Starting phenix.refine on Sun Dec 29 09:24:42 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6024882.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=2 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_6024882.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6024882.pdb" 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 = 2 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } 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 6 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: 1.90, per 1000 atoms: 0.56 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: 0.57 Conformation dependent library (CDL) restraints added in 112.2 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.91: 489 0.91 - 1.16: 1142 1.16 - 1.41: 599 1.41 - 1.65: 864 1.65 - 1.90: 59 Bond restraints: 3153 Sorted by residual: bond pdb=" N GLY A 108 " pdb=" CA GLY A 108 " ideal model delta sigma weight residual 1.444 1.641 -0.198 8.80e-03 1.29e+04 5.05e+02 bond pdb=" CA GLY A 108 " pdb=" C GLY A 108 " ideal model delta sigma weight residual 1.511 1.385 0.126 6.90e-03 2.10e+04 3.35e+02 bond pdb=" CA VAL A 35 " pdb=" CB VAL A 35 " ideal model delta sigma weight residual 1.533 1.325 0.208 1.14e-02 7.69e+03 3.33e+02 bond pdb=" N GLY A 174 " pdb=" CA GLY A 174 " ideal model delta sigma weight residual 1.447 1.267 0.179 9.90e-03 1.02e+04 3.28e+02 bond pdb=" C LEU A 7 " pdb=" O LEU A 7 " ideal model delta sigma weight residual 1.236 1.035 0.201 1.14e-02 7.69e+03 3.10e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.69: 3154 4.69 - 9.37: 1888 9.37 - 14.06: 613 14.06 - 18.75: 109 18.75 - 23.44: 13 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O GLY A 108 " pdb=" C GLY A 108 " pdb=" N PRO A 109 " ideal model delta sigma weight residual 121.07 110.85 10.22 3.60e-01 7.72e+00 8.05e+02 angle pdb=" CA GLY A 74 " pdb=" C GLY A 74 " pdb=" O GLY A 74 " ideal model delta sigma weight residual 121.28 137.77 -16.49 1.01e+00 9.80e-01 2.67e+02 angle pdb=" CA ACYS A 53 " pdb=" C ACYS A 53 " pdb=" O ACYS A 53 " ideal model delta sigma weight residual 119.71 107.68 12.03 8.10e-01 1.52e+00 2.20e+02 angle pdb=" OD1 ASN A 173 " pdb=" CG ASN A 173 " pdb=" ND2 ASN A 173 " ideal model delta sigma weight residual 122.60 108.37 14.23 1.00e+00 1.00e+00 2.03e+02 angle pdb=" CA ALA A 56 " pdb=" C ALA A 56 " pdb=" O ALA A 56 " ideal model delta sigma weight residual 121.10 105.54 15.56 1.10e+00 8.26e-01 2.00e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.36: 1367 21.36 - 42.71: 86 42.71 - 64.07: 22 64.07 - 85.43: 4 85.43 - 106.78: 2 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C LEU A 128 " pdb=" N LEU A 128 " pdb=" CA LEU A 128 " pdb=" CB LEU A 128 " ideal model delta harmonic sigma weight residual -122.60 -146.02 23.42 0 2.50e+00 1.60e-01 8.78e+01 dihedral pdb=" N LEU A 128 " pdb=" C LEU A 128 " pdb=" CA LEU A 128 " pdb=" CB LEU A 128 " ideal model delta harmonic sigma weight residual 122.80 145.80 -23.00 0 2.50e+00 1.60e-01 8.46e+01 dihedral pdb=" N ACYS A 53 " pdb=" C ACYS A 53 " pdb=" CA ACYS A 53 " pdb=" CB ACYS A 53 " ideal model delta harmonic sigma weight residual 122.80 140.89 -18.09 0 2.50e+00 1.60e-01 5.24e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.003 - 0.233: 113 0.233 - 0.462: 76 0.462 - 0.692: 35 0.692 - 0.922: 13 0.922 - 1.151: 6 Chirality restraints: 243 Sorted by residual: 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 3.66 -1.15 2.00e-01 2.50e+01 3.31e+01 chirality pdb=" CA LEU A 128 " pdb=" N LEU A 128 " pdb=" C LEU A 128 " pdb=" CB LEU A 128 " both_signs ideal model delta sigma weight residual False 2.51 1.48 1.03 2.00e-01 2.50e+01 2.64e+01 chirality pdb=" CG LEU A 112 " pdb=" CB LEU A 112 " pdb=" CD1 LEU A 112 " pdb=" CD2 LEU A 112 " both_signs ideal model delta sigma weight residual False -2.59 -1.57 -1.02 2.00e-01 2.50e+01 2.59e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.134 2.00e-02 2.50e+03 6.91e-02 1.43e+02 pdb=" CG PHE A 119 " -0.109 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.104 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.043 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " -0.045 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.086 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.022 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.046 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.038 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.102 2.00e-02 2.50e+03 6.56e-02 1.29e+02 pdb=" CG PHE A 164 " 0.061 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.045 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.142 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.043 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.040 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.026 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.004 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.005 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.104 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 98 " 0.063 9.50e-02 1.11e+02 7.48e-02 1.16e+02 pdb=" NE ARG A 98 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG A 98 " 0.059 2.00e-02 2.50e+03 pdb=" NH1 ARG A 98 " 0.077 2.00e-02 2.50e+03 pdb=" NH2 ARG A 98 " -0.123 2.00e-02 2.50e+03 pdb="HH11 ARG A 98 " 0.002 2.00e-02 2.50e+03 pdb="HH12 ARG A 98 " -0.100 2.00e-02 2.50e+03 pdb="HH21 ARG A 98 " -0.009 2.00e-02 2.50e+03 pdb="HH22 ARG A 98 " 0.108 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.34: 1176 2.34 - 2.91: 8301 2.91 - 3.47: 10440 3.47 - 4.04: 15158 4.04 - 4.60: 21573 Nonbonded interactions: 56648 Sorted by model distance: nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.777 2.100 nonbonded pdb=" OE2 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.793 2.450 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.836 2.450 nonbonded pdb=" H VAL A 44 " pdb=" O ILE A 52 " model vdw 1.837 2.450 nonbonded pdb=" H THR A 125 " pdb=" HH TYR A 141 " model vdw 1.841 2.100 ... (remaining 56643 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 6 Type Number sf(0) Gaussians S 10 15.96 2 O1- 2 8.97 2 O 551 7.97 2 N 265 6.97 2 C 957 5.97 2 H 1596 1.00 2 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_6024882_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: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2796 r_free= 0.1824 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.402269 | | target function (ml) not normalized (work): 71506.061543 | | target function (ml) not normalized (free): 3242.933973 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 49.25 - 3.64 1.00 2819 159 0.3197 0.2104 7.536 5.0305| | 2: 3.63 - 2.88 1.00 2711 122 0.2651 0.1788 4.3315 4.329| | 3: 2.88 - 2.52 1.00 2682 148 0.2549 0.1758 4.1814 4.1925| | 4: 2.52 - 2.29 1.00 2661 139 0.2563 0.1502 3.5057 3.5295| | 5: 2.29 - 2.13 1.00 2678 122 0.2684 0.1562 3.3901 3.4199| | 6: 2.13 - 2.00 1.00 2692 117 0.2764 0.1776 3.3051 3.3045| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 - 3.64 2819 159 0.88 17.61 0.77 0.23 1297.06| | 2: 3.63 - 2.88 2711 122 0.83 23.84 1.32 0.23 1297.06| | 3: 2.88 - 2.52 2682 148 0.73 32.83 1.28 0.23 1297.06| | 4: 2.52 - 2.29 2661 139 0.94 10.66 1.30 0.26 124.10| | 5: 2.29 - 2.13 2678 122 0.93 12.73 1.32 0.26 124.10| | 6: 2.13 - 2.00 2692 117 0.91 15.39 1.34 0.26 124.10| |alpha: min = 0.23 max = 0.26 mean = 0.25| |beta: min = 124.10 max = 1297.06 mean = 717.11| |figures of merit: min = 0.00 max = 1.00 mean = 0.87| |phase err.(work): min = 0.00 max = 89.99 mean = 18.85| |phase err.(test): min = 0.00 max = 88.31 mean = 18.94| |-----------------------------------------------------------------------------| ----------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 : 0.083 0.226 1557 Z= 5.599 Angle : 5.311 18.178 2118 Z= 3.853 Chirality : 0.388 1.151 243 Planarity : 0.032 0.111 284 Dihedral : 14.207 106.782 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.24 % Favored : 96.22 % Rotamer: Outliers : 1.86 % Allowed : 3.11 % Favored : 95.03 % Cbeta Deviations : 31.89 % 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: -2.70 (0.48), residues: 224 helix: -2.67 (0.37), residues: 109 sheet: -0.75 (0.80), residues: 38 loop : -0.49 (0.64), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.058 0.016 ARG A 98 TYR 0.077 0.032 TYR A 141 PHE 0.127 0.044 PHE A 119 HIS 0.040 0.023 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: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2796 r_free= 0.1824 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.402269 | | target function (ml) not normalized (work): 71506.061543 | | target function (ml) not normalized (free): 3242.933973 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.3346 percent. r_work = 0.2929 r_free = 0.1996 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2875 0.2929 0.1996 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2875 0.2929 0.1996 n_refl.: 17050 remove outliers: r(all,work,free)=0.2163 0.2174 0.1996 n_refl.: 17045 overall B=-0.42 to atoms: r(all,work,free)=0.2134 0.2145 0.1975 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1620 0.1618 0.1657 n_refl.: 17045 remove outliers: r(all,work,free)=0.1619 0.1617 0.1657 n_refl.: 17044 ======================== 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 0.4033 394.811 364.775 0.663 1.010 0.406 11.894-9.307 99.02 97 4 0.1808 633.683 615.726 0.938 1.011 0.396 9.237-7.194 100.00 213 7 0.2166 518.289 508.684 0.959 1.011 0.357 7.162-5.571 100.00 427 22 0.2269 388.976 376.320 0.926 1.010 0.305 5.546-4.326 100.00 867 58 0.1382 534.002 528.743 0.964 1.009 0.220 4.315-3.360 100.00 1859 96 0.1286 507.841 503.804 1.018 1.006 0.181 3.356-2.611 100.00 3867 181 0.1678 333.623 328.732 1.011 1.001 0.015 2.608-2.000 99.99 8818 434 0.1658 217.465 213.542 1.029 0.993 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.5143 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1617 r_free=0.1657 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN A ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 80 GLN A Total number of N/Q/H flips: 3 r_work=0.1624 r_free=0.1663 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.248953 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.815459 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 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 0.1348 0.1637 0.0289 0.010 1.0 1.3 0.5 0.0 0 13.624 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.48 16.37 2.89 3.012 18.435 0.815 0.023 12.76 16.59 3.83 3.579 18.709 0.815 0.020 Individual atomic B min max mean iso aniso Overall: 6.37 113.88 19.98 4.03 1785 0 Protein: 6.37 112.80 17.23 4.03 1519 0 Water: 8.78 113.88 35.98 N/A 258 0 Other: 22.18 35.70 26.24 N/A 8 0 Chain A: 6.37 113.88 19.98 N/A 1785 0 Histogram: Values Number of atoms 6.37 - 17.12 1095 17.12 - 27.87 338 27.87 - 38.62 179 38.62 - 49.37 98 49.37 - 60.12 48 60.12 - 70.87 13 70.87 - 81.62 6 81.62 - 92.37 4 92.37 - 103.12 1 103.12 - 113.88 3 =========================== Idealize ADP of riding H ========================== r_work=0.1276 r_free=0.1659 r_work=0.1279 r_free=0.1668 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1279 r_free = 0.1668 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1273 r_free = 0.1657 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17044 (all), 4.73 % free)------------| | | | r_work= 0.1273 r_free= 0.1657 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.019931 | | target function (ls_wunit_k1) not normalized (work): 323.624303 | | target function (ls_wunit_k1) not normalized (free): 27.432046 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1292 0.1273 0.1657 n_refl.: 17044 re-set all scales: r(all,work,free)=0.1916 0.1915 0.1990 n_refl.: 17044 remove outliers: r(all,work,free)=0.1916 0.1915 0.1990 n_refl.: 17044 overall B=-0.40 to atoms: r(all,work,free)=0.1886 0.1885 0.1973 n_refl.: 17044 bulk-solvent and scaling: r(all,work,free)=0.1291 0.1273 0.1654 n_refl.: 17044 remove outliers: r(all,work,free)=0.1290 0.1272 0.1654 n_refl.: 17043 ======================== 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 0.3629 301.701 282.228 0.640 1.010 0.380 11.894-9.307 99.02 97 4 0.1659 488.408 478.490 0.921 1.010 0.372 9.237-7.194 100.00 213 7 0.1817 399.469 396.788 0.958 1.010 0.351 7.162-5.571 100.00 427 22 0.1827 299.802 294.986 0.931 1.009 0.301 5.546-4.326 100.00 867 58 0.1049 411.580 409.330 0.959 1.007 0.205 4.315-3.360 100.00 1859 96 0.0928 391.416 391.076 1.018 1.005 0.191 3.356-2.611 100.00 3867 181 0.1298 257.138 255.805 1.014 1.000 0.081 2.608-2.000 99.99 8818 434 0.1343 167.610 166.117 1.024 0.992 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.4178 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1272 r_free=0.1654 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A A 80 GLN A Total number of N/Q/H flips: 2 r_work=0.1274 r_free=0.1654 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1274 r_free=0.1654 | n_water=258 | time (s): 0.610 (total time: 0.610) Filter (dist) r_work=0.1281 r_free=0.1639 | n_water=254 | time (s): 20.030 (total time: 20.640) Filter (q & B) r_work=0.1282 r_free=0.1639 | n_water=252 | time (s): 1.500 (total time: 22.140) Compute maps r_work=0.1282 r_free=0.1639 | n_water=252 | time (s): 0.690 (total time: 22.830) Filter (map) r_work=0.1319 r_free=0.1626 | n_water=208 | time (s): 1.810 (total time: 24.640) Find peaks r_work=0.1319 r_free=0.1626 | n_water=208 | time (s): 0.430 (total time: 25.070) Add new water r_work=0.1550 r_free=0.1870 | n_water=369 | time (s): 1.610 (total time: 26.680) Refine new water occ: r_work=0.1341 r_free=0.1615 adp: r_work=0.1277 r_free=0.1605 occ: r_work=0.1285 r_free=0.1586 adp: r_work=0.1248 r_free=0.1584 occ: r_work=0.1250 r_free=0.1581 adp: r_work=0.1239 r_free=0.1574 ADP+occupancy (water only), MIN, final r_work=0.1239 r_free=0.1574 r_work=0.1239 r_free=0.1574 | n_water=369 | time (s): 18.300 (total time: 44.980) Filter (q & B) r_work=0.1241 r_free=0.1573 | n_water=362 | time (s): 1.980 (total time: 46.960) Filter (dist only) r_work=0.1242 r_free=0.1576 | n_water=361 | time (s): 27.700 (total time: 74.660) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.901016 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.989146 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 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 0.1217 0.1587 0.0370 0.008 0.9 2.2 0.5 0.0 0 12.451 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.17 15.87 3.70 4.147 21.031 0.989 0.018 11.98 16.04 4.06 4.219 21.283 0.989 0.018 Individual atomic B min max mean iso aniso Overall: 6.57 107.40 21.26 4.26 1888 0 Protein: 6.57 107.40 17.66 4.25 1519 0 Water: 8.66 66.89 36.09 N/A 361 0 Other: 25.60 44.16 34.52 N/A 8 0 Chain A: 6.57 107.40 19.35 N/A 1735 0 Chain S: 18.16 66.89 42.88 N/A 153 0 Histogram: Values Number of atoms 6.57 - 16.65 1022 16.65 - 26.74 378 26.74 - 36.82 229 36.82 - 46.90 151 46.90 - 56.98 72 56.98 - 67.07 25 67.07 - 77.15 4 77.15 - 87.23 4 87.23 - 97.32 1 97.32 - 107.40 2 =========================== Idealize ADP of riding H ========================== r_work=0.1198 r_free=0.1604 r_work=0.1199 r_free=0.1606 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 r_free = 0.1606 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1195 r_free = 0.1611 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17043 (all), 4.74 % free)------------| | | | r_work= 0.1195 r_free= 0.1611 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.017143 | | target function (ls_wunit_k1) not normalized (work): 278.328129 | | target function (ls_wunit_k1) not normalized (free): 24.791834 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1215 0.1195 0.1611 n_refl.: 17043 re-set all scales: r(all,work,free)=0.1810 0.1806 0.1954 n_refl.: 17043 remove outliers: r(all,work,free)=0.1810 0.1806 0.1954 n_refl.: 17043 overall B=-0.37 to atoms: r(all,work,free)=0.1784 0.1779 0.1939 n_refl.: 17043 bulk-solvent and scaling: r(all,work,free)=0.1209 0.1190 0.1601 n_refl.: 17043 remove outliers: r(all,work,free)=0.1208 0.1189 0.1601 n_refl.: 17042 ======================== 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 0.3438 303.672 277.016 0.593 1.007 0.360 11.894-9.307 99.02 97 4 0.1476 488.408 484.700 0.918 1.007 0.360 9.237-7.194 100.00 213 7 0.1691 399.469 399.156 0.972 1.006 0.310 7.162-5.571 100.00 427 22 0.1548 299.802 296.434 0.935 1.006 0.261 5.546-4.326 100.00 867 58 0.0884 411.580 408.931 0.959 1.005 0.206 4.315-3.360 100.00 1859 96 0.0836 391.416 390.472 1.014 1.004 0.201 3.356-2.611 100.00 3867 181 0.1183 257.138 256.403 1.010 1.001 0.058 2.608-2.000 99.99 8818 434 0.1330 167.610 166.558 1.015 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.3159 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1189 r_free=0.1601 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN B Total number of N/Q/H flips: 1 r_work=0.1189 r_free=0.1602 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1189 r_free=0.1602 | n_water=361 | time (s): 0.850 (total time: 0.850) Filter (dist) r_work=0.1189 r_free=0.1602 | n_water=361 | time (s): 25.520 (total time: 26.370) Filter (q & B) r_work=0.1189 r_free=0.1602 | n_water=361 | time (s): 1.320 (total time: 27.690) Compute maps r_work=0.1189 r_free=0.1602 | n_water=361 | time (s): 0.840 (total time: 28.530) Filter (map) r_work=0.1271 r_free=0.1632 | n_water=256 | time (s): 1.780 (total time: 30.310) Find peaks r_work=0.1271 r_free=0.1632 | n_water=256 | time (s): 0.530 (total time: 30.840) Add new water r_work=0.1459 r_free=0.1839 | n_water=410 | time (s): 1.830 (total time: 32.670) Refine new water occ: r_work=0.1247 r_free=0.1616 adp: r_work=0.1241 r_free=0.1617 occ: r_work=0.1219 r_free=0.1585 adp: r_work=0.1209 r_free=0.1585 occ: r_work=0.1200 r_free=0.1567 adp: r_work=0.1191 r_free=0.1564 ADP+occupancy (water only), MIN, final r_work=0.1191 r_free=0.1564 r_work=0.1191 r_free=0.1564 | n_water=410 | time (s): 32.430 (total time: 65.100) Filter (q & B) r_work=0.1192 r_free=0.1572 | n_water=404 | time (s): 1.760 (total time: 66.860) Filter (dist only) r_work=0.1192 r_free=0.1572 | n_water=404 | time (s): 31.050 (total time: 97.910) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.840990 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.170291 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 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 0.1176 0.1539 0.0363 0.009 1.0 3.5 0.5 0.0 0 0.920 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.76 15.39 3.63 4.320 21.425 0.170 4.995 11.57 15.61 4.04 4.858 21.340 0.170 4.976 Individual atomic B min max mean iso aniso Overall: 6.09 105.78 20.75 4.70 1931 0 Protein: 6.09 105.78 16.97 4.70 1519 0 Water: 8.85 62.18 34.69 N/A 404 0 Other: 26.30 45.84 34.73 N/A 8 0 Chain A: 6.09 105.78 18.63 N/A 1729 0 Chain S: 16.87 62.18 38.91 N/A 202 0 Histogram: Values Number of atoms 6.09 - 16.05 1061 16.05 - 26.02 355 26.02 - 35.99 235 35.99 - 45.96 169 45.96 - 55.93 74 55.93 - 65.90 24 65.90 - 75.87 5 75.87 - 85.84 4 85.84 - 95.81 2 95.81 - 105.78 2 =========================== Idealize ADP of riding H ========================== r_work=0.1157 r_free=0.1561 r_work=0.1157 r_free=0.1562 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1157 r_free = 0.1562 target_work(ml) = 4.976 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1150 r_free = 0.1575 target_work(ml) = 4.973 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17042 (all), 4.74 % free)------------| | | | r_work= 0.1150 r_free= 0.1575 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.973193 | | target function (ml) not normalized (work): 80739.785390 | | target function (ml) not normalized (free): 4201.353948 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1170 0.1150 0.1575 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1687 0.1681 0.1860 n_refl.: 17042 remove outliers: r(all,work,free)=0.1687 0.1681 0.1860 n_refl.: 17042 overall B=-0.47 to atoms: r(all,work,free)=0.1655 0.1648 0.1847 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1169 0.1148 0.1582 n_refl.: 17042 remove outliers: r(all,work,free)=0.1168 0.1147 0.1582 n_refl.: 17041 ======================== 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 0.3685 300.178 277.035 0.568 1.006 0.340 11.894-9.307 99.02 97 4 0.1781 488.408 478.749 0.909 1.007 0.327 9.237-7.194 100.00 213 7 0.1825 399.469 400.028 0.985 1.007 0.265 7.162-5.571 100.00 427 22 0.1595 299.802 295.091 0.942 1.006 0.230 5.546-4.326 100.00 867 58 0.0957 411.580 407.884 0.966 1.006 0.218 4.315-3.360 100.00 1859 96 0.0895 391.416 389.350 1.011 1.004 0.217 3.356-2.611 100.00 3867 181 0.1288 257.138 254.669 1.010 1.001 0.112 2.608-2.000 99.99 8818 434 0.1078 167.610 166.274 1.013 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-1.1753 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1147 r_free=0.1582 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=0.1149 r_free=0.1580 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1149 r_free=0.1580 | n_water=404 | time (s): 0.880 (total time: 0.880) Filter (dist) r_work=0.1149 r_free=0.1580 | n_water=404 | time (s): 30.040 (total time: 30.920) Filter (q & B) r_work=0.1149 r_free=0.1580 | n_water=404 | time (s): 1.280 (total time: 32.200) Compute maps r_work=0.1149 r_free=0.1580 | n_water=404 | time (s): 0.870 (total time: 33.070) Filter (map) r_work=0.1203 r_free=0.1563 | n_water=306 | time (s): 2.120 (total time: 35.190) Find peaks r_work=0.1203 r_free=0.1563 | n_water=306 | time (s): 0.660 (total time: 35.850) Add new water r_work=0.1359 r_free=0.1717 | n_water=456 | time (s): 2.060 (total time: 37.910) Refine new water occ: r_work=0.1185 r_free=0.1542 adp: r_work=0.1178 r_free=0.1544 occ: r_work=0.1163 r_free=0.1521 adp: r_work=0.1153 r_free=0.1518 occ: r_work=0.1146 r_free=0.1510 adp: r_work=0.1137 r_free=0.1507 ADP+occupancy (water only), MIN, final r_work=0.1137 r_free=0.1507 r_work=0.1137 r_free=0.1507 | n_water=456 | time (s): 30.780 (total time: 68.690) Filter (q & B) r_work=0.1142 r_free=0.1520 | n_water=443 | time (s): 1.800 (total time: 70.490) Filter (dist only) r_work=0.1142 r_free=0.1519 | n_water=442 | time (s): 39.260 (total time: 109.750) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.943716 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.166923 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 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 0.1126 0.1557 0.0431 0.010 1.0 4.5 0.5 0.0 0 0.972 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.26 15.57 4.31 4.500 20.913 0.167 4.963 11.15 15.36 4.22 4.697 20.952 0.167 4.951 Individual atomic B min max mean iso aniso Overall: 5.70 104.72 20.79 4.93 1969 0 Protein: 5.70 104.72 16.42 4.92 1519 0 Water: 8.24 66.62 35.57 N/A 442 0 Other: 25.14 44.20 32.94 N/A 8 0 Chain A: 5.70 104.72 18.04 N/A 1729 0 Chain S: 13.98 66.62 40.62 N/A 240 0 Histogram: Values Number of atoms 5.70 - 15.60 1073 15.60 - 25.50 346 25.50 - 35.40 232 35.40 - 45.30 186 45.30 - 55.21 95 55.21 - 65.11 23 65.11 - 75.01 6 75.01 - 84.91 3 84.91 - 94.81 3 94.81 - 104.72 2 =========================== Idealize ADP of riding H ========================== r_work=0.1115 r_free=0.1536 r_work=0.1115 r_free=0.1537 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1115 r_free = 0.1537 target_work(ml) = 4.952 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1107 r_free = 0.1537 target_work(ml) = 4.946 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1107 r_free= 0.1537 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ml) (work): 4.945509 | | target function (ml) not normalized (work): 80285.389927 | | target function (ml) not normalized (free): 4180.915245 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1128 0.1107 0.1537 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1596 0.1584 0.1868 n_refl.: 17041 remove outliers: r(all,work,free)=0.1596 0.1584 0.1868 n_refl.: 17041 overall B=-0.26 to atoms: r(all,work,free)=0.1581 0.1568 0.1860 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1126 0.1106 0.1532 n_refl.: 17041 remove outliers: r(all,work,free)=0.1126 0.1106 0.1532 n_refl.: 17041 ======================== 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 0.3662 300.178 277.552 0.547 1.003 0.324 11.894-9.307 99.02 97 4 0.1708 488.408 479.855 0.913 1.004 0.320 9.237-7.194 100.00 213 7 0.1742 399.469 401.162 0.991 1.004 0.239 7.162-5.571 100.00 427 22 0.1521 299.802 294.398 0.932 1.004 0.205 5.546-4.326 100.00 867 58 0.0914 411.580 408.499 0.965 1.004 0.201 4.315-3.360 100.00 1859 96 0.0871 391.416 389.167 1.005 1.003 0.201 3.356-2.611 100.00 3867 181 0.1232 257.138 254.732 1.004 1.001 0.063 2.608-2.000 99.99 8818 434 0.1045 167.610 166.391 0.996 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.8910 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1106 r_free=0.1532 After: r_work=0.1108 r_free=0.1531 ================================== NQH flips ================================== r_work=0.1108 r_free=0.1531 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1108 r_free=0.1531 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1108 r_free=0.1531 | n_water=442 | time (s): 0.610 (total time: 0.610) Filter (dist) r_work=0.1108 r_free=0.1531 | n_water=442 | time (s): 35.720 (total time: 36.330) Filter (q & B) r_work=0.1108 r_free=0.1531 | n_water=441 | time (s): 2.070 (total time: 38.400) Compute maps r_work=0.1108 r_free=0.1531 | n_water=441 | time (s): 0.700 (total time: 39.100) Filter (map) r_work=0.1180 r_free=0.1541 | n_water=334 | time (s): 2.140 (total time: 41.240) Find peaks r_work=0.1180 r_free=0.1541 | n_water=334 | time (s): 0.450 (total time: 41.690) Add new water r_work=0.1296 r_free=0.1681 | n_water=463 | time (s): 1.640 (total time: 43.330) Refine new water occ: r_work=0.1143 r_free=0.1539 adp: r_work=0.1138 r_free=0.1536 occ: r_work=0.1122 r_free=0.1519 adp: r_work=0.1116 r_free=0.1512 occ: r_work=0.1107 r_free=0.1500 adp: r_work=0.1102 r_free=0.1496 ADP+occupancy (water only), MIN, final r_work=0.1102 r_free=0.1496 r_work=0.1102 r_free=0.1496 | n_water=463 | time (s): 21.370 (total time: 64.700) Filter (q & B) r_work=0.1105 r_free=0.1505 | n_water=454 | time (s): 2.010 (total time: 66.710) Filter (dist only) r_work=0.1105 r_free=0.1503 | n_water=453 | time (s): 36.570 (total time: 103.280) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.942577 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.165549 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 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 0.1118 0.1496 0.0378 0.010 1.0 5.4 0.5 0.0 0 0.971 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.18 14.96 3.78 4.581 20.661 0.166 4.942 11.07 14.94 3.86 4.620 20.743 0.166 4.934 Individual atomic B min max mean iso aniso Overall: 5.32 103.73 20.77 5.03 1980 0 Protein: 5.32 103.73 16.19 5.02 1519 0 Water: 7.94 68.85 35.91 N/A 453 0 Other: 25.82 45.77 33.70 N/A 8 0 Chain A: 5.32 103.73 17.76 N/A 1728 0 Chain S: 15.29 68.85 41.45 N/A 252 0 Histogram: Values Number of atoms 5.32 - 15.16 1054 15.16 - 25.00 360 25.00 - 34.84 218 34.84 - 44.68 193 44.68 - 54.53 108 54.53 - 64.37 31 64.37 - 74.21 7 74.21 - 84.05 4 84.05 - 93.89 2 93.89 - 103.73 3 =========================== Idealize ADP of riding H ========================== r_work=0.1107 r_free=0.1494 r_work=0.1107 r_free=0.1494 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1107 r_free = 0.1494 target_work(ml) = 4.934 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1102 r_free = 0.1496 target_work(ml) = 4.930 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1102 r_free= 0.1496 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.929758 | | target function (ml) not normalized (work): 80029.692812 | | target function (ml) not normalized (free): 4160.869926 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.64 1.00 2811 159 0.1119 0.1373 5.4586 5.6544| | 2: 3.63 - 2.88 1.00 2711 122 0.1085 0.1437 5.2144 5.3307| | 3: 2.88 - 2.52 1.00 2681 148 0.1349 0.1725 5.1239 5.2115| | 4: 2.52 - 2.29 1.00 2661 139 0.0920 0.1507 4.6139 4.9551| | 5: 2.29 - 2.13 1.00 2678 122 0.0954 0.1473 4.5711 4.8768| | 6: 2.13 - 2.00 1.00 2692 117 0.1119 0.1685 4.5665 4.7559| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 - 3.64 2811 159 0.95 8.97 1.00 0.96 6285.51| | 2: 3.63 - 2.88 2711 122 0.92 12.77 1.01 0.96 6285.51| | 3: 2.88 - 2.52 2681 148 0.88 18.84 0.99 0.96 6285.51| | 4: 2.52 - 2.29 2661 139 0.93 11.88 1.01 0.98 2071.96| | 5: 2.29 - 2.13 2678 122 0.92 13.97 1.00 0.98 2071.96| | 6: 2.13 - 2.00 2692 117 0.90 16.66 0.99 0.98 2071.96| |alpha: min = 0.96 max = 0.98 mean = 0.97| |beta: min = 2071.96 max = 6285.51 mean = 4201.06| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.82 mean = 13.81| |phase err.(test): min = 0.00 max = 88.49 mean = 13.32| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1121 0.1102 0.1496 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1571 0.1558 0.1844 n_refl.: 17041 remove outliers: r(all,work,free)=0.1571 0.1558 0.1844 n_refl.: 17041 overall B=-0.22 to atoms: r(all,work,free)=0.1558 0.1545 0.1836 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1121 0.1102 0.1495 n_refl.: 17041 remove outliers: r(all,work,free)=0.1121 0.1102 0.1495 n_refl.: 17041 ======================== 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 0.3531 300.178 278.658 0.545 1.005 0.324 11.894-9.307 99.02 97 4 0.1715 488.408 480.929 0.918 1.006 0.320 9.237-7.194 100.00 213 7 0.1777 399.469 399.718 0.988 1.006 0.250 7.162-5.571 100.00 427 22 0.1557 299.802 293.323 0.927 1.005 0.202 5.546-4.326 100.00 867 58 0.0917 411.580 408.021 0.965 1.005 0.193 4.315-3.360 100.00 1859 96 0.0888 391.416 389.372 1.003 1.003 0.191 3.356-2.611 100.00 3867 181 0.1221 257.138 254.830 1.001 1.001 0.131 2.608-2.000 99.99 8818 434 0.1031 167.610 166.283 0.992 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.7706 ================= 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 : 0.2796 0.1824 0.083 5.311 8.8 119.3 19.9 258 0.000 1_bss: 0.1617 0.1657 0.083 5.311 8.4 118.9 19.5 258 0.000 1_settarget: 0.1617 0.1657 0.083 5.311 8.4 118.9 19.5 258 0.000 1_nqh: 0.1624 0.1663 0.083 5.311 8.4 118.9 19.5 258 0.010 1_weight: 0.1624 0.1663 0.083 5.311 8.4 118.9 19.5 258 0.010 1_xyzrec: 0.1348 0.1637 0.010 1.024 8.4 118.9 19.5 258 0.146 1_adp: 0.1276 0.1659 0.010 1.024 6.4 113.9 20.0 258 0.146 1_regHadp: 0.1279 0.1668 0.010 1.024 6.4 113.9 20.0 258 0.146 1_occ: 0.1273 0.1657 0.010 1.024 6.4 113.9 20.0 258 0.146 2_bss: 0.1272 0.1654 0.010 1.024 6.0 113.5 19.6 258 0.146 2_settarget: 0.1272 0.1654 0.010 1.024 6.0 113.5 19.6 258 0.146 2_updatecdl: 0.1272 0.1654 0.010 1.041 6.0 113.5 19.6 258 0.146 2_nqh: 0.1274 0.1654 0.010 1.041 6.0 113.5 19.6 258 0.140 2_sol: 0.1242 0.1576 0.010 1.041 6.0 112.4 20.8 361 n/a 2_weight: 0.1242 0.1576 0.010 1.041 6.0 112.4 20.8 361 n/a 2_xyzrec: 0.1217 0.1587 0.008 0.945 6.0 112.4 20.8 361 n/a 2_adp: 0.1198 0.1604 0.008 0.945 6.6 107.4 21.3 361 n/a 2_regHadp: 0.1199 0.1606 0.008 0.945 6.6 107.4 21.3 361 n/a 2_occ: 0.1195 0.1611 0.008 0.945 6.6 107.4 21.3 361 n/a 3_bss: 0.1189 0.1601 0.008 0.945 6.2 107.0 20.9 361 n/a 3_settarget: 0.1189 0.1601 0.008 0.945 6.2 107.0 20.9 361 n/a 3_updatecdl: 0.1189 0.1601 0.008 0.942 6.2 107.0 20.9 361 n/a 3_nqh: 0.1189 0.1602 0.008 0.942 6.2 107.0 20.9 361 n/a 3_sol: 0.1192 0.1572 0.008 0.942 6.2 107.0 20.9 404 n/a 3_weight: 0.1192 0.1572 0.008 0.942 6.2 107.0 20.9 404 n/a 3_xyzrec: 0.1176 0.1539 0.009 0.952 6.2 107.0 20.9 404 n/a 3_adp: 0.1157 0.1561 0.009 0.952 6.1 105.8 20.8 404 n/a 3_regHadp: 0.1157 0.1562 0.009 0.952 6.1 105.8 20.8 404 n/a 3_occ: 0.1150 0.1575 0.009 0.952 6.1 105.8 20.8 404 n/a 4_bss: 0.1147 0.1582 0.009 0.952 5.6 105.3 20.3 404 n/a 4_settarget: 0.1147 0.1582 0.009 0.952 5.6 105.3 20.3 404 n/a 4_updatecdl: 0.1147 0.1582 0.009 0.952 5.6 105.3 20.3 404 n/a 4_nqh: 0.1149 0.1580 0.009 0.952 5.6 105.3 20.3 404 n/a 4_sol: 0.1142 0.1519 0.009 0.952 5.6 105.3 20.7 442 n/a 4_weight: 0.1142 0.1519 0.009 0.952 5.6 105.3 20.7 442 n/a 4_xyzrec: 0.1126 0.1557 0.010 0.977 5.6 105.3 20.7 442 n/a 4_adp: 0.1115 0.1536 0.010 0.977 5.7 104.7 20.8 442 n/a 4_regHadp: 0.1115 0.1537 0.010 0.977 5.7 104.7 20.8 442 n/a 4_occ: 0.1107 0.1537 0.010 0.977 5.7 104.7 20.8 442 n/a 5_bss: 0.1106 0.1532 0.010 0.977 5.4 104.5 20.5 442 n/a 5_settarget: 0.1106 0.1532 0.010 0.977 5.4 104.5 20.5 442 n/a 5_updatecdl: 0.1106 0.1532 0.010 0.978 5.4 104.5 20.5 442 n/a 5_setrh: 0.1108 0.1531 0.010 0.978 5.4 104.5 20.5 442 n/a 5_nqh: 0.1108 0.1531 0.010 0.978 5.4 104.5 20.5 442 n/a 5_sol: 0.1105 0.1503 0.010 0.978 5.4 104.5 20.6 453 n/a 5_weight: 0.1105 0.1503 0.010 0.978 5.4 104.5 20.6 453 n/a 5_xyzrec: 0.1118 0.1496 0.010 1.020 5.4 104.5 20.6 453 n/a 5_adp: 0.1107 0.1494 0.010 1.020 5.3 103.7 20.8 453 n/a 5_regHadp: 0.1107 0.1494 0.010 1.020 5.3 103.7 20.8 453 n/a 5_occ: 0.1102 0.1496 0.010 1.020 5.3 103.7 20.8 453 n/a end: 0.1102 0.1495 0.010 1.020 5.1 103.5 20.6 453 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_6024882_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_6024882_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.8700 Refinement macro-cycles (run) : 904.1600 Write final files (write_after_run_outputs) : 19.9700 Total : 928.0000 Total CPU time: 15.87 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:40:53 PST -0800 (1735494053.80 s) Start R-work = 0.1617, R-free = 0.1657 Final R-work = 0.1102, R-free = 0.1495 =============================================================================== Job complete usr+sys time: 978.92 seconds wall clock time: 16 minutes 42.13 seconds (1002.13 seconds total)