Starting phenix.refine on Sun Dec 29 09:24:41 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_5239121.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 { phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_5239121.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_5239121.pdb" 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 =============================================================================== 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: 1.36, per 1000 atoms: 0.40 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.29 Conformation dependent library (CDL) restraints added in 105.1 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.64 - 0.89: 412 0.89 - 1.14: 1190 1.14 - 1.40: 598 1.40 - 1.65: 883 1.65 - 1.90: 70 Bond restraints: 3153 Sorted by residual: bond pdb=" N ILE A 31 " pdb=" CA ILE A 31 " ideal model delta sigma weight residual 1.459 1.193 0.266 1.24e-02 6.50e+03 4.60e+02 bond pdb=" N ILE A 105 " pdb=" CA ILE A 105 " ideal model delta sigma weight residual 1.458 1.223 0.235 1.19e-02 7.06e+03 3.89e+02 bond pdb=" C GLU A 16 " pdb=" O GLU A 16 " ideal model delta sigma weight residual 1.236 1.000 0.236 1.25e-02 6.40e+03 3.58e+02 bond pdb=" C AGLU A 96 " pdb=" O AGLU A 96 " ideal model delta sigma weight residual 1.237 1.443 -0.206 1.17e-02 7.31e+03 3.10e+02 bond pdb=" N VAL A 44 " pdb=" CA VAL A 44 " ideal model delta sigma weight residual 1.458 1.253 0.205 1.17e-02 7.31e+03 3.07e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.15: 2745 4.15 - 8.30: 1953 8.30 - 12.44: 831 12.44 - 16.59: 224 16.59 - 20.74: 24 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O BGLY A 65 " pdb=" C BGLY A 65 " pdb=" N BPRO A 66 " ideal model delta sigma weight residual 121.77 137.73 -15.96 1.00e+00 1.00e+00 2.55e+02 angle pdb=" CA LYS A 182 " pdb=" C LYS A 182 " pdb=" O LYS A 182 " ideal model delta sigma weight residual 121.07 137.12 -16.05 1.10e+00 8.26e-01 2.13e+02 angle pdb=" O ILE A 102 " pdb=" C ILE A 102 " pdb=" N ALA A 103 " ideal model delta sigma weight residual 123.20 137.69 -14.49 1.06e+00 8.90e-01 1.87e+02 angle pdb=" NE ARG A 156 " pdb=" CZ ARG A 156 " pdb=" NH2 ARG A 156 " ideal model delta sigma weight residual 119.20 131.37 -12.17 9.00e-01 1.23e+00 1.83e+02 angle pdb=" O ILE A 52 " pdb=" C ILE A 52 " pdb=" N ACYS A 53 " ideal model delta sigma weight residual 123.03 137.34 -14.31 1.11e+00 8.12e-01 1.66e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.32: 1280 15.32 - 30.63: 131 30.63 - 45.95: 45 45.95 - 61.27: 21 61.27 - 76.58: 4 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C VAL A 25 " pdb=" N VAL A 25 " pdb=" CA VAL A 25 " pdb=" CB VAL A 25 " ideal model delta harmonic sigma weight residual -122.00 -146.63 24.63 0 2.50e+00 1.60e-01 9.71e+01 dihedral pdb=" C LYS A 182 " pdb=" N LYS A 182 " pdb=" CA LYS A 182 " pdb=" CB LYS A 182 " ideal model delta harmonic sigma weight residual -122.60 -143.33 20.73 0 2.50e+00 1.60e-01 6.88e+01 dihedral pdb=" N VAL A 25 " pdb=" C VAL A 25 " pdb=" CA VAL A 25 " pdb=" CB VAL A 25 " ideal model delta harmonic sigma weight residual 123.40 143.55 -20.15 0 2.50e+00 1.60e-01 6.49e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.003 - 0.242: 102 0.242 - 0.482: 75 0.482 - 0.721: 44 0.721 - 0.960: 18 0.960 - 1.199: 4 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA VAL A 25 " pdb=" N VAL A 25 " pdb=" C VAL A 25 " pdb=" CB VAL A 25 " both_signs ideal model delta sigma weight residual False 2.44 1.24 1.20 2.00e-01 2.50e+01 3.60e+01 chirality pdb=" CA LYS A 182 " pdb=" N LYS A 182 " pdb=" C LYS A 182 " pdb=" CB LYS A 182 " both_signs ideal model delta sigma weight residual False 2.51 1.39 1.12 2.00e-01 2.50e+01 3.12e+01 chirality pdb=" CA ALA A 6 " pdb=" N ALA A 6 " pdb=" C ALA A 6 " pdb=" CB ALA A 6 " both_signs ideal model delta sigma weight residual False 2.48 3.47 -0.98 2.00e-01 2.50e+01 2.40e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " -0.002 2.00e-02 2.50e+03 6.68e-02 1.34e+02 pdb=" CG BTYR A 67 " 0.103 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " -0.081 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " -0.056 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " 0.070 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " -0.077 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " 0.094 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " 0.005 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " -0.067 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " 0.071 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " 0.004 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " -0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " -0.088 2.00e-02 2.50e+03 6.13e-02 1.13e+02 pdb=" CG TYR A 141 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " -0.069 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " 0.069 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " 0.091 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " -0.087 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " 0.027 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " 0.047 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " -0.075 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 68 " -0.042 2.00e-02 2.50e+03 8.69e-02 7.54e+01 pdb=" CG ASP A 68 " 0.150 2.00e-02 2.50e+03 pdb=" OD1 ASP A 68 " -0.051 2.00e-02 2.50e+03 pdb=" OD2 ASP A 68 " -0.057 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.29: 851 2.29 - 2.87: 7855 2.87 - 3.44: 10617 3.44 - 4.02: 15259 4.02 - 4.60: 22059 Nonbonded interactions: 56641 Sorted by model distance: nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.711 2.450 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.771 2.450 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.808 2.450 nonbonded pdb=" H LEU A 10 " pdb=" O ALA A 36 " model vdw 1.812 2.450 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.812 2.100 ... (remaining 56636 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_5239121_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= 0.2792 r_free= 0.1832 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.404668 | | target function (ml) not normalized (work): 71545.020690 | | target function (ml) not normalized (free): 3255.218212 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3202 0.2142 7.5451 5.025| | 2: 3.63 - 2.88 1.00 2711 122 0.2666 0.1742 4.3313 4.3452| | 3: 2.88 - 2.52 1.00 2682 148 0.2528 0.1778 4.1831 4.1924| | 4: 2.52 - 2.29 1.00 2661 139 0.2587 0.1526 3.5059 3.5497| | 5: 2.29 - 2.13 1.00 2678 122 0.2654 0.1396 3.3836 3.3448| | 6: 2.13 - 2.00 1.00 2692 117 0.2711 0.1972 3.3149 3.4546| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 1308.96| | 2: 3.63 - 2.88 2711 122 0.83 23.88 1.32 0.23 1308.96| | 3: 2.88 - 2.52 2682 148 0.73 32.78 1.28 0.23 1308.96| | 4: 2.52 - 2.29 2661 139 0.94 11.04 1.30 0.26 128.85| | 5: 2.29 - 2.13 2678 122 0.92 13.23 1.31 0.26 128.85| | 6: 2.13 - 2.00 2692 117 0.90 15.78 1.33 0.26 128.85| |alpha: min = 0.23 max = 0.26 mean = 0.25| |beta: min = 128.85 max = 1308.96 mean = 725.48| |figures of merit: min = 0.00 max = 1.00 mean = 0.87| |phase err.(work): min = 0.00 max = 89.87 mean = 19.06| |phase err.(test): min = 0.00 max = 89.87 mean = 19.20| |-----------------------------------------------------------------------------| ----------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 0.266 1557 Z= 5.538 Angle : 5.610 17.491 2118 Z= 3.877 Chirality : 0.426 1.199 243 Planarity : 0.033 0.128 284 Dihedral : 13.512 76.582 611 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 : 1.24 % Allowed : 2.48 % Favored : 96.27 % Cbeta Deviations : 32.43 % 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: -2.34 (0.51), residues: 224 helix: -3.09 (0.35), residues: 102 sheet: -0.83 (0.90), residues: 30 loop : 0.48 (0.66), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.075 0.013 ARG A 156 TYR 0.100 0.040 TYR A 141 PHE 0.087 0.036 PHE A 164 HIS 0.054 0.018 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= 0.2792 r_free= 0.1832 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.404668 | | target function (ml) not normalized (work): 71545.020690 | | target function (ml) not normalized (free): 3255.218212 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.3000 percent. r_work = 0.2922 r_free = 0.2005 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2869 0.2922 0.2005 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2869 0.2922 0.2005 n_refl.: 17050 remove outliers: r(all,work,free)=0.2158 0.2169 0.2005 n_refl.: 17045 overall B=-0.39 to atoms: r(all,work,free)=0.2133 0.2143 0.1987 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1620 0.1617 0.1685 n_refl.: 17045 remove outliers: r(all,work,free)=0.1619 0.1616 0.1685 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 0.4075 394.626 361.956 0.646 1.013 0.393 11.894-9.307 99.02 97 4 0.1839 633.387 616.702 0.924 1.014 0.380 9.237-7.194 100.00 213 7 0.2163 518.046 509.838 0.957 1.014 0.355 7.162-5.571 100.00 427 22 0.2341 388.794 376.476 0.921 1.012 0.288 5.546-4.326 100.00 867 58 0.1361 533.752 528.875 0.960 1.010 0.226 4.315-3.360 100.00 1859 96 0.1312 507.604 503.125 1.015 1.006 0.222 3.356-2.611 100.00 3867 181 0.1651 333.467 329.250 1.011 1.000 0.101 2.608-2.000 99.99 8818 434 0.1656 217.363 212.990 1.027 0.988 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.3773 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1616 r_free=0.1685 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1616 r_free=0.1685 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.320641 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.937834 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 0.1353 0.1627 0.0274 0.009 1.0 1.3 0.5 0.0 0 11.660 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.53 16.27 2.74 3.013 18.473 0.938 0.023 12.81 16.49 3.68 3.587 18.669 0.938 0.021 Individual atomic B min max mean iso aniso Overall: 6.06 113.91 19.87 4.10 1785 0 Protein: 6.06 112.99 17.10 4.10 1519 0 Water: 8.53 113.91 36.01 N/A 258 0 Other: 21.58 36.69 26.17 N/A 8 0 Chain A: 6.06 113.91 19.87 N/A 1785 0 Histogram: Values Number of atoms 6.06 - 16.85 1089 16.85 - 27.63 338 27.63 - 38.42 185 38.42 - 49.20 93 49.20 - 59.99 53 59.99 - 70.77 12 70.77 - 81.56 7 81.56 - 92.34 4 92.34 - 103.13 1 103.13 - 113.91 3 =========================== Idealize ADP of riding H ========================== r_work=0.1281 r_free=0.1649 r_work=0.1284 r_free=0.1657 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1284 r_free = 0.1657 target_work(ls_wunit_k1) = 0.021 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1279 r_free = 0.1651 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.25 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= 0.1279 r_free= 0.1651 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.020225 | | target function (ls_wunit_k1) not normalized (work): 328.388575 | | target function (ls_wunit_k1) not normalized (free): 26.850728 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1297 0.1279 0.1651 n_refl.: 17044 re-set all scales: r(all,work,free)=0.1905 0.1904 0.1978 n_refl.: 17044 remove outliers: r(all,work,free)=0.1905 0.1904 0.1978 n_refl.: 17044 overall B=-0.46 to atoms: r(all,work,free)=0.1872 0.1870 0.1960 n_refl.: 17044 bulk-solvent and scaling: r(all,work,free)=0.1295 0.1277 0.1643 n_refl.: 17044 remove outliers: r(all,work,free)=0.1293 0.1276 0.1643 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 0.3535 303.676 278.812 0.625 1.006 0.368 11.894-9.307 99.02 97 4 0.1698 488.415 477.577 0.918 1.007 0.358 9.237-7.194 100.00 213 7 0.1836 399.474 395.616 0.962 1.007 0.351 7.162-5.571 100.00 427 22 0.1840 299.806 294.230 0.932 1.006 0.301 5.546-4.326 100.00 867 58 0.1053 411.585 408.900 0.959 1.006 0.211 4.315-3.360 100.00 1859 96 0.0932 391.422 390.849 1.015 1.004 0.202 3.356-2.611 100.00 3867 181 0.1295 257.142 255.811 1.010 1.001 0.101 2.608-2.000 99.99 8818 434 0.1350 167.612 166.296 1.011 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9583 b_overall=-1.1495 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1276 r_free=0.1643 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1276 r_free=0.1643 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1276 r_free=0.1643 | n_water=258 | time (s): 0.820 (total time: 0.820) Filter (dist) r_work=0.1282 r_free=0.1632 | n_water=253 | time (s): 21.040 (total time: 21.860) Filter (q & B) r_work=0.1282 r_free=0.1632 | n_water=251 | time (s): 1.690 (total time: 23.550) Compute maps r_work=0.1282 r_free=0.1632 | n_water=251 | time (s): 0.620 (total time: 24.170) Filter (map) r_work=0.1314 r_free=0.1629 | n_water=215 | time (s): 2.240 (total time: 26.410) Find peaks r_work=0.1314 r_free=0.1629 | n_water=215 | time (s): 0.560 (total time: 26.970) Add new water r_work=0.1526 r_free=0.1881 | n_water=369 | time (s): 1.970 (total time: 28.940) Refine new water occ: r_work=0.1332 r_free=0.1568 adp: r_work=0.1273 r_free=0.1580 occ: r_work=0.1281 r_free=0.1537 adp: r_work=0.1248 r_free=0.1550 occ: r_work=0.1250 r_free=0.1537 adp: r_work=0.1239 r_free=0.1539 ADP+occupancy (water only), MIN, final r_work=0.1239 r_free=0.1539 r_work=0.1239 r_free=0.1539 | n_water=369 | time (s): 18.970 (total time: 47.910) Filter (q & B) r_work=0.1241 r_free=0.1546 | n_water=360 | time (s): 1.570 (total time: 49.480) Filter (dist only) r_work=0.1240 r_free=0.1546 | n_water=359 | time (s): 28.620 (total time: 78.100) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.107666 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.002200 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 0.1211 0.1574 0.0363 0.008 0.9 2.2 0.5 0.0 0 12.554 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.11 15.74 3.63 4.173 20.839 1.002 0.018 11.97 15.94 3.97 4.266 21.162 1.002 0.018 Individual atomic B min max mean iso aniso Overall: 6.95 107.53 21.21 4.34 1886 0 Protein: 6.95 107.53 17.63 4.32 1519 0 Water: 8.85 67.14 36.05 N/A 359 0 Other: 25.81 46.55 36.75 N/A 8 0 Chain A: 6.95 107.53 19.44 N/A 1742 0 Chain S: 18.62 67.14 42.64 N/A 144 0 Histogram: Values Number of atoms 6.95 - 17.00 1057 17.00 - 27.06 354 27.06 - 37.12 212 37.12 - 47.18 160 47.18 - 57.24 64 57.24 - 67.29 28 67.29 - 77.35 4 77.35 - 87.41 3 87.41 - 97.47 2 97.47 - 107.53 2 =========================== Idealize ADP of riding H ========================== r_work=0.1197 r_free=0.1594 r_work=0.1199 r_free=0.1595 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 r_free = 0.1595 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1193 r_free = 0.1595 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17042 (all), 4.74 % free)------------| | | | r_work= 0.1193 r_free= 0.1595 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.017023 | | target function (ls_wunit_k1) not normalized (work): 276.363200 | | target function (ls_wunit_k1) not normalized (free): 24.526165 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1213 0.1193 0.1595 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1739 0.1730 0.1934 n_refl.: 17042 remove outliers: r(all,work,free)=0.1739 0.1730 0.1934 n_refl.: 17042 overall B=-0.46 to atoms: r(all,work,free)=0.1710 0.1701 0.1913 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1208 0.1189 0.1588 n_refl.: 17042 remove outliers: r(all,work,free)=0.1207 0.1187 0.1588 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 0.3162 300.511 285.814 0.597 1.005 0.340 11.894-9.307 99.02 97 4 0.1562 488.415 485.112 0.918 1.006 0.334 9.237-7.194 100.00 213 7 0.1698 399.474 399.702 0.973 1.006 0.311 7.162-5.571 100.00 427 22 0.1537 299.806 296.220 0.936 1.005 0.261 5.546-4.326 100.00 867 58 0.0869 411.585 409.324 0.962 1.005 0.211 4.315-3.360 100.00 1859 96 0.0813 391.422 390.773 1.016 1.003 0.202 3.356-2.611 100.00 3867 181 0.1199 257.142 256.315 1.010 1.000 0.122 2.608-2.000 99.99 8818 434 0.1334 167.612 166.525 1.011 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-1.1517 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1187 r_free=0.1588 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1187 r_free=0.1588 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1187 r_free=0.1588 | n_water=359 | time (s): 0.800 (total time: 0.800) Filter (dist) r_work=0.1187 r_free=0.1587 | n_water=358 | time (s): 29.520 (total time: 30.320) Filter (q & B) r_work=0.1187 r_free=0.1587 | n_water=358 | time (s): 0.820 (total time: 31.140) Compute maps r_work=0.1187 r_free=0.1587 | n_water=358 | time (s): 0.600 (total time: 31.740) Filter (map) r_work=0.1253 r_free=0.1619 | n_water=271 | time (s): 1.840 (total time: 33.580) Find peaks r_work=0.1253 r_free=0.1619 | n_water=271 | time (s): 0.450 (total time: 34.030) Add new water r_work=0.1427 r_free=0.1797 | n_water=418 | time (s): 1.760 (total time: 35.790) Refine new water occ: r_work=0.1239 r_free=0.1553 adp: r_work=0.1232 r_free=0.1566 occ: r_work=0.1215 r_free=0.1522 adp: r_work=0.1205 r_free=0.1534 occ: r_work=0.1198 r_free=0.1507 adp: r_work=0.1189 r_free=0.1512 ADP+occupancy (water only), MIN, final r_work=0.1189 r_free=0.1512 r_work=0.1189 r_free=0.1512 | n_water=418 | time (s): 23.080 (total time: 58.870) Filter (q & B) r_work=0.1193 r_free=0.1514 | n_water=406 | time (s): 2.150 (total time: 61.020) Filter (dist only) r_work=0.1193 r_free=0.1514 | n_water=406 | time (s): 31.700 (total time: 92.720) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.863348 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.150594 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 0.1168 0.1515 0.0347 0.009 1.0 4.2 0.5 0.0 0 0.932 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.68 15.15 3.47 4.369 21.366 0.151 4.985 11.44 15.16 3.72 4.903 21.273 0.151 4.962 Individual atomic B min max mean iso aniso Overall: 6.07 104.44 20.73 4.69 1933 0 Protein: 6.07 104.44 16.79 4.67 1519 0 Water: 8.90 63.92 35.20 N/A 406 0 Other: 26.72 46.77 34.85 N/A 8 0 Chain A: 6.07 104.44 18.62 N/A 1739 0 Chain S: 17.32 63.92 39.68 N/A 194 0 Histogram: Values Number of atoms 6.07 - 15.91 1061 15.91 - 25.74 347 25.74 - 35.58 230 35.58 - 45.42 176 45.42 - 55.26 74 55.26 - 65.09 33 65.09 - 74.93 3 74.93 - 84.77 4 84.77 - 94.60 3 94.60 - 104.44 2 =========================== Idealize ADP of riding H ========================== r_work=0.1144 r_free=0.1516 r_work=0.1144 r_free=0.1517 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1144 r_free = 0.1517 target_work(ml) = 4.962 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1140 r_free = 0.1526 target_work(ml) = 4.959 | | 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.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1140 r_free= 0.1526 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.959353 | | target function (ml) not normalized (work): 80510.139916 | | target function (ml) not normalized (free): 4179.337616 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1159 0.1140 0.1526 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1644 0.1638 0.1815 n_refl.: 17041 remove outliers: r(all,work,free)=0.1644 0.1638 0.1815 n_refl.: 17041 overall B=-0.31 to atoms: r(all,work,free)=0.1624 0.1617 0.1805 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1155 0.1137 0.1520 n_refl.: 17041 remove outliers: r(all,work,free)=0.1155 0.1136 0.1520 n_refl.: 17040 ======================== 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 93.75 85 5 0.3387 296.943 281.523 0.570 1.000 0.334 11.894-9.307 99.02 97 4 0.1750 488.415 483.721 0.922 1.002 0.330 9.237-7.194 100.00 213 7 0.1749 399.474 400.377 0.989 1.002 0.270 7.162-5.571 100.00 427 22 0.1591 299.806 294.385 0.940 1.002 0.240 5.546-4.326 100.00 867 58 0.0920 411.585 408.078 0.965 1.003 0.221 4.315-3.360 100.00 1859 96 0.0884 391.422 388.884 1.009 1.002 0.211 3.356-2.611 100.00 3867 181 0.1271 257.142 254.710 1.005 1.002 0.151 2.608-2.000 99.99 8818 434 0.1088 167.612 166.371 1.003 1.001 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-1.0790 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1136 r_free=0.1520 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1136 r_free=0.1520 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1136 r_free=0.1520 | n_water=406 | time (s): 0.740 (total time: 0.740) Filter (dist) r_work=0.1136 r_free=0.1520 | n_water=406 | time (s): 30.950 (total time: 31.690) Filter (q & B) r_work=0.1136 r_free=0.1520 | n_water=406 | time (s): 1.120 (total time: 32.810) Compute maps r_work=0.1136 r_free=0.1520 | n_water=406 | time (s): 0.830 (total time: 33.640) Filter (map) r_work=0.1199 r_free=0.1529 | n_water=311 | time (s): 2.120 (total time: 35.760) Find peaks r_work=0.1199 r_free=0.1529 | n_water=311 | time (s): 0.580 (total time: 36.340) Add new water r_work=0.1347 r_free=0.1675 | n_water=454 | time (s): 2.160 (total time: 38.500) Refine new water occ: r_work=0.1173 r_free=0.1513 adp: r_work=0.1166 r_free=0.1517 occ: r_work=0.1150 r_free=0.1494 adp: r_work=0.1142 r_free=0.1496 occ: r_work=0.1134 r_free=0.1485 adp: r_work=0.1127 r_free=0.1485 ADP+occupancy (water only), MIN, final r_work=0.1127 r_free=0.1485 r_work=0.1127 r_free=0.1485 | n_water=454 | time (s): 25.720 (total time: 64.220) Filter (q & B) r_work=0.1131 r_free=0.1485 | n_water=443 | time (s): 1.630 (total time: 65.850) Filter (dist only) r_work=0.1131 r_free=0.1486 | n_water=442 | time (s): 37.150 (total time: 103.000) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.851330 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.165692 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 0.1117 0.1522 0.0405 0.010 1.0 3.5 0.5 0.0 0 0.926 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.17 15.22 4.05 4.481 20.935 0.166 4.944 11.04 15.22 4.18 4.641 20.954 0.166 4.939 Individual atomic B min max mean iso aniso Overall: 5.26 101.26 20.84 4.84 1969 0 Protein: 5.26 101.26 16.37 4.83 1519 0 Water: 8.22 64.55 35.88 N/A 442 0 Other: 29.24 50.30 37.97 N/A 8 0 Chain A: 5.26 101.26 18.16 N/A 1738 0 Chain S: 17.00 64.55 41.00 N/A 231 0 Histogram: Values Number of atoms 5.26 - 14.86 1000 14.86 - 24.46 392 24.46 - 34.06 212 34.06 - 43.66 193 43.66 - 53.26 115 53.26 - 62.86 39 62.86 - 72.46 7 72.46 - 82.06 5 82.06 - 91.66 3 91.66 - 101.26 3 =========================== Idealize ADP of riding H ========================== r_work=0.1104 r_free=0.1522 r_work=0.1104 r_free=0.1522 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1104 r_free = 0.1522 target_work(ml) = 4.939 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1094 r_free = 0.1522 target_work(ml) = 4.934 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1094 r_free= 0.1522 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ml) (work): 4.933502 | | target function (ml) not normalized (work): 80085.531925 | | target function (ml) not normalized (free): 4170.286745 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1115 0.1094 0.1522 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1571 0.1561 0.1788 n_refl.: 17040 remove outliers: r(all,work,free)=0.1571 0.1561 0.1788 n_refl.: 17040 overall B=-0.24 to atoms: r(all,work,free)=0.1556 0.1546 0.1781 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1115 0.1095 0.1517 n_refl.: 17040 remove outliers: r(all,work,free)=0.1115 0.1095 0.1517 n_refl.: 17040 ======================== 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 93.75 85 5 0.3521 296.943 279.073 0.546 1.004 0.316 11.894-9.307 99.02 97 4 0.1668 488.415 485.164 0.922 1.005 0.307 9.237-7.194 100.00 213 7 0.1698 399.474 401.703 0.995 1.005 0.250 7.162-5.571 100.00 427 22 0.1512 299.806 294.646 0.935 1.005 0.215 5.546-4.326 100.00 867 58 0.0897 411.585 408.723 0.963 1.005 0.205 4.315-3.360 100.00 1859 96 0.0855 391.422 389.130 1.004 1.003 0.201 3.356-2.611 100.00 3867 181 0.1231 257.142 254.994 1.000 1.001 0.131 2.608-2.000 99.99 8818 434 0.1037 167.612 166.374 0.995 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.8446 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1095 r_free=0.1517 After: r_work=0.1097 r_free=0.1516 ================================== NQH flips ================================== r_work=0.1097 r_free=0.1516 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1097 r_free=0.1516 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1097 r_free=0.1516 | n_water=442 | time (s): 0.950 (total time: 0.950) Filter (dist) r_work=0.1100 r_free=0.1520 | n_water=441 | time (s): 38.920 (total time: 39.870) Filter (q & B) r_work=0.1101 r_free=0.1520 | n_water=440 | time (s): 1.770 (total time: 41.640) Compute maps r_work=0.1101 r_free=0.1520 | n_water=440 | time (s): 0.580 (total time: 42.220) Filter (map) r_work=0.1178 r_free=0.1542 | n_water=334 | time (s): 1.700 (total time: 43.920) Find peaks r_work=0.1178 r_free=0.1542 | n_water=334 | time (s): 0.460 (total time: 44.380) Add new water r_work=0.1306 r_free=0.1643 | n_water=470 | time (s): 1.460 (total time: 45.840) Refine new water occ: r_work=0.1141 r_free=0.1508 adp: r_work=0.1132 r_free=0.1510 occ: r_work=0.1119 r_free=0.1489 adp: r_work=0.1111 r_free=0.1491 occ: r_work=0.1104 r_free=0.1473 adp: r_work=0.1098 r_free=0.1477 ADP+occupancy (water only), MIN, final r_work=0.1098 r_free=0.1477 r_work=0.1098 r_free=0.1477 | n_water=470 | time (s): 37.860 (total time: 83.700) Filter (q & B) r_work=0.1102 r_free=0.1481 | n_water=457 | time (s): 1.900 (total time: 85.600) Filter (dist only) r_work=0.1102 r_free=0.1481 | n_water=456 | time (s): 39.890 (total time: 125.490) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.017740 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.174397 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 0.1116 0.1514 0.0398 0.010 1.0 5.1 0.5 0.0 0 1.009 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.16 15.14 3.98 4.537 20.698 0.174 4.944 11.06 15.00 3.94 4.655 20.758 0.174 4.933 Individual atomic B min max mean iso aniso Overall: 5.29 98.95 20.80 5.04 1983 0 Protein: 5.29 98.95 16.13 5.03 1519 0 Water: 8.04 71.14 36.12 N/A 456 0 Other: 27.98 45.57 35.37 N/A 8 0 Chain A: 5.29 98.95 17.87 N/A 1737 0 Chain S: 14.62 71.14 41.54 N/A 246 0 Histogram: Values Number of atoms 5.29 - 14.66 1005 14.66 - 24.02 386 24.02 - 33.39 205 33.39 - 42.76 192 42.76 - 52.12 136 52.12 - 61.49 32 61.49 - 70.86 17 70.86 - 80.22 1 80.22 - 89.59 5 89.59 - 98.95 4 =========================== Idealize ADP of riding H ========================== r_work=0.1106 r_free=0.1500 r_work=0.1105 r_free=0.1500 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1105 r_free = 0.1500 target_work(ml) = 4.933 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1099 r_free = 0.1498 target_work(ml) = 4.928 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1099 r_free= 0.1498 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.928340 | | target function (ml) not normalized (work): 80001.748637 | | target function (ml) not normalized (free): 4159.125829 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.64 1.00 2810 159 0.1114 0.1351 5.4516 5.6233| | 2: 3.63 - 2.88 1.00 2711 122 0.1076 0.1527 5.2126 5.3768| | 3: 2.88 - 2.52 1.00 2681 148 0.1346 0.1709 5.1234 5.1908| | 4: 2.52 - 2.29 1.00 2661 139 0.0926 0.1480 4.6177 4.9234| | 5: 2.29 - 2.13 1.00 2678 122 0.0960 0.1445 4.5708 4.892| | 6: 2.13 - 2.00 1.00 2692 117 0.1119 0.1716 4.5643 4.7832| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2810 159 0.95 8.77 1.00 0.96 6270.06| | 2: 3.63 - 2.88 2711 122 0.92 12.65 1.01 0.96 6270.06| | 3: 2.88 - 2.52 2681 148 0.88 18.77 0.99 0.96 6270.06| | 4: 2.52 - 2.29 2661 139 0.93 11.99 1.01 0.97 2067.12| | 5: 2.29 - 2.13 2678 122 0.92 13.98 1.00 0.97 2067.12| | 6: 2.13 - 2.00 2692 117 0.90 16.60 0.99 0.97 2067.12| |alpha: min = 0.96 max = 0.97 mean = 0.97| |beta: min = 2067.12 max = 6270.06 mean = 4190.73| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.86 mean = 13.76| |phase err.(test): min = 0.00 max = 87.03 mean = 13.32| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1119 0.1099 0.1498 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1560 0.1551 0.1780 n_refl.: 17040 remove outliers: r(all,work,free)=0.1560 0.1551 0.1780 n_refl.: 17040 overall B=-0.22 to atoms: r(all,work,free)=0.1548 0.1538 0.1773 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1119 0.1100 0.1499 n_refl.: 17040 remove outliers: r(all,work,free)=0.1119 0.1100 0.1499 n_refl.: 17040 ======================== 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 93.75 85 5 0.3584 296.943 278.876 0.565 1.005 0.330 11.894-9.307 99.02 97 4 0.1726 488.415 484.674 0.954 1.006 0.330 9.237-7.194 100.00 213 7 0.1725 399.474 401.542 1.033 1.006 0.230 7.162-5.571 100.00 427 22 0.1531 299.806 295.159 0.972 1.005 0.215 5.546-4.326 100.00 867 58 0.0931 411.585 408.819 0.999 1.005 0.193 4.315-3.360 100.00 1859 96 0.0875 391.422 389.025 1.040 1.003 0.177 3.356-2.611 100.00 3867 181 0.1225 257.142 254.817 1.037 1.000 0.121 2.608-2.000 99.99 8818 434 0.1030 167.612 166.291 1.025 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9964 b_overall=-0.6471 ================= 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 : 0.2792 0.1832 0.083 5.610 8.8 119.3 19.9 258 0.000 1_bss: 0.1616 0.1685 0.083 5.610 8.5 118.9 19.5 258 0.000 1_settarget: 0.1616 0.1685 0.083 5.610 8.5 118.9 19.5 258 0.000 1_nqh: 0.1616 0.1685 0.083 5.610 8.5 118.9 19.5 258 0.000 1_weight: 0.1616 0.1685 0.083 5.610 8.5 118.9 19.5 258 0.000 1_xyzrec: 0.1353 0.1627 0.009 0.983 8.5 118.9 19.5 258 0.142 1_adp: 0.1281 0.1649 0.009 0.983 6.1 113.9 19.9 258 0.142 1_regHadp: 0.1284 0.1657 0.009 0.983 6.1 113.9 19.9 258 0.142 1_occ: 0.1279 0.1651 0.009 0.983 6.1 113.9 19.9 258 0.142 2_bss: 0.1276 0.1643 0.009 0.983 5.6 113.5 19.4 258 0.142 2_settarget: 0.1276 0.1643 0.009 0.983 5.6 113.5 19.4 258 0.142 2_updatecdl: 0.1276 0.1643 0.009 1.004 5.6 113.5 19.4 258 0.142 2_nqh: 0.1276 0.1643 0.009 1.004 5.6 113.5 19.4 258 0.142 2_sol: 0.1240 0.1546 0.009 1.004 5.6 112.5 20.6 359 n/a 2_weight: 0.1240 0.1546 0.009 1.004 5.6 112.5 20.6 359 n/a 2_xyzrec: 0.1211 0.1574 0.008 0.942 5.6 112.5 20.6 359 n/a 2_adp: 0.1197 0.1594 0.008 0.942 6.9 107.5 21.2 359 n/a 2_regHadp: 0.1199 0.1595 0.008 0.942 6.9 107.5 21.2 359 n/a 2_occ: 0.1193 0.1595 0.008 0.942 6.9 107.5 21.2 359 n/a 3_bss: 0.1187 0.1588 0.008 0.942 6.5 107.1 20.8 359 n/a 3_settarget: 0.1187 0.1588 0.008 0.942 6.5 107.1 20.8 359 n/a 3_updatecdl: 0.1187 0.1588 0.008 0.940 6.5 107.1 20.8 359 n/a 3_nqh: 0.1187 0.1588 0.008 0.940 6.5 107.1 20.8 359 n/a 3_sol: 0.1193 0.1514 0.008 0.940 6.5 107.1 20.9 406 n/a 3_weight: 0.1193 0.1514 0.008 0.940 6.5 107.1 20.9 406 n/a 3_xyzrec: 0.1168 0.1515 0.009 0.963 6.5 107.1 20.9 406 n/a 3_adp: 0.1144 0.1516 0.009 0.963 6.1 104.4 20.7 406 n/a 3_regHadp: 0.1144 0.1517 0.009 0.963 6.1 104.4 20.7 406 n/a 3_occ: 0.1140 0.1526 0.009 0.963 6.1 104.4 20.7 406 n/a 4_bss: 0.1136 0.1520 0.009 0.963 5.8 104.1 20.4 406 n/a 4_settarget: 0.1136 0.1520 0.009 0.963 5.8 104.1 20.4 406 n/a 4_updatecdl: 0.1136 0.1520 0.009 0.962 5.8 104.1 20.4 406 n/a 4_nqh: 0.1136 0.1520 0.009 0.962 5.8 104.1 20.4 406 n/a 4_sol: 0.1131 0.1486 0.009 0.962 5.8 104.1 20.8 442 n/a 4_weight: 0.1131 0.1486 0.009 0.962 5.8 104.1 20.8 442 n/a 4_xyzrec: 0.1117 0.1522 0.010 0.973 5.8 104.1 20.8 442 n/a 4_adp: 0.1104 0.1522 0.010 0.973 5.3 101.3 20.8 442 n/a 4_regHadp: 0.1104 0.1522 0.010 0.973 5.3 101.3 20.8 442 n/a 4_occ: 0.1094 0.1522 0.010 0.973 5.3 101.3 20.8 442 n/a 5_bss: 0.1095 0.1517 0.010 0.973 5.0 101.0 20.6 442 n/a 5_settarget: 0.1095 0.1517 0.010 0.973 5.0 101.0 20.6 442 n/a 5_updatecdl: 0.1095 0.1517 0.010 0.974 5.0 101.0 20.6 442 n/a 5_setrh: 0.1097 0.1516 0.010 0.974 5.0 101.0 20.6 442 n/a 5_nqh: 0.1097 0.1516 0.010 0.974 5.0 101.0 20.6 442 n/a 5_sol: 0.1102 0.1481 0.010 0.974 5.0 101.0 20.7 456 n/a 5_weight: 0.1102 0.1481 0.010 0.974 5.0 101.0 20.7 456 n/a 5_xyzrec: 0.1116 0.1514 0.010 1.020 5.0 101.0 20.7 456 n/a 5_adp: 0.1106 0.1500 0.010 1.020 5.3 99.0 20.8 456 n/a 5_regHadp: 0.1105 0.1500 0.010 1.020 5.3 99.0 20.8 456 n/a 5_occ: 0.1099 0.1498 0.010 1.020 5.3 99.0 20.8 456 n/a end: 0.1100 0.1499 0.010 1.020 5.1 98.7 20.6 456 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_5239121_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_5239121_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.0300 Refinement macro-cycles (run) : 944.7300 Write final files (write_after_run_outputs) : 21.0800 Total : 968.8400 Total CPU time: 16.49 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:31 PST -0800 (1735494091.31 s) Start R-work = 0.1616, R-free = 0.1685 Final R-work = 0.1100, R-free = 0.1499 =============================================================================== Job complete usr+sys time: 1011.60 seconds wall clock time: 17 minutes 15.08 seconds (1035.08 seconds total)