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_8530424.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_8530424.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8530424.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.53, per 1000 atoms: 0.45 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.29 Conformation dependent library (CDL) restraints added in 108.4 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.67 - 0.91: 556 0.91 - 1.16: 1074 1.16 - 1.40: 593 1.40 - 1.65: 869 1.65 - 1.89: 61 Bond restraints: 3153 Sorted by residual: bond pdb=" N LYS A 130 " pdb=" CA LYS A 130 " ideal model delta sigma weight residual 1.459 1.204 0.256 1.19e-02 7.06e+03 4.61e+02 bond pdb=" N LYS A 63 " pdb=" CA LYS A 63 " ideal model delta sigma weight residual 1.457 1.729 -0.272 1.33e-02 5.65e+03 4.18e+02 bond pdb=" CA HIS A 126 " pdb=" C HIS A 126 " ideal model delta sigma weight residual 1.528 1.729 -0.200 1.11e-02 8.12e+03 3.25e+02 bond pdb=" N THR A 154 " pdb=" CA THR A 154 " ideal model delta sigma weight residual 1.454 1.688 -0.234 1.33e-02 5.65e+03 3.09e+02 bond pdb=" CA BGLU A 90 " pdb=" C BGLU A 90 " ideal model delta sigma weight residual 1.523 1.757 -0.234 1.35e-02 5.49e+03 3.00e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.02: 2729 4.02 - 8.04: 1893 8.04 - 12.06: 872 12.06 - 16.08: 230 16.08 - 20.10: 53 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O VAL A 181 " pdb=" C VAL A 181 " pdb=" N LYS A 182 " ideal model delta sigma weight residual 121.83 138.67 -16.84 1.03e+00 9.43e-01 2.67e+02 angle pdb=" NE ARG A 28 " pdb=" CZ ARG A 28 " pdb=" NH1 ARG A 28 " ideal model delta sigma weight residual 121.50 135.63 -14.13 1.00e+00 1.00e+00 2.00e+02 angle pdb=" NE ARG A 98 " pdb=" CZ ARG A 98 " pdb=" NH1 ARG A 98 " ideal model delta sigma weight residual 121.50 134.91 -13.41 1.00e+00 1.00e+00 1.80e+02 angle pdb=" OE1 GLN A 180 " pdb=" CD GLN A 180 " pdb=" NE2 GLN A 180 " ideal model delta sigma weight residual 122.60 135.98 -13.38 1.00e+00 1.00e+00 1.79e+02 angle pdb=" CA LYS A 130 " pdb=" C LYS A 130 " pdb=" O LYS A 130 " ideal model delta sigma weight residual 120.82 134.78 -13.96 1.05e+00 9.07e-01 1.77e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.66: 1302 16.66 - 33.32: 128 33.32 - 49.98: 33 49.98 - 66.63: 14 66.63 - 83.29: 4 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C LEU A 166 " pdb=" N LEU A 166 " pdb=" CA LEU A 166 " pdb=" CB LEU A 166 " ideal model delta harmonic sigma weight residual -122.60 -144.87 22.27 0 2.50e+00 1.60e-01 7.93e+01 dihedral pdb=" N LEU A 166 " pdb=" C LEU A 166 " pdb=" CA LEU A 166 " pdb=" CB LEU A 166 " ideal model delta harmonic sigma weight residual 122.80 142.71 -19.91 0 2.50e+00 1.60e-01 6.34e+01 dihedral pdb=" C AGLU A 90 " pdb=" N AGLU A 90 " pdb=" CA AGLU A 90 " pdb=" CB AGLU A 90 " ideal model delta harmonic sigma weight residual -122.60 -140.75 18.15 0 2.50e+00 1.60e-01 5.27e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.211: 100 0.211 - 0.422: 81 0.422 - 0.633: 41 0.633 - 0.843: 16 0.843 - 1.054: 5 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA LEU A 166 " pdb=" N LEU A 166 " pdb=" C LEU A 166 " pdb=" CB LEU A 166 " both_signs ideal model delta sigma weight residual False 2.51 1.46 1.05 2.00e-01 2.50e+01 2.78e+01 chirality pdb=" CB ILE A 117 " pdb=" CA ILE A 117 " pdb=" CG1 ILE A 117 " pdb=" CG2 ILE A 117 " both_signs ideal model delta sigma weight residual False 2.64 1.62 1.03 2.00e-01 2.50e+01 2.64e+01 chirality pdb=" CA BLEU A 153 " pdb=" N BLEU A 153 " pdb=" C BLEU A 153 " pdb=" CB BLEU A 153 " both_signs ideal model delta sigma weight residual False 2.51 3.51 -1.00 2.00e-01 2.50e+01 2.48e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.067 2.00e-02 2.50e+03 6.69e-02 1.34e+02 pdb=" CG PHE A 119 " -0.095 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.067 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.079 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.100 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.011 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.104 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.009 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.062 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " -0.026 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " -0.002 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 138 " 0.048 2.00e-02 2.50e+03 6.63e-02 9.88e+01 pdb=" CG HIS A 138 " 0.001 2.00e-02 2.50e+03 pdb=" ND1 HIS A 138 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 HIS A 138 " 0.054 2.00e-02 2.50e+03 pdb=" CE1 HIS A 138 " -0.129 2.00e-02 2.50e+03 pdb=" NE2 HIS A 138 " 0.002 2.00e-02 2.50e+03 pdb=" HD1 HIS A 138 " -0.036 2.00e-02 2.50e+03 pdb=" HD2 HIS A 138 " -0.046 2.00e-02 2.50e+03 pdb=" HE1 HIS A 138 " 0.118 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " -0.031 2.00e-02 2.50e+03 5.53e-02 9.18e+01 pdb=" CG TYR A 141 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " 0.099 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " -0.082 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " 0.021 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " -0.049 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " -0.030 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " 0.056 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " -0.025 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " 0.015 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " 0.086 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.32: 1010 2.32 - 2.89: 8126 2.89 - 3.46: 10504 3.46 - 4.03: 15263 4.03 - 4.60: 21626 Nonbonded interactions: 56529 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.748 2.100 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.755 2.450 x-y,-y,-z-4/3 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.812 2.100 nonbonded pdb=" H THR A 125 " pdb=" HH TYR A 141 " model vdw 1.826 2.100 nonbonded pdb=" HD3 ARG A 5 " pdb="HH11 ARG A 5 " model vdw 1.832 2.270 ... (remaining 56524 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_8530424_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= 0.3610 r_free= 0.1994 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.464864 | | target function (ml) not normalized (work): 22011.781644 | | target function (ml) not normalized (free): 1154.185719 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 49.25 - 3.79 1.00 2500 142 0.3805 0.2174 4.8491 4.9057| | 2: 3.78 - 3.00 1.00 2430 110 0.3371 0.1691 4.0695 4.1597| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 48.83 0.83 0.13 6602.90| | 2: 3.78 - 3.00 2430 110 0.94 11.09 1.48 0.26 441.17| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 371.49 max = 12057.29 mean = 3565.78| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 89.99 mean = 30.23| |phase err.(test): min = 0.00 max = 89.97 mean = 33.22| |-----------------------------------------------------------------------------| ----------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 : 0.084 0.272 1557 Z= 5.609 Angle : 5.432 16.836 2118 Z= 3.905 Chirality : 0.375 1.054 243 Planarity : 0.030 0.083 284 Dihedral : 14.044 83.291 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.24 % Favored : 96.22 % Rotamer: Outliers : 0.62 % Allowed : 3.73 % Favored : 95.65 % Cbeta Deviations : 33.51 % 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: -2.04 (0.50), residues: 224 helix: -2.30 (0.39), residues: 109 sheet: -0.50 (0.86), residues: 30 loop : 0.07 (0.66), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.130 0.031 ARG A 27 TYR 0.116 0.039 TYR A 141 PHE 0.113 0.044 PHE A 119 HIS 0.072 0.030 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= 0.3610 r_free= 0.1994 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.464864 | | target function (ml) not normalized (work): 22011.781644 | | target function (ml) not normalized (free): 1154.185719 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3562 0.3642 0.2091 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3562 0.3642 0.2091 n_refl.: 5182 remove outliers: r(all,work,free)=0.2515 0.2541 0.2091 n_refl.: 5178 overall B=-1.15 to atoms: r(all,work,free)=0.2469 0.2493 0.2072 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1557 0.1555 0.1583 n_refl.: 5178 remove outliers: r(all,work,free)=0.1553 0.1551 0.1583 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 98.94 88 5 0.3848 449.631 410.861 0.631 1.097 0.409 11.894-9.307 99.02 97 4 0.1895 714.274 691.913 0.878 1.090 0.381 9.237-7.194 100.00 213 7 0.2231 584.134 575.420 0.911 1.080 0.362 7.162-5.571 100.00 427 22 0.2375 438.322 423.287 0.897 1.062 0.302 5.546-4.326 100.00 867 58 0.1384 601.754 593.397 0.946 1.033 0.217 4.315-3.360 100.00 1859 96 0.1297 572.274 566.488 1.043 0.985 0.194 3.356-3.002 100.00 1373 60 0.1553 440.790 434.238 1.088 0.936 0.062 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9173 b_overall=-5.1324 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1551 r_free=0.1583 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=0.1552 r_free=0.1586 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 19.051673 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.614600 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 0.1160 0.1791 0.0631 0.010 1.0 1.9 0.5 0.0 0 9.526 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.60 17.91 6.31 3.013 17.710 1.615 0.018 10.21 17.74 7.53 4.827 17.855 1.615 0.014 Individual atomic B min max mean iso aniso Overall: 3.36 113.15 19.01 5.21 1785 0 Protein: 3.36 113.04 16.31 5.21 1519 0 Water: 5.72 113.15 34.67 N/A 258 0 Other: 18.50 37.92 25.87 N/A 8 0 Chain A: 3.36 113.15 19.01 N/A 1785 0 Histogram: Values Number of atoms 3.36 - 14.34 893 14.34 - 25.32 502 25.32 - 36.30 191 36.30 - 47.28 111 47.28 - 58.26 55 58.26 - 69.24 16 69.24 - 80.21 8 80.21 - 91.19 5 91.19 - 102.17 1 102.17 - 113.15 3 =========================== Idealize ADP of riding H ========================== r_work=0.1021 r_free=0.1774 r_work=0.1015 r_free=0.1777 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1015 r_free = 0.1777 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 = 0.1007 r_free = 0.1776 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.1007 r_free= 0.1776 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ls_wunit_k1) (work): 0.013824 | | target function (ls_wunit_k1) not normalized (work): 68.068962 | | target function (ls_wunit_k1) not normalized (free): 10.406975 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1046 0.1007 0.1776 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2157 0.2159 0.2249 n_refl.: 5176 remove outliers: r(all,work,free)=0.2157 0.2159 0.2249 n_refl.: 5176 overall B=-1.09 to atoms: r(all,work,free)=0.2108 0.2108 0.2235 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.1049 0.1010 0.1774 n_refl.: 5176 remove outliers: r(all,work,free)=0.1049 0.1010 0.1774 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 0.3414 315.839 295.848 0.633 1.028 0.377 11.894-9.307 99.02 97 4 0.1512 501.736 494.993 0.931 1.027 0.361 9.237-7.194 100.00 213 7 0.1644 410.320 409.702 0.969 1.025 0.331 7.162-5.571 100.00 427 22 0.1611 307.896 304.509 0.946 1.019 0.292 5.546-4.326 100.00 867 58 0.0906 422.697 419.924 0.966 1.010 0.197 4.315-3.360 100.00 1859 96 0.0764 401.989 402.009 1.031 0.995 0.193 3.356-3.002 100.00 1373 60 0.1000 309.629 308.061 1.028 0.979 0.051 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-4.9239 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1010 r_free=0.1774 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1010 r_free=0.1774 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1010 r_free=0.1774 | n_water=258 | time (s): 0.580 (total time: 0.580) Filter (dist) r_work=0.1043 r_free=0.1779 | n_water=247 | time (s): 21.050 (total time: 21.630) Filter (q & B) r_work=0.1043 r_free=0.1780 | n_water=244 | time (s): 1.580 (total time: 23.210) Compute maps r_work=0.1043 r_free=0.1780 | n_water=244 | time (s): 0.570 (total time: 23.780) Filter (map) r_work=0.1346 r_free=0.1868 | n_water=139 | time (s): 1.500 (total time: 25.280) Find peaks r_work=0.1346 r_free=0.1868 | n_water=139 | time (s): 0.460 (total time: 25.740) Add new water r_work=0.1707 r_free=0.2189 | n_water=227 | time (s): 1.200 (total time: 26.940) Refine new water occ: r_work=0.1183 r_free=0.1678 adp: r_work=0.1158 r_free=0.1694 occ: r_work=0.1153 r_free=0.1663 adp: r_work=0.1141 r_free=0.1677 occ: r_work=0.1140 r_free=0.1667 adp: r_work=0.1140 r_free=0.1667 ADP+occupancy (water only), MIN, final r_work=0.1140 r_free=0.1667 r_work=0.1140 r_free=0.1667 | n_water=227 | time (s): 4.850 (total time: 31.790) Filter (q & B) r_work=0.1140 r_free=0.1667 | n_water=227 | time (s): 1.000 (total time: 32.790) Filter (dist only) r_work=0.1144 r_free=0.1665 | n_water=225 | time (s): 17.780 (total time: 50.570) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.383300 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.482765 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 0.1022 0.1796 0.0773 0.009 1.0 4.2 0.5 0.6 0 11.192 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.22 17.96 7.73 4.732 18.294 2.483 0.014 9.52 18.35 8.83 5.475 18.600 2.483 0.013 Individual atomic B min max mean iso aniso Overall: 0.80 110.27 17.69 6.40 1752 0 Protein: 2.33 110.27 16.26 6.40 1519 0 Water: 0.80 64.34 27.06 N/A 225 0 Other: 13.96 35.08 24.38 N/A 8 0 Chain A: 0.80 110.27 16.93 N/A 1664 0 Chain S: 1.99 58.29 31.98 N/A 88 0 Histogram: Values Number of atoms 0.80 - 11.75 664 11.75 - 22.70 679 22.70 - 33.64 231 33.64 - 44.59 103 44.59 - 55.54 41 55.54 - 66.48 21 66.48 - 77.43 6 77.43 - 88.38 3 88.38 - 99.33 2 99.33 - 110.27 2 =========================== Idealize ADP of riding H ========================== r_work=0.0952 r_free=0.1835 r_work=0.0950 r_free=0.1839 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0950 r_free = 0.1839 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0947 r_free = 0.1831 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.29 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= 0.0947 r_free= 0.1831 coordinate error (max.-lik. estimate): 0.31 A | | | | normalized target function (ls_wunit_k1) (work): 0.012210 | | target function (ls_wunit_k1) not normalized (work): 60.119674 | | target function (ls_wunit_k1) not normalized (free): 10.419419 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0992 0.0947 0.1831 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2193 0.2197 0.2263 n_refl.: 5176 remove outliers: r(all,work,free)=0.2193 0.2197 0.2263 n_refl.: 5176 overall B=-0.80 to atoms: r(all,work,free)=0.2155 0.2158 0.2248 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0992 0.0947 0.1847 n_refl.: 5176 remove outliers: r(all,work,free)=0.0992 0.0947 0.1847 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 0.3279 315.839 301.577 0.681 1.007 0.388 11.894-9.307 99.02 97 4 0.1420 501.736 493.630 0.940 1.009 0.346 9.237-7.194 100.00 213 7 0.1498 410.320 410.052 0.977 1.008 0.305 7.162-5.571 100.00 427 22 0.1423 307.896 304.344 0.957 1.007 0.292 5.546-4.326 100.00 867 58 0.0793 422.697 419.404 0.971 1.004 0.232 4.315-3.360 100.00 1859 96 0.0738 401.989 402.256 1.024 0.998 0.193 3.356-3.002 100.00 1373 60 0.0977 309.629 309.862 1.010 0.993 0.061 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-4.7899 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0947 r_free=0.1847 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=0.0950 r_free=0.1847 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0950 r_free=0.1847 | n_water=225 | time (s): 0.460 (total time: 0.460) Filter (dist) r_work=0.0974 r_free=0.1837 | n_water=218 | time (s): 18.000 (total time: 18.460) Filter (q & B) r_work=0.1006 r_free=0.1833 | n_water=217 | time (s): 1.510 (total time: 19.970) Compute maps r_work=0.1006 r_free=0.1833 | n_water=217 | time (s): 0.490 (total time: 20.460) Filter (map) r_work=0.1264 r_free=0.1889 | n_water=144 | time (s): 1.280 (total time: 21.740) Find peaks r_work=0.1264 r_free=0.1889 | n_water=144 | time (s): 0.480 (total time: 22.220) Add new water r_work=0.1657 r_free=0.2250 | n_water=230 | time (s): 1.480 (total time: 23.700) Refine new water occ: r_work=0.1060 r_free=0.1781 adp: r_work=0.1058 r_free=0.1794 occ: r_work=0.1047 r_free=0.1775 adp: r_work=0.1046 r_free=0.1782 occ: r_work=0.1036 r_free=0.1764 adp: r_work=0.1035 r_free=0.1768 ADP+occupancy (water only), MIN, final r_work=0.1035 r_free=0.1768 r_work=0.1035 r_free=0.1768 | n_water=230 | time (s): 10.540 (total time: 34.240) Filter (q & B) r_work=0.1038 r_free=0.1771 | n_water=228 | time (s): 1.510 (total time: 35.750) Filter (dist only) r_work=0.1050 r_free=0.1766 | n_water=224 | time (s): 16.130 (total time: 51.880) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.099227 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.215698 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 0.0955 0.1858 0.0903 0.010 1.0 4.2 0.5 0.6 0 0.550 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.55 18.58 9.03 5.436 18.256 0.216 5.134 9.09 18.37 9.29 7.181 18.244 0.216 5.035 Individual atomic B min max mean iso aniso Overall: 0.00 108.95 16.67 8.72 1751 0 Protein: 0.00 108.95 15.52 8.70 1519 0 Water: 0.00 58.75 24.17 N/A 224 0 Other: 8.16 40.92 24.81 N/A 8 0 Chain A: 0.00 108.95 16.10 N/A 1649 0 Chain S: 0.00 58.75 25.93 N/A 102 0 Histogram: Values Number of atoms 0.00 - 10.90 637 10.90 - 21.79 699 21.79 - 32.68 236 32.68 - 43.58 115 43.58 - 54.47 32 54.47 - 65.37 17 65.37 - 76.26 7 76.26 - 87.16 3 87.16 - 98.05 4 98.05 - 108.95 1 =========================== Idealize ADP of riding H ========================== r_work=0.0909 r_free=0.1837 r_work=0.0914 r_free=0.1846 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0914 r_free = 0.1846 target_work(ml) = 5.038 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0903 r_free = 0.1828 target_work(ml) = 5.031 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.0903 r_free= 0.1828 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ml) (work): 5.031487 | | target function (ml) not normalized (work): 24775.039906 | | target function (ml) not normalized (free): 1818.293328 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0951 0.0903 0.1828 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2174 0.2184 0.2173 n_refl.: 5176 remove outliers: r(all,work,free)=0.2174 0.2184 0.2173 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2174 0.2184 0.2173 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0946 0.0900 0.1816 n_refl.: 5176 remove outliers: r(all,work,free)=0.0942 0.0895 0.1816 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 0.3523 315.262 290.756 0.612 0.992 0.340 11.894-9.307 99.02 97 4 0.1854 501.736 484.942 0.956 0.996 0.333 9.237-7.194 100.00 213 7 0.1892 410.320 406.005 1.003 0.998 0.285 7.162-5.571 100.00 427 22 0.1880 307.896 298.460 0.984 0.999 0.280 5.546-4.326 100.00 867 58 0.0911 422.697 417.958 1.006 1.000 0.250 4.315-3.360 100.00 1859 96 0.0600 401.989 401.532 1.066 1.002 0.200 3.356-3.002 100.00 1373 60 0.0614 309.629 309.607 1.049 1.004 0.050 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9175 b_overall=-6.9472 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0895 r_free=0.1816 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A A 76 ASN B Total number of N/Q/H flips: 2 r_work=0.0897 r_free=0.1817 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0897 r_free=0.1817 | n_water=224 | time (s): 0.640 (total time: 0.640) Filter (dist) r_work=0.0904 r_free=0.1816 | n_water=223 | time (s): 19.950 (total time: 20.590) Filter (q & B) r_work=0.0948 r_free=0.1847 | n_water=221 | time (s): 1.480 (total time: 22.070) Compute maps r_work=0.0948 r_free=0.1847 | n_water=221 | time (s): 0.480 (total time: 22.550) Filter (map) r_work=0.1237 r_free=0.1913 | n_water=149 | time (s): 1.530 (total time: 24.080) Find peaks r_work=0.1237 r_free=0.1913 | n_water=149 | time (s): 0.470 (total time: 24.550) Add new water r_work=0.1554 r_free=0.2220 | n_water=223 | time (s): 1.630 (total time: 26.180) Refine new water occ: r_work=0.1020 r_free=0.1826 adp: r_work=0.1018 r_free=0.1834 occ: r_work=0.1008 r_free=0.1810 adp: r_work=0.1008 r_free=0.1820 occ: r_work=0.0998 r_free=0.1795 adp: r_work=0.0998 r_free=0.1807 ADP+occupancy (water only), MIN, final r_work=0.0998 r_free=0.1807 r_work=0.0998 r_free=0.1807 | n_water=223 | time (s): 11.990 (total time: 38.170) Filter (q & B) r_work=0.0998 r_free=0.1807 | n_water=223 | time (s): 0.980 (total time: 39.150) Filter (dist only) r_work=0.1010 r_free=0.1820 | n_water=222 | time (s): 17.960 (total time: 57.110) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.079451 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.207759 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 0.0920 0.1887 0.0967 0.011 1.1 4.8 0.5 0.0 0 0.540 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.20 18.87 9.67 6.830 18.274 0.208 5.014 8.94 18.98 10.04 7.928 18.373 0.208 4.944 Individual atomic B min max mean iso aniso Overall: 0.00 108.38 16.99 10.28 1749 0 Protein: 0.00 108.38 15.94 10.27 1519 0 Water: 0.00 57.83 23.84 N/A 222 0 Other: 11.27 42.86 25.46 N/A 8 0 Chain A: 0.00 108.38 16.42 N/A 1636 0 Chain S: 0.00 57.83 25.26 N/A 113 0 Histogram: Values Number of atoms 0.00 - 10.84 617 10.84 - 21.68 682 21.68 - 32.51 259 32.51 - 43.35 122 43.35 - 54.19 36 54.19 - 65.03 16 65.03 - 75.87 8 75.87 - 86.70 4 86.70 - 97.54 4 97.54 - 108.38 1 =========================== Idealize ADP of riding H ========================== r_work=0.0894 r_free=0.1898 r_work=0.0898 r_free=0.1901 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0898 r_free = 0.1901 target_work(ml) = 4.948 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0887 r_free = 0.1886 target_work(ml) = 4.940 | | occupancies: max = 1.00 min = 0.23 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= 0.0887 r_free= 0.1886 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ml) (work): 4.939797 | | target function (ml) not normalized (work): 24313.683149 | | target function (ml) not normalized (free): 2090.965313 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0937 0.0887 0.1886 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2108 0.2108 0.2230 n_refl.: 5174 remove outliers: r(all,work,free)=0.2108 0.2108 0.2230 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2108 0.2108 0.2230 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0938 0.0887 0.1890 n_refl.: 5174 remove outliers: r(all,work,free)=0.0938 0.0887 0.1890 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 0.3728 315.262 289.754 0.592 0.991 0.324 11.894-9.307 99.02 97 4 0.1897 501.736 487.543 0.952 0.995 0.320 9.237-7.194 100.00 213 7 0.2089 410.320 403.028 1.001 0.998 0.280 7.162-5.571 100.00 427 22 0.2026 307.896 298.190 0.993 0.999 0.280 5.546-4.326 100.00 867 58 0.0987 422.697 417.069 1.017 1.000 0.240 4.315-3.360 100.00 1859 96 0.0569 401.989 401.727 1.086 1.002 0.210 3.356-3.002 100.00 1373 60 0.0467 309.629 309.462 1.071 1.003 0.050 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.8808 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0887 r_free=0.1890 After: r_work=0.0890 r_free=0.1889 ================================== NQH flips ================================== r_work=0.0890 r_free=0.1889 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0890 r_free=0.1889 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0890 r_free=0.1889 | n_water=222 | time (s): 0.530 (total time: 0.530) Filter (dist) r_work=0.0909 r_free=0.1882 | n_water=218 | time (s): 17.530 (total time: 18.060) Filter (q & B) r_work=0.0985 r_free=0.1887 | n_water=215 | time (s): 1.700 (total time: 19.760) Compute maps r_work=0.0985 r_free=0.1887 | n_water=215 | time (s): 0.500 (total time: 20.260) Filter (map) r_work=0.1285 r_free=0.1975 | n_water=147 | time (s): 1.790 (total time: 22.050) Find peaks r_work=0.1285 r_free=0.1975 | n_water=147 | time (s): 0.580 (total time: 22.630) Add new water r_work=0.1580 r_free=0.2274 | n_water=216 | time (s): 1.560 (total time: 24.190) Refine new water occ: r_work=0.1024 r_free=0.1937 adp: r_work=0.1019 r_free=0.1951 occ: r_work=0.1012 r_free=0.1931 adp: r_work=0.1012 r_free=0.1941 occ: r_work=0.1005 r_free=0.1920 adp: r_work=0.1005 r_free=0.1929 ADP+occupancy (water only), MIN, final r_work=0.1005 r_free=0.1929 r_work=0.1005 r_free=0.1929 | n_water=216 | time (s): 12.130 (total time: 36.320) Filter (q & B) r_work=0.1005 r_free=0.1930 | n_water=215 | time (s): 1.490 (total time: 37.810) Filter (dist only) r_work=0.1005 r_free=0.1930 | n_water=215 | time (s): 14.470 (total time: 52.280) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.985089 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.206945 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 0.0947 0.1931 0.0984 0.010 1.1 7.0 0.5 0.0 0 0.493 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.47 19.31 9.84 7.864 18.653 0.207 5.018 9.25 19.75 10.50 8.776 18.763 0.207 4.958 Individual atomic B min max mean iso aniso Overall: 0.00 108.47 17.28 11.53 1742 0 Protein: 0.00 108.47 16.29 11.51 1519 0 Water: 0.00 59.59 23.93 N/A 215 0 Other: 9.22 42.19 25.75 N/A 8 0 Chain A: 0.00 108.47 16.67 N/A 1627 0 Chain S: 0.00 59.59 25.82 N/A 115 0 Histogram: Values Number of atoms 0.00 - 10.85 623 10.85 - 21.69 651 21.69 - 32.54 276 32.54 - 43.39 118 43.39 - 54.24 29 54.24 - 65.08 22 65.08 - 75.93 10 75.93 - 86.78 6 86.78 - 97.63 5 97.63 - 108.47 2 =========================== Idealize ADP of riding H ========================== r_work=0.0925 r_free=0.1975 r_work=0.0927 r_free=0.1981 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0927 r_free = 0.1981 target_work(ml) = 4.961 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0921 r_free = 0.1961 target_work(ml) = 4.956 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0921 r_free= 0.1961 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ml) (work): 4.956436 | | target function (ml) not normalized (work): 24395.575984 | | target function (ml) not normalized (free): 2091.141999 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1300 0.2015 5.5202 6.2233| | 2: 3.78 - 3.00 1.00 2430 110 0.0459 0.1868 4.3783 10.977| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 12.51 1.00 0.94 12578.47| | 2: 3.78 - 3.00 2430 110 0.99 2.06 1.00 0.96 936.80| |alpha: min = 0.92 max = 0.96 mean = 0.95| |beta: min = 603.24 max = 20918.13 mean = 6830.96| |figures of merit: min = 0.01 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.10 mean = 7.35| |phase err.(test): min = 0.00 max = 86.04 mean = 7.98| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0974 0.0921 0.1961 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2163 0.2166 0.2238 n_refl.: 5174 remove outliers: r(all,work,free)=0.2163 0.2166 0.2238 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2163 0.2166 0.2238 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0972 0.0920 0.1969 n_refl.: 5174 remove outliers: r(all,work,free)=0.0972 0.0920 0.1969 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 0.3894 315.262 284.229 0.596 0.988 0.309 11.894-9.307 99.02 97 4 0.1923 501.736 486.479 1.002 0.994 0.304 9.237-7.194 100.00 213 7 0.2213 410.320 401.996 1.053 0.997 0.300 7.162-5.571 100.00 427 22 0.2080 307.896 298.681 1.044 0.998 0.300 5.546-4.326 100.00 867 58 0.1050 422.697 416.161 1.071 1.000 0.236 4.315-3.360 100.00 1859 96 0.0604 401.989 401.748 1.154 1.002 0.222 3.356-3.002 100.00 1373 60 0.0437 309.629 309.353 1.141 1.003 0.040 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-8.8529 ================= 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 : 0.3610 0.1994 0.084 5.432 8.8 119.3 19.9 258 0.000 1_bss: 0.1551 0.1583 0.084 5.432 7.7 118.2 18.7 258 0.000 1_settarget: 0.1551 0.1583 0.084 5.432 7.7 118.2 18.7 258 0.000 1_nqh: 0.1552 0.1586 0.084 5.432 7.7 118.2 18.7 258 0.003 1_weight: 0.1552 0.1586 0.084 5.432 7.7 118.2 18.7 258 0.003 1_xyzrec: 0.1160 0.1791 0.010 0.971 7.7 118.2 18.7 258 0.211 1_adp: 0.1021 0.1774 0.010 0.971 3.4 113.2 19.0 258 0.211 1_regHadp: 0.1015 0.1777 0.010 0.971 3.4 113.2 19.0 258 0.211 1_occ: 0.1007 0.1776 0.010 0.971 3.4 113.2 19.0 258 0.211 2_bss: 0.1010 0.1774 0.010 0.971 2.3 112.1 17.9 258 0.211 2_settarget: 0.1010 0.1774 0.010 0.971 2.3 112.1 17.9 258 0.211 2_updatecdl: 0.1010 0.1774 0.010 0.989 2.3 112.1 17.9 258 0.211 2_nqh: 0.1010 0.1774 0.010 0.989 2.3 112.1 17.9 258 0.211 2_sol: 0.1144 0.1665 0.010 0.989 1.0 111.9 17.1 225 n/a 2_weight: 0.1144 0.1665 0.010 0.989 1.0 111.9 17.1 225 n/a 2_xyzrec: 0.1022 0.1796 0.009 0.967 1.0 111.9 17.1 225 n/a 2_adp: 0.0952 0.1835 0.009 0.967 0.8 110.3 17.7 225 n/a 2_regHadp: 0.0950 0.1839 0.009 0.967 0.8 110.3 17.7 225 n/a 2_occ: 0.0947 0.1831 0.009 0.967 0.8 110.3 17.7 225 n/a 3_bss: 0.0947 0.1847 0.009 0.967 0.0 109.5 16.9 225 n/a 3_settarget: 0.0947 0.1847 0.009 0.967 0.0 109.5 16.9 225 n/a 3_updatecdl: 0.0947 0.1847 0.009 0.973 0.0 109.5 16.9 225 n/a 3_nqh: 0.0950 0.1847 0.009 0.973 0.0 109.5 16.9 225 n/a 3_sol: 0.1050 0.1766 0.009 0.973 1.2 109.5 16.7 224 n/a 3_weight: 0.1050 0.1766 0.009 0.973 1.2 109.5 16.7 224 n/a 3_xyzrec: 0.0955 0.1858 0.010 1.049 1.2 109.5 16.7 224 n/a 3_adp: 0.0909 0.1837 0.010 1.049 0.0 108.9 16.7 224 n/a 3_regHadp: 0.0914 0.1846 0.010 1.049 0.0 108.9 16.7 224 n/a 3_occ: 0.0903 0.1828 0.010 1.049 0.0 108.9 16.7 224 n/a 4_bss: 0.0895 0.1816 0.010 1.049 0.0 108.9 16.7 224 n/a 4_settarget: 0.0895 0.1816 0.010 1.049 0.0 108.9 16.7 224 n/a 4_updatecdl: 0.0895 0.1816 0.010 1.058 0.0 108.9 16.7 224 n/a 4_nqh: 0.0897 0.1817 0.010 1.058 0.0 108.9 16.7 224 n/a 4_sol: 0.1010 0.1820 0.010 1.058 0.0 108.9 16.8 222 n/a 4_weight: 0.1010 0.1820 0.010 1.058 0.0 108.9 16.8 222 n/a 4_xyzrec: 0.0920 0.1887 0.011 1.056 0.0 108.9 16.8 222 n/a 4_adp: 0.0894 0.1898 0.011 1.056 0.0 108.4 17.0 222 n/a 4_regHadp: 0.0898 0.1901 0.011 1.056 0.0 108.4 17.0 222 n/a 4_occ: 0.0887 0.1886 0.011 1.056 0.0 108.4 17.0 222 n/a 5_bss: 0.0887 0.1890 0.011 1.056 0.0 108.4 17.0 222 n/a 5_settarget: 0.0887 0.1890 0.011 1.056 0.0 108.4 17.0 222 n/a 5_updatecdl: 0.0887 0.1890 0.011 1.049 0.0 108.4 17.0 222 n/a 5_setrh: 0.0890 0.1889 0.011 1.049 0.0 108.4 17.0 222 n/a 5_nqh: 0.0890 0.1889 0.011 1.049 0.0 108.4 17.0 222 n/a 5_sol: 0.1005 0.1930 0.011 1.049 0.0 108.4 17.1 215 n/a 5_weight: 0.1005 0.1930 0.011 1.049 0.0 108.4 17.1 215 n/a 5_xyzrec: 0.0947 0.1931 0.010 1.074 0.0 108.4 17.1 215 n/a 5_adp: 0.0925 0.1975 0.010 1.074 0.0 108.5 17.3 215 n/a 5_regHadp: 0.0927 0.1981 0.010 1.074 0.0 108.5 17.3 215 n/a 5_occ: 0.0921 0.1961 0.010 1.074 0.0 108.5 17.3 215 n/a end: 0.0920 0.1969 0.010 1.074 0.0 108.5 17.3 215 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_8530424_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_8530424_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.2100 Refinement macro-cycles (run) : 479.5100 Write final files (write_after_run_outputs) : 11.1100 Total : 493.8300 Total CPU time: 8.56 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:18:55 PST -0800 (1735492735.23 s) Start R-work = 0.1551, R-free = 0.1583 Final R-work = 0.0920, R-free = 0.1969 =============================================================================== Job complete usr+sys time: 521.69 seconds wall clock time: 9 minutes 4.21 seconds (544.21 seconds total)