Starting phenix.refine on Mon May 20 17:15:26 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+individual_sites_real_space ramachandran_plot_restraints.enabled=True secondary_structure.enabled=True main.nqh_flips=True Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { 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" 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" } 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 { max_number_of_iterations = 100 nproc = 20 } modify_start_model { modify { selection = element H occupancies { set = 1 } } } pdb_interpretation { secondary_structure { enabled = True } ramachandran_plot_restraints { 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: 1.03, per 1000 atoms: 0.21 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: 1.16 Conformation dependent library (CDL) restraints added in 204.0 milliseconds 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. 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: 0.34 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: 1.21 Time building geometry restraints manager: 1.34 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 { 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 } ramachandran_plot_restraints { 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 ============================ Update phi&psi targets =========================== 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ================================== NQH flips ================================== r_work=0.2277 r_free=0.2633 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.2277 r_free=0.2633 ========================= Local real-space refinement ========================= Before: r_work=0.2277 r_free=0.2633 101 residues out of total 262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 84 time to evaluate : 0.276 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 13 residues processed: 17 average time/residue: 0.4083 time to fit residues: 8.9648 After: r_work=0.2284 r_free=0.2627 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 16.720703 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.218368 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 0.2468 0.2684 0.0216 0.002 0.6 6.9 1.3 4.5 0 0.125 0.2422 0.2662 0.0240 0.002 0.6 7.1 1.7 4.5 0 0.250 0.2377 0.2651 0.0275 0.003 0.6 7.5 1.7 4.5 0 0.500 0.2307 0.2629 0.0322 0.004 0.6 10.1 1.7 4.5 0 1.000 0.2222 0.2617 0.0395 0.005 0.7 13.5 2.3 5.6 0 2.000 0.2175 0.2616 0.0441 0.007 0.8 14.7 2.3 6.0 0 3.000 0.2135 0.2628 0.0492 0.008 0.9 14.9 2.7 6.0 0 4.000 0.2109 0.2635 0.0526 0.010 1.0 15.5 2.7 6.0 0 5.000 0.2088 0.2647 0.0559 0.011 1.1 17.8 2.7 6.8 0 6.000 0.2067 0.2630 0.0564 0.012 1.1 18.0 2.7 6.8 0 7.000 0.2052 0.2644 0.0592 0.013 1.2 18.2 2.7 7.5 0 8.000 0.2039 0.2663 0.0624 0.014 1.3 18.6 2.7 7.9 0 9.000 0.2027 0.2661 0.0634 0.015 1.3 19.2 2.7 8.3 0 10.000 0.2050 0.2655 0.0605 0.013 1.2 19.0 2.7 7.5 0 8.360 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2468 0.2684 0.0216 0.002 0.6 6.9 1.3 4.5 0 0.125 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.2468 r_free=0.2684 99 residues out of total 262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 88 time to evaluate : 0.755 revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 3 residues processed: 11 average time/residue: 0.7030 time to fit residues: 11.0647 After: r_work=0.2515 r_free=0.2736 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 25.15 27.36 2.21 5.550 67.315 0.218 0.072 25.03 26.78 1.74 6.220 68.244 0.007 0.071 24.72 26.70 1.98 6.245 68.235 0.027 0.069 23.90 26.52 2.62 6.896 68.309 0.109 0.065 23.36 26.44 3.09 7.946 68.474 0.218 0.062 23.07 26.45 3.38 8.808 68.610 0.328 0.061 22.77 26.47 3.69 10.136 68.990 0.437 0.060 22.64 26.47 3.84 10.790 69.120 0.546 0.059 22.54 26.50 3.96 11.342 69.232 0.655 0.058 22.46 26.52 4.06 11.812 69.333 0.764 0.058 22.39 26.54 4.14 12.282 69.442 0.873 0.058 22.27 26.56 4.29 13.173 69.693 0.983 0.057 22.27 26.59 4.32 13.248 69.686 1.092 0.057 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.218 Accepted refinement result: 23.36 26.44 3.09 7.946 68.474 0.218 0.062 Individual atomic B min max mean iso aniso Overall: 29.71 116.79 69.96 6.83 2452 0 Protein: 29.71 116.79 69.96 6.83 2452 0 Chain A: 36.43 116.79 76.69 N/A 1226 0 Chain B: 29.71 113.90 63.24 N/A 1226 0 Histogram: Values Number of atoms 29.71 - 38.42 52 38.42 - 47.13 245 47.13 - 55.84 403 55.84 - 64.54 413 64.54 - 73.25 331 73.25 - 81.96 237 81.96 - 90.67 318 90.67 - 99.37 304 99.37 - 108.08 131 108.08 - 116.79 18 =========================== Idealize ADP of riding H ========================== r_work=0.2336 r_free=0.2644 r_work=0.2303 r_free=0.2626 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.10 - 25.19 A, n_refl.=9446 (all), 10.30 % free)-------------| | | | r_work= 0.2303 r_free= 0.2626 coordinate error (max.-lik. estimate): 0.41 A | | | | normalized target function (ls_wunit_k1) (work): 0.060918 | | target function (ls_wunit_k1) not normalized (work): 516.161671 | | target function (ls_wunit_k1) not normalized (free): 79.172524 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2338 0.2303 0.2626 n_refl.: 9446 re-set all scales: r(all,work,free)=0.3701 0.3677 0.3906 n_refl.: 9446 remove outliers: r(all,work,free)=0.3701 0.3677 0.3906 n_refl.: 9446 overall B=0.00 to atoms: r(all,work,free)=0.3701 0.3677 0.3906 n_refl.: 9446 bulk-solvent and scaling: r(all,work,free)=0.2336 0.2301 0.2628 n_refl.: 9446 remove outliers: r(all,work,free)=0.2336 0.2301 0.2628 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 0.3349 1508.866 1386.584 1.285 1.026 0.390 14.006-11.401 95.00 85 10 0.2264 1691.824 1705.947 1.178 1.024 0.330 11.401-9.290 97.27 153 25 0.1555 2015.124 1974.699 1.119 1.022 0.320 9.217-7.555 99.08 294 28 0.1756 1378.164 1368.863 1.123 1.019 0.320 7.516-6.153 99.14 515 63 0.2412 898.627 862.120 1.000 1.013 0.310 6.131-5.015 99.81 954 115 0.2330 843.471 805.510 0.905 1.005 0.270 5.003-4.077 99.75 1757 207 0.1870 927.583 904.214 1.031 0.992 0.220 4.074-3.318 98.51 3188 384 0.2545 554.288 526.823 1.061 0.971 0.085 3.316-3.104 91.27 1438 130 0.3441 313.215 277.640 0.924 0.955 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0577 b_overall=3.9224 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.2301 r_free=0.2628 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 31 ASN Total number of N/Q/H flips: 1 r_work=0.2301 r_free=0.2629 ========================= Local real-space refinement ========================= Before: r_work=0.2301 r_free=0.2629 95 residues out of total 262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 93 time to evaluate : 1.029 outliers start: 3 outliers final: 2 residues processed: 2 average time/residue: 2.9307 time to fit residues: 7.9698 After: r_work=0.2297 r_free=0.2628 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 5.417768 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.053650 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 0.2223 0.2573 0.0351 0.002 0.5 5.6 1.3 2.6 0 0.125 0.2156 0.2553 0.0397 0.003 0.6 6.3 1.3 3.0 0 0.250 0.2094 0.2544 0.0451 0.004 0.7 6.3 1.7 4.1 0 0.500 0.2038 0.2544 0.0506 0.006 0.8 9.1 1.7 5.3 0 1.000 0.1976 0.2543 0.0566 0.011 1.1 11.1 2.0 6.4 0 2.000 0.1945 0.2559 0.0614 0.014 1.3 14.5 2.0 9.4 0 3.000 0.1924 0.2565 0.0641 0.018 1.5 16.3 2.0 10.5 0 4.000 0.1911 0.2582 0.0672 0.021 1.7 15.1 2.0 12.0 0 5.000 0.1897 0.2585 0.0688 0.024 1.9 15.1 2.0 12.4 0 6.000 0.1889 0.2591 0.0702 0.027 2.1 16.9 2.3 15.0 0 7.000 0.1882 0.2591 0.0709 0.029 2.2 18.0 2.3 15.8 0 8.000 0.1872 0.2594 0.0722 0.032 2.4 18.0 2.3 17.7 0 9.000 0.1871 0.2597 0.0726 0.034 2.5 20.2 2.3 18.8 0 10.000 0.1951 0.2557 0.0606 0.013 1.2 12.9 2.0 8.3 0 2.709 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2223 0.2573 0.0351 0.002 0.5 5.6 1.3 2.6 0 0.125 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.2223 r_free=0.2573 96 residues out of total 262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 91 time to evaluate : 1.543 revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 5 average time/residue: 1.8163 time to fit residues: 12.7140 After: r_work=0.2228 r_free=0.2588 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 22.28 25.88 3.60 11.417 77.391 0.054 6.664 25.91 26.99 1.08 11.337 82.542 0.002 6.717 24.68 26.10 1.42 10.779 81.509 0.007 6.697 22.95 25.66 2.71 11.286 79.452 0.027 6.658 21.99 25.64 3.65 12.067 78.550 0.054 6.639 21.70 25.76 4.06 12.689 78.704 0.080 6.634 21.51 25.73 4.22 12.904 78.646 0.107 6.630 21.41 25.80 4.39 13.300 78.828 0.134 6.628 21.37 25.86 4.49 13.525 78.896 0.161 6.628 21.32 25.91 4.59 13.837 79.038 0.188 6.627 21.28 25.95 4.67 14.075 79.142 0.215 6.627 21.27 25.96 4.69 14.076 79.109 0.241 6.627 21.28 25.96 4.68 13.920 78.991 0.268 6.628 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.054 Accepted refinement result: 21.99 25.64 3.65 12.067 78.550 0.054 6.639 Individual atomic B min max mean iso aniso Overall: 24.80 126.40 72.31 9.20 2452 0 Protein: 24.80 126.40 72.31 9.20 2452 0 Chain A: 33.14 124.06 79.47 N/A 1226 0 Chain B: 24.80 126.40 65.14 N/A 1226 0 Histogram: Values Number of atoms 24.80 - 34.96 16 34.96 - 45.12 155 45.12 - 55.28 414 55.28 - 65.44 447 65.44 - 75.60 428 75.60 - 85.76 337 85.76 - 95.92 293 95.92 - 106.08 209 106.08 - 116.24 120 116.24 - 126.40 33 =========================== Idealize ADP of riding H ========================== r_work=0.2199 r_free=0.2564 r_work=0.2203 r_free=0.2564 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.10 - 25.19 A, n_refl.=9446 (all), 10.30 % free)-------------| | | | r_work= 0.2203 r_free= 0.2564 coordinate error (max.-lik. estimate): 0.41 A | | | | normalized target function (ml) (work): 6.638407 | | target function (ml) not normalized (work): 56247.221156 | | target function (ml) not normalized (free): 6605.205933 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2242 0.2203 0.2564 n_refl.: 9446 re-set all scales: r(all,work,free)=0.3746 0.3720 0.3964 n_refl.: 9446 remove outliers: r(all,work,free)=0.3746 0.3720 0.3964 n_refl.: 9446 overall B=0.00 to atoms: r(all,work,free)=0.3746 0.3720 0.3964 n_refl.: 9446 bulk-solvent and scaling: r(all,work,free)=0.2239 0.2200 0.2564 n_refl.: 9446 remove outliers: r(all,work,free)=0.2239 0.2200 0.2564 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 0.3201 1508.866 1380.187 1.251 1.015 0.390 14.006-11.401 95.00 85 10 0.2167 1691.824 1702.126 1.129 1.015 0.320 11.401-9.290 97.27 153 25 0.1496 2015.124 1978.625 1.093 1.014 0.320 9.217-7.555 99.08 294 28 0.1756 1378.164 1363.477 1.122 1.012 0.320 7.516-6.153 99.14 515 63 0.2424 898.627 857.972 1.015 1.008 0.310 6.131-5.015 99.81 954 115 0.2401 843.471 798.861 0.897 1.003 0.260 5.003-4.077 99.75 1757 207 0.1852 927.583 900.077 1.023 0.994 0.230 4.074-3.318 98.51 3188 384 0.2291 554.288 526.677 1.065 0.980 0.080 3.316-3.104 91.27 1438 130 0.3098 313.215 280.553 0.955 0.969 0.030 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0231 b_overall=1.1802 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.2200 r_free=0.2564 After: r_work=0.2200 r_free=0.2564 ================================== NQH flips ================================== r_work=0.2200 r_free=0.2564 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.2200 r_free=0.2564 ========================= Local real-space refinement ========================= Before: r_work=0.2200 r_free=0.2564 99 residues out of total 262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 98 time to evaluate : 1.005 outliers start: 3 outliers final: 3 residues processed: 1 average time/residue: 2.6939 time to fit residues: 4.0760 After: r_work=0.2200 r_free=0.2564 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 5.968183 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.049188 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 0.2199 0.2554 0.0355 0.003 0.5 7.7 1.3 1.1 0 0.125 0.2193 0.2553 0.0360 0.003 0.5 7.7 1.3 1.1 0 0.250 0.2171 0.2544 0.0373 0.005 0.6 8.7 1.3 1.1 0 0.500 0.2068 0.2529 0.0461 0.012 1.1 9.7 1.3 1.5 0 1.000 0.1990 0.2544 0.0554 0.012 1.3 12.7 1.3 3.4 0 2.000 0.1949 0.2551 0.0601 0.016 1.7 16.3 1.3 4.5 0 3.000 0.1943 0.2532 0.0589 0.016 1.6 19.6 1.7 5.3 0 4.000 0.1940 0.2535 0.0596 0.017 1.7 15.7 1.7 4.9 0 5.000 0.1888 0.2570 0.0682 0.023 2.2 24.0 1.7 7.5 0 6.000 0.1866 0.2575 0.0709 0.028 2.6 24.0 2.0 7.1 0 7.000 0.1883 0.2552 0.0669 0.026 2.3 21.8 2.0 7.1 0 8.000 0.1878 0.2553 0.0675 0.027 2.4 20.6 2.0 7.1 0 9.000 0.1859 0.2572 0.0713 0.032 2.7 22.8 2.0 9.4 0 10.000 0.1950 0.2551 0.0601 0.016 1.7 16.3 1.3 4.5 0 2.984 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2193 0.2553 0.0360 0.003 0.5 7.7 1.3 1.1 0 0.250 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.2193 r_free=0.2553 98 residues out of total 262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 97 time to evaluate : 0.644 revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 1 average time/residue: 1.1124 time to fit residues: 1.9996 After: r_work=0.2193 r_free=0.2553 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 21.93 25.53 3.60 12.479 79.777 0.049 6.637 25.85 26.74 0.89 11.301 85.469 0.001 6.706 24.85 26.16 1.31 10.974 84.544 0.006 6.694 23.11 25.20 2.09 11.543 81.364 0.025 6.662 21.89 25.36 3.48 11.543 80.892 0.049 6.637 21.17 25.66 4.49 12.538 80.900 0.074 6.624 20.97 25.84 4.87 13.362 80.772 0.098 6.621 20.95 25.89 4.94 13.689 80.622 0.123 6.621 20.88 25.97 5.10 14.070 80.740 0.148 6.621 20.83 26.03 5.21 14.383 80.845 0.172 6.620 20.81 26.07 5.27 14.584 80.895 0.197 6.620 20.78 26.12 5.34 14.803 80.981 0.221 6.620 20.76 26.15 5.39 15.003 81.064 0.246 6.621 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.025 Accepted refinement result: 23.11 25.20 2.09 11.543 81.364 0.025 6.662 Individual atomic B min max mean iso aniso Overall: 34.64 133.03 75.52 5.50 2452 0 Protein: 34.64 133.03 75.52 5.50 2452 0 Chain A: 42.82 133.03 83.41 N/A 1226 0 Chain B: 34.64 121.40 67.63 N/A 1226 0 Histogram: Values Number of atoms 34.64 - 44.47 49 44.47 - 54.31 274 54.31 - 64.15 457 64.15 - 73.99 559 73.99 - 83.83 351 83.83 - 93.67 255 93.67 - 103.51 248 103.51 - 113.35 174 113.35 - 123.19 73 123.19 - 133.03 12 =========================== Idealize ADP of riding H ========================== r_work=0.2311 r_free=0.2520 r_work=0.2327 r_free=0.2531 ----------X-ray data---------- |--(resolution: 3.10 - 25.19 A, n_refl.=9446 (all), 10.30 % free)-------------| | | | r_work= 0.2327 r_free= 0.2531 coordinate error (max.-lik. estimate): 0.37 A | | | | normalized target function (ml) (work): 6.666913 | | target function (ml) not normalized (work): 56488.757814 | | target function (ml) not normalized (free): 6596.387796 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2182 0.2462 7.1734 7.3705| | 2: 5.91 - 4.71 1.00 1245 142 0.2181 0.2354 6.9445 7.0472| | 3: 4.70 - 4.12 1.00 1230 149 0.1992 0.2136 6.8528 6.9245| | 4: 4.11 - 3.74 0.99 1195 141 0.2447 0.2659 6.6713 6.7314| | 5: 3.74 - 3.47 0.99 1236 140 0.2442 0.2640 6.5101 6.6148| | 6: 3.47 - 3.27 0.98 1167 145 0.2803 0.3155 6.3012 6.3556| | 7: 3.27 - 3.10 0.90 1124 101 0.3418 0.3654 6.1286 6.1855| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 25.47 0.98 1.00 299225.36| | 2: 5.91 - 4.71 1245 142 0.76 29.98 1.01 1.01 268437.78| | 3: 4.70 - 4.12 1230 149 0.84 23.43 1.01 1.03 177153.57| | 4: 4.11 - 3.74 1195 141 0.78 28.99 1.07 1.02 136106.00| | 5: 3.74 - 3.47 1236 140 0.79 28.01 1.02 1.01 94851.81| | 6: 3.47 - 3.27 1167 145 0.75 31.36 0.96 0.94 62342.57| | 7: 3.27 - 3.10 1124 101 0.65 40.69 1.03 0.92 52320.10| |alpha: min = 0.92 max = 1.03 mean = 0.99| |beta: min = 52320.10 max = 299225.36 mean = 158782.08| |figures of merit: min = 0.00 max = 1.00 mean = 0.77| |phase err.(work): min = 0.00 max = 89.94 mean = 29.53| |phase err.(test): min = 0.00 max = 88.08 mean = 28.45| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2349 0.2327 0.2531 n_refl.: 9446 re-set all scales: r(all,work,free)=0.3930 0.3911 0.4098 n_refl.: 9446 remove outliers: r(all,work,free)=0.3930 0.3911 0.4098 n_refl.: 9446 overall B=-1.89 to atoms: r(all,work,free)=0.3861 0.3840 0.4033 n_refl.: 9446 bulk-solvent and scaling: r(all,work,free)=0.2336 0.2313 0.2531 n_refl.: 9446 remove outliers: r(all,work,free)=0.2336 0.2313 0.2531 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 0.3226 1508.866 1379.479 1.172 1.049 0.391 14.006-11.401 95.00 85 10 0.2138 1691.824 1699.143 1.087 1.046 0.329 11.401-9.290 97.27 153 25 0.1504 2015.124 1980.659 1.042 1.042 0.328 9.217-7.555 99.08 294 28 0.1771 1378.164 1361.090 1.066 1.035 0.319 7.516-6.153 99.14 515 63 0.2468 898.627 857.901 0.962 1.025 0.303 6.131-5.015 99.81 954 115 0.2401 843.471 801.648 0.884 1.009 0.274 5.003-4.077 99.75 1757 207 0.1982 927.583 897.515 1.016 0.985 0.236 4.074-3.318 98.51 3188 384 0.2502 554.288 524.676 1.086 0.948 0.067 3.316-3.104 91.27 1438 130 0.3276 313.215 280.481 1.009 0.918 0.052 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9978 b_overall=0.3946 ================= 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_updatephipsi: 0.2277 0.2633 0.009 1.390 16.6 95.6 67.6 0 0.000 1_nqh: 0.2277 0.2633 0.009 1.390 16.6 95.6 67.6 0 0.000 1_realsrl: 0.2284 0.2627 0.009 1.390 16.6 95.6 67.6 0 0.013 1_weight: 0.2284 0.2627 0.009 1.390 16.6 95.6 67.6 0 0.013 1_xyzrec: 0.2468 0.2684 0.002 0.551 16.6 95.6 67.6 0 0.228 1_realsrl2: 0.2515 0.2736 0.002 0.551 16.6 95.6 67.6 0 0.247 1_adp: 0.2336 0.2644 0.002 0.551 29.7 116.8 70.0 0 0.247 1_regHadp: 0.2303 0.2626 0.002 0.551 29.7 116.8 70.0 0 0.247 2_bss: 0.2301 0.2628 0.002 0.551 29.7 116.8 70.0 0 0.247 2_settarget: 0.2301 0.2628 0.002 0.551 29.7 116.8 70.0 0 0.247 2_updatephipsi: 0.2301 0.2628 0.002 0.551 29.7 116.8 70.0 0 0.247 2_updatecdl: 0.2301 0.2628 0.003 0.612 29.7 116.8 70.0 0 0.247 2_nqh: 0.2301 0.2629 0.003 0.612 29.7 116.8 70.0 0 0.249 2_realsrl: 0.2297 0.2628 0.003 0.612 29.7 116.8 70.0 0 0.254 2_weight: 0.2297 0.2628 0.003 0.612 29.7 116.8 70.0 0 0.254 2_xyzrec: 0.2223 0.2573 0.002 0.510 29.7 116.8 70.0 0 0.293 2_realsrl2: 0.2228 0.2588 0.002 0.510 29.7 116.8 70.0 0 0.292 2_adp: 0.2199 0.2564 0.002 0.510 24.8 126.4 72.3 0 0.292 2_regHadp: 0.2203 0.2564 0.002 0.510 24.8 126.4 72.3 0 0.292 3_bss: 0.2200 0.2564 0.002 0.510 24.8 126.4 72.3 0 0.292 3_settarget: 0.2200 0.2564 0.002 0.510 24.8 126.4 72.3 0 0.292 3_updatephipsi: 0.2200 0.2564 0.002 0.510 24.8 126.4 72.3 0 0.292 3_updatecdl: 0.2200 0.2564 0.002 0.544 24.8 126.4 72.3 0 0.292 3_setrh: 0.2200 0.2564 0.002 0.544 24.8 126.4 72.3 0 0.292 3_nqh: 0.2200 0.2564 0.002 0.544 24.8 126.4 72.3 0 0.292 3_realsrl: 0.2200 0.2564 0.002 0.544 24.8 126.4 72.3 0 0.292 3_weight: 0.2200 0.2564 0.002 0.544 24.8 126.4 72.3 0 0.292 3_xyzrec: 0.2193 0.2553 0.003 0.546 24.8 126.4 72.3 0 0.293 3_realsrl2: 0.2193 0.2553 0.003 0.546 24.8 126.4 72.3 0 0.293 3_adp: 0.2311 0.2520 0.003 0.546 34.6 133.0 75.5 0 0.293 3_regHadp: 0.2327 0.2531 0.003 0.546 34.6 133.0 75.5 0 0.293 end: 0.2313 0.2531 0.003 0.546 32.7 131.1 73.6 0 0.293 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V0/1x24_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V0/1x24_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.9900 Refinement macro-cycles (run) : 309.6200 Write final files (write_after_run_outputs) : 24.6100 Total : 338.2200 Total CPU time: 6.00 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:33:52 PDT -0700 (1716251632.49 s) Start R-work = 0.2277, R-free = 0.2633 Final R-work = 0.2313, R-free = 0.2531 =============================================================================== Job complete usr+sys time: 385.46 seconds wall clock time: 18 minutes 56.21 seconds (1136.21 seconds total)