Starting phenix.refine on Sun Dec 29 09:10:03 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7798058.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 { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7798058.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7798058.pdb" 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" } 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: 1.97, per 1000 atoms: 0.58 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: 0.41 Conformation dependent library (CDL) restraints added in 127.4 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.64 - 0.92: 590 0.92 - 1.21: 1105 1.21 - 1.49: 885 1.49 - 1.78: 562 1.78 - 2.06: 11 Bond restraints: 3153 Sorted by residual: bond pdb=" C VAL A 186 " pdb=" N LEU A 187 " ideal model delta sigma weight residual 1.330 1.069 0.262 1.38e-02 5.25e+03 3.59e+02 bond pdb=" C VAL A 123 " pdb=" O VAL A 123 " ideal model delta sigma weight residual 1.235 1.417 -0.182 1.02e-02 9.61e+03 3.20e+02 bond pdb=" CA LYS A 182 " pdb=" C LYS A 182 " ideal model delta sigma weight residual 1.523 1.283 0.240 1.35e-02 5.49e+03 3.16e+02 bond pdb=" C ILE A 9 " pdb=" O ILE A 9 " ideal model delta sigma weight residual 1.236 1.043 0.193 1.09e-02 8.42e+03 3.13e+02 bond pdb=" N SER A 155 " pdb=" CA SER A 155 " ideal model delta sigma weight residual 1.457 1.668 -0.211 1.20e-02 6.94e+03 3.09e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.17: 2906 4.17 - 8.33: 1891 8.33 - 12.49: 756 12.49 - 16.65: 197 16.65 - 20.81: 27 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O VAL A 50 " pdb=" C VAL A 50 " pdb=" N VAL A 51 " ideal model delta sigma weight residual 122.67 136.07 -13.40 1.02e+00 9.61e-01 1.73e+02 angle pdb=" O ALA A 114 " pdb=" C ALA A 114 " pdb=" N HIS A 115 " ideal model delta sigma weight residual 122.12 135.44 -13.32 1.06e+00 8.90e-01 1.58e+02 angle pdb=" CA AGLN A 80 " pdb=" C AGLN A 80 " pdb=" N ASN A 81 " ideal model delta sigma weight residual 117.39 102.01 15.38 1.24e+00 6.50e-01 1.54e+02 angle pdb=" NE ARG A 156 " pdb=" CZ ARG A 156 " pdb=" NH1 ARG A 156 " ideal model delta sigma weight residual 121.50 109.34 12.16 1.00e+00 1.00e+00 1.48e+02 angle pdb=" O ALYS A 99 " pdb=" C ALYS A 99 " pdb=" N GLY A 100 " ideal model delta sigma weight residual 122.59 138.13 -15.54 1.33e+00 5.65e-01 1.37e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.49: 1292 16.49 - 32.99: 135 32.99 - 49.48: 36 49.48 - 65.97: 16 65.97 - 82.46: 2 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C THR A 19 " pdb=" N THR A 19 " pdb=" CA THR A 19 " pdb=" CB THR A 19 " ideal model delta harmonic sigma weight residual -122.00 -141.58 19.58 0 2.50e+00 1.60e-01 6.13e+01 dihedral pdb=" C ALA A 167 " pdb=" N ALA A 167 " pdb=" CA ALA A 167 " pdb=" CB ALA A 167 " ideal model delta harmonic sigma weight residual -122.60 -140.97 18.37 0 2.50e+00 1.60e-01 5.40e+01 dihedral pdb=" C ALA A 61 " pdb=" N ALA A 61 " pdb=" CA ALA A 61 " pdb=" CB ALA A 61 " ideal model delta harmonic sigma weight residual -122.60 -140.02 17.42 0 2.50e+00 1.60e-01 4.85e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.005 - 0.194: 104 0.194 - 0.384: 58 0.384 - 0.574: 37 0.574 - 0.764: 37 0.764 - 0.954: 7 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA VAL A 35 " pdb=" N VAL A 35 " pdb=" C VAL A 35 " pdb=" CB VAL A 35 " both_signs ideal model delta sigma weight residual False 2.44 3.40 -0.95 2.00e-01 2.50e+01 2.28e+01 chirality pdb=" CG LEU A 72 " pdb=" CB LEU A 72 " pdb=" CD1 LEU A 72 " pdb=" CD2 LEU A 72 " both_signs ideal model delta sigma weight residual False -2.59 -1.68 -0.91 2.00e-01 2.50e+01 2.05e+01 chirality pdb=" CA LYS A 32 " pdb=" N LYS A 32 " pdb=" C LYS A 32 " pdb=" CB LYS A 32 " both_signs ideal model delta sigma weight residual False 2.51 3.39 -0.88 2.00e-01 2.50e+01 1.94e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " 0.037 2.00e-02 2.50e+03 6.63e-02 1.32e+02 pdb=" CG PHE A 162 " 0.111 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " -0.053 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " -0.099 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " -0.045 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " -0.063 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " 0.109 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " -0.013 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " -0.037 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " 0.013 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " 0.075 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " -0.046 2.00e-02 2.50e+03 6.51e-02 1.27e+02 pdb=" CG TYR A 139 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " -0.080 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " 0.053 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.057 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " -0.090 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.028 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " 0.087 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " 0.104 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.075 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " 0.024 2.00e-02 2.50e+03 6.37e-02 1.22e+02 pdb=" CG TYR A 141 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " -0.097 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " -0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " -0.056 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " 0.080 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " -0.118 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " 0.033 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " 0.010 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " -0.009 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " 0.103 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " 0.004 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.32: 1068 2.32 - 2.89: 8155 2.89 - 3.46: 10516 3.46 - 4.03: 15147 4.03 - 4.60: 21742 Nonbonded interactions: 56628 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.756 2.100 nonbonded pdb=" HD2 LYS A 32 " pdb=" HZ2 LYS A 32 " model vdw 1.796 2.270 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.818 2.450 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.826 2.450 nonbonded pdb=" O ALA A 6 " pdb=" H THR A 34 " model vdw 1.830 2.450 ... (remaining 56623 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_7798058_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= 0.3620 r_free= 0.2080 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.462663 | | target function (ml) not normalized (work): 22000.930283 | | target function (ml) not normalized (free): 1160.789940 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2241 4.8487 4.9332| | 2: 3.78 - 3.00 1.00 2430 110 0.3406 0.1809 4.0655 4.1843| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 48.88 0.83 0.13 6612.79| | 2: 3.78 - 3.00 2430 110 0.94 11.13 1.48 0.26 438.59| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 366.55 max = 12069.03 mean = 3569.52| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 90.00 mean = 30.28| |phase err.(test): min = 0.00 max = 89.95 mean = 33.35| |-----------------------------------------------------------------------------| ----------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 : 0.081 0.262 1557 Z= 5.405 Angle : 5.160 17.447 2118 Z= 3.572 Chirality : 0.380 0.954 243 Planarity : 0.030 0.097 284 Dihedral : 13.674 82.465 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 1.08 % Allowed : 3.24 % Favored : 95.68 % Rotamer: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Cbeta Deviations : 24.86 % 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: -2.66 (0.47), residues: 224 helix: -2.44 (0.36), residues: 108 sheet: -1.19 (0.71), residues: 38 loop : -0.58 (0.67), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.101 0.025 ARG A 98 TYR 0.098 0.044 TYR A 141 PHE 0.121 0.043 PHE A 162 HIS 0.060 0.029 HIS A 115 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= 0.3620 r_free= 0.2080 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.462663 | | target function (ml) not normalized (work): 22000.930283 | | target function (ml) not normalized (free): 1160.789940 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3577 0.3651 0.2156 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3577 0.3651 0.2156 n_refl.: 5182 remove outliers: r(all,work,free)=0.2527 0.2549 0.2156 n_refl.: 5178 overall B=-2.82 to atoms: r(all,work,free)=0.2419 0.2438 0.2108 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1568 0.1565 0.1629 n_refl.: 5178 remove outliers: r(all,work,free)=0.1566 0.1563 0.1629 n_refl.: 5177 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 100.00 89 5 0.4102 444.919 404.246 0.681 1.009 0.400 11.894-9.307 99.02 97 4 0.1891 714.263 690.018 0.965 1.011 0.393 9.237-7.194 100.00 213 7 0.2171 584.125 570.860 0.982 1.010 0.358 7.162-5.571 100.00 427 22 0.2328 438.315 422.617 0.940 1.008 0.336 5.546-4.326 100.00 867 58 0.1379 601.744 590.702 0.974 1.005 0.220 4.315-3.360 100.00 1859 96 0.1311 572.265 567.327 1.026 0.998 0.189 3.356-3.002 100.00 1373 60 0.1597 440.783 435.462 1.015 0.992 0.086 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9170 b_overall=-4.9152 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1563 r_free=0.1629 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1563 r_free=0.1629 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 18.657556 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.845998 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 0.1165 0.1847 0.0682 0.010 1.0 3.5 0.5 0.0 0 9.329 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.65 18.47 6.82 3.013 16.040 1.846 0.018 10.25 18.29 8.04 4.987 16.354 1.846 0.015 Individual atomic B min max mean iso aniso Overall: 2.26 111.48 17.66 5.31 1785 0 Protein: 2.26 110.75 14.97 5.29 1519 0 Water: 4.05 111.48 33.29 N/A 258 0 Other: 15.93 40.97 24.19 N/A 8 0 Chain A: 2.26 111.48 17.66 N/A 1785 0 Histogram: Values Number of atoms 2.26 - 13.18 895 13.18 - 24.11 503 24.11 - 35.03 190 35.03 - 45.95 106 45.95 - 56.87 59 56.87 - 67.79 15 67.79 - 78.71 8 78.71 - 89.64 5 89.64 - 100.56 1 100.56 - 111.48 3 =========================== Idealize ADP of riding H ========================== r_work=0.1025 r_free=0.1829 r_work=0.1019 r_free=0.1834 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1019 r_free = 0.1834 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1021 r_free = 0.1842 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5177 (all), 4.87 % free)-------------| | | | r_work= 0.1021 r_free= 0.1842 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ls_wunit_k1) (work): 0.014328 | | target function (ls_wunit_k1) not normalized (work): 70.566246 | | target function (ls_wunit_k1) not normalized (free): 10.832420 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1063 0.1021 0.1842 n_refl.: 5177 re-set all scales: r(all,work,free)=0.2139 0.2140 0.2247 n_refl.: 5177 remove outliers: r(all,work,free)=0.2139 0.2140 0.2247 n_refl.: 5177 overall B=-1.06 to atoms: r(all,work,free)=0.2093 0.2091 0.2235 n_refl.: 5177 bulk-solvent and scaling: r(all,work,free)=0.1058 0.1017 0.1819 n_refl.: 5177 remove outliers: r(all,work,free)=0.1054 0.1013 0.1819 n_refl.: 5175 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3322 317.475 294.039 0.631 0.999 0.360 11.894-9.307 99.02 97 4 0.1543 510.718 501.096 0.965 1.001 0.361 9.237-7.194 100.00 213 7 0.1677 417.666 417.932 1.000 1.002 0.316 7.162-5.571 100.00 427 22 0.1655 313.407 309.420 0.959 1.002 0.312 5.546-4.326 100.00 867 58 0.0905 430.264 426.931 0.975 1.001 0.202 4.315-3.360 100.00 1859 96 0.0766 409.186 409.256 1.023 1.001 0.194 3.356-3.002 100.00 1373 60 0.0997 315.172 314.296 1.000 1.000 0.072 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9174 b_overall=-4.7183 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1013 r_free=0.1819 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=0.1015 r_free=0.1821 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1015 r_free=0.1821 | n_water=258 | time (s): 0.670 (total time: 0.670) Filter (dist) r_work=0.1032 r_free=0.1791 | n_water=249 | time (s): 21.020 (total time: 21.690) Filter (q & B) r_work=0.1033 r_free=0.1798 | n_water=247 | time (s): 1.870 (total time: 23.560) Compute maps r_work=0.1033 r_free=0.1798 | n_water=247 | time (s): 0.510 (total time: 24.070) Filter (map) r_work=0.1333 r_free=0.1940 | n_water=147 | time (s): 1.350 (total time: 25.420) Find peaks r_work=0.1333 r_free=0.1940 | n_water=147 | time (s): 0.410 (total time: 25.830) Add new water r_work=0.1699 r_free=0.2309 | n_water=237 | time (s): 1.430 (total time: 27.260) Refine new water occ: r_work=0.1175 r_free=0.1737 adp: r_work=0.1146 r_free=0.1738 occ: r_work=0.1141 r_free=0.1711 adp: r_work=0.1127 r_free=0.1718 occ: r_work=0.1126 r_free=0.1696 adp: r_work=0.1123 r_free=0.1702 ADP+occupancy (water only), MIN, final r_work=0.1123 r_free=0.1702 r_work=0.1123 r_free=0.1702 | n_water=237 | time (s): 4.010 (total time: 31.270) Filter (q & B) r_work=0.1123 r_free=0.1702 | n_water=237 | time (s): 0.770 (total time: 32.040) Filter (dist only) r_work=0.1130 r_free=0.1696 | n_water=234 | time (s): 18.970 (total time: 51.010) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.234236 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.454723 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 0.1025 0.1789 0.0764 0.009 1.0 3.8 0.5 0.6 0 11.117 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.25 17.89 7.64 4.689 17.046 2.455 0.014 9.61 18.26 8.65 5.413 17.460 2.455 0.013 Individual atomic B min max mean iso aniso Overall: 0.00 108.14 16.94 6.30 1761 0 Protein: 0.00 108.14 15.20 6.29 1519 0 Water: 0.00 62.70 28.09 N/A 234 0 Other: 9.87 34.91 21.40 N/A 8 0 Chain A: 0.00 108.14 15.96 N/A 1672 0 Chain S: 2.18 59.14 35.29 N/A 89 0 Histogram: Values Number of atoms 0.00 - 10.81 664 10.81 - 21.63 676 21.63 - 32.44 217 32.44 - 43.26 120 43.26 - 54.07 38 54.07 - 64.89 35 64.89 - 75.70 4 75.70 - 86.51 4 86.51 - 97.33 1 97.33 - 108.14 2 =========================== Idealize ADP of riding H ========================== r_work=0.0961 r_free=0.1826 r_work=0.0958 r_free=0.1827 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0958 r_free = 0.1827 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0951 r_free = 0.1815 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0951 r_free= 0.1815 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ls_wunit_k1) (work): 0.012300 | | target function (ls_wunit_k1) not normalized (work): 60.551184 | | target function (ls_wunit_k1) not normalized (free): 9.758189 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0994 0.0951 0.1815 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2059 0.2063 0.2094 n_refl.: 5175 remove outliers: r(all,work,free)=0.2059 0.2063 0.2094 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2059 0.2063 0.2094 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0991 0.0949 0.1807 n_refl.: 5175 remove outliers: r(all,work,free)=0.0991 0.0949 0.1807 n_refl.: 5175 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3356 317.475 301.877 0.619 1.000 0.340 11.894-9.307 99.02 97 4 0.1517 510.718 505.396 0.949 1.003 0.330 9.237-7.194 100.00 213 7 0.1495 417.666 419.575 0.999 1.004 0.300 7.162-5.571 100.00 427 22 0.1489 313.407 310.039 0.968 1.003 0.300 5.546-4.326 100.00 867 58 0.0781 430.264 427.886 0.983 1.002 0.214 4.315-3.360 100.00 1859 96 0.0723 409.186 409.110 1.035 1.000 0.200 3.356-3.002 100.00 1373 60 0.0989 315.172 314.258 1.018 0.998 0.080 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-5.4031 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0949 r_free=0.1807 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN A Total number of N/Q/H flips: 2 r_work=0.0951 r_free=0.1810 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0951 r_free=0.1810 | n_water=234 | time (s): 0.510 (total time: 0.510) Filter (dist) r_work=0.0962 r_free=0.1791 | n_water=230 | time (s): 18.320 (total time: 18.830) Filter (q & B) r_work=0.1022 r_free=0.1840 | n_water=228 | time (s): 1.290 (total time: 20.120) Compute maps r_work=0.1022 r_free=0.1840 | n_water=228 | time (s): 0.550 (total time: 20.670) Filter (map) r_work=0.1316 r_free=0.1896 | n_water=147 | time (s): 1.570 (total time: 22.240) Find peaks r_work=0.1316 r_free=0.1896 | n_water=147 | time (s): 0.590 (total time: 22.830) Add new water r_work=0.1681 r_free=0.2252 | n_water=241 | time (s): 1.850 (total time: 24.680) Refine new water occ: r_work=0.1060 r_free=0.1797 adp: r_work=0.1054 r_free=0.1791 occ: r_work=0.1044 r_free=0.1779 adp: r_work=0.1042 r_free=0.1782 occ: r_work=0.1034 r_free=0.1770 adp: r_work=0.1032 r_free=0.1773 ADP+occupancy (water only), MIN, final r_work=0.1032 r_free=0.1773 r_work=0.1032 r_free=0.1773 | n_water=241 | time (s): 14.170 (total time: 38.850) Filter (q & B) r_work=0.1033 r_free=0.1780 | n_water=239 | time (s): 1.320 (total time: 40.170) Filter (dist only) r_work=0.1043 r_free=0.1791 | n_water=237 | time (s): 18.280 (total time: 58.450) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.080973 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.229818 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 0.0935 0.1894 0.0959 0.011 1.1 3.8 0.5 0.6 0 0.540 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.35 18.94 9.59 5.312 17.989 0.230 5.132 8.86 18.93 10.06 7.076 17.975 0.230 5.027 Individual atomic B min max mean iso aniso Overall: 0.00 109.83 16.60 8.67 1764 0 Protein: 0.00 109.83 15.30 8.67 1519 0 Water: 0.00 57.80 24.81 N/A 237 0 Other: 9.00 34.93 20.93 N/A 8 0 Chain A: 0.00 109.83 15.98 N/A 1653 0 Chain S: 0.00 57.80 25.85 N/A 111 0 Histogram: Values Number of atoms 0.00 - 10.98 663 10.98 - 21.97 699 21.97 - 32.95 223 32.95 - 43.93 105 43.93 - 54.92 41 54.92 - 65.90 17 65.90 - 76.88 8 76.88 - 87.87 4 87.87 - 98.85 3 98.85 - 109.83 1 =========================== Idealize ADP of riding H ========================== r_work=0.0886 r_free=0.1893 r_work=0.0893 r_free=0.1903 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0893 r_free = 0.1903 target_work(ml) = 5.031 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0882 r_free = 0.1881 target_work(ml) = 5.024 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0882 r_free= 0.1881 coordinate error (max.-lik. estimate): 0.31 A | | | | normalized target function (ml) (work): 5.023605 | | target function (ml) not normalized (work): 24731.208713 | | target function (ml) not normalized (free): 1871.105888 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0933 0.0882 0.1881 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2076 0.2077 0.2172 n_refl.: 5175 remove outliers: r(all,work,free)=0.2076 0.2077 0.2172 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2076 0.2077 0.2172 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0929 0.0878 0.1881 n_refl.: 5175 remove outliers: r(all,work,free)=0.0929 0.0878 0.1881 n_refl.: 5175 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3678 317.475 293.220 0.599 0.989 0.324 11.894-9.307 99.02 97 4 0.1752 510.718 498.767 0.963 0.994 0.320 9.237-7.194 100.00 213 7 0.1880 417.666 410.793 1.010 0.997 0.290 7.162-5.571 100.00 427 22 0.1806 313.407 304.255 0.987 0.998 0.290 5.546-4.326 100.00 867 58 0.0909 430.264 425.328 1.009 1.000 0.220 4.315-3.360 100.00 1859 96 0.0581 409.186 408.832 1.069 1.001 0.210 3.356-3.002 100.00 1373 60 0.0603 315.172 315.103 1.055 1.003 0.065 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.1692 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0878 r_free=0.1881 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B Total number of N/Q/H flips: 1 r_work=0.0880 r_free=0.1880 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0880 r_free=0.1880 | n_water=237 | time (s): 0.670 (total time: 0.670) Filter (dist) r_work=0.0897 r_free=0.1879 | n_water=233 | time (s): 19.140 (total time: 19.810) Filter (q & B) r_work=0.0970 r_free=0.1871 | n_water=228 | time (s): 1.350 (total time: 21.160) Compute maps r_work=0.0970 r_free=0.1871 | n_water=228 | time (s): 0.530 (total time: 21.690) Filter (map) r_work=0.1277 r_free=0.1946 | n_water=159 | time (s): 1.520 (total time: 23.210) Find peaks r_work=0.1277 r_free=0.1946 | n_water=159 | time (s): 0.560 (total time: 23.770) Add new water r_work=0.1579 r_free=0.2224 | n_water=236 | time (s): 1.740 (total time: 25.510) Refine new water occ: r_work=0.0993 r_free=0.1829 adp: r_work=0.0987 r_free=0.1839 occ: r_work=0.0979 r_free=0.1825 adp: r_work=0.0978 r_free=0.1830 occ: r_work=0.0971 r_free=0.1816 adp: r_work=0.0970 r_free=0.1820 ADP+occupancy (water only), MIN, final r_work=0.0970 r_free=0.1820 r_work=0.0970 r_free=0.1820 | n_water=236 | time (s): 9.710 (total time: 35.220) Filter (q & B) r_work=0.0970 r_free=0.1820 | n_water=236 | time (s): 0.900 (total time: 36.120) Filter (dist only) r_work=0.0971 r_free=0.1815 | n_water=234 | time (s): 18.070 (total time: 54.190) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.993243 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.267112 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 0.0881 0.1880 0.0999 0.011 1.0 4.8 0.5 0.0 0 0.497 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 8.81 18.80 9.99 6.793 18.077 0.267 4.991 8.60 19.09 10.48 8.188 18.194 0.267 4.923 Individual atomic B min max mean iso aniso Overall: 0.00 109.66 16.91 10.70 1761 0 Protein: 0.00 109.66 15.71 10.69 1519 0 Water: 0.00 57.31 24.58 N/A 234 0 Other: 7.34 36.09 21.21 N/A 8 0 Chain A: 0.00 109.66 16.28 N/A 1643 0 Chain S: 0.00 57.31 25.61 N/A 118 0 Histogram: Values Number of atoms 0.00 - 10.97 659 10.97 - 21.93 668 21.93 - 32.90 241 32.90 - 43.86 115 43.86 - 54.83 45 54.83 - 65.80 13 65.80 - 76.76 11 76.76 - 87.73 6 87.73 - 98.69 2 98.69 - 109.66 1 =========================== Idealize ADP of riding H ========================== r_work=0.0860 r_free=0.1909 r_work=0.0865 r_free=0.1913 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0865 r_free = 0.1913 target_work(ml) = 4.929 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0855 r_free = 0.1898 target_work(ml) = 4.922 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0855 r_free= 0.1898 coordinate error (max.-lik. estimate): 0.31 A | | | | normalized target function (ml) (work): 4.921802 | | target function (ml) not normalized (work): 24230.033022 | | target function (ml) not normalized (free): 2231.230857 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0908 0.0855 0.1898 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2130 0.2130 0.2246 n_refl.: 5175 remove outliers: r(all,work,free)=0.2130 0.2130 0.2246 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2130 0.2130 0.2246 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0909 0.0857 0.1897 n_refl.: 5175 remove outliers: r(all,work,free)=0.0909 0.0857 0.1897 n_refl.: 5175 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3771 317.475 283.718 0.570 0.983 0.318 11.894-9.307 99.02 97 4 0.1795 510.718 500.341 0.970 0.990 0.317 9.237-7.194 100.00 213 7 0.2085 417.666 410.761 1.023 0.993 0.293 7.162-5.571 100.00 427 22 0.1993 313.407 306.311 1.002 0.995 0.277 5.546-4.326 100.00 867 58 0.0947 430.264 424.292 1.021 0.998 0.230 4.315-3.360 100.00 1859 96 0.0536 409.186 409.367 1.089 1.002 0.220 3.356-3.002 100.00 1373 60 0.0448 315.172 315.110 1.075 1.005 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-8.0596 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0857 r_free=0.1897 After: r_work=0.0860 r_free=0.1896 ================================== NQH flips ================================== r_work=0.0860 r_free=0.1896 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B Total number of N/Q/H flips: 1 r_work=0.0860 r_free=0.1897 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0860 r_free=0.1897 | n_water=234 | time (s): 0.680 (total time: 0.680) Filter (dist) r_work=0.0873 r_free=0.1892 | n_water=231 | time (s): 19.260 (total time: 19.940) Filter (q & B) r_work=0.0978 r_free=0.1963 | n_water=228 | time (s): 1.850 (total time: 21.790) Compute maps r_work=0.0978 r_free=0.1963 | n_water=228 | time (s): 0.570 (total time: 22.360) Filter (map) r_work=0.1260 r_free=0.2017 | n_water=162 | time (s): 1.560 (total time: 23.920) Find peaks r_work=0.1260 r_free=0.2017 | n_water=162 | time (s): 0.570 (total time: 24.490) Add new water r_work=0.1521 r_free=0.2250 | n_water=226 | time (s): 1.490 (total time: 25.980) Refine new water occ: r_work=0.0993 r_free=0.1930 adp: r_work=0.0983 r_free=0.1921 occ: r_work=0.0978 r_free=0.1916 adp: r_work=0.0977 r_free=0.1916 occ: r_work=0.0972 r_free=0.1912 adp: r_work=0.0972 r_free=0.1912 ADP+occupancy (water only), MIN, final r_work=0.0972 r_free=0.1912 r_work=0.0972 r_free=0.1912 | n_water=226 | time (s): 9.270 (total time: 35.250) Filter (q & B) r_work=0.0971 r_free=0.1916 | n_water=225 | time (s): 1.290 (total time: 36.540) Filter (dist only) r_work=0.0974 r_free=0.1928 | n_water=224 | time (s): 18.460 (total time: 55.000) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.935801 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.214724 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 0.0902 0.1894 0.0992 0.010 1.1 7.4 0.5 0.0 0 0.468 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.02 18.94 9.92 8.140 18.402 0.215 4.982 8.86 19.04 10.18 8.822 18.478 0.215 4.927 Individual atomic B min max mean iso aniso Overall: 0.00 110.34 17.01 11.63 1751 0 Protein: 0.00 110.34 16.01 11.61 1519 0 Water: 0.00 54.72 23.64 N/A 224 0 Other: 6.13 36.46 21.27 N/A 8 0 Chain A: 0.00 110.34 16.50 N/A 1637 0 Chain S: 0.00 54.19 24.21 N/A 114 0 Histogram: Values Number of atoms 0.00 - 11.03 648 11.03 - 22.07 656 22.07 - 33.10 266 33.10 - 44.14 110 44.14 - 55.17 39 55.17 - 66.20 10 66.20 - 77.24 12 77.24 - 88.27 5 88.27 - 99.31 3 99.31 - 110.34 2 =========================== Idealize ADP of riding H ========================== r_work=0.0886 r_free=0.1904 r_work=0.0889 r_free=0.1906 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0889 r_free = 0.1906 target_work(ml) = 4.931 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0884 r_free = 0.1895 target_work(ml) = 4.927 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0884 r_free= 0.1895 coordinate error (max.-lik. estimate): 0.31 A | | | | normalized target function (ml) (work): 4.926525 | | target function (ml) not normalized (work): 24253.281477 | | target function (ml) not normalized (free): 2288.179359 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.79 1.00 2493 142 0.1255 0.1860 5.4939 6.2942| | 2: 3.78 - 3.00 1.00 2430 110 0.0432 0.1952 4.3445 12.676| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.79 2493 142 0.92 11.96 1.00 0.94 12349.29| | 2: 3.78 - 3.00 2430 110 0.99 1.83 1.00 0.97 870.73| |alpha: min = 0.93 max = 0.97 mean = 0.96| |beta: min = 565.67 max = 20819.39 mean = 6683.46| |figures of merit: min = 0.00 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.97 mean = 6.96| |phase err.(test): min = 0.00 max = 85.34 mean = 7.25| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0935 0.0884 0.1895 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2186 0.2190 0.2246 n_refl.: 5175 remove outliers: r(all,work,free)=0.2186 0.2190 0.2246 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2186 0.2190 0.2246 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0932 0.0881 0.1907 n_refl.: 5175 remove outliers: r(all,work,free)=0.0932 0.0881 0.1907 n_refl.: 5175 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3706 317.475 293.331 0.630 0.983 0.320 11.894-9.307 99.02 97 4 0.1871 510.718 494.983 1.006 0.991 0.320 9.237-7.194 100.00 213 7 0.2202 417.666 408.072 1.057 0.995 0.299 7.162-5.571 100.00 427 22 0.2065 313.407 304.176 1.036 0.997 0.283 5.546-4.326 100.00 867 58 0.1014 430.264 424.901 1.069 0.999 0.250 4.315-3.360 100.00 1859 96 0.0552 409.186 409.284 1.148 1.001 0.229 3.356-3.002 100.00 1373 60 0.0414 315.172 314.861 1.138 1.003 0.061 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-8.6693 ================= 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 : 0.3620 0.2080 0.081 5.160 8.8 119.3 19.9 258 0.000 1_bss: 0.1563 0.1629 0.081 5.160 6.0 116.5 17.1 258 0.000 1_settarget: 0.1563 0.1629 0.081 5.160 6.0 116.5 17.1 258 0.000 1_nqh: 0.1563 0.1629 0.081 5.160 6.0 116.5 17.1 258 0.000 1_weight: 0.1563 0.1629 0.081 5.160 6.0 116.5 17.1 258 0.000 1_xyzrec: 0.1165 0.1847 0.010 0.968 6.0 116.5 17.1 258 0.216 1_adp: 0.1025 0.1829 0.010 0.968 2.3 111.5 17.7 258 0.216 1_regHadp: 0.1019 0.1834 0.010 0.968 2.3 111.5 17.7 258 0.216 1_occ: 0.1021 0.1842 0.010 0.968 2.3 111.5 17.7 258 0.216 2_bss: 0.1013 0.1819 0.010 0.968 1.2 110.4 16.6 258 0.216 2_settarget: 0.1013 0.1819 0.010 0.968 1.2 110.4 16.6 258 0.216 2_updatecdl: 0.1013 0.1819 0.010 0.984 1.2 110.4 16.6 258 0.216 2_nqh: 0.1015 0.1821 0.010 0.984 1.2 110.4 16.6 258 0.219 2_sol: 0.1130 0.1696 0.010 0.984 1.0 109.7 16.1 234 n/a 2_weight: 0.1130 0.1696 0.010 0.984 1.0 109.7 16.1 234 n/a 2_xyzrec: 0.1025 0.1789 0.009 0.959 1.0 109.7 16.1 234 n/a 2_adp: 0.0961 0.1826 0.009 0.959 0.0 108.1 16.9 234 n/a 2_regHadp: 0.0958 0.1827 0.009 0.959 0.0 108.1 16.9 234 n/a 2_occ: 0.0951 0.1815 0.009 0.959 0.0 108.1 16.9 234 n/a 3_bss: 0.0949 0.1807 0.009 0.959 0.0 108.1 16.9 234 n/a 3_settarget: 0.0949 0.1807 0.009 0.959 0.0 108.1 16.9 234 n/a 3_updatecdl: 0.0949 0.1807 0.009 0.966 0.0 108.1 16.9 234 n/a 3_nqh: 0.0951 0.1810 0.009 0.966 0.0 108.1 16.9 234 n/a 3_sol: 0.1043 0.1791 0.009 0.966 0.0 108.1 16.6 237 n/a 3_weight: 0.1043 0.1791 0.009 0.966 0.0 108.1 16.6 237 n/a 3_xyzrec: 0.0935 0.1894 0.011 1.050 0.0 108.1 16.6 237 n/a 3_adp: 0.0886 0.1893 0.011 1.050 0.0 109.8 16.6 237 n/a 3_regHadp: 0.0893 0.1903 0.011 1.050 0.0 109.8 16.6 237 n/a 3_occ: 0.0882 0.1881 0.011 1.050 0.0 109.8 16.6 237 n/a 4_bss: 0.0878 0.1881 0.011 1.050 0.0 109.8 16.6 237 n/a 4_settarget: 0.0878 0.1881 0.011 1.050 0.0 109.8 16.6 237 n/a 4_updatecdl: 0.0878 0.1881 0.011 1.060 0.0 109.8 16.6 237 n/a 4_nqh: 0.0880 0.1880 0.011 1.060 0.0 109.8 16.6 237 n/a 4_sol: 0.0971 0.1815 0.011 1.060 0.0 109.8 16.7 234 n/a 4_weight: 0.0971 0.1815 0.011 1.060 0.0 109.8 16.7 234 n/a 4_xyzrec: 0.0881 0.1880 0.011 1.045 0.0 109.8 16.7 234 n/a 4_adp: 0.0860 0.1909 0.011 1.045 0.0 109.7 16.9 234 n/a 4_regHadp: 0.0865 0.1913 0.011 1.045 0.0 109.7 16.9 234 n/a 4_occ: 0.0855 0.1898 0.011 1.045 0.0 109.7 16.9 234 n/a 5_bss: 0.0857 0.1897 0.011 1.045 0.0 109.7 16.9 234 n/a 5_settarget: 0.0857 0.1897 0.011 1.045 0.0 109.7 16.9 234 n/a 5_updatecdl: 0.0857 0.1897 0.011 1.059 0.0 109.7 16.9 234 n/a 5_setrh: 0.0860 0.1896 0.011 1.059 0.0 109.7 16.9 234 n/a 5_nqh: 0.0860 0.1897 0.011 1.059 0.0 109.7 16.9 234 n/a 5_sol: 0.0974 0.1928 0.011 1.059 0.0 109.7 16.9 224 n/a 5_weight: 0.0974 0.1928 0.011 1.059 0.0 109.7 16.9 224 n/a 5_xyzrec: 0.0902 0.1894 0.010 1.110 0.0 109.7 16.9 224 n/a 5_adp: 0.0886 0.1904 0.010 1.110 0.0 110.3 17.0 224 n/a 5_regHadp: 0.0889 0.1906 0.010 1.110 0.0 110.3 17.0 224 n/a 5_occ: 0.0884 0.1895 0.010 1.110 0.0 110.3 17.0 224 n/a end: 0.0881 0.1907 0.010 1.110 0.0 110.3 17.0 224 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_7798058_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_7798058_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.2900 Refinement macro-cycles (run) : 483.8300 Write final files (write_after_run_outputs) : 10.2800 Total : 498.4000 Total CPU time: 8.67 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:19:01 PST -0800 (1735492742.00 s) Start R-work = 0.1563, R-free = 0.1629 Final R-work = 0.0881, R-free = 0.1907 =============================================================================== Job complete usr+sys time: 528.46 seconds wall clock time: 9 minutes 10.64 seconds (550.64 seconds total)