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_4813131.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Adding command-line PHIL: ------------------------- xray_data.high_resolution=2 ordered_solvent.low_resolution=4 No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_4813131.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_4813131.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 2 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.38, per 1000 atoms: 0.41 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.28 Conformation dependent library (CDL) restraints added in 105.3 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.63 - 0.89: 406 0.89 - 1.15: 1203 1.15 - 1.41: 628 1.41 - 1.67: 881 1.67 - 1.93: 35 Bond restraints: 3153 Sorted by residual: bond pdb=" C ALA A 11 " pdb=" N LYS A 12 " ideal model delta sigma weight residual 1.332 1.626 -0.295 1.35e-02 5.49e+03 4.76e+02 bond pdb=" CA ALA A 104 " pdb=" C ALA A 104 " ideal model delta sigma weight residual 1.520 1.294 0.227 1.22e-02 6.72e+03 3.46e+02 bond pdb=" N ALA A 39 " pdb=" CA ALA A 39 " ideal model delta sigma weight residual 1.456 1.214 0.242 1.32e-02 5.74e+03 3.36e+02 bond pdb=" N GLU A 163 " pdb=" CA GLU A 163 " ideal model delta sigma weight residual 1.459 1.671 -0.212 1.19e-02 7.06e+03 3.18e+02 bond pdb=" C ARG A 145 " pdb=" O ARG A 145 " ideal model delta sigma weight residual 1.237 1.441 -0.205 1.16e-02 7.43e+03 3.11e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.94: 3333 4.94 - 9.87: 1811 9.87 - 14.81: 548 14.81 - 19.74: 79 19.74 - 24.68: 6 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA BLYS A 175 " pdb=" C BLYS A 175 " pdb=" O BLYS A 175 " ideal model delta sigma weight residual 120.55 136.26 -15.71 1.06e+00 8.90e-01 2.20e+02 angle pdb=" CA ATYR A 67 " pdb=" C ATYR A 67 " pdb=" O ATYR A 67 " ideal model delta sigma weight residual 120.71 135.51 -14.80 1.06e+00 8.90e-01 1.95e+02 angle pdb=" O BGLU A 94 " pdb=" C BGLU A 94 " pdb=" N GLN A 95 " ideal model delta sigma weight residual 122.15 106.38 15.77 1.14e+00 7.69e-01 1.91e+02 angle pdb=" CA MET A 133 " pdb=" C MET A 133 " pdb=" O MET A 133 " ideal model delta sigma weight residual 120.76 107.13 13.63 1.03e+00 9.43e-01 1.75e+02 angle pdb=" O GLU A 163 " pdb=" C GLU A 163 " pdb=" N PHE A 164 " ideal model delta sigma weight residual 122.07 109.11 12.96 1.03e+00 9.43e-01 1.58e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.33: 1308 17.33 - 34.66: 115 34.66 - 51.98: 40 51.98 - 69.31: 16 69.31 - 86.64: 2 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C GLN A 180 " pdb=" N GLN A 180 " pdb=" CA GLN A 180 " pdb=" CB GLN A 180 " ideal model delta harmonic sigma weight residual -122.60 -138.25 15.65 0 2.50e+00 1.60e-01 3.92e+01 dihedral pdb=" C LEU A 113 " pdb=" N LEU A 113 " pdb=" CA LEU A 113 " pdb=" CB LEU A 113 " ideal model delta harmonic sigma weight residual -122.60 -138.20 15.60 0 2.50e+00 1.60e-01 3.90e+01 dihedral pdb=" N MET A 134 " pdb=" C MET A 134 " pdb=" CA MET A 134 " pdb=" CB MET A 134 " ideal model delta harmonic sigma weight residual 122.80 138.40 -15.60 0 2.50e+00 1.60e-01 3.90e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.215: 103 0.215 - 0.427: 77 0.427 - 0.640: 41 0.640 - 0.852: 19 0.852 - 1.065: 3 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA VAL A 51 " pdb=" N VAL A 51 " pdb=" C VAL A 51 " pdb=" CB VAL A 51 " both_signs ideal model delta sigma weight residual False 2.44 3.51 -1.06 2.00e-01 2.50e+01 2.83e+01 chirality pdb=" CA VAL A 35 " pdb=" N VAL A 35 " pdb=" C VAL A 35 " pdb=" CB VAL A 35 " both_signs ideal model delta sigma weight residual False 2.44 3.41 -0.97 2.00e-01 2.50e+01 2.37e+01 chirality pdb=" CG LEU A 187 " pdb=" CB LEU A 187 " pdb=" CD1 LEU A 187 " pdb=" CD2 LEU A 187 " both_signs ideal model delta sigma weight residual False -2.59 -3.56 0.97 2.00e-01 2.50e+01 2.34e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 27 " -0.105 9.50e-02 1.11e+02 8.77e-02 1.47e+02 pdb=" NE ARG A 27 " 0.057 2.00e-02 2.50e+03 pdb=" CZ ARG A 27 " 0.091 2.00e-02 2.50e+03 pdb=" NH1 ARG A 27 " 0.046 2.00e-02 2.50e+03 pdb=" NH2 ARG A 27 " -0.131 2.00e-02 2.50e+03 pdb="HH11 ARG A 27 " -0.096 2.00e-02 2.50e+03 pdb="HH12 ARG A 27 " -0.009 2.00e-02 2.50e+03 pdb="HH21 ARG A 27 " -0.069 2.00e-02 2.50e+03 pdb="HH22 ARG A 27 " 0.115 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.073 2.00e-02 2.50e+03 6.18e-02 1.15e+02 pdb=" CG PHE A 164 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.071 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.035 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.062 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.069 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.092 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.078 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.019 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.007 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.082 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " 0.042 2.00e-02 2.50e+03 5.78e-02 1.00e+02 pdb=" CG TYR A 139 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " -0.127 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " 0.037 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " -0.058 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.045 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " -0.040 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.047 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " 0.033 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " -0.044 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.062 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " 0.034 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.29: 869 2.29 - 2.87: 7884 2.87 - 3.44: 10567 3.44 - 4.02: 15298 4.02 - 4.60: 22023 Nonbonded interactions: 56641 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.710 2.100 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.805 2.450 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.834 2.450 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.870 2.100 nonbonded pdb=" O GLY A 75 " pdb=" H ALA A 79 " model vdw 1.895 2.450 ... (remaining 56636 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_4813131_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= 0.1846 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.399740 | | target function (ml) not normalized (work): 71464.969777 | | target function (ml) not normalized (free): 3263.153338 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3203 0.2150 7.5287 5.0299| | 2: 3.63 - 2.88 1.00 2711 122 0.2646 0.1760 4.3291 4.3303| | 3: 2.88 - 2.52 1.00 2682 148 0.2563 0.1752 4.1866 4.192| | 4: 2.52 - 2.29 1.00 2661 139 0.2514 0.1612 3.4908 3.5919| | 5: 2.29 - 2.13 1.00 2678 122 0.2664 0.1525 3.396 3.4557| | 6: 2.13 - 2.00 1.00 2692 117 0.2732 0.1809 3.3037 3.3659| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 17.66 0.77 0.23 1303.73| | 2: 3.63 - 2.88 2711 122 0.83 23.88 1.32 0.23 1303.73| | 3: 2.88 - 2.52 2682 148 0.73 32.84 1.29 0.23 1303.73| | 4: 2.52 - 2.29 2661 139 0.93 11.36 1.29 0.26 136.24| | 5: 2.29 - 2.13 2678 122 0.92 13.50 1.32 0.26 136.24| | 6: 2.13 - 2.00 2692 117 0.90 16.24 1.33 0.26 136.24| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 136.24 max = 1303.73 mean = 726.49| |figures of merit: min = 0.00 max = 1.00 mean = 0.87| |phase err.(work): min = 0.00 max = 89.93 mean = 19.25| |phase err.(test): min = 0.00 max = 88.95 mean = 19.75| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.080 0.295 1557 Z= 5.317 Angle : 5.198 18.421 2118 Z= 3.650 Chirality : 0.370 1.065 243 Planarity : 0.032 0.132 284 Dihedral : 14.016 86.638 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.24 % Allowed : 2.48 % Favored : 96.27 % Cbeta Deviations : 28.65 % 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: -2.38 (0.47), residues: 224 helix: -1.87 (0.39), residues: 109 sheet: -1.46 (0.77), residues: 38 loop : -0.76 (0.62), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.125 0.030 ARG A 28 TYR 0.076 0.029 TYR A 139 PHE 0.121 0.037 PHE A 164 HIS 0.088 0.036 HIS A 115 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= 0.1846 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.399740 | | target function (ml) not normalized (work): 71464.969777 | | target function (ml) not normalized (free): 3263.153338 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.3449 percent. r_work = 0.2922 r_free = 0.2023 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2869 0.2922 0.2023 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2869 0.2922 0.2023 n_refl.: 17050 remove outliers: r(all,work,free)=0.2154 0.2164 0.2023 n_refl.: 17045 overall B=-0.40 to atoms: r(all,work,free)=0.2128 0.2137 0.2006 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1607 0.1603 0.1693 n_refl.: 17045 remove outliers: r(all,work,free)=0.1607 0.1602 0.1693 n_refl.: 17044 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 100.00 89 5 0.4080 394.422 359.910 0.644 1.019 0.393 11.894-9.307 99.02 97 4 0.1896 633.060 615.896 0.927 1.020 0.380 9.237-7.194 100.00 213 7 0.2190 517.779 507.785 0.953 1.019 0.353 7.162-5.571 100.00 427 22 0.2299 388.594 375.648 0.915 1.017 0.346 5.546-4.326 100.00 867 58 0.1394 533.477 528.429 0.953 1.013 0.215 4.315-3.360 100.00 1859 96 0.1299 507.342 503.104 1.012 1.008 0.191 3.356-2.611 100.00 3867 181 0.1635 333.295 329.044 1.015 0.999 0.039 2.608-2.000 99.99 8818 434 0.1630 217.251 213.491 1.035 0.983 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.4139 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1602 r_free=0.1693 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1602 r_free=0.1693 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.689748 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.763202 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 0.1349 0.1641 0.0292 0.009 1.0 1.3 0.5 0.0 0 11.845 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.49 16.41 2.92 3.013 18.463 0.763 0.023 12.78 16.59 3.81 3.491 18.682 0.763 0.020 Individual atomic B min max mean iso aniso Overall: 6.19 113.90 19.91 3.99 1785 0 Protein: 6.19 112.96 17.14 3.99 1519 0 Water: 8.78 113.90 36.02 N/A 258 0 Other: 21.45 36.53 25.85 N/A 8 0 Chain A: 6.19 113.90 19.91 N/A 1785 0 Histogram: Values Number of atoms 6.19 - 16.96 1087 16.96 - 27.74 344 27.74 - 38.51 181 38.51 - 49.28 96 49.28 - 60.05 50 60.05 - 70.82 13 70.82 - 81.59 6 81.59 - 92.36 4 92.36 - 103.13 1 103.13 - 113.90 3 =========================== Idealize ADP of riding H ========================== r_work=0.1278 r_free=0.1659 r_work=0.1281 r_free=0.1665 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1281 r_free = 0.1665 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 = 0.1654 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17044 (all), 4.73 % free)------------| | | | r_work= 0.1275 r_free= 0.1654 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.020001 | | target function (ls_wunit_k1) not normalized (work): 324.751521 | | target function (ls_wunit_k1) not normalized (free): 27.006644 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1294 0.1275 0.1654 n_refl.: 17044 re-set all scales: r(all,work,free)=0.1913 0.1912 0.1987 n_refl.: 17044 remove outliers: r(all,work,free)=0.1913 0.1912 0.1987 n_refl.: 17044 overall B=-0.39 to atoms: r(all,work,free)=0.1885 0.1883 0.1971 n_refl.: 17044 bulk-solvent and scaling: r(all,work,free)=0.1294 0.1276 0.1651 n_refl.: 17044 remove outliers: r(all,work,free)=0.1293 0.1275 0.1651 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 0.3624 301.184 282.535 0.626 1.010 0.370 11.894-9.307 99.02 97 4 0.1664 487.571 477.195 0.918 1.010 0.367 9.237-7.194 100.00 213 7 0.1798 398.784 397.206 0.958 1.010 0.325 7.162-5.571 100.00 427 22 0.1853 299.288 294.108 0.930 1.009 0.301 5.546-4.326 100.00 867 58 0.1051 410.874 408.722 0.956 1.007 0.205 4.315-3.360 100.00 1859 96 0.0923 390.745 390.352 1.018 1.005 0.191 3.356-2.611 100.00 3867 181 0.1298 256.697 255.393 1.016 1.000 0.091 2.608-2.000 99.99 8818 434 0.1352 167.323 165.812 1.022 0.991 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.3832 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1275 r_free=0.1651 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1275 r_free=0.1651 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1275 r_free=0.1651 | n_water=258 | time (s): 0.920 (total time: 0.920) Filter (dist) r_work=0.1279 r_free=0.1644 | n_water=254 | time (s): 20.520 (total time: 21.440) Filter (q & B) r_work=0.1279 r_free=0.1642 | n_water=251 | time (s): 1.690 (total time: 23.130) Compute maps r_work=0.1279 r_free=0.1642 | n_water=251 | time (s): 0.710 (total time: 23.840) Filter (map) r_work=0.1319 r_free=0.1630 | n_water=211 | time (s): 1.510 (total time: 25.350) Find peaks r_work=0.1319 r_free=0.1630 | n_water=211 | time (s): 0.460 (total time: 25.810) Add new water r_work=0.1540 r_free=0.1891 | n_water=375 | time (s): 1.690 (total time: 27.500) Refine new water occ: r_work=0.1327 r_free=0.1569 adp: r_work=0.1267 r_free=0.1573 occ: r_work=0.1273 r_free=0.1537 adp: r_work=0.1238 r_free=0.1546 occ: r_work=0.1240 r_free=0.1534 adp: r_work=0.1228 r_free=0.1537 ADP+occupancy (water only), MIN, final r_work=0.1228 r_free=0.1537 r_work=0.1228 r_free=0.1537 | n_water=375 | time (s): 16.080 (total time: 43.580) Filter (q & B) r_work=0.1230 r_free=0.1540 | n_water=366 | time (s): 2.370 (total time: 45.950) Filter (dist only) r_work=0.1231 r_free=0.1541 | n_water=365 | time (s): 30.210 (total time: 76.160) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.143932 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.975326 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 0.1206 0.1579 0.0373 0.009 0.9 3.5 0.5 0.0 0 12.572 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.06 15.79 3.73 4.117 21.004 0.975 0.018 11.90 16.11 4.21 4.142 21.320 0.975 0.017 Individual atomic B min max mean iso aniso Overall: 6.59 107.58 21.43 4.26 1892 0 Protein: 6.59 107.58 17.79 4.25 1519 0 Water: 8.22 66.06 36.35 N/A 365 0 Other: 23.50 41.47 31.79 N/A 8 0 Chain A: 6.59 107.58 19.50 N/A 1738 0 Chain S: 16.75 66.06 43.28 N/A 154 0 Histogram: Values Number of atoms 6.59 - 16.69 1022 16.69 - 26.79 371 26.79 - 36.89 228 36.89 - 46.99 158 46.99 - 57.09 75 57.09 - 67.18 28 67.18 - 77.28 3 77.28 - 87.38 5 87.38 - 97.48 0 97.48 - 107.58 2 =========================== Idealize ADP of riding H ========================== r_work=0.1190 r_free=0.1611 r_work=0.1191 r_free=0.1612 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1191 r_free = 0.1612 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1188 r_free = 0.1618 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.=17043 (all), 4.74 % free)------------| | | | r_work= 0.1188 r_free= 0.1618 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.016820 | | target function (ls_wunit_k1) not normalized (work): 273.097424 | | target function (ls_wunit_k1) not normalized (free): 24.650957 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1208 0.1188 0.1618 n_refl.: 17043 re-set all scales: r(all,work,free)=0.1819 0.1817 0.1924 n_refl.: 17043 remove outliers: r(all,work,free)=0.1819 0.1817 0.1924 n_refl.: 17043 overall B=-0.38 to atoms: r(all,work,free)=0.1793 0.1790 0.1908 n_refl.: 17043 bulk-solvent and scaling: r(all,work,free)=0.1202 0.1182 0.1605 n_refl.: 17043 remove outliers: r(all,work,free)=0.1201 0.1181 0.1605 n_refl.: 17042 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3340 303.151 276.771 0.592 1.006 0.350 11.894-9.307 99.02 97 4 0.1434 487.571 483.713 0.914 1.006 0.348 9.237-7.194 100.00 213 7 0.1634 398.784 400.625 0.974 1.006 0.280 7.162-5.571 100.00 427 22 0.1523 299.288 295.556 0.933 1.006 0.244 5.546-4.326 100.00 867 58 0.0868 410.874 408.415 0.958 1.005 0.216 4.315-3.360 100.00 1859 96 0.0822 390.745 390.015 1.016 1.004 0.211 3.356-2.611 100.00 3867 181 0.1187 256.697 255.770 1.011 1.002 0.111 2.608-2.000 99.99 8818 434 0.1325 167.323 166.355 1.015 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.3441 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1181 r_free=0.1605 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** Total number of N/Q/H flips: 0 r_work=0.1181 r_free=0.1605 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1181 r_free=0.1605 | n_water=365 | time (s): 0.810 (total time: 0.810) Filter (dist) r_work=0.1181 r_free=0.1610 | n_water=363 | time (s): 28.210 (total time: 29.020) Filter (q & B) r_work=0.1181 r_free=0.1613 | n_water=362 | time (s): 1.860 (total time: 30.880) Compute maps r_work=0.1181 r_free=0.1613 | n_water=362 | time (s): 0.670 (total time: 31.550) Filter (map) r_work=0.1253 r_free=0.1628 | n_water=266 | time (s): 2.090 (total time: 33.640) Find peaks r_work=0.1253 r_free=0.1628 | n_water=266 | time (s): 0.660 (total time: 34.300) Add new water r_work=0.1442 r_free=0.1776 | n_water=415 | time (s): 1.720 (total time: 36.020) Refine new water occ: r_work=0.1238 r_free=0.1553 adp: r_work=0.1231 r_free=0.1554 occ: r_work=0.1211 r_free=0.1522 adp: r_work=0.1201 r_free=0.1521 occ: r_work=0.1194 r_free=0.1512 adp: r_work=0.1184 r_free=0.1509 ADP+occupancy (water only), MIN, final r_work=0.1184 r_free=0.1509 r_work=0.1184 r_free=0.1509 | n_water=415 | time (s): 40.460 (total time: 76.480) Filter (q & B) r_work=0.1185 r_free=0.1511 | n_water=407 | time (s): 1.550 (total time: 78.030) Filter (dist only) r_work=0.1187 r_free=0.1516 | n_water=405 | time (s): 32.420 (total time: 110.450) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.209665 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.188691 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1166 0.1535 0.0369 0.010 1.0 5.1 0.5 0.0 0 1.105 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.66 15.35 3.69 4.336 21.559 0.189 4.993 11.42 15.39 3.96 4.918 21.494 0.189 4.970 Individual atomic B min max mean iso aniso Overall: 6.06 105.47 20.95 4.78 1932 0 Protein: 6.06 105.47 17.08 4.78 1519 0 Water: 8.70 60.42 35.25 N/A 405 0 Other: 23.61 43.17 31.08 N/A 8 0 Chain A: 6.06 105.47 18.80 N/A 1734 0 Chain S: 16.21 59.87 39.74 N/A 198 0 Histogram: Values Number of atoms 6.06 - 16.00 1044 16.00 - 25.94 374 25.94 - 35.88 211 35.88 - 45.82 181 45.82 - 55.76 82 55.76 - 65.71 25 65.71 - 75.65 7 75.65 - 85.59 3 85.59 - 95.53 3 95.53 - 105.47 2 =========================== Idealize ADP of riding H ========================== r_work=0.1142 r_free=0.1539 r_work=0.1142 r_free=0.1540 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1142 r_free = 0.1540 target_work(ml) = 4.970 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1135 r_free = 0.1548 target_work(ml) = 4.966 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17042 (all), 4.74 % free)------------| | | | r_work= 0.1135 r_free= 0.1548 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.966038 | | target function (ml) not normalized (work): 80623.621705 | | target function (ml) not normalized (free): 4189.772287 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1155 0.1135 0.1548 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1666 0.1660 0.1854 n_refl.: 17042 remove outliers: r(all,work,free)=0.1666 0.1660 0.1854 n_refl.: 17042 overall B=-0.37 to atoms: r(all,work,free)=0.1641 0.1633 0.1842 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1154 0.1133 0.1550 n_refl.: 17042 remove outliers: r(all,work,free)=0.1154 0.1133 0.1550 n_refl.: 17042 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3704 303.151 278.975 0.567 1.003 0.340 11.894-9.307 99.02 97 4 0.1658 487.571 479.861 0.916 1.004 0.340 9.237-7.194 100.00 213 7 0.1764 398.784 400.082 0.985 1.004 0.280 7.162-5.571 100.00 427 22 0.1571 299.288 294.244 0.936 1.004 0.230 5.546-4.326 100.00 867 58 0.0925 410.874 407.124 0.966 1.004 0.221 4.315-3.360 100.00 1859 96 0.0865 390.745 388.426 1.014 1.003 0.221 3.356-2.611 100.00 3867 181 0.1259 256.697 254.432 1.012 1.002 0.121 2.608-2.000 99.99 8818 434 0.1093 167.323 165.940 1.014 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-1.3413 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1133 r_free=0.1550 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1133 r_free=0.1550 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1133 r_free=0.1550 | n_water=405 | time (s): 0.680 (total time: 0.680) Filter (dist) r_work=0.1133 r_free=0.1550 | n_water=405 | time (s): 33.540 (total time: 34.220) Filter (q & B) r_work=0.1134 r_free=0.1552 | n_water=404 | time (s): 1.960 (total time: 36.180) Compute maps r_work=0.1134 r_free=0.1552 | n_water=404 | time (s): 0.610 (total time: 36.790) Filter (map) r_work=0.1190 r_free=0.1567 | n_water=317 | time (s): 1.670 (total time: 38.460) Find peaks r_work=0.1190 r_free=0.1567 | n_water=317 | time (s): 0.660 (total time: 39.120) Add new water r_work=0.1334 r_free=0.1672 | n_water=466 | time (s): 2.040 (total time: 41.160) Refine new water occ: r_work=0.1164 r_free=0.1513 adp: r_work=0.1155 r_free=0.1512 occ: r_work=0.1142 r_free=0.1503 adp: r_work=0.1132 r_free=0.1501 occ: r_work=0.1127 r_free=0.1498 adp: r_work=0.1118 r_free=0.1496 ADP+occupancy (water only), MIN, final r_work=0.1118 r_free=0.1496 r_work=0.1118 r_free=0.1496 | n_water=466 | time (s): 24.780 (total time: 65.940) Filter (q & B) r_work=0.1122 r_free=0.1503 | n_water=449 | time (s): 1.480 (total time: 67.420) Filter (dist only) r_work=0.1122 r_free=0.1503 | n_water=449 | time (s): 32.450 (total time: 99.870) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.012164 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.166417 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 0.1118 0.1567 0.0449 0.010 1.0 3.8 0.5 0.0 0 1.006 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.18 15.67 4.49 4.562 21.231 0.166 4.966 11.09 15.80 4.71 4.737 21.238 0.166 4.959 Individual atomic B min max mean iso aniso Overall: 5.57 103.37 21.13 4.88 1976 0 Protein: 5.57 103.37 16.60 4.88 1519 0 Water: 8.43 65.63 36.31 N/A 449 0 Other: 22.98 40.18 29.62 N/A 8 0 Chain A: 5.57 103.37 18.26 N/A 1734 0 Chain S: 18.74 65.63 41.70 N/A 242 0 Histogram: Values Number of atoms 5.57 - 15.35 1015 15.35 - 25.13 398 25.13 - 34.91 211 34.91 - 44.69 193 44.69 - 54.47 110 54.47 - 64.25 33 64.25 - 74.03 9 74.03 - 83.81 3 83.81 - 93.59 2 93.59 - 103.37 2 =========================== Idealize ADP of riding H ========================== r_work=0.1109 r_free=0.1580 r_work=0.1109 r_free=0.1582 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1109 r_free = 0.1582 target_work(ml) = 4.960 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1100 r_free = 0.1586 target_work(ml) = 4.957 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17042 (all), 4.74 % free)------------| | | | r_work= 0.1100 r_free= 0.1586 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.956977 | | target function (ml) not normalized (work): 80476.524408 | | target function (ml) not normalized (free): 4197.662651 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1123 0.1100 0.1586 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1592 0.1578 0.1882 n_refl.: 17042 remove outliers: r(all,work,free)=0.1592 0.1578 0.1882 n_refl.: 17042 overall B=-0.33 to atoms: r(all,work,free)=0.1571 0.1557 0.1872 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1119 0.1096 0.1578 n_refl.: 17042 remove outliers: r(all,work,free)=0.1118 0.1095 0.1578 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 0.3762 299.663 278.564 0.553 1.000 0.330 11.894-9.307 99.02 97 4 0.1811 487.571 478.549 0.915 1.001 0.300 9.237-7.194 100.00 213 7 0.1740 398.784 399.670 0.988 1.002 0.230 7.162-5.571 100.00 427 22 0.1513 299.288 293.670 0.946 1.002 0.230 5.546-4.326 100.00 867 58 0.0915 410.874 406.384 0.967 1.002 0.201 4.315-3.360 100.00 1859 96 0.0831 390.745 388.043 1.011 1.002 0.191 3.356-2.611 100.00 3867 181 0.1228 256.697 254.597 1.007 1.001 0.131 2.608-2.000 99.99 8818 434 0.1036 167.323 166.431 1.006 1.000 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-1.1218 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1095 r_free=0.1578 After: r_work=0.1097 r_free=0.1577 ================================== NQH flips ================================== r_work=0.1097 r_free=0.1577 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1097 r_free=0.1577 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1097 r_free=0.1577 | n_water=449 | time (s): 0.620 (total time: 0.620) Filter (dist) r_work=0.1100 r_free=0.1579 | n_water=447 | time (s): 34.410 (total time: 35.030) Filter (q & B) r_work=0.1100 r_free=0.1579 | n_water=447 | time (s): 0.940 (total time: 35.970) Compute maps r_work=0.1100 r_free=0.1579 | n_water=447 | time (s): 0.610 (total time: 36.580) Filter (map) r_work=0.1182 r_free=0.1586 | n_water=339 | time (s): 1.550 (total time: 38.130) Find peaks r_work=0.1182 r_free=0.1586 | n_water=339 | time (s): 0.460 (total time: 38.590) Add new water r_work=0.1305 r_free=0.1686 | n_water=484 | time (s): 1.580 (total time: 40.170) Refine new water occ: r_work=0.1140 r_free=0.1506 adp: r_work=0.1132 r_free=0.1508 occ: r_work=0.1118 r_free=0.1492 adp: r_work=0.1110 r_free=0.1491 occ: r_work=0.1103 r_free=0.1487 adp: r_work=0.1097 r_free=0.1486 ADP+occupancy (water only), MIN, final r_work=0.1097 r_free=0.1486 r_work=0.1097 r_free=0.1486 | n_water=484 | time (s): 29.220 (total time: 69.390) Filter (q & B) r_work=0.1101 r_free=0.1499 | n_water=472 | time (s): 2.090 (total time: 71.480) Filter (dist only) r_work=0.1101 r_free=0.1499 | n_water=472 | time (s): 37.340 (total time: 108.820) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.953018 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.171122 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 0.1114 0.1549 0.0435 0.010 1.1 7.4 0.5 0.0 0 0.977 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.14 15.49 4.35 4.569 20.937 0.171 4.955 11.06 15.37 4.30 4.589 21.003 0.171 4.947 Individual atomic B min max mean iso aniso Overall: 5.32 101.31 21.13 4.94 1999 0 Protein: 5.32 101.31 16.32 4.94 1519 0 Water: 8.22 65.70 36.49 N/A 472 0 Other: 22.10 37.12 28.21 N/A 8 0 Chain A: 5.32 101.31 17.95 N/A 1733 0 Chain S: 15.32 65.70 41.84 N/A 266 0 Histogram: Values Number of atoms 5.32 - 14.92 1008 14.92 - 24.52 400 24.52 - 34.12 208 34.12 - 43.71 193 43.71 - 53.31 131 53.31 - 62.91 38 62.91 - 72.51 12 72.51 - 82.11 3 82.11 - 91.71 3 91.71 - 101.31 3 =========================== Idealize ADP of riding H ========================== r_work=0.1106 r_free=0.1537 r_work=0.1106 r_free=0.1536 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1106 r_free = 0.1536 target_work(ml) = 4.946 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1098 r_free = 0.1533 target_work(ml) = 4.943 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1098 r_free= 0.1533 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.942586 | | target function (ml) not normalized (work): 80237.947095 | | target function (ml) not normalized (free): 4176.561020 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.64 1.00 2811 159 0.1106 0.1386 5.4461 5.6438| | 2: 3.63 - 2.88 1.00 2711 122 0.1065 0.1582 5.2114 5.3874| | 3: 2.88 - 2.52 1.00 2681 148 0.1354 0.1719 5.1307 5.2134| | 4: 2.52 - 2.29 1.00 2661 139 0.0936 0.1506 4.6444 4.9648| | 5: 2.29 - 2.13 1.00 2678 122 0.0967 0.1515 4.6011 4.9242| | 6: 2.13 - 2.00 1.00 2692 117 0.1124 0.1720 4.5931 4.7821| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.64 2811 159 0.95 9.06 1.00 0.96 6453.77| | 2: 3.63 - 2.88 2711 122 0.92 12.97 1.01 0.96 6453.77| | 3: 2.88 - 2.52 2681 148 0.87 19.06 0.99 0.96 6453.77| | 4: 2.52 - 2.29 2661 139 0.92 12.57 1.01 0.97 2255.79| | 5: 2.29 - 2.13 2678 122 0.91 14.66 1.00 0.97 2255.79| | 6: 2.13 - 2.00 2692 117 0.89 17.41 0.99 0.97 2255.79| |alpha: min = 0.96 max = 0.97 mean = 0.96| |beta: min = 2255.79 max = 6453.77 mean = 4377.02| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.99 mean = 14.25| |phase err.(test): min = 0.00 max = 85.89 mean = 13.89| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1119 0.1098 0.1533 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1563 0.1549 0.1871 n_refl.: 17041 remove outliers: r(all,work,free)=0.1563 0.1549 0.1871 n_refl.: 17041 overall B=-0.25 to atoms: r(all,work,free)=0.1548 0.1533 0.1862 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1118 0.1098 0.1531 n_refl.: 17041 remove outliers: r(all,work,free)=0.1118 0.1098 0.1531 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 0.3753 299.663 278.948 0.541 1.007 0.330 11.894-9.307 99.02 97 4 0.1703 487.571 477.390 0.906 1.008 0.320 9.237-7.194 100.00 213 7 0.1771 398.784 398.952 0.978 1.008 0.228 7.162-5.571 100.00 427 22 0.1518 299.288 294.551 0.937 1.007 0.207 5.546-4.326 100.00 867 58 0.0904 410.874 407.568 0.963 1.006 0.191 4.315-3.360 100.00 1859 96 0.0861 390.745 388.546 1.004 1.003 0.181 3.356-2.611 100.00 3867 181 0.1220 256.697 254.449 1.003 1.000 0.101 2.608-2.000 99.99 8818 434 0.1037 167.323 166.042 1.000 0.993 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.8689 ================= 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 0.1846 0.080 5.198 8.8 119.3 19.9 258 0.000 1_bss: 0.1602 0.1693 0.080 5.198 8.5 118.9 19.5 258 0.000 1_settarget: 0.1602 0.1693 0.080 5.198 8.5 118.9 19.5 258 0.000 1_nqh: 0.1602 0.1693 0.080 5.198 8.5 118.9 19.5 258 0.000 1_weight: 0.1602 0.1693 0.080 5.198 8.5 118.9 19.5 258 0.000 1_xyzrec: 0.1349 0.1641 0.009 0.982 8.5 118.9 19.5 258 0.149 1_adp: 0.1278 0.1659 0.009 0.982 6.2 113.9 19.9 258 0.149 1_regHadp: 0.1281 0.1665 0.009 0.982 6.2 113.9 19.9 258 0.149 1_occ: 0.1275 0.1654 0.009 0.982 6.2 113.9 19.9 258 0.149 2_bss: 0.1275 0.1651 0.009 0.982 5.8 113.5 19.5 258 0.149 2_settarget: 0.1275 0.1651 0.009 0.982 5.8 113.5 19.5 258 0.149 2_updatecdl: 0.1275 0.1651 0.009 1.002 5.8 113.5 19.5 258 0.149 2_nqh: 0.1275 0.1651 0.009 1.002 5.8 113.5 19.5 258 0.149 2_sol: 0.1231 0.1541 0.009 1.002 5.8 112.6 20.9 365 n/a 2_weight: 0.1231 0.1541 0.009 1.002 5.8 112.6 20.9 365 n/a 2_xyzrec: 0.1206 0.1579 0.009 0.936 5.8 112.6 20.9 365 n/a 2_adp: 0.1190 0.1611 0.009 0.936 6.6 107.6 21.4 365 n/a 2_regHadp: 0.1191 0.1612 0.009 0.936 6.6 107.6 21.4 365 n/a 2_occ: 0.1188 0.1618 0.009 0.936 6.6 107.6 21.4 365 n/a 3_bss: 0.1181 0.1605 0.009 0.936 6.2 107.2 21.1 365 n/a 3_settarget: 0.1181 0.1605 0.009 0.936 6.2 107.2 21.1 365 n/a 3_updatecdl: 0.1181 0.1605 0.009 0.937 6.2 107.2 21.1 365 n/a 3_nqh: 0.1181 0.1605 0.009 0.937 6.2 107.2 21.1 365 n/a 3_sol: 0.1187 0.1516 0.009 0.937 6.2 107.2 21.1 405 n/a 3_weight: 0.1187 0.1516 0.009 0.937 6.2 107.2 21.1 405 n/a 3_xyzrec: 0.1166 0.1535 0.010 1.013 6.2 107.2 21.1 405 n/a 3_adp: 0.1142 0.1539 0.010 1.013 6.1 105.5 20.9 405 n/a 3_regHadp: 0.1142 0.1540 0.010 1.013 6.1 105.5 20.9 405 n/a 3_occ: 0.1135 0.1548 0.010 1.013 6.1 105.5 20.9 405 n/a 4_bss: 0.1133 0.1550 0.010 1.013 5.7 105.1 20.6 405 n/a 4_settarget: 0.1133 0.1550 0.010 1.013 5.7 105.1 20.6 405 n/a 4_updatecdl: 0.1133 0.1550 0.010 1.011 5.7 105.1 20.6 405 n/a 4_nqh: 0.1133 0.1550 0.010 1.011 5.7 105.1 20.6 405 n/a 4_sol: 0.1122 0.1503 0.010 1.011 5.7 105.1 21.1 449 n/a 4_weight: 0.1122 0.1503 0.010 1.011 5.7 105.1 21.1 449 n/a 4_xyzrec: 0.1118 0.1567 0.010 0.979 5.7 105.1 21.1 449 n/a 4_adp: 0.1109 0.1580 0.010 0.979 5.6 103.4 21.1 449 n/a 4_regHadp: 0.1109 0.1582 0.010 0.979 5.6 103.4 21.1 449 n/a 4_occ: 0.1100 0.1586 0.010 0.979 5.6 103.4 21.1 449 n/a 5_bss: 0.1095 0.1578 0.010 0.979 5.2 103.0 20.8 449 n/a 5_settarget: 0.1095 0.1578 0.010 0.979 5.2 103.0 20.8 449 n/a 5_updatecdl: 0.1095 0.1578 0.010 0.982 5.2 103.0 20.8 449 n/a 5_setrh: 0.1097 0.1577 0.010 0.982 5.2 103.0 20.8 449 n/a 5_nqh: 0.1097 0.1577 0.010 0.982 5.2 103.0 20.8 449 n/a 5_sol: 0.1101 0.1499 0.010 0.982 5.2 103.0 21.0 472 n/a 5_weight: 0.1101 0.1499 0.010 0.982 5.2 103.0 21.0 472 n/a 5_xyzrec: 0.1114 0.1549 0.010 1.101 5.2 103.0 21.0 472 n/a 5_adp: 0.1106 0.1537 0.010 1.101 5.3 101.3 21.1 472 n/a 5_regHadp: 0.1106 0.1536 0.010 1.101 5.3 101.3 21.1 472 n/a 5_occ: 0.1098 0.1533 0.010 1.101 5.3 101.3 21.1 472 n/a end: 0.1098 0.1531 0.010 1.101 5.1 101.1 20.9 472 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_4813131_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_4813131_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.7000 Refinement macro-cycles (run) : 928.3100 Write final files (write_after_run_outputs) : 20.7900 Total : 952.8000 Total CPU time: 16.23 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:16 PST -0800 (1735494076.86 s) Start R-work = 0.1602, R-free = 0.1693 Final R-work = 0.1098, R-free = 0.1531 =============================================================================== Job complete usr+sys time: 995.85 seconds wall clock time: 17 minutes 0.48 seconds (1020.48 seconds total)