Starting phenix.refine on Fri Aug 9 09:31:39 2024 by nigel =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, 4phenix_2yhj.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/2yhj/2yhj.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 amber.topology_file_name=4amber_2yhj.prmtop amber.coordinate_file_name=4amber_2yhj.rst7 amber.order_file_name=4amber_2yhj.order use_amber=True strategy=individual_sites+individual_adp ramachandran_plot_restraints.enabled=False secondary_structure.enabled=True main.nqh_flips=False Processing files from PHIL: ------------------------------------------------------------------------------- Files not used by program: -------------------------- 4amber_2yhj.order 4amber_2yhj.prmtop 4amber_2yhj.rst7 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/2yhj/2yhj.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/2yhj/2yhj.mtz" model { file = "4phenix_2yhj.pdb" } default_model = "4phenix_2yhj.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls occupancies group_anomalous \ den } main { nqh_flips = False max_number_of_iterations = 100 nproc = 20 } modify_start_model { modify { selection = element H occupancies { set = 1 } } } pdb_interpretation { secondary_structure { enabled = True } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = true optimize_adp_weight = true } amber { use_amber = True topology_file_name = 4amber_2yhj.prmtop coordinate_file_name = 4amber_2yhj.rst7 order_file_name = 4amber_2yhj.order } } Starting job =============================================================================== Symmetric amino acids flipped None Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/bootstrap/modules/chem_data/mon_lib" Total number of atoms: 8782 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 4391 Classifications: {'peptide': 285} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 277} Chain: "B" Number of atoms: 4391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 4391 Classifications: {'peptide': 285} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 277} Time building chain proxies: 0.98, per 1000 atoms: 0.11 Number of scatterers: 8782 At special positions: 0 Unit cell: (159.697, 159.697, 159.697, 90, 90, 90) Space group: P 21 3 (No. 198) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 4 16.00 O 904 8.00 N 728 7.00 C 2814 6.00 H 4332 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: 1.50 Conformation dependent library (CDL) restraints added in 182.1 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 1052 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 12 helices and 10 sheets defined 10.7% alpha, 44.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 54 through 56 No H-bonds generated for 'chain 'A' and resid 54 through 56' Processing helix chain 'A' and resid 93 through 104 Processing helix chain 'A' and resid 171 through 173 No H-bonds generated for 'chain 'A' and resid 171 through 173' Processing helix chain 'A' and resid 176 through 179 Processing helix chain 'A' and resid 211 through 216 Processing helix chain 'A' and resid 267 through 269 No H-bonds generated for 'chain 'A' and resid 267 through 269' Processing helix chain 'B' and resid 54 through 56 No H-bonds generated for 'chain 'B' and resid 54 through 56' Processing helix chain 'B' and resid 93 through 104 Processing helix chain 'B' and resid 171 through 173 No H-bonds generated for 'chain 'B' and resid 171 through 173' Processing helix chain 'B' and resid 176 through 179 Processing helix chain 'B' and resid 211 through 215 Processing helix chain 'B' and resid 267 through 269 No H-bonds generated for 'chain 'B' and resid 267 through 269' Processing sheet with id= A, first strand: chain 'A' and resid 195 through 199 removed outlier: 4.183A pdb=" N LEU A 41 " --> pdb=" O ILE A 199 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ARG A 137 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N LEU A 158 " --> pdb=" O ARG A 137 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N TYR A 139 " --> pdb=" O TYR A 156 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N TYR A 156 " --> pdb=" O TYR A 139 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ALA A 141 " --> pdb=" O SER A 154 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N SER A 154 " --> pdb=" O ALA A 141 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ARG A 143 " --> pdb=" O ASP A 152 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N ASP A 152 " --> pdb=" O ARG A 143 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 68 through 78 removed outlier: 3.602A pdb=" N ARG A 116 " --> pdb=" O GLN A 73 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 205 through 210 removed outlier: 5.984A pdb=" N SER A 265 " --> pdb=" O LYS A 273 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N LYS A 273 " --> pdb=" O SER A 265 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 223 through 227 removed outlier: 4.011A pdb=" N GLN A 249 " --> pdb=" O LEU A 291 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 57 through 63 removed outlier: 6.380A pdb=" N VAL A 132 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N SER A 60 " --> pdb=" O TYR A 130 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N TYR A 130 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ILE A 62 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL A 128 " --> pdb=" O ILE A 62 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 195 through 199 removed outlier: 4.199A pdb=" N LEU B 41 " --> pdb=" O ILE B 199 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N ARG B 137 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N LEU B 158 " --> pdb=" O ARG B 137 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N TYR B 139 " --> pdb=" O TYR B 156 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N TYR B 156 " --> pdb=" O TYR B 139 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ALA B 141 " --> pdb=" O SER B 154 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N SER B 154 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ARG B 143 " --> pdb=" O ASP B 152 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ASP B 152 " --> pdb=" O ARG B 143 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 68 through 78 removed outlier: 3.575A pdb=" N ARG B 116 " --> pdb=" O GLN B 73 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 204 through 210 removed outlier: 6.658A pdb=" N LYS B 237 " --> pdb=" O ALA B 205 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N GLU B 207 " --> pdb=" O LYS B 237 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ASN B 239 " --> pdb=" O GLU B 207 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N LEU B 209 " --> pdb=" O ASN B 239 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N HIS B 241 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N SER B 265 " --> pdb=" O LYS B 273 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N LYS B 273 " --> pdb=" O SER B 265 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 223 through 227 removed outlier: 3.998A pdb=" N GLN B 249 " --> pdb=" O LEU B 291 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 57 through 63 removed outlier: 6.378A pdb=" N VAL B 132 " --> pdb=" O VAL B 58 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N SER B 60 " --> pdb=" O TYR B 130 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N TYR B 130 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ILE B 62 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL B 128 " --> pdb=" O ILE B 62 " (cutoff:3.500A) 162 hydrogen bonds defined for protein. 441 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.56 Time building geometry restraints manager: 1.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.15: 4330 1.15 - 1.31: 765 1.31 - 1.48: 1860 1.48 - 1.64: 1909 1.64 - 1.81: 6 Bond restraints: 8870 Sorted by residual: bond pdb=" NE2 GLN B 140 " pdb="HE22 GLN B 140 " 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 B 292 " pdb=" H ASP B 292 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N ILE A 253 " pdb=" H ILE A 253 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N THR A 121 " pdb=" H THR A 121 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N LYS A 157 " pdb=" H LYS A 157 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 8865 not shown) Histogram of bond angle deviations from ideal: 97.03 - 104.43: 162 104.43 - 111.82: 9279 111.82 - 119.21: 2643 119.21 - 126.60: 3803 126.60 - 133.99: 67 Bond angle restraints: 15954 Sorted by residual: angle pdb=" N LEU B 37 " pdb=" CA LEU B 37 " pdb=" C LEU B 37 " ideal model delta sigma weight residual 110.14 119.17 -9.03 1.47e+00 4.63e-01 3.78e+01 angle pdb=" N VAL B 89 " pdb=" CA VAL B 89 " pdb=" CB VAL B 89 " ideal model delta sigma weight residual 111.00 117.48 -6.48 1.14e+00 7.69e-01 3.23e+01 angle pdb=" N ILE A 108 " pdb=" CA ILE A 108 " pdb=" C ILE A 108 " ideal model delta sigma weight residual 110.53 115.72 -5.19 9.40e-01 1.13e+00 3.04e+01 angle pdb=" C GLU A 181 " pdb=" N THR A 182 " pdb=" CA THR A 182 " ideal model delta sigma weight residual 120.31 128.30 -7.99 1.52e+00 4.33e-01 2.76e+01 angle pdb=" N ILE A 289 " pdb=" CA ILE A 289 " pdb=" C ILE A 289 " ideal model delta sigma weight residual 108.27 115.35 -7.08 1.37e+00 5.33e-01 2.67e+01 ... (remaining 15949 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 3811 17.72 - 35.43: 237 35.43 - 53.15: 106 53.15 - 70.87: 43 70.87 - 88.58: 11 Dihedral angle restraints: 4208 sinusoidal: 2252 harmonic: 1956 Sorted by residual: dihedral pdb=" C THR B 212 " pdb=" N THR B 212 " pdb=" CA THR B 212 " pdb=" CB THR B 212 " ideal model delta harmonic sigma weight residual -122.00 -135.87 13.87 0 2.50e+00 1.60e-01 3.08e+01 dihedral pdb=" C GLU B 184 " pdb=" N GLU B 184 " pdb=" CA GLU B 184 " pdb=" CB GLU B 184 " ideal model delta harmonic sigma weight residual -122.60 -135.02 12.42 0 2.50e+00 1.60e-01 2.47e+01 dihedral pdb=" C ASN B 86 " pdb=" N ASN B 86 " pdb=" CA ASN B 86 " pdb=" CB ASN B 86 " ideal model delta harmonic sigma weight residual -122.60 -134.99 12.39 0 2.50e+00 1.60e-01 2.46e+01 ... (remaining 4205 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 495 0.107 - 0.213: 154 0.213 - 0.320: 30 0.320 - 0.427: 15 0.427 - 0.533: 6 Chirality restraints: 700 Sorted by residual: chirality pdb=" CA GLU B 184 " pdb=" N GLU B 184 " pdb=" C GLU B 184 " pdb=" CB GLU B 184 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 7.11e+00 chirality pdb=" CA ASN B 86 " pdb=" N ASN B 86 " pdb=" C ASN B 86 " pdb=" CB ASN B 86 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.73e+00 chirality pdb=" CA ASN A 86 " pdb=" N ASN A 86 " pdb=" C ASN A 86 " pdb=" CB ASN A 86 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.28e+00 ... (remaining 697 not shown) Planarity restraints: 1346 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN B 61 " -0.013 2.00e-02 2.50e+03 3.89e-02 2.26e+01 pdb=" CD GLN B 61 " -0.051 2.00e-02 2.50e+03 pdb=" OE1 GLN B 61 " 0.052 2.00e-02 2.50e+03 pdb=" NE2 GLN B 61 " -0.008 2.00e-02 2.50e+03 pdb="HE21 GLN B 61 " 0.050 2.00e-02 2.50e+03 pdb="HE22 GLN B 61 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 264 " -0.005 2.00e-02 2.50e+03 2.57e-02 1.99e+01 pdb=" CG TYR B 264 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 TYR B 264 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR B 264 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B 264 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 264 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR B 264 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 264 " 0.007 2.00e-02 2.50e+03 pdb=" HD1 TYR B 264 " 0.040 2.00e-02 2.50e+03 pdb=" HD2 TYR B 264 " 0.047 2.00e-02 2.50e+03 pdb=" HE1 TYR B 264 " -0.004 2.00e-02 2.50e+03 pdb=" HE2 TYR B 264 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 130 " 0.014 2.00e-02 2.50e+03 2.57e-02 1.99e+01 pdb=" CG TYR B 130 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR B 130 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR B 130 " -0.017 2.00e-02 2.50e+03 pdb=" CE1 TYR B 130 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR B 130 " 0.014 2.00e-02 2.50e+03 pdb=" CZ TYR B 130 " 0.011 2.00e-02 2.50e+03 pdb=" OH TYR B 130 " -0.004 2.00e-02 2.50e+03 pdb=" HD1 TYR B 130 " 0.042 2.00e-02 2.50e+03 pdb=" HD2 TYR B 130 " -0.039 2.00e-02 2.50e+03 pdb=" HE1 TYR B 130 " -0.039 2.00e-02 2.50e+03 pdb=" HE2 TYR B 130 " 0.041 2.00e-02 2.50e+03 ... (remaining 1343 not shown) Histogram of nonbonded interaction distances: 0.76 - 1.53: 35 1.53 - 2.30: 1545 2.30 - 3.06: 26132 3.06 - 3.83: 38081 3.83 - 4.60: 61387 Warning: very small nonbonded interaction distances. Nonbonded interactions: 127180 Sorted by model distance: nonbonded pdb=" HG1 THR B 76 " pdb=" HG1 THR B 113 " model vdw 0.760 2.100 nonbonded pdb=" HG1 THR B 68 " pdb=" HG1 THR B 121 " model vdw 0.787 2.100 nonbonded pdb=" HG1 THR A 76 " pdb=" HG1 THR A 113 " model vdw 0.790 2.100 nonbonded pdb=" HG1 THR A 68 " pdb=" HG1 THR A 121 " model vdw 0.794 2.100 nonbonded pdb="HH12 ARG A 227 " pdb=" HB2 PRO A 311 " model vdw 0.896 2.270 ... (remaining 127175 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Initializing Amber ============================= topology : 4amber_2yhj.prmtop atom order : 4amber_2yhj.order coordinates : 4amber_2yhj.rst7 ===================================== ... ===================================== ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 5 Type Number sf(0) Gaussians S 4 15.91 1 O 904 7.97 1 N 728 6.97 1 C 2814 5.97 1 H 4332 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: 4332 of 8782 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 8782 n_use_u_iso = 8782 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 = 8782 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (8782 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 8782 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 54 through 56 helix_type = alpha pi *3_10 unknown } helix { serial_number = "2" helix_identifier = "2" selection = chain 'A' and resid 93 through 104 } helix { serial_number = "3" helix_identifier = "3" selection = chain 'A' and resid 171 through 173 helix_type = alpha pi *3_10 unknown } helix { serial_number = "4" helix_identifier = "4" selection = chain 'A' and resid 176 through 179 helix_type = alpha pi *3_10 unknown } helix { serial_number = "5" helix_identifier = "5" selection = chain 'A' and resid 211 through 216 } helix { serial_number = "6" helix_identifier = "6" selection = chain 'A' and resid 267 through 269 helix_type = alpha pi *3_10 unknown } helix { serial_number = "7" helix_identifier = "7" selection = chain 'B' and resid 54 through 56 helix_type = alpha pi *3_10 unknown } helix { serial_number = "8" helix_identifier = "8" selection = chain 'B' and resid 93 through 104 } helix { serial_number = "9" helix_identifier = "9" selection = chain 'B' and resid 171 through 173 helix_type = alpha pi *3_10 unknown } helix { serial_number = "10" helix_identifier = "10" selection = chain 'B' and resid 176 through 179 helix_type = alpha pi *3_10 unknown } helix { serial_number = "11" helix_identifier = "11" selection = chain 'B' and resid 211 through 215 } helix { serial_number = "12" helix_identifier = "12" selection = chain 'B' and resid 267 through 269 helix_type = alpha pi *3_10 unknown } sheet { first_strand = chain 'A' and resid 195 through 199 sheet_id = " A" strand { selection = chain 'A' and resid 40 through 45 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 45 and name N bond_start_previous = chain 'A' and resid 195 and name O } strand { selection = chain 'A' and resid 127 through 144 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 144 and name N bond_start_previous = chain 'A' and resid 40 and name O } strand { selection = chain 'A' and resid 151 through 168 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 168 and name N bond_start_previous = chain 'A' and resid 127 and name O } strand { selection = chain 'A' and resid 80 through 82 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 82 and name N bond_start_previous = chain 'A' and resid 154 and name O } } sheet { first_strand = chain 'A' and resid 68 through 78 sheet_id = " B" strand { selection = chain 'A' and resid 111 through 121 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 120 and name N bond_start_previous = chain 'A' and resid 69 and name O } } sheet { first_strand = chain 'A' and resid 205 through 210 sheet_id = " C" strand { selection = chain 'A' and resid 238 through 244 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 239 and name N bond_start_previous = chain 'A' and resid 205 and name O } strand { selection = chain 'A' and resid 294 through 302 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 300 and name N bond_start_previous = chain 'A' and resid 238 and name O } strand { selection = chain 'A' and resid 259 through 265 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 264 and name N bond_start_previous = chain 'A' and resid 297 and name O } strand { selection = chain 'A' and resid 272 through 277 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 277 and name N bond_start_previous = chain 'A' and resid 261 and name O } } sheet { first_strand = chain 'A' and resid 223 through 227 sheet_id = " D" strand { selection = chain 'A' and resid 313 through 318 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 316 and name N bond_start_previous = chain 'A' and resid 224 and name O } strand { selection = chain 'A' and resid 249 through 255 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 254 and name N bond_start_previous = chain 'A' and resid 315 and name O } strand { selection = chain 'A' and resid 285 through 291 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 291 and name N bond_start_previous = chain 'A' and resid 249 and name O } } sheet { first_strand = chain 'A' and resid 57 through 63 sheet_id = " E" strand { selection = chain 'A' and resid 128 through 133 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 132 and name N bond_start_previous = chain 'A' and resid 58 and name O } } sheet { first_strand = chain 'B' and resid 195 through 199 sheet_id = " F" strand { selection = chain 'B' and resid 40 through 45 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 45 and name N bond_start_previous = chain 'B' and resid 195 and name O } strand { selection = chain 'B' and resid 127 through 144 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 144 and name N bond_start_previous = chain 'B' and resid 40 and name O } strand { selection = chain 'B' and resid 151 through 168 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 168 and name N bond_start_previous = chain 'B' and resid 127 and name O } strand { selection = chain 'B' and resid 80 through 82 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 82 and name N bond_start_previous = chain 'B' and resid 154 and name O } } sheet { first_strand = chain 'B' and resid 68 through 78 sheet_id = " G" strand { selection = chain 'B' and resid 111 through 121 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 120 and name N bond_start_previous = chain 'B' and resid 69 and name O } } sheet { first_strand = chain 'B' and resid 204 through 210 sheet_id = " H" strand { selection = chain 'B' and resid 237 through 244 sense = *parallel antiparallel unknown bond_start_current = chain 'B' and resid 237 and name N bond_start_previous = chain 'B' and resid 205 and name O } strand { selection = chain 'B' and resid 294 through 302 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 300 and name N bond_start_previous = chain 'B' and resid 238 and name O } strand { selection = chain 'B' and resid 259 through 265 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 264 and name N bond_start_previous = chain 'B' and resid 297 and name O } strand { selection = chain 'B' and resid 272 through 277 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 277 and name N bond_start_previous = chain 'B' and resid 261 and name O } } sheet { first_strand = chain 'B' and resid 223 through 227 sheet_id = " I" strand { selection = chain 'B' and resid 313 through 318 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 316 and name N bond_start_previous = chain 'B' and resid 224 and name O } strand { selection = chain 'B' and resid 249 through 255 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 254 and name N bond_start_previous = chain 'B' and resid 315 and name O } strand { selection = chain 'B' and resid 285 through 291 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 291 and name N bond_start_previous = chain 'B' and resid 249 and name O } } sheet { first_strand = chain 'B' and resid 57 through 63 sheet_id = " J" strand { selection = chain 'B' and resid 128 through 133 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 132 and name N bond_start_previous = chain 'B' and resid 58 and name O } } } enabled = True } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } amber { use_amber = True topology_file_name = "4amber_2yhj.prmtop" coordinate_file_name = "4amber_2yhj.rst7" order_file_name = "4amber_2yhj.order" } } output { prefix = "4phenix_2yhj_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== WARNING: failed to analyze molecule topology. Atomic model may be wrong. ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 4.00 - 65.20 A, n_refl.=11707 (all), 4.74 % free)------------| | | | r_work= 0.5891 r_free= 0.4408 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.177950 | | target function (ml) not normalized (work): 46592.495139 | | target function (ml) not normalized (free): 2298.034255 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 65.20 - 6.35 1.00 2869 154 0.5472 0.4512 5.0221 4.6886| | 2: 6.35 - 5.04 1.00 2777 143 0.5706 0.3862 4.0914 4.1462| | 3: 5.04 - 4.40 1.00 2783 123 0.6250 0.4333 3.954 4.0164| | 4: 4.40 - 4.00 0.99 2723 135 0.6723 0.5104 3.6057 3.6227| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 65.20 - 6.35 2869 154 0.51 50.29 0.85 0.03 2263.90| | 2: 6.35 - 5.04 2777 143 0.43 57.41 2.00 0.04 1475.16| | 3: 5.04 - 4.40 2783 123 0.59 44.87 2.34 0.05 842.17| | 4: 4.40 - 4.00 2723 135 0.61 43.59 2.67 0.06 379.02| |alpha: min = 0.03 max = 0.06 mean = 0.04| |beta: min = 379.02 max = 2263.90 mean = 1252.46| |figures of merit: min = 0.00 max = 1.00 mean = 0.54| |phase err.(work): min = 0.00 max = 89.88 mean = 49.07| |phase err.(test): min = 0.00 max = 89.66 mean = 49.14| |-----------------------------------------------------------------------------| ----------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 : 0.010 0.113 4538 Z= 0.660 Angle : 1.541 9.034 6170 Z= 1.009 Chirality : 0.123 0.533 700 Planarity : 0.007 0.028 792 Dihedral : 15.468 88.583 1622 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.22 % Allowed : 6.83 % Favored : 88.96 % Cbeta Deviations : 2.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.32), residues: 566 helix: -0.38 (0.69), residues: 42 sheet: 0.26 (0.29), residues: 286 loop : -0.96 (0.35), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.002 ARG A 116 TYR 0.045 0.007 TYR B 264 PHE 0.018 0.005 PHE B 316 TRP 0.046 0.009 TRP A 162 HIS 0.008 0.002 HIS A 146 Individual atomic B min max mean iso aniso Overall: 34.09 300.00 115.49 16.58 4450 0 Protein: 34.09 300.00 115.49 16.58 4450 0 Chain A: 34.09 300.00 113.10 N/A 2225 0 Chain B: 38.50 300.00 117.88 N/A 2225 0 Histogram: Values Number of atoms 34.09 - 60.68 195 60.68 - 87.27 913 87.27 - 113.86 1318 113.86 - 140.45 1013 140.45 - 167.04 585 167.04 - 193.64 250 193.64 - 220.23 97 220.23 - 246.82 41 246.82 - 273.41 14 273.41 - 300.00 24 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 3 ************************* |--(resolution: 4.00 - 65.20 A, n_refl.=11707 (all), 4.74 % free)------------| | | | r_work= 0.5891 r_free= 0.4408 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.177950 | | target function (ml) not normalized (work): 46592.495139 | | target function (ml) not normalized (free): 2298.034255 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.5850 0.5891 0.4408 n_refl.: 11707 re-set all scales: r(all,work,free)=0.5850 0.5891 0.4408 n_refl.: 11707 remove outliers: r(all,work,free)=0.5853 0.5894 0.4408 n_refl.: 11703 overall B=1.75 to atoms: r(all,work,free)=0.5901 0.5942 0.4439 n_refl.: 11703 bulk-solvent and scaling: r(all,work,free)=0.3022 0.3000 0.3467 n_refl.: 11703 remove outliers: r(all,work,free)=0.3022 0.3000 0.3467 n_refl.: 11703 ======================== 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 65.196-20.791 100.00 98 1 0.3718 4797.131 4481.903 1.350 1.186 0.370 20.447-16.215 100.00 96 3 0.3150 3372.133 3175.189 1.068 1.173 0.340 16.132-12.745 100.00 194 11 0.2768 3265.866 3052.880 1.142 1.157 0.329 12.705-10.080 100.00 377 16 0.2680 3068.255 2814.173 1.084 1.130 0.309 10.040-7.926 100.00 749 47 0.2592 2378.286 2226.841 1.046 1.086 0.278 7.906-6.254 99.81 1487 80 0.3020 1468.322 1345.455 1.041 1.015 0.228 6.249-4.933 100.00 3011 157 0.3076 1268.459 1120.402 1.062 0.900 0.177 4.931-4.001 99.68 5136 240 0.3095 1069.047 941.662 1.390 0.733 0.127 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=7.8534 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ==================== Compute data/restraints target weights =================== Setting wxc_scale using amber.wxc_factor : 0.500 * 1.000 = 0.500 |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 4.161496 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.153669 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 5.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2944 0.3583 0.0639 0.014 1.8 0.3 0.4 2.8 0 0.125 0.2852 0.3576 0.0724 0.014 1.9 0.5 0.4 2.8 0 0.250 0.2770 0.3553 0.0783 0.015 2.0 0.5 0.5 2.6 0 0.500 0.2682 0.3560 0.0878 0.017 2.3 1.1 0.4 4.6 2 1.000 0.2615 0.3536 0.0921 0.021 2.9 1.9 1.2 6.4 4 2.000 0.2560 0.3562 0.1002 0.026 3.6 4.4 1.1 4.8 12 3.000 0.2647 0.3533 0.0886 0.028 3.1 4.9 0.0 3.8 4 4.000 0.2745 0.3482 0.0737 0.026 2.5 6.6 0.0 4.0 1 5.000 0.2769 0.3477 0.0708 0.026 2.4 6.8 0.0 3.8 1 6.000 0.2746 0.3479 0.0733 0.029 2.6 7.5 0.0 4.0 1 7.000 0.2880 0.3455 0.0575 0.021 1.8 8.5 0.0 4.2 1 8.000 0.2861 0.3454 0.0593 0.024 1.9 8.8 0.0 4.2 1 9.000 0.2838 0.3453 0.0616 0.028 2.0 8.7 0.0 4.2 1 10.000 0.2608 0.3548 0.0941 0.022 2.9 3.0 0.4 3.4 5 2.081 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2861 0.3454 0.0593 0.024 1.9 8.8 0.0 4.2 1 9.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 28.61 34.54 5.93 11.857 115.384 0.154 0.104 29.07 33.11 4.05 15.689 119.831 0.005 0.107 28.85 33.07 4.22 15.627 119.737 0.019 0.105 28.16 33.06 4.90 15.670 119.477 0.077 0.101 27.56 33.10 5.54 16.024 119.272 0.154 0.098 27.15 33.20 6.05 16.506 119.155 0.231 0.096 26.88 33.32 6.44 17.009 119.100 0.307 0.094 26.69 33.41 6.71 17.488 119.081 0.384 0.093 26.55 33.56 7.00 17.850 119.063 0.461 0.092 26.45 33.63 7.19 18.284 119.104 0.538 0.092 26.33 33.74 7.42 19.028 119.326 0.615 0.091 26.25 33.79 7.54 19.421 119.389 0.692 0.091 26.19 33.88 7.69 19.707 119.418 0.768 0.091 max suggested for this run: 23.08 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.077 Accepted refinement result: 28.16 33.06 4.90 15.670 119.477 0.077 0.101 Individual atomic B min max mean iso aniso Overall: 42.44 296.75 125.31 12.01 4450 0 Protein: 42.44 296.75 125.31 12.01 4450 0 Chain A: 42.44 296.75 123.07 N/A 2225 0 Chain B: 65.22 296.75 127.56 N/A 2225 0 Histogram: Values Number of atoms 42.44 - 67.87 10 67.87 - 93.30 569 93.30 - 118.73 1601 118.73 - 144.16 1291 144.16 - 169.59 585 169.59 - 195.02 245 195.02 - 220.45 79 220.45 - 245.88 33 245.88 - 271.31 15 271.31 - 296.75 22 =========================== Idealize ADP of riding H ========================== r_work=0.2816 r_free=0.3306 r_work=0.2810 r_free=0.3310 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 4.00 - 65.20 A, n_refl.=11703 (all), 4.74 % free)------------| | | | r_work= 0.2810 r_free= 0.3310 coordinate error (max.-lik. estimate): 0.60 A | | | | normalized target function (ls_wunit_k1) (work): 0.100927 | | target function (ls_wunit_k1) not normalized (work): 1125.133756 | | target function (ls_wunit_k1) not normalized (free): 75.778336 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2833 0.2810 0.3310 n_refl.: 11703 re-set all scales: r(all,work,free)=0.6181 0.6220 0.4619 n_refl.: 11703 remove outliers: r(all,work,free)=0.6181 0.6220 0.4619 n_refl.: 11703 overall B=-2.77 to atoms: r(all,work,free)=0.6109 0.6148 0.4560 n_refl.: 11703 bulk-solvent and scaling: r(all,work,free)=0.2805 0.2781 0.3298 n_refl.: 11703 remove outliers: r(all,work,free)=0.2805 0.2781 0.3298 n_refl.: 11703 ======================== 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 65.196-20.791 100.00 98 1 0.3629 1634.108 1529.948 1.226 1.172 0.370 20.447-16.215 100.00 96 3 0.3036 1148.693 1090.611 0.955 1.159 0.338 16.132-12.745 100.00 194 11 0.2515 1112.494 1052.671 1.035 1.143 0.328 12.705-10.080 100.00 377 16 0.2487 1045.179 974.163 0.998 1.119 0.312 10.040-7.926 100.00 749 47 0.2271 810.146 769.553 0.962 1.078 0.272 7.906-6.254 99.81 1487 80 0.2636 500.173 467.011 0.974 1.013 0.223 6.249-4.933 100.00 3011 157 0.2804 432.091 388.906 1.030 0.908 0.184 4.931-4.001 99.68 5136 240 0.2989 364.163 325.351 1.330 0.754 0.114 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.6087 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ==================== Compute data/restraints target weights =================== Setting wxc_scale using amber.wxc_factor : 0.500 * 1.000 = 0.500 |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.462961 wxc_scale = 0.074 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.074587 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 5.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2968 0.3467 0.0499 0.014 1.8 0.5 0.4 2.4 0 0.018 0.2884 0.3392 0.0508 0.013 1.9 0.1 0.4 2.6 0 0.055 0.2820 0.3400 0.0579 0.013 1.9 0.2 0.4 2.8 0 0.109 0.2771 0.3416 0.0645 0.013 1.9 0.5 0.5 2.0 0 0.164 0.2742 0.3421 0.0679 0.014 2.0 0.3 0.5 2.8 0 0.218 0.2720 0.3433 0.0712 0.014 2.0 0.3 0.5 3.0 0 0.273 0.2712 0.3444 0.0732 0.015 2.2 0.7 0.5 3.2 0 0.327 0.2748 0.3371 0.0622 0.017 2.2 0.7 0.0 3.6 0 0.382 0.2761 0.3438 0.0676 0.013 1.9 0.3 0.5 2.0 0 0.182 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2968 0.3467 0.0499 0.014 1.8 0.5 0.4 2.4 0 0.018 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 29.68 34.67 4.99 19.727 133.764 0.075 6.492 32.53 34.49 1.96 18.138 144.007 0.002 6.504 31.93 34.40 2.46 17.685 144.170 0.009 6.493 29.79 34.26 4.47 18.597 140.379 0.037 6.462 28.76 34.29 5.52 19.479 137.635 0.075 6.453 28.49 34.44 5.95 20.019 136.500 0.112 6.454 28.35 34.44 6.09 20.561 136.294 0.149 6.453 28.24 34.49 6.26 20.982 136.383 0.186 6.452 28.15 34.52 6.36 21.428 136.576 0.224 6.451 28.08 34.55 6.47 21.821 136.751 0.261 6.451 28.08 34.55 6.47 21.721 136.601 0.298 6.452 28.04 34.59 6.54 21.994 136.737 0.336 6.451 27.99 34.61 6.62 22.314 136.911 0.373 6.451 max suggested for this run: 26.75 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.037 Accepted refinement result: 29.79 34.26 4.47 18.597 140.379 0.037 6.462 Individual atomic B min max mean iso aniso Overall: 55.19 288.97 135.60 12.39 4450 0 Protein: 55.19 288.97 135.60 12.39 4450 0 Chain A: 55.19 288.97 132.86 N/A 2225 0 Chain B: 69.27 288.97 138.33 N/A 2225 0 Histogram: Values Number of atoms 55.19 - 78.57 40 78.57 - 101.95 625 101.95 - 125.33 1124 125.33 - 148.70 1310 148.70 - 172.08 816 172.08 - 195.46 347 195.46 - 218.84 116 218.84 - 242.22 35 242.22 - 265.59 15 265.59 - 288.97 22 =========================== Idealize ADP of riding H ========================== r_work=0.2979 r_free=0.3426 r_work=0.2987 r_free=0.3429 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 4.00 - 65.20 A, n_refl.=11703 (all), 4.74 % free)------------| | | | r_work= 0.2987 r_free= 0.3429 coordinate error (max.-lik. estimate): 0.62 A | | | | normalized target function (ml) (work): 6.462118 | | target function (ml) not normalized (work): 72039.694333 | | target function (ml) not normalized (free): 3620.916799 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3007 0.2987 0.3429 n_refl.: 11703 re-set all scales: r(all,work,free)=0.6488 0.6523 0.4940 n_refl.: 11703 remove outliers: r(all,work,free)=0.6488 0.6523 0.4940 n_refl.: 11703 overall B=-10.99 to atoms: r(all,work,free)=0.6217 0.6254 0.4712 n_refl.: 11703 bulk-solvent and scaling: r(all,work,free)=0.2974 0.2952 0.3425 n_refl.: 11703 remove outliers: r(all,work,free)=0.2974 0.2952 0.3425 n_refl.: 11703 ======================== 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 65.196-20.791 100.00 98 1 0.3641 1432.287 1306.094 1.075 1.142 0.361 20.447-16.215 100.00 96 3 0.3011 1006.823 948.934 0.986 1.133 0.336 16.132-12.745 100.00 194 11 0.2730 975.095 913.201 1.051 1.120 0.328 12.705-10.080 100.00 377 16 0.2531 916.093 853.382 1.048 1.099 0.327 10.040-7.926 100.00 749 47 0.2435 710.088 664.270 0.989 1.064 0.280 7.906-6.254 99.81 1487 80 0.2916 438.399 397.254 1.008 1.008 0.222 6.249-4.933 100.00 3011 157 0.3031 378.726 332.911 1.047 0.917 0.186 4.931-4.001 99.68 5136 240 0.3129 319.187 280.451 1.252 0.783 0.115 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0265 b_overall=4.0224 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ==================== Compute data/restraints target weights =================== Setting wxc_scale using amber.wxc_factor : 0.500 * 1.000 = 0.500 |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.554964 wxc_scale = 0.029 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.084795 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 5.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2975 0.3424 0.0449 0.014 1.8 0.2 0.4 2.0 0 0.007 0.2946 0.3428 0.0482 0.013 1.8 0.2 0.4 2.0 0 0.022 0.2913 0.3420 0.0507 0.013 1.8 0.2 0.4 2.0 0 0.045 0.2883 0.3410 0.0527 0.013 1.8 0.2 0.4 2.0 0 0.067 0.2901 0.3406 0.0504 0.013 1.8 0.5 0.4 2.4 0 0.089 0.2910 0.3417 0.0507 0.013 1.8 0.5 0.4 2.6 0 0.111 0.2946 0.3422 0.0476 0.013 1.8 0.5 0.4 2.4 0 0.134 0.2945 0.3421 0.0476 0.013 1.8 0.5 0.4 2.4 0 0.156 0.2875 0.3411 0.0536 0.013 1.8 0.2 0.4 2.0 0 0.074 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2946 0.3428 0.0482 0.013 1.8 0.2 0.4 2.0 0 0.022 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 29.46 34.28 4.82 21.345 137.859 0.085 6.332 31.89 34.66 2.77 18.223 144.929 0.003 6.373 31.43 34.57 3.14 17.845 145.082 0.011 6.364 29.14 34.28 5.14 20.321 141.718 0.042 6.334 28.28 34.36 6.08 22.037 140.164 0.085 6.319 28.25 34.23 5.98 22.089 138.982 0.127 6.314 28.04 34.35 6.31 22.637 139.606 0.170 6.311 27.95 34.37 6.41 23.030 139.845 0.212 6.310 27.91 34.39 6.48 23.321 140.030 0.254 6.308 27.89 34.42 6.53 23.361 140.056 0.297 6.308 27.86 34.45 6.59 23.537 140.201 0.339 6.308 27.82 34.49 6.67 23.778 140.389 0.382 6.307 27.78 34.52 6.73 23.991 140.546 0.424 6.307 max suggested for this run: 27.57 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.127 Accepted refinement result: 28.25 34.23 5.98 22.089 138.982 0.127 6.314 Individual atomic B min max mean iso aniso Overall: 51.05 272.98 126.82 14.76 4450 0 Protein: 51.05 272.98 126.82 14.76 4450 0 Chain A: 51.05 272.98 124.74 N/A 2225 0 Chain B: 53.28 272.98 128.90 N/A 2225 0 Histogram: Values Number of atoms 51.05 - 73.25 99 73.25 - 95.44 703 95.44 - 117.63 1063 117.63 - 139.82 1166 139.82 - 162.02 825 162.02 - 184.21 362 184.21 - 206.40 149 206.40 - 228.59 46 228.59 - 250.79 16 250.79 - 272.98 21 =========================== Idealize ADP of riding H ========================== r_work=0.2825 r_free=0.3423 r_work=0.2814 r_free=0.3424 ----------X-ray data---------- |--(resolution: 4.00 - 65.20 A, n_refl.=11703 (all), 4.74 % free)------------| | | | r_work= 0.2814 r_free= 0.3424 coordinate error (max.-lik. estimate): 0.70 A | | | | normalized target function (ml) (work): 6.312841 | | target function (ml) not normalized (work): 70375.549040 | | target function (ml) not normalized (free): 3551.417767 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 65.20 - 6.35 1.00 2866 154 0.2664 0.3324 6.7846 6.8428| | 2: 6.35 - 5.04 1.00 2776 143 0.2921 0.3275 6.2878 6.3692| | 3: 5.04 - 4.40 1.00 2783 123 0.2811 0.3550 6.2169 6.3198| | 4: 4.40 - 4.00 0.99 2723 135 0.3056 0.3755 5.9399 5.9963| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 65.20 - 6.35 2866 154 0.74 31.28 0.99 0.84 128057.85| | 2: 6.35 - 5.04 2776 143 0.62 42.86 1.02 0.82 94780.70| | 3: 5.04 - 4.40 2783 123 0.70 36.05 1.03 0.80 66140.98| | 4: 4.40 - 4.00 2723 135 0.64 41.15 0.99 0.77 42767.83| |alpha: min = 0.77 max = 0.84 mean = 0.81| |beta: min = 42767.83 max = 128057.85 mean = 83481.54| |figures of merit: min = 0.00 max = 1.00 mean = 0.67| |phase err.(work): min = 0.00 max = 90.00 mean = 37.76| |phase err.(test): min = 0.00 max = 89.34 mean = 37.63| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2843 0.2814 0.3424 n_refl.: 11703 re-set all scales: r(all,work,free)=0.6265 0.6301 0.4751 n_refl.: 11703 remove outliers: r(all,work,free)=0.6265 0.6301 0.4751 n_refl.: 11703 overall B=2.99 to atoms: r(all,work,free)=0.6340 0.6376 0.4813 n_refl.: 11703 bulk-solvent and scaling: r(all,work,free)=0.2839 0.2810 0.3435 n_refl.: 11703 remove outliers: r(all,work,free)=0.2839 0.2810 0.3435 n_refl.: 11703 ======================== 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 65.196-20.791 100.00 98 1 0.3619 1432.287 1307.712 0.976 1.185 0.360 20.447-16.215 100.00 96 3 0.2996 1006.823 953.252 0.924 1.173 0.338 16.132-12.745 100.00 194 11 0.2672 975.095 911.948 1.002 1.157 0.330 12.705-10.080 100.00 377 16 0.2456 916.093 858.478 0.994 1.130 0.328 10.040-7.926 100.00 749 47 0.2335 710.088 666.943 0.936 1.087 0.267 7.906-6.254 99.81 1487 80 0.2811 438.399 399.145 1.008 1.016 0.217 6.249-4.933 100.00 3011 157 0.2868 378.726 336.146 1.074 0.901 0.176 4.931-4.001 99.68 5136 240 0.2931 319.187 283.042 1.369 0.733 0.106 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.6797 ================= 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 : 0.5891 0.4408 0.010 1.541 34.1 300.0 115.5 0 0.000 1_bss: 0.3000 0.3467 0.010 1.541 35.8 301.7 117.2 0 0.000 1_settarget: 0.3000 0.3467 0.010 1.541 35.8 301.7 117.2 0 0.000 1_weight: 0.3000 0.3467 0.010 1.541 35.8 301.7 117.2 0 0.000 1_xyzrec: 0.2861 0.3454 0.024 1.908 35.8 301.7 117.2 0 0.027 1_adp: 0.2816 0.3306 0.024 1.908 42.4 296.7 125.3 0 0.027 1_regHadp: 0.2810 0.3310 0.024 1.908 42.4 296.7 125.3 0 0.027 2_bss: 0.2781 0.3298 0.024 1.908 39.7 294.0 122.5 0 0.027 2_settarget: 0.2781 0.3298 0.024 1.908 39.7 294.0 122.5 0 0.027 2_updatecdl: 0.2781 0.3298 0.024 1.907 39.7 294.0 122.5 0 0.027 2_weight: 0.2781 0.3298 0.024 1.907 39.7 294.0 122.5 0 0.027 2_xyzrec: 0.2968 0.3467 0.014 1.838 39.7 294.0 122.5 0 0.274 2_adp: 0.2979 0.3426 0.014 1.838 55.2 289.0 135.6 0 0.274 2_regHadp: 0.2987 0.3429 0.014 1.838 55.2 289.0 135.6 0 0.274 3_bss: 0.2952 0.3425 0.014 1.838 44.2 278.0 124.6 0 0.274 3_settarget: 0.2952 0.3425 0.014 1.838 44.2 278.0 124.6 0 0.274 3_updatecdl: 0.2952 0.3425 0.014 1.840 44.2 278.0 124.6 0 0.274 3_setrh: 0.2952 0.3425 0.014 1.840 44.2 278.0 124.6 0 0.274 3_weight: 0.2952 0.3425 0.014 1.840 44.2 278.0 124.6 0 0.274 3_xyzrec: 0.2946 0.3428 0.013 1.806 44.2 278.0 124.6 0 0.288 3_adp: 0.2825 0.3423 0.013 1.806 51.1 273.0 126.8 0 0.288 3_regHadp: 0.2814 0.3424 0.013 1.806 51.1 273.0 126.8 0 0.288 end: 0.2810 0.3435 0.013 1.806 54.0 276.0 129.8 0 0.288 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/cci-filer3/home/nigel/work/ANI/result/xray/pairs/4phenix_2yhj_refine_001.cif Writing default parameters for subsequent refinement: /net/cci-filer3/home/nigel/work/ANI/result/xray/pairs/4phenix_2yhj_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 5.1900 Refinement macro-cycles (run) : 430.5600 Write final files (write_after_run_outputs) : 13.0700 Total : 448.8200 Total CPU time: 8.51 minutes =========================== phenix.refine: finished =========================== # Date 2024-08-09 Time 09:52:01 PDT -0700 (1723222321.22 s) Start R-work = 0.3000, R-free = 0.3467 Final R-work = 0.2810, R-free = 0.3435 =============================================================================== Job complete usr+sys time: 523.01 seconds wall clock time: 20 minutes 36.61 seconds (1236.61 seconds total)