Starting phenix.refine on Sun Dec 29 09:10:03 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_9291273.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Adding command-line PHIL: ------------------------- xray_data.high_resolution=3 ordered_solvent.low_resolution=4 No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 3 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_9291273.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_9291273.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 2 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: 1.27, per 1000 atoms: 0.38 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.31 Conformation dependent library (CDL) restraints added in 124.5 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.64 - 0.90: 454 0.90 - 1.17: 1203 1.17 - 1.44: 682 1.44 - 1.70: 798 1.70 - 1.97: 16 Bond restraints: 3153 Sorted by residual: bond pdb=" C GLY A 136 " pdb=" N GLY A 137 " ideal model delta sigma weight residual 1.329 1.121 0.208 1.00e-02 1.00e+04 4.32e+02 bond pdb=" N PRO A 127 " pdb=" CD PRO A 127 " ideal model delta sigma weight residual 1.473 1.198 0.275 1.40e-02 5.10e+03 3.85e+02 bond pdb=" C SER A 142 " pdb=" O SER A 142 " ideal model delta sigma weight residual 1.234 1.017 0.216 1.22e-02 6.72e+03 3.15e+02 bond pdb=" CG HIS A 126 " pdb=" ND1 HIS A 126 " ideal model delta sigma weight residual 1.378 1.189 0.189 1.10e-02 8.26e+03 2.95e+02 bond pdb=" C BTYR A 67 " pdb=" N ASP A 68 " ideal model delta sigma weight residual 1.333 1.584 -0.251 1.49e-02 4.50e+03 2.83e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.24: 2960 4.24 - 8.48: 1845 8.48 - 12.72: 762 12.72 - 16.96: 180 16.96 - 21.20: 30 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O ILE A 21 " pdb=" C ILE A 21 " pdb=" N PRO A 22 " ideal model delta sigma weight residual 120.07 108.45 11.62 7.10e-01 1.98e+00 2.68e+02 angle pdb=" OD1 ASN A 81 " pdb=" CG ASN A 81 " pdb=" ND2 ASN A 81 " ideal model delta sigma weight residual 122.60 137.39 -14.79 1.00e+00 1.00e+00 2.19e+02 angle pdb=" NE ARG A 27 " pdb=" CZ ARG A 27 " pdb=" NH2 ARG A 27 " ideal model delta sigma weight residual 119.20 106.48 12.72 9.00e-01 1.23e+00 2.00e+02 angle pdb=" O ILE A 117 " pdb=" C ILE A 117 " pdb=" N GLY A 118 " ideal model delta sigma weight residual 122.93 108.17 14.76 1.06e+00 8.90e-01 1.94e+02 angle pdb=" O LEU A 72 " pdb=" C LEU A 72 " pdb=" N PRO A 73 " ideal model delta sigma weight residual 120.85 134.61 -13.76 1.01e+00 9.80e-01 1.86e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.66: 1269 15.66 - 31.32: 145 31.32 - 46.97: 46 46.97 - 62.63: 19 62.63 - 78.28: 2 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C GLU A 116 " pdb=" N GLU A 116 " pdb=" CA GLU A 116 " pdb=" CB GLU A 116 " ideal model delta harmonic sigma weight residual -122.60 -142.73 20.13 0 2.50e+00 1.60e-01 6.48e+01 dihedral pdb=" C VAL A 186 " pdb=" N VAL A 186 " pdb=" CA VAL A 186 " pdb=" CB VAL A 186 " ideal model delta harmonic sigma weight residual -122.00 -141.43 19.43 0 2.50e+00 1.60e-01 6.04e+01 dihedral pdb=" C ARG A 27 " pdb=" N ARG A 27 " pdb=" CA ARG A 27 " pdb=" CB ARG A 27 " ideal model delta harmonic sigma weight residual -122.60 -141.59 18.99 0 2.50e+00 1.60e-01 5.77e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.004 - 0.244: 104 0.244 - 0.485: 83 0.485 - 0.725: 39 0.725 - 0.966: 15 0.966 - 1.206: 2 Chirality restraints: 243 Sorted by residual: chirality pdb=" CG LEU A 172 " pdb=" CB LEU A 172 " pdb=" CD1 LEU A 172 " pdb=" CD2 LEU A 172 " both_signs ideal model delta sigma weight residual False -2.59 -1.38 -1.21 2.00e-01 2.50e+01 3.64e+01 chirality pdb=" CB THR A 110 " pdb=" CA THR A 110 " pdb=" OG1 THR A 110 " pdb=" CG2 THR A 110 " both_signs ideal model delta sigma weight residual False 2.55 1.57 0.98 2.00e-01 2.50e+01 2.42e+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 3.44 -0.96 2.00e-01 2.50e+01 2.29e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.049 2.00e-02 2.50e+03 7.54e-02 1.71e+02 pdb=" CG PHE A 119 " -0.127 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " 0.042 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.074 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.067 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " 0.071 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.064 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.007 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.083 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " -0.078 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " -0.122 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " -0.053 2.00e-02 2.50e+03 6.15e-02 1.14e+02 pdb=" CG ATYR A 67 " 0.023 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " -0.132 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " 0.085 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " 0.068 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " -0.033 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " -0.056 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " -0.031 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " 0.027 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " 0.040 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " 0.072 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " 0.055 2.00e-02 2.50e+03 5.97e-02 1.07e+02 pdb=" CG TYR A 141 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " -0.073 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " -0.079 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " 0.057 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " -0.086 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " 0.036 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " -0.015 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " 0.093 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " 0.068 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " -0.014 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.30: 911 2.30 - 2.87: 7913 2.87 - 3.45: 10588 3.45 - 4.02: 15323 4.02 - 4.60: 21834 Nonbonded interactions: 56569 Sorted by model distance: nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.719 2.100 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.823 2.100 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.830 2.450 nonbonded pdb=" O VAL A 8 " pdb=" H ALA A 36 " model vdw 1.844 2.450 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.849 2.100 ... (remaining 56564 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 6 Type Number sf(0) Gaussians S 10 15.96 2 O1- 2 8.97 2 O 551 7.97 1 N 265 6.97 1 C 957 5.97 2 H 1596 1.00 1 sf(0) = scattering factor at diffraction angle 0. =========================== Regularize ADP if needed ========================== ========================== Anomalous scatterer groups ========================= All atoms refined with f_prime=0 and f_double_prime=0. ====================== Modifying start model if requested ===================== ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 3381 n_use_u_iso = 1596 n_use_u_aniso = 1785 n_grad_site = 0 n_grad_u_iso = 0 n_grad_u_aniso = 0 n_grad_occupancy = 0 n_grad_fp = 0 n_grad_fdp = 0 total number of scatterers = 3381 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (3381 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 1596 aniso = 1785) group_adp = False (0 atoms in 0 groups) tls = False (0 atoms in 0 groups) occupancies = True (876 atoms) group_anomalous = False ============================ Non-default parameters =========================== A complete record of all parameters was written to the .eff file above. Below are only the non-defaults. #phil __ON__ refinement { electron_density_maps { map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT" mtz_label_phases = "PH2FOFCWT" fill_missing_f_obs = True } map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT_no_fill" mtz_label_phases = "PH2FOFCWT_no_fill" } map_coefficients { map_type = "mFo-DFc" mtz_label_amplitudes = "FOFCWT" mtz_label_phases = "PHFOFCWT" } map_coefficients { map_type = "anomalous" mtz_label_amplitudes = "ANOM" mtz_label_phases = "PANOM" } map { map_type = "2mFo-DFc" fill_missing_f_obs = True } map { map_type = "2mFo-DFc" } map { map_type = "mFo-DFc" } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } hydrogens { refine = individual *riding Auto } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } output { prefix = "shake_9291273_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1596 occupancy sum: 1438.50 (% of total atoms 46.85) Rotatable: count: 507 occupancy sum: 483.00 (% of total atoms 15.73) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.00 - 49.25 A, n_refl.=5182 (all), 4.86 % free)-------------| | | | r_work= 0.3623 r_free= 0.1992 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.469573 | | target function (ml) not normalized (work): 22034.994874 | | target function (ml) not normalized (free): 1145.734009 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 49.25 - 3.79 1.00 2500 142 0.3810 0.2205 4.8583 4.9013| | 2: 3.78 - 3.00 1.00 2430 110 0.3396 0.1630 4.0697 4.0887| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 49.25 - 3.79 2500 142 0.50 48.93 0.83 0.13 6619.33| | 2: 3.78 - 3.00 2430 110 0.94 11.21 1.48 0.26 443.91| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 373.55 max = 12085.90 mean = 3575.46| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 90.00 mean = 30.34| |phase err.(test): min = 0.00 max = 89.87 mean = 33.19| |-----------------------------------------------------------------------------| ----------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 0.275 1557 Z= 5.463 Angle : 5.274 19.994 2118 Z= 3.722 Chirality : 0.402 1.206 243 Planarity : 0.031 0.090 284 Dihedral : 13.567 78.285 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.24 % Favored : 96.22 % Rotamer: Outliers : 2.48 % Allowed : 3.11 % Favored : 94.41 % 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: -3.03 (0.45), residues: 224 helix: -2.85 (0.34), residues: 108 sheet: -2.04 (0.68), residues: 30 loop : -0.39 (0.61), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.094 0.019 ARG A 5 TYR 0.076 0.045 TYR A 141 PHE 0.119 0.031 PHE A 119 HIS 0.069 0.020 HIS A 138 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 1785 0 Protein: 8.85 115.78 16.79 3.90 1519 0 Water: 11.36 119.30 38.03 N/A 258 0 Other: 19.04 26.29 21.71 N/A 8 0 Chain A: 8.85 119.30 19.89 N/A 1785 0 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 3.00 - 49.25 A, n_refl.=5182 (all), 4.86 % free)-------------| | | | r_work= 0.3623 r_free= 0.1992 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.469573 | | target function (ml) not normalized (work): 22034.994874 | | target function (ml) not normalized (free): 1145.734009 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3577 0.3655 0.2073 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3577 0.3655 0.2073 n_refl.: 5182 remove outliers: r(all,work,free)=0.2528 0.2555 0.2073 n_refl.: 5178 overall B=-2.83 to atoms: r(all,work,free)=0.2419 0.2443 0.2033 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1559 0.1558 0.1576 n_refl.: 5178 remove outliers: r(all,work,free)=0.1555 0.1554 0.1576 n_refl.: 5176 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 98.94 88 5 0.3848 449.751 407.094 0.642 1.110 0.414 11.894-9.307 99.02 97 4 0.1889 714.465 689.088 0.903 1.103 0.385 9.237-7.194 100.00 213 7 0.2241 584.291 574.480 0.943 1.091 0.369 7.162-5.571 100.00 427 22 0.2299 438.439 426.226 0.910 1.071 0.331 5.546-4.326 100.00 867 58 0.1355 601.915 595.685 0.966 1.038 0.231 4.315-3.360 100.00 1859 96 0.1314 572.428 566.667 1.061 0.983 0.210 3.356-3.002 100.00 1373 60 0.1586 440.908 434.033 1.099 0.928 0.086 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9555 b_overall=-3.6154 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1554 r_free=0.1576 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=0.1554 r_free=0.1576 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 19.772458 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.945926 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1164 0.1792 0.0628 0.010 1.0 2.6 0.5 0.0 0 9.886 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.64 17.92 6.28 3.013 16.031 1.946 0.018 10.26 17.94 7.68 4.859 16.170 1.946 0.015 Individual atomic B min max mean iso aniso Overall: 2.09 111.70 17.32 5.27 1785 0 Protein: 2.09 111.70 14.63 5.26 1519 0 Water: 4.04 111.47 32.98 N/A 258 0 Other: 17.12 37.66 24.17 N/A 8 0 Chain A: 2.09 111.70 17.32 N/A 1785 0 Histogram: Values Number of atoms 2.09 - 13.05 926 13.05 - 24.01 479 24.01 - 34.97 183 34.97 - 45.93 109 45.93 - 56.90 55 56.90 - 67.86 16 67.86 - 78.82 8 78.82 - 89.78 5 89.78 - 100.74 1 100.74 - 111.70 3 =========================== Idealize ADP of riding H ========================== r_work=0.1026 r_free=0.1794 r_work=0.1021 r_free=0.1800 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1021 r_free = 0.1800 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1021 r_free = 0.1791 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.1021 r_free= 0.1791 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ls_wunit_k1) (work): 0.014073 | | target function (ls_wunit_k1) not normalized (work): 69.294568 | | target function (ls_wunit_k1) not normalized (free): 10.382603 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1059 0.1021 0.1791 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2098 0.2098 0.2212 n_refl.: 5176 remove outliers: r(all,work,free)=0.2098 0.2098 0.2212 n_refl.: 5176 overall B=-0.96 to atoms: r(all,work,free)=0.2059 0.2056 0.2200 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.1058 0.1020 0.1777 n_refl.: 5176 remove outliers: r(all,work,free)=0.1058 0.1020 0.1777 n_refl.: 5176 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 96.88 88 5 0.3373 330.610 313.859 0.654 1.041 0.386 11.894-9.307 99.02 97 4 0.1506 525.200 517.093 0.953 1.040 0.354 9.237-7.194 100.00 213 7 0.1653 429.509 429.727 0.996 1.035 0.326 7.162-5.571 100.00 427 22 0.1625 322.295 318.623 0.960 1.027 0.312 5.546-4.326 100.00 867 58 0.0931 442.465 439.460 0.985 1.014 0.207 4.315-3.360 100.00 1859 96 0.0773 420.789 420.904 1.049 0.992 0.204 3.356-3.002 100.00 1373 60 0.1005 324.109 322.548 1.040 0.971 0.069 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-3.4301 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1020 r_free=0.1777 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 80 GLN A Total number of N/Q/H flips: 2 r_work=0.1023 r_free=0.1776 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1023 r_free=0.1776 | n_water=258 | time (s): 0.650 (total time: 0.650) Filter (dist) r_work=0.1040 r_free=0.1774 | n_water=249 | time (s): 20.170 (total time: 20.820) Filter (q & B) r_work=0.1040 r_free=0.1776 | n_water=246 | time (s): 2.040 (total time: 22.860) Compute maps r_work=0.1040 r_free=0.1776 | n_water=246 | time (s): 0.550 (total time: 23.410) Filter (map) r_work=0.1333 r_free=0.1845 | n_water=144 | time (s): 1.610 (total time: 25.020) Find peaks r_work=0.1333 r_free=0.1845 | n_water=144 | time (s): 0.400 (total time: 25.420) Add new water r_work=0.1669 r_free=0.2120 | n_water=230 | time (s): 1.280 (total time: 26.700) Refine new water occ: r_work=0.1160 r_free=0.1707 adp: r_work=0.1137 r_free=0.1698 occ: r_work=0.1136 r_free=0.1692 adp: r_work=0.1124 r_free=0.1689 occ: r_work=0.1123 r_free=0.1683 adp: r_work=0.1120 r_free=0.1682 ADP+occupancy (water only), MIN, final r_work=0.1120 r_free=0.1682 r_work=0.1120 r_free=0.1682 | n_water=230 | time (s): 3.970 (total time: 30.670) Filter (q & B) r_work=0.1121 r_free=0.1688 | n_water=228 | time (s): 1.730 (total time: 32.400) Filter (dist only) r_work=0.1129 r_free=0.1686 | n_water=224 | time (s): 18.710 (total time: 51.110) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.369768 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.786988 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1021 0.1802 0.0781 0.009 1.0 4.2 0.5 0.6 0 11.185 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.21 18.02 7.81 4.646 16.657 2.787 0.014 9.52 18.08 8.55 5.454 17.110 2.787 0.013 Individual atomic B min max mean iso aniso Overall: 0.00 108.48 16.55 6.47 1751 0 Protein: 0.00 108.48 15.03 6.46 1519 0 Water: 0.00 62.80 26.76 N/A 224 0 Other: 11.16 31.70 19.39 N/A 8 0 Chain A: 0.00 108.48 15.73 N/A 1667 0 Chain S: 2.02 57.82 32.86 N/A 84 0 Histogram: Values Number of atoms 0.00 - 10.85 695 10.85 - 21.70 656 21.70 - 32.55 206 32.55 - 43.39 117 43.39 - 54.24 40 54.24 - 65.09 24 65.09 - 75.94 6 75.94 - 86.79 3 86.79 - 97.64 2 97.64 - 108.48 2 =========================== Idealize ADP of riding H ========================== r_work=0.0952 r_free=0.1808 r_work=0.0950 r_free=0.1809 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0950 r_free = 0.1809 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0947 r_free = 0.1793 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.0947 r_free= 0.1793 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ls_wunit_k1) (work): 0.012141 | | target function (ls_wunit_k1) not normalized (work): 59.783139 | | target function (ls_wunit_k1) not normalized (free): 10.031777 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0989 0.0947 0.1793 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2153 0.2155 0.2270 n_refl.: 5176 remove outliers: r(all,work,free)=0.2153 0.2155 0.2270 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2153 0.2155 0.2270 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0990 0.0947 0.1800 n_refl.: 5176 remove outliers: r(all,work,free)=0.0988 0.0946 0.1800 n_refl.: 5175 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3241 327.825 313.083 0.673 1.029 0.377 11.894-9.307 99.02 97 4 0.1443 525.200 521.162 0.957 1.030 0.340 9.237-7.194 100.00 213 7 0.1490 429.509 430.432 0.994 1.027 0.304 7.162-5.571 100.00 427 22 0.1405 322.295 320.699 0.977 1.021 0.290 5.546-4.326 100.00 867 58 0.0802 442.465 439.866 0.995 1.012 0.240 4.315-3.360 100.00 1859 96 0.0738 420.789 420.647 1.054 0.995 0.200 3.356-3.002 100.00 1373 60 0.0973 324.109 322.502 1.043 0.979 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9552 b_overall=-3.8837 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0946 r_free=0.1800 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN A Total number of N/Q/H flips: 2 r_work=0.0947 r_free=0.1800 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0947 r_free=0.1800 | n_water=224 | time (s): 0.670 (total time: 0.670) Filter (dist) r_work=0.0968 r_free=0.1798 | n_water=218 | time (s): 17.810 (total time: 18.480) Filter (q & B) r_work=0.1044 r_free=0.1812 | n_water=215 | time (s): 1.250 (total time: 19.730) Compute maps r_work=0.1044 r_free=0.1812 | n_water=215 | time (s): 0.450 (total time: 20.180) Filter (map) r_work=0.1277 r_free=0.1868 | n_water=145 | time (s): 1.490 (total time: 21.670) Find peaks r_work=0.1277 r_free=0.1868 | n_water=145 | time (s): 0.460 (total time: 22.130) Add new water r_work=0.1649 r_free=0.2245 | n_water=234 | time (s): 1.350 (total time: 23.480) Refine new water occ: r_work=0.1064 r_free=0.1756 adp: r_work=0.1056 r_free=0.1777 occ: r_work=0.1046 r_free=0.1756 adp: r_work=0.1045 r_free=0.1766 occ: r_work=0.1036 r_free=0.1746 adp: r_work=0.1035 r_free=0.1756 ADP+occupancy (water only), MIN, final r_work=0.1035 r_free=0.1756 r_work=0.1035 r_free=0.1756 | n_water=234 | time (s): 8.950 (total time: 32.430) Filter (q & B) r_work=0.1034 r_free=0.1755 | n_water=233 | time (s): 1.530 (total time: 33.960) Filter (dist only) r_work=0.1040 r_free=0.1772 | n_water=231 | time (s): 17.010 (total time: 50.970) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.073837 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.230671 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.0951 0.1794 0.0844 0.011 1.0 5.1 0.5 0.6 0 0.537 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.51 17.94 8.44 5.402 17.778 0.231 5.165 9.12 17.84 8.72 7.111 17.729 0.231 5.073 Individual atomic B min max mean iso aniso Overall: 0.00 106.97 16.27 8.74 1758 0 Protein: 0.00 106.97 15.04 8.74 1519 0 Water: 0.00 57.80 24.21 N/A 231 0 Other: 11.20 32.41 21.21 N/A 8 0 Chain A: 0.00 106.97 15.65 N/A 1653 0 Chain S: 0.00 56.56 26.07 N/A 105 0 Histogram: Values Number of atoms 0.00 - 10.70 675 10.70 - 21.39 665 21.39 - 32.09 228 32.09 - 42.79 122 42.79 - 53.49 32 53.49 - 64.18 16 64.18 - 74.88 12 74.88 - 85.58 3 85.58 - 96.27 4 96.27 - 106.97 1 =========================== Idealize ADP of riding H ========================== r_work=0.0912 r_free=0.1784 r_work=0.0918 r_free=0.1792 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0918 r_free = 0.1792 target_work(ml) = 5.077 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0901 r_free = 0.1766 target_work(ml) = 5.068 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0901 r_free= 0.1766 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 5.067709 | | target function (ml) not normalized (work): 24948.331812 | | target function (ml) not normalized (free): 1780.781115 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0945 0.0901 0.1766 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2115 0.2124 0.2089 n_refl.: 5175 remove outliers: r(all,work,free)=0.2115 0.2124 0.2089 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2115 0.2124 0.2089 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0939 0.0896 0.1769 n_refl.: 5175 remove outliers: r(all,work,free)=0.0937 0.0894 0.1769 n_refl.: 5174 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 94.79 86 5 0.3690 330.006 296.465 0.605 0.994 0.347 11.894-9.307 99.02 97 4 0.1730 525.200 511.314 0.953 0.998 0.341 9.237-7.194 100.00 213 7 0.1887 429.509 422.183 0.994 0.999 0.336 7.162-5.571 100.00 427 22 0.1828 322.295 313.069 0.981 1.000 0.290 5.546-4.326 100.00 867 58 0.0921 442.465 437.715 0.996 1.001 0.244 4.315-3.360 100.00 1859 96 0.0601 420.789 420.765 1.054 1.002 0.210 3.356-3.002 100.00 1373 60 0.0619 324.109 323.747 1.031 1.003 0.050 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9171 b_overall=-6.2785 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0894 r_free=0.1769 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B Total number of N/Q/H flips: 1 r_work=0.0895 r_free=0.1766 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0895 r_free=0.1766 | n_water=231 | time (s): 0.540 (total time: 0.540) Filter (dist) r_work=0.0919 r_free=0.1771 | n_water=224 | time (s): 17.930 (total time: 18.470) Filter (q & B) r_work=0.0989 r_free=0.1798 | n_water=221 | time (s): 1.880 (total time: 20.350) Compute maps r_work=0.0989 r_free=0.1798 | n_water=221 | time (s): 0.630 (total time: 20.980) Filter (map) r_work=0.1257 r_free=0.1839 | n_water=144 | time (s): 1.810 (total time: 22.790) Find peaks r_work=0.1257 r_free=0.1839 | n_water=144 | time (s): 0.610 (total time: 23.400) Add new water r_work=0.1599 r_free=0.2221 | n_water=229 | time (s): 1.450 (total time: 24.850) Refine new water occ: r_work=0.1001 r_free=0.1726 adp: r_work=0.0996 r_free=0.1737 occ: r_work=0.0987 r_free=0.1710 adp: r_work=0.0987 r_free=0.1724 occ: r_work=0.0979 r_free=0.1698 adp: r_work=0.0978 r_free=0.1710 ADP+occupancy (water only), MIN, final r_work=0.0978 r_free=0.1710 r_work=0.0978 r_free=0.1710 | n_water=229 | time (s): 11.420 (total time: 36.270) Filter (q & B) r_work=0.0978 r_free=0.1710 | n_water=227 | time (s): 1.410 (total time: 37.680) Filter (dist only) r_work=0.0991 r_free=0.1693 | n_water=225 | time (s): 16.570 (total time: 54.250) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.008434 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.248590 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.0900 0.1724 0.0824 0.011 1.0 4.5 0.5 0.0 0 0.504 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.00 17.24 8.24 6.823 17.779 0.249 5.043 8.78 17.50 8.72 8.289 17.943 0.249 4.976 Individual atomic B min max mean iso aniso Overall: 0.00 107.68 16.62 10.82 1752 0 Protein: 0.00 107.68 15.55 10.82 1519 0 Water: 0.00 60.71 23.63 N/A 225 0 Other: 10.08 34.47 22.20 N/A 8 0 Chain A: 0.00 107.68 16.08 N/A 1641 0 Chain S: 0.00 60.71 24.57 N/A 111 0 Histogram: Values Number of atoms 0.00 - 10.77 652 10.77 - 21.54 659 21.54 - 32.30 256 32.30 - 43.07 113 43.07 - 53.84 33 53.84 - 64.61 19 64.61 - 75.38 8 75.38 - 86.14 7 86.14 - 96.91 3 96.91 - 107.68 2 =========================== Idealize ADP of riding H ========================== r_work=0.0878 r_free=0.1750 r_work=0.0883 r_free=0.1760 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0883 r_free = 0.1760 target_work(ml) = 4.982 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0873 r_free = 0.1743 target_work(ml) = 4.974 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0873 r_free= 0.1743 coordinate error (max.-lik. estimate): 0.26 A | | | | normalized target function (ml) (work): 4.974269 | | target function (ml) not normalized (work): 24483.352720 | | target function (ml) not normalized (free): 2000.019418 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0916 0.0873 0.1743 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2088 0.2095 0.2096 n_refl.: 5174 remove outliers: r(all,work,free)=0.2088 0.2095 0.2096 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2088 0.2095 0.2096 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0916 0.0872 0.1747 n_refl.: 5174 remove outliers: r(all,work,free)=0.0916 0.0872 0.1747 n_refl.: 5174 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 94.79 86 5 0.3821 330.006 299.293 0.607 0.988 0.340 11.894-9.307 99.02 97 4 0.1783 525.200 511.335 0.953 0.994 0.340 9.237-7.194 100.00 213 7 0.2072 429.509 419.611 0.992 0.997 0.340 7.162-5.571 100.00 427 22 0.1916 322.295 312.596 0.988 0.998 0.280 5.546-4.326 100.00 867 58 0.0972 442.465 437.009 1.007 1.000 0.260 4.315-3.360 100.00 1859 96 0.0564 420.789 420.717 1.068 1.002 0.210 3.356-3.002 100.00 1373 60 0.0467 324.109 324.269 1.048 1.004 0.040 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.0190 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0872 r_free=0.1747 After: r_work=0.0875 r_free=0.1746 ================================== NQH flips ================================== r_work=0.0875 r_free=0.1746 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B A 80 GLN A Total number of N/Q/H flips: 2 r_work=0.0875 r_free=0.1749 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0875 r_free=0.1749 | n_water=225 | time (s): 0.490 (total time: 0.490) Filter (dist) r_work=0.0879 r_free=0.1760 | n_water=224 | time (s): 18.420 (total time: 18.910) Filter (q & B) r_work=0.1023 r_free=0.1793 | n_water=220 | time (s): 1.620 (total time: 20.530) Compute maps r_work=0.1023 r_free=0.1793 | n_water=220 | time (s): 0.630 (total time: 21.160) Filter (map) r_work=0.1267 r_free=0.1855 | n_water=152 | time (s): 1.470 (total time: 22.630) Find peaks r_work=0.1267 r_free=0.1855 | n_water=152 | time (s): 0.490 (total time: 23.120) Add new water r_work=0.1564 r_free=0.2124 | n_water=222 | time (s): 1.420 (total time: 24.540) Refine new water occ: r_work=0.1025 r_free=0.1760 adp: r_work=0.1014 r_free=0.1780 occ: r_work=0.1004 r_free=0.1758 adp: r_work=0.1003 r_free=0.1767 occ: r_work=0.0994 r_free=0.1746 adp: r_work=0.0993 r_free=0.1754 ADP+occupancy (water only), MIN, final r_work=0.0993 r_free=0.1754 r_work=0.0993 r_free=0.1754 | n_water=222 | time (s): 11.810 (total time: 36.350) Filter (q & B) r_work=0.0993 r_free=0.1756 | n_water=221 | time (s): 1.840 (total time: 38.190) Filter (dist only) r_work=0.0993 r_free=0.1756 | n_water=221 | time (s): 14.540 (total time: 52.730) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.974754 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.232426 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.0937 0.1809 0.0872 0.010 1.1 7.4 0.5 0.6 0 0.487 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.37 18.09 8.72 8.216 18.323 0.232 5.054 9.19 18.48 9.29 9.054 18.462 0.232 4.993 Individual atomic B min max mean iso aniso Overall: 0.00 106.81 17.01 11.94 1748 0 Protein: 0.00 106.81 15.97 11.95 1519 0 Water: 0.00 65.48 23.98 N/A 221 0 Other: 9.77 35.63 22.98 N/A 8 0 Chain A: 0.00 106.81 16.39 N/A 1631 0 Chain S: 0.00 65.48 25.72 N/A 117 0 Histogram: Values Number of atoms 0.00 - 10.68 657 10.68 - 21.36 606 21.36 - 32.04 289 32.04 - 42.72 115 42.72 - 53.40 36 53.40 - 64.08 21 64.08 - 74.77 11 74.77 - 85.45 6 85.45 - 96.13 4 96.13 - 106.81 3 =========================== Idealize ADP of riding H ========================== r_work=0.0919 r_free=0.1848 r_work=0.0922 r_free=0.1850 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0922 r_free = 0.1850 target_work(ml) = 4.999 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0914 r_free = 0.1843 target_work(ml) = 4.993 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0914 r_free= 0.1843 coordinate error (max.-lik. estimate): 0.27 A | | | | normalized target function (ml) (work): 4.993356 | | target function (ml) not normalized (work): 24577.297445 | | target function (ml) not normalized (free): 2070.502371 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.79 1.00 2492 142 0.1297 0.1842 5.5701 6.1856| | 2: 3.78 - 3.00 1.00 2430 110 0.0448 0.1843 4.4018 10.838| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.79 2492 142 0.91 12.42 1.00 0.98 13376.59| | 2: 3.78 - 3.00 2430 110 0.99 2.04 1.01 1.01 1009.28| |alpha: min = 0.97 max = 1.01 mean = 1.00| |beta: min = 641.04 max = 21995.73 mean = 7270.83| |figures of merit: min = 0.00 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.73 mean = 7.29| |phase err.(test): min = 0.00 max = 88.36 mean = 7.86| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0961 0.0914 0.1843 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2158 0.2161 0.2219 n_refl.: 5174 remove outliers: r(all,work,free)=0.2158 0.2161 0.2219 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2158 0.2161 0.2219 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0957 0.0912 0.1836 n_refl.: 5174 remove outliers: r(all,work,free)=0.0957 0.0912 0.1836 n_refl.: 5174 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 94.79 86 5 0.3958 330.006 293.324 0.606 0.986 0.317 11.894-9.307 99.02 97 4 0.1891 525.200 512.237 0.996 0.993 0.316 9.237-7.194 100.00 213 7 0.2169 429.509 417.907 1.050 0.996 0.300 7.162-5.571 100.00 427 22 0.1977 322.295 311.466 1.040 0.998 0.300 5.546-4.326 100.00 867 58 0.1061 442.465 436.069 1.066 1.000 0.260 4.315-3.360 100.00 1859 96 0.0603 420.789 420.853 1.147 1.003 0.228 3.356-3.002 100.00 1373 60 0.0433 324.109 324.355 1.128 1.005 0.030 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-8.4810 ================= 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 : 0.3623 0.1992 0.083 5.274 8.8 119.3 19.9 258 0.000 1_bss: 0.1554 0.1576 0.083 5.274 6.0 116.5 17.1 258 0.000 1_settarget: 0.1554 0.1576 0.083 5.274 6.0 116.5 17.1 258 0.000 1_nqh: 0.1554 0.1576 0.083 5.274 6.0 116.5 17.1 258 0.000 1_weight: 0.1554 0.1576 0.083 5.274 6.0 116.5 17.1 258 0.000 1_xyzrec: 0.1164 0.1792 0.010 0.997 6.0 116.5 17.1 258 0.203 1_adp: 0.1026 0.1794 0.010 0.997 2.1 111.7 17.3 258 0.203 1_regHadp: 0.1021 0.1800 0.010 0.997 2.1 111.7 17.3 258 0.203 1_occ: 0.1021 0.1791 0.010 0.997 2.1 111.7 17.3 258 0.203 2_bss: 0.1020 0.1777 0.010 0.997 1.1 110.7 16.4 258 0.203 2_settarget: 0.1020 0.1777 0.010 0.997 1.1 110.7 16.4 258 0.203 2_updatecdl: 0.1020 0.1777 0.010 1.007 1.1 110.7 16.4 258 0.203 2_nqh: 0.1023 0.1776 0.010 1.007 1.1 110.7 16.4 258 0.209 2_sol: 0.1129 0.1686 0.010 1.007 1.0 110.7 15.7 224 n/a 2_weight: 0.1129 0.1686 0.010 1.007 1.0 110.7 15.7 224 n/a 2_xyzrec: 0.1021 0.1802 0.009 0.962 1.0 110.7 15.7 224 n/a 2_adp: 0.0952 0.1808 0.009 0.962 0.0 108.5 16.6 224 n/a 2_regHadp: 0.0950 0.1809 0.009 0.962 0.0 108.5 16.6 224 n/a 2_occ: 0.0947 0.1793 0.009 0.962 0.0 108.5 16.6 224 n/a 3_bss: 0.0946 0.1800 0.009 0.962 0.0 108.5 16.6 224 n/a 3_settarget: 0.0946 0.1800 0.009 0.962 0.0 108.5 16.6 224 n/a 3_updatecdl: 0.0946 0.1800 0.009 0.969 0.0 108.5 16.6 224 n/a 3_nqh: 0.0947 0.1800 0.009 0.969 0.0 108.5 16.6 224 n/a 3_sol: 0.1040 0.1772 0.009 0.969 0.0 108.5 16.4 231 n/a 3_weight: 0.1040 0.1772 0.009 0.969 0.0 108.5 16.4 231 n/a 3_xyzrec: 0.0951 0.1794 0.011 1.036 0.0 108.5 16.4 231 n/a 3_adp: 0.0912 0.1784 0.011 1.036 0.0 107.0 16.3 231 n/a 3_regHadp: 0.0918 0.1792 0.011 1.036 0.0 107.0 16.3 231 n/a 3_occ: 0.0901 0.1766 0.011 1.036 0.0 107.0 16.3 231 n/a 4_bss: 0.0894 0.1769 0.011 1.036 0.0 107.0 16.3 231 n/a 4_settarget: 0.0894 0.1769 0.011 1.036 0.0 107.0 16.3 231 n/a 4_updatecdl: 0.0894 0.1769 0.011 1.038 0.0 107.0 16.3 231 n/a 4_nqh: 0.0895 0.1766 0.011 1.038 0.0 107.0 16.3 231 n/a 4_sol: 0.0991 0.1693 0.011 1.038 0.0 107.0 16.3 225 n/a 4_weight: 0.0991 0.1693 0.011 1.038 0.0 107.0 16.3 225 n/a 4_xyzrec: 0.0900 0.1724 0.011 1.036 0.0 107.0 16.3 225 n/a 4_adp: 0.0878 0.1750 0.011 1.036 0.0 107.7 16.6 225 n/a 4_regHadp: 0.0883 0.1760 0.011 1.036 0.0 107.7 16.6 225 n/a 4_occ: 0.0873 0.1743 0.011 1.036 0.0 107.7 16.6 225 n/a 5_bss: 0.0872 0.1747 0.011 1.036 0.0 107.7 16.6 225 n/a 5_settarget: 0.0872 0.1747 0.011 1.036 0.0 107.7 16.6 225 n/a 5_updatecdl: 0.0872 0.1747 0.011 1.046 0.0 107.7 16.6 225 n/a 5_setrh: 0.0875 0.1746 0.011 1.046 0.0 107.7 16.6 225 n/a 5_nqh: 0.0875 0.1749 0.011 1.046 0.0 107.7 16.6 225 n/a 5_sol: 0.0993 0.1756 0.011 1.046 0.0 107.7 16.7 221 n/a 5_weight: 0.0993 0.1756 0.011 1.046 0.0 107.7 16.7 221 n/a 5_xyzrec: 0.0937 0.1809 0.010 1.124 0.0 107.7 16.7 221 n/a 5_adp: 0.0919 0.1848 0.010 1.124 0.0 106.8 17.0 221 n/a 5_regHadp: 0.0922 0.1850 0.010 1.124 0.0 106.8 17.0 221 n/a 5_occ: 0.0914 0.1843 0.010 1.124 0.0 106.8 17.0 221 n/a end: 0.0912 0.1835 0.010 1.124 0.0 106.8 17.0 221 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_9291273_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_9291273_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.2100 Refinement macro-cycles (run) : 478.7100 Write final files (write_after_run_outputs) : 11.2500 Total : 493.1700 Total CPU time: 8.60 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:18:59 PST -0800 (1735492739.02 s) Start R-work = 0.1554, R-free = 0.1576 Final R-work = 0.0912, R-free = 0.1835 =============================================================================== Job complete usr+sys time: 524.39 seconds wall clock time: 9 minutes 8.11 seconds (548.11 seconds total)