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/2h1g.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/2h1g/2h1g.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 { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/2h1g/2h1g.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/2h1g/2h1g.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/2h1g.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/2h1g.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 { 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 None Time to flip residues: 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 4293 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 2139 Classifications: {'peptide': 136} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 127} Chain: "B" Number of atoms: 2154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 2154 Classifications: {'peptide': 137} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 128} Time building chain proxies: 0.81, per 1000 atoms: 0.19 Number of scatterers: 4293 At special positions: 0 Unit cell: (47.031, 59.522, 109.562, 90, 90, 90) Space group: P 21 21 21 (No. 19) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 O 405 8.00 N 349 7.00 C 1391 6.00 H 2138 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 0.90 Conformation dependent library (CDL) restraints added in 127.4 milliseconds 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 506 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 10 helices and 4 sheets defined 37.0% alpha, 19.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 57 through 60 Processing helix chain 'A' and resid 75 through 94 removed outlier: 3.530A pdb=" N LYS A 79 " --> pdb=" O GLU A 75 " (cutoff:3.500A) Proline residue: A 82 - end of helix removed outlier: 3.782A pdb=" N HIS A 90 " --> pdb=" O ASN A 86 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N SER A 93 " --> pdb=" O LYS A 89 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLN A 94 " --> pdb=" O HIS A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 116 Processing helix chain 'A' and resid 130 through 135 Processing helix chain 'A' and resid 162 through 172 Processing helix chain 'B' and resid 57 through 60 Processing helix chain 'B' and resid 75 through 94 removed outlier: 3.792A pdb=" N GLU B 80 " --> pdb=" O ALA B 77 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N PHE B 81 " --> pdb=" O LYS B 78 " (cutoff:3.500A) Proline residue: B 82 - end of helix removed outlier: 3.504A pdb=" N ALA B 85 " --> pdb=" O PRO B 82 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR B 88 " --> pdb=" O ALA B 85 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE B 91 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LYS B 92 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N SER B 93 " --> pdb=" O HIS B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 116 Processing helix chain 'B' and resid 130 through 134 Processing helix chain 'B' and resid 162 through 172 Processing sheet with id= A, first strand: chain 'A' and resid 46 through 48 Processing sheet with id= B, first strand: chain 'A' and resid 152 through 157 removed outlier: 6.765A pdb=" N LEU A 145 " --> pdb=" O VAL A 153 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N VAL A 155 " --> pdb=" O THR A 143 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N THR A 143 " --> pdb=" O VAL A 155 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 46 through 48 Processing sheet with id= D, first strand: chain 'B' and resid 152 through 157 removed outlier: 6.774A pdb=" N LEU B 145 " --> pdb=" O VAL B 153 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N VAL B 155 " --> pdb=" O THR B 143 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N THR B 143 " --> pdb=" O VAL B 155 " (cutoff:3.500A) 81 hydrogen bonds defined for protein. 210 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: 0.91 Time building geometry restraints manager: 1.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.16: 2140 1.16 - 1.33: 536 1.33 - 1.51: 996 1.51 - 1.68: 655 1.68 - 1.86: 20 Bond restraints: 4347 Sorted by residual: bond pdb=" N LYS B 89 " pdb=" H LYS B 89 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N ASP A 41 " pdb=" H ASP A 41 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N MET A 164 " pdb=" H MET A 164 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N HIS B 166 " pdb=" H HIS B 166 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" NE1 TRP B 70 " pdb=" HE1 TRP B 70 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 4342 not shown) Histogram of bond angle deviations from ideal: 98.40 - 106.27: 294 106.27 - 114.14: 5068 114.14 - 122.01: 1765 122.01 - 129.88: 740 129.88 - 137.75: 22 Bond angle restraints: 7889 Sorted by residual: angle pdb=" N TRP B 73 " pdb=" CA TRP B 73 " pdb=" C TRP B 73 " ideal model delta sigma weight residual 111.82 119.27 -7.45 1.16e+00 7.43e-01 4.13e+01 angle pdb=" N ASP A 41 " pdb=" CA ASP A 41 " pdb=" C ASP A 41 " ideal model delta sigma weight residual 110.23 118.37 -8.14 1.45e+00 4.76e-01 3.15e+01 angle pdb=" N ASP B 41 " pdb=" CA ASP B 41 " pdb=" C ASP B 41 " ideal model delta sigma weight residual 110.24 118.13 -7.89 1.41e+00 5.03e-01 3.13e+01 angle pdb=" O VAL A 137 " pdb=" C VAL A 137 " pdb=" N SER A 138 " ideal model delta sigma weight residual 122.72 129.05 -6.33 1.18e+00 7.18e-01 2.88e+01 angle pdb=" C LYS B 173 " pdb=" N PRO B 174 " pdb=" CA PRO B 174 " ideal model delta sigma weight residual 119.84 126.44 -6.60 1.25e+00 6.40e-01 2.79e+01 ... (remaining 7884 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 1802 17.76 - 35.52: 158 35.52 - 53.28: 75 53.28 - 71.04: 15 71.04 - 88.80: 5 Dihedral angle restraints: 2055 sinusoidal: 1106 harmonic: 949 Sorted by residual: dihedral pdb=" C SER B 138 " pdb=" N SER B 138 " pdb=" CA SER B 138 " pdb=" CB SER B 138 " ideal model delta harmonic sigma weight residual -122.60 -144.10 21.50 0 2.50e+00 1.60e-01 7.39e+01 dihedral pdb=" N SER B 138 " pdb=" C SER B 138 " pdb=" CA SER B 138 " pdb=" CB SER B 138 " ideal model delta harmonic sigma weight residual 122.80 143.41 -20.61 0 2.50e+00 1.60e-01 6.80e+01 dihedral pdb=" CA PRO B 139 " pdb=" C PRO B 139 " pdb=" N LEU B 140 " pdb=" CA LEU B 140 " ideal model delta harmonic sigma weight residual -180.00 -150.85 -29.15 0 5.00e+00 4.00e-02 3.40e+01 ... (remaining 2052 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.153: 264 0.153 - 0.305: 60 0.305 - 0.456: 4 0.456 - 0.607: 2 0.607 - 0.759: 1 Chirality restraints: 331 Sorted by residual: chirality pdb=" CA SER B 138 " pdb=" N SER B 138 " pdb=" C SER B 138 " pdb=" CB SER B 138 " both_signs ideal model delta sigma weight residual False 2.51 1.75 0.76 2.00e-01 2.50e+01 1.44e+01 chirality pdb=" CA VAL B 137 " pdb=" N VAL B 137 " pdb=" C VAL B 137 " pdb=" CB VAL B 137 " both_signs ideal model delta sigma weight residual False 2.44 2.91 -0.47 2.00e-01 2.50e+01 5.54e+00 chirality pdb=" CA MET A 169 " pdb=" N MET A 169 " pdb=" C MET A 169 " pdb=" CB MET A 169 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.34e+00 ... (remaining 328 not shown) Planarity restraints: 641 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 73 " 0.047 2.00e-02 2.50e+03 1.93e-02 1.48e+01 pdb=" CG TRP B 73 " 0.014 2.00e-02 2.50e+03 pdb=" CD1 TRP B 73 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP B 73 " -0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP B 73 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TRP B 73 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP B 73 " -0.019 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 73 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 73 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP B 73 " 0.010 2.00e-02 2.50e+03 pdb=" HD1 TRP B 73 " -0.004 2.00e-02 2.50e+03 pdb=" HE1 TRP B 73 " -0.025 2.00e-02 2.50e+03 pdb=" HE3 TRP B 73 " -0.040 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 73 " 0.005 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 73 " -0.001 2.00e-02 2.50e+03 pdb=" HH2 TRP B 73 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 135 " -0.025 2.00e-02 2.50e+03 2.02e-02 1.23e+01 pdb=" CG TYR A 135 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR A 135 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR A 135 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR A 135 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR A 135 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A 135 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 135 " -0.006 2.00e-02 2.50e+03 pdb=" HD1 TYR A 135 " -0.030 2.00e-02 2.50e+03 pdb=" HD2 TYR A 135 " 0.023 2.00e-02 2.50e+03 pdb=" HE1 TYR A 135 " 0.021 2.00e-02 2.50e+03 pdb=" HE2 TYR A 135 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 135 " 0.039 2.00e-02 2.50e+03 1.86e-02 1.03e+01 pdb=" CG TYR B 135 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR B 135 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR B 135 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR B 135 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR B 135 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR B 135 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 135 " 0.034 2.00e-02 2.50e+03 pdb=" HD1 TYR B 135 " 0.009 2.00e-02 2.50e+03 pdb=" HD2 TYR B 135 " -0.009 2.00e-02 2.50e+03 pdb=" HE1 TYR B 135 " -0.019 2.00e-02 2.50e+03 pdb=" HE2 TYR B 135 " -0.000 2.00e-02 2.50e+03 ... (remaining 638 not shown) Histogram of nonbonded interaction distances: 1.38 - 2.03: 161 2.03 - 2.67: 5935 2.67 - 3.31: 13205 3.31 - 3.96: 17955 3.96 - 4.60: 26972 Nonbonded interactions: 64228 Sorted by model distance: nonbonded pdb="HD12 LEU B 145 " pdb=" HB3 LYS B 154 " model vdw 1.385 2.440 nonbonded pdb="HD21 ASN B 44 " pdb=" HB3 SER B 58 " model vdw 1.410 2.270 nonbonded pdb=" HH TYR A 88 " pdb=" OE1 GLU A 97 " model vdw 1.440 1.850 nonbonded pdb=" OD1 ASP A 49 " pdb=" H ASN A 51 " model vdw 1.472 1.850 nonbonded pdb=" OD1 ASP B 49 " pdb=" H ASN B 51 " model vdw 1.500 1.850 ... (remaining 64223 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 10 15.96 2 O 405 7.97 1 N 349 6.97 1 C 1391 5.97 2 H 2138 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: 2138 of 4293 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 4293 n_use_u_iso = 4293 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 = 4293 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (4293 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 4293 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 57 through 60 helix_type = alpha pi *3_10 unknown } helix { serial_number = "2" helix_identifier = "2" selection = chain 'A' and resid 75 through 94 } helix { serial_number = "3" helix_identifier = "3" selection = chain 'A' and resid 107 through 116 } helix { serial_number = "4" helix_identifier = "4" selection = chain 'A' and resid 130 through 135 } helix { serial_number = "5" helix_identifier = "5" selection = chain 'A' and resid 162 through 172 } helix { serial_number = "6" helix_identifier = "6" selection = chain 'B' and resid 57 through 60 helix_type = alpha pi *3_10 unknown } helix { serial_number = "7" helix_identifier = "7" selection = chain 'B' and resid 75 through 94 helix_type = alpha pi *3_10 unknown } helix { serial_number = "8" helix_identifier = "8" selection = chain 'B' and resid 107 through 116 } helix { serial_number = "9" helix_identifier = "9" selection = chain 'B' and resid 130 through 134 } helix { serial_number = "10" helix_identifier = "10" selection = chain 'B' and resid 162 through 172 } sheet { first_strand = chain 'A' and resid 46 through 48 sheet_id = " A" strand { selection = chain 'A' and resid 54 through 56 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 55 and name N bond_start_previous = chain 'A' and resid 47 and name O } } sheet { first_strand = chain 'A' and resid 152 through 157 sheet_id = " B" strand { selection = chain 'A' and resid 142 through 146 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 145 and name N bond_start_previous = chain 'A' and resid 153 and name O } strand { selection = chain 'A' and resid 64 through 70 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 69 and name N bond_start_previous = chain 'A' and resid 142 and name O } strand { selection = chain 'A' and resid 96 through 102 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 97 and name N bond_start_previous = chain 'A' and resid 64 and name O } strand { selection = chain 'A' and resid 123 through 125 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 124 and name N bond_start_previous = chain 'A' and resid 100 and name O } } sheet { first_strand = chain 'B' and resid 46 through 48 sheet_id = " C" strand { selection = chain 'B' and resid 54 through 56 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 55 and name N bond_start_previous = chain 'B' and resid 47 and name O } } sheet { first_strand = chain 'B' and resid 152 through 157 sheet_id = " D" strand { selection = chain 'B' and resid 142 through 146 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 145 and name N bond_start_previous = chain 'B' and resid 153 and name O } strand { selection = chain 'B' and resid 64 through 70 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 69 and name N bond_start_previous = chain 'B' and resid 142 and name O } strand { selection = chain 'B' and resid 96 through 102 sense = *parallel antiparallel unknown bond_start_current = chain 'B' and resid 97 and name N bond_start_previous = chain 'B' and resid 64 and name O } strand { selection = chain 'B' and resid 123 through 125 sense = *parallel antiparallel unknown bond_start_current = chain 'B' and resid 124 and name N bond_start_previous = chain 'B' and resid 100 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 = "2h1g_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 2138 occupancy sum: 2138.00 (% of total atoms 49.80) Rotatable: count: 610 occupancy sum: 610.00 (% of total atoms 14.21) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.10 - 36.90 A, n_refl.=5695 (all), 5.23 % free)-------------| | | | r_work= 0.3523 r_free= 0.3456 coordinate error (max.-lik. estimate): 0.23 A | | | | normalized target function (ml) (work): 6.129983 | | target function (ml) not normalized (work): 33083.515704 | | target function (ml) not normalized (free): 1923.593214 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 36.90 - 3.91 0.97 2809 138 0.3665 0.3354 6.3578 6.4558| | 2: 3.91 - 3.10 0.94 2588 160 0.3327 0.3587 5.8828 6.4544| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 36.90 - 3.91 2809 138 0.76 28.35 0.89 0.78 61335.00| | 2: 3.91 - 3.10 2588 160 0.88 18.54 1.37 1.02 18111.74| |alpha: min = 0.10 max = 1.08 mean = 0.90| |beta: min = 12794.24 max = 259712.65 mean = 40608.33| |figures of merit: min = 0.00 max = 1.00 mean = 0.82| |phase err.(work): min = 0.00 max = 89.81 mean = 23.65| |phase err.(test): min = 0.00 max = 89.70 mean = 22.17| |-----------------------------------------------------------------------------| ----------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 : 0.024 0.153 2209 Z= 1.602 Angle : 2.035 10.752 2998 Z= 1.276 Chirality : 0.130 0.759 331 Planarity : 0.006 0.021 386 Dihedral : 17.709 88.802 808 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 1.49 % Allowed : 4.83 % Favored : 93.68 % Rotamer: Outliers : 6.69 % Allowed : 12.55 % Favored : 80.75 % Cbeta Deviations : 0.79 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.45), residues: 269 helix: -2.28 (0.39), residues: 93 sheet: -1.31 (0.58), residues: 77 loop : -1.82 (0.56), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 129 TYR 0.040 0.010 TYR B 135 PHE 0.021 0.006 PHE A 91 TRP 0.027 0.008 TRP B 73 HIS 0.010 0.006 HIS A 90 Individual atomic B min max mean iso aniso Overall: 2.00 37.24 13.06 1.53 2155 0 Protein: 2.00 37.24 13.06 1.53 2155 0 Chain A: 2.00 33.66 13.04 N/A 1073 0 Chain B: 2.00 37.24 13.09 N/A 1082 0 Histogram: Values Number of atoms 2.00 - 5.52 154 5.52 - 9.05 509 9.05 - 12.57 430 12.57 - 16.10 443 16.10 - 19.62 315 19.62 - 23.14 170 23.14 - 26.67 71 26.67 - 30.19 32 30.19 - 33.72 26 33.72 - 37.24 5 |-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 - 36.90 A, n_refl.=5695 (all), 5.23 % free)-------------| | | | r_work= 0.3523 r_free= 0.3456 coordinate error (max.-lik. estimate): 0.23 A | | | | normalized target function (ml) (work): 6.129983 | | target function (ml) not normalized (work): 33083.515704 | | target function (ml) not normalized (free): 1923.593214 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3517 0.3523 0.3456 n_refl.: 5695 re-set all scales: r(all,work,free)=0.3517 0.3523 0.3456 n_refl.: 5695 remove outliers: r(all,work,free)=0.3515 0.3522 0.3456 n_refl.: 5694 overall B=1.09 to atoms: r(all,work,free)=0.3563 0.3570 0.3478 n_refl.: 5694 bulk-solvent and scaling: r(all,work,free)=0.1927 0.1895 0.2493 n_refl.: 5694 remove outliers: r(all,work,free)=0.1927 0.1895 0.2493 n_refl.: 5694 ======================== 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 36.902-12.728 94.29 95 4 0.2921 541.895 491.160 0.931 1.188 0.390 12.598-9.947 96.15 96 4 0.1369 773.478 775.898 1.022 1.165 0.399 9.931-7.830 97.01 189 6 0.1608 683.507 672.379 1.067 1.151 0.409 7.826-6.174 96.81 381 14 0.2165 462.055 446.916 0.988 1.121 0.461 6.172-4.868 97.27 748 36 0.1786 518.967 507.654 0.949 1.073 0.470 4.862-3.836 96.79 1456 84 0.1625 627.947 611.330 1.027 0.996 0.471 3.836-3.102 94.30 2431 150 0.2128 446.506 421.037 1.121 0.883 0.195 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=4.9144 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update phi&psi targets =========================== 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ================================== NQH flips ================================== r_work=0.1895 r_free=0.2493 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1895 r_free=0.2493 ========================= Local real-space refinement ========================= Before: r_work=0.1895 r_free=0.2493 67 residues out of total 239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 51 time to evaluate : 0.166 revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 6 residues processed: 16 average time/residue: 0.1242 time to fit residues: 2.6275 After: r_work=0.1933 r_free=0.2545 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 15.302078 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.979445 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 0.2141 0.2458 0.0317 0.004 0.6 2.1 0.0 2.5 0 0.125 0.2105 0.2456 0.0352 0.003 0.6 2.1 0.0 2.5 0 0.250 0.2030 0.2463 0.0433 0.003 0.6 2.1 0.0 2.5 0 0.500 0.1935 0.2465 0.0530 0.004 0.7 2.8 0.0 2.1 0 1.000 0.1843 0.2484 0.0641 0.005 0.8 3.0 0.0 2.5 0 2.000 0.1787 0.2499 0.0712 0.007 0.9 3.7 0.0 5.0 0 3.000 0.1754 0.2505 0.0751 0.008 1.0 4.0 0.0 5.0 0 4.000 0.1726 0.2486 0.0760 0.010 1.0 4.9 0.0 5.9 0 5.000 0.1703 0.2486 0.0783 0.011 1.1 4.9 0.0 5.9 0 6.000 0.1684 0.2482 0.0798 0.012 1.2 4.7 0.0 5.9 0 7.000 0.1668 0.2474 0.0806 0.013 1.3 5.1 0.0 6.3 0 8.000 0.1654 0.2478 0.0824 0.015 1.3 5.4 0.0 6.7 0 9.000 0.1641 0.2463 0.0823 0.016 1.4 5.1 0.0 6.7 0 10.000 0.1669 0.2470 0.0801 0.013 1.2 5.1 0.0 6.3 0 7.651 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2105 0.2456 0.0352 0.003 0.6 2.1 0.0 2.5 0 0.250 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.2105 r_free=0.2456 64 residues out of total 239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 58 time to evaluate : 0.176 outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0837 time to fit residues: 0.8289 After: r_work=0.2126 r_free=0.2461 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 21.26 24.61 3.36 1.092 14.008 0.979 0.054 21.42 24.82 3.40 1.816 14.213 0.029 0.055 20.67 24.82 4.15 2.211 14.248 0.122 0.051 19.60 24.81 5.21 3.650 14.328 0.490 0.046 18.50 25.00 6.49 7.058 15.059 0.979 0.041 18.07 25.09 7.02 8.984 15.617 1.469 0.039 17.81 25.14 7.33 10.490 16.040 1.959 0.038 17.61 25.24 7.63 11.820 16.428 2.449 0.037 17.43 25.82 8.39 15.088 17.376 2.938 0.037 17.41 25.92 8.51 15.895 17.587 3.428 0.037 17.40 26.03 8.63 16.589 17.761 3.918 0.037 17.40 26.07 8.67 17.187 17.917 4.408 0.037 17.41 26.11 8.71 17.576 18.016 4.897 0.037 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.490 Accepted refinement result: 19.60 24.81 5.21 3.650 14.328 0.490 0.046 Individual atomic B min max mean iso aniso Overall: 1.79 50.99 14.79 3.89 2155 0 Protein: 1.79 50.99 14.79 3.89 2155 0 Chain A: 2.20 50.99 14.97 N/A 1073 0 Chain B: 1.79 45.37 14.61 N/A 1082 0 Histogram: Values Number of atoms 1.79 - 6.71 219 6.71 - 11.63 613 11.63 - 16.55 576 16.55 - 21.47 389 21.47 - 26.39 186 26.39 - 31.31 95 31.31 - 36.23 51 36.23 - 41.15 21 41.15 - 46.07 4 46.07 - 50.99 1 =========================== Idealize ADP of riding H ========================== r_work=0.1960 r_free=0.2481 r_work=0.1941 r_free=0.2473 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.10 - 36.90 A, n_refl.=5694 (all), 5.23 % free)-------------| | | | r_work= 0.1941 r_free= 0.2473 coordinate error (max.-lik. estimate): 0.33 A | | | | normalized target function (ls_wunit_k1) (work): 0.045305 | | target function (ls_wunit_k1) not normalized (work): 244.464514 | | target function (ls_wunit_k1) not normalized (free): 21.537190 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1969 0.1941 0.2473 n_refl.: 5694 re-set all scales: r(all,work,free)=0.3554 0.3561 0.3498 n_refl.: 5694 remove outliers: r(all,work,free)=0.3554 0.3561 0.3498 n_refl.: 5694 overall B=1.16 to atoms: r(all,work,free)=0.3604 0.3611 0.3520 n_refl.: 5694 bulk-solvent and scaling: r(all,work,free)=0.1978 0.1951 0.2467 n_refl.: 5694 remove outliers: r(all,work,free)=0.1978 0.1951 0.2467 n_refl.: 5694 ======================== 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 36.902-12.728 94.29 95 4 0.2720 392.341 364.616 1.169 1.120 0.411 12.598-9.947 96.15 96 4 0.1405 560.011 562.611 1.125 1.103 0.412 9.931-7.830 97.01 189 6 0.1626 494.870 489.509 1.153 1.095 0.445 7.826-6.174 96.81 381 14 0.2238 334.535 326.010 1.009 1.077 0.466 6.172-4.868 97.27 748 36 0.1867 375.740 368.189 0.952 1.046 0.471 4.862-3.836 96.79 1456 84 0.1683 454.644 443.807 1.016 0.997 0.471 3.836-3.102 94.30 2431 150 0.2183 323.278 308.142 1.066 0.925 0.195 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=5.2074 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1951 r_free=0.2467 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 HIS Total number of N/Q/H flips: 1 r_work=0.1951 r_free=0.2468 ========================= Local real-space refinement ========================= Before: r_work=0.1951 r_free=0.2468 62 residues out of total 239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.507 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6835 After: r_work=0.1951 r_free=0.2468 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.824440 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.131480 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 0.1808 0.2352 0.0544 0.003 0.6 3.7 0.0 0.4 0 0.091 0.1709 0.2373 0.0664 0.006 0.7 3.5 0.0 0.8 0 0.274 0.1639 0.2376 0.0737 0.010 0.9 4.2 0.0 2.1 0 0.547 0.1605 0.2386 0.0781 0.013 1.1 4.4 0.0 2.1 0 0.821 0.1580 0.2391 0.0811 0.015 1.3 4.9 0.0 2.5 0 1.095 0.1558 0.2396 0.0838 0.018 1.5 5.1 0.0 2.5 0 1.368 0.1543 0.2385 0.0842 0.021 1.6 4.9 0.0 2.5 0 1.642 0.1528 0.2396 0.0868 0.023 1.8 5.6 0.4 2.5 0 1.916 0.1592 0.2385 0.0793 0.014 1.2 4.4 0.0 2.5 0 0.912 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1808 0.2352 0.0544 0.003 0.6 3.7 0.0 0.4 0 0.091 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.1808 r_free=0.2352 62 residues out of total 239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 61 time to evaluate : 0.725 outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1545 time to fit residues: 0.9053 After: r_work=0.1808 r_free=0.2349 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 18.08 23.49 5.41 3.608 17.434 0.131 5.785 19.43 23.42 4.00 3.480 17.870 0.004 5.846 18.34 23.33 4.99 3.377 17.743 0.016 5.787 17.01 23.86 6.85 5.776 17.926 0.066 5.703 16.54 24.28 7.74 7.454 18.134 0.131 5.673 16.34 24.44 8.10 8.539 18.343 0.197 5.660 16.25 24.51 8.26 9.336 18.519 0.263 5.653 16.23 24.55 8.32 9.554 18.567 0.329 5.652 16.17 24.60 8.43 10.206 18.723 0.394 5.648 16.17 24.62 8.45 10.286 18.744 0.460 5.647 16.16 24.65 8.48 10.427 18.779 0.526 5.647 16.15 24.68 8.53 10.626 18.829 0.592 5.646 16.14 24.70 8.55 10.820 18.879 0.657 5.645 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.016 Accepted refinement result: 18.34 23.33 4.99 3.377 17.743 0.016 5.787 Individual atomic B min max mean iso aniso Overall: 4.93 61.18 16.56 3.14 2155 0 Protein: 4.93 61.18 16.56 3.14 2155 0 Chain A: 5.92 61.18 16.91 N/A 1073 0 Chain B: 4.93 46.64 16.22 N/A 1082 0 Histogram: Values Number of atoms 4.93 - 10.56 371 10.56 - 16.18 887 16.18 - 21.81 485 21.81 - 27.43 220 27.43 - 33.05 119 33.05 - 38.68 40 38.68 - 44.30 27 44.30 - 49.93 5 49.93 - 55.55 0 55.55 - 61.18 1 =========================== Idealize ADP of riding H ========================== r_work=0.1834 r_free=0.2333 r_work=0.1839 r_free=0.2330 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.10 - 36.90 A, n_refl.=5694 (all), 5.23 % free)-------------| | | | r_work= 0.1839 r_free= 0.2330 coordinate error (max.-lik. estimate): 0.31 A | | | | normalized target function (ml) (work): 5.787885 | | target function (ml) not normalized (work): 31231.426831 | | target function (ml) not normalized (free): 1846.987488 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1865 0.1839 0.2330 n_refl.: 5694 re-set all scales: r(all,work,free)=0.3589 0.3600 0.3441 n_refl.: 5694 remove outliers: r(all,work,free)=0.3589 0.3600 0.3441 n_refl.: 5694 overall B=0.00 to atoms: r(all,work,free)=0.3589 0.3600 0.3441 n_refl.: 5694 bulk-solvent and scaling: r(all,work,free)=0.1808 0.1779 0.2335 n_refl.: 5694 remove outliers: r(all,work,free)=0.1808 0.1779 0.2335 n_refl.: 5694 ======================== 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 36.902-12.728 94.29 95 4 0.2759 392.341 349.119 0.926 1.352 0.411 12.598-9.947 96.15 96 4 0.1357 560.011 550.175 0.913 1.313 0.412 9.931-7.830 97.01 189 6 0.1456 494.870 480.510 0.942 1.284 0.420 7.826-6.174 96.81 381 14 0.2058 334.535 319.319 0.867 1.228 0.480 6.172-4.868 97.27 748 36 0.1634 375.740 366.663 0.869 1.139 0.480 4.862-3.836 96.79 1456 84 0.1578 454.644 443.946 1.013 0.997 0.390 3.836-3.102 94.30 2431 150 0.1976 323.278 314.077 1.263 0.790 0.200 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=5.3672 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1779 r_free=0.2335 After: r_work=0.1779 r_free=0.2335 ================================== NQH flips ================================== r_work=0.1779 r_free=0.2335 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN Total number of N/Q/H flips: 1 r_work=0.1780 r_free=0.2333 ========================= Local real-space refinement ========================= Before: r_work=0.1780 r_free=0.2333 63 residues out of total 239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.981 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8962 After: r_work=0.1780 r_free=0.2333 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.781675 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.106408 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 0.1777 0.2336 0.0559 0.003 0.6 4.0 0.0 0.0 0 0.089 0.1719 0.2348 0.0629 0.008 0.7 4.0 0.0 0.0 0 0.267 0.1596 0.2343 0.0747 0.013 1.3 5.6 0.0 0.4 0 0.535 0.1572 0.2377 0.0805 0.014 1.3 7.7 0.0 1.3 0 0.802 0.1532 0.2400 0.0868 0.017 1.6 9.1 0.4 1.7 0 1.069 0.1523 0.2406 0.0883 0.019 1.6 9.6 0.4 2.1 0 1.336 0.1496 0.2429 0.0933 0.022 1.8 10.5 0.4 2.1 0 1.604 0.1463 0.2450 0.0986 0.025 2.2 10.7 0.4 2.9 0 1.871 0.1558 0.2378 0.0820 0.015 1.4 7.5 0.0 1.3 0 0.891 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1777 0.2336 0.0559 0.003 0.6 4.0 0.0 0.0 0 0.089 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.1777 r_free=0.2336 63 residues out of total 239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 1.075 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9940 After: r_work=0.1777 r_free=0.2336 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 17.77 23.36 5.59 3.387 18.268 0.106 5.785 19.02 23.58 4.57 3.385 18.763 0.003 5.848 17.91 23.29 5.37 2.907 18.693 0.013 5.791 16.61 23.73 7.12 4.838 18.578 0.053 5.716 15.92 24.07 8.16 7.005 18.882 0.106 5.672 15.76 24.13 8.37 7.787 19.020 0.160 5.662 15.63 24.20 8.56 8.585 19.208 0.213 5.654 15.56 24.27 8.72 9.234 19.370 0.266 5.649 15.56 24.31 8.75 9.325 19.398 0.319 5.649 15.52 24.35 8.83 9.683 19.492 0.372 5.646 15.50 24.39 8.89 9.976 19.570 0.426 5.644 15.48 24.42 8.94 10.229 19.637 0.479 5.643 15.47 24.45 8.99 10.445 19.695 0.532 5.642 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.013 Accepted refinement result: 17.91 23.29 5.37 2.907 18.693 0.013 5.791 Individual atomic B min max mean iso aniso Overall: 6.08 70.61 17.41 2.87 2155 0 Protein: 6.08 70.61 17.41 2.87 2155 0 Chain A: 8.04 70.61 17.90 N/A 1073 0 Chain B: 6.08 51.79 16.93 N/A 1082 0 Histogram: Values Number of atoms 6.08 - 12.53 570 12.53 - 18.99 933 18.99 - 25.44 368 25.44 - 31.89 181 31.89 - 38.35 66 38.35 - 44.80 24 44.80 - 51.25 11 51.25 - 57.71 1 57.71 - 64.16 0 64.16 - 70.61 1 =========================== Idealize ADP of riding H ========================== r_work=0.1791 r_free=0.2329 r_work=0.1792 r_free=0.2325 ----------X-ray data---------- |--(resolution: 3.10 - 36.90 A, n_refl.=5694 (all), 5.23 % free)-------------| | | | r_work= 0.1792 r_free= 0.2325 coordinate error (max.-lik. estimate): 0.35 A | | | | normalized target function (ml) (work): 5.790790 | | target function (ml) not normalized (work): 31247.103872 | | target function (ml) not normalized (free): 1837.565095 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 36.90 - 3.91 0.97 2808 138 0.1658 0.1919 5.8328 6.1137| | 2: 3.91 - 3.10 0.94 2588 160 0.1978 0.2842 5.7452 6.2117| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 36.90 - 3.91 2808 138 0.91 13.38 1.00 1.03 13846.58| | 2: 3.91 - 3.10 2588 160 0.91 15.87 1.00 1.03 12845.36| |alpha: min = 0.95 max = 1.10 mean = 1.03| |beta: min = 7671.92 max = 23719.78 mean = 13366.38| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.87 mean = 14.58| |phase err.(test): min = 0.00 max = 89.23 mean = 14.61| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1820 0.1792 0.2325 n_refl.: 5694 re-set all scales: r(all,work,free)=0.3628 0.3641 0.3454 n_refl.: 5694 remove outliers: r(all,work,free)=0.3628 0.3641 0.3454 n_refl.: 5694 overall B=0.00 to atoms: r(all,work,free)=0.3628 0.3641 0.3454 n_refl.: 5694 bulk-solvent and scaling: r(all,work,free)=0.1839 0.1813 0.2302 n_refl.: 5694 remove outliers: r(all,work,free)=0.1839 0.1813 0.2302 n_refl.: 5694 ======================== 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 36.902-12.728 94.29 95 4 0.2768 392.341 356.787 1.021 1.241 0.411 12.598-9.947 96.15 96 4 0.1357 560.011 562.320 1.000 1.212 0.412 9.931-7.830 97.01 189 6 0.1456 494.870 490.580 1.027 1.193 0.420 7.826-6.174 96.81 381 14 0.2063 334.535 325.440 0.933 1.155 0.480 6.172-4.868 97.27 748 36 0.1631 375.740 370.345 0.910 1.093 0.480 4.862-3.836 96.79 1456 84 0.1571 454.644 444.704 1.023 0.995 0.476 3.836-3.102 94.30 2431 150 0.2058 323.278 309.127 1.162 0.851 0.180 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=5.2732 ================= 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 : 0.3523 0.3456 0.024 2.035 2.0 37.2 13.1 0 0.000 1_bss: 0.1895 0.2493 0.024 2.035 3.1 38.3 14.2 0 0.000 1_settarget: 0.1895 0.2493 0.024 2.035 3.1 38.3 14.2 0 0.000 1_updatephipsi: 0.1895 0.2493 0.024 2.035 3.1 38.3 14.2 0 0.000 1_nqh: 0.1895 0.2493 0.024 2.035 3.1 38.3 14.2 0 0.000 1_realsrl: 0.1933 0.2545 0.025 2.045 3.1 38.3 14.2 0 0.022 1_weight: 0.1933 0.2545 0.025 2.045 3.1 38.3 14.2 0 0.022 1_xyzrec: 0.2105 0.2456 0.003 0.626 3.1 38.3 14.2 0 0.218 1_realsrl2: 0.2126 0.2461 0.003 0.626 3.1 38.3 14.2 0 0.226 1_adp: 0.1960 0.2481 0.003 0.626 1.8 51.0 14.8 0 0.226 1_regHadp: 0.1941 0.2473 0.003 0.626 1.8 51.0 14.8 0 0.226 2_bss: 0.1951 0.2467 0.003 0.626 2.9 52.2 16.0 0 0.226 2_settarget: 0.1951 0.2467 0.003 0.626 2.9 52.2 16.0 0 0.226 2_updatephipsi: 0.1951 0.2467 0.003 0.626 2.9 52.2 16.0 0 0.226 2_updatecdl: 0.1951 0.2467 0.003 0.661 2.9 52.2 16.0 0 0.226 2_nqh: 0.1951 0.2468 0.003 0.661 2.9 52.2 16.0 0 0.229 2_realsrl: 0.1951 0.2468 0.003 0.661 2.9 52.2 16.0 0 0.229 2_weight: 0.1951 0.2468 0.003 0.661 2.9 52.2 16.0 0 0.229 2_xyzrec: 0.1808 0.2352 0.003 0.579 2.9 52.2 16.0 0 0.276 2_realsrl2: 0.1808 0.2349 0.003 0.579 2.9 52.2 16.0 0 0.277 2_adp: 0.1834 0.2333 0.003 0.579 4.9 61.2 16.6 0 0.277 2_regHadp: 0.1839 0.2330 0.003 0.579 4.9 61.2 16.6 0 0.277 3_bss: 0.1779 0.2335 0.003 0.579 4.9 61.2 16.6 0 0.277 3_settarget: 0.1779 0.2335 0.003 0.579 4.9 61.2 16.6 0 0.277 3_updatephipsi: 0.1779 0.2335 0.003 0.579 4.9 61.2 16.6 0 0.277 3_updatecdl: 0.1779 0.2335 0.003 0.603 4.9 61.2 16.6 0 0.277 3_setrh: 0.1779 0.2335 0.003 0.603 4.9 61.2 16.6 0 0.277 3_nqh: 0.1780 0.2333 0.003 0.603 4.9 61.2 16.6 0 0.279 3_realsrl: 0.1780 0.2333 0.003 0.603 4.9 61.2 16.6 0 0.279 3_weight: 0.1780 0.2333 0.003 0.603 4.9 61.2 16.6 0 0.279 3_xyzrec: 0.1777 0.2336 0.003 0.592 4.9 61.2 16.6 0 0.279 3_realsrl2: 0.1777 0.2336 0.003 0.592 4.9 61.2 16.6 0 0.279 3_adp: 0.1791 0.2329 0.003 0.592 6.1 70.6 17.4 0 0.279 3_regHadp: 0.1792 0.2325 0.003 0.592 6.1 70.6 17.4 0 0.279 end: 0.1813 0.2302 0.003 0.592 6.1 70.6 17.4 0 0.279 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V0/2h1g_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V0/2h1g_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.3200 Refinement macro-cycles (run) : 199.4700 Write final files (write_after_run_outputs) : 20.6100 Total : 223.4000 Total CPU time: 4.02 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:26:14 PDT -0700 (1716251174.44 s) Start R-work = 0.1895, R-free = 0.2493 Final R-work = 0.1813, R-free = 0.2302 =============================================================================== Job complete usr+sys time: 260.67 seconds wall clock time: 11 minutes 39.43 seconds (699.43 seconds total)