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_7410891.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 { 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" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7410891.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7410891.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 1 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.70, per 1000 atoms: 0.50 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 169.4 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.63 - 0.89: 410 0.89 - 1.14: 1196 1.14 - 1.40: 576 1.40 - 1.65: 902 1.65 - 1.90: 69 Bond restraints: 3153 Sorted by residual: bond pdb=" N ALA A 165 " pdb=" CA ALA A 165 " ideal model delta sigma weight residual 1.459 1.238 0.221 1.21e-02 6.83e+03 3.35e+02 bond pdb=" ND1 HIS A 126 " pdb=" CE1 HIS A 126 " ideal model delta sigma weight residual 1.321 1.156 0.165 1.00e-02 1.00e+04 2.72e+02 bond pdb=" CA VAL A 33 " pdb=" CB VAL A 33 " ideal model delta sigma weight residual 1.539 1.730 -0.191 1.18e-02 7.18e+03 2.63e+02 bond pdb=" C BLYS A 175 " pdb=" N GLU A 176 " ideal model delta sigma weight residual 1.334 1.540 -0.206 1.27e-02 6.20e+03 2.62e+02 bond pdb=" C GLY A 78 " pdb=" O GLY A 78 " ideal model delta sigma weight residual 1.234 1.428 -0.195 1.21e-02 6.83e+03 2.59e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.93: 3251 4.93 - 9.86: 1858 9.86 - 14.79: 582 14.79 - 19.71: 81 19.71 - 24.64: 5 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA ALEU A 153 " pdb=" C ALEU A 153 " pdb=" O ALEU A 153 " ideal model delta sigma weight residual 120.30 134.74 -14.44 1.07e+00 8.73e-01 1.82e+02 angle pdb=" O LEU A 92 " pdb=" C LEU A 92 " pdb=" N BLYS A 93 " ideal model delta sigma weight residual 122.07 135.58 -13.51 1.03e+00 9.43e-01 1.72e+02 angle pdb=" O ASP A 60 " pdb=" C ASP A 60 " pdb=" N ALA A 61 " ideal model delta sigma weight residual 122.07 135.53 -13.46 1.03e+00 9.43e-01 1.71e+02 angle pdb=" CA LEU A 82 " pdb=" C LEU A 82 " pdb=" O LEU A 82 " ideal model delta sigma weight residual 120.90 134.82 -13.92 1.07e+00 8.73e-01 1.69e+02 angle pdb=" NE ARG A 28 " pdb=" CZ ARG A 28 " pdb=" NH2 ARG A 28 " ideal model delta sigma weight residual 119.20 108.24 10.96 9.00e-01 1.23e+00 1.48e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.42: 1283 16.42 - 32.83: 140 32.83 - 49.24: 41 49.24 - 65.66: 14 65.66 - 82.07: 3 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" N MET A 26 " pdb=" C MET A 26 " pdb=" CA MET A 26 " pdb=" CB MET A 26 " ideal model delta harmonic sigma weight residual 122.80 144.29 -21.49 0 2.50e+00 1.60e-01 7.39e+01 dihedral pdb=" N ALA A 104 " pdb=" C ALA A 104 " pdb=" CA ALA A 104 " pdb=" CB ALA A 104 " ideal model delta harmonic sigma weight residual 122.90 142.59 -19.69 0 2.50e+00 1.60e-01 6.20e+01 dihedral pdb=" C BASN A 76 " pdb=" N BASN A 76 " pdb=" CA BASN A 76 " pdb=" CB BASN A 76 " ideal model delta harmonic sigma weight residual -122.60 -104.39 -18.21 0 2.50e+00 1.60e-01 5.30e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.270: 111 0.270 - 0.539: 83 0.539 - 0.809: 39 0.809 - 1.079: 8 1.079 - 1.348: 2 Chirality restraints: 243 Sorted by residual: chirality pdb=" CG LEU A 172 " pdb=" CB LEU A 172 " pdb=" CD1 LEU A 172 " pdb=" CD2 LEU A 172 " both_signs ideal model delta sigma weight residual False -2.59 -1.24 -1.35 2.00e-01 2.50e+01 4.55e+01 chirality pdb=" CA MET A 26 " pdb=" N MET A 26 " pdb=" C MET A 26 " pdb=" CB MET A 26 " both_signs ideal model delta sigma weight residual False 2.51 1.35 1.16 2.00e-01 2.50e+01 3.35e+01 chirality pdb=" CA PRO A 22 " pdb=" N PRO A 22 " pdb=" C PRO A 22 " pdb=" CB PRO A 22 " both_signs ideal model delta sigma weight residual False 2.72 1.70 1.01 2.00e-01 2.50e+01 2.57e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.102 2.00e-02 2.50e+03 7.30e-02 1.60e+02 pdb=" CG PHE A 164 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " -0.087 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.128 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " -0.091 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.083 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.082 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.008 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.046 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.055 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " -0.065 2.00e-02 2.50e+03 6.85e-02 1.41e+02 pdb=" CG ATYR A 67 " 0.032 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " -0.015 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " 0.098 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " 0.080 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " 0.068 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " 0.064 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " -0.121 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " -0.066 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " -0.022 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " 0.027 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " -0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 138 " 0.070 2.00e-02 2.50e+03 6.39e-02 9.18e+01 pdb=" CG HIS A 138 " -0.055 2.00e-02 2.50e+03 pdb=" ND1 HIS A 138 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 HIS A 138 " -0.060 2.00e-02 2.50e+03 pdb=" CE1 HIS A 138 " 0.068 2.00e-02 2.50e+03 pdb=" NE2 HIS A 138 " -0.078 2.00e-02 2.50e+03 pdb=" HD1 HIS A 138 " -0.084 2.00e-02 2.50e+03 pdb=" HD2 HIS A 138 " 0.053 2.00e-02 2.50e+03 pdb=" HE1 HIS A 138 " 0.061 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.34: 1162 2.34 - 2.90: 8204 2.90 - 3.47: 10467 3.47 - 4.03: 15210 4.03 - 4.60: 21605 Nonbonded interactions: 56648 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.771 2.100 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.817 2.450 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.853 2.450 nonbonded pdb=" HE2 HIS A 126 " pdb=" O PRO A 184 " model vdw sym.op. 1.873 2.450 x-y,-y,-z-4/3 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.878 2.450 ... (remaining 56643 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_7410891_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= 0.3618 r_free= 0.2001 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.474882 | | target function (ml) not normalized (work): 22061.169027 | | target function (ml) not normalized (free): 1150.556988 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3795 0.2212 4.8555 4.9135| | 2: 3.78 - 3.00 1.00 2430 110 0.3401 0.1643 4.0833 4.1168| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 48.92 0.83 0.13 6621.54| | 2: 3.78 - 3.00 2430 110 0.93 11.51 1.48 0.26 458.33| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 390.92 max = 12086.64 mean = 3583.69| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 89.99 mean = 30.48| |phase err.(test): min = 0.00 max = 89.94 mean = 33.78| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.080 0.247 1557 Z= 5.376 Angle : 5.408 18.959 2118 Z= 3.798 Chirality : 0.413 1.348 243 Planarity : 0.034 0.086 284 Dihedral : 13.735 82.074 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.48 % Allowed : 1.86 % Favored : 95.65 % Cbeta Deviations : 36.22 % 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: -2.44 (0.44), residues: 224 helix: -2.57 (0.34), residues: 103 sheet: -0.77 (0.90), residues: 28 loop : -0.42 (0.52), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.101 0.024 ARG A 5 TYR 0.069 0.030 TYR A 139 PHE 0.120 0.045 PHE A 164 HIS 0.042 0.017 HIS A 138 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 1785 0 Protein: 8.85 115.78 16.79 3.90 1519 0 Water: 11.36 119.30 38.03 N/A 258 0 Other: 19.04 26.29 21.71 N/A 8 0 Chain A: 8.85 119.30 19.89 N/A 1785 0 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 3.00 - 49.25 A, n_refl.=5182 (all), 4.86 % free)-------------| | | | r_work= 0.3618 r_free= 0.2001 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.474882 | | target function (ml) not normalized (work): 22061.169027 | | target function (ml) not normalized (free): 1150.556988 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3576 0.3653 0.2124 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3576 0.3653 0.2124 n_refl.: 5182 remove outliers: r(all,work,free)=0.2531 0.2555 0.2124 n_refl.: 5178 overall B=-2.77 to atoms: r(all,work,free)=0.2426 0.2447 0.2083 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1580 0.1579 0.1587 n_refl.: 5178 remove outliers: r(all,work,free)=0.1573 0.1572 0.1587 n_refl.: 5174 ======================== 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 96.81 86 5 0.3843 447.758 398.433 0.655 1.027 0.381 11.894-9.307 99.02 97 4 0.1847 714.211 691.352 0.943 1.027 0.379 9.237-7.194 100.00 213 7 0.2223 584.083 572.108 0.974 1.024 0.350 7.162-5.571 100.00 427 22 0.2355 438.283 421.330 0.927 1.019 0.300 5.546-4.326 100.00 867 58 0.1385 601.700 592.027 0.970 1.010 0.234 4.315-3.360 100.00 1859 96 0.1318 572.224 567.490 1.027 0.996 0.208 3.356-3.002 100.00 1373 60 0.1628 440.751 435.639 1.024 0.982 0.096 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9180 b_overall=-4.7754 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1572 r_free=0.1587 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1572 r_free=0.1587 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 19.143896 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.775435 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 0.1840 0.0683 0.010 1.0 2.9 0.5 0.0 0 9.572 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.57 18.40 6.83 3.013 16.089 1.775 0.018 10.14 18.43 8.29 4.895 16.394 1.775 0.014 Individual atomic B min max mean iso aniso Overall: 2.31 111.53 17.69 5.24 1785 0 Protein: 2.31 111.53 15.01 5.23 1519 0 Water: 4.10 111.53 33.29 N/A 258 0 Other: 17.95 36.47 24.72 N/A 8 0 Chain A: 2.31 111.53 17.69 N/A 1785 0 Histogram: Values Number of atoms 2.31 - 13.23 907 13.23 - 24.16 489 24.16 - 35.08 190 35.08 - 46.00 111 46.00 - 56.92 54 56.92 - 67.84 17 67.84 - 78.77 8 78.77 - 89.69 5 89.69 - 100.61 1 100.61 - 111.53 3 =========================== Idealize ADP of riding H ========================== r_work=0.1014 r_free=0.1843 r_work=0.1008 r_free=0.1845 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1008 r_free = 0.1845 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 = 0.1008 r_free = 0.1857 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.1008 r_free= 0.1857 coordinate error (max.-lik. estimate): 0.33 A | | | | normalized target function (ls_wunit_k1) (work): 0.013862 | | target function (ls_wunit_k1) not normalized (work): 68.231097 | | target function (ls_wunit_k1) not normalized (free): 10.777538 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1051 0.1008 0.1857 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2032 0.2022 0.2288 n_refl.: 5174 remove outliers: r(all,work,free)=0.2032 0.2022 0.2288 n_refl.: 5174 overall B=-0.98 to atoms: r(all,work,free)=0.1992 0.1981 0.2277 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.1048 0.1005 0.1846 n_refl.: 5174 remove outliers: r(all,work,free)=0.1048 0.1005 0.1846 n_refl.: 5174 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 94.79 86 5 0.3243 319.339 299.534 0.646 0.997 0.360 11.894-9.307 99.02 97 4 0.1507 509.372 501.341 0.965 1.000 0.361 9.237-7.194 100.00 213 7 0.1654 416.565 417.910 0.997 1.001 0.310 7.162-5.571 100.00 427 22 0.1599 312.582 308.698 0.951 1.001 0.292 5.546-4.326 100.00 867 58 0.0913 429.130 425.996 0.972 1.001 0.212 4.315-3.360 100.00 1859 96 0.0759 408.107 408.019 1.017 1.000 0.204 3.356-3.002 100.00 1373 60 0.1000 314.341 313.234 0.993 0.999 0.082 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-4.4153 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1005 r_free=0.1846 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=0.1008 r_free=0.1846 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1008 r_free=0.1846 | n_water=258 | time (s): 0.710 (total time: 0.710) Filter (dist) r_work=0.1033 r_free=0.1838 | n_water=247 | time (s): 21.200 (total time: 21.910) Filter (q & B) r_work=0.1033 r_free=0.1835 | n_water=244 | time (s): 1.790 (total time: 23.700) Compute maps r_work=0.1033 r_free=0.1835 | n_water=244 | time (s): 0.670 (total time: 24.370) Filter (map) r_work=0.1306 r_free=0.1900 | n_water=152 | time (s): 1.540 (total time: 25.910) Find peaks r_work=0.1306 r_free=0.1900 | n_water=152 | time (s): 0.470 (total time: 26.380) Add new water r_work=0.1651 r_free=0.2172 | n_water=235 | time (s): 1.220 (total time: 27.600) Refine new water occ: r_work=0.1154 r_free=0.1699 adp: r_work=0.1131 r_free=0.1717 occ: r_work=0.1128 r_free=0.1682 adp: r_work=0.1117 r_free=0.1705 occ: r_work=0.1117 r_free=0.1680 adp: r_work=0.1114 r_free=0.1691 ADP+occupancy (water only), MIN, final r_work=0.1114 r_free=0.1691 r_work=0.1114 r_free=0.1691 | n_water=235 | time (s): 6.920 (total time: 34.520) Filter (q & B) r_work=0.1114 r_free=0.1691 | n_water=235 | time (s): 1.200 (total time: 35.720) Filter (dist only) r_work=0.1126 r_free=0.1690 | n_water=231 | time (s): 18.260 (total time: 53.980) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.280596 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.538815 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 0.1821 0.0803 0.010 1.0 4.5 0.5 0.0 0 12.140 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.18 18.21 8.03 4.650 17.097 2.539 0.014 9.53 18.24 8.71 5.434 17.489 2.539 0.012 Individual atomic B min max mean iso aniso Overall: 0.00 108.91 16.89 6.41 1758 0 Protein: 0.00 108.91 15.29 6.40 1519 0 Water: 0.00 64.10 27.18 N/A 231 0 Other: 11.97 38.06 25.08 N/A 8 0 Chain A: 0.00 108.91 16.06 N/A 1676 0 Chain S: 6.32 61.96 34.03 N/A 82 0 Histogram: Values Number of atoms 0.00 - 10.89 661 10.89 - 21.78 691 21.78 - 32.67 212 32.67 - 43.56 116 43.56 - 54.45 41 54.45 - 65.34 26 65.34 - 76.23 5 76.23 - 87.12 3 87.12 - 98.02 1 98.02 - 108.91 2 =========================== Idealize ADP of riding H ========================== r_work=0.0953 r_free=0.1824 r_work=0.0951 r_free=0.1824 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0951 r_free = 0.1824 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0945 r_free = 0.1815 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0945 r_free= 0.1815 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ls_wunit_k1) (work): 0.011953 | | target function (ls_wunit_k1) not normalized (work): 58.833562 | | target function (ls_wunit_k1) not normalized (free): 9.880994 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0989 0.0945 0.1815 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2047 0.2046 0.2155 n_refl.: 5174 remove outliers: r(all,work,free)=0.2047 0.2046 0.2155 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2047 0.2046 0.2155 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0989 0.0945 0.1813 n_refl.: 5174 remove outliers: r(all,work,free)=0.0989 0.0945 0.1813 n_refl.: 5174 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 94.79 86 5 0.3262 319.339 305.282 0.671 1.001 0.350 11.894-9.307 99.02 97 4 0.1487 509.372 505.140 0.989 1.004 0.337 9.237-7.194 100.00 213 7 0.1485 416.565 417.726 1.034 1.004 0.295 7.162-5.571 100.00 427 22 0.1429 312.582 310.302 1.000 1.004 0.290 5.546-4.326 100.00 867 58 0.0800 429.130 426.838 1.017 1.002 0.210 4.315-3.360 100.00 1859 96 0.0743 408.107 407.965 1.071 0.999 0.200 3.356-3.002 100.00 1373 60 0.0954 314.341 313.277 1.052 0.996 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-4.9813 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0945 r_free=0.1813 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN A A 76 ASN B A 80 GLN A Total number of N/Q/H flips: 4 r_work=0.0949 r_free=0.1816 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0949 r_free=0.1816 | n_water=231 | time (s): 0.550 (total time: 0.550) Filter (dist) r_work=0.0972 r_free=0.1815 | n_water=226 | time (s): 18.240 (total time: 18.790) Filter (q & B) r_work=0.1001 r_free=0.1827 | n_water=225 | time (s): 1.700 (total time: 20.490) Compute maps r_work=0.1001 r_free=0.1827 | n_water=225 | time (s): 0.650 (total time: 21.140) Filter (map) r_work=0.1261 r_free=0.1906 | n_water=154 | time (s): 1.960 (total time: 23.100) Find peaks r_work=0.1261 r_free=0.1906 | n_water=154 | time (s): 0.440 (total time: 23.540) Add new water r_work=0.1649 r_free=0.2251 | n_water=240 | time (s): 1.390 (total time: 24.930) Refine new water occ: r_work=0.1073 r_free=0.1792 adp: r_work=0.1071 r_free=0.1814 occ: r_work=0.1058 r_free=0.1778 adp: r_work=0.1058 r_free=0.1795 occ: r_work=0.1047 r_free=0.1759 adp: r_work=0.1046 r_free=0.1777 ADP+occupancy (water only), MIN, final r_work=0.1046 r_free=0.1777 r_work=0.1046 r_free=0.1777 | n_water=240 | time (s): 12.240 (total time: 37.170) Filter (q & B) r_work=0.1047 r_free=0.1781 | n_water=238 | time (s): 1.490 (total time: 38.660) Filter (dist only) r_work=0.1047 r_free=0.1781 | n_water=238 | time (s): 16.210 (total time: 54.870) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.119838 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.228309 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 0.1871 0.0927 0.011 1.1 5.1 0.5 0.0 0 0.560 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.44 18.71 9.27 5.380 18.118 0.228 5.118 8.95 18.78 9.83 7.242 18.130 0.228 5.016 Individual atomic B min max mean iso aniso Overall: 0.00 108.06 16.75 8.88 1765 0 Protein: 0.00 108.06 15.44 8.85 1519 0 Water: 0.00 59.10 24.84 N/A 238 0 Other: 8.32 42.62 25.17 N/A 8 0 Chain A: 0.00 108.06 16.12 N/A 1663 0 Chain S: 0.00 57.09 27.03 N/A 102 0 Histogram: Values Number of atoms 0.00 - 10.81 654 10.81 - 21.61 677 21.61 - 32.42 242 32.42 - 43.23 125 43.23 - 54.03 29 54.03 - 64.84 21 64.84 - 75.64 9 75.64 - 86.45 3 86.45 - 97.26 4 97.26 - 108.06 1 =========================== Idealize ADP of riding H ========================== r_work=0.0895 r_free=0.1878 r_work=0.0902 r_free=0.1879 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0902 r_free = 0.1879 target_work(ml) = 5.021 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0889 r_free = 0.1843 target_work(ml) = 5.011 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0889 r_free= 0.1843 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ml) (work): 5.011248 | | target function (ml) not normalized (work): 24665.363233 | | target function (ml) not normalized (free): 1908.571113 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0937 0.0889 0.1843 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2035 0.2033 0.2178 n_refl.: 5174 remove outliers: r(all,work,free)=0.2035 0.2033 0.2178 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2035 0.2033 0.2178 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0930 0.0883 0.1834 n_refl.: 5174 remove outliers: r(all,work,free)=0.0930 0.0883 0.1834 n_refl.: 5174 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 94.79 86 5 0.3812 319.339 289.502 0.586 0.991 0.330 11.894-9.307 99.02 97 4 0.1848 509.372 493.977 0.955 0.996 0.330 9.237-7.194 100.00 213 7 0.1943 416.565 410.115 1.005 0.998 0.290 7.162-5.571 100.00 427 22 0.1821 312.582 304.237 0.987 0.999 0.280 5.546-4.326 100.00 867 58 0.0928 429.130 424.132 1.008 1.000 0.215 4.315-3.360 100.00 1859 96 0.0581 408.107 407.917 1.069 1.002 0.210 3.356-3.002 100.00 1373 60 0.0569 314.341 314.261 1.050 1.003 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.0411 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0883 r_free=0.1834 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN B Total number of N/Q/H flips: 2 r_work=0.0884 r_free=0.1836 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0884 r_free=0.1836 | n_water=238 | time (s): 0.690 (total time: 0.690) Filter (dist) r_work=0.0901 r_free=0.1846 | n_water=235 | time (s): 19.920 (total time: 20.610) Filter (q & B) r_work=0.1008 r_free=0.1887 | n_water=232 | time (s): 1.540 (total time: 22.150) Compute maps r_work=0.1008 r_free=0.1887 | n_water=232 | time (s): 0.470 (total time: 22.620) Filter (map) r_work=0.1267 r_free=0.1937 | n_water=161 | time (s): 1.270 (total time: 23.890) Find peaks r_work=0.1267 r_free=0.1937 | n_water=161 | time (s): 0.440 (total time: 24.330) Add new water r_work=0.1561 r_free=0.2208 | n_water=232 | time (s): 1.390 (total time: 25.720) Refine new water occ: r_work=0.1007 r_free=0.1870 adp: r_work=0.0998 r_free=0.1882 occ: r_work=0.0991 r_free=0.1859 adp: r_work=0.0989 r_free=0.1870 occ: r_work=0.0982 r_free=0.1844 adp: r_work=0.0981 r_free=0.1856 ADP+occupancy (water only), MIN, final r_work=0.0981 r_free=0.1856 r_work=0.0981 r_free=0.1856 | n_water=232 | time (s): 12.990 (total time: 38.710) Filter (q & B) r_work=0.0981 r_free=0.1856 | n_water=232 | time (s): 0.750 (total time: 39.460) Filter (dist only) r_work=0.0985 r_free=0.1875 | n_water=231 | time (s): 17.060 (total time: 56.520) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.969831 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.241154 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 0.0898 0.1908 0.1011 0.010 1.1 4.5 0.5 0.6 0 0.485 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 8.98 19.08 10.11 6.930 18.241 0.241 4.987 8.73 18.96 10.22 7.957 18.342 0.241 4.920 Individual atomic B min max mean iso aniso Overall: 0.00 106.50 16.96 10.37 1758 0 Protein: 0.00 106.50 15.77 10.35 1519 0 Water: 0.00 54.10 24.48 N/A 231 0 Other: 8.51 40.72 25.90 N/A 8 0 Chain A: 0.00 106.50 16.41 N/A 1655 0 Chain S: 0.00 51.74 25.82 N/A 103 0 Histogram: Values Number of atoms 0.00 - 10.65 628 10.65 - 21.30 676 21.30 - 31.95 254 31.95 - 42.60 114 42.60 - 53.25 47 53.25 - 63.90 20 63.90 - 74.55 8 74.55 - 85.20 7 85.20 - 95.85 1 95.85 - 106.50 3 =========================== Idealize ADP of riding H ========================== r_work=0.0873 r_free=0.1896 r_work=0.0877 r_free=0.1898 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0877 r_free = 0.1898 target_work(ml) = 4.925 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0866 r_free = 0.1882 target_work(ml) = 4.917 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0866 r_free= 0.1882 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ml) (work): 4.916874 | | target function (ml) not normalized (work): 24200.853195 | | target function (ml) not normalized (free): 2209.593377 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0917 0.0866 0.1882 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2092 0.2089 0.2245 n_refl.: 5174 remove outliers: r(all,work,free)=0.2092 0.2089 0.2245 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2092 0.2089 0.2245 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0915 0.0864 0.1874 n_refl.: 5174 remove outliers: r(all,work,free)=0.0915 0.0864 0.1874 n_refl.: 5174 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 94.79 86 5 0.3734 319.339 292.829 0.582 0.987 0.320 11.894-9.307 99.02 97 4 0.1910 509.372 493.537 0.949 0.992 0.305 9.237-7.194 100.00 213 7 0.2173 416.565 407.159 1.008 0.995 0.285 7.162-5.571 100.00 427 22 0.2007 312.582 303.225 0.993 0.997 0.280 5.546-4.326 100.00 867 58 0.0956 429.130 424.536 1.022 0.999 0.224 4.315-3.360 100.00 1859 96 0.0543 408.107 408.134 1.088 1.002 0.210 3.356-3.002 100.00 1373 60 0.0429 314.341 314.440 1.070 1.004 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.9474 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0864 r_free=0.1874 After: r_work=0.0867 r_free=0.1873 ================================== NQH flips ================================== r_work=0.0867 r_free=0.1873 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=0.0868 r_free=0.1874 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0868 r_free=0.1874 | n_water=231 | time (s): 0.500 (total time: 0.500) Filter (dist) r_work=0.0883 r_free=0.1879 | n_water=227 | time (s): 17.830 (total time: 18.330) Filter (q & B) r_work=0.0955 r_free=0.1914 | n_water=224 | time (s): 1.350 (total time: 19.680) Compute maps r_work=0.0955 r_free=0.1914 | n_water=224 | time (s): 0.450 (total time: 20.130) Filter (map) r_work=0.1248 r_free=0.2006 | n_water=160 | time (s): 1.730 (total time: 21.860) Find peaks r_work=0.1248 r_free=0.2006 | n_water=160 | time (s): 0.580 (total time: 22.440) Add new water r_work=0.1544 r_free=0.2301 | n_water=238 | time (s): 2.090 (total time: 24.530) Refine new water occ: r_work=0.1001 r_free=0.1875 adp: r_work=0.0997 r_free=0.1886 occ: r_work=0.0988 r_free=0.1861 adp: r_work=0.0987 r_free=0.1874 occ: r_work=0.0978 r_free=0.1848 adp: r_work=0.0977 r_free=0.1858 ADP+occupancy (water only), MIN, final r_work=0.0977 r_free=0.1858 r_work=0.0977 r_free=0.1858 | n_water=238 | time (s): 8.010 (total time: 32.540) Filter (q & B) r_work=0.0977 r_free=0.1856 | n_water=235 | time (s): 1.860 (total time: 34.400) Filter (dist only) r_work=0.0980 r_free=0.1862 | n_water=233 | time (s): 20.090 (total time: 54.490) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.928064 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.203507 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 0.0913 0.1872 0.0959 0.010 1.1 7.0 0.5 0.6 0 0.464 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.13 18.72 9.59 7.920 18.568 0.204 4.974 8.91 18.72 9.81 8.786 18.661 0.204 4.915 Individual atomic B min max mean iso aniso Overall: 0.00 106.60 17.25 11.57 1760 0 Protein: 0.00 106.60 16.16 11.55 1519 0 Water: 0.00 61.81 24.06 N/A 233 0 Other: 8.47 43.34 25.34 N/A 8 0 Chain A: 0.00 106.60 16.65 N/A 1641 0 Chain S: 0.00 61.81 25.56 N/A 119 0 Histogram: Values Number of atoms 0.00 - 10.66 625 10.66 - 21.32 651 21.32 - 31.98 279 31.98 - 42.64 124 42.64 - 53.30 40 53.30 - 63.96 19 63.96 - 74.62 11 74.62 - 85.28 5 85.28 - 95.94 2 95.94 - 106.60 4 =========================== Idealize ADP of riding H ========================== r_work=0.0891 r_free=0.1872 r_work=0.0894 r_free=0.1872 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0894 r_free = 0.1872 target_work(ml) = 4.921 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0884 r_free = 0.1843 target_work(ml) = 4.912 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0884 r_free= 0.1843 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ml) (work): 4.911870 | | target function (ml) not normalized (work): 24176.222185 | | target function (ml) not normalized (free): 2212.779897 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.79 1.00 2492 142 0.1268 0.1870 5.5143 6.2704| | 2: 3.78 - 3.00 1.00 2430 110 0.0415 0.1799 4.294 12.022| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2492 142 0.91 12.28 1.00 0.94 12854.64| | 2: 3.78 - 3.00 2430 110 0.99 1.66 1.00 0.97 793.96| |alpha: min = 0.93 max = 0.97 mean = 0.96| |beta: min = 499.13 max = 21671.95 mean = 6900.26| |figures of merit: min = 0.00 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.86 mean = 7.04| |phase err.(test): min = 0.00 max = 72.67 mean = 6.89| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0932 0.0884 0.1843 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2142 0.2140 0.2272 n_refl.: 5174 remove outliers: r(all,work,free)=0.2142 0.2140 0.2272 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2142 0.2140 0.2272 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0934 0.0887 0.1836 n_refl.: 5174 remove outliers: r(all,work,free)=0.0934 0.0887 0.1836 n_refl.: 5174 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 94.79 86 5 0.3801 319.339 288.854 0.586 0.983 0.316 11.894-9.307 99.02 97 4 0.1871 509.372 493.716 0.966 0.990 0.308 9.237-7.194 100.00 213 7 0.2253 416.565 406.462 1.012 0.994 0.279 7.162-5.571 100.00 427 22 0.2069 312.582 303.011 0.996 0.996 0.257 5.546-4.326 100.00 867 58 0.1028 429.130 424.245 1.036 0.998 0.210 4.315-3.360 100.00 1859 96 0.0561 408.107 408.112 1.114 1.002 0.210 3.356-3.002 100.00 1373 60 0.0395 314.341 314.628 1.101 1.005 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-9.1337 ================= 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 : 0.3618 0.2001 0.080 5.408 8.8 119.3 19.9 258 0.000 1_bss: 0.1572 0.1587 0.080 5.408 6.1 116.5 17.1 258 0.000 1_settarget: 0.1572 0.1587 0.080 5.408 6.1 116.5 17.1 258 0.000 1_nqh: 0.1572 0.1587 0.080 5.408 6.1 116.5 17.1 258 0.000 1_weight: 0.1572 0.1587 0.080 5.408 6.1 116.5 17.1 258 0.000 1_xyzrec: 0.1157 0.1840 0.010 0.981 6.1 116.5 17.1 258 0.209 1_adp: 0.1014 0.1843 0.010 0.981 2.3 111.5 17.7 258 0.209 1_regHadp: 0.1008 0.1845 0.010 0.981 2.3 111.5 17.7 258 0.209 1_occ: 0.1008 0.1857 0.010 0.981 2.3 111.5 17.7 258 0.209 2_bss: 0.1005 0.1846 0.010 0.981 1.3 110.6 16.7 258 0.209 2_settarget: 0.1005 0.1846 0.010 0.981 1.3 110.6 16.7 258 0.209 2_updatecdl: 0.1005 0.1846 0.010 1.008 1.3 110.6 16.7 258 0.209 2_nqh: 0.1008 0.1846 0.010 1.008 1.3 110.6 16.7 258 0.214 2_sol: 0.1126 0.1690 0.010 1.008 1.3 110.6 16.1 231 n/a 2_weight: 0.1126 0.1690 0.010 1.008 1.3 110.6 16.1 231 n/a 2_xyzrec: 0.1018 0.1821 0.010 1.005 1.3 110.6 16.1 231 n/a 2_adp: 0.0953 0.1824 0.010 1.005 0.0 108.9 16.9 231 n/a 2_regHadp: 0.0951 0.1824 0.010 1.005 0.0 108.9 16.9 231 n/a 2_occ: 0.0945 0.1815 0.010 1.005 0.0 108.9 16.9 231 n/a 3_bss: 0.0945 0.1813 0.010 1.005 0.0 108.9 16.9 231 n/a 3_settarget: 0.0945 0.1813 0.010 1.005 0.0 108.9 16.9 231 n/a 3_updatecdl: 0.0945 0.1813 0.010 1.014 0.0 108.9 16.9 231 n/a 3_nqh: 0.0949 0.1816 0.010 1.014 0.0 108.9 16.9 231 n/a 3_sol: 0.1047 0.1781 0.010 1.014 0.0 108.9 16.7 238 n/a 3_weight: 0.1047 0.1781 0.010 1.014 0.0 108.9 16.7 238 n/a 3_xyzrec: 0.0944 0.1871 0.011 1.099 0.0 108.9 16.7 238 n/a 3_adp: 0.0895 0.1878 0.011 1.099 0.0 108.1 16.7 238 n/a 3_regHadp: 0.0902 0.1879 0.011 1.099 0.0 108.1 16.7 238 n/a 3_occ: 0.0889 0.1843 0.011 1.099 0.0 108.1 16.7 238 n/a 4_bss: 0.0883 0.1834 0.011 1.099 0.0 108.1 16.7 238 n/a 4_settarget: 0.0883 0.1834 0.011 1.099 0.0 108.1 16.7 238 n/a 4_updatecdl: 0.0883 0.1834 0.011 1.114 0.0 108.1 16.7 238 n/a 4_nqh: 0.0884 0.1836 0.011 1.114 0.0 108.1 16.7 238 n/a 4_sol: 0.0985 0.1875 0.011 1.114 0.0 108.1 16.8 231 n/a 4_weight: 0.0985 0.1875 0.011 1.114 0.0 108.1 16.8 231 n/a 4_xyzrec: 0.0898 0.1908 0.010 1.054 0.0 108.1 16.8 231 n/a 4_adp: 0.0873 0.1896 0.010 1.054 0.0 106.5 17.0 231 n/a 4_regHadp: 0.0877 0.1898 0.010 1.054 0.0 106.5 17.0 231 n/a 4_occ: 0.0866 0.1882 0.010 1.054 0.0 106.5 17.0 231 n/a 5_bss: 0.0864 0.1874 0.010 1.054 0.0 106.5 17.0 231 n/a 5_settarget: 0.0864 0.1874 0.010 1.054 0.0 106.5 17.0 231 n/a 5_updatecdl: 0.0864 0.1874 0.010 1.055 0.0 106.5 17.0 231 n/a 5_setrh: 0.0867 0.1873 0.010 1.055 0.0 106.5 17.0 231 n/a 5_nqh: 0.0868 0.1874 0.010 1.055 0.0 106.5 17.0 231 n/a 5_sol: 0.0980 0.1862 0.010 1.055 0.0 106.5 17.1 233 n/a 5_weight: 0.0980 0.1862 0.010 1.055 0.0 106.5 17.1 233 n/a 5_xyzrec: 0.0913 0.1872 0.010 1.113 0.0 106.5 17.1 233 n/a 5_adp: 0.0891 0.1872 0.010 1.113 0.0 106.6 17.2 233 n/a 5_regHadp: 0.0894 0.1872 0.010 1.113 0.0 106.6 17.2 233 n/a 5_occ: 0.0884 0.1843 0.010 1.113 0.0 106.6 17.2 233 n/a end: 0.0887 0.1836 0.010 1.113 0.0 106.6 17.2 233 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_7410891_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_7410891_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.8500 Refinement macro-cycles (run) : 491.3900 Write final files (write_after_run_outputs) : 9.5400 Total : 504.7800 Total CPU time: 8.78 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:19:07 PST -0800 (1735492747.59 s) Start R-work = 0.1572, R-free = 0.1587 Final R-work = 0.0887, R-free = 0.1836 =============================================================================== Job complete usr+sys time: 534.05 seconds wall clock time: 9 minutes 15.98 seconds (555.98 seconds total)