Starting phenix.refine on Sun Dec 29 09:10:02 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=3 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 = 3 } } 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: 1.67, 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: 0.29 Conformation dependent library (CDL) restraints added in 108.0 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.62 - 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 1 N 265 6.97 1 C 957 5.97 2 H 1596 1.00 1 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: 3.00 - 49.25 A, n_refl.=5182 (all), 4.86 % free)-------------| | | | r_work= 0.3611 r_free= 0.1982 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.471379 | | target function (ml) not normalized (work): 22043.896438 | | target function (ml) not normalized (free): 1144.461872 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 49.25 - 3.79 1.00 2500 142 0.3805 0.2143 4.8551 4.8834| | 2: 3.78 - 3.00 1.00 2430 110 0.3374 0.1710 4.0766 4.1002| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 - 3.79 2500 142 0.50 48.78 0.83 0.13 6609.29| | 2: 3.78 - 3.00 2430 110 0.94 11.14 1.48 0.26 445.30| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 376.99 max = 12072.74 mean = 3571.05| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 89.97 mean = 30.23| |phase err.(test): min = 0.00 max = 89.99 mean = 33.04| |-----------------------------------------------------------------------------| ----------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: 3.00 - 49.25 A, n_refl.=5182 (all), 4.86 % free)-------------| | | | r_work= 0.3611 r_free= 0.1982 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.471379 | | target function (ml) not normalized (work): 22043.896438 | | target function (ml) not normalized (free): 1144.461872 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3568 0.3645 0.2096 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3568 0.3645 0.2096 n_refl.: 5182 remove outliers: r(all,work,free)=0.2517 0.2542 0.2096 n_refl.: 5178 overall B=-2.93 to atoms: r(all,work,free)=0.2407 0.2429 0.2045 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1569 0.1569 0.1569 n_refl.: 5178 remove outliers: r(all,work,free)=0.1563 0.1562 0.1569 n_refl.: 5175 ======================== 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 97.87 87 5 0.3724 453.601 406.404 0.673 1.051 0.392 11.894-9.307 99.02 97 4 0.1912 714.532 695.552 0.955 1.049 0.373 9.237-7.194 100.00 213 7 0.2241 584.346 574.663 0.987 1.044 0.353 7.162-5.571 100.00 427 22 0.2301 438.480 424.245 0.947 1.034 0.336 5.546-4.326 100.00 867 58 0.1378 601.971 594.306 0.988 1.018 0.229 4.315-3.360 100.00 1859 96 0.1322 572.481 567.456 1.055 0.991 0.187 3.356-3.002 100.00 1373 60 0.1591 440.949 432.621 1.059 0.964 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9559 b_overall=-3.7329 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1562 r_free=0.1569 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=0.1563 r_free=0.1572 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 18.962274 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.194182 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 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 0.1157 0.1782 0.0625 0.010 1.0 3.2 0.5 0.0 0 9.481 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.57 17.82 6.25 3.013 15.928 2.194 0.018 10.15 17.60 7.45 5.090 16.129 2.194 0.014 Individual atomic B min max mean iso aniso Overall: 1.89 112.13 17.34 5.51 1785 0 Protein: 1.89 112.13 14.62 5.50 1519 0 Water: 3.93 111.37 33.13 N/A 258 0 Other: 15.68 36.48 23.73 N/A 8 0 Chain A: 1.89 112.13 17.34 N/A 1785 0 Histogram: Values Number of atoms 1.89 - 12.91 915 12.91 - 23.94 482 23.94 - 34.96 191 34.96 - 45.98 107 45.98 - 57.01 57 57.01 - 68.03 17 68.03 - 79.06 7 79.06 - 90.08 5 90.08 - 101.10 1 101.10 - 112.13 3 =========================== Idealize ADP of riding H ========================== r_work=0.1015 r_free=0.1760 r_work=0.1010 r_free=0.1764 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1010 r_free = 0.1764 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1004 r_free = 0.1773 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.1004 r_free= 0.1773 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ls_wunit_k1) (work): 0.013649 | | target function (ls_wunit_k1) not normalized (work): 67.192490 | | target function (ls_wunit_k1) not normalized (free): 10.245499 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1043 0.1004 0.1773 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2081 0.2081 0.2206 n_refl.: 5175 remove outliers: r(all,work,free)=0.2081 0.2081 0.2206 n_refl.: 5175 overall B=-0.97 to atoms: r(all,work,free)=0.2041 0.2039 0.2194 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.1046 0.1007 0.1773 n_refl.: 5175 remove outliers: r(all,work,free)=0.1046 0.1007 0.1773 n_refl.: 5175 ======================== 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 0.3263 334.056 325.185 0.708 0.997 0.381 11.894-9.307 99.02 97 4 0.1455 526.220 518.885 0.998 1.000 0.351 9.237-7.194 100.00 213 7 0.1663 430.344 430.249 1.032 1.000 0.321 7.162-5.571 100.00 427 22 0.1586 322.921 319.601 0.984 1.000 0.302 5.546-4.326 100.00 867 58 0.0903 443.324 439.572 0.998 1.000 0.201 4.315-3.360 100.00 1859 96 0.0770 421.606 421.465 1.041 1.000 0.183 3.356-3.002 100.00 1373 60 0.0999 324.739 323.243 1.011 0.999 0.051 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-3.4658 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1007 r_free=0.1773 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 80 GLN A Total number of N/Q/H flips: 2 r_work=0.1010 r_free=0.1771 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1010 r_free=0.1771 | n_water=258 | time (s): 0.460 (total time: 0.460) Filter (dist) r_work=0.1047 r_free=0.1754 | n_water=247 | time (s): 20.170 (total time: 20.630) Filter (q & B) r_work=0.1046 r_free=0.1757 | n_water=244 | time (s): 1.940 (total time: 22.570) Compute maps r_work=0.1046 r_free=0.1757 | n_water=244 | time (s): 0.600 (total time: 23.170) Filter (map) r_work=0.1384 r_free=0.1828 | n_water=137 | time (s): 1.790 (total time: 24.960) Find peaks r_work=0.1384 r_free=0.1828 | n_water=137 | time (s): 0.420 (total time: 25.380) Add new water r_work=0.1736 r_free=0.2101 | n_water=232 | time (s): 1.250 (total time: 26.630) Refine new water occ: r_work=0.1173 r_free=0.1652 adp: r_work=0.1145 r_free=0.1656 occ: r_work=0.1143 r_free=0.1636 adp: r_work=0.1129 r_free=0.1644 occ: r_work=0.1127 r_free=0.1621 adp: r_work=0.1124 r_free=0.1631 ADP+occupancy (water only), MIN, final r_work=0.1124 r_free=0.1631 r_work=0.1124 r_free=0.1631 | n_water=232 | time (s): 5.100 (total time: 31.730) Filter (q & B) r_work=0.1124 r_free=0.1631 | n_water=232 | time (s): 0.840 (total time: 32.570) Filter (dist only) r_work=0.1134 r_free=0.1619 | n_water=227 | time (s): 17.930 (total time: 50.500) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.022324 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.808139 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 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 0.1018 0.1838 0.0820 0.009 1.0 4.2 0.5 0.6 0 11.011 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.18 18.38 8.20 4.790 16.723 2.808 0.014 9.55 18.34 8.79 5.445 17.044 2.808 0.013 Individual atomic B min max mean iso aniso Overall: 0.00 110.19 16.42 6.46 1754 0 Protein: 0.00 110.19 14.78 6.45 1519 0 Water: 0.00 62.68 27.24 N/A 227 0 Other: 10.30 30.77 20.96 N/A 8 0 Chain A: 0.00 110.19 15.45 N/A 1660 0 Chain S: 0.54 61.50 33.62 N/A 94 0 Histogram: Values Number of atoms 0.00 - 11.02 716 11.02 - 22.04 658 22.04 - 33.06 197 33.06 - 44.07 104 44.07 - 55.09 46 55.09 - 66.11 22 66.11 - 77.13 5 77.13 - 88.15 3 88.15 - 99.17 1 99.17 - 110.19 2 =========================== Idealize ADP of riding H ========================== r_work=0.0955 r_free=0.1834 r_work=0.0952 r_free=0.1832 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0952 r_free = 0.1832 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0952 r_free = 0.1825 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0952 r_free= 0.1825 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ls_wunit_k1) (work): 0.012311 | | target function (ls_wunit_k1) not normalized (work): 60.604952 | | target function (ls_wunit_k1) not normalized (free): 9.737602 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0996 0.0952 0.1825 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2108 0.2116 0.2107 n_refl.: 5175 remove outliers: r(all,work,free)=0.2108 0.2116 0.2107 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2108 0.2116 0.2107 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0997 0.0953 0.1832 n_refl.: 5175 remove outliers: r(all,work,free)=0.0993 0.0949 0.1832 n_refl.: 5173 ======================== 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 0.3145 333.506 312.785 0.659 1.005 0.360 11.894-9.307 99.02 97 4 0.1503 526.220 520.238 0.987 1.006 0.350 9.237-7.194 100.00 213 7 0.1511 430.344 432.081 1.028 1.007 0.305 7.162-5.571 100.00 427 22 0.1490 322.921 320.201 0.994 1.006 0.300 5.546-4.326 100.00 867 58 0.0795 443.324 440.971 1.010 1.004 0.240 4.315-3.360 100.00 1859 96 0.0733 421.606 421.212 1.056 1.000 0.190 3.356-3.002 100.00 1373 60 0.0973 324.739 323.435 1.031 0.997 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9557 b_overall=-4.2289 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0949 r_free=0.1832 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN Total number of N/Q/H flips: 1 r_work=0.0949 r_free=0.1831 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0949 r_free=0.1831 | n_water=227 | time (s): 0.510 (total time: 0.510) Filter (dist) r_work=0.0964 r_free=0.1802 | n_water=222 | time (s): 18.110 (total time: 18.620) Filter (q & B) r_work=0.1052 r_free=0.1790 | n_water=218 | time (s): 1.460 (total time: 20.080) Compute maps r_work=0.1052 r_free=0.1790 | n_water=218 | time (s): 0.650 (total time: 20.730) Filter (map) r_work=0.1288 r_free=0.1866 | n_water=146 | time (s): 1.890 (total time: 22.620) Find peaks r_work=0.1288 r_free=0.1866 | n_water=146 | time (s): 0.470 (total time: 23.090) Add new water r_work=0.1643 r_free=0.2196 | n_water=229 | time (s): 1.550 (total time: 24.640) Refine new water occ: r_work=0.1060 r_free=0.1775 adp: r_work=0.1053 r_free=0.1798 occ: r_work=0.1044 r_free=0.1773 adp: r_work=0.1044 r_free=0.1784 occ: r_work=0.1035 r_free=0.1759 adp: r_work=0.1035 r_free=0.1770 ADP+occupancy (water only), MIN, final r_work=0.1035 r_free=0.1770 r_work=0.1035 r_free=0.1770 | n_water=229 | time (s): 10.060 (total time: 34.700) Filter (q & B) r_work=0.1036 r_free=0.1773 | n_water=228 | time (s): 1.650 (total time: 36.350) Filter (dist only) r_work=0.1046 r_free=0.1776 | n_water=226 | time (s): 17.340 (total time: 53.690) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.063980 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.186706 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 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 0.0944 0.1854 0.0910 0.011 1.0 3.8 0.5 0.0 0 0.532 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.44 18.54 9.10 5.380 17.478 0.187 5.170 8.99 18.44 9.45 7.131 17.463 0.187 5.076 Individual atomic B min max mean iso aniso Overall: 0.00 110.85 16.04 8.73 1753 0 Protein: 0.00 110.85 14.92 8.71 1519 0 Water: 0.00 57.68 23.47 N/A 226 0 Other: 5.42 32.26 20.16 N/A 8 0 Chain A: 0.00 110.85 15.54 N/A 1652 0 Chain S: 0.00 52.12 24.27 N/A 101 0 Histogram: Values Number of atoms 0.00 - 11.09 720 11.09 - 22.17 647 22.17 - 33.26 223 33.26 - 44.34 104 44.34 - 55.43 29 55.43 - 66.51 15 66.51 - 77.60 8 77.60 - 88.68 3 88.68 - 99.77 3 99.77 - 110.85 1 =========================== Idealize ADP of riding H ========================== r_work=0.0899 r_free=0.1844 r_work=0.0904 r_free=0.1856 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0904 r_free = 0.1856 target_work(ml) = 5.079 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0897 r_free = 0.1840 target_work(ml) = 5.073 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5173 (all), 4.87 % free)-------------| | | | r_work= 0.0897 r_free= 0.1840 coordinate error (max.-lik. estimate): 0.27 A | | | | normalized target function (ml) (work): 5.073206 | | target function (ml) not normalized (work): 24965.249090 | | target function (ml) not normalized (free): 1824.009226 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0944 0.0897 0.1840 n_refl.: 5173 re-set all scales: r(all,work,free)=0.2032 0.2033 0.2150 n_refl.: 5173 remove outliers: r(all,work,free)=0.2032 0.2033 0.2150 n_refl.: 5173 overall B=-0.00 to atoms: r(all,work,free)=0.2032 0.2033 0.2150 n_refl.: 5173 bulk-solvent and scaling: r(all,work,free)=0.0937 0.0890 0.1821 n_refl.: 5173 remove outliers: r(all,work,free)=0.0937 0.0890 0.1821 n_refl.: 5173 ======================== 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 0.3591 333.506 307.378 0.601 0.989 0.330 11.894-9.307 99.02 97 4 0.1781 526.220 510.960 0.957 0.994 0.330 9.237-7.194 100.00 213 7 0.1905 430.344 424.326 1.007 0.997 0.330 7.162-5.571 100.00 427 22 0.1869 322.921 313.858 0.971 0.998 0.284 5.546-4.326 100.00 867 58 0.0896 443.324 438.352 1.002 1.000 0.234 4.315-3.360 100.00 1859 96 0.0603 421.606 421.265 1.053 1.003 0.210 3.356-3.002 100.00 1373 60 0.0607 324.739 324.254 1.029 1.005 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-6.3023 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0890 r_free=0.1821 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=0.0891 r_free=0.1818 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0891 r_free=0.1818 | n_water=226 | time (s): 0.680 (total time: 0.680) Filter (dist) r_work=0.0894 r_free=0.1819 | n_water=224 | time (s): 19.120 (total time: 19.800) Filter (q & B) r_work=0.0955 r_free=0.1843 | n_water=221 | time (s): 1.530 (total time: 21.330) Compute maps r_work=0.0955 r_free=0.1843 | n_water=221 | time (s): 0.640 (total time: 21.970) Filter (map) r_work=0.1234 r_free=0.1886 | n_water=152 | time (s): 1.910 (total time: 23.880) Find peaks r_work=0.1234 r_free=0.1886 | n_water=152 | time (s): 0.470 (total time: 24.350) Add new water r_work=0.1535 r_free=0.2147 | n_water=225 | time (s): 1.460 (total time: 25.810) Refine new water occ: r_work=0.1006 r_free=0.1785 adp: r_work=0.1002 r_free=0.1808 occ: r_work=0.0995 r_free=0.1785 adp: r_work=0.0994 r_free=0.1795 occ: r_work=0.0988 r_free=0.1777 adp: r_work=0.0987 r_free=0.1786 ADP+occupancy (water only), MIN, final r_work=0.0987 r_free=0.1786 r_work=0.0987 r_free=0.1786 | n_water=225 | time (s): 18.320 (total time: 44.130) Filter (q & B) r_work=0.0987 r_free=0.1786 | n_water=225 | time (s): 0.900 (total time: 45.030) Filter (dist only) r_work=0.0986 r_free=0.1786 | n_water=224 | time (s): 16.540 (total time: 61.570) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.019988 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.239947 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 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 0.0905 0.1853 0.0948 0.011 1.1 4.5 0.5 0.0 0 0.510 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.05 18.53 9.48 6.810 17.619 0.240 5.043 8.82 18.76 9.94 8.116 17.746 0.240 4.982 Individual atomic B min max mean iso aniso Overall: 0.00 109.89 16.42 10.59 1751 0 Protein: 0.00 109.89 15.32 10.56 1519 0 Water: 0.00 58.68 23.69 N/A 224 0 Other: 5.68 35.22 21.53 N/A 8 0 Chain A: 0.00 109.89 15.84 N/A 1640 0 Chain S: 0.00 58.68 24.97 N/A 111 0 Histogram: Values Number of atoms 0.00 - 10.99 696 10.99 - 21.98 632 21.98 - 32.97 254 32.97 - 43.96 99 43.96 - 54.94 37 54.94 - 65.93 15 65.93 - 76.92 10 76.92 - 87.91 4 87.91 - 98.90 3 98.90 - 109.89 1 =========================== Idealize ADP of riding H ========================== r_work=0.0882 r_free=0.1876 r_work=0.0887 r_free=0.1880 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0887 r_free = 0.1880 target_work(ml) = 4.987 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0876 r_free = 0.1877 target_work(ml) = 4.979 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5173 (all), 4.87 % free)-------------| | | | r_work= 0.0876 r_free= 0.1877 coordinate error (max.-lik. estimate): 0.27 A | | | | normalized target function (ml) (work): 4.978678 | | target function (ml) not normalized (work): 24500.073392 | | target function (ml) not normalized (free): 2078.754302 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0925 0.0876 0.1877 n_refl.: 5173 re-set all scales: r(all,work,free)=0.2079 0.2079 0.2233 n_refl.: 5173 remove outliers: r(all,work,free)=0.2079 0.2079 0.2233 n_refl.: 5173 overall B=-0.00 to atoms: r(all,work,free)=0.2079 0.2079 0.2233 n_refl.: 5173 bulk-solvent and scaling: r(all,work,free)=0.0927 0.0877 0.1888 n_refl.: 5173 remove outliers: r(all,work,free)=0.0927 0.0877 0.1888 n_refl.: 5173 ======================== 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 0.3831 333.506 302.409 0.579 0.986 0.320 11.894-9.307 99.02 97 4 0.1902 526.220 507.121 0.952 0.993 0.320 9.237-7.194 100.00 213 7 0.2082 430.344 420.353 1.012 0.996 0.310 7.162-5.571 100.00 427 22 0.2032 322.921 312.215 0.987 0.997 0.300 5.546-4.326 100.00 867 58 0.0956 443.324 437.960 1.014 0.999 0.229 4.315-3.360 100.00 1859 96 0.0562 421.606 421.963 1.077 1.002 0.210 3.356-3.002 100.00 1373 60 0.0453 324.739 324.648 1.056 1.005 0.058 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.3903 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0877 r_free=0.1888 After: r_work=0.0880 r_free=0.1886 ================================== NQH flips ================================== r_work=0.0880 r_free=0.1886 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B Total number of N/Q/H flips: 1 r_work=0.0881 r_free=0.1880 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0881 r_free=0.1880 | n_water=224 | time (s): 0.520 (total time: 0.520) Filter (dist) r_work=0.0892 r_free=0.1875 | n_water=222 | time (s): 17.820 (total time: 18.340) Filter (q & B) r_work=0.1005 r_free=0.1924 | n_water=218 | time (s): 1.720 (total time: 20.060) Compute maps r_work=0.1005 r_free=0.1924 | n_water=218 | time (s): 0.570 (total time: 20.630) Filter (map) r_work=0.1273 r_free=0.2020 | n_water=151 | time (s): 1.820 (total time: 22.450) Find peaks r_work=0.1273 r_free=0.2020 | n_water=151 | time (s): 0.590 (total time: 23.040) Add new water r_work=0.1556 r_free=0.2289 | n_water=222 | time (s): 1.690 (total time: 24.730) Refine new water occ: r_work=0.0984 r_free=0.1858 adp: r_work=0.0971 r_free=0.1866 occ: r_work=0.0966 r_free=0.1848 adp: r_work=0.0964 r_free=0.1857 occ: r_work=0.0959 r_free=0.1839 adp: r_work=0.0958 r_free=0.1849 ADP+occupancy (water only), MIN, final r_work=0.0958 r_free=0.1849 r_work=0.0958 r_free=0.1849 | n_water=222 | time (s): 9.510 (total time: 34.240) Filter (q & B) r_work=0.0958 r_free=0.1854 | n_water=221 | time (s): 1.430 (total time: 35.670) Filter (dist only) r_work=0.0957 r_free=0.1856 | n_water=220 | time (s): 16.750 (total time: 52.420) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.894607 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.206504 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 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 0.0914 0.1844 0.0931 0.010 1.1 6.1 0.5 0.0 0 0.447 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.14 18.44 9.31 8.037 17.929 0.207 5.010 9.00 18.52 9.51 8.717 18.024 0.207 4.965 Individual atomic B min max mean iso aniso Overall: 0.00 108.27 16.59 11.56 1747 0 Protein: 0.00 108.27 15.64 11.54 1519 0 Water: 0.00 55.00 22.95 N/A 220 0 Other: 6.87 37.37 22.30 N/A 8 0 Chain A: 0.00 108.27 16.10 N/A 1635 0 Chain S: 0.00 55.00 23.70 N/A 112 0 Histogram: Values Number of atoms 0.00 - 10.83 663 10.83 - 21.65 646 21.65 - 32.48 270 32.48 - 43.31 95 43.31 - 54.14 40 54.14 - 64.96 13 64.96 - 75.79 8 75.79 - 86.62 7 86.62 - 97.45 3 97.45 - 108.27 2 =========================== Idealize ADP of riding H ========================== r_work=0.0900 r_free=0.1852 r_work=0.0903 r_free=0.1854 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0903 r_free = 0.1854 target_work(ml) = 4.969 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0899 r_free = 0.1848 target_work(ml) = 4.965 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5173 (all), 4.87 % free)-------------| | | | r_work= 0.0899 r_free= 0.1848 coordinate error (max.-lik. estimate): 0.26 A | | | | normalized target function (ml) (work): 4.965489 | | target function (ml) not normalized (work): 24435.169869 | | target function (ml) not normalized (free): 2176.664180 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.79 1.00 2491 142 0.1281 0.1781 5.5465 6.1718| | 2: 3.78 - 3.00 1.00 2430 110 0.0434 0.1961 4.3699 11.821| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 - 3.79 2491 142 0.91 12.34 1.00 0.98 13455.61| | 2: 3.78 - 3.00 2430 110 0.99 1.87 1.00 1.00 916.95| |alpha: min = 0.97 max = 1.00 mean = 0.99| |beta: min = 582.14 max = 22506.37 mean = 7263.99| |figures of merit: min = 0.00 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.94 mean = 7.17| |phase err.(test): min = 0.00 max = 81.11 mean = 7.39| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0946 0.0899 0.1848 n_refl.: 5173 re-set all scales: r(all,work,free)=0.2135 0.2135 0.2277 n_refl.: 5173 remove outliers: r(all,work,free)=0.2135 0.2135 0.2277 n_refl.: 5173 overall B=-0.00 to atoms: r(all,work,free)=0.2135 0.2135 0.2277 n_refl.: 5173 bulk-solvent and scaling: r(all,work,free)=0.0946 0.0899 0.1852 n_refl.: 5173 remove outliers: r(all,work,free)=0.0946 0.0899 0.1852 n_refl.: 5173 ======================== 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 0.3871 333.506 303.751 0.615 0.982 0.319 11.894-9.307 99.02 97 4 0.1944 526.220 503.693 0.996 0.990 0.319 9.237-7.194 100.00 213 7 0.2177 430.344 418.690 1.051 0.994 0.302 7.162-5.571 100.00 427 22 0.2073 322.921 312.269 1.035 0.996 0.291 5.546-4.326 100.00 867 58 0.1043 443.324 437.177 1.066 0.999 0.235 4.315-3.360 100.00 1859 96 0.0577 421.606 422.254 1.141 1.003 0.220 3.356-3.002 100.00 1373 60 0.0408 324.739 324.519 1.119 1.006 0.054 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-8.2218 ================= 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 : 0.3611 0.1982 0.082 5.302 8.8 119.3 19.9 258 0.000 1_bss: 0.1562 0.1569 0.082 5.302 5.9 116.4 17.0 258 0.000 1_settarget: 0.1562 0.1569 0.082 5.302 5.9 116.4 17.0 258 0.000 1_nqh: 0.1563 0.1572 0.082 5.302 5.9 116.4 17.0 258 0.006 1_weight: 0.1563 0.1572 0.082 5.302 5.9 116.4 17.0 258 0.006 1_xyzrec: 0.1157 0.1782 0.010 0.980 5.9 116.4 17.0 258 0.216 1_adp: 0.1015 0.1760 0.010 0.980 1.9 112.1 17.3 258 0.216 1_regHadp: 0.1010 0.1764 0.010 0.980 1.9 112.1 17.3 258 0.216 1_occ: 0.1004 0.1773 0.010 0.980 1.9 112.1 17.3 258 0.216 2_bss: 0.1007 0.1773 0.010 0.980 0.9 111.2 16.4 258 0.216 2_settarget: 0.1007 0.1773 0.010 0.980 0.9 111.2 16.4 258 0.216 2_updatecdl: 0.1007 0.1773 0.010 1.002 0.9 111.2 16.4 258 0.216 2_nqh: 0.1010 0.1771 0.010 1.002 0.9 111.2 16.4 258 0.216 2_sol: 0.1134 0.1619 0.010 1.002 0.9 111.2 15.8 227 n/a 2_weight: 0.1134 0.1619 0.010 1.002 0.9 111.2 15.8 227 n/a 2_xyzrec: 0.1018 0.1838 0.009 0.964 0.9 111.2 15.8 227 n/a 2_adp: 0.0955 0.1834 0.009 0.964 0.0 110.2 16.4 227 n/a 2_regHadp: 0.0952 0.1832 0.009 0.964 0.0 110.2 16.4 227 n/a 2_occ: 0.0952 0.1825 0.009 0.964 0.0 110.2 16.4 227 n/a 3_bss: 0.0949 0.1832 0.009 0.964 0.0 110.2 16.4 227 n/a 3_settarget: 0.0949 0.1832 0.009 0.964 0.0 110.2 16.4 227 n/a 3_updatecdl: 0.0949 0.1832 0.009 0.970 0.0 110.2 16.4 227 n/a 3_nqh: 0.0949 0.1831 0.009 0.970 0.0 110.2 16.4 227 n/a 3_sol: 0.1046 0.1776 0.009 0.970 0.0 110.2 16.1 226 n/a 3_weight: 0.1046 0.1776 0.009 0.970 0.0 110.2 16.1 226 n/a 3_xyzrec: 0.0944 0.1854 0.011 1.036 0.0 110.2 16.1 226 n/a 3_adp: 0.0899 0.1844 0.011 1.036 0.0 110.9 16.0 226 n/a 3_regHadp: 0.0904 0.1856 0.011 1.036 0.0 110.9 16.0 226 n/a 3_occ: 0.0897 0.1840 0.011 1.036 0.0 110.9 16.0 226 n/a 4_bss: 0.0890 0.1821 0.011 1.036 0.0 110.9 16.0 226 n/a 4_settarget: 0.0890 0.1821 0.011 1.036 0.0 110.9 16.0 226 n/a 4_updatecdl: 0.0890 0.1821 0.011 1.052 0.0 110.9 16.0 226 n/a 4_nqh: 0.0891 0.1818 0.011 1.052 0.0 110.9 16.0 226 n/a 4_sol: 0.0986 0.1786 0.011 1.052 0.0 110.9 16.2 224 n/a 4_weight: 0.0986 0.1786 0.011 1.052 0.0 110.9 16.2 224 n/a 4_xyzrec: 0.0905 0.1853 0.011 1.055 0.0 110.9 16.2 224 n/a 4_adp: 0.0882 0.1876 0.011 1.055 0.0 109.9 16.4 224 n/a 4_regHadp: 0.0887 0.1880 0.011 1.055 0.0 109.9 16.4 224 n/a 4_occ: 0.0876 0.1877 0.011 1.055 0.0 109.9 16.4 224 n/a 5_bss: 0.0877 0.1888 0.011 1.055 0.0 109.9 16.4 224 n/a 5_settarget: 0.0877 0.1888 0.011 1.055 0.0 109.9 16.4 224 n/a 5_updatecdl: 0.0877 0.1888 0.011 1.061 0.0 109.9 16.4 224 n/a 5_setrh: 0.0880 0.1886 0.011 1.061 0.0 109.9 16.4 224 n/a 5_nqh: 0.0881 0.1880 0.011 1.061 0.0 109.9 16.4 224 n/a 5_sol: 0.0957 0.1856 0.011 1.061 0.0 109.9 16.4 220 n/a 5_weight: 0.0957 0.1856 0.011 1.061 0.0 109.9 16.4 220 n/a 5_xyzrec: 0.0914 0.1844 0.010 1.099 0.0 109.9 16.4 220 n/a 5_adp: 0.0900 0.1852 0.010 1.099 0.0 108.3 16.6 220 n/a 5_regHadp: 0.0903 0.1854 0.010 1.099 0.0 108.3 16.6 220 n/a 5_occ: 0.0899 0.1848 0.010 1.099 0.0 108.3 16.6 220 n/a end: 0.0899 0.1852 0.010 1.099 0.0 108.3 16.6 220 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_3473948_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_3473948_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.1500 Refinement macro-cycles (run) : 492.4200 Write final files (write_after_run_outputs) : 9.6600 Total : 505.2300 Total CPU time: 8.76 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:19:07 PST -0800 (1735492747.14 s) Start R-work = 0.1562, R-free = 0.1569 Final R-work = 0.0899, R-free = 0.1852 =============================================================================== Job complete usr+sys time: 532.85 seconds wall clock time: 9 minutes 15.38 seconds (555.38 seconds total)