 181 0.1668 333.572 328.962 1.015 0.999 0.044 2.608-2.000 99.99 8818 434 0.1652 217.432 213.714 1.031 0.984 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.3888 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1618 r_free=0.1699 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** A 80 GLN A Total number of N/Q/H flips: 2 r_work=0.1620 r_free=0.1706 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.956985 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.030010 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 0.1627 0.0280 0.009 1.0 1.3 0.5 0.0 0 11.478 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.48 16.27 2.80 3.013 18.469 1.030 0.022 12.72 16.51 3.79 3.714 18.729 1.030 0.020 Individual atomic B min max mean iso aniso Overall: 5.85 113.91 19.99 4.20 1785 0 Protein: 5.85 113.51 17.19 4.21 1519 0 Water: 8.40 113.91 36.27 N/A 258 0 Other: 21.67 36.79 26.38 N/A 8 0 Chain A: 5.85 113.91 19.99 N/A 1785 0 Histogram: Values Number of atoms 5.85 - 16.65 1065 16.65 - 27.46 354 27.46 - 38.27 188 38.27 - 49.07 97 49.07 - 59.88 52 59.88 - 70.69 13 70.69 - 81.49 8 81.49 - 92.30 4 92.30 - 103.10 1 103.10 - 113.91 3 =========================== Idealize ADP of riding H ========================== r_work=0.1272 r_free=0.1651 r_work=0.1275 r_free=0.1661 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1275 r_free = 0.1661 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 = 0.1271 r_free = 0.1655 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17043 (all), 4.74 % free)------------| | | | r_work= 0.1271 r_free= 0.1655 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.019842 | | target function (ls_wunit_k1) not normalized (work): 322.158939 | | target function (ls_wunit_k1) not normalized (free): 27.200395 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1290 0.1271 0.1655 n_refl.: 17043 re-set all scales: r(all,work,free)=0.1899 0.1897 0.1994 n_refl.: 17043 remove outliers: r(all,work,free)=0.1899 0.1897 0.1994 n_refl.: 17043 overall B=-0.52 to atoms: r(all,work,free)=0.1861 0.1859 0.1972 n_refl.: 17043 bulk-solvent and scaling: r(all,work,free)=0.1288 0.1270 0.1646 n_refl.: 17043 remove outliers: r(all,work,free)=0.1288 0.1270 0.1646 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 96.88 88 5 0.3557 306.878 291.240 0.676 1.001 0.393 11.894-9.307 99.02 97 4 0.1688 487.394 476.630 0.923 1.002 0.360 9.237-7.194 100.00 213 7 0.1844 398.640 394.020 0.962 1.002 0.341 7.162-5.571 100.00 427 22 0.1834 299.179 293.702 0.934 1.002 0.301 5.546-4.326 100.00 867 58 0.1034 410.725 407.877 0.960 1.002 0.196 4.315-3.360 100.00 1859 96 0.0920 390.604 390.179 1.015 1.002 0.140 3.356-2.611 100.00 3867 181 0.1292 256.604 255.087 1.011 1.001 0.102 2.608-2.000 99.99 8818 434 0.1347 167.262 166.005 1.009 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-1.1847 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1270 r_free=0.1646 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=0.1270 r_free=0.1647 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1270 r_free=0.1647 | n_water=258 | time (s): 0.630 (total time: 0.630) Filter (dist) r_work=0.1275 r_free=0.1632 | n_water=255 | time (s): 20.260 (total time: 20.890) Filter (q & B) r_work=0.1275 r_free=0.1632 | n_water=253 | time (s): 1.410 (total time: 22.300) Compute maps r_work=0.1275 r_free=0.1632 | n_water=253 | time (s): 0.570 (total time: 22.870) Filter (map) r_work=0.1321 r_free=0.1642 | n_water=207 | time (s): 1.600 (total time: 24.470) Find peaks r_work=0.1321 r_free=0.1642 | n_water=207 | time (s): 0.450 (total time: 24.920) Add new water r_work=0.1542 r_free=0.1863 | n_water=380 | time (s): 1.450 (total time: 26.370) Refine new water occ: r_work=0.1336 r_free=0.1575 adp: r_work=0.1273 r_free=0.1559 occ: r_work=0.1281 r_free=0.1539 adp: r_work=0.1245 r_free=0.1533 occ: r_work=0.1246 r_free=0.1526 adp: r_work=0.1236 r_free=0.1524 ADP+occupancy (water only), MIN, final r_work=0.1236 r_free=0.1524 r_work=0.1236 r_free=0.1524 | n_water=380 | time (s): 19.580 (total time: 45.950) Filter (q & B) r_work=0.1239 r_free=0.1532 | n_water=368 | time (s): 1.960 (total time: 47.910) Filter (dist only) r_work=0.1240 r_free=0.1528 | n_water=366 | time (s): 28.240 (total time: 76.150) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.500876 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.994636 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 0.1214 0.1603 0.0389 0.008 0.9 2.6 0.5 0.0 0 12.250 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.14 16.03 3.89 4.237 20.968 0.995 0.018 12.00 16.26 4.25 4.362 21.264 0.995 0.018 Individual atomic B min max mean iso aniso Overall: 6.39 107.99 21.34 4.52 1893 0 Protein: 6.39 107.99 17.70 4.50 1519 0 Water: 8.32 65.67 36.13 N/A 366 0 Other: 25.10 48.13 36.88 N/A 8 0 Chain A: 6.39 107.99 19.33 N/A 1734 0 Chain S: 18.69 64.97 43.30 N/A 159 0 Histogram: Values Number of atoms 6.39 - 16.55 1019 16.55 - 26.71 381 26.71 - 36.87 212 36.87 - 47.03 170 47.03 - 57.19 77 57.19 - 67.35 21 67.35 - 77.51 5 77.51 - 87.67 4 87.67 - 97.83 2 97.83 - 107.99 2 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1626 r_work=0.1203 r_free=0.1628 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1203 r_free = 0.1628 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1198 r_free = 0.1642 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17043 (all), 4.74 % free)------------| | | | r_work= 0.1198 r_free= 0.1642 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.017105 | | target function (ls_wunit_k1) not normalized (work): 277.709820 | | target function (ls_wunit_k1) not normalized (free): 26.373072 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1220 0.1198 0.1642 n_refl.: 17043 re-set all scales: r(all,work,free)=0.1782 0.1777 0.1950 n_refl.: 17043 remove outliers: r(all,work,free)=0.1782 0.1777 0.1950 n_refl.: 17043 overall B=-0.41 to atoms: r(all,work,free)=0.1755 0.1749 0.1934 n_refl.: 17043 bulk-solvent and scaling: r(all,work,free)=0.1215 0.1194 0.1634 n_refl.: 17043 remove outliers: r(all,work,free)=0.1214 0.1192 0.1634 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 0.3386 306.316 277.584 0.622 1.008 0.370 11.894-9.307 99.02 97 4 0.1497 487.394 483.852 0.919 1.008 0.370 9.237-7.194 100.00 213 7 0.1698 398.640 398.202 0.967 1.008 0.300 7.162-5.571 100.00 427 22 0.1549 299.179 296.104 0.931 1.007 0.251 5.546-4.326 100.00 867 58 0.0865 410.725 407.942 0.959 1.006 0.195 4.315-3.360 100.00 1859 96 0.0828 390.604 390.034 1.012 1.004 0.181 3.356-2.611 100.00 3867 181 0.1211 256.604 255.760 1.010 1.001 0.048 2.608-2.000 99.99 8818 434 0.1329 167.262 166.240 1.010 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9583 b_overall=-1.1272 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1192 r_free=0.1634 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A Total number of N/Q/H flips: 1 r_work=0.1193 r_free=0.1635 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1635 | n_water=366 | time (s): 0.600 (total time: 0.600) Filter (dist) r_work=0.1193 r_free=0.1635 | n_water=366 | time (s): 27.900 (total time: 28.500) Filter (q & B) r_work=0.1193 r_free=0.1635 | n_water=366 | time (s): 0.790 (total time: 29.290) Compute maps r_work=0.1193 r_free=0.1635 | n_water=366 | time (s): 0.770 (total time: 30.060) Filter (map) r_work=0.1265 r_free=0.1643 | n_water=260 | time (s): 1.970 (total time: 32.030) Find peaks r_work=0.1265 r_free=0.1643 | n_water=260 | time (s): 0.520 (total time: 32.550) Add new water r_work=0.1443 r_free=0.1815 | n_water=413 | time (s): 1.630 (total time: 34.180) Refine new water occ: r_work=0.1248 r_free=0.1559 adp: r_work=0.1240 r_free=0.1568 occ: r_work=0.1222 r_free=0.1530 adp: r_work=0.1211 r_free=0.1538 occ: r_work=0.1202 r_free=0.1521 adp: r_work=0.1194 r_free=0.1524 ADP+occupancy (water only), MIN, final r_work=0.1194 r_free=0.1524 r_work=0.1194 r_free=0.1524 | n_water=413 | time (s): 20.050 (total time: 54.230) Filter (q & B) r_work=0.1196 r_free=0.1528 | n_water=403 | time (s): 1.880 (total time: 56.110) Filter (dist only) r_work=0.1196 r_free=0.1528 | n_water=403 | time (s): 31.040 (total time: 87.150) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.766513 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.174323 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 0.1178 0.1510 0.0331 0.009 1.0 5.1 0.5 0.0 0 0.883 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.78 15.10 3.31 4.477 21.526 0.174 4.992 11.60 15.04 3.44 5.057 21.405 0.174 4.963 Individual atomic B min max mean iso aniso Overall: 6.28 105.41 20.82 4.83 1930 0 Protein: 6.28 105.41 16.84 4.82 1519 0 Water: 8.26 66.97 35.55 N/A 403 0 Other: 27.22 48.89 36.19 N/A 8 0 Chain A: 6.28 105.41 18.51 N/A 1731 0 Chain S: 18.25 66.97 40.94 N/A 199 0 Histogram: Values Number of atoms 6.28 - 16.20 1074 16.20 - 26.11 341 26.11 - 36.02 219 36.02 - 45.93 175 45.93 - 55.85 77 55.85 - 65.76 29 65.76 - 75.67 6 75.67 - 85.59 4 85.59 - 95.50 3 95.50 - 105.41 2 =========================== Idealize ADP of riding H ========================== r_work=0.1160 r_free=0.1504 r_work=0.1160 r_free=0.1503 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1160 r_free = 0.1503 target_work(ml) = 4.962 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1150 r_free = 0.1496 target_work(ml) = 4.956 | | occupancies: max = 1.00 min = 0.18 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= 0.1150 r_free= 0.1496 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.955656 | | target function (ml) not normalized (work): 80450.118005 | | target function (ml) not normalized (free): 4166.635516 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1167 0.1150 0.1496 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1642 0.1637 0.1790 n_refl.: 17041 remove outliers: r(all,work,free)=0.1642 0.1637 0.1790 n_refl.: 17041 overall B=-0.33 to atoms: r(all,work,free)=0.1621 0.1615 0.1781 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1164 0.1148 0.1491 n_refl.: 17041 remove outliers: r(all,work,free)=0.1163 0.1146 0.1491 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 0.3545 299.595 281.527 0.565 1.006 0.327 11.894-9.307 99.02 97 4 0.1772 487.394 480.244 0.912 1.007 0.318 9.237-7.194 100.00 213 7 0.1780 398.640 399.970 0.985 1.007 0.270 7.162-5.571 100.00 427 22 0.1609 299.179 294.292 0.940 1.007 0.220 5.546-4.326 100.00 867 58 0.0942 410.725 407.343 0.965 1.006 0.196 4.315-3.360 100.00 1859 96 0.0896 390.604 388.520 1.012 1.004 0.191 3.356-2.611 100.00 3867 181 0.1284 256.604 254.593 1.011 1.001 0.131 2.608-2.000 99.99 8818 434 0.1088 167.262 165.808 1.012 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9584 b_overall=-1.1474 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1146 r_free=0.1491 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1146 r_free=0.1491 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1146 r_free=0.1491 | n_water=403 | time (s): 0.700 (total time: 0.700) Filter (dist) r_work=0.1146 r_free=0.1491 | n_water=403 | time (s): 30.180 (total time: 30.880) Filter (q & B) r_work=0.1147 r_free=0.1493 | n_water=401 | time (s): 1.780 (total time: 32.660) Compute maps r_work=0.1147 r_free=0.1493 | n_water=401 | time (s): 0.810 (total time: 33.470) Filter (map) r_work=0.1230 r_free=0.1551 | n_water=295 | time (s): 1.640 (total time: 35.110) Find peaks r_work=0.1230 r_free=0.1551 | n_water=295 | time (s): 0.540 (total time: 35.650) Add new water r_work=0.1375 r_free=0.1705 | n_water=452 | time (s): 1.590 (total time: 37.240) Refine new water occ: r_work=0.1187 r_free=0.1483 adp: r_work=0.1181 r_free=0.1493 occ: r_work=0.1161 r_free=0.1455 adp: r_work=0.1153 r_free=0.1463 occ: r_work=0.1143 r_free=0.1439 adp: r_work=0.1136 r_free=0.1448 ADP+occupancy (water only), MIN, final r_work=0.1136 r_free=0.1448 r_work=0.1136 r_free=0.1448 | n_water=452 | time (s): 30.690 (total time: 67.930) Filter (q & B) r_work=0.1141 r_free=0.1459 | n_water=438 | time (s): 2.120 (total time: 70.050) Filter (dist only) r_work=0.1143 r_free=0.1458 | n_water=437 | time (s): 35.310 (total time: 105.360) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.838517 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.175041 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 0.1127 0.1499 0.0372 0.010 1.0 3.5 0.5 0.0 0 0.919 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.27 14.99 3.72 4.570 20.977 0.175 4.939 11.17 15.11 3.94 4.724 21.007 0.175 4.936 Individual atomic B min max mean iso aniso Overall: 5.76 102.72 20.91 5.08 1964 0 Protein: 5.76 102.72 16.51 5.07 1519 0 Water: 8.57 64.71 35.94 N/A 437 0 Other: 26.91 49.14 35.11 N/A 8 0 Chain A: 5.76 102.72 18.14 N/A 1730 0 Chain S: 16.91 64.71 41.36 N/A 234 0 Histogram: Values Number of atoms 5.76 - 15.45 1042 15.45 - 25.15 368 25.15 - 34.85 207 34.85 - 44.54 194 44.54 - 54.24 102 54.24 - 63.94 31 63.94 - 73.63 11 73.63 - 83.33 2 83.33 - 93.03 3 93.03 - 102.72 4 =========================== Idealize ADP of riding H ========================== r_work=0.1117 r_free=0.1511 r_work=0.1117 r_free=0.1512 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1117 r_free = 0.1512 target_work(ml) = 4.936 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1110 r_free = 0.1511 target_work(ml) = 4.930 | | 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.=17039 (all), 4.74 % free)------------| | | | r_work= 0.1110 r_free= 0.1511 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.930383 | | target function (ml) not normalized (work): 80029.971595 | | target function (ml) not normalized (free): 4157.803723 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1129 0.1110 0.1511 n_refl.: 17039 re-set all scales: r(all,work,free)=0.1569 0.1558 0.1822 n_refl.: 17039 remove outliers: r(all,work,free)=0.1569 0.1558 0.1822 n_refl.: 17039 overall B=-0.27 to atoms: r(all,work,free)=0.1553 0.1542 0.1814 n_refl.: 17039 bulk-solvent and scaling: r(all,work,free)=0.1127 0.1108 0.1511 n_refl.: 17039 remove outliers: r(all,work,free)=0.1127 0.1108 0.1511 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 0.3657 299.595 275.845 0.553 1.003 0.331 11.894-9.307 99.02 97 4 0.1778 487.394 481.644 0.918 1.004 0.325 9.237-7.194 100.00 213 7 0.1739 398.640 399.846 0.990 1.004 0.230 7.162-5.571 100.00 427 22 0.1516 299.179 293.009 0.938 1.004 0.205 5.546-4.326 100.00 867 58 0.0912 410.725 407.743 0.962 1.004 0.191 4.315-3.360 100.00 1859 96 0.0863 390.604 388.134 1.007 1.003 0.191 3.356-2.611 100.00 3867 181 0.1253 256.604 254.527 1.002 1.001 0.131 2.608-2.000 99.99 8818 434 0.1040 167.262 166.123 0.998 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.9190 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1108 r_free=0.1511 After: r_work=0.1110 r_free=0.1511 ================================== NQH flips ================================== r_work=0.1110 r_free=0.1511 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1110 r_free=0.1511 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1110 r_free=0.1511 | n_water=437 | time (s): 0.690 (total time: 0.690) Filter (dist) r_work=0.1110 r_free=0.1511 | n_water=437 | time (s): 36.040 (total time: 36.730) Filter (q & B) r_work=0.1110 r_free=0.1511 | n_water=437 | time (s): 0.840 (total time: 37.570) Compute maps r_work=0.1110 r_free=0.1511 | n_water=437 | time (s): 0.520 (total time: 38.090) Filter (map) r_work=0.1180 r_free=0.1526 | n_water=332 | time (s): 1.710 (total time: 39.800) Find peaks r_work=0.1180 r_free=0.1526 | n_water=332 | time (s): 0.480 (total time: 40.280) Add new water r_work=0.1299 r_free=0.1639 | n_water=474 | time (s): 1.650 (total time: 41.930) Refine new water occ: r_work=0.1144 r_free=0.1493 adp: r_work=0.1137 r_free=0.1490 occ: r_work=0.1122 r_free=0.1480 adp: r_work=0.1114 r_free=0.1476 occ: r_work=0.1107 r_free=0.1471 adp: r_work=0.1101 r_free=0.1472 ADP+occupancy (water only), MIN, final r_work=0.1101 r_free=0.1472 r_work=0.1101 r_free=0.1472 | n_water=474 | time (s): 33.730 (total time: 75.660) Filter (q & B) r_work=0.1105 r_free=0.1481 | n_water=463 | time (s): 1.670 (total time: 77.330) Filter (dist only) r_work=0.1105 r_free=0.1481 | n_water=461 | time (s): 37.700 (total time: 115.030) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.947963 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.175071 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1123 0.1508 0.0385 0.010 1.0 5.4 0.5 0.0 0 0.974 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.23 15.08 3.85 4.687 20.839 0.175 4.938 11.13 15.01 3.88 4.760 20.891 0.175 4.929 Individual atomic B min max mean iso aniso Overall: 5.39 101.89 20.92 5.16 1988 0 Protein: 5.39 101.89 16.26 5.15 1519 0 Water: 8.02 64.72 36.08 N/A 461 0 Other: 25.90 46.28 33.00 N/A 8 0 Chain A: 5.39 101.89 17.86 N/A 1730 0 Chain S: 16.22 64.72 41.47 N/A 258 0 Histogram: Values Number of atoms 5.39 - 15.04 1038 15.04 - 24.69 362 24.69 - 34.34 224 34.34 - 43.99 193 43.99 - 53.64 117 53.64 - 63.29 33 63.29 - 72.94 12 72.94 - 82.59 1 82.59 - 92.24 3 92.24 - 101.89 5 =========================== Idealize ADP of riding H ========================== r_work=0.1113 r_free=0.1501 r_work=0.1113 r_free=0.1501 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1113 r_free = 0.1501 target_work(ml) = 4.929 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1106 r_free = 0.1497 target_work(ml) = 4.924 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17039 (all), 4.74 % free)------------| | | | r_work= 0.1106 r_free= 0.1497 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.923741 | | target function (ml) not normalized (work): 79922.165321 | | target function (ml) not normalized (free): 4148.129552 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1111 0.1429 5.441 5.6588| | 2: 3.63 - 2.88 1.00 2711 122 0.1095 0.1391 5.2102 5.3143| | 3: 2.88 - 2.52 1.00 2681 148 0.1368 0.1712 5.1251 5.1905| | 4: 2.52 - 2.29 1.00 2661 139 0.0921 0.1455 4.6134 4.8967| | 5: 2.29 - 2.13 1.00 2678 122 0.0961 0.1440 4.5649 4.8613| | 6: 2.13 - 2.00 1.00 2692 117 0.1121 0.1739 4.5587 4.7702| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.64 2809 159 0.95 8.83 1.00 0.96 6199.42| | 2: 3.63 - 2.88 2711 122 0.92 12.67 1.01 0.96 6199.42| | 3: 2.88 - 2.52 2681 148 0.88 18.63 0.99 0.96 6199.42| | 4: 2.52 - 2.29 2661 139 0.93 11.75 1.01 0.97 2025.09| | 5: 2.29 - 2.13 2678 122 0.92 13.84 1.00 0.97 2025.09| | 6: 2.13 - 2.00 2692 117 0.90 16.46 0.99 0.97 2025.09| |alpha: min = 0.96 max = 0.97 mean = 0.96| |beta: min = 2025.09 max = 6199.42 mean = 4134.11| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.87 mean = 13.66| |phase err.(test): min = 0.00 max = 88.63 mean = 13.42| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1125 0.1106 0.1497 n_refl.: 17039 re-set all scales: r(all,work,free)=0.1550 0.1538 0.1812 n_refl.: 17039 remove outliers: r(all,work,free)=0.1550 0.1538 0.1812 n_refl.: 17039 overall B=-0.21 to atoms: r(all,work,free)=0.1539 0.1526 0.1805 n_refl.: 17039 bulk-solvent and scaling: r(all,work,free)=0.1126 0.1107 0.1499 n_refl.: 17039 remove outliers: r(all,work,free)=0.1126 0.1107 0.1499 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 0.3548 299.595 276.695 0.540 1.003 0.313 11.894-9.307 99.02 97 4 0.1766 487.394 481.150 0.915 1.005 0.301 9.237-7.194 100.00 213 7 0.1706 398.640 400.429 0.993 1.005 0.220 7.162-5.571 100.00 427 22 0.1537 299.179 293.676 0.933 1.005 0.203 5.546-4.326 100.00 867 58 0.0934 410.725 407.665 0.962 1.004 0.197 4.315-3.360 100.00 1859 96 0.0880 390.604 388.230 1.003 1.003 0.191 3.356-2.611 100.00 3867 181 0.1242 256.604 254.517 0.999 1.000 0.131 2.608-2.000 99.99 8818 434 0.1034 167.262 165.965 0.989 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.7174 ================= 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 0.1860 0.084 5.299 8.8 119.3 19.9 258 0.000 1_bss: 0.1618 0.1699 0.084 5.299 8.5 118.9 19.5 258 0.000 1_settarget: 0.1618 0.1699 0.084 5.299 8.5 118.9 19.5 258 0.000 1_nqh: 0.1620 0.1706 0.084 5.299 8.5 118.9 19.5 258 0.006 1_weight: 0.1620 0.1706 0.084 5.299 8.5 118.9 19.5 258 0.006 1_xyzrec: 0.1348 0.1627 0.009 0.976 8.5 118.9 19.5 258 0.150 1_adp: 0.1272 0.1651 0.009 0.976 5.8 113.9 20.0 258 0.150 1_regHadp: 0.1275 0.1661 0.009 0.976 5.8 113.9 20.0 258 0.150 1_occ: 0.1271 0.1655 0.009 0.976 5.8 113.9 20.0 258 0.150 2_bss: 0.1270 0.1646 0.009 0.976 5.3 113.4 19.5 258 0.150 2_settarget: 0.1270 0.1646 0.009 0.976 5.3 113.4 19.5 258 0.150 2_updatecdl: 0.1270 0.1646 0.009 0.988 5.3 113.4 19.5 258 0.150 2_nqh: 0.1270 0.1647 0.009 0.988 5.3 113.4 19.5 258 0.147 2_sol: 0.1240 0.1528 0.009 0.988 5.3 113.0 20.8 366 n/a 2_weight: 0.1240 0.1528 0.009 0.988 5.3 113.0 20.8 366 n/a 2_xyzrec: 0.1214 0.1603 0.008 0.934 5.3 113.0 20.8 366 n/a 2_adp: 0.1200 0.1626 0.008 0.934 6.4 108.0 21.3 366 n/a 2_regHadp: 0.1203 0.1628 0.008 0.934 6.4 108.0 21.3 366 n/a 2_occ: 0.1198 0.1642 0.008 0.934 6.4 108.0 21.3 366 n/a 3_bss: 0.1192 0.1634 0.008 0.934 6.0 107.6 20.9 366 n/a 3_settarget: 0.1192 0.1634 0.008 0.934 6.0 107.6 20.9 366 n/a 3_updatecdl: 0.1192 0.1634 0.008 0.934 6.0 107.6 20.9 366 n/a 3_nqh: 0.1193 0.1635 0.008 0.934 6.0 107.6 20.9 366 n/a 3_sol: 0.1196 0.1528 0.008 0.934 6.0 107.6 21.0 403 n/a 3_weight: 0.1196 0.1528 0.008 0.934 6.0 107.6 21.0 403 n/a 3_xyzrec: 0.1178 0.1510 0.009 0.953 6.0 107.6 21.0 403 n/a 3_adp: 0.1160 0.1504 0.009 0.953 6.3 105.4 20.8 403 n/a 3_regHadp: 0.1160 0.1503 0.009 0.953 6.3 105.4 20.8 403 n/a 3_occ: 0.1150 0.1496 0.009 0.953 6.3 105.4 20.8 403 n/a 4_bss: 0.1146 0.1491 0.009 0.953 6.0 105.1 20.5 403 n/a 4_settarget: 0.1146 0.1491 0.009 0.953 6.0 105.1 20.5 403 n/a 4_updatecdl: 0.1146 0.1491 0.009 0.953 6.0 105.1 20.5 403 n/a 4_nqh: 0.1146 0.1491 0.009 0.953 6.0 105.1 20.5 403 n/a 4_sol: 0.1143 0.1458 0.009 0.953 6.0 105.1 20.9 437 n/a 4_weight: 0.1143 0.1458 0.009 0.953 6.0 105.1 20.9 437 n/a 4_xyzrec: 0.1127 0.1499 0.010 0.987 6.0 105.1 20.9 437 n/a 4_adp: 0.1117 0.1511 0.010 0.987 5.8 102.7 20.9 437 n/a 4_regHadp: 0.1117 0.1512 0.010 0.987 5.8 102.7 20.9 437 n/a 4_occ: 0.1110 0.1511 0.010 0.987 5.8 102.7 20.9 437 n/a 5_bss: 0.1108 0.1511 0.010 0.987 5.5 102.5 20.6 437 n/a 5_settarget: 0.1108 0.1511 0.010 0.987 5.5 102.5 20.6 437 n/a 5_updatecdl: 0.1108 0.1511 0.010 0.987 5.5 102.5 20.6 437 n/a 5_setrh: 0.1110 0.1511 0.010 0.987 5.5 102.5 20.6 437 n/a 5_nqh: 0.1110 0.1511 0.010 0.987 5.5 102.5 20.6 437 n/a 5_sol: 0.1105 0.1481 0.010 0.987 5.5 102.5 20.8 461 n/a 5_weight: 0.1105 0.1481 0.010 0.987 5.5 102.5 20.8 461 n/a 5_xyzrec: 0.1123 0.1508 0.010 1.044 5.5 102.5 20.8 461 n/a 5_adp: 0.1113 0.1501 0.010 1.044 5.4 101.9 20.9 461 n/a 5_regHadp: 0.1113 0.1501 0.010 1.044 5.4 101.9 20.9 461 n/a 5_occ: 0.1106 0.1497 0.010 1.044 5.4 101.9 20.9 461 n/a end: 0.1107 0.1499 0.010 1.044 5.2 101.7 20.7 461 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_6369642_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_6369642_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.1800 Refinement macro-cycles (run) : 911.0800 Write final files (write_after_run_outputs) : 21.7800 Total : 936.0400 Total CPU time: 15.96 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:40:57 PST -0800 (1735494057.99 s) Start R-work = 0.1618, R-free = 0.1699 Final R-work = 0.1107, R-free = 0.1499 =============================================================================== Job complete usr+sys time: 983.19 seconds wall clock time: 16 minutes 45.66 seconds (1005.66 seconds total)