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_5382129.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 { 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" 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_5382129.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_5382129.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 1 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.64, per 1000 atoms: 0.49 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: 0.40 Conformation dependent library (CDL) restraints added in 148.4 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.65 - 0.90: 485 0.90 - 1.16: 1157 1.16 - 1.41: 569 1.41 - 1.66: 886 1.66 - 1.91: 56 Bond restraints: 3153 Sorted by residual: bond pdb=" C VAL A 20 " pdb=" O VAL A 20 " ideal model delta sigma weight residual 1.237 0.986 0.251 1.19e-02 7.06e+03 4.45e+02 bond pdb=" C THR A 34 " pdb=" N VAL A 35 " ideal model delta sigma weight residual 1.329 1.538 -0.209 1.15e-02 7.56e+03 3.30e+02 bond pdb=" CE1 HIS A 138 " pdb=" NE2 HIS A 138 " ideal model delta sigma weight residual 1.321 1.501 -0.180 1.00e-02 1.00e+04 3.23e+02 bond pdb=" C THR A 34 " pdb=" O THR A 34 " ideal model delta sigma weight residual 1.236 1.029 0.207 1.17e-02 7.31e+03 3.12e+02 bond pdb=" CA ALA A 183 " pdb=" C ALA A 183 " ideal model delta sigma weight residual 1.520 1.732 -0.212 1.23e-02 6.61e+03 2.96e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.88: 3268 4.88 - 9.75: 1836 9.75 - 14.62: 581 14.62 - 19.49: 83 19.49 - 24.37: 9 Bond angle restraints: 5777 Sorted by residual: angle pdb=" NE ARG A 27 " pdb=" CZ ARG A 27 " pdb=" NH2 ARG A 27 " ideal model delta sigma weight residual 119.20 105.62 13.58 9.00e-01 1.23e+00 2.28e+02 angle pdb=" O LEU A 82 " pdb=" C LEU A 82 " pdb=" N SER A 83 " ideal model delta sigma weight residual 122.12 137.98 -15.86 1.06e+00 8.90e-01 2.24e+02 angle pdb=" CA GLY A 40 " pdb=" C GLY A 40 " pdb=" O GLY A 40 " ideal model delta sigma weight residual 121.76 134.45 -12.69 8.70e-01 1.32e+00 2.13e+02 angle pdb=" CA BGLU A 96 " pdb=" C BGLU A 96 " pdb=" O BGLU A 96 " ideal model delta sigma weight residual 120.82 107.13 13.69 1.05e+00 9.07e-01 1.70e+02 angle pdb=" O ALA A 36 " pdb=" C ALA A 36 " pdb=" N GLY A 37 " ideal model delta sigma weight residual 123.22 137.81 -14.59 1.14e+00 7.69e-01 1.64e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.64: 1357 20.64 - 41.28: 88 41.28 - 61.92: 31 61.92 - 82.55: 3 82.55 - 103.19: 2 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C BLYS A 99 " pdb=" N BLYS A 99 " pdb=" CA BLYS A 99 " pdb=" CB BLYS A 99 " ideal model delta harmonic sigma weight residual -122.60 -145.39 22.79 0 2.50e+00 1.60e-01 8.31e+01 dihedral pdb=" N BLYS A 99 " pdb=" C BLYS A 99 " pdb=" CA BLYS A 99 " pdb=" CB BLYS A 99 " ideal model delta harmonic sigma weight residual 122.80 144.44 -21.64 0 2.50e+00 1.60e-01 7.49e+01 dihedral pdb=" N ARG A 48 " pdb=" C ARG A 48 " pdb=" CA ARG A 48 " pdb=" CB ARG A 48 " ideal model delta harmonic sigma weight residual 122.80 142.51 -19.71 0 2.50e+00 1.60e-01 6.22e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.007 - 0.228: 111 0.228 - 0.449: 71 0.449 - 0.670: 44 0.670 - 0.892: 13 0.892 - 1.113: 4 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA BLYS A 99 " pdb=" N BLYS A 99 " pdb=" C BLYS A 99 " pdb=" CB BLYS A 99 " both_signs ideal model delta sigma weight residual False 2.51 1.40 1.11 2.00e-01 2.50e+01 3.10e+01 chirality pdb=" CA ILE A 102 " pdb=" N ILE A 102 " pdb=" C ILE A 102 " pdb=" CB ILE A 102 " both_signs ideal model delta sigma weight residual False 2.43 3.52 -1.09 2.00e-01 2.50e+01 2.96e+01 chirality pdb=" CA ARG A 48 " pdb=" N ARG A 48 " pdb=" C ARG A 48 " pdb=" CB ARG A 48 " both_signs ideal model delta sigma weight residual False 2.51 1.48 1.03 2.00e-01 2.50e+01 2.63e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.007 2.00e-02 2.50e+03 6.01e-02 1.08e+02 pdb=" CG PHE A 164 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.112 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.020 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.037 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " -0.032 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.009 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.112 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.058 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.025 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.066 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " -0.043 2.00e-02 2.50e+03 5.35e-02 8.59e+01 pdb=" CG BTYR A 67 " 0.073 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " -0.025 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " -0.049 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " -0.086 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " 0.093 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " -0.028 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " -0.030 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " 0.019 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " 0.013 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " 0.075 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 49 " -0.052 2.00e-02 2.50e+03 9.22e-02 8.51e+01 pdb=" C ASP A 49 " 0.160 2.00e-02 2.50e+03 pdb=" O ASP A 49 " -0.053 2.00e-02 2.50e+03 pdb=" N VAL A 50 " -0.055 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.35: 1282 2.35 - 2.91: 8208 2.91 - 3.48: 10502 3.48 - 4.04: 15144 4.04 - 4.60: 21424 Nonbonded interactions: 56560 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.788 2.100 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.795 2.450 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.820 2.100 nonbonded pdb=" H LEU A 72 " pdb=" O ALA A 103 " model vdw 1.837 2.450 nonbonded pdb=" HG SER A 47 " pdb="HH11 ARG A 48 " model vdw 1.839 2.100 ... (remaining 56555 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_5382129_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= 0.2776 r_free= 0.1831 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.416501 | | target function (ml) not normalized (work): 71737.218480 | | target function (ml) not normalized (free): 3273.994432 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3188 0.2098 7.6205 5.0214| | 2: 3.63 - 2.88 1.00 2711 122 0.2633 0.1697 4.3237 4.315| | 3: 2.88 - 2.52 1.00 2682 148 0.2545 0.1706 4.1714 4.1733| | 4: 2.52 - 2.29 1.00 2661 139 0.2532 0.1577 3.5018 3.5908| | 5: 2.29 - 2.13 1.00 2678 122 0.2646 0.1577 3.3974 3.4823| | 6: 2.13 - 2.00 1.00 2692 117 0.2719 0.2046 3.317 3.4833| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 17.36 0.77 0.23 1268.53| | 2: 3.63 - 2.88 2711 122 0.83 23.47 1.32 0.23 1268.53| | 3: 2.88 - 2.52 2682 148 0.74 32.44 1.29 0.23 1268.53| | 4: 2.52 - 2.29 2661 139 0.93 11.66 1.30 0.26 141.61| | 5: 2.29 - 2.13 2678 122 0.92 13.95 1.32 0.26 141.61| | 6: 2.13 - 2.00 2692 117 0.90 16.77 1.33 0.26 141.61| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 141.61 max = 1268.53 mean = 711.35| |figures of merit: min = 0.00 max = 1.00 mean = 0.87| |phase err.(work): min = 0.00 max = 89.97 mean = 19.28| |phase err.(test): min = 0.00 max = 88.26 mean = 19.44| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.081 0.258 1557 Z= 5.355 Angle : 5.248 15.864 2118 Z= 3.666 Chirality : 0.382 1.113 243 Planarity : 0.031 0.092 284 Dihedral : 14.092 103.191 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 1.08 % Allowed : 2.16 % Favored : 96.76 % Rotamer: Outliers : 0.62 % Allowed : 3.73 % Favored : 95.65 % 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: -1.73 (0.51), residues: 224 helix: -1.88 (0.44), residues: 102 sheet: -2.14 (0.85), residues: 28 loop : 0.45 (0.60), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.121 0.024 ARG A 48 TYR 0.089 0.028 TYR A 141 PHE 0.078 0.032 PHE A 119 HIS 0.069 0.031 HIS A 126 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 1785 0 Protein: 8.85 115.78 16.79 3.90 1519 0 Water: 11.36 119.30 38.03 N/A 258 0 Other: 19.04 26.29 21.71 N/A 8 0 Chain A: 8.85 119.30 19.89 N/A 1785 0 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2776 r_free= 0.1831 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.416501 | | target function (ml) not normalized (work): 71737.218480 | | target function (ml) not normalized (free): 3273.994432 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.3241 percent. r_work = 0.2909 r_free = 0.1991 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2855 0.2909 0.1991 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2855 0.2909 0.1991 n_refl.: 17050 remove outliers: r(all,work,free)=0.2150 0.2160 0.1991 n_refl.: 17045 overall B=-0.40 to atoms: r(all,work,free)=0.2123 0.2133 0.1972 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1607 0.1605 0.1655 n_refl.: 17045 remove outliers: r(all,work,free)=0.1605 0.1603 0.1655 n_refl.: 17043 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 98.94 88 5 0.3972 398.959 360.950 0.659 1.012 0.403 11.894-9.307 99.02 97 4 0.1895 633.641 612.385 0.933 1.012 0.390 9.237-7.194 100.00 213 7 0.2191 518.255 508.842 0.960 1.012 0.351 7.162-5.571 100.00 427 22 0.2290 388.951 375.420 0.921 1.010 0.284 5.546-4.326 100.00 867 58 0.1396 533.967 528.334 0.962 1.009 0.225 4.315-3.360 100.00 1859 96 0.1296 507.808 503.654 1.016 1.005 0.201 3.356-2.611 100.00 3867 181 0.1644 333.601 329.370 1.013 1.000 0.061 2.608-2.000 99.99 8818 434 0.1629 217.450 213.848 1.028 0.990 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.4319 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1603 r_free=0.1655 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1603 r_free=0.1655 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.302850 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.960405 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 0.1350 0.1645 0.0295 0.009 1.0 1.0 0.5 0.0 0 11.651 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.50 16.45 2.95 3.013 18.457 0.960 0.023 12.76 16.62 3.86 3.707 18.729 0.960 0.020 Individual atomic B min max mean iso aniso Overall: 5.93 113.90 20.00 4.16 1785 0 Protein: 5.93 113.05 17.24 4.16 1519 0 Water: 8.96 113.90 36.07 N/A 258 0 Other: 21.54 37.58 26.77 N/A 8 0 Chain A: 5.93 113.90 20.00 N/A 1785 0 Histogram: Values Number of atoms 5.93 - 16.73 1068 16.73 - 27.52 351 27.52 - 38.32 189 38.32 - 49.12 100 49.12 - 59.91 48 59.91 - 70.71 14 70.71 - 81.51 7 81.51 - 92.30 4 92.30 - 103.10 1 103.10 - 113.90 3 =========================== Idealize ADP of riding H ========================== r_work=0.1276 r_free=0.1662 r_work=0.1279 r_free=0.1669 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1279 r_free = 0.1669 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1273 r_free = 0.1660 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17043 (all), 4.74 % free)------------| | | | r_work= 0.1273 r_free= 0.1660 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.019876 | | target function (ls_wunit_k1) not normalized (work): 322.714556 | | target function (ls_wunit_k1) not normalized (free): 27.431606 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1291 0.1273 0.1660 n_refl.: 17043 re-set all scales: r(all,work,free)=0.1901 0.1900 0.1993 n_refl.: 17043 remove outliers: r(all,work,free)=0.1901 0.1900 0.1993 n_refl.: 17043 overall B=-0.51 to atoms: r(all,work,free)=0.1865 0.1863 0.1971 n_refl.: 17043 bulk-solvent and scaling: r(all,work,free)=0.1288 0.1270 0.1652 n_refl.: 17043 remove outliers: r(all,work,free)=0.1288 0.1270 0.1652 n_refl.: 17043 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 96.88 88 5 0.3566 306.951 286.049 0.655 1.006 0.393 11.894-9.307 99.02 97 4 0.1660 487.511 476.098 0.919 1.006 0.381 9.237-7.194 100.00 213 7 0.1807 398.735 395.491 0.958 1.006 0.341 7.162-5.571 100.00 427 22 0.1806 299.251 293.956 0.931 1.006 0.301 5.546-4.326 100.00 867 58 0.1041 410.824 408.278 0.958 1.005 0.211 4.315-3.360 100.00 1859 96 0.0922 390.697 390.161 1.015 1.003 0.202 3.356-2.611 100.00 3867 181 0.1290 256.666 255.381 1.009 1.001 0.091 2.608-2.000 99.99 8818 434 0.1351 167.302 165.971 1.011 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-1.1575 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1270 r_free=0.1652 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1270 r_free=0.1652 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1270 r_free=0.1652 | n_water=258 | time (s): 0.790 (total time: 0.790) Filter (dist) r_work=0.1279 r_free=0.1644 | n_water=252 | time (s): 19.690 (total time: 20.480) Filter (q & B) r_work=0.1279 r_free=0.1643 | n_water=250 | time (s): 1.740 (total time: 22.220) Compute maps r_work=0.1279 r_free=0.1643 | n_water=250 | time (s): 0.790 (total time: 23.010) Filter (map) r_work=0.1317 r_free=0.1632 | n_water=207 | time (s): 1.740 (total time: 24.750) Find peaks r_work=0.1317 r_free=0.1632 | n_water=207 | time (s): 0.570 (total time: 25.320) Add new water r_work=0.1549 r_free=0.1872 | n_water=363 | time (s): 1.540 (total time: 26.860) Refine new water occ: r_work=0.1334 r_free=0.1579 adp: r_work=0.1275 r_free=0.1575 occ: r_work=0.1277 r_free=0.1534 adp: r_work=0.1245 r_free=0.1546 occ: r_work=0.1246 r_free=0.1528 adp: r_work=0.1234 r_free=0.1535 ADP+occupancy (water only), MIN, final r_work=0.1234 r_free=0.1535 r_work=0.1234 r_free=0.1535 | n_water=363 | time (s): 12.120 (total time: 38.980) Filter (q & B) r_work=0.1236 r_free=0.1541 | n_water=355 | time (s): 2.210 (total time: 41.190) Filter (dist only) r_work=0.1236 r_free=0.1545 | n_water=354 | time (s): 27.230 (total time: 68.420) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.413844 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.993969 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 0.1214 0.1584 0.0370 0.008 0.9 2.2 0.5 0.0 0 12.207 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.14 15.84 3.70 4.218 20.943 0.994 0.018 12.00 16.03 4.02 4.263 21.185 0.994 0.018 Individual atomic B min max mean iso aniso Overall: 6.43 107.54 21.14 4.29 1881 0 Protein: 6.43 107.54 17.59 4.28 1519 0 Water: 8.45 67.10 36.05 N/A 354 0 Other: 24.42 46.37 34.29 N/A 8 0 Chain A: 6.43 107.54 19.25 N/A 1734 0 Chain S: 17.87 67.10 43.45 N/A 147 0 Histogram: Values Number of atoms 6.43 - 16.54 1024 16.54 - 26.65 375 26.65 - 36.76 222 36.76 - 46.87 151 46.87 - 56.99 77 56.99 - 67.10 22 67.10 - 77.21 3 77.21 - 87.32 4 87.32 - 97.43 1 97.43 - 107.54 2 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1603 r_work=0.1202 r_free=0.1603 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1202 r_free = 0.1603 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 = 0.1200 r_free = 0.1605 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17043 (all), 4.74 % free)------------| | | | r_work= 0.1200 r_free= 0.1605 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.017172 | | target function (ls_wunit_k1) not normalized (work): 278.809210 | | target function (ls_wunit_k1) not normalized (free): 24.979314 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1220 0.1200 0.1605 n_refl.: 17043 re-set all scales: r(all,work,free)=0.1806 0.1802 0.1944 n_refl.: 17043 remove outliers: r(all,work,free)=0.1806 0.1802 0.1944 n_refl.: 17043 overall B=-0.46 to atoms: r(all,work,free)=0.1775 0.1770 0.1923 n_refl.: 17043 bulk-solvent and scaling: r(all,work,free)=0.1216 0.1197 0.1601 n_refl.: 17043 remove outliers: r(all,work,free)=0.1215 0.1195 0.1601 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 0.3419 306.389 278.208 0.613 1.005 0.360 11.894-9.307 99.02 97 4 0.1522 487.511 483.248 0.922 1.005 0.360 9.237-7.194 100.00 213 7 0.1669 398.735 400.147 0.977 1.005 0.291 7.162-5.571 100.00 427 22 0.1534 299.251 296.529 0.938 1.004 0.261 5.546-4.326 100.00 867 58 0.0872 410.824 408.814 0.960 1.004 0.201 4.315-3.360 100.00 1859 96 0.0839 390.697 389.881 1.015 1.003 0.192 3.356-2.611 100.00 3867 181 0.1208 256.666 255.704 1.009 1.001 0.112 2.608-2.000 99.99 8818 434 0.1332 167.302 166.198 1.008 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9584 b_overall=-1.1462 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1195 r_free=0.1601 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN Total number of N/Q/H flips: 1 r_work=0.1197 r_free=0.1602 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1197 r_free=0.1602 | n_water=354 | time (s): 0.900 (total time: 0.900) Filter (dist) r_work=0.1197 r_free=0.1606 | n_water=352 | time (s): 30.420 (total time: 31.320) Filter (q & B) r_work=0.1197 r_free=0.1606 | n_water=352 | time (s): 0.990 (total time: 32.310) Compute maps r_work=0.1197 r_free=0.1606 | n_water=352 | time (s): 0.640 (total time: 32.950) Filter (map) r_work=0.1260 r_free=0.1613 | n_water=262 | time (s): 1.520 (total time: 34.470) Find peaks r_work=0.1260 r_free=0.1613 | n_water=262 | time (s): 0.430 (total time: 34.900) Add new water r_work=0.1441 r_free=0.1823 | n_water=409 | time (s): 1.730 (total time: 36.630) Refine new water occ: r_work=0.1245 r_free=0.1578 adp: r_work=0.1239 r_free=0.1580 occ: r_work=0.1221 r_free=0.1551 adp: r_work=0.1211 r_free=0.1552 occ: r_work=0.1203 r_free=0.1525 adp: r_work=0.1194 r_free=0.1526 ADP+occupancy (water only), MIN, final r_work=0.1194 r_free=0.1526 r_work=0.1194 r_free=0.1526 | n_water=409 | time (s): 34.770 (total time: 71.400) Filter (q & B) r_work=0.1198 r_free=0.1529 | n_water=399 | time (s): 2.070 (total time: 73.470) Filter (dist only) r_work=0.1198 r_free=0.1529 | n_water=399 | time (s): 31.870 (total time: 105.340) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.896320 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.174004 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 0.1178 0.1536 0.0358 0.009 1.0 4.2 0.5 0.0 0 0.948 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.78 15.36 3.58 4.335 21.269 0.174 4.999 11.59 15.49 3.90 4.980 21.172 0.174 4.977 Individual atomic B min max mean iso aniso Overall: 6.11 105.40 20.60 4.75 1926 0 Protein: 6.11 105.40 16.71 4.74 1519 0 Water: 7.97 63.55 35.12 N/A 399 0 Other: 26.73 47.82 35.44 N/A 8 0 Chain A: 6.11 105.40 18.46 N/A 1732 0 Chain S: 15.25 63.55 39.72 N/A 194 0 Histogram: Values Number of atoms 6.11 - 16.04 1077 16.04 - 25.97 341 25.97 - 35.90 227 35.90 - 45.83 160 45.83 - 55.76 78 55.76 - 65.69 31 65.69 - 75.61 4 75.61 - 85.54 3 85.54 - 95.47 3 95.47 - 105.40 2 =========================== Idealize ADP of riding H ========================== r_work=0.1159 r_free=0.1549 r_work=0.1160 r_free=0.1552 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1160 r_free = 0.1552 target_work(ml) = 4.977 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1150 r_free = 0.1539 target_work(ml) = 4.970 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1150 r_free= 0.1539 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.969533 | | target function (ml) not normalized (work): 80675.395602 | | target function (ml) not normalized (free): 4190.430391 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1169 0.1150 0.1539 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1644 0.1638 0.1793 n_refl.: 17041 remove outliers: r(all,work,free)=0.1644 0.1638 0.1793 n_refl.: 17041 overall B=-0.34 to atoms: r(all,work,free)=0.1622 0.1616 0.1783 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1166 0.1148 0.1536 n_refl.: 17041 remove outliers: r(all,work,free)=0.1166 0.1148 0.1536 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 0.3654 306.389 280.712 0.582 1.004 0.344 11.894-9.307 99.02 97 4 0.1801 487.511 478.974 0.917 1.004 0.340 9.237-7.194 100.00 213 7 0.1842 398.735 400.710 0.991 1.004 0.250 7.162-5.571 100.00 427 22 0.1634 299.251 293.754 0.941 1.004 0.241 5.546-4.326 100.00 867 58 0.0938 410.824 407.202 0.966 1.004 0.191 4.315-3.360 100.00 1859 96 0.0896 390.697 388.809 1.013 1.003 0.191 3.356-2.611 100.00 3867 181 0.1287 256.666 254.505 1.010 1.001 0.141 2.608-2.000 99.99 8818 434 0.1079 167.302 165.884 1.009 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-1.1715 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1148 r_free=0.1536 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1148 r_free=0.1536 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1148 r_free=0.1536 | n_water=399 | time (s): 0.800 (total time: 0.800) Filter (dist) r_work=0.1148 r_free=0.1536 | n_water=399 | time (s): 32.510 (total time: 33.310) Filter (q & B) r_work=0.1148 r_free=0.1533 | n_water=397 | time (s): 1.540 (total time: 34.850) Compute maps r_work=0.1148 r_free=0.1533 | n_water=397 | time (s): 0.670 (total time: 35.520) Filter (map) r_work=0.1200 r_free=0.1544 | n_water=316 | time (s): 2.030 (total time: 37.550) Find peaks r_work=0.1200 r_free=0.1544 | n_water=316 | time (s): 0.660 (total time: 38.210) Add new water r_work=0.1328 r_free=0.1681 | n_water=445 | time (s): 1.910 (total time: 40.120) Refine new water occ: r_work=0.1176 r_free=0.1530 adp: r_work=0.1170 r_free=0.1532 occ: r_work=0.1155 r_free=0.1500 adp: r_work=0.1147 r_free=0.1501 occ: r_work=0.1141 r_free=0.1481 adp: r_work=0.1135 r_free=0.1480 ADP+occupancy (water only), MIN, final r_work=0.1135 r_free=0.1480 r_work=0.1135 r_free=0.1480 | n_water=445 | time (s): 28.280 (total time: 68.400) Filter (q & B) r_work=0.1138 r_free=0.1494 | n_water=435 | time (s): 1.650 (total time: 70.050) Filter (dist only) r_work=0.1138 r_free=0.1494 | n_water=434 | time (s): 36.220 (total time: 106.270) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.940381 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.152567 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 0.1123 0.1556 0.0433 0.009 1.0 3.8 0.5 0.0 0 0.970 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.23 15.56 4.33 4.502 20.781 0.153 4.963 11.13 15.58 4.45 4.604 20.794 0.153 4.959 Individual atomic B min max mean iso aniso Overall: 5.72 102.69 20.66 4.78 1961 0 Protein: 5.72 102.69 16.37 4.77 1519 0 Water: 8.34 65.02 35.43 N/A 434 0 Other: 26.36 47.02 34.56 N/A 8 0 Chain A: 5.72 102.69 18.04 N/A 1732 0 Chain S: 15.03 65.02 40.49 N/A 229 0 Histogram: Values Number of atoms 5.72 - 15.42 1039 15.42 - 25.11 369 25.11 - 34.81 228 34.81 - 44.51 182 44.51 - 54.20 99 54.20 - 63.90 29 63.90 - 73.60 6 73.60 - 83.29 3 83.29 - 92.99 4 92.99 - 102.69 2 =========================== Idealize ADP of riding H ========================== r_work=0.1113 r_free=0.1558 r_work=0.1113 r_free=0.1559 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1113 r_free = 0.1559 target_work(ml) = 4.960 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1104 r_free = 0.1559 target_work(ml) = 4.954 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1104 r_free= 0.1559 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.954378 | | target function (ml) not normalized (work): 80429.366301 | | target function (ml) not normalized (free): 4192.917048 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1126 0.1104 0.1559 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1567 0.1555 0.1834 n_refl.: 17041 remove outliers: r(all,work,free)=0.1567 0.1555 0.1834 n_refl.: 17041 overall B=-0.27 to atoms: r(all,work,free)=0.1551 0.1539 0.1826 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1122 0.1101 0.1551 n_refl.: 17041 remove outliers: r(all,work,free)=0.1122 0.1100 0.1551 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 0.3615 302.900 280.265 0.566 1.004 0.350 11.894-9.307 99.02 97 4 0.1799 487.511 482.072 0.915 1.004 0.330 9.237-7.194 100.00 213 7 0.1800 398.735 400.582 0.983 1.004 0.220 7.162-5.571 100.00 427 22 0.1559 299.251 293.334 0.939 1.004 0.210 5.546-4.326 100.00 867 58 0.0902 410.824 407.546 0.966 1.004 0.201 4.315-3.360 100.00 1859 96 0.0842 390.697 388.666 1.005 1.003 0.181 3.356-2.611 100.00 3867 181 0.1235 256.666 254.452 1.002 1.001 0.053 2.608-2.000 99.99 8818 434 0.1037 167.302 166.096 0.998 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-0.9168 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1100 r_free=0.1551 After: r_work=0.1102 r_free=0.1550 ================================== NQH flips ================================== r_work=0.1102 r_free=0.1550 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1102 r_free=0.1550 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1102 r_free=0.1550 | n_water=434 | time (s): 0.630 (total time: 0.630) Filter (dist) r_work=0.1108 r_free=0.1551 | n_water=432 | time (s): 36.010 (total time: 36.640) Filter (q & B) r_work=0.1108 r_free=0.1551 | n_water=432 | time (s): 1.190 (total time: 37.830) Compute maps r_work=0.1108 r_free=0.1551 | n_water=432 | time (s): 0.670 (total time: 38.500) Filter (map) r_work=0.1187 r_free=0.1579 | n_water=340 | time (s): 1.530 (total time: 40.030) Find peaks r_work=0.1187 r_free=0.1579 | n_water=340 | time (s): 0.440 (total time: 40.470) Add new water r_work=0.1298 r_free=0.1661 | n_water=476 | time (s): 1.770 (total time: 42.240) Refine new water occ: r_work=0.1141 r_free=0.1518 adp: r_work=0.1133 r_free=0.1515 occ: r_work=0.1122 r_free=0.1501 adp: r_work=0.1113 r_free=0.1498 occ: r_work=0.1108 r_free=0.1492 adp: r_work=0.1102 r_free=0.1491 ADP+occupancy (water only), MIN, final r_work=0.1102 r_free=0.1491 r_work=0.1102 r_free=0.1491 | n_water=476 | time (s): 29.430 (total time: 71.670) Filter (q & B) r_work=0.1107 r_free=0.1507 | n_water=462 | time (s): 2.030 (total time: 73.700) Filter (dist only) r_work=0.1107 r_free=0.1505 | n_water=460 | time (s): 39.580 (total time: 113.280) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.962741 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.171178 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 0.1119 0.1532 0.0413 0.010 1.1 5.1 0.5 0.0 0 0.981 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.19 15.32 4.13 4.489 20.662 0.171 4.945 11.08 15.15 4.07 4.583 20.767 0.171 4.934 Individual atomic B min max mean iso aniso Overall: 5.49 101.44 20.88 5.05 1987 0 Protein: 5.49 101.44 16.18 5.03 1519 0 Water: 7.89 66.27 36.18 N/A 460 0 Other: 26.44 45.02 34.51 N/A 8 0 Chain A: 5.49 101.44 17.84 N/A 1731 0 Chain S: 15.24 66.27 41.49 N/A 256 0 Histogram: Values Number of atoms 5.49 - 15.09 1046 15.09 - 24.68 359 24.68 - 34.28 216 34.28 - 43.87 198 43.87 - 53.47 113 53.47 - 63.06 33 63.06 - 72.66 12 72.66 - 82.25 3 82.25 - 91.85 3 91.85 - 101.44 4 =========================== Idealize ADP of riding H ========================== r_work=0.1108 r_free=0.1515 r_work=0.1108 r_free=0.1515 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1108 r_free = 0.1515 target_work(ml) = 4.934 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1101 r_free = 0.1523 target_work(ml) = 4.930 | | 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= 0.1101 r_free= 0.1523 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.930116 | | target function (ml) not normalized (work): 80030.572979 | | target function (ml) not normalized (free): 4166.912919 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1108 0.1450 5.4453 5.6957| | 2: 3.63 - 2.88 1.00 2711 122 0.1089 0.1438 5.2189 5.3419| | 3: 2.88 - 2.52 1.00 2681 148 0.1349 0.1704 5.1331 5.2064| | 4: 2.52 - 2.29 1.00 2661 139 0.0933 0.1533 4.6187 4.9426| | 5: 2.29 - 2.13 1.00 2678 122 0.0960 0.1519 4.5712 4.8944| | 6: 2.13 - 2.00 1.00 2692 117 0.1115 0.1649 4.5641 4.7428| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 9.15 1.00 0.96 6524.81| | 2: 3.63 - 2.88 2711 122 0.92 12.98 1.01 0.96 6524.81| | 3: 2.88 - 2.52 2681 148 0.87 19.17 0.99 0.96 6524.81| | 4: 2.52 - 2.29 2661 139 0.93 12.03 1.01 0.97 2085.91| | 5: 2.29 - 2.13 2678 122 0.91 14.10 1.00 0.97 2085.91| | 6: 2.13 - 2.00 2692 117 0.89 16.79 0.99 0.97 2085.91| |alpha: min = 0.96 max = 0.97 mean = 0.97| |beta: min = 2085.91 max = 6524.81 mean = 4328.74| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.92 mean = 14.00| |phase err.(test): min = 0.00 max = 87.78 mean = 13.57| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1122 0.1101 0.1523 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1553 0.1542 0.1805 n_refl.: 17040 remove outliers: r(all,work,free)=0.1553 0.1542 0.1805 n_refl.: 17040 overall B=-0.21 to atoms: r(all,work,free)=0.1541 0.1530 0.1799 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1122 0.1101 0.1525 n_refl.: 17040 remove outliers: r(all,work,free)=0.1122 0.1101 0.1525 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 0.3523 302.900 281.919 0.558 1.006 0.340 11.894-9.307 99.02 97 4 0.1727 487.511 482.520 0.917 1.006 0.320 9.237-7.194 100.00 213 7 0.1743 398.735 402.103 0.982 1.006 0.220 7.162-5.571 100.00 427 22 0.1548 299.251 293.509 0.934 1.006 0.220 5.546-4.326 100.00 867 58 0.0910 410.824 407.535 0.963 1.005 0.200 4.315-3.360 100.00 1859 96 0.0871 390.697 388.551 1.001 1.003 0.191 3.356-2.611 100.00 3867 181 0.1234 256.666 254.407 0.998 1.001 0.131 2.608-2.000 99.99 8818 434 0.1033 167.302 166.048 0.990 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.7371 ================= 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 : 0.2776 0.1831 0.081 5.248 8.8 119.3 19.9 258 0.000 1_bss: 0.1603 0.1655 0.081 5.248 8.4 118.9 19.5 258 0.000 1_settarget: 0.1603 0.1655 0.081 5.248 8.4 118.9 19.5 258 0.000 1_nqh: 0.1603 0.1655 0.081 5.248 8.4 118.9 19.5 258 0.000 1_weight: 0.1603 0.1655 0.081 5.248 8.4 118.9 19.5 258 0.000 1_xyzrec: 0.1350 0.1645 0.009 0.982 8.4 118.9 19.5 258 0.151 1_adp: 0.1276 0.1662 0.009 0.982 5.9 113.9 20.0 258 0.151 1_regHadp: 0.1279 0.1669 0.009 0.982 5.9 113.9 20.0 258 0.151 1_occ: 0.1273 0.1660 0.009 0.982 5.9 113.9 20.0 258 0.151 2_bss: 0.1270 0.1652 0.009 0.982 5.4 113.4 19.5 258 0.151 2_settarget: 0.1270 0.1652 0.009 0.982 5.4 113.4 19.5 258 0.151 2_updatecdl: 0.1270 0.1652 0.009 0.994 5.4 113.4 19.5 258 0.151 2_nqh: 0.1270 0.1652 0.009 0.994 5.4 113.4 19.5 258 0.151 2_sol: 0.1236 0.1545 0.009 0.994 5.4 112.5 20.7 354 n/a 2_weight: 0.1236 0.1545 0.009 0.994 5.4 112.5 20.7 354 n/a 2_xyzrec: 0.1214 0.1584 0.008 0.922 5.4 112.5 20.7 354 n/a 2_adp: 0.1200 0.1603 0.008 0.922 6.4 107.5 21.1 354 n/a 2_regHadp: 0.1202 0.1603 0.008 0.922 6.4 107.5 21.1 354 n/a 2_occ: 0.1200 0.1605 0.008 0.922 6.4 107.5 21.1 354 n/a 3_bss: 0.1195 0.1601 0.008 0.922 6.0 107.1 20.7 354 n/a 3_settarget: 0.1195 0.1601 0.008 0.922 6.0 107.1 20.7 354 n/a 3_updatecdl: 0.1195 0.1601 0.008 0.927 6.0 107.1 20.7 354 n/a 3_nqh: 0.1197 0.1602 0.008 0.927 6.0 107.1 20.7 354 n/a 3_sol: 0.1198 0.1529 0.008 0.927 6.0 107.1 20.8 399 n/a 3_weight: 0.1198 0.1529 0.008 0.927 6.0 107.1 20.8 399 n/a 3_xyzrec: 0.1178 0.1536 0.009 0.969 6.0 107.1 20.8 399 n/a 3_adp: 0.1159 0.1549 0.009 0.969 6.1 105.4 20.6 399 n/a 3_regHadp: 0.1160 0.1552 0.009 0.969 6.1 105.4 20.6 399 n/a 3_occ: 0.1150 0.1539 0.009 0.969 6.1 105.4 20.6 399 n/a 4_bss: 0.1148 0.1536 0.009 0.969 5.8 105.1 20.3 399 n/a 4_settarget: 0.1148 0.1536 0.009 0.969 5.8 105.1 20.3 399 n/a 4_updatecdl: 0.1148 0.1536 0.009 0.967 5.8 105.1 20.3 399 n/a 4_nqh: 0.1148 0.1536 0.009 0.967 5.8 105.1 20.3 399 n/a 4_sol: 0.1138 0.1494 0.009 0.967 5.8 105.1 20.6 434 n/a 4_weight: 0.1138 0.1494 0.009 0.967 5.8 105.1 20.6 434 n/a 4_xyzrec: 0.1123 0.1556 0.009 0.981 5.8 105.1 20.6 434 n/a 4_adp: 0.1113 0.1558 0.009 0.981 5.7 102.7 20.7 434 n/a 4_regHadp: 0.1113 0.1559 0.009 0.981 5.7 102.7 20.7 434 n/a 4_occ: 0.1104 0.1559 0.009 0.981 5.7 102.7 20.7 434 n/a 5_bss: 0.1100 0.1551 0.009 0.981 5.5 102.4 20.4 434 n/a 5_settarget: 0.1100 0.1551 0.009 0.981 5.5 102.4 20.4 434 n/a 5_updatecdl: 0.1100 0.1551 0.009 0.982 5.5 102.4 20.4 434 n/a 5_setrh: 0.1102 0.1550 0.009 0.982 5.5 102.4 20.4 434 n/a 5_nqh: 0.1102 0.1550 0.009 0.982 5.5 102.4 20.4 434 n/a 5_sol: 0.1107 0.1505 0.009 0.982 5.5 102.4 20.7 460 n/a 5_weight: 0.1107 0.1505 0.009 0.982 5.5 102.4 20.7 460 n/a 5_xyzrec: 0.1119 0.1532 0.010 1.089 5.5 102.4 20.7 460 n/a 5_adp: 0.1108 0.1515 0.010 1.089 5.5 101.4 20.9 460 n/a 5_regHadp: 0.1108 0.1515 0.010 1.089 5.5 101.4 20.9 460 n/a 5_occ: 0.1101 0.1523 0.010 1.089 5.5 101.4 20.9 460 n/a end: 0.1101 0.1525 0.010 1.089 5.3 101.2 20.7 460 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_5382129_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_5382129_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.1500 Refinement macro-cycles (run) : 934.4200 Write final files (write_after_run_outputs) : 19.9600 Total : 957.5300 Total CPU time: 16.35 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:23 PST -0800 (1735494083.07 s) Start R-work = 0.1603, R-free = 0.1655 Final R-work = 0.1101, R-free = 0.1525 =============================================================================== Job complete usr+sys time: 1003.52 seconds wall clock time: 17 minutes 6.82 seconds (1026.82 seconds total)