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_5155044.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_5155044.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_5155044.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: 0.36 Conformation dependent library (CDL) restraints added in 140.2 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.64 - 0.91: 552 0.91 - 1.19: 1117 1.19 - 1.46: 769 1.46 - 1.74: 706 1.74 - 2.01: 9 Bond restraints: 3153 Sorted by residual: bond pdb=" C BLYS A 132 " pdb=" O BLYS A 132 " ideal model delta sigma weight residual 1.236 1.026 0.210 1.15e-02 7.56e+03 3.35e+02 bond pdb=" CE1 HIS A 138 " pdb=" NE2 HIS A 138 " ideal model delta sigma weight residual 1.321 1.143 0.178 1.00e-02 1.00e+04 3.16e+02 bond pdb=" C ILE A 102 " pdb=" O ILE A 102 " ideal model delta sigma weight residual 1.236 1.060 0.176 9.90e-03 1.02e+04 3.16e+02 bond pdb=" CZ ARG A 48 " pdb=" NH2 ARG A 48 " ideal model delta sigma weight residual 1.330 1.553 -0.223 1.30e-02 5.92e+03 2.95e+02 bond pdb=" C VAL A 71 " pdb=" O VAL A 71 " ideal model delta sigma weight residual 1.237 1.426 -0.189 1.11e-02 8.12e+03 2.89e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.49: 3108 4.49 - 8.99: 1818 8.99 - 13.48: 707 13.48 - 17.97: 124 17.97 - 22.46: 20 Bond angle restraints: 5777 Sorted by residual: angle pdb=" N VAL A 20 " pdb=" CA VAL A 20 " pdb=" C VAL A 20 " ideal model delta sigma weight residual 111.05 132.28 -21.23 1.25e+00 6.40e-01 2.89e+02 angle pdb=" O GLY A 118 " pdb=" C GLY A 118 " pdb=" N PHE A 119 " ideal model delta sigma weight residual 122.41 136.93 -14.52 1.08e+00 8.57e-01 1.81e+02 angle pdb=" CA GLY A 108 " pdb=" C GLY A 108 " pdb=" O GLY A 108 " ideal model delta sigma weight residual 119.69 111.84 7.85 6.30e-01 2.52e+00 1.55e+02 angle pdb=" CA ARG A 156 " pdb=" C ARG A 156 " pdb=" O ARG A 156 " ideal model delta sigma weight residual 119.41 105.48 13.93 1.13e+00 7.83e-01 1.52e+02 angle pdb=" O BASN A 76 " pdb=" C BASN A 76 " pdb=" N LEU A 77 " ideal model delta sigma weight residual 122.09 134.79 -12.70 1.04e+00 9.25e-01 1.49e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.04: 1295 17.04 - 34.08: 135 34.08 - 51.12: 32 51.12 - 68.16: 16 68.16 - 85.20: 3 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" N PRO A 127 " pdb=" C PRO A 127 " pdb=" CA PRO A 127 " pdb=" CB PRO A 127 " ideal model delta harmonic sigma weight residual 115.10 137.05 -21.95 0 2.50e+00 1.60e-01 7.71e+01 dihedral pdb=" N ASP A 49 " pdb=" C ASP A 49 " pdb=" CA ASP A 49 " pdb=" CB ASP A 49 " ideal model delta harmonic sigma weight residual 122.80 142.70 -19.90 0 2.50e+00 1.60e-01 6.33e+01 dihedral pdb=" N HIS A 115 " pdb=" C HIS A 115 " pdb=" CA HIS A 115 " pdb=" CB HIS A 115 " ideal model delta harmonic sigma weight residual 122.80 141.89 -19.09 0 2.50e+00 1.60e-01 5.83e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.241: 99 0.241 - 0.481: 85 0.481 - 0.720: 38 0.720 - 0.960: 16 0.960 - 1.200: 5 Chirality restraints: 243 Sorted by residual: chirality pdb=" CB VAL A 69 " pdb=" CA VAL A 69 " pdb=" CG1 VAL A 69 " pdb=" CG2 VAL A 69 " both_signs ideal model delta sigma weight residual False -2.63 -1.43 -1.20 2.00e-01 2.50e+01 3.60e+01 chirality pdb=" CA PRO A 127 " pdb=" N PRO A 127 " pdb=" C PRO A 127 " pdb=" CB PRO A 127 " both_signs ideal model delta sigma weight residual False 2.72 1.57 1.14 2.00e-01 2.50e+01 3.27e+01 chirality pdb=" CA ASP A 49 " pdb=" N ASP A 49 " pdb=" C ASP A 49 " pdb=" CB ASP A 49 " both_signs ideal model delta sigma weight residual False 2.51 1.46 1.05 2.00e-01 2.50e+01 2.74e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 126 " 0.125 2.00e-02 2.50e+03 9.34e-02 1.96e+02 pdb=" CG HIS A 126 " -0.095 2.00e-02 2.50e+03 pdb=" ND1 HIS A 126 " -0.079 2.00e-02 2.50e+03 pdb=" CD2 HIS A 126 " 0.031 2.00e-02 2.50e+03 pdb=" CE1 HIS A 126 " 0.104 2.00e-02 2.50e+03 pdb=" NE2 HIS A 126 " 0.103 2.00e-02 2.50e+03 pdb=" HD2 HIS A 126 " -0.131 2.00e-02 2.50e+03 pdb=" HE1 HIS A 126 " -0.085 2.00e-02 2.50e+03 pdb=" HE2 HIS A 126 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " 0.052 2.00e-02 2.50e+03 6.73e-02 1.36e+02 pdb=" CG TYR A 139 " 0.005 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " -0.122 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " -0.109 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.067 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " 0.124 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.029 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " 0.048 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " 0.006 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.041 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " 0.029 2.00e-02 2.50e+03 5.51e-02 9.11e+01 pdb=" CG ATYR A 67 " 0.033 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " -0.105 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " 0.061 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " 0.015 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " -0.087 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " -0.026 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " 0.089 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " 0.044 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " -0.024 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " -0.030 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " 0.000 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 409 2.20 - 2.80: 7174 2.80 - 3.40: 10810 3.40 - 4.00: 15518 4.00 - 4.60: 22781 Nonbonded interactions: 56692 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.600 2.100 nonbonded pdb=" HB2BGLN A 80 " pdb="HE21BGLN A 80 " model vdw 1.786 2.270 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.805 2.450 x-y,-y,-z-4/3 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.812 2.100 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.829 2.450 ... (remaining 56687 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_5155044_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= 0.2797 r_free= 0.1835 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.416724 | | target function (ml) not normalized (work): 71740.841935 | | target function (ml) not normalized (free): 3274.133157 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3206 0.2138 7.5869 5.032| | 2: 3.63 - 2.88 1.00 2711 122 0.2650 0.1676 4.3249 4.3173| | 3: 2.88 - 2.52 1.00 2682 148 0.2553 0.1709 4.1768 4.1819| | 4: 2.52 - 2.29 1.00 2661 139 0.2538 0.1671 3.495 3.63| | 5: 2.29 - 2.13 1.00 2678 122 0.2712 0.1508 3.4242 3.468| | 6: 2.13 - 2.00 1.00 2692 117 0.2746 0.1923 3.327 3.4251| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 17.46 0.77 0.23 1282.53| | 2: 3.63 - 2.88 2711 122 0.83 23.67 1.31 0.23 1282.53| | 3: 2.88 - 2.52 2682 148 0.73 32.58 1.28 0.23 1282.53| | 4: 2.52 - 2.29 2661 139 0.93 11.34 1.30 0.26 138.29| | 5: 2.29 - 2.13 2678 122 0.92 13.86 1.32 0.26 138.29| | 6: 2.13 - 2.00 2692 117 0.90 16.47 1.33 0.26 138.29| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 138.29 max = 1282.53 mean = 716.79| |figures of merit: min = 0.00 max = 1.00 mean = 0.87| |phase err.(work): min = 0.00 max = 90.00 mean = 19.23| |phase err.(test): min = 0.00 max = 89.79 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 : 0.084 0.243 1557 Z= 5.592 Angle : 5.321 21.233 2118 Z= 3.749 Chirality : 0.416 1.200 243 Planarity : 0.032 0.094 284 Dihedral : 14.211 85.196 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.24 % Favored : 96.22 % Rotamer: Outliers : 2.48 % Allowed : 3.73 % Favored : 93.79 % Cbeta Deviations : 32.97 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.46), residues: 224 helix: -2.56 (0.37), residues: 102 sheet: -0.71 (0.75), residues: 38 loop : -0.64 (0.57), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.140 0.030 ARG A 156 TYR 0.135 0.040 TYR A 139 PHE 0.117 0.033 PHE A 164 HIS 0.035 0.019 HIS A 115 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 1785 0 Protein: 8.85 115.78 16.79 3.90 1519 0 Water: 11.36 119.30 38.03 N/A 258 0 Other: 19.04 26.29 21.71 N/A 8 0 Chain A: 8.85 119.30 19.89 N/A 1785 0 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2797 r_free= 0.1835 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.416724 | | target function (ml) not normalized (work): 71740.841935 | | target function (ml) not normalized (free): 3274.133157 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.2983 percent. r_work = 0.2927 r_free = 0.1992 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2874 0.2927 0.1992 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2874 0.2927 0.1992 n_refl.: 17050 remove outliers: r(all,work,free)=0.2166 0.2178 0.1992 n_refl.: 17045 overall B=-0.41 to atoms: r(all,work,free)=0.2139 0.2150 0.1976 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1620 0.1617 0.1676 n_refl.: 17045 remove outliers: r(all,work,free)=0.1619 0.1616 0.1676 n_refl.: 17044 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 100.00 89 5 0.4049 394.874 362.837 0.660 1.011 0.403 11.894-9.307 99.02 97 4 0.1829 633.784 615.866 0.934 1.012 0.390 9.237-7.194 100.00 213 7 0.2136 518.372 510.616 0.959 1.012 0.371 7.162-5.571 100.00 427 22 0.2320 389.038 376.704 0.924 1.011 0.294 5.546-4.326 100.00 867 58 0.1385 534.087 527.690 0.963 1.009 0.219 4.315-3.360 100.00 1859 96 0.1285 507.922 504.126 1.019 1.005 0.181 3.356-2.611 100.00 3867 181 0.1666 333.676 329.357 1.010 1.000 0.081 2.608-2.000 99.99 8818 434 0.1656 217.500 213.413 1.031 0.989 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.4690 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1616 r_free=0.1676 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1616 r_free=0.1676 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.464595 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.915967 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 0.1634 0.0283 0.009 1.0 1.3 0.5 0.0 0 11.732 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.50 16.34 2.83 3.013 18.448 0.916 0.023 12.78 16.51 3.74 3.582 18.666 0.916 0.020 Individual atomic B min max mean iso aniso Overall: 6.13 113.89 19.89 4.09 1785 0 Protein: 6.13 113.16 17.11 4.09 1519 0 Water: 8.64 113.89 36.05 N/A 258 0 Other: 21.61 36.83 26.25 N/A 8 0 Chain A: 6.13 113.89 19.89 N/A 1785 0 Histogram: Values Number of atoms 6.13 - 16.91 1093 16.91 - 27.69 337 27.69 - 38.46 182 38.46 - 49.24 95 49.24 - 60.01 51 60.01 - 70.79 12 70.79 - 81.56 7 81.56 - 92.34 4 92.34 - 103.11 1 103.11 - 113.89 3 =========================== Idealize ADP of riding H ========================== r_work=0.1278 r_free=0.1651 r_work=0.1281 r_free=0.1658 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1281 r_free = 0.1658 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 = 0.1277 r_free = 0.1651 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17044 (all), 4.73 % free)------------| | | | r_work= 0.1277 r_free= 0.1651 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.020088 | | target function (ls_wunit_k1) not normalized (work): 326.176657 | | target function (ls_wunit_k1) not normalized (free): 27.069625 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1295 0.1277 0.1651 n_refl.: 17044 re-set all scales: r(all,work,free)=0.1906 0.1905 0.1971 n_refl.: 17044 remove outliers: r(all,work,free)=0.1906 0.1905 0.1971 n_refl.: 17044 overall B=-0.51 to atoms: r(all,work,free)=0.1869 0.1868 0.1952 n_refl.: 17044 bulk-solvent and scaling: r(all,work,free)=0.1293 0.1275 0.1649 n_refl.: 17044 remove outliers: r(all,work,free)=0.1291 0.1273 0.1649 n_refl.: 17042 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3531 304.374 279.298 0.628 1.006 0.370 11.894-9.307 99.02 97 4 0.1695 489.537 478.636 0.921 1.007 0.367 9.237-7.194 100.00 213 7 0.1826 400.392 396.736 0.962 1.007 0.351 7.162-5.571 100.00 427 22 0.1837 300.495 295.205 0.931 1.007 0.301 5.546-4.326 100.00 867 58 0.1057 412.531 410.067 0.959 1.006 0.201 4.315-3.360 100.00 1859 96 0.0929 392.321 391.846 1.016 1.004 0.192 3.356-2.611 100.00 3867 181 0.1295 257.732 256.422 1.008 1.001 0.081 2.608-2.000 99.99 8818 434 0.1345 167.997 166.684 1.012 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9583 b_overall=-1.1540 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1273 r_free=0.1649 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1273 r_free=0.1649 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1273 r_free=0.1649 | n_water=258 | time (s): 0.740 (total time: 0.740) Filter (dist) r_work=0.1281 r_free=0.1636 | n_water=253 | time (s): 20.220 (total time: 20.960) Filter (q & B) r_work=0.1281 r_free=0.1636 | n_water=251 | time (s): 1.850 (total time: 22.810) Compute maps r_work=0.1281 r_free=0.1636 | n_water=251 | time (s): 0.800 (total time: 23.610) Filter (map) r_work=0.1320 r_free=0.1621 | n_water=212 | time (s): 1.840 (total time: 25.450) Find peaks r_work=0.1320 r_free=0.1621 | n_water=212 | time (s): 0.490 (total time: 25.940) Add new water r_work=0.1543 r_free=0.1862 | n_water=373 | time (s): 1.500 (total time: 27.440) Refine new water occ: r_work=0.1330 r_free=0.1575 adp: r_work=0.1270 r_free=0.1579 occ: r_work=0.1276 r_free=0.1541 adp: r_work=0.1241 r_free=0.1553 occ: r_work=0.1243 r_free=0.1534 adp: r_work=0.1231 r_free=0.1536 ADP+occupancy (water only), MIN, final r_work=0.1231 r_free=0.1536 r_work=0.1231 r_free=0.1536 | n_water=373 | time (s): 15.210 (total time: 42.650) Filter (q & B) r_work=0.1232 r_free=0.1539 | n_water=365 | time (s): 1.570 (total time: 44.220) Filter (dist only) r_work=0.1233 r_free=0.1543 | n_water=364 | time (s): 29.110 (total time: 73.330) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.657348 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.988193 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 0.1206 0.1580 0.0374 0.008 0.9 3.2 0.5 0.0 0 12.329 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.06 15.80 3.74 4.170 20.824 0.988 0.018 11.91 16.04 4.13 4.221 21.163 0.988 0.017 Individual atomic B min max mean iso aniso Overall: 6.39 107.65 21.25 4.36 1891 0 Protein: 6.39 107.65 17.64 4.34 1519 0 Water: 8.59 65.66 36.00 N/A 364 0 Other: 25.36 49.52 37.06 N/A 8 0 Chain A: 6.39 107.65 19.40 N/A 1739 0 Chain S: 19.13 64.75 42.50 N/A 152 0 Histogram: Values Number of atoms 6.39 - 16.52 1017 16.52 - 26.64 386 26.64 - 36.77 212 36.77 - 46.89 173 46.89 - 57.02 67 57.02 - 67.14 25 67.14 - 77.27 4 77.27 - 87.39 3 87.39 - 97.52 2 97.52 - 107.65 2 =========================== Idealize ADP of riding H ========================== r_work=0.1191 r_free=0.1604 r_work=0.1193 r_free=0.1603 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1193 r_free = 0.1603 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1190 r_free = 0.1612 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17042 (all), 4.74 % free)------------| | | | r_work= 0.1190 r_free= 0.1612 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.016868 | | target function (ls_wunit_k1) not normalized (work): 273.858814 | | target function (ls_wunit_k1) not normalized (free): 24.838059 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1210 0.1190 0.1612 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1751 0.1744 0.1930 n_refl.: 17042 remove outliers: r(all,work,free)=0.1751 0.1744 0.1930 n_refl.: 17042 overall B=-0.38 to atoms: r(all,work,free)=0.1727 0.1719 0.1915 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1206 0.1185 0.1607 n_refl.: 17042 remove outliers: r(all,work,free)=0.1206 0.1185 0.1607 n_refl.: 17042 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3386 304.374 284.895 0.602 1.006 0.350 11.894-9.307 99.02 97 4 0.1443 489.537 488.567 0.917 1.007 0.337 9.237-7.194 100.00 213 7 0.1668 400.392 402.751 0.974 1.007 0.288 7.162-5.571 100.00 427 22 0.1534 300.495 296.702 0.937 1.006 0.267 5.546-4.326 100.00 867 58 0.0872 412.531 410.027 0.961 1.005 0.221 4.315-3.360 100.00 1859 96 0.0819 392.321 391.806 1.016 1.004 0.191 3.356-2.611 100.00 3867 181 0.1191 257.732 256.909 1.009 1.000 0.101 2.608-2.000 99.99 8818 434 0.1331 167.997 166.887 1.013 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-1.1691 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1185 r_free=0.1607 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=0.1185 r_free=0.1607 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1185 r_free=0.1607 | n_water=364 | time (s): 0.730 (total time: 0.730) Filter (dist) r_work=0.1185 r_free=0.1613 | n_water=362 | time (s): 28.450 (total time: 29.180) Filter (q & B) r_work=0.1185 r_free=0.1613 | n_water=362 | time (s): 1.200 (total time: 30.380) Compute maps r_work=0.1185 r_free=0.1613 | n_water=362 | time (s): 0.700 (total time: 31.080) Filter (map) r_work=0.1255 r_free=0.1594 | n_water=268 | time (s): 1.700 (total time: 32.780) Find peaks r_work=0.1255 r_free=0.1594 | n_water=268 | time (s): 0.640 (total time: 33.420) Add new water r_work=0.1437 r_free=0.1768 | n_water=418 | time (s): 1.890 (total time: 35.310) Refine new water occ: r_work=0.1243 r_free=0.1552 adp: r_work=0.1236 r_free=0.1555 occ: r_work=0.1219 r_free=0.1524 adp: r_work=0.1208 r_free=0.1529 occ: r_work=0.1201 r_free=0.1503 adp: r_work=0.1191 r_free=0.1508 ADP+occupancy (water only), MIN, final r_work=0.1191 r_free=0.1508 r_work=0.1191 r_free=0.1508 | n_water=418 | time (s): 48.520 (total time: 83.830) Filter (q & B) r_work=0.1194 r_free=0.1508 | n_water=408 | time (s): 1.670 (total time: 85.500) Filter (dist only) r_work=0.1194 r_free=0.1508 | n_water=408 | time (s): 29.800 (total time: 115.300) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.821669 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.173427 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 0.1175 0.1539 0.0364 0.009 1.0 4.8 0.5 0.0 0 0.911 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.75 15.39 3.64 4.387 21.477 0.173 4.996 11.52 15.37 3.85 4.948 21.414 0.173 4.972 Individual atomic B min max mean iso aniso Overall: 6.37 105.35 20.87 4.82 1935 0 Protein: 6.37 105.35 16.90 4.81 1519 0 Water: 8.79 63.22 35.36 N/A 408 0 Other: 25.75 47.82 34.09 N/A 8 0 Chain A: 6.37 105.35 18.69 N/A 1736 0 Chain S: 16.00 63.22 39.87 N/A 199 0 Histogram: Values Number of atoms 6.37 - 16.27 1072 16.27 - 26.17 349 26.17 - 36.06 216 36.06 - 45.96 179 45.96 - 55.86 74 55.86 - 65.76 32 65.76 - 75.65 4 75.65 - 85.55 4 85.55 - 95.45 3 95.45 - 105.35 2 =========================== Idealize ADP of riding H ========================== r_work=0.1152 r_free=0.1537 r_work=0.1153 r_free=0.1539 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1153 r_free = 0.1539 target_work(ml) = 4.971 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1145 r_free = 0.1546 target_work(ml) = 4.967 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17042 (all), 4.74 % free)------------| | | | r_work= 0.1145 r_free= 0.1546 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.966608 | | target function (ml) not normalized (work): 80632.884050 | | target function (ml) not normalized (free): 4185.526084 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1165 0.1145 0.1546 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1667 0.1662 0.1829 n_refl.: 17042 remove outliers: r(all,work,free)=0.1667 0.1662 0.1829 n_refl.: 17042 overall B=-0.37 to atoms: r(all,work,free)=0.1643 0.1637 0.1818 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1164 0.1144 0.1545 n_refl.: 17042 remove outliers: r(all,work,free)=0.1163 0.1143 0.1545 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 0.3564 300.872 282.750 0.574 1.002 0.340 11.894-9.307 99.02 97 4 0.1814 489.537 482.779 0.918 1.004 0.340 9.237-7.194 100.00 213 7 0.1790 400.392 400.595 0.987 1.004 0.300 7.162-5.571 100.00 427 22 0.1625 300.495 294.817 0.940 1.004 0.251 5.546-4.326 100.00 867 58 0.0942 412.531 409.071 0.966 1.004 0.210 4.315-3.360 100.00 1859 96 0.0882 392.321 390.026 1.013 1.003 0.201 3.356-2.611 100.00 3867 181 0.1274 257.732 255.475 1.010 1.002 0.152 2.608-2.000 99.99 8818 434 0.1090 167.997 166.501 1.007 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-1.1411 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1143 r_free=0.1545 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1143 r_free=0.1545 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1143 r_free=0.1545 | n_water=408 | time (s): 0.820 (total time: 0.820) Filter (dist) r_work=0.1143 r_free=0.1549 | n_water=407 | time (s): 35.230 (total time: 36.050) Filter (q & B) r_work=0.1143 r_free=0.1549 | n_water=407 | time (s): 0.840 (total time: 36.890) Compute maps r_work=0.1143 r_free=0.1549 | n_water=407 | time (s): 0.590 (total time: 37.480) Filter (map) r_work=0.1207 r_free=0.1582 | n_water=310 | time (s): 1.800 (total time: 39.280) Find peaks r_work=0.1207 r_free=0.1582 | n_water=310 | time (s): 0.450 (total time: 39.730) Add new water r_work=0.1352 r_free=0.1693 | n_water=449 | time (s): 2.210 (total time: 41.940) Refine new water occ: r_work=0.1180 r_free=0.1538 adp: r_work=0.1172 r_free=0.1542 occ: r_work=0.1157 r_free=0.1523 adp: r_work=0.1148 r_free=0.1528 occ: r_work=0.1142 r_free=0.1514 adp: r_work=0.1134 r_free=0.1517 ADP+occupancy (water only), MIN, final r_work=0.1134 r_free=0.1517 r_work=0.1134 r_free=0.1517 | n_water=449 | time (s): 38.350 (total time: 80.290) Filter (q & B) r_work=0.1139 r_free=0.1530 | n_water=436 | time (s): 1.510 (total time: 81.800) Filter (dist only) r_work=0.1139 r_free=0.1530 | n_water=436 | time (s): 33.000 (total time: 114.800) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.934284 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.166290 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 0.1124 0.1563 0.0439 0.009 1.0 4.5 0.5 0.0 0 0.967 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.24 15.63 4.39 4.579 21.044 0.166 4.961 11.17 15.65 4.48 4.724 21.052 0.166 4.957 Individual atomic B min max mean iso aniso Overall: 5.75 103.00 20.90 4.91 1963 0 Protein: 5.75 103.00 16.47 4.90 1519 0 Water: 8.67 65.19 36.07 N/A 436 0 Other: 26.43 45.41 33.85 N/A 8 0 Chain A: 5.75 103.00 18.19 N/A 1735 0 Chain S: 12.98 65.19 41.49 N/A 228 0 Histogram: Values Number of atoms 5.75 - 15.47 1038 15.47 - 25.20 371 25.20 - 34.92 213 34.92 - 44.65 182 44.65 - 54.38 107 54.38 - 64.10 36 64.10 - 73.83 7 73.83 - 83.55 4 83.55 - 93.28 3 93.28 - 103.00 2 =========================== Idealize ADP of riding H ========================== r_work=0.1117 r_free=0.1565 r_work=0.1117 r_free=0.1566 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1117 r_free = 0.1566 target_work(ml) = 4.957 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1110 r_free = 0.1584 target_work(ml) = 4.957 | | occupancies: max = 1.00 min = 0.21 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= 0.1110 r_free= 0.1584 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.957069 | | target function (ml) not normalized (work): 80473.053976 | | target function (ml) not normalized (free): 4193.250094 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1133 0.1110 0.1584 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1598 0.1586 0.1875 n_refl.: 17041 remove outliers: r(all,work,free)=0.1598 0.1586 0.1875 n_refl.: 17041 overall B=-0.28 to atoms: r(all,work,free)=0.1580 0.1568 0.1866 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1129 0.1106 0.1576 n_refl.: 17041 remove outliers: r(all,work,free)=0.1128 0.1105 0.1576 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 0.3687 297.625 276.467 0.550 1.003 0.330 11.894-9.307 99.02 97 4 0.1891 489.537 481.327 0.914 1.005 0.324 9.237-7.194 100.00 213 7 0.1755 400.392 401.563 0.988 1.005 0.250 7.162-5.571 100.00 427 22 0.1593 300.495 295.140 0.942 1.005 0.230 5.546-4.326 100.00 867 58 0.0910 412.531 409.661 0.962 1.004 0.195 4.315-3.360 100.00 1859 96 0.0845 392.321 389.913 1.006 1.003 0.191 3.356-2.611 100.00 3867 181 0.1253 257.732 255.590 1.003 1.001 0.131 2.608-2.000 99.99 8818 434 0.1031 167.997 166.783 1.000 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-0.9534 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1105 r_free=0.1576 After: r_work=0.1107 r_free=0.1575 ================================== NQH flips ================================== r_work=0.1107 r_free=0.1575 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1107 r_free=0.1575 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1107 r_free=0.1575 | n_water=436 | time (s): 0.800 (total time: 0.800) Filter (dist) r_work=0.1114 r_free=0.1575 | n_water=434 | time (s): 33.850 (total time: 34.650) Filter (q & B) r_work=0.1114 r_free=0.1575 | n_water=434 | time (s): 0.800 (total time: 35.450) Compute maps r_work=0.1114 r_free=0.1575 | n_water=434 | time (s): 0.650 (total time: 36.100) Filter (map) r_work=0.1201 r_free=0.1598 | n_water=321 | time (s): 1.860 (total time: 37.960) Find peaks r_work=0.1201 r_free=0.1598 | n_water=321 | time (s): 0.470 (total time: 38.430) Add new water r_work=0.1318 r_free=0.1686 | n_water=463 | time (s): 1.610 (total time: 40.040) Refine new water occ: r_work=0.1148 r_free=0.1521 adp: r_work=0.1142 r_free=0.1527 occ: r_work=0.1126 r_free=0.1500 adp: r_work=0.1119 r_free=0.1503 occ: r_work=0.1112 r_free=0.1491 adp: r_work=0.1106 r_free=0.1495 ADP+occupancy (water only), MIN, final r_work=0.1106 r_free=0.1495 r_work=0.1106 r_free=0.1495 | n_water=463 | time (s): 22.930 (total time: 62.970) Filter (q & B) r_work=0.1108 r_free=0.1503 | n_water=458 | time (s): 2.120 (total time: 65.090) Filter (dist only) r_work=0.1108 r_free=0.1505 | n_water=457 | time (s): 36.410 (total time: 101.500) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.931571 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.139733 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 0.1130 0.1540 0.0410 0.009 1.1 8.0 0.5 0.0 0 0.966 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.30 15.40 4.10 4.587 20.783 0.140 4.960 11.21 15.20 3.99 4.592 20.810 0.140 4.952 Individual atomic B min max mean iso aniso Overall: 5.64 100.96 20.81 4.87 1984 0 Protein: 5.64 100.96 16.23 4.86 1519 0 Water: 8.25 66.78 35.84 N/A 457 0 Other: 26.66 43.96 33.79 N/A 8 0 Chain A: 5.64 100.96 17.88 N/A 1733 0 Chain S: 15.66 66.78 41.08 N/A 251 0 Histogram: Values Number of atoms 5.64 - 15.17 1045 15.17 - 24.70 360 24.70 - 34.23 213 34.23 - 43.76 192 43.76 - 53.30 121 53.30 - 62.83 35 62.83 - 72.36 8 72.36 - 81.89 2 81.89 - 91.43 4 91.43 - 100.96 4 =========================== Idealize ADP of riding H ========================== r_work=0.1121 r_free=0.1520 r_work=0.1121 r_free=0.1520 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1121 r_free = 0.1520 target_work(ml) = 4.952 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1113 r_free = 0.1530 target_work(ml) = 4.948 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1113 r_free= 0.1530 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.948090 | | target function (ml) not normalized (work): 80322.342612 | | target function (ml) not normalized (free): 4172.735545 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1118 0.1392 5.4637 5.6303| | 2: 3.63 - 2.88 1.00 2711 122 0.1098 0.1548 5.2209 5.3561| | 3: 2.88 - 2.52 1.00 2681 148 0.1364 0.1710 5.132 5.2065| | 4: 2.52 - 2.29 1.00 2661 139 0.0947 0.1470 4.6482 4.9656| | 5: 2.29 - 2.13 1.00 2678 122 0.0974 0.1564 4.601 4.9399| | 6: 2.13 - 2.00 1.00 2692 117 0.1127 0.1744 4.5937 4.7917| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.64 2810 159 0.95 8.90 1.00 0.96 6320.72| | 2: 3.63 - 2.88 2711 122 0.92 12.74 1.01 0.96 6320.72| | 3: 2.88 - 2.52 2681 148 0.88 18.84 0.99 0.96 6320.72| | 4: 2.52 - 2.29 2661 139 0.93 12.41 1.01 0.98 2226.10| | 5: 2.29 - 2.13 2678 122 0.91 14.45 1.00 0.98 2226.10| | 6: 2.13 - 2.00 2692 117 0.89 17.18 0.99 0.98 2226.10| |alpha: min = 0.96 max = 0.98 mean = 0.97| |beta: min = 2226.10 max = 6320.72 mean = 4294.97| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.95 mean = 14.05| |phase err.(test): min = 0.00 max = 89.86 mean = 13.79| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1133 0.1113 0.1530 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1582 0.1572 0.1797 n_refl.: 17040 remove outliers: r(all,work,free)=0.1582 0.1572 0.1797 n_refl.: 17040 overall B=-0.23 to atoms: r(all,work,free)=0.1568 0.1559 0.1790 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1133 0.1113 0.1531 n_refl.: 17040 remove outliers: r(all,work,free)=0.1133 0.1113 0.1531 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 0.3636 297.625 277.860 0.543 1.005 0.324 11.894-9.307 99.02 97 4 0.1813 489.537 482.366 0.916 1.006 0.320 9.237-7.194 100.00 213 7 0.1755 400.392 402.214 0.986 1.006 0.230 7.162-5.571 100.00 427 22 0.1549 300.495 295.535 0.938 1.005 0.230 5.546-4.326 100.00 867 58 0.0938 412.531 409.249 0.960 1.005 0.195 4.315-3.360 100.00 1859 96 0.0862 392.321 390.130 1.002 1.003 0.191 3.356-2.611 100.00 3867 181 0.1248 257.732 255.569 1.000 1.001 0.067 2.608-2.000 99.99 8818 434 0.1047 167.997 166.638 0.992 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.7802 ================= 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 : 0.2797 0.1835 0.084 5.321 8.8 119.3 19.9 258 0.000 1_bss: 0.1616 0.1676 0.084 5.321 8.4 118.9 19.5 258 0.000 1_settarget: 0.1616 0.1676 0.084 5.321 8.4 118.9 19.5 258 0.000 1_nqh: 0.1616 0.1676 0.084 5.321 8.4 118.9 19.5 258 0.000 1_weight: 0.1616 0.1676 0.084 5.321 8.4 118.9 19.5 258 0.000 1_xyzrec: 0.1350 0.1634 0.009 0.975 8.4 118.9 19.5 258 0.146 1_adp: 0.1278 0.1651 0.009 0.975 6.1 113.9 19.9 258 0.146 1_regHadp: 0.1281 0.1658 0.009 0.975 6.1 113.9 19.9 258 0.146 1_occ: 0.1277 0.1651 0.009 0.975 6.1 113.9 19.9 258 0.146 2_bss: 0.1273 0.1649 0.009 0.975 5.6 113.4 19.4 258 0.146 2_settarget: 0.1273 0.1649 0.009 0.975 5.6 113.4 19.4 258 0.146 2_updatecdl: 0.1273 0.1649 0.009 0.991 5.6 113.4 19.4 258 0.146 2_nqh: 0.1273 0.1649 0.009 0.991 5.6 113.4 19.4 258 0.146 2_sol: 0.1233 0.1543 0.009 0.991 5.6 112.6 20.6 364 n/a 2_weight: 0.1233 0.1543 0.009 0.991 5.6 112.6 20.6 364 n/a 2_xyzrec: 0.1206 0.1580 0.008 0.938 5.6 112.6 20.6 364 n/a 2_adp: 0.1191 0.1604 0.008 0.938 6.4 107.6 21.3 364 n/a 2_regHadp: 0.1193 0.1603 0.008 0.938 6.4 107.6 21.3 364 n/a 2_occ: 0.1190 0.1612 0.008 0.938 6.4 107.6 21.3 364 n/a 3_bss: 0.1185 0.1607 0.008 0.938 6.0 107.3 20.9 364 n/a 3_settarget: 0.1185 0.1607 0.008 0.938 6.0 107.3 20.9 364 n/a 3_updatecdl: 0.1185 0.1607 0.008 0.944 6.0 107.3 20.9 364 n/a 3_nqh: 0.1185 0.1607 0.008 0.944 6.0 107.3 20.9 364 n/a 3_sol: 0.1194 0.1508 0.008 0.944 6.0 107.3 21.0 408 n/a 3_weight: 0.1194 0.1508 0.008 0.944 6.0 107.3 21.0 408 n/a 3_xyzrec: 0.1175 0.1539 0.009 0.966 6.0 107.3 21.0 408 n/a 3_adp: 0.1152 0.1537 0.009 0.966 6.4 105.3 20.9 408 n/a 3_regHadp: 0.1153 0.1539 0.009 0.966 6.4 105.3 20.9 408 n/a 3_occ: 0.1145 0.1546 0.009 0.966 6.4 105.3 20.9 408 n/a 4_bss: 0.1143 0.1545 0.009 0.966 6.0 105.0 20.5 408 n/a 4_settarget: 0.1143 0.1545 0.009 0.966 6.0 105.0 20.5 408 n/a 4_updatecdl: 0.1143 0.1545 0.009 0.966 6.0 105.0 20.5 408 n/a 4_nqh: 0.1143 0.1545 0.009 0.966 6.0 105.0 20.5 408 n/a 4_sol: 0.1139 0.1530 0.009 0.966 6.0 105.0 20.9 436 n/a 4_weight: 0.1139 0.1530 0.009 0.966 6.0 105.0 20.9 436 n/a 4_xyzrec: 0.1124 0.1563 0.009 0.973 6.0 105.0 20.9 436 n/a 4_adp: 0.1117 0.1565 0.009 0.973 5.7 103.0 20.9 436 n/a 4_regHadp: 0.1117 0.1566 0.009 0.973 5.7 103.0 20.9 436 n/a 4_occ: 0.1110 0.1584 0.009 0.973 5.7 103.0 20.9 436 n/a 5_bss: 0.1105 0.1576 0.009 0.973 5.5 102.7 20.6 436 n/a 5_settarget: 0.1105 0.1576 0.009 0.973 5.5 102.7 20.6 436 n/a 5_updatecdl: 0.1105 0.1576 0.009 0.973 5.5 102.7 20.6 436 n/a 5_setrh: 0.1107 0.1575 0.009 0.973 5.5 102.7 20.6 436 n/a 5_nqh: 0.1107 0.1575 0.009 0.973 5.5 102.7 20.6 436 n/a 5_sol: 0.1108 0.1505 0.009 0.973 5.5 102.7 20.8 457 n/a 5_weight: 0.1108 0.1505 0.009 0.973 5.5 102.7 20.8 457 n/a 5_xyzrec: 0.1130 0.1540 0.009 1.057 5.5 102.7 20.8 457 n/a 5_adp: 0.1121 0.1520 0.009 1.057 5.6 101.0 20.8 457 n/a 5_regHadp: 0.1121 0.1520 0.009 1.057 5.6 101.0 20.8 457 n/a 5_occ: 0.1113 0.1530 0.009 1.057 5.6 101.0 20.8 457 n/a end: 0.1113 0.1531 0.009 1.057 5.4 100.7 20.6 457 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_5155044_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_5155044_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.7400 Refinement macro-cycles (run) : 937.9800 Write final files (write_after_run_outputs) : 18.5300 Total : 960.2500 Total CPU time: 16.36 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:23 PST -0800 (1735494083.40 s) Start R-work = 0.1616, R-free = 0.1676 Final R-work = 0.1113, R-free = 0.1531 =============================================================================== Job complete usr+sys time: 1002.20 seconds wall clock time: 17 minutes 5.77 seconds (1025.77 seconds total)