Starting phenix.refine on Mon May 20 17:17:37 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/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 ramachandran_plot_restraints.enabled=False secondary_structure.enabled=True main.nqh_flips=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { 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" 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" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls occupancies group_anomalous \ den } main { nqh_flips = False max_number_of_iterations = 100 nproc = 20 } modify_start_model { modify { selection = element H occupancies { set = 1 } } } pdb_interpretation { secondary_structure { enabled = True } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = true optimize_adp_weight = true } } Starting job =============================================================================== Symmetric amino acids flipped 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: 1.60, per 1000 atoms: 0.37 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: 3.15 Conformation dependent library (CDL) restraints added in 386.7 milliseconds 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: 0.86 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: 3.08 Time building geometry restraints manager: 2.09 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 { nqh_flips = False max_number_of_iterations = 100 nproc = 20 } modify_start_model { modify { selection = element H occupancies { set = 1 } } } hydrogens { refine = individual *riding Auto } pdb_interpretation { secondary_structure { protein { helix { serial_number = "1" helix_identifier = "1" selection = chain 'A' and resid 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 } 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 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 14.882811 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.982810 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 0.2108 0.2504 0.0396 0.004 0.7 2.6 0.7 5.0 0 0.125 0.2091 0.2504 0.0414 0.004 0.7 2.6 0.7 5.0 0 0.250 0.2051 0.2517 0.0466 0.004 0.7 2.8 0.7 5.0 0 0.500 0.1991 0.2522 0.0531 0.004 0.8 3.3 0.7 5.0 0 1.000 0.1891 0.2531 0.0640 0.006 0.8 3.0 1.1 4.6 0 2.000 0.1830 0.2516 0.0687 0.007 0.9 4.0 1.1 5.0 0 3.000 0.1783 0.2524 0.0741 0.009 1.0 5.4 1.1 5.4 0 4.000 0.1745 0.2504 0.0759 0.010 1.0 5.6 1.5 6.3 0 5.000 0.1717 0.2508 0.0791 0.011 1.1 5.4 1.5 6.7 0 6.000 0.1696 0.2505 0.0809 0.013 1.2 5.6 1.5 6.7 0 7.000 0.1679 0.2488 0.0809 0.014 1.3 6.1 1.5 7.1 0 8.000 0.1660 0.2471 0.0810 0.015 1.4 5.1 1.5 8.4 0 9.000 0.1650 0.2487 0.0837 0.016 1.4 6.1 1.5 8.4 0 10.000 0.1690 0.2497 0.0807 0.013 1.2 6.1 1.5 7.1 0 7.441 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2108 0.2504 0.0396 0.004 0.7 2.6 0.7 5.0 0 0.125 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 21.08 25.04 3.96 1.092 14.008 0.983 0.054 21.21 25.25 4.04 1.802 14.209 0.029 0.055 20.45 25.12 4.67 2.183 14.239 0.123 0.051 19.37 25.06 5.69 3.660 14.336 0.491 0.045 18.40 25.12 6.72 6.398 14.839 0.983 0.041 17.80 25.27 7.47 8.812 15.581 1.474 0.039 17.58 25.37 7.80 9.948 15.899 1.966 0.038 17.25 25.89 8.64 13.471 17.005 2.457 0.036 17.22 26.03 8.82 14.357 17.248 2.948 0.036 17.14 26.15 9.00 15.407 17.562 3.440 0.036 17.13 26.27 9.14 16.167 17.778 3.931 0.036 17.14 26.36 9.21 16.563 17.873 4.423 0.036 17.13 26.43 9.30 17.185 18.049 4.914 0.036 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.491 Accepted refinement result: 19.37 25.06 5.69 3.660 14.336 0.491 0.045 Individual atomic B min max mean iso aniso Overall: 2.05 43.57 14.81 3.94 2155 0 Protein: 2.05 43.57 14.81 3.94 2155 0 Chain A: 2.73 39.03 15.04 N/A 1073 0 Chain B: 2.05 43.57 14.58 N/A 1082 0 Histogram: Values Number of atoms 2.05 - 6.20 158 6.20 - 10.35 514 10.35 - 14.50 523 14.50 - 18.66 420 18.66 - 22.81 232 22.81 - 26.96 159 26.96 - 31.11 68 31.11 - 35.27 49 35.27 - 39.42 26 39.42 - 43.57 6 =========================== Idealize ADP of riding H ========================== r_work=0.1937 r_free=0.2506 r_work=0.1918 r_free=0.2499 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.10 - 36.90 A, n_refl.=5694 (all), 5.23 % free)-------------| | | | r_work= 0.1918 r_free= 0.2499 coordinate error (max.-lik. estimate): 0.35 A | | | | normalized target function (ls_wunit_k1) (work): 0.044515 | | target function (ls_wunit_k1) not normalized (work): 240.204089 | | target function (ls_wunit_k1) not normalized (free): 21.693682 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1948 0.1918 0.2499 n_refl.: 5694 re-set all scales: r(all,work,free)=0.3560 0.3566 0.3493 n_refl.: 5694 remove outliers: r(all,work,free)=0.3560 0.3566 0.3493 n_refl.: 5694 overall B=1.08 to atoms: r(all,work,free)=0.3607 0.3614 0.3515 n_refl.: 5694 bulk-solvent and scaling: r(all,work,free)=0.1956 0.1926 0.2498 n_refl.: 5694 remove outliers: r(all,work,free)=0.1956 0.1926 0.2498 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 0.2877 391.052 353.674 1.088 1.153 0.410 12.598-9.947 96.15 96 4 0.1398 558.172 557.824 1.095 1.132 0.412 9.931-7.830 97.01 189 6 0.1620 493.245 486.094 1.124 1.121 0.428 7.826-6.174 96.81 381 14 0.2172 333.437 324.289 0.997 1.097 0.461 6.172-4.868 97.27 748 36 0.1846 374.507 366.972 0.950 1.057 0.462 4.862-3.836 96.79 1456 84 0.1674 453.151 441.639 1.019 0.995 0.459 3.836-3.102 94.30 2431 150 0.2139 322.216 306.764 1.102 0.903 0.186 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=4.8650 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.807651 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.125590 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 0.1797 0.2376 0.0580 0.003 0.6 2.8 0.7 2.9 0 0.090 0.1672 0.2403 0.0731 0.006 0.8 4.2 0.7 3.8 0 0.271 0.1606 0.2406 0.0801 0.009 1.0 5.1 1.1 5.0 0 0.542 0.1568 0.2431 0.0863 0.013 1.1 5.6 1.5 5.9 0 0.813 0.1545 0.2439 0.0894 0.015 1.3 6.3 1.5 6.3 0 1.085 0.1524 0.2439 0.0915 0.018 1.4 6.5 1.5 7.1 0 1.356 0.1504 0.2431 0.0927 0.020 1.6 7.2 1.5 7.1 0 1.627 0.1491 0.2415 0.0923 0.022 1.7 7.7 1.5 7.5 0 1.898 0.1560 0.2439 0.0879 0.014 1.2 6.3 1.5 6.3 0 0.904 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1797 0.2376 0.0580 0.003 0.6 2.8 0.7 2.9 0 0.090 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 17.97 23.76 5.80 3.638 17.395 0.126 5.778 19.26 23.68 4.42 3.519 17.785 0.004 5.837 18.22 23.47 5.25 3.416 17.712 0.016 5.781 16.88 23.49 6.62 5.627 17.883 0.063 5.696 16.44 23.77 7.33 7.147 18.055 0.126 5.666 16.24 23.95 7.71 8.191 18.264 0.188 5.652 16.14 24.06 7.92 8.918 18.423 0.251 5.645 16.11 24.11 8.01 9.252 18.499 0.314 5.643 16.08 24.17 8.09 9.548 18.569 0.377 5.641 16.06 24.23 8.17 9.909 18.659 0.440 5.638 16.04 24.26 8.22 10.150 18.720 0.502 5.637 16.03 24.30 8.27 10.378 18.776 0.565 5.636 16.02 24.33 8.31 10.575 18.826 0.628 5.635 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: 18.22 23.47 5.25 3.416 17.712 0.016 5.781 Individual atomic B min max mean iso aniso Overall: 5.90 47.32 16.52 3.04 2155 0 Protein: 5.90 47.32 16.52 3.04 2155 0 Chain A: 6.71 42.46 16.91 N/A 1073 0 Chain B: 5.90 47.32 16.14 N/A 1082 0 Histogram: Values Number of atoms 5.90 - 10.04 295 10.04 - 14.19 683 14.19 - 18.33 513 18.33 - 22.47 294 22.47 - 26.61 170 26.61 - 30.75 94 30.75 - 34.90 53 34.90 - 39.04 31 39.04 - 43.18 16 43.18 - 47.32 6 =========================== Idealize ADP of riding H ========================== r_work=0.1822 r_free=0.2347 r_work=0.1827 r_free=0.2343 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.10 - 36.90 A, n_refl.=5694 (all), 5.23 % free)-------------| | | | r_work= 0.1827 r_free= 0.2343 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ml) (work): 5.782156 | | target function (ml) not normalized (work): 31200.515508 | | target function (ml) not normalized (free): 1848.106390 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1854 0.1827 0.2343 n_refl.: 5694 re-set all scales: r(all,work,free)=0.3589 0.3603 0.3388 n_refl.: 5694 remove outliers: r(all,work,free)=0.3589 0.3603 0.3388 n_refl.: 5694 overall B=0.00 to atoms: r(all,work,free)=0.3589 0.3603 0.3388 n_refl.: 5694 bulk-solvent and scaling: r(all,work,free)=0.1865 0.1839 0.2337 n_refl.: 5694 remove outliers: r(all,work,free)=0.1865 0.1839 0.2337 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 0.2700 391.052 360.587 1.159 1.110 0.411 12.598-9.947 96.15 96 4 0.1375 558.172 563.763 1.132 1.092 0.412 9.931-7.830 97.01 189 6 0.1487 493.245 494.951 1.169 1.085 0.420 7.826-6.174 96.81 381 14 0.2066 333.437 326.061 1.012 1.067 0.466 6.172-4.868 97.27 748 36 0.1599 374.507 370.006 0.969 1.037 0.476 4.862-3.836 96.79 1456 84 0.1600 453.151 442.068 1.030 0.990 0.479 3.836-3.102 94.30 2431 150 0.2103 322.216 306.907 1.076 0.920 0.180 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=4.9106 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1839 r_free=0.2337 After: r_work=0.1839 r_free=0.2337 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.755328 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.105126 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 0.1839 0.2343 0.0504 0.003 0.6 3.7 0.7 2.9 0 0.088 0.1786 0.2338 0.0552 0.008 0.7 3.7 0.7 3.3 0 0.263 0.1642 0.2354 0.0712 0.012 1.4 7.2 1.1 4.2 0 0.527 0.1620 0.2368 0.0747 0.014 1.4 7.9 1.1 4.2 0 0.790 0.1591 0.2380 0.0789 0.017 1.6 10.7 1.5 4.6 0 1.053 0.1593 0.2372 0.0780 0.019 1.5 9.6 1.5 5.4 0 1.316 0.1574 0.2377 0.0803 0.019 1.7 10.7 1.5 5.4 0 1.580 0.1553 0.2381 0.0827 0.023 1.9 11.0 1.9 7.5 0 1.843 0.1605 0.2374 0.0769 0.016 1.5 10.5 1.1 4.6 0 0.878 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1839 0.2343 0.0504 0.003 0.6 3.7 0.7 2.9 0 0.088 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 18.39 23.43 5.04 3.319 18.202 0.105 5.782 19.59 23.83 4.24 3.382 18.685 0.003 5.845 18.54 23.48 4.94 2.940 18.586 0.013 5.789 17.37 23.51 6.14 4.690 18.454 0.053 5.716 16.67 23.63 6.96 7.024 18.837 0.105 5.668 16.56 23.76 7.20 7.736 18.952 0.158 5.660 16.48 23.86 7.39 8.423 19.111 0.210 5.653 16.45 23.91 7.47 8.752 19.191 0.263 5.651 16.40 23.99 7.59 9.308 19.334 0.315 5.647 16.39 24.02 7.63 9.537 19.394 0.368 5.645 16.37 24.06 7.69 9.844 19.474 0.421 5.643 16.36 24.08 7.72 10.102 19.542 0.473 5.642 16.35 24.12 7.77 10.331 19.601 0.526 5.641 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: 18.54 23.48 4.94 2.940 18.586 0.013 5.789 Individual atomic B min max mean iso aniso Overall: 6.74 49.18 17.29 2.80 2155 0 Protein: 6.74 49.18 17.29 2.80 2155 0 Chain A: 8.02 42.96 17.84 N/A 1073 0 Chain B: 6.74 49.18 16.74 N/A 1082 0 Histogram: Values Number of atoms 6.74 - 10.99 282 10.99 - 15.23 730 15.23 - 19.47 544 19.47 - 23.72 255 23.72 - 27.96 165 27.96 - 32.20 90 32.20 - 36.45 44 36.45 - 40.69 23 40.69 - 44.93 16 44.93 - 49.18 6 =========================== Idealize ADP of riding H ========================== r_work=0.1854 r_free=0.2348 r_work=0.1855 r_free=0.2346 ----------X-ray data---------- |--(resolution: 3.10 - 36.90 A, n_refl.=5694 (all), 5.23 % free)-------------| | | | r_work= 0.1855 r_free= 0.2346 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ml) (work): 5.789553 | | target function (ml) not normalized (work): 31240.429388 | | target function (ml) not normalized (free): 1846.693560 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1677 0.1917 5.83 6.1387| | 2: 3.91 - 3.10 0.94 2588 160 0.2100 0.2893 5.7457 6.2472| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 13.45 0.99 1.02 13621.02| | 2: 3.91 - 3.10 2588 160 0.91 16.08 1.02 1.03 13059.16| |alpha: min = 0.88 max = 1.18 mean = 1.02| |beta: min = 8275.66 max = 22184.92 mean = 13351.55| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.68 mean = 14.71| |phase err.(test): min = 0.00 max = 81.78 mean = 14.57| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1881 0.1855 0.2346 n_refl.: 5694 re-set all scales: r(all,work,free)=0.3632 0.3647 0.3423 n_refl.: 5694 remove outliers: r(all,work,free)=0.3632 0.3647 0.3423 n_refl.: 5694 overall B=0.00 to atoms: r(all,work,free)=0.3632 0.3647 0.3423 n_refl.: 5694 bulk-solvent and scaling: r(all,work,free)=0.1841 0.1813 0.2332 n_refl.: 5694 remove outliers: r(all,work,free)=0.1841 0.1813 0.2332 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 0.2707 391.052 357.764 1.020 1.233 0.410 12.598-9.947 96.15 96 4 0.1366 558.172 558.892 1.007 1.204 0.410 9.931-7.830 97.01 189 6 0.1492 493.245 490.950 1.046 1.186 0.410 7.826-6.174 96.81 381 14 0.2059 333.437 324.008 0.929 1.149 0.468 6.172-4.868 97.27 748 36 0.1597 374.507 369.352 0.923 1.088 0.480 4.862-3.836 96.79 1456 84 0.1599 453.151 442.310 1.029 0.993 0.479 3.836-3.102 94.30 2431 150 0.2046 322.216 308.127 1.169 0.853 0.200 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=4.8862 ================= 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_weight: 0.1895 0.2493 0.024 2.035 3.1 38.3 14.2 0 0.000 1_xyzrec: 0.2108 0.2504 0.004 0.729 3.1 38.3 14.2 0 0.149 1_adp: 0.1937 0.2506 0.004 0.729 2.0 43.6 14.8 0 0.149 1_regHadp: 0.1918 0.2499 0.004 0.729 2.0 43.6 14.8 0 0.149 2_bss: 0.1926 0.2498 0.004 0.729 3.1 44.7 15.9 0 0.149 2_settarget: 0.1926 0.2498 0.004 0.729 3.1 44.7 15.9 0 0.149 2_updatecdl: 0.1926 0.2498 0.004 0.760 3.1 44.7 15.9 0 0.149 2_weight: 0.1926 0.2498 0.004 0.760 3.1 44.7 15.9 0 0.149 2_xyzrec: 0.1797 0.2376 0.003 0.594 3.1 44.7 15.9 0 0.242 2_adp: 0.1822 0.2347 0.003 0.594 5.9 47.3 16.5 0 0.242 2_regHadp: 0.1827 0.2343 0.003 0.594 5.9 47.3 16.5 0 0.242 3_bss: 0.1839 0.2337 0.003 0.594 5.9 47.3 16.5 0 0.242 3_settarget: 0.1839 0.2337 0.003 0.594 5.9 47.3 16.5 0 0.242 3_updatecdl: 0.1839 0.2337 0.003 0.633 5.9 47.3 16.5 0 0.242 3_setrh: 0.1839 0.2337 0.003 0.633 5.9 47.3 16.5 0 0.242 3_weight: 0.1839 0.2337 0.003 0.633 5.9 47.3 16.5 0 0.242 3_xyzrec: 0.1839 0.2343 0.003 0.601 5.9 47.3 16.5 0 0.242 3_adp: 0.1854 0.2348 0.003 0.601 6.7 49.2 17.3 0 0.242 3_regHadp: 0.1855 0.2346 0.003 0.601 6.7 49.2 17.3 0 0.242 end: 0.1813 0.2332 0.003 0.601 6.7 49.2 17.3 0 0.242 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V3/2h1g_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V3/2h1g_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 6.4400 Refinement macro-cycles (run) : 166.2400 Write final files (write_after_run_outputs) : 19.8800 Total : 192.5600 Total CPU time: 3.73 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:30:07 PDT -0700 (1716251407.85 s) Start R-work = 0.1895, R-free = 0.2493 Final R-work = 0.1813, R-free = 0.2332 =============================================================================== Job complete usr+sys time: 242.99 seconds wall clock time: 13 minutes 9.46 seconds (789.46 seconds total)