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_3473948.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" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 2 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3473948.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3473948.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 =============================================================================== 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: 1.64, per 1000 atoms: 0.49 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: 0.35 Conformation dependent library (CDL) restraints added in 145.1 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.62 - 0.89: 405 0.89 - 1.15: 1221 1.15 - 1.42: 638 1.42 - 1.69: 852 1.69 - 1.95: 37 Bond restraints: 3153 Sorted by residual: bond pdb=" CA ILE A 21 " pdb=" CB ILE A 21 " ideal model delta sigma weight residual 1.534 1.701 -0.166 6.80e-03 2.16e+04 5.97e+02 bond pdb=" N VAL A 146 " pdb=" CA VAL A 146 " ideal model delta sigma weight residual 1.458 1.683 -0.225 1.19e-02 7.06e+03 3.58e+02 bond pdb=" C THR A 154 " pdb=" O THR A 154 " ideal model delta sigma weight residual 1.234 1.018 0.216 1.28e-02 6.10e+03 2.84e+02 bond pdb=" CA GLU A 16 " pdb=" C GLU A 16 " ideal model delta sigma weight residual 1.523 1.750 -0.227 1.35e-02 5.49e+03 2.83e+02 bond pdb=" CA VAL A 50 " pdb=" CB VAL A 50 " ideal model delta sigma weight residual 1.538 1.727 -0.189 1.13e-02 7.83e+03 2.79e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.82: 3216 4.82 - 9.63: 1845 9.63 - 14.45: 610 14.45 - 19.26: 99 19.26 - 24.08: 7 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O AGLY A 65 " pdb=" C AGLY A 65 " pdb=" N APRO A 66 " ideal model delta sigma weight residual 121.77 106.84 14.93 1.00e+00 1.00e+00 2.23e+02 angle pdb=" CA PHE A 164 " pdb=" CB PHE A 164 " pdb=" CG PHE A 164 " ideal model delta sigma weight residual 113.80 128.52 -14.72 1.00e+00 1.00e+00 2.17e+02 angle pdb=" CA AGLU A 90 " pdb=" C AGLU A 90 " pdb=" O AGLU A 90 " ideal model delta sigma weight residual 120.82 135.89 -15.07 1.05e+00 9.07e-01 2.06e+02 angle pdb=" C ASP A 42 " pdb=" N PRO A 43 " pdb=" CA PRO A 43 " ideal model delta sigma weight residual 119.76 105.07 14.69 1.03e+00 9.43e-01 2.03e+02 angle pdb=" NE ARG A 5 " pdb=" CZ ARG A 5 " pdb=" NH2 ARG A 5 " ideal model delta sigma weight residual 119.20 131.62 -12.42 9.00e-01 1.23e+00 1.90e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.61: 1283 15.61 - 31.21: 134 31.21 - 46.81: 37 46.81 - 62.42: 21 62.42 - 78.02: 6 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" N ASP A 49 " pdb=" C ASP A 49 " pdb=" CA ASP A 49 " pdb=" CB ASP A 49 " ideal model delta harmonic sigma weight residual 122.80 145.18 -22.38 0 2.50e+00 1.60e-01 8.01e+01 dihedral pdb=" C ASP A 49 " pdb=" N ASP A 49 " pdb=" CA ASP A 49 " pdb=" CB ASP A 49 " ideal model delta harmonic sigma weight residual -122.60 -142.98 20.38 0 2.50e+00 1.60e-01 6.65e+01 dihedral pdb=" N ALA A 29 " pdb=" C ALA A 29 " pdb=" CA ALA A 29 " pdb=" CB ALA A 29 " ideal model delta harmonic sigma weight residual 122.90 142.23 -19.33 0 2.50e+00 1.60e-01 5.98e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.217: 91 0.217 - 0.433: 82 0.433 - 0.649: 46 0.649 - 0.866: 18 0.866 - 1.082: 6 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA ASP A 49 " pdb=" N ASP A 49 " pdb=" C ASP A 49 " pdb=" CB ASP A 49 " both_signs ideal model delta sigma weight residual False 2.51 1.43 1.08 2.00e-01 2.50e+01 2.93e+01 chirality pdb=" CA LEU A 7 " pdb=" N LEU A 7 " pdb=" C LEU A 7 " pdb=" CB LEU A 7 " both_signs ideal model delta sigma weight residual False 2.51 3.54 -1.03 2.00e-01 2.50e+01 2.67e+01 chirality pdb=" CA GLN A 180 " pdb=" N GLN A 180 " pdb=" C GLN A 180 " pdb=" CB GLN A 180 " both_signs ideal model delta sigma weight residual False 2.51 3.51 -1.00 2.00e-01 2.50e+01 2.52e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.003 2.00e-02 2.50e+03 7.23e-02 1.57e+02 pdb=" CG PHE A 164 " -0.095 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.128 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.073 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.057 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.061 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.096 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.023 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.075 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.084 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " -0.109 2.00e-02 2.50e+03 6.28e-02 1.18e+02 pdb=" CG ATYR A 67 " 0.097 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " -0.073 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " 0.065 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " 0.030 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " -0.002 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " -0.009 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " -0.091 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " 0.058 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " -0.035 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " 0.018 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " 0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.042 2.00e-02 2.50e+03 5.38e-02 8.68e+01 pdb=" CG PHE A 119 " 0.009 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.053 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.124 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.039 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.061 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.019 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.047 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " -0.080 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.007 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.017 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.33: 1126 2.33 - 2.90: 8225 2.90 - 3.47: 10447 3.47 - 4.03: 15200 4.03 - 4.60: 21578 Nonbonded interactions: 56576 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.766 2.100 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.794 2.450 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.808 2.450 nonbonded pdb=" H THR A 125 " pdb=" HH TYR A 141 " model vdw 1.835 2.100 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.847 2.450 ... (remaining 56571 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_3473948_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1596 occupancy sum: 1438.50 (% of total atoms 46.85) Rotatable: count: 507 occupancy sum: 483.00 (% of total atoms 15.73) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2783 r_free= 0.1811 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.408256 | | target function (ml) not normalized (work): 71603.301667 | | target function (ml) not normalized (free): 3261.788208 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3197 0.2053 7.5736 5.012| | 2: 3.63 - 2.88 1.00 2711 122 0.2626 0.1726 4.3248 4.327| | 3: 2.88 - 2.52 1.00 2682 148 0.2556 0.1789 4.1762 4.1804| | 4: 2.52 - 2.29 1.00 2661 139 0.2568 0.1498 3.5084 3.5404| | 5: 2.29 - 2.13 1.00 2678 122 0.2633 0.1524 3.3832 3.4593| | 6: 2.13 - 2.00 1.00 2692 117 0.2725 0.1964 3.318 3.4543| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 17.40 0.77 0.23 1277.64| | 2: 3.63 - 2.88 2711 122 0.83 23.55 1.31 0.23 1277.64| | 3: 2.88 - 2.52 2682 148 0.73 32.60 1.29 0.23 1277.64| | 4: 2.52 - 2.29 2661 139 0.93 11.63 1.30 0.26 140.25| | 5: 2.29 - 2.13 2678 122 0.92 13.72 1.32 0.26 140.25| | 6: 2.13 - 2.00 2692 117 0.90 16.42 1.33 0.26 140.25| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 140.25 max = 1277.64 mean = 715.28| |figures of merit: min = 0.00 max = 1.00 mean = 0.87| |phase err.(work): min = 0.00 max = 90.00 mean = 19.22| |phase err.(test): min = 0.00 max = 89.07 mean = 19.61| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.082 0.246 1557 Z= 5.496 Angle : 5.302 19.071 2118 Z= 3.752 Chirality : 0.400 1.082 243 Planarity : 0.033 0.096 284 Dihedral : 13.800 78.020 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.16 % Favored : 97.30 % Rotamer: Outliers : 0.62 % Allowed : 3.11 % Favored : 96.27 % Cbeta Deviations : 32.97 % 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: -3.15 (0.45), residues: 224 helix: -2.90 (0.38), residues: 102 sheet: -0.55 (0.68), residues: 38 loop : -1.43 (0.56), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.041 0.012 ARG A 5 TYR 0.088 0.042 TYR A 141 PHE 0.108 0.043 PHE A 164 HIS 0.104 0.029 HIS A 126 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 1785 0 Protein: 8.85 115.78 16.79 3.90 1519 0 Water: 11.36 119.30 38.03 N/A 258 0 Other: 19.04 26.29 21.71 N/A 8 0 Chain A: 8.85 119.30 19.89 N/A 1785 0 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2783 r_free= 0.1811 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.408256 | | target function (ml) not normalized (work): 71603.301667 | | target function (ml) not normalized (free): 3261.788208 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.3017 percent. r_work = 0.2913 r_free = 0.1991 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2861 0.2913 0.1991 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2861 0.2913 0.1991 n_refl.: 17050 remove outliers: r(all,work,free)=0.2151 0.2161 0.1991 n_refl.: 17045 overall B=-0.40 to atoms: r(all,work,free)=0.2124 0.2134 0.1971 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1618 0.1616 0.1670 n_refl.: 17045 remove outliers: r(all,work,free)=0.1616 0.1614 0.1670 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 0.3888 399.094 361.972 0.662 1.013 0.403 11.894-9.307 99.02 97 4 0.1931 633.856 612.571 0.926 1.013 0.375 9.237-7.194 100.00 213 7 0.2253 518.430 507.488 0.957 1.013 0.361 7.162-5.571 100.00 427 22 0.2295 389.082 375.850 0.918 1.012 0.331 5.546-4.326 100.00 867 58 0.1388 534.147 528.048 0.959 1.010 0.251 4.315-3.360 100.00 1859 96 0.1305 507.979 505.209 1.016 1.006 0.191 3.356-2.611 100.00 3867 181 0.1652 333.714 329.282 1.014 1.000 0.034 2.608-2.000 99.99 8818 434 0.1646 217.524 213.638 1.030 0.988 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.4416 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1614 r_free=0.1670 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A A 80 GLN A Total number of N/Q/H flips: 2 r_work=0.1615 r_free=0.1673 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.154632 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.012880 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 0.1352 0.1644 0.0292 0.009 1.0 1.6 0.5 0.0 0 11.577 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.52 16.44 2.92 3.013 18.454 1.013 0.023 12.78 16.62 3.83 3.675 18.709 1.013 0.020 Individual atomic B min max mean iso aniso Overall: 5.91 113.89 19.96 4.16 1785 0 Protein: 5.91 113.41 17.19 4.16 1519 0 Water: 8.78 113.89 36.12 N/A 258 0 Other: 21.66 37.26 26.44 N/A 8 0 Chain A: 5.91 113.89 19.96 N/A 1785 0 Histogram: Values Number of atoms 5.91 - 16.71 1067 16.71 - 27.51 349 27.51 - 38.31 192 38.31 - 49.10 97 49.10 - 59.90 52 59.90 - 70.70 13 70.70 - 81.50 7 81.50 - 92.30 4 92.30 - 103.10 1 103.10 - 113.89 3 =========================== Idealize ADP of riding H ========================== r_work=0.1278 r_free=0.1662 r_work=0.1281 r_free=0.1670 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1281 r_free = 0.1670 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1277 r_free = 0.1659 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17043 (all), 4.74 % free)------------| | | | r_work= 0.1277 r_free= 0.1659 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.019998 | | target function (ls_wunit_k1) not normalized (work): 324.688821 | | target function (ls_wunit_k1) not normalized (free): 27.201273 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1295 0.1277 0.1659 n_refl.: 17043 re-set all scales: r(all,work,free)=0.1907 0.1906 0.1987 n_refl.: 17043 remove outliers: r(all,work,free)=0.1907 0.1906 0.1987 n_refl.: 17043 overall B=-0.51 to atoms: r(all,work,free)=0.1871 0.1869 0.1967 n_refl.: 17043 bulk-solvent and scaling: r(all,work,free)=0.1292 0.1274 0.1650 n_refl.: 17043 remove outliers: r(all,work,free)=0.1292 0.1274 0.1650 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 0.3539 307.107 285.116 0.652 1.007 0.389 11.894-9.307 99.02 97 4 0.1707 487.758 476.926 0.920 1.007 0.380 9.237-7.194 100.00 213 7 0.1824 398.937 395.372 0.960 1.007 0.341 7.162-5.571 100.00 427 22 0.1858 299.403 293.954 0.929 1.006 0.301 5.546-4.326 100.00 867 58 0.1051 411.032 408.017 0.956 1.005 0.215 4.315-3.360 100.00 1859 96 0.0930 390.895 390.185 1.014 1.004 0.192 3.356-2.611 100.00 3867 181 0.1290 256.796 255.474 1.009 1.001 0.091 2.608-2.000 99.99 8818 434 0.1348 167.387 166.072 1.011 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-1.1554 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1274 r_free=0.1650 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A Total number of N/Q/H flips: 1 r_work=0.1275 r_free=0.1649 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1275 r_free=0.1649 | n_water=258 | time (s): 0.740 (total time: 0.740) Filter (dist) r_work=0.1284 r_free=0.1637 | n_water=253 | time (s): 22.760 (total time: 23.500) Filter (q & B) r_work=0.1284 r_free=0.1636 | n_water=251 | time (s): 1.600 (total time: 25.100) Compute maps r_work=0.1284 r_free=0.1636 | n_water=251 | time (s): 0.740 (total time: 25.840) Filter (map) r_work=0.1326 r_free=0.1625 | n_water=205 | time (s): 2.260 (total time: 28.100) Find peaks r_work=0.1326 r_free=0.1625 | n_water=205 | time (s): 0.620 (total time: 28.720) Add new water r_work=0.1557 r_free=0.1871 | n_water=364 | time (s): 1.560 (total time: 30.280) Refine new water occ: r_work=0.1341 r_free=0.1579 adp: r_work=0.1280 r_free=0.1562 occ: r_work=0.1286 r_free=0.1542 adp: r_work=0.1251 r_free=0.1542 occ: r_work=0.1251 r_free=0.1536 adp: r_work=0.1241 r_free=0.1536 ADP+occupancy (water only), MIN, final r_work=0.1241 r_free=0.1536 r_work=0.1241 r_free=0.1536 | n_water=364 | time (s): 16.090 (total time: 46.370) Filter (q & B) r_work=0.1242 r_free=0.1543 | n_water=357 | time (s): 1.660 (total time: 48.030) Filter (dist only) r_work=0.1243 r_free=0.1549 | n_water=356 | time (s): 28.600 (total time: 76.630) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.883163 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.013723 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 0.1587 0.0373 0.008 0.9 1.9 0.5 0.0 0 12.442 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.14 15.87 3.73 4.213 20.912 1.014 0.018 12.00 16.13 4.13 4.252 21.253 1.014 0.018 Individual atomic B min max mean iso aniso Overall: 6.74 107.90 21.32 4.35 1883 0 Protein: 6.74 107.90 17.76 4.34 1519 0 Water: 8.57 74.93 36.18 N/A 356 0 Other: 24.65 46.59 35.49 N/A 8 0 Chain A: 6.74 107.90 19.38 N/A 1732 0 Chain S: 17.05 66.41 43.48 N/A 151 0 Histogram: Values Number of atoms 6.74 - 16.86 1029 16.86 - 26.98 368 26.98 - 37.09 232 37.09 - 47.21 144 47.21 - 57.32 76 57.32 - 67.44 22 67.44 - 77.55 5 77.55 - 87.67 5 87.67 - 97.78 0 97.78 - 107.90 2 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1613 r_work=0.1202 r_free=0.1614 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1202 r_free = 0.1614 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 = 0.1197 r_free = 0.1610 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.26 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= 0.1197 r_free= 0.1610 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.016929 | | target function (ls_wunit_k1) not normalized (work): 274.858411 | | target function (ls_wunit_k1) not normalized (free): 25.110505 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1217 0.1197 0.1610 n_refl.: 17043 re-set all scales: r(all,work,free)=0.1817 0.1813 0.1949 n_refl.: 17043 remove outliers: r(all,work,free)=0.1817 0.1813 0.1949 n_refl.: 17043 overall B=-0.41 to atoms: r(all,work,free)=0.1789 0.1784 0.1929 n_refl.: 17043 bulk-solvent and scaling: r(all,work,free)=0.1214 0.1194 0.1605 n_refl.: 17043 remove outliers: r(all,work,free)=0.1213 0.1193 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 0.3360 309.138 279.934 0.629 1.008 0.370 11.894-9.307 99.02 97 4 0.1436 487.758 484.574 0.919 1.008 0.370 9.237-7.194 100.00 213 7 0.1609 398.937 400.118 0.970 1.008 0.286 7.162-5.571 100.00 427 22 0.1567 299.403 295.820 0.934 1.007 0.271 5.546-4.326 100.00 867 58 0.0869 411.032 408.120 0.956 1.006 0.211 4.315-3.360 100.00 1859 96 0.0826 390.895 390.319 1.014 1.004 0.201 3.356-2.611 100.00 3867 181 0.1201 256.796 255.995 1.009 1.001 0.058 2.608-2.000 99.99 8818 434 0.1343 167.387 166.292 1.011 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-1.1450 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1193 r_free=0.1605 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=0.1605 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1605 | n_water=356 | time (s): 0.800 (total time: 0.800) Filter (dist) r_work=0.1194 r_free=0.1607 | n_water=353 | time (s): 29.920 (total time: 30.720) Filter (q & B) r_work=0.1194 r_free=0.1607 | n_water=353 | time (s): 0.850 (total time: 31.570) Compute maps r_work=0.1194 r_free=0.1607 | n_water=353 | time (s): 0.630 (total time: 32.200) Filter (map) r_work=0.1266 r_free=0.1614 | n_water=255 | time (s): 2.080 (total time: 34.280) Find peaks r_work=0.1266 r_free=0.1614 | n_water=255 | time (s): 0.670 (total time: 34.950) Add new water r_work=0.1459 r_free=0.1815 | n_water=405 | time (s): 1.970 (total time: 36.920) Refine new water occ: r_work=0.1259 r_free=0.1589 adp: r_work=0.1250 r_free=0.1593 occ: r_work=0.1233 r_free=0.1556 adp: r_work=0.1220 r_free=0.1561 occ: r_work=0.1213 r_free=0.1539 adp: r_work=0.1202 r_free=0.1541 ADP+occupancy (water only), MIN, final r_work=0.1202 r_free=0.1541 r_work=0.1202 r_free=0.1541 | n_water=405 | time (s): 39.410 (total time: 76.330) Filter (q & B) r_work=0.1204 r_free=0.1545 | n_water=395 | time (s): 1.650 (total time: 77.980) Filter (dist only) r_work=0.1205 r_free=0.1546 | n_water=394 | time (s): 31.730 (total time: 109.710) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.939094 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.176781 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 0.1187 0.1531 0.0345 0.009 1.0 2.9 0.5 0.0 0 0.970 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.87 15.31 3.45 4.389 21.485 0.177 5.001 11.67 15.40 3.72 5.010 21.373 0.177 4.974 Individual atomic B min max mean iso aniso Overall: 6.08 105.05 20.73 4.75 1921 0 Protein: 6.08 105.05 16.89 4.75 1519 0 Water: 8.69 69.52 35.27 N/A 394 0 Other: 25.27 45.43 33.83 N/A 8 0 Chain A: 6.08 105.05 18.54 N/A 1729 0 Chain S: 16.34 61.10 40.43 N/A 192 0 Histogram: Values Number of atoms 6.08 - 15.98 1062 15.98 - 25.88 350 25.88 - 35.78 224 35.78 - 45.67 158 45.67 - 55.57 84 55.57 - 65.47 29 65.47 - 75.36 6 75.36 - 85.26 3 85.26 - 95.16 3 95.16 - 105.05 2 =========================== Idealize ADP of riding H ========================== r_work=0.1167 r_free=0.1540 r_work=0.1168 r_free=0.1541 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1168 r_free = 0.1541 target_work(ml) = 4.974 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1162 r_free = 0.1538 target_work(ml) = 4.968 | | occupancies: max = 1.00 min = 0.24 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= 0.1162 r_free= 0.1538 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.968059 | | target function (ml) not normalized (work): 80656.436697 | | target function (ml) not normalized (free): 4182.679793 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1180 0.1162 0.1538 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1680 0.1673 0.1844 n_refl.: 17042 remove outliers: r(all,work,free)=0.1680 0.1673 0.1844 n_refl.: 17042 overall B=-0.38 to atoms: r(all,work,free)=0.1654 0.1646 0.1831 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1179 0.1160 0.1532 n_refl.: 17042 remove outliers: r(all,work,free)=0.1178 0.1160 0.1532 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 0.3516 306.545 283.542 0.594 1.005 0.350 11.894-9.307 99.02 97 4 0.1770 487.758 479.356 0.915 1.006 0.330 9.237-7.194 100.00 213 7 0.1768 398.937 400.196 0.988 1.006 0.265 7.162-5.571 100.00 427 22 0.1672 299.403 294.675 0.943 1.006 0.251 5.546-4.326 100.00 867 58 0.0947 411.032 407.412 0.963 1.005 0.200 4.315-3.360 100.00 1859 96 0.0922 390.895 388.829 1.011 1.003 0.181 3.356-2.611 100.00 3867 181 0.1296 256.796 254.533 1.011 1.000 0.131 2.608-2.000 99.99 8818 434 0.1095 167.387 165.910 1.013 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-1.1741 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1160 r_free=0.1532 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=0.1160 r_free=0.1532 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1160 r_free=0.1532 | n_water=394 | time (s): 0.600 (total time: 0.600) Filter (dist) r_work=0.1160 r_free=0.1532 | n_water=394 | time (s): 28.390 (total time: 28.990) Filter (q & B) r_work=0.1160 r_free=0.1532 | n_water=394 | time (s): 1.190 (total time: 30.180) Compute maps r_work=0.1160 r_free=0.1532 | n_water=394 | time (s): 0.870 (total time: 31.050) Filter (map) r_work=0.1204 r_free=0.1554 | n_water=306 | time (s): 1.940 (total time: 32.990) Find peaks r_work=0.1204 r_free=0.1554 | n_water=306 | time (s): 0.520 (total time: 33.510) Add new water r_work=0.1343 r_free=0.1695 | n_water=452 | time (s): 2.180 (total time: 35.690) Refine new water occ: r_work=0.1178 r_free=0.1499 adp: r_work=0.1172 r_free=0.1508 occ: r_work=0.1156 r_free=0.1474 adp: r_work=0.1148 r_free=0.1484 occ: r_work=0.1140 r_free=0.1456 adp: r_work=0.1133 r_free=0.1464 ADP+occupancy (water only), MIN, final r_work=0.1133 r_free=0.1464 r_work=0.1133 r_free=0.1464 | n_water=452 | time (s): 27.510 (total time: 63.200) Filter (q & B) r_work=0.1138 r_free=0.1471 | n_water=442 | time (s): 1.810 (total time: 65.010) Filter (dist only) r_work=0.1138 r_free=0.1471 | n_water=442 | time (s): 31.270 (total time: 96.280) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.891513 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.167518 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 0.1514 0.0396 0.010 1.0 6.1 0.5 0.0 0 0.946 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.18 15.14 3.96 4.525 20.961 0.168 4.952 11.07 15.18 4.11 4.646 20.974 0.168 4.946 Individual atomic B min max mean iso aniso Overall: 5.50 103.65 20.83 4.87 1969 0 Protein: 5.50 103.65 16.47 4.86 1519 0 Water: 8.27 64.14 35.58 N/A 442 0 Other: 25.27 44.62 33.96 N/A 8 0 Chain A: 5.50 103.65 18.09 N/A 1729 0 Chain S: 15.02 62.51 40.64 N/A 240 0 Histogram: Values Number of atoms 5.50 - 15.31 1028 15.31 - 25.13 384 25.13 - 34.94 224 34.94 - 44.76 185 44.76 - 54.57 107 54.57 - 64.39 27 64.39 - 74.20 5 74.20 - 84.02 3 84.02 - 93.83 4 93.83 - 103.65 2 =========================== Idealize ADP of riding H ========================== r_work=0.1107 r_free=0.1518 r_work=0.1107 r_free=0.1519 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1107 r_free = 0.1519 target_work(ml) = 4.946 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1097 r_free = 0.1521 target_work(ml) = 4.942 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1097 r_free= 0.1521 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ml) (work): 4.941816 | | target function (ml) not normalized (work): 80225.440996 | | target function (ml) not normalized (free): 4175.235747 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1118 0.1097 0.1521 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1562 0.1551 0.1818 n_refl.: 17041 remove outliers: r(all,work,free)=0.1562 0.1551 0.1818 n_refl.: 17041 overall B=-0.26 to atoms: r(all,work,free)=0.1547 0.1535 0.1812 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1115 0.1095 0.1516 n_refl.: 17041 remove outliers: r(all,work,free)=0.1115 0.1094 0.1516 n_refl.: 17040 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 93.75 85 5 0.3492 303.053 280.873 0.570 1.003 0.340 11.894-9.307 99.02 97 4 0.1695 487.758 479.944 0.919 1.004 0.330 9.237-7.194 100.00 213 7 0.1703 398.937 399.782 0.988 1.004 0.235 7.162-5.571 100.00 427 22 0.1583 299.403 292.937 0.937 1.004 0.230 5.546-4.326 100.00 867 58 0.0904 411.032 407.855 0.965 1.004 0.201 4.315-3.360 100.00 1859 96 0.0838 390.895 388.736 1.003 1.003 0.181 3.356-2.611 100.00 3867 181 0.1213 256.796 254.681 1.002 1.001 0.063 2.608-2.000 99.99 8818 434 0.1048 167.387 166.251 0.996 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-0.8810 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1094 r_free=0.1516 After: r_work=0.1096 r_free=0.1515 ================================== NQH flips ================================== r_work=0.1096 r_free=0.1515 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=0.1096 r_free=0.1515 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1096 r_free=0.1515 | n_water=442 | time (s): 0.660 (total time: 0.660) Filter (dist) r_work=0.1099 r_free=0.1516 | n_water=439 | time (s): 34.070 (total time: 34.730) Filter (q & B) r_work=0.1099 r_free=0.1517 | n_water=438 | time (s): 2.120 (total time: 36.850) Compute maps r_work=0.1099 r_free=0.1517 | n_water=438 | time (s): 0.710 (total time: 37.560) Filter (map) r_work=0.1176 r_free=0.1550 | n_water=334 | time (s): 1.660 (total time: 39.220) Find peaks r_work=0.1176 r_free=0.1550 | n_water=334 | time (s): 0.430 (total time: 39.650) Add new water r_work=0.1307 r_free=0.1651 | n_water=484 | time (s): 1.460 (total time: 41.110) Refine new water occ: r_work=0.1145 r_free=0.1493 adp: r_work=0.1137 r_free=0.1496 occ: r_work=0.1123 r_free=0.1481 adp: r_work=0.1114 r_free=0.1479 occ: r_work=0.1107 r_free=0.1474 adp: r_work=0.1100 r_free=0.1469 ADP+occupancy (water only), MIN, final r_work=0.1100 r_free=0.1469 r_work=0.1100 r_free=0.1469 | n_water=484 | time (s): 35.080 (total time: 76.190) Filter (q & B) r_work=0.1104 r_free=0.1475 | n_water=472 | time (s): 1.780 (total time: 77.970) Filter (dist only) r_work=0.1104 r_free=0.1477 | n_water=471 | time (s): 38.050 (total time: 116.020) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.902475 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.169540 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1126 0.1484 0.0359 0.010 1.0 5.1 0.5 0.0 0 0.951 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.26 14.84 3.59 4.559 20.845 0.170 4.944 11.14 14.80 3.66 4.671 20.890 0.170 4.935 Individual atomic B min max mean iso aniso Overall: 5.15 103.61 20.97 5.07 1998 0 Protein: 5.15 103.61 16.20 5.06 1519 0 Water: 7.87 64.47 36.16 N/A 471 0 Other: 25.21 42.93 32.76 N/A 8 0 Chain A: 5.15 103.61 17.79 N/A 1729 0 Chain S: 18.08 64.47 41.44 N/A 269 0 Histogram: Values Number of atoms 5.15 - 15.00 1033 15.00 - 24.84 374 24.84 - 34.69 217 34.69 - 44.54 211 44.54 - 54.38 115 54.38 - 64.23 31 64.23 - 74.07 8 74.07 - 83.92 4 83.92 - 93.76 2 93.76 - 103.61 3 =========================== Idealize ADP of riding H ========================== r_work=0.1114 r_free=0.1480 r_work=0.1114 r_free=0.1479 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1114 r_free = 0.1479 target_work(ml) = 4.935 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1107 r_free = 0.1481 target_work(ml) = 4.931 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1107 r_free= 0.1481 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ml) (work): 4.930702 | | target function (ml) not normalized (work): 80040.093004 | | target function (ml) not normalized (free): 4162.435019 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.64 1.00 2810 159 0.1119 0.1410 5.447 5.6806| | 2: 3.63 - 2.88 1.00 2711 122 0.1086 0.1460 5.2168 5.3687| | 3: 2.88 - 2.52 1.00 2681 148 0.1363 0.1579 5.135 5.1862| | 4: 2.52 - 2.29 1.00 2661 139 0.0933 0.1463 4.621 4.9202| | 5: 2.29 - 2.13 1.00 2678 122 0.0964 0.1424 4.5733 4.8706| | 6: 2.13 - 2.00 1.00 2692 117 0.1117 0.1731 4.5618 4.7738| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2810 159 0.95 9.11 1.00 0.96 6426.21| | 2: 3.63 - 2.88 2711 122 0.92 13.01 1.01 0.96 6426.21| | 3: 2.88 - 2.52 2681 148 0.87 19.04 0.99 0.96 6426.21| | 4: 2.52 - 2.29 2661 139 0.93 11.94 1.01 0.97 2071.82| | 5: 2.29 - 2.13 2678 122 0.92 13.96 1.00 0.97 2071.82| | 6: 2.13 - 2.00 2692 117 0.90 16.63 0.99 0.97 2071.82| |alpha: min = 0.96 max = 0.97 mean = 0.96| |beta: min = 2071.82 max = 6426.21 mean = 4271.95| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.99 mean = 13.91| |phase err.(test): min = 0.00 max = 88.56 mean = 13.55| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1125 0.1107 0.1481 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1545 0.1534 0.1792 n_refl.: 17040 remove outliers: r(all,work,free)=0.1545 0.1534 0.1792 n_refl.: 17040 overall B=-0.20 to atoms: r(all,work,free)=0.1534 0.1522 0.1786 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1126 0.1108 0.1483 n_refl.: 17040 remove outliers: r(all,work,free)=0.1126 0.1108 0.1483 n_refl.: 17040 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 93.75 85 5 0.3518 303.053 279.603 0.558 1.001 0.340 11.894-9.307 99.02 97 4 0.1709 487.758 481.864 0.919 1.003 0.330 9.237-7.194 100.00 213 7 0.1734 398.937 399.188 0.988 1.003 0.225 7.162-5.571 100.00 427 22 0.1593 299.403 293.091 0.936 1.003 0.220 5.546-4.326 100.00 867 58 0.0917 411.032 407.961 0.966 1.003 0.190 4.315-3.360 100.00 1859 96 0.0877 390.895 388.918 1.002 1.002 0.181 3.356-2.611 100.00 3867 181 0.1240 256.796 254.190 0.997 1.001 0.121 2.608-2.000 99.99 8818 434 0.1038 167.387 166.074 0.985 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.7019 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2783 0.1811 0.082 5.302 8.8 119.3 19.9 258 0.000 1_bss: 0.1614 0.1670 0.082 5.302 8.4 118.9 19.5 258 0.000 1_settarget: 0.1614 0.1670 0.082 5.302 8.4 118.9 19.5 258 0.000 1_nqh: 0.1615 0.1673 0.082 5.302 8.4 118.9 19.5 258 0.006 1_weight: 0.1615 0.1673 0.082 5.302 8.4 118.9 19.5 258 0.006 1_xyzrec: 0.1352 0.1644 0.009 0.971 8.4 118.9 19.5 258 0.151 1_adp: 0.1278 0.1662 0.009 0.971 5.9 113.9 20.0 258 0.151 1_regHadp: 0.1281 0.1670 0.009 0.971 5.9 113.9 20.0 258 0.151 1_occ: 0.1277 0.1659 0.009 0.971 5.9 113.9 20.0 258 0.151 2_bss: 0.1274 0.1650 0.009 0.971 5.4 113.4 19.5 258 0.151 2_settarget: 0.1274 0.1650 0.009 0.971 5.4 113.4 19.5 258 0.151 2_updatecdl: 0.1274 0.1650 0.009 0.988 5.4 113.4 19.5 258 0.151 2_nqh: 0.1275 0.1649 0.009 0.988 5.4 113.4 19.5 258 0.148 2_sol: 0.1243 0.1549 0.009 0.988 5.4 112.9 20.7 356 n/a 2_weight: 0.1243 0.1549 0.009 0.988 5.4 112.9 20.7 356 n/a 2_xyzrec: 0.1214 0.1587 0.008 0.929 5.4 112.9 20.7 356 n/a 2_adp: 0.1200 0.1613 0.008 0.929 6.7 107.9 21.3 356 n/a 2_regHadp: 0.1202 0.1614 0.008 0.929 6.7 107.9 21.3 356 n/a 2_occ: 0.1197 0.1610 0.008 0.929 6.7 107.9 21.3 356 n/a 3_bss: 0.1193 0.1605 0.008 0.929 6.3 107.5 20.9 356 n/a 3_settarget: 0.1193 0.1605 0.008 0.929 6.3 107.5 20.9 356 n/a 3_updatecdl: 0.1193 0.1605 0.008 0.929 6.3 107.5 20.9 356 n/a 3_nqh: 0.1193 0.1605 0.008 0.929 6.3 107.5 20.9 356 n/a 3_sol: 0.1205 0.1546 0.008 0.929 6.3 107.5 20.9 394 n/a 3_weight: 0.1205 0.1546 0.008 0.929 6.3 107.5 20.9 394 n/a 3_xyzrec: 0.1187 0.1531 0.009 0.959 6.3 107.5 20.9 394 n/a 3_adp: 0.1167 0.1540 0.009 0.959 6.1 105.1 20.7 394 n/a 3_regHadp: 0.1168 0.1541 0.009 0.959 6.1 105.1 20.7 394 n/a 3_occ: 0.1162 0.1538 0.009 0.959 6.1 105.1 20.7 394 n/a 4_bss: 0.1160 0.1532 0.009 0.959 5.7 104.7 20.3 394 n/a 4_settarget: 0.1160 0.1532 0.009 0.959 5.7 104.7 20.3 394 n/a 4_updatecdl: 0.1160 0.1532 0.009 0.958 5.7 104.7 20.3 394 n/a 4_nqh: 0.1160 0.1532 0.009 0.958 5.7 104.7 20.3 394 n/a 4_sol: 0.1138 0.1471 0.009 0.958 5.7 104.7 20.8 442 n/a 4_weight: 0.1138 0.1471 0.009 0.958 5.7 104.7 20.8 442 n/a 4_xyzrec: 0.1118 0.1514 0.010 0.980 5.7 104.7 20.8 442 n/a 4_adp: 0.1107 0.1518 0.010 0.980 5.5 103.6 20.8 442 n/a 4_regHadp: 0.1107 0.1519 0.010 0.980 5.5 103.6 20.8 442 n/a 4_occ: 0.1097 0.1521 0.010 0.980 5.5 103.6 20.8 442 n/a 5_bss: 0.1094 0.1516 0.010 0.980 5.2 103.4 20.6 442 n/a 5_settarget: 0.1094 0.1516 0.010 0.980 5.2 103.4 20.6 442 n/a 5_updatecdl: 0.1094 0.1516 0.010 0.983 5.2 103.4 20.6 442 n/a 5_setrh: 0.1096 0.1515 0.010 0.983 5.2 103.4 20.6 442 n/a 5_nqh: 0.1096 0.1515 0.010 0.983 5.2 103.4 20.6 442 n/a 5_sol: 0.1104 0.1477 0.010 0.983 5.2 103.4 20.9 471 n/a 5_weight: 0.1104 0.1477 0.010 0.983 5.2 103.4 20.9 471 n/a 5_xyzrec: 0.1126 0.1484 0.010 1.010 5.2 103.4 20.9 471 n/a 5_adp: 0.1114 0.1480 0.010 1.010 5.2 103.6 21.0 471 n/a 5_regHadp: 0.1114 0.1479 0.010 1.010 5.2 103.6 21.0 471 n/a 5_occ: 0.1107 0.1481 0.010 1.010 5.2 103.6 21.0 471 n/a end: 0.1108 0.1483 0.010 1.010 5.0 103.4 20.8 471 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_3473948_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_3473948_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.8800 Refinement macro-cycles (run) : 932.9600 Write final files (write_after_run_outputs) : 21.9700 Total : 958.8100 Total CPU time: 16.35 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:21 PST -0800 (1735494081.75 s) Start R-work = 0.1614, R-free = 0.1670 Final R-work = 0.1108, R-free = 0.1483 =============================================================================== Job complete usr+sys time: 1003.09 seconds wall clock time: 17 minutes 5.51 seconds (1025.51 seconds total)