Starting phenix.refine on Sun Dec 29 09:10:03 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2659048.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_2659048.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2659048.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.99, per 1000 atoms: 0.59 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: 0.31 Conformation dependent library (CDL) restraints added in 143.7 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.64 - 0.90: 481 0.90 - 1.17: 1162 1.17 - 1.44: 717 1.44 - 1.70: 775 1.70 - 1.97: 18 Bond restraints: 3153 Sorted by residual: bond pdb=" CA GLY A 100 " pdb=" C GLY A 100 " ideal model delta sigma weight residual 1.518 1.719 -0.201 1.00e-02 1.00e+04 4.04e+02 bond pdb=" CA LYS A 122 " pdb=" C LYS A 122 " ideal model delta sigma weight residual 1.523 1.755 -0.232 1.30e-02 5.92e+03 3.19e+02 bond pdb=" CA ALA A 178 " pdb=" C ALA A 178 " ideal model delta sigma weight residual 1.523 1.292 0.231 1.30e-02 5.92e+03 3.17e+02 bond pdb=" CG HIS A 115 " pdb=" ND1 HIS A 115 " ideal model delta sigma weight residual 1.378 1.187 0.191 1.10e-02 8.26e+03 3.02e+02 bond pdb=" N ACYS A 53 " pdb=" CA ACYS A 53 " ideal model delta sigma weight residual 1.456 1.662 -0.205 1.20e-02 6.94e+03 2.93e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.62: 3624 5.62 - 11.25: 1728 11.25 - 16.87: 393 16.87 - 22.49: 25 22.49 - 28.11: 7 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O ILE A 168 " pdb=" C ILE A 168 " pdb=" N VAL A 169 " ideal model delta sigma weight residual 121.91 104.91 17.00 9.80e-01 1.04e+00 3.01e+02 angle pdb=" NE ARG A 48 " pdb=" CZ ARG A 48 " pdb=" NH1 ARG A 48 " ideal model delta sigma weight residual 121.50 137.32 -15.82 1.00e+00 1.00e+00 2.50e+02 angle pdb=" CA ACYS A 53 " pdb=" C ACYS A 53 " pdb=" O ACYS A 53 " ideal model delta sigma weight residual 119.29 129.38 -10.09 6.50e-01 2.37e+00 2.41e+02 angle pdb=" NE ARG A 48 " pdb=" CZ ARG A 48 " pdb=" NH2 ARG A 48 " ideal model delta sigma weight residual 119.20 105.33 13.87 9.00e-01 1.23e+00 2.37e+02 angle pdb=" C GLY A 108 " pdb=" N PRO A 109 " pdb=" CA PRO A 109 " ideal model delta sigma weight residual 119.82 105.61 14.21 9.80e-01 1.04e+00 2.10e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.56: 1341 19.56 - 39.13: 97 39.13 - 58.69: 34 58.69 - 78.26: 8 78.26 - 97.82: 1 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: 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 -143.24 20.64 0 2.50e+00 1.60e-01 6.82e+01 dihedral pdb=" C ALA A 14 " pdb=" N ALA A 14 " pdb=" CA ALA A 14 " pdb=" CB ALA A 14 " ideal model delta harmonic sigma weight residual -122.60 -102.92 -19.68 0 2.50e+00 1.60e-01 6.20e+01 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 122.80 142.01 -19.21 0 2.50e+00 1.60e-01 5.91e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.208: 104 0.208 - 0.416: 65 0.416 - 0.624: 46 0.624 - 0.832: 21 0.832 - 1.040: 7 Chirality restraints: 243 Sorted by residual: chirality pdb=" CB VAL A 51 " pdb=" CA VAL A 51 " pdb=" CG1 VAL A 51 " pdb=" CG2 VAL A 51 " both_signs ideal model delta sigma weight residual False -2.63 -1.59 -1.04 2.00e-01 2.50e+01 2.70e+01 chirality pdb=" CA ALA A 14 " pdb=" N ALA A 14 " pdb=" C ALA A 14 " pdb=" CB ALA A 14 " both_signs ideal model delta sigma weight residual False 2.48 3.51 -1.02 2.00e-01 2.50e+01 2.60e+01 chirality pdb=" CB VAL A 33 " pdb=" CA VAL A 33 " pdb=" CG1 VAL A 33 " pdb=" CG2 VAL A 33 " both_signs ideal model delta sigma weight residual False -2.63 -1.66 -0.97 2.00e-01 2.50e+01 2.37e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.044 2.00e-02 2.50e+03 6.38e-02 1.22e+02 pdb=" CG PHE A 119 " -0.009 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.043 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.029 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " -0.096 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " 0.026 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.137 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.027 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.007 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.045 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " -0.112 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " -0.005 2.00e-02 2.50e+03 5.42e-02 8.81e+01 pdb=" CG BTYR A 67 " -0.097 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " -0.016 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " 0.037 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " 0.069 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " 0.107 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " -0.041 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " -0.015 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " 0.039 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " 0.011 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " -0.032 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " -0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.020 2.00e-02 2.50e+03 4.81e-02 6.95e+01 pdb=" CG PHE A 164 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.090 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.019 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.042 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.004 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.077 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.060 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.036 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.062 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.31: 935 2.31 - 2.88: 8022 2.88 - 3.45: 10610 3.45 - 4.03: 15159 4.03 - 4.60: 21975 Nonbonded interactions: 56701 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.733 2.100 nonbonded pdb="HH21 ARG A 145 " pdb=" OE1 GLU A 163 " model vdw 1.834 2.450 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.858 2.450 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.870 2.450 nonbonded pdb=" H LYS A 12 " pdb=" O HOH A 396 " model vdw 1.888 2.450 ... (remaining 56696 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_2659048_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= 0.3614 r_free= 0.2049 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.463030 | | target function (ml) not normalized (work): 22002.739048 | | target function (ml) not normalized (free): 1149.526769 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3793 0.2255 4.8479 4.9261| | 2: 3.78 - 3.00 1.00 2430 110 0.3395 0.1702 4.0671 4.091| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 48.82 0.83 0.13 6606.53| | 2: 3.78 - 3.00 2430 110 0.94 11.08 1.48 0.26 437.47| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 369.19 max = 12070.15 mean = 3565.80| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 90.00 mean = 30.22| |phase err.(test): min = 0.00 max = 89.95 mean = 33.14| |-----------------------------------------------------------------------------| ----------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 : 0.085 0.281 1557 Z= 5.601 Angle : 5.394 24.633 2118 Z= 3.839 Chirality : 0.390 1.040 243 Planarity : 0.031 0.098 284 Dihedral : 14.130 97.822 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.11 % Allowed : 3.73 % Favored : 93.17 % Cbeta Deviations : 30.81 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.46), residues: 224 helix: -2.41 (0.40), residues: 109 sheet: -1.87 (0.85), residues: 28 loop : -0.59 (0.54), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.062 0.024 ARG A 27 TYR 0.067 0.027 TYR A 139 PHE 0.111 0.037 PHE A 119 HIS 0.038 0.020 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= 0.3614 r_free= 0.2049 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.463030 | | target function (ml) not normalized (work): 22002.739048 | | target function (ml) not normalized (free): 1149.526769 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3568 0.3645 0.2156 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3568 0.3645 0.2156 n_refl.: 5182 remove outliers: r(all,work,free)=0.2512 0.2534 0.2156 n_refl.: 5178 overall B=-2.95 to atoms: r(all,work,free)=0.2398 0.2416 0.2106 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1558 0.1555 0.1616 n_refl.: 5178 remove outliers: r(all,work,free)=0.1556 0.1553 0.1616 n_refl.: 5177 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 100.00 89 5 0.4102 445.039 406.961 0.690 1.019 0.394 11.894-9.307 99.02 97 4 0.1916 714.455 693.458 0.983 1.019 0.383 9.237-7.194 100.00 213 7 0.2225 584.282 574.827 1.017 1.017 0.364 7.162-5.571 100.00 427 22 0.2328 438.433 423.604 0.976 1.013 0.302 5.546-4.326 100.00 867 58 0.1365 601.906 594.625 0.998 1.007 0.226 4.315-3.360 100.00 1859 96 0.1290 572.419 566.303 1.047 0.997 0.190 3.356-3.002 100.00 1373 60 0.1586 440.901 433.882 1.037 0.986 0.065 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9552 b_overall=-3.7885 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1553 r_free=0.1616 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN A Total number of N/Q/H flips: 2 r_work=0.1554 r_free=0.1612 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 19.101884 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.831154 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 0.1797 0.0639 0.010 1.0 3.2 0.5 0.0 0 9.551 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.57 17.97 6.39 3.013 15.911 1.831 0.018 10.24 17.91 7.67 4.709 16.084 1.831 0.015 Individual atomic B min max mean iso aniso Overall: 1.79 111.35 17.27 5.13 1785 0 Protein: 1.79 110.60 14.55 5.13 1519 0 Water: 3.92 111.35 33.04 N/A 258 0 Other: 16.74 38.14 23.75 N/A 8 0 Chain A: 1.79 111.35 17.27 N/A 1785 0 Histogram: Values Number of atoms 1.79 - 12.75 898 12.75 - 23.70 502 23.70 - 34.66 189 34.66 - 45.62 107 45.62 - 56.57 59 56.57 - 67.53 13 67.53 - 78.48 8 78.48 - 89.44 5 89.44 - 100.40 1 100.40 - 111.35 3 =========================== Idealize ADP of riding H ========================== r_work=0.1024 r_free=0.1791 r_work=0.1018 r_free=0.1797 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1018 r_free = 0.1797 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 = 0.1020 r_free = 0.1803 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5177 (all), 4.87 % free)-------------| | | | r_work= 0.1020 r_free= 0.1803 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ls_wunit_k1) (work): 0.014200 | | target function (ls_wunit_k1) not normalized (work): 69.932990 | | target function (ls_wunit_k1) not normalized (free): 10.632447 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1059 0.1020 0.1803 n_refl.: 5177 re-set all scales: r(all,work,free)=0.2101 0.2100 0.2234 n_refl.: 5177 remove outliers: r(all,work,free)=0.2101 0.2100 0.2234 n_refl.: 5177 overall B=-1.02 to atoms: r(all,work,free)=0.2058 0.2055 0.2223 n_refl.: 5177 bulk-solvent and scaling: r(all,work,free)=0.1061 0.1021 0.1803 n_refl.: 5177 remove outliers: r(all,work,free)=0.1059 0.1019 0.1803 n_refl.: 5176 ======================== 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 0.3420 324.984 309.518 0.663 1.000 0.365 11.894-9.307 99.02 97 4 0.1546 526.213 517.959 0.998 1.002 0.361 9.237-7.194 100.00 213 7 0.1701 430.338 431.279 1.039 1.002 0.315 7.162-5.571 100.00 427 22 0.1634 322.916 319.530 0.998 1.002 0.292 5.546-4.326 100.00 867 58 0.0914 443.318 440.012 1.001 1.001 0.197 4.315-3.360 100.00 1859 96 0.0765 421.600 421.482 1.044 1.000 0.183 3.356-3.002 100.00 1373 60 0.1012 324.734 323.364 1.016 0.998 0.062 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9553 b_overall=-3.6446 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1019 r_free=0.1803 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1019 r_free=0.1803 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1019 r_free=0.1803 | n_water=258 | time (s): 0.600 (total time: 0.600) Filter (dist) r_work=0.1044 r_free=0.1794 | n_water=248 | time (s): 20.010 (total time: 20.610) Filter (q & B) r_work=0.1046 r_free=0.1799 | n_water=246 | time (s): 1.380 (total time: 21.990) Compute maps r_work=0.1046 r_free=0.1799 | n_water=246 | time (s): 0.420 (total time: 22.410) Filter (map) r_work=0.1341 r_free=0.1902 | n_water=150 | time (s): 1.550 (total time: 23.960) Find peaks r_work=0.1341 r_free=0.1902 | n_water=150 | time (s): 0.510 (total time: 24.470) Add new water r_work=0.1705 r_free=0.2238 | n_water=244 | time (s): 1.550 (total time: 26.020) Refine new water occ: r_work=0.1167 r_free=0.1753 adp: r_work=0.1132 r_free=0.1766 occ: r_work=0.1127 r_free=0.1721 adp: r_work=0.1112 r_free=0.1734 occ: r_work=0.1110 r_free=0.1715 adp: r_work=0.1108 r_free=0.1715 ADP+occupancy (water only), MIN, final r_work=0.1108 r_free=0.1715 r_work=0.1108 r_free=0.1715 | n_water=244 | time (s): 4.100 (total time: 30.120) Filter (q & B) r_work=0.1108 r_free=0.1715 | n_water=244 | time (s): 1.170 (total time: 31.290) Filter (dist only) r_work=0.1108 r_free=0.1714 | n_water=243 | time (s): 18.680 (total time: 49.970) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.941099 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.649961 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 0.0995 0.1811 0.0816 0.010 1.0 4.8 0.5 0.6 0 12.471 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.95 18.11 8.16 4.556 16.698 2.650 0.014 9.28 18.30 9.01 5.277 17.005 2.650 0.012 Individual atomic B min max mean iso aniso Overall: 0.00 105.76 16.54 6.19 1770 0 Protein: 0.00 105.76 14.60 6.17 1519 0 Water: 0.00 62.76 28.48 N/A 243 0 Other: 13.29 35.43 22.00 N/A 8 0 Chain A: 0.00 105.76 15.45 N/A 1677 0 Chain S: 2.25 61.62 36.23 N/A 93 0 Histogram: Values Number of atoms 0.00 - 10.58 703 10.58 - 21.15 639 21.15 - 31.73 213 31.73 - 42.30 117 42.30 - 52.88 50 52.88 - 63.45 34 63.45 - 74.03 7 74.03 - 84.61 2 84.61 - 95.18 3 95.18 - 105.76 2 =========================== Idealize ADP of riding H ========================== r_work=0.0928 r_free=0.1830 r_work=0.0925 r_free=0.1829 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0925 r_free = 0.1829 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0923 r_free = 0.1818 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.0923 r_free= 0.1818 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ls_wunit_k1) (work): 0.011727 | | target function (ls_wunit_k1) not normalized (work): 57.745150 | | target function (ls_wunit_k1) not normalized (free): 10.081982 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0968 0.0923 0.1818 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2071 0.2071 0.2196 n_refl.: 5176 remove outliers: r(all,work,free)=0.2071 0.2071 0.2196 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2071 0.2071 0.2196 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0963 0.0918 0.1809 n_refl.: 5176 remove outliers: r(all,work,free)=0.0961 0.0916 0.1809 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 0.3172 327.107 305.734 0.631 1.004 0.344 11.894-9.307 99.02 97 4 0.1408 526.213 522.447 0.990 1.006 0.340 9.237-7.194 100.00 213 7 0.1447 430.338 433.192 1.039 1.006 0.290 7.162-5.571 100.00 427 22 0.1393 322.916 320.427 1.005 1.005 0.280 5.546-4.326 100.00 867 58 0.0770 443.318 440.702 1.014 1.003 0.220 4.315-3.360 100.00 1859 96 0.0701 421.600 421.389 1.057 1.000 0.200 3.356-3.002 100.00 1373 60 0.0962 324.734 324.033 1.036 0.997 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9553 b_overall=-4.4235 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0916 r_free=0.1809 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=0.0919 r_free=0.1810 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0919 r_free=0.1810 | n_water=243 | time (s): 0.590 (total time: 0.590) Filter (dist) r_work=0.0936 r_free=0.1811 | n_water=238 | time (s): 20.640 (total time: 21.230) Filter (q & B) r_work=0.0996 r_free=0.1814 | n_water=236 | time (s): 1.930 (total time: 23.160) Compute maps r_work=0.0996 r_free=0.1814 | n_water=236 | time (s): 0.550 (total time: 23.710) Filter (map) r_work=0.1272 r_free=0.1919 | n_water=161 | time (s): 1.830 (total time: 25.540) Find peaks r_work=0.1272 r_free=0.1919 | n_water=161 | time (s): 0.500 (total time: 26.040) Add new water r_work=0.1642 r_free=0.2286 | n_water=246 | time (s): 1.710 (total time: 27.750) Refine new water occ: r_work=0.1048 r_free=0.1816 adp: r_work=0.1044 r_free=0.1825 occ: r_work=0.1031 r_free=0.1800 adp: r_work=0.1031 r_free=0.1810 occ: r_work=0.1020 r_free=0.1783 adp: r_work=0.1020 r_free=0.1796 ADP+occupancy (water only), MIN, final r_work=0.1020 r_free=0.1796 r_work=0.1020 r_free=0.1796 | n_water=246 | time (s): 11.810 (total time: 39.560) Filter (q & B) r_work=0.1020 r_free=0.1796 | n_water=246 | time (s): 0.970 (total time: 40.530) Filter (dist only) r_work=0.1023 r_free=0.1784 | n_water=245 | time (s): 19.390 (total time: 59.920) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.113813 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.214622 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 0.0923 0.1832 0.0908 0.011 1.1 4.8 0.5 0.6 0 0.557 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.23 18.32 9.08 5.205 17.417 0.215 5.135 8.80 18.24 9.44 7.057 17.434 0.215 5.039 Individual atomic B min max mean iso aniso Overall: 0.00 104.08 16.25 8.71 1772 0 Protein: 0.00 104.08 14.75 8.70 1519 0 Water: 0.00 57.76 25.27 N/A 245 0 Other: 15.13 39.25 23.67 N/A 8 0 Chain A: 0.00 104.08 15.56 N/A 1662 0 Chain S: 0.00 56.66 26.65 N/A 110 0 Histogram: Values Number of atoms 0.00 - 10.41 689 10.41 - 20.82 634 20.82 - 31.22 236 31.22 - 41.63 122 41.63 - 52.04 52 52.04 - 62.45 20 62.45 - 72.85 10 72.85 - 83.26 4 83.26 - 93.67 3 93.67 - 104.08 2 =========================== Idealize ADP of riding H ========================== r_work=0.0880 r_free=0.1824 r_work=0.0884 r_free=0.1835 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0884 r_free = 0.1835 target_work(ml) = 5.044 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0874 r_free = 0.1819 target_work(ml) = 5.036 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0874 r_free= 0.1819 coordinate error (max.-lik. estimate): 0.27 A | | | | normalized target function (ml) (work): 5.036256 | | target function (ml) not normalized (work): 24793.489795 | | target function (ml) not normalized (free): 1871.128043 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0922 0.0874 0.1819 n_refl.: 5175 re-set all scales: r(all,work,free)=0.1999 0.2001 0.2114 n_refl.: 5175 remove outliers: r(all,work,free)=0.1999 0.2001 0.2114 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.1999 0.2001 0.2114 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0914 0.0867 0.1806 n_refl.: 5175 remove outliers: r(all,work,free)=0.0914 0.0867 0.1806 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 0.3753 327.107 297.905 0.587 0.989 0.323 11.894-9.307 99.02 97 4 0.1834 526.213 511.399 0.951 0.993 0.318 9.237-7.194 100.00 213 7 0.1915 430.338 424.126 1.010 0.996 0.290 7.162-5.571 100.00 427 22 0.1811 322.916 313.582 0.986 0.997 0.270 5.546-4.326 100.00 867 58 0.0887 443.318 438.258 1.003 1.000 0.220 4.315-3.360 100.00 1859 96 0.0562 421.600 421.048 1.054 1.003 0.210 3.356-3.002 100.00 1373 60 0.0586 324.734 324.519 1.034 1.006 0.076 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-6.4641 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0867 r_free=0.1806 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=0.0868 r_free=0.1800 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0868 r_free=0.1800 | n_water=245 | time (s): 0.600 (total time: 0.600) Filter (dist) r_work=0.0892 r_free=0.1807 | n_water=241 | time (s): 17.780 (total time: 18.380) Filter (q & B) r_work=0.0947 r_free=0.1837 | n_water=238 | time (s): 1.570 (total time: 19.950) Compute maps r_work=0.0947 r_free=0.1837 | n_water=238 | time (s): 0.490 (total time: 20.440) Filter (map) r_work=0.1216 r_free=0.1923 | n_water=168 | time (s): 1.320 (total time: 21.760) Find peaks r_work=0.1216 r_free=0.1923 | n_water=168 | time (s): 0.420 (total time: 22.180) Add new water r_work=0.1528 r_free=0.2198 | n_water=247 | time (s): 1.440 (total time: 23.620) Refine new water occ: r_work=0.0997 r_free=0.1797 adp: r_work=0.0995 r_free=0.1810 occ: r_work=0.0986 r_free=0.1788 adp: r_work=0.0986 r_free=0.1799 occ: r_work=0.0978 r_free=0.1777 adp: r_work=0.0978 r_free=0.1789 ADP+occupancy (water only), MIN, final r_work=0.0978 r_free=0.1789 r_work=0.0978 r_free=0.1789 | n_water=247 | time (s): 9.580 (total time: 33.200) Filter (q & B) r_work=0.0978 r_free=0.1786 | n_water=246 | time (s): 1.220 (total time: 34.420) Filter (dist only) r_work=0.0988 r_free=0.1795 | n_water=245 | time (s): 19.910 (total time: 54.330) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.078587 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.220711 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 0.0896 0.1866 0.0969 0.012 1.1 4.2 0.5 0.0 0 0.539 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 8.96 18.66 9.69 6.796 17.654 0.221 5.012 8.71 19.07 10.36 8.184 17.773 0.221 4.942 Individual atomic B min max mean iso aniso Overall: 0.00 105.22 16.59 10.69 1772 0 Protein: 0.00 105.22 15.16 10.68 1519 0 Water: 0.00 58.64 25.24 N/A 245 0 Other: 12.38 41.20 23.39 N/A 8 0 Chain A: 0.00 105.22 15.89 N/A 1653 0 Chain S: 0.00 57.50 26.35 N/A 119 0 Histogram: Values Number of atoms 0.00 - 10.52 666 10.52 - 21.05 639 21.05 - 31.57 252 31.57 - 42.09 122 42.09 - 52.61 54 52.61 - 63.13 19 63.13 - 73.66 9 73.66 - 84.18 7 84.18 - 94.70 2 94.70 - 105.22 2 =========================== Idealize ADP of riding H ========================== r_work=0.0871 r_free=0.1907 r_work=0.0876 r_free=0.1913 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0876 r_free = 0.1913 target_work(ml) = 4.948 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0866 r_free = 0.1885 target_work(ml) = 4.940 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0866 r_free= 0.1885 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 4.939959 | | target function (ml) not normalized (work): 24319.417952 | | target function (ml) not normalized (free): 2218.296236 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0918 0.0866 0.1885 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2036 0.2035 0.2190 n_refl.: 5175 remove outliers: r(all,work,free)=0.2036 0.2035 0.2190 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2036 0.2035 0.2190 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0919 0.0868 0.1886 n_refl.: 5175 remove outliers: r(all,work,free)=0.0919 0.0868 0.1886 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 0.3976 327.107 293.209 0.579 0.988 0.318 11.894-9.307 99.02 97 4 0.1924 526.213 508.141 0.958 0.992 0.316 9.237-7.194 100.00 213 7 0.2170 430.338 420.375 1.009 0.995 0.286 7.162-5.571 100.00 427 22 0.2060 322.916 311.736 0.988 0.997 0.265 5.546-4.326 100.00 867 58 0.0954 443.318 438.387 1.023 0.999 0.220 4.315-3.360 100.00 1859 96 0.0537 421.600 421.599 1.081 1.002 0.210 3.356-3.002 100.00 1373 60 0.0422 324.734 324.917 1.064 1.005 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.6917 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0868 r_free=0.1886 After: r_work=0.0871 r_free=0.1885 ================================== NQH flips ================================== r_work=0.0871 r_free=0.1885 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=0.0871 r_free=0.1886 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0871 r_free=0.1886 | n_water=245 | time (s): 0.520 (total time: 0.520) Filter (dist) r_work=0.0898 r_free=0.1907 | n_water=238 | time (s): 20.050 (total time: 20.570) Filter (q & B) r_work=0.0971 r_free=0.1937 | n_water=236 | time (s): 1.900 (total time: 22.470) Compute maps r_work=0.0971 r_free=0.1937 | n_water=236 | time (s): 0.540 (total time: 23.010) Filter (map) r_work=0.1233 r_free=0.2086 | n_water=170 | time (s): 1.830 (total time: 24.840) Find peaks r_work=0.1233 r_free=0.2086 | n_water=170 | time (s): 0.600 (total time: 25.440) Add new water r_work=0.1484 r_free=0.2320 | n_water=234 | time (s): 1.690 (total time: 27.130) Refine new water occ: r_work=0.1002 r_free=0.1888 adp: r_work=0.0993 r_free=0.1888 occ: r_work=0.0989 r_free=0.1874 adp: r_work=0.0988 r_free=0.1881 occ: r_work=0.0984 r_free=0.1867 adp: r_work=0.0983 r_free=0.1874 ADP+occupancy (water only), MIN, final r_work=0.0983 r_free=0.1874 r_work=0.0983 r_free=0.1874 | n_water=234 | time (s): 8.310 (total time: 35.440) Filter (q & B) r_work=0.0983 r_free=0.1874 | n_water=234 | time (s): 0.930 (total time: 36.370) Filter (dist only) r_work=0.0986 r_free=0.1886 | n_water=231 | time (s): 17.380 (total time: 53.750) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.959892 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.233939 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 0.0937 0.1906 0.0969 0.011 1.1 6.4 0.5 0.0 0 0.480 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.37 19.06 9.69 8.108 17.967 0.234 5.040 9.12 19.49 10.37 8.897 18.048 0.234 4.974 Individual atomic B min max mean iso aniso Overall: 0.00 104.54 16.71 11.76 1758 0 Protein: 0.00 104.54 15.52 11.75 1519 0 Water: 0.00 64.67 24.31 N/A 231 0 Other: 14.52 43.86 23.18 N/A 8 0 Chain A: 0.00 104.54 16.07 N/A 1641 0 Chain S: 0.00 54.54 25.68 N/A 117 0 Histogram: Values Number of atoms 0.00 - 10.45 631 10.45 - 20.91 655 20.91 - 31.36 259 31.36 - 41.82 113 41.82 - 52.27 58 52.27 - 62.72 20 62.72 - 73.18 10 73.18 - 83.63 6 83.63 - 94.09 4 94.09 - 104.54 2 =========================== Idealize ADP of riding H ========================== r_work=0.0912 r_free=0.1949 r_work=0.0916 r_free=0.1957 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0916 r_free = 0.1957 target_work(ml) = 4.979 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0908 r_free = 0.1935 target_work(ml) = 4.974 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0908 r_free= 0.1935 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ml) (work): 4.973508 | | target function (ml) not normalized (work): 24484.580698 | | target function (ml) not normalized (free): 2278.441782 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.79 1.00 2493 142 0.1295 0.1867 5.5494 6.3423| | 2: 3.78 - 3.00 1.00 2430 110 0.0437 0.2051 4.3827 12.526| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2493 142 0.91 12.47 1.00 0.97 13648.84| | 2: 3.78 - 3.00 2430 110 0.99 1.96 1.00 0.99 947.06| |alpha: min = 0.96 max = 0.99 mean = 0.98| |beta: min = 607.04 max = 22866.77 mean = 7379.22| |figures of merit: min = 0.00 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.99 mean = 7.29| |phase err.(test): min = 0.00 max = 82.70 mean = 7.72| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0960 0.0908 0.1935 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2119 0.2116 0.2277 n_refl.: 5175 remove outliers: r(all,work,free)=0.2119 0.2116 0.2277 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2119 0.2116 0.2277 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0959 0.0907 0.1934 n_refl.: 5175 remove outliers: r(all,work,free)=0.0959 0.0907 0.1934 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 0.3965 327.107 285.849 0.579 0.982 0.309 11.894-9.307 99.02 97 4 0.1873 526.213 517.266 1.021 0.989 0.309 9.237-7.194 100.00 213 7 0.2226 430.338 422.320 1.068 0.992 0.293 7.162-5.571 100.00 427 22 0.2121 322.916 311.726 1.042 0.995 0.280 5.546-4.326 100.00 867 58 0.1054 443.318 436.686 1.072 0.998 0.239 4.315-3.360 100.00 1859 96 0.0576 421.600 421.167 1.143 1.002 0.220 3.356-3.002 100.00 1373 60 0.0411 324.734 324.396 1.127 1.005 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-8.4222 ================= 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 : 0.3614 0.2049 0.085 5.394 8.8 119.3 19.9 258 0.000 1_bss: 0.1553 0.1616 0.085 5.394 5.9 116.4 16.9 258 0.000 1_settarget: 0.1553 0.1616 0.085 5.394 5.9 116.4 16.9 258 0.000 1_nqh: 0.1554 0.1612 0.085 5.394 5.9 116.4 16.9 258 0.006 1_weight: 0.1554 0.1612 0.085 5.394 5.9 116.4 16.9 258 0.006 1_xyzrec: 0.1157 0.1797 0.010 0.970 5.9 116.4 16.9 258 0.218 1_adp: 0.1024 0.1791 0.010 0.970 1.8 111.4 17.3 258 0.218 1_regHadp: 0.1018 0.1797 0.010 0.970 1.8 111.4 17.3 258 0.218 1_occ: 0.1020 0.1803 0.010 0.970 1.8 111.4 17.3 258 0.218 2_bss: 0.1019 0.1803 0.010 0.970 0.8 110.3 16.2 258 0.218 2_settarget: 0.1019 0.1803 0.010 0.970 0.8 110.3 16.2 258 0.218 2_updatecdl: 0.1019 0.1803 0.010 0.998 0.8 110.3 16.2 258 0.218 2_nqh: 0.1019 0.1803 0.010 0.998 0.8 110.3 16.2 258 0.218 2_sol: 0.1108 0.1714 0.010 0.998 0.8 109.6 16.0 243 n/a 2_weight: 0.1108 0.1714 0.010 0.998 0.8 109.6 16.0 243 n/a 2_xyzrec: 0.0995 0.1811 0.010 1.022 0.8 109.6 16.0 243 n/a 2_adp: 0.0928 0.1830 0.010 1.022 0.0 105.8 16.5 243 n/a 2_regHadp: 0.0925 0.1829 0.010 1.022 0.0 105.8 16.5 243 n/a 2_occ: 0.0923 0.1818 0.010 1.022 0.0 105.8 16.5 243 n/a 3_bss: 0.0916 0.1809 0.010 1.022 0.0 105.8 16.5 243 n/a 3_settarget: 0.0916 0.1809 0.010 1.022 0.0 105.8 16.5 243 n/a 3_updatecdl: 0.0916 0.1809 0.010 1.025 0.0 105.8 16.5 243 n/a 3_nqh: 0.0919 0.1810 0.010 1.025 0.0 105.8 16.5 243 n/a 3_sol: 0.1023 0.1784 0.010 1.025 0.0 105.8 16.2 245 n/a 3_weight: 0.1023 0.1784 0.010 1.025 0.0 105.8 16.2 245 n/a 3_xyzrec: 0.0923 0.1832 0.011 1.087 0.0 105.8 16.2 245 n/a 3_adp: 0.0880 0.1824 0.011 1.087 0.0 104.1 16.2 245 n/a 3_regHadp: 0.0884 0.1835 0.011 1.087 0.0 104.1 16.2 245 n/a 3_occ: 0.0874 0.1819 0.011 1.087 0.0 104.1 16.2 245 n/a 4_bss: 0.0867 0.1806 0.011 1.087 0.0 104.1 16.2 245 n/a 4_settarget: 0.0867 0.1806 0.011 1.087 0.0 104.1 16.2 245 n/a 4_updatecdl: 0.0867 0.1806 0.011 1.105 0.0 104.1 16.2 245 n/a 4_nqh: 0.0868 0.1800 0.011 1.105 0.0 104.1 16.2 245 n/a 4_sol: 0.0988 0.1795 0.011 1.105 0.0 104.1 16.4 245 n/a 4_weight: 0.0988 0.1795 0.011 1.105 0.0 104.1 16.4 245 n/a 4_xyzrec: 0.0896 0.1866 0.012 1.079 0.0 104.1 16.4 245 n/a 4_adp: 0.0871 0.1907 0.012 1.079 0.0 105.2 16.6 245 n/a 4_regHadp: 0.0876 0.1913 0.012 1.079 0.0 105.2 16.6 245 n/a 4_occ: 0.0866 0.1885 0.012 1.079 0.0 105.2 16.6 245 n/a 5_bss: 0.0868 0.1886 0.012 1.079 0.0 105.2 16.6 245 n/a 5_settarget: 0.0868 0.1886 0.012 1.079 0.0 105.2 16.6 245 n/a 5_updatecdl: 0.0868 0.1886 0.012 1.081 0.0 105.2 16.6 245 n/a 5_setrh: 0.0871 0.1885 0.012 1.081 0.0 105.2 16.6 245 n/a 5_nqh: 0.0871 0.1886 0.012 1.081 0.0 105.2 16.6 245 n/a 5_sol: 0.0986 0.1886 0.012 1.081 0.0 105.2 16.6 231 n/a 5_weight: 0.0986 0.1886 0.012 1.081 0.0 105.2 16.6 231 n/a 5_xyzrec: 0.0937 0.1906 0.011 1.140 0.0 105.2 16.6 231 n/a 5_adp: 0.0912 0.1949 0.011 1.140 0.0 104.5 16.7 231 n/a 5_regHadp: 0.0916 0.1957 0.011 1.140 0.0 104.5 16.7 231 n/a 5_occ: 0.0908 0.1935 0.011 1.140 0.0 104.5 16.7 231 n/a end: 0.0907 0.1934 0.011 1.140 0.0 104.5 16.7 231 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_2659048_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_2659048_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.0000 Refinement macro-cycles (run) : 486.2700 Write final files (write_after_run_outputs) : 10.4600 Total : 499.7300 Total CPU time: 8.71 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:19:03 PST -0800 (1735492743.35 s) Start R-work = 0.1553, R-free = 0.1616 Final R-work = 0.0907, R-free = 0.1934 =============================================================================== Job complete usr+sys time: 530.75 seconds wall clock time: 9 minutes 12.00 seconds (552.00 seconds total)