Starting phenix.refine on Mon May 20 17:17:37 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/1x24.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1x24/1x24.mtz Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- optimize_xyz=true optimize_adp=true main.number_of_mac=3 main.max_number_of_iterations=100 main.nproc=20 nonbonded_weight=100 modify_start_model.modify.selection=element H modify_start_model.modify.occupancies.set=1 strategy=individual_sites+individual_adp ramachandran_plot_restraints.enabled=False secondary_structure.enabled=True main.nqh_flips=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1x24/1x24.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1x24/1x24.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/1x24.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/1x24.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 } main { nqh_flips = False max_number_of_iterations = 100 nproc = 20 } modify_start_model { modify { selection = element H occupancies { set = 1 } } } pdb_interpretation { secondary_structure { enabled = True } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = true optimize_adp_weight = true } } Starting job =============================================================================== Symmetric amino acids flipped Residue "B TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 4962 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 2481 Classifications: {'peptide': 152} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 7, 'TRANS': 144} Chain: "B" Number of atoms: 2481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 2481 Classifications: {'peptide': 152} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 7, 'TRANS': 144} Time building chain proxies: 1.83, per 1000 atoms: 0.37 Number of scatterers: 4962 At special positions: 0 Unit cell: (146.891, 146.891, 146.891, 90, 90, 90) Space group: I 21 3 (No. 199) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 O 434 8.00 N 424 7.00 C 1580 6.00 H 2510 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 104 " distance=2.01 Simple disulfide: pdb=" SG CYS B 49 " - pdb=" SG CYS B 104 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 3.42 Conformation dependent library (CDL) restraints added in 755.9 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 572 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 12 helices and 2 sheets defined 42.4% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 30 through 39 Processing helix chain 'A' and resid 56 through 61 removed outlier: 3.847A pdb=" N GLU A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 94 removed outlier: 3.865A pdb=" N PHE A 92 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ARG A 93 " --> pdb=" O LYS A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 121 removed outlier: 3.616A pdb=" N VAL A 115 " --> pdb=" O ALA A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 137 removed outlier: 4.210A pdb=" N LYS A 136 " --> pdb=" O PHE A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 151 Processing helix chain 'B' and resid 30 through 39 Processing helix chain 'B' and resid 55 through 61 removed outlier: 3.721A pdb=" N GLU B 59 " --> pdb=" O THR B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 94 removed outlier: 3.830A pdb=" N PHE B 92 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ARG B 93 " --> pdb=" O LYS B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 121 removed outlier: 3.642A pdb=" N VAL B 115 " --> pdb=" O ALA B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 137 removed outlier: 4.186A pdb=" N LYS B 136 " --> pdb=" O PHE B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 151 Processing sheet with id= A, first strand: chain 'A' and resid 10 through 14 removed outlier: 6.401A pdb=" N ILE A 100 " --> pdb=" O LEU A 20 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N THR A 22 " --> pdb=" O ILE A 100 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL A 102 " --> pdb=" O THR A 22 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N ALA A 101 " --> pdb=" O THR A 43 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ILE A 45 " --> pdb=" O ALA A 101 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N HIS A 103 " --> pdb=" O ILE A 45 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ARG A 47 " --> pdb=" O HIS A 103 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N HIS A 64 " --> pdb=" O ILE A 45 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N ARG A 47 " --> pdb=" O HIS A 64 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU A 66 " --> pdb=" O ARG A 47 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 10 through 14 removed outlier: 6.440A pdb=" N ILE B 100 " --> pdb=" O LEU B 20 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N THR B 22 " --> pdb=" O ILE B 100 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL B 102 " --> pdb=" O THR B 22 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N ALA B 101 " --> pdb=" O THR B 43 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ILE B 45 " --> pdb=" O ALA B 101 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N HIS B 103 " --> pdb=" O ILE B 45 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ARG B 47 " --> pdb=" O HIS B 103 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N HIS B 64 " --> pdb=" O ILE B 45 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ARG B 47 " --> pdb=" O HIS B 64 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LEU B 66 " --> pdb=" O ARG B 47 " (cutoff:3.500A) 86 hydrogen bonds defined for protein. 237 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.71 Time building geometry restraints manager: 2.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.15: 2506 1.15 - 1.32: 455 1.32 - 1.50: 983 1.50 - 1.67: 1052 1.67 - 1.84: 20 Bond restraints: 5016 Sorted by residual: bond pdb=" N GLY B 73 " pdb=" H GLY B 73 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" N TYR A 14 " pdb=" H TYR A 14 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N ILE A 45 " pdb=" H ILE A 45 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N PHE A 160 " pdb=" H PHE A 160 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" NE ARG A 153 " pdb=" HE ARG A 153 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 5011 not shown) Histogram of bond angle deviations from ideal: 100.47 - 107.19: 382 107.19 - 113.90: 5754 113.90 - 120.62: 1661 120.62 - 127.33: 1294 127.33 - 134.05: 19 Bond angle restraints: 9110 Sorted by residual: angle pdb=" N ARG B 93 " pdb=" CA ARG B 93 " pdb=" C ARG B 93 " ideal model delta sigma weight residual 111.40 103.59 7.81 1.22e+00 6.72e-01 4.10e+01 angle pdb=" C GLU B 95 " pdb=" N PRO B 96 " pdb=" CA PRO B 96 " ideal model delta sigma weight residual 119.84 127.73 -7.89 1.25e+00 6.40e-01 3.99e+01 angle pdb=" N ARG A 93 " pdb=" CA ARG A 93 " pdb=" C ARG A 93 " ideal model delta sigma weight residual 111.40 103.82 7.58 1.22e+00 6.72e-01 3.86e+01 angle pdb=" C GLU A 95 " pdb=" N PRO A 96 " pdb=" CA PRO A 96 " ideal model delta sigma weight residual 119.84 127.01 -7.17 1.25e+00 6.40e-01 3.29e+01 angle pdb=" N LYS A 91 " pdb=" CA LYS A 91 " pdb=" C LYS A 91 " ideal model delta sigma weight residual 110.80 120.32 -9.52 2.13e+00 2.20e-01 2.00e+01 ... (remaining 9105 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.13: 2041 15.13 - 30.26: 170 30.26 - 45.39: 74 45.39 - 60.52: 51 60.52 - 75.65: 6 Dihedral angle restraints: 2342 sinusoidal: 1294 harmonic: 1048 Sorted by residual: dihedral pdb=" CB CYS B 49 " pdb=" SG CYS B 49 " pdb=" SG CYS B 104 " pdb=" CB CYS B 104 " ideal model delta sinusoidal sigma weight residual 93.00 59.98 33.02 1 1.00e+01 1.00e-02 1.55e+01 dihedral pdb=" N LEU A 158 " pdb=" CA LEU A 158 " pdb=" CB LEU A 158 " pdb=" CG LEU A 158 " ideal model delta sinusoidal sigma weight residual -60.00 -117.55 57.55 3 1.50e+01 4.44e-03 9.44e+00 dihedral pdb=" N VAL B 12 " pdb=" CA VAL B 12 " pdb=" CB VAL B 12 " pdb=" CG1 VAL B 12 " ideal model delta sinusoidal sigma weight residual 60.00 3.29 56.71 3 1.50e+01 4.44e-03 9.41e+00 ... (remaining 2339 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.065: 177 0.065 - 0.129: 129 0.129 - 0.193: 56 0.193 - 0.257: 12 0.257 - 0.322: 6 Chirality restraints: 380 Sorted by residual: chirality pdb=" CA LYS A 91 " pdb=" N LYS A 91 " pdb=" C LYS A 91 " pdb=" CB LYS A 91 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" CA ILE B 100 " pdb=" N ILE B 100 " pdb=" C ILE B 100 " pdb=" CB ILE B 100 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" CA LYS B 91 " pdb=" N LYS B 91 " pdb=" C LYS B 91 " pdb=" CB LYS B 91 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.24e+00 ... (remaining 377 not shown) Planarity restraints: 718 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 14 " -0.055 2.00e-02 2.50e+03 2.08e-02 1.30e+01 pdb=" CG TYR B 14 " 0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR B 14 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR B 14 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR B 14 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 14 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR B 14 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 14 " -0.028 2.00e-02 2.50e+03 pdb=" HD1 TYR B 14 " 0.019 2.00e-02 2.50e+03 pdb=" HD2 TYR B 14 " 0.020 2.00e-02 2.50e+03 pdb=" HE1 TYR B 14 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 TYR B 14 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 14 " 0.053 2.00e-02 2.50e+03 2.01e-02 1.21e+01 pdb=" CG TYR A 14 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR A 14 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR A 14 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR A 14 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 14 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 14 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 14 " 0.027 2.00e-02 2.50e+03 pdb=" HD1 TYR A 14 " -0.017 2.00e-02 2.50e+03 pdb=" HD2 TYR A 14 " -0.022 2.00e-02 2.50e+03 pdb=" HE1 TYR A 14 " -0.003 2.00e-02 2.50e+03 pdb=" HE2 TYR A 14 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 70 " 0.053 2.00e-02 2.50e+03 1.96e-02 1.16e+01 pdb=" CG PHE B 70 " -0.014 2.00e-02 2.50e+03 pdb=" CD1 PHE B 70 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE B 70 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE B 70 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 70 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 70 " 0.007 2.00e-02 2.50e+03 pdb=" HD1 PHE B 70 " -0.022 2.00e-02 2.50e+03 pdb=" HD2 PHE B 70 " -0.021 2.00e-02 2.50e+03 pdb=" HE1 PHE B 70 " 0.004 2.00e-02 2.50e+03 pdb=" HE2 PHE B 70 " 0.002 2.00e-02 2.50e+03 pdb=" HZ PHE B 70 " 0.019 2.00e-02 2.50e+03 ... (remaining 715 not shown) Histogram of nonbonded interaction distances: 1.10 - 1.80: 84 1.80 - 2.50: 3854 2.50 - 3.20: 15870 3.20 - 3.90: 21680 3.90 - 4.60: 32886 Nonbonded interactions: 74374 Sorted by model distance: nonbonded pdb=" HB3 CYS B 104 " pdb=" H VAL B 105 " model vdw 1.099 2.270 nonbonded pdb="HD11 ILE A 34 " pdb="HG22 VAL A 58 " model vdw 1.159 2.440 nonbonded pdb="HD11 ILE B 34 " pdb="HG22 VAL B 58 " model vdw 1.174 2.440 nonbonded pdb=" HE2 MET A 156 " pdb=" HE2 MET B 156 " model vdw 1.336 2.440 nonbonded pdb=" OE1 GLU A 127 " pdb=" H GLU A 127 " model vdw 1.401 1.850 ... (remaining 74369 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: 5 Type Number sf(0) Gaussians S 14 15.96 2 O 434 7.97 1 N 424 6.97 1 C 1580 5.97 2 H 2510 1.00 1 sf(0) = scattering factor at diffraction angle 0. =========================== Regularize ADP if needed ========================== ========================== Anomalous scatterer groups ========================= All atoms refined with f_prime=0 and f_double_prime=0. ====================== Modifying start model if requested ===================== Setting occupancies to: 1.000: selected atoms: 2510 of 4962 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 4962 n_use_u_iso = 4962 n_use_u_aniso = 0 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 = 4962 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (4962 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 4962 aniso = 0) group_adp = False (0 atoms in 0 groups) tls = False (0 atoms in 0 groups) occupancies = False (0 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 } main { nqh_flips = False max_number_of_iterations = 100 nproc = 20 } modify_start_model { modify { selection = element H occupancies { set = 1 } } } hydrogens { refine = individual *riding Auto } pdb_interpretation { secondary_structure { protein { helix { serial_number = "1" helix_identifier = "1" selection = chain 'A' and resid 30 through 39 } helix { serial_number = "2" helix_identifier = "2" selection = chain 'A' and resid 56 through 61 } helix { serial_number = "3" helix_identifier = "3" selection = chain 'A' and resid 79 through 94 } helix { serial_number = "4" helix_identifier = "4" selection = chain 'A' and resid 111 through 121 } helix { serial_number = "5" helix_identifier = "5" selection = chain 'A' and resid 126 through 137 } helix { serial_number = "6" helix_identifier = "6" selection = chain 'A' and resid 143 through 151 } helix { serial_number = "7" helix_identifier = "7" selection = chain 'B' and resid 30 through 39 } helix { serial_number = "8" helix_identifier = "8" selection = chain 'B' and resid 55 through 61 helix_type = alpha pi *3_10 unknown } helix { serial_number = "9" helix_identifier = "9" selection = chain 'B' and resid 79 through 94 } helix { serial_number = "10" helix_identifier = "10" selection = chain 'B' and resid 111 through 121 } helix { serial_number = "11" helix_identifier = "11" selection = chain 'B' and resid 126 through 137 } helix { serial_number = "12" helix_identifier = "12" selection = chain 'B' and resid 143 through 151 } sheet { first_strand = chain 'A' and resid 10 through 14 sheet_id = " A" strand { selection = chain 'A' and resid 17 through 22 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 21 and name N bond_start_previous = chain 'A' and resid 10 and name O } strand { selection = chain 'A' and resid 99 through 103 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 100 and name N bond_start_previous = chain 'A' and resid 20 and name O } strand { selection = chain 'A' and resid 42 through 47 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 43 and name N bond_start_previous = chain 'A' and resid 99 and name O } strand { selection = chain 'A' and resid 64 through 66 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 64 and name N bond_start_previous = chain 'A' and resid 45 and name O } } sheet { first_strand = chain 'B' and resid 10 through 14 sheet_id = " B" strand { selection = chain 'B' and resid 17 through 22 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 21 and name N bond_start_previous = chain 'B' and resid 10 and name O } strand { selection = chain 'B' and resid 99 through 103 sense = *parallel antiparallel unknown bond_start_current = chain 'B' and resid 100 and name N bond_start_previous = chain 'B' and resid 20 and name O } strand { selection = chain 'B' and resid 42 through 47 sense = *parallel antiparallel unknown bond_start_current = chain 'B' and resid 43 and name N bond_start_previous = chain 'B' and resid 99 and name O } strand { selection = chain 'B' and resid 64 through 66 sense = *parallel antiparallel unknown bond_start_current = chain 'B' and resid 64 and name N bond_start_previous = chain 'B' and resid 45 and name O } } } enabled = True } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } output { prefix = "1x24_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 2510 occupancy sum: 2510.00 (% of total atoms 50.58) Rotatable: count: 700 occupancy sum: 700.00 (% of total atoms 14.11) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.10 - 25.19 A, n_refl.=9450 (all), 10.31 % free)-------------| | | | r_work= 0.3217 r_free= 0.3511 coordinate error (max.-lik. estimate): 0.34 A | | | | normalized target function (ml) (work): 3.705103 | | target function (ml) not normalized (work): 31404.451511 | | target function (ml) not normalized (free): 3715.470795 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 25.19 - 5.92 0.99 1279 156 0.3984 0.4374 4.5731 4.6595| | 2: 5.91 - 4.71 1.00 1245 142 0.2750 0.3052 4.1105 4.2067| | 3: 4.70 - 4.12 1.00 1230 149 0.2995 0.3165 3.9373 3.9737| | 4: 4.11 - 3.74 0.99 1195 141 0.3075 0.3413 3.6254 3.7264| | 5: 3.74 - 3.47 0.99 1236 140 0.2850 0.3008 3.3831 3.5066| | 6: 3.47 - 3.27 0.98 1167 145 0.2752 0.2989 3.1427 3.2223| | 7: 3.27 - 3.10 0.90 1124 101 0.3715 0.4011 3.037 3.1246| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 25.19 - 5.92 1279 156 0.60 43.52 0.86 0.02 1484.45| | 2: 5.91 - 4.71 1245 142 0.54 48.68 1.00 0.02 1282.82| | 3: 4.70 - 4.12 1230 149 0.68 37.31 1.29 0.03 685.00| | 4: 4.11 - 3.74 1195 141 0.66 39.30 1.28 0.03 455.35| | 5: 3.74 - 3.47 1236 140 0.73 33.45 1.21 0.03 224.54| | 6: 3.47 - 3.27 1167 145 0.72 34.52 1.11 0.02 131.69| | 7: 3.27 - 3.10 1124 101 0.65 40.46 0.93 0.02 103.07| |alpha: min = 0.02 max = 0.03 mean = 0.02| |beta: min = 103.07 max = 1484.45 mean = 640.57| |figures of merit: min = 0.00 max = 1.00 mean = 0.65| |phase err.(work): min = 0.00 max = 89.99 mean = 39.67| |phase err.(test): min = 0.00 max = 89.17 mean = 39.22| |-----------------------------------------------------------------------------| ----------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 : 0.009 0.077 2506 Z= 0.592 Angle : 1.390 9.518 3390 Z= 0.917 Chirality : 0.099 0.322 380 Planarity : 0.006 0.038 430 Dihedral : 16.447 75.649 948 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 24.21 Ramachandran Plot: Outliers : 2.67 % Allowed : 8.33 % Favored : 89.00 % Rotamer: Outliers : 7.14 % Allowed : 9.77 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.35 (0.35), residues: 300 helix: -2.77 (0.30), residues: 134 sheet: -1.20 (0.62), residues: 48 loop : -3.64 (0.41), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.002 ARG A 18 TYR 0.044 0.013 TYR B 14 PHE 0.031 0.006 PHE B 70 TRP 0.014 0.003 TRP B 68 HIS 0.001 0.001 HIS B 64 Individual atomic B min max mean iso aniso Overall: 3.07 82.07 54.06 7.85 2452 0 Protein: 3.07 82.07 54.06 7.85 2452 0 Chain A: 19.98 82.07 60.93 N/A 1226 0 Chain B: 3.07 82.07 47.19 N/A 1226 0 Histogram: Values Number of atoms 3.07 - 10.97 7 10.97 - 18.87 37 18.87 - 26.77 157 26.77 - 34.67 269 34.67 - 42.57 432 42.57 - 50.47 311 50.47 - 58.37 225 58.37 - 66.27 175 66.27 - 74.17 168 74.17 - 82.07 671 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 3 ************************* |--(resolution: 3.10 - 25.19 A, n_refl.=9450 (all), 10.31 % free)-------------| | | | r_work= 0.3217 r_free= 0.3511 coordinate error (max.-lik. estimate): 0.34 A | | | | normalized target function (ml) (work): 3.705103 | | target function (ml) not normalized (work): 31404.451511 | | target function (ml) not normalized (free): 3715.470795 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3247 0.3217 0.3511 n_refl.: 9450 re-set all scales: r(all,work,free)=0.3247 0.3217 0.3511 n_refl.: 9450 remove outliers: r(all,work,free)=0.3236 0.3204 0.3511 n_refl.: 9446 overall B=13.55 to atoms: r(all,work,free)=0.3613 0.3590 0.3804 n_refl.: 9446 bulk-solvent and scaling: r(all,work,free)=0.2315 0.2277 0.2633 n_refl.: 9446 remove outliers: r(all,work,free)=0.2315 0.2277 0.2633 n_refl.: 9446 ======================== 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 25.192-14.006 95.24 89 11 0.3157 2409.358 2177.841 1.252 1.038 0.395 14.006-11.401 95.00 85 10 0.2454 2701.504 2688.352 1.107 1.036 0.323 11.401-9.290 97.27 153 25 0.1596 3217.750 3143.081 1.127 1.033 0.319 9.217-7.555 99.08 294 28 0.1790 2200.652 2184.414 1.105 1.028 0.314 7.516-6.153 99.14 515 63 0.2361 1434.928 1379.068 0.969 1.020 0.306 6.131-5.015 99.81 954 115 0.2370 1346.854 1284.162 0.869 1.007 0.241 5.003-4.077 99.75 1757 207 0.1907 1481.164 1430.652 1.031 0.989 0.219 4.074-3.318 98.51 3188 384 0.2391 885.086 840.039 1.055 0.960 0.089 3.316-3.104 91.27 1438 130 0.3486 500.142 441.212 0.903 0.937 0.072 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0493 b_overall=4.7319 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 16.293943 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.217311 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2443 0.2696 0.0253 0.002 0.5 5.2 2.7 6.8 0 0.125 0.2409 0.2690 0.0280 0.002 0.5 5.4 2.7 6.8 0 0.250 0.2347 0.2659 0.0312 0.003 0.5 6.1 2.7 6.8 0 0.500 0.2271 0.2658 0.0387 0.003 0.6 8.9 3.3 7.1 0 1.000 0.2194 0.2652 0.0458 0.005 0.7 10.9 3.3 7.1 0 2.000 0.2164 0.2649 0.0484 0.007 0.8 12.5 3.3 7.1 0 3.000 0.2149 0.2676 0.0527 0.009 1.0 14.7 3.3 7.1 0 4.000 0.2125 0.2676 0.0551 0.011 1.1 15.7 3.3 7.1 0 5.000 0.2114 0.2694 0.0580 0.012 1.2 15.7 3.0 7.1 0 6.000 0.2097 0.2687 0.0589 0.014 1.3 15.7 3.0 7.5 0 7.000 0.2084 0.2687 0.0602 0.015 1.4 16.9 3.0 7.5 0 8.000 0.2073 0.2687 0.0614 0.017 1.5 18.4 3.0 7.5 0 9.000 0.2064 0.2685 0.0621 0.018 1.5 18.8 2.7 7.5 0 10.000 0.2083 0.2687 0.0604 0.015 1.4 17.2 3.0 7.5 0 8.147 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2443 0.2696 0.0253 0.002 0.5 5.2 2.7 6.8 0 0.125 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 24.43 26.96 2.53 5.550 67.315 0.217 0.067 24.34 26.17 1.83 6.168 68.238 0.007 0.066 24.05 26.11 2.07 6.221 68.249 0.027 0.065 23.29 25.93 2.64 6.814 68.340 0.109 0.061 22.78 25.82 3.04 7.812 68.502 0.217 0.059 22.47 25.79 3.32 8.708 68.688 0.326 0.057 22.17 25.77 3.61 9.924 69.062 0.435 0.056 22.03 25.79 3.76 10.563 69.197 0.543 0.055 21.93 25.80 3.87 11.071 69.304 0.652 0.055 21.82 25.78 3.96 11.686 69.468 0.761 0.055 21.74 25.79 4.05 12.245 69.610 0.869 0.054 21.69 25.82 4.14 12.701 69.715 0.978 0.054 21.65 25.84 4.19 13.028 69.792 1.087 0.054 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.435 Accepted refinement result: 22.17 25.77 3.61 9.924 69.062 0.435 0.056 Individual atomic B min max mean iso aniso Overall: 22.37 125.55 71.15 8.92 2452 0 Protein: 22.37 125.55 71.15 8.92 2452 0 Chain A: 35.01 125.55 77.89 N/A 1226 0 Chain B: 22.37 124.98 64.42 N/A 1226 0 Histogram: Values Number of atoms 22.37 - 32.69 9 32.69 - 43.00 138 43.00 - 53.32 404 53.32 - 63.64 460 63.64 - 73.96 410 73.96 - 84.28 257 84.28 - 94.60 424 94.60 - 104.92 238 104.92 - 115.24 95 115.24 - 125.55 17 =========================== Idealize ADP of riding H ========================== r_work=0.2217 r_free=0.2577 r_work=0.2186 r_free=0.2563 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.10 - 25.19 A, n_refl.=9446 (all), 10.30 % free)-------------| | | | r_work= 0.2186 r_free= 0.2563 coordinate error (max.-lik. estimate): 0.41 A | | | | normalized target function (ls_wunit_k1) (work): 0.054715 | | target function (ls_wunit_k1) not normalized (work): 463.603033 | | target function (ls_wunit_k1) not normalized (free): 76.037507 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2227 0.2186 0.2563 n_refl.: 9446 re-set all scales: r(all,work,free)=0.3674 0.3648 0.3885 n_refl.: 9446 remove outliers: r(all,work,free)=0.3674 0.3648 0.3885 n_refl.: 9446 overall B=0.00 to atoms: r(all,work,free)=0.3674 0.3648 0.3885 n_refl.: 9446 bulk-solvent and scaling: r(all,work,free)=0.2227 0.2186 0.2566 n_refl.: 9446 remove outliers: r(all,work,free)=0.2227 0.2186 0.2566 n_refl.: 9446 ======================== 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 25.192-14.006 95.24 89 11 0.3192 1492.110 1368.559 1.322 1.007 0.390 14.006-11.401 95.00 85 10 0.2173 1673.036 1709.376 1.209 1.007 0.325 11.401-9.290 97.27 153 25 0.1484 1992.746 1946.991 1.144 1.007 0.320 9.217-7.555 99.08 294 28 0.1672 1362.859 1360.445 1.153 1.006 0.320 7.516-6.153 99.14 515 63 0.2273 888.648 859.713 1.015 1.005 0.300 6.131-5.015 99.81 954 115 0.2213 834.104 799.227 0.921 1.001 0.270 5.003-4.077 99.75 1757 207 0.1736 917.282 894.511 1.042 0.996 0.230 4.074-3.318 98.51 3188 384 0.2439 548.132 523.840 1.066 0.989 0.064 3.316-3.104 91.27 1438 130 0.3330 309.737 276.217 0.927 0.982 0.040 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0610 b_overall=2.8412 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 5.420524 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.050672 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2117 0.2517 0.0400 0.002 0.5 5.6 2.7 6.8 0 0.125 0.2069 0.2511 0.0442 0.003 0.5 6.3 3.0 6.8 0 0.250 0.2025 0.2534 0.0508 0.004 0.6 8.5 3.0 7.1 0 0.500 0.1984 0.2561 0.0577 0.007 0.8 10.1 3.0 7.9 0 1.000 0.1952 0.2559 0.0607 0.011 1.1 13.7 3.3 8.3 0 2.000 0.1927 0.2569 0.0642 0.016 1.5 15.9 3.3 8.3 0 3.000 0.1913 0.2541 0.0628 0.017 1.5 14.3 3.3 8.3 0 4.000 0.1901 0.2562 0.0661 0.022 1.8 17.6 3.3 8.3 0 5.000 0.1893 0.2568 0.0675 0.026 2.0 17.2 3.3 8.3 0 6.000 0.1881 0.2569 0.0687 0.030 2.2 17.8 3.3 8.3 0 7.000 0.1849 0.2614 0.0765 0.029 2.2 18.4 6.3 13.5 0 8.000 0.1842 0.2620 0.0778 0.031 2.4 19.6 6.3 13.2 0 9.000 0.1839 0.2626 0.0787 0.033 2.5 20.4 7.0 13.5 0 10.000 0.1932 0.2553 0.0621 0.014 1.3 14.5 3.3 8.3 0 2.710 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2117 0.2517 0.0400 0.002 0.5 5.6 2.7 6.8 0 0.125 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 21.17 25.17 4.00 12.320 78.887 0.051 6.628 25.31 26.27 0.96 11.731 84.597 0.002 6.679 24.11 25.42 1.31 11.530 83.471 0.006 6.662 22.47 24.90 2.44 12.123 80.614 0.025 6.628 21.54 24.89 3.35 12.584 79.933 0.051 6.610 21.19 24.98 3.78 13.105 79.927 0.076 6.603 20.87 25.05 4.18 13.472 79.995 0.101 6.597 20.76 25.11 4.35 13.741 80.000 0.127 6.596 20.70 25.17 4.46 13.988 80.066 0.152 6.595 20.67 25.21 4.54 14.099 80.064 0.177 6.595 20.63 25.25 4.62 14.319 80.161 0.203 6.595 20.61 25.29 4.68 14.519 80.247 0.228 6.594 20.59 25.32 4.73 14.704 80.330 0.253 6.594 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.051 Accepted refinement result: 21.54 24.89 3.35 12.584 79.933 0.051 6.610 Individual atomic B min max mean iso aniso Overall: 26.60 126.98 73.27 8.93 2452 0 Protein: 26.60 126.98 73.27 8.93 2452 0 Chain A: 33.14 126.98 80.68 N/A 1226 0 Chain B: 26.60 126.88 65.86 N/A 1226 0 Histogram: Values Number of atoms 26.60 - 36.64 21 36.64 - 46.68 164 46.68 - 56.71 410 56.71 - 66.75 451 66.75 - 76.79 415 76.79 - 86.83 368 86.83 - 96.86 250 96.86 - 106.90 225 106.90 - 116.94 104 116.94 - 126.98 44 =========================== Idealize ADP of riding H ========================== r_work=0.2154 r_free=0.2489 r_work=0.2166 r_free=0.2500 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.10 - 25.19 A, n_refl.=9446 (all), 10.30 % free)-------------| | | | r_work= 0.2166 r_free= 0.2500 coordinate error (max.-lik. estimate): 0.39 A | | | | normalized target function (ml) (work): 6.610930 | | target function (ml) not normalized (work): 56014.411382 | | target function (ml) not normalized (free): 6576.082853 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2202 0.2166 0.2500 n_refl.: 9446 re-set all scales: r(all,work,free)=0.3764 0.3745 0.3933 n_refl.: 9446 remove outliers: r(all,work,free)=0.3764 0.3745 0.3933 n_refl.: 9446 overall B=0.00 to atoms: r(all,work,free)=0.3764 0.3745 0.3933 n_refl.: 9446 bulk-solvent and scaling: r(all,work,free)=0.2196 0.2160 0.2499 n_refl.: 9446 remove outliers: r(all,work,free)=0.2196 0.2160 0.2499 n_refl.: 9446 ======================== 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 25.192-14.006 95.24 89 11 0.3107 1492.110 1367.821 1.256 1.022 0.390 14.006-11.401 95.00 85 10 0.2092 1673.036 1681.830 1.165 1.021 0.330 11.401-9.290 97.27 153 25 0.1435 1992.746 1947.014 1.110 1.020 0.330 9.217-7.555 99.08 294 28 0.1758 1362.859 1349.520 1.130 1.017 0.320 7.516-6.153 99.14 515 63 0.2432 888.648 850.757 1.011 1.012 0.300 6.131-5.015 99.81 954 115 0.2377 834.104 791.056 0.917 1.005 0.270 5.003-4.077 99.75 1757 207 0.1784 917.282 891.220 1.045 0.993 0.220 4.074-3.318 98.51 3188 384 0.2266 548.132 521.452 1.095 0.975 0.065 3.316-3.104 91.27 1438 130 0.3030 309.737 278.654 0.978 0.961 0.050 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0393 b_overall=0.9210 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.2160 r_free=0.2499 After: r_work=0.2160 r_free=0.2498 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 5.630866 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.046998 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2159 0.2499 0.0340 0.002 0.5 6.3 2.7 6.8 0 0.125 0.2155 0.2498 0.0343 0.003 0.5 6.5 2.7 6.8 0 0.250 0.2137 0.2495 0.0358 0.004 0.5 6.9 3.0 6.8 0 0.500 0.2050 0.2493 0.0443 0.011 1.0 9.1 2.7 7.1 0 1.000 0.1949 0.2515 0.0566 0.014 1.4 18.0 2.7 8.6 0 2.000 0.1945 0.2497 0.0552 0.014 1.3 14.7 2.7 7.5 0 3.000 0.1900 0.2509 0.0609 0.019 1.8 18.8 3.3 9.0 0 4.000 0.1884 0.2524 0.0640 0.022 2.1 20.0 3.7 9.0 0 5.000 0.1866 0.2534 0.0668 0.024 2.3 21.2 3.7 9.4 0 6.000 0.1862 0.2537 0.0674 0.026 2.4 22.4 4.0 10.2 0 7.000 0.1848 0.2543 0.0695 0.029 2.7 24.0 4.7 10.2 0 8.000 0.1848 0.2541 0.0694 0.031 2.6 22.8 4.0 10.2 0 9.000 0.1843 0.2572 0.0729 0.031 2.9 27.4 5.0 12.4 0 10.000 0.1949 0.2500 0.0551 0.013 1.3 14.1 2.7 7.5 0 2.815 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2159 0.2499 0.0340 0.002 0.5 6.3 2.7 6.8 0 0.125 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 21.59 24.99 3.40 12.502 80.887 0.047 6.611 25.40 26.41 1.01 11.256 86.402 0.001 6.680 24.50 25.70 1.20 11.153 85.483 0.006 6.670 22.69 24.84 2.15 11.912 82.419 0.023 6.638 21.41 24.89 3.49 12.040 81.842 0.047 6.609 20.82 24.91 4.09 12.905 81.738 0.070 6.595 20.71 25.04 4.32 13.448 81.605 0.094 6.593 20.63 25.13 4.50 13.866 81.699 0.117 6.592 20.57 25.18 4.61 14.205 81.821 0.141 6.591 20.54 25.22 4.69 14.452 81.916 0.164 6.590 20.53 25.26 4.73 14.573 81.926 0.188 6.590 20.48 25.31 4.83 14.895 82.086 0.211 6.590 20.49 25.34 4.85 14.939 82.076 0.235 6.590 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.023 Accepted refinement result: 22.69 24.84 2.15 11.912 82.419 0.023 6.638 Individual atomic B min max mean iso aniso Overall: 36.23 135.37 76.37 6.11 2452 0 Protein: 36.23 135.37 76.37 6.11 2452 0 Chain A: 43.23 135.37 84.23 N/A 1226 0 Chain B: 36.23 121.88 68.51 N/A 1226 0 Histogram: Values Number of atoms 36.23 - 46.15 39 46.15 - 56.06 298 56.06 - 65.97 501 65.97 - 75.89 549 75.89 - 85.80 351 85.80 - 95.72 245 95.72 - 105.63 243 105.63 - 115.54 152 115.54 - 125.46 64 125.46 - 135.37 10 =========================== Idealize ADP of riding H ========================== r_work=0.2269 r_free=0.2484 r_work=0.2286 r_free=0.2486 ----------X-ray data---------- |--(resolution: 3.10 - 25.19 A, n_refl.=9446 (all), 10.30 % free)-------------| | | | r_work= 0.2286 r_free= 0.2486 coordinate error (max.-lik. estimate): 0.37 A | | | | normalized target function (ml) (work): 6.642377 | | target function (ml) not normalized (work): 56280.863194 | | target function (ml) not normalized (free): 6572.753923 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 25.19 - 5.92 0.99 1276 155 0.2169 0.2474 7.1563 7.3679| | 2: 5.91 - 4.71 1.00 1245 142 0.2140 0.2316 6.9214 7.0371| | 3: 4.70 - 4.12 1.00 1230 149 0.1880 0.2029 6.8042 6.8874| | 4: 4.11 - 3.74 0.99 1195 141 0.2427 0.2562 6.6542 6.6886| | 5: 3.74 - 3.47 0.99 1236 140 0.2394 0.2552 6.4782 6.5654| | 6: 3.47 - 3.27 0.98 1167 145 0.2759 0.3157 6.2819 6.3436| | 7: 3.27 - 3.10 0.90 1124 101 0.3458 0.3683 6.1149 6.1702| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 25.19 - 5.92 1276 155 0.80 25.31 0.97 0.98 290046.05| | 2: 5.91 - 4.71 1245 142 0.77 29.71 1.01 0.99 259552.12| | 3: 4.70 - 4.12 1230 149 0.84 23.36 1.02 1.02 169138.57| | 4: 4.11 - 3.74 1195 141 0.79 28.31 1.07 1.01 129328.03| | 5: 3.74 - 3.47 1236 140 0.79 27.93 1.02 1.00 89317.10| | 6: 3.47 - 3.27 1167 145 0.76 30.98 0.97 0.93 59709.55| | 7: 3.27 - 3.10 1124 101 0.65 40.62 1.03 0.91 50581.66| |alpha: min = 0.91 max = 1.02 mean = 0.98| |beta: min = 50581.66 max = 290046.05 mean = 152573.98| |figures of merit: min = 0.00 max = 1.00 mean = 0.77| |phase err.(work): min = 0.00 max = 89.87 mean = 29.29| |phase err.(test): min = 0.00 max = 87.65 mean = 28.31| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2308 0.2286 0.2486 n_refl.: 9446 re-set all scales: r(all,work,free)=0.3961 0.3948 0.4075 n_refl.: 9446 remove outliers: r(all,work,free)=0.3961 0.3948 0.4075 n_refl.: 9446 overall B=-4.36 to atoms: r(all,work,free)=0.3800 0.3785 0.3928 n_refl.: 9446 bulk-solvent and scaling: r(all,work,free)=0.2302 0.2279 0.2489 n_refl.: 9446 remove outliers: r(all,work,free)=0.2302 0.2279 0.2489 n_refl.: 9446 ======================== 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 25.192-14.006 95.24 89 11 0.3084 1492.110 1379.092 1.158 1.017 0.370 14.006-11.401 95.00 85 10 0.2159 1673.036 1679.336 1.182 1.017 0.341 11.401-9.290 97.27 153 25 0.1438 1992.746 1952.811 1.098 1.016 0.330 9.217-7.555 99.08 294 28 0.1805 1362.859 1346.236 1.117 1.014 0.325 7.516-6.153 99.14 515 63 0.2478 888.648 852.970 0.995 1.010 0.307 6.131-5.015 99.81 954 115 0.2375 834.104 793.127 0.915 1.004 0.290 5.003-4.077 99.75 1757 207 0.1889 917.282 890.011 1.021 0.995 0.222 4.074-3.318 98.51 3188 384 0.2489 548.132 518.938 1.055 0.980 0.064 3.316-3.104 91.27 1438 130 0.3291 309.737 276.575 0.954 0.968 0.044 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0265 b_overall=1.5937 ================= 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) ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.3217 0.3511 0.009 1.390 3.1 82.1 54.1 0 0.000 1_bss: 0.2277 0.2633 0.009 1.390 16.6 95.6 67.6 0 0.000 1_settarget: 0.2277 0.2633 0.009 1.390 16.6 95.6 67.6 0 0.000 1_weight: 0.2277 0.2633 0.009 1.390 16.6 95.6 67.6 0 0.000 1_xyzrec: 0.2443 0.2696 0.002 0.500 16.6 95.6 67.6 0 0.199 1_adp: 0.2217 0.2577 0.002 0.500 22.4 125.6 71.2 0 0.199 1_regHadp: 0.2186 0.2563 0.002 0.500 22.4 125.6 71.2 0 0.199 2_bss: 0.2186 0.2566 0.002 0.500 22.4 125.6 71.2 0 0.199 2_settarget: 0.2186 0.2566 0.002 0.500 22.4 125.6 71.2 0 0.199 2_updatecdl: 0.2186 0.2566 0.002 0.586 22.4 125.6 71.2 0 0.199 2_weight: 0.2186 0.2566 0.002 0.586 22.4 125.6 71.2 0 0.199 2_xyzrec: 0.2117 0.2517 0.002 0.497 22.4 125.6 71.2 0 0.223 2_adp: 0.2154 0.2489 0.002 0.497 26.6 127.0 73.3 0 0.223 2_regHadp: 0.2166 0.2500 0.002 0.497 26.6 127.0 73.3 0 0.223 3_bss: 0.2160 0.2499 0.002 0.497 26.6 127.0 73.3 0 0.223 3_settarget: 0.2160 0.2499 0.002 0.497 26.6 127.0 73.3 0 0.223 3_updatecdl: 0.2160 0.2499 0.002 0.539 26.6 127.0 73.3 0 0.223 3_setrh: 0.2160 0.2498 0.002 0.539 26.6 127.0 73.3 0 0.224 3_weight: 0.2160 0.2498 0.002 0.539 26.6 127.0 73.3 0 0.224 3_xyzrec: 0.2159 0.2499 0.002 0.503 26.6 127.0 73.3 0 0.224 3_adp: 0.2269 0.2484 0.002 0.503 36.2 135.4 76.4 0 0.224 3_regHadp: 0.2286 0.2486 0.002 0.503 36.2 135.4 76.4 0 0.224 end: 0.2279 0.2489 0.002 0.503 31.9 131.0 72.0 0 0.224 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V3/1x24_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V3/1x24_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 8.0600 Refinement macro-cycles (run) : 230.8100 Write final files (write_after_run_outputs) : 24.1000 Total : 262.9700 Total CPU time: 5.00 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:34:41 PDT -0700 (1716251681.77 s) Start R-work = 0.2277, R-free = 0.2633 Final R-work = 0.2279, R-free = 0.2489 =============================================================================== Job complete usr+sys time: 324.76 seconds wall clock time: 17 minutes 34.25 seconds (1054.25 seconds total)