Starting phenix.real_space_refine on Wed Aug 5 05:50:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vnq_65215/08_2026/9vnq_65215.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vnq_65215/08_2026/9vnq_65215.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vnq_65215/08_2026/9vnq_65215.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vnq_65215/08_2026/9vnq_65215.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vnq_65215/08_2026/9vnq_65215.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vnq_65215/08_2026/9vnq_65215.map" } resolution = 2.74 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 62 5.49 5 S 28 5.16 5 C 5226 2.51 5 N 1450 2.21 5 O 1793 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8559 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1829 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 9, 'TRANS': 217} Chain: "B" Number of atoms: 1801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1801 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 9, 'TRANS': 214} Chain breaks: 1 Chain: "C" Number of atoms: 1829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1829 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 9, 'TRANS': 217} Chain: "D" Number of atoms: 1829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1829 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 9, 'TRANS': 217} Chain: "E" Number of atoms: 642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 642 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "F" Number of atoms: 629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 629 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Time building chain proxies: 1.54, per 1000 atoms: 0.18 Number of scatterers: 8559 At special positions: 0 Unit cell: (91.5528, 89.9032, 131.143, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 28 16.00 P 62 15.00 O 1793 8.00 N 1450 7.00 C 5226 6.00 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.56 Conformation dependent library (CDL) restraints added in 374.5 milliseconds 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1730 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 10 sheets defined 33.9% alpha, 34.7% beta 27 base pairs and 52 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 73 through 75 No H-bonds generated for 'chain 'A' and resid 73 through 75' Processing helix chain 'A' and resid 92 through 100 Processing helix chain 'A' and resid 117 through 119 No H-bonds generated for 'chain 'A' and resid 117 through 119' Processing helix chain 'A' and resid 136 through 151 Processing helix chain 'A' and resid 189 through 193 removed outlier: 3.802A pdb=" N VAL A 193 " --> pdb=" O ALA A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 218 Processing helix chain 'A' and resid 222 through 226 removed outlier: 3.615A pdb=" N TYR A 226 " --> pdb=" O PRO A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 244 Processing helix chain 'B' and resid 73 through 75 No H-bonds generated for 'chain 'B' and resid 73 through 75' Processing helix chain 'B' and resid 92 through 102 removed outlier: 3.726A pdb=" N GLU B 102 " --> pdb=" O SER B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 119 No H-bonds generated for 'chain 'B' and resid 117 through 119' Processing helix chain 'B' and resid 136 through 151 Processing helix chain 'B' and resid 183 through 187 Processing helix chain 'B' and resid 189 through 193 removed outlier: 3.536A pdb=" N VAL B 193 " --> pdb=" O ALA B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 218 Processing helix chain 'B' and resid 228 through 244 Processing helix chain 'C' and resid 73 through 75 No H-bonds generated for 'chain 'C' and resid 73 through 75' Processing helix chain 'C' and resid 92 through 100 Processing helix chain 'C' and resid 117 through 119 No H-bonds generated for 'chain 'C' and resid 117 through 119' Processing helix chain 'C' and resid 137 through 151 Processing helix chain 'C' and resid 183 through 187 Processing helix chain 'C' and resid 189 through 193 removed outlier: 3.532A pdb=" N VAL C 193 " --> pdb=" O ALA C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 218 Processing helix chain 'C' and resid 222 through 226 removed outlier: 3.542A pdb=" N TYR C 226 " --> pdb=" O PRO C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 244 Processing helix chain 'D' and resid 73 through 75 No H-bonds generated for 'chain 'D' and resid 73 through 75' Processing helix chain 'D' and resid 92 through 100 Processing helix chain 'D' and resid 117 through 119 No H-bonds generated for 'chain 'D' and resid 117 through 119' Processing helix chain 'D' and resid 136 through 151 Processing helix chain 'D' and resid 183 through 187 Processing helix chain 'D' and resid 189 through 193 removed outlier: 3.768A pdb=" N VAL D 193 " --> pdb=" O ALA D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 218 Processing helix chain 'D' and resid 222 through 226 removed outlier: 3.515A pdb=" N TYR D 226 " --> pdb=" O PRO D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 244 Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 28 removed outlier: 6.496A pdb=" N LEU A 37 " --> pdb=" O MET A 21 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N LYS A 23 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ILE A 35 " --> pdb=" O LYS A 23 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N SER A 25 " --> pdb=" O ILE A 33 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N ILE A 33 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N SER A 27 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL A 31 " --> pdb=" O SER A 27 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG A 126 " --> pdb=" O SER A 180 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ILE A 176 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LEU A 166 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N VAL A 171 " --> pdb=" O LYS A 152 " (cutoff:3.500A) removed outlier: 8.896A pdb=" N LYS A 152 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ASN A 157 " --> pdb=" O ILE A 110 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N ILE A 110 " --> pdb=" O ASN A 157 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N VAL A 108 " --> pdb=" O LYS A 23 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N SER A 25 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ILE A 110 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N SER A 27 " --> pdb=" O ILE A 110 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N ASP A 112 " --> pdb=" O SER A 27 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 52 removed outlier: 4.576A pdb=" N LYS B 79 " --> pdb=" O LEU B 91 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LYS B 87 " --> pdb=" O TYR B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 59 through 65 Processing sheet with id=AA4, first strand: chain 'A' and resid 87 through 91 removed outlier: 7.113A pdb=" N LYS A 87 " --> pdb=" O TYR A 83 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LYS A 79 " --> pdb=" O LEU A 91 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 22 through 28 removed outlier: 3.635A pdb=" N TRP B 22 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ILE B 176 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LEU B 166 " --> pdb=" O ILE B 181 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N VAL B 171 " --> pdb=" O LYS B 152 " (cutoff:3.500A) removed outlier: 8.860A pdb=" N LYS B 152 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP B 112 " --> pdb=" O ILE B 155 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ASN B 157 " --> pdb=" O ILE B 110 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N ILE B 110 " --> pdb=" O ASN B 157 " (cutoff:3.500A) removed outlier: 8.504A pdb=" N THR B 159 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N VAL B 108 " --> pdb=" O THR B 159 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 20 through 28 removed outlier: 6.555A pdb=" N LEU C 37 " --> pdb=" O MET C 21 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N LYS C 23 " --> pdb=" O ILE C 35 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ILE C 35 " --> pdb=" O LYS C 23 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N SER C 25 " --> pdb=" O ILE C 33 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N ILE C 33 " --> pdb=" O SER C 25 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N SER C 27 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N VAL C 31 " --> pdb=" O SER C 27 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG C 126 " --> pdb=" O SER C 180 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ILE C 176 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU C 166 " --> pdb=" O ILE C 181 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N VAL C 171 " --> pdb=" O LYS C 152 " (cutoff:3.500A) removed outlier: 8.802A pdb=" N LYS C 152 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASN C 157 " --> pdb=" O ILE C 110 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N ILE C 110 " --> pdb=" O ASN C 157 " (cutoff:3.500A) removed outlier: 8.597A pdb=" N THR C 159 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N VAL C 108 " --> pdb=" O THR C 159 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N VAL C 108 " --> pdb=" O LYS C 23 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N SER C 25 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ILE C 110 " --> pdb=" O SER C 25 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N SER C 27 " --> pdb=" O ILE C 110 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N ASP C 112 " --> pdb=" O SER C 27 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 49 through 52 removed outlier: 4.141A pdb=" N LYS D 79 " --> pdb=" O LEU D 91 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR D 83 " --> pdb=" O LYS D 87 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N LYS D 87 " --> pdb=" O TYR D 83 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 59 through 65 Processing sheet with id=AA9, first strand: chain 'C' and resid 87 through 91 removed outlier: 7.494A pdb=" N LYS C 87 " --> pdb=" O TYR C 83 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TYR C 83 " --> pdb=" O LYS C 87 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LYS C 79 " --> pdb=" O LEU C 91 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 22 through 28 removed outlier: 3.646A pdb=" N TRP D 22 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N SER D 180 " --> pdb=" O ASN D 125 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N SER D 127 " --> pdb=" O MET D 178 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N MET D 178 " --> pdb=" O SER D 127 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N PHE D 129 " --> pdb=" O ILE D 176 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ILE D 176 " --> pdb=" O PHE D 129 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LEU D 166 " --> pdb=" O ILE D 181 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N VAL D 171 " --> pdb=" O LYS D 152 " (cutoff:3.500A) removed outlier: 8.736A pdb=" N LYS D 152 " --> pdb=" O VAL D 171 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP D 112 " --> pdb=" O ILE D 155 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ASN D 157 " --> pdb=" O ILE D 110 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N ILE D 110 " --> pdb=" O ASN D 157 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N THR D 159 " --> pdb=" O VAL D 108 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N VAL D 108 " --> pdb=" O THR D 159 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N VAL D 108 " --> pdb=" O LYS D 23 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N SER D 25 " --> pdb=" O VAL D 108 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ILE D 110 " --> pdb=" O SER D 25 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N SER D 27 " --> pdb=" O ILE D 110 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N ASP D 112 " --> pdb=" O SER D 27 " (cutoff:3.500A) 338 hydrogen bonds defined for protein. 942 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 66 hydrogen bonds 132 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 52 stacking parallelities Total time for adding SS restraints: 1.31 Time building geometry restraints manager: 0.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2398 1.34 - 1.45: 1591 1.45 - 1.57: 4683 1.57 - 1.69: 122 1.69 - 1.81: 44 Bond restraints: 8838 Sorted by residual: bond pdb=" C3' DC F 22 " pdb=" C2' DC F 22 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.20e+01 bond pdb=" C3' DA E 25 " pdb=" C2' DA E 25 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.18e+01 bond pdb=" C3' DT F 24 " pdb=" C2' DT F 24 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.17e+01 bond pdb=" C3' DC F 3 " pdb=" C2' DC F 3 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.15e+01 bond pdb=" C3' DT E 4 " pdb=" C2' DT E 4 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.08e+01 ... (remaining 8833 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 11975 1.99 - 3.98: 233 3.98 - 5.97: 2 5.97 - 7.96: 0 7.96 - 9.95: 1 Bond angle restraints: 12211 Sorted by residual: angle pdb=" N3 DT E 28 " pdb=" C4 DT E 28 " pdb=" O4 DT E 28 " ideal model delta sigma weight residual 119.90 122.66 -2.76 6.00e-01 2.78e+00 2.12e+01 angle pdb=" N3 DT F 27 " pdb=" C4 DT F 27 " pdb=" O4 DT F 27 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.89e+01 angle pdb=" N3 DT E 15 " pdb=" C4 DT E 15 " pdb=" O4 DT E 15 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.87e+01 angle pdb=" N3 DT E 24 " pdb=" C4 DT E 24 " pdb=" O4 DT E 24 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.86e+01 angle pdb=" N3 DT F 25 " pdb=" C4 DT F 25 " pdb=" O4 DT F 25 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.84e+01 ... (remaining 12206 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.80: 4761 34.80 - 69.59: 486 69.59 - 104.39: 16 104.39 - 139.19: 0 139.19 - 173.98: 1 Dihedral angle restraints: 5264 sinusoidal: 2586 harmonic: 2678 Sorted by residual: dihedral pdb=" C4' DC E 1 " pdb=" C3' DC E 1 " pdb=" O3' DC E 1 " pdb=" P DT E 2 " ideal model delta sinusoidal sigma weight residual -140.00 33.98 -173.98 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" CA GLU D 179 " pdb=" C GLU D 179 " pdb=" N SER D 180 " pdb=" CA SER D 180 " ideal model delta harmonic sigma weight residual 180.00 163.70 16.30 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CG ARG C 148 " pdb=" CD ARG C 148 " pdb=" NE ARG C 148 " pdb=" CZ ARG C 148 " ideal model delta sinusoidal sigma weight residual 90.00 134.75 -44.75 2 1.50e+01 4.44e-03 1.06e+01 ... (remaining 5261 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 764 0.028 - 0.055: 367 0.055 - 0.083: 118 0.083 - 0.111: 95 0.111 - 0.138: 37 Chirality restraints: 1381 Sorted by residual: chirality pdb=" CA VAL D 108 " pdb=" N VAL D 108 " pdb=" C VAL D 108 " pdb=" CB VAL D 108 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.77e-01 chirality pdb=" CA ILE C 26 " pdb=" N ILE C 26 " pdb=" C ILE C 26 " pdb=" CB ILE C 26 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.59e-01 chirality pdb=" CA ILE D 26 " pdb=" N ILE D 26 " pdb=" C ILE D 26 " pdb=" CB ILE D 26 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.56e-01 ... (remaining 1378 not shown) Planarity restraints: 1351 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP D 120 " 0.033 5.00e-02 4.00e+02 4.94e-02 3.90e+00 pdb=" N PRO D 121 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO D 121 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 121 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 120 " -0.029 5.00e-02 4.00e+02 4.43e-02 3.14e+00 pdb=" N PRO C 121 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO C 121 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 121 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 120 " -0.029 5.00e-02 4.00e+02 4.36e-02 3.05e+00 pdb=" N PRO B 121 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 121 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 121 " -0.024 5.00e-02 4.00e+02 ... (remaining 1348 not shown) Histogram of nonbonded interaction distances: 2.49 - 2.97: 3798 2.97 - 3.45: 7886 3.45 - 3.94: 14948 3.94 - 4.42: 17010 4.42 - 4.90: 26956 Nonbonded interactions: 70598 Sorted by model distance: nonbonded pdb=" N ASP B 134 " pdb=" OD1 ASP B 134 " model vdw 2.490 3.120 nonbonded pdb=" O ASP B 228 " pdb=" NE2 GLN B 232 " model vdw 2.568 3.120 nonbonded pdb=" N1 DG E 16 " pdb=" C4 DG E 16 " model vdw 2.598 2.672 nonbonded pdb=" N1 DG E 29 " pdb=" C4 DG E 29 " model vdw 2.598 2.672 nonbonded pdb=" N1 DG E 3 " pdb=" C4 DG E 3 " model vdw 2.600 2.672 ... (remaining 70593 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 18 through 102 or resid 106 through 244)) selection = chain 'B' selection = (chain 'C' and (resid 18 through 102 or resid 106 through 244)) selection = (chain 'D' and (resid 18 through 102 or resid 106 through 244)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.320 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8838 Z= 0.309 Angle : 0.571 9.952 12211 Z= 0.439 Chirality : 0.044 0.138 1381 Planarity : 0.004 0.049 1351 Dihedral : 22.273 173.984 3534 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.98 % Allowed : 28.66 % Favored : 70.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.27), residues: 895 helix: 2.86 (0.32), residues: 229 sheet: 0.23 (0.47), residues: 125 loop : 0.12 (0.24), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 237 TYR 0.018 0.001 TYR B 81 PHE 0.010 0.001 PHE C 28 TRP 0.008 0.002 TRP B 22 HIS 0.006 0.001 HIS B 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.31 ( 8838) covalent geometry : angle 0.57057 / 0.44 (12211) hydrogen bonds : bond 0.09933 / 6.39 ( 404) hydrogen bonds : angle 5.43976 / 3.73 ( 1074) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.184 Fit side-chains REVERT: A 70 LYS cc_start: 0.7627 (ptmm) cc_final: 0.7182 (ttmt) REVERT: B 164 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.7694 (tp40) REVERT: C 192 GLN cc_start: 0.8254 (mt0) cc_final: 0.7466 (tm-30) outliers start: 8 outliers final: 7 residues processed: 92 average time/residue: 0.5176 time to fit residues: 50.6263 Evaluate side-chains 98 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 164 GLN Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain C residue 85 LYS Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 240 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.0980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 232 GLN ** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.163800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.127212 restraints weight = 9389.095| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.77 r_work: 0.3378 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.0538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8838 Z= 0.175 Angle : 0.572 8.648 12211 Z= 0.323 Chirality : 0.046 0.230 1381 Planarity : 0.004 0.052 1351 Dihedral : 22.767 175.530 1684 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.44 % Allowed : 25.71 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.27), residues: 895 helix: 2.92 (0.31), residues: 229 sheet: 0.17 (0.46), residues: 128 loop : 0.06 (0.25), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 188 TYR 0.011 0.001 TYR B 83 PHE 0.018 0.002 PHE C 28 TRP 0.008 0.002 TRP B 22 HIS 0.003 0.001 HIS B 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 ( 8838) covalent geometry : angle 0.57245 / 0.32 (12211) hydrogen bonds : bond 0.03841 / 2.54 ( 404) hydrogen bonds : angle 4.54559 / 3.10 ( 1074) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 96 time to evaluate : 0.209 Fit side-chains REVERT: A 70 LYS cc_start: 0.7461 (ptmm) cc_final: 0.7050 (ttmt) REVERT: B 161 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7661 (mtt180) REVERT: B 241 LYS cc_start: 0.7387 (OUTLIER) cc_final: 0.6687 (mtmm) REVERT: B 243 GLU cc_start: 0.7251 (tt0) cc_final: 0.6821 (mm-30) REVERT: C 94 GLU cc_start: 0.7086 (mp0) cc_final: 0.6840 (mp0) REVERT: C 192 GLN cc_start: 0.8132 (mt0) cc_final: 0.7058 (tm-30) REVERT: C 217 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7328 (mp) REVERT: D 217 LEU cc_start: 0.7662 (OUTLIER) cc_final: 0.7428 (mp) outliers start: 28 outliers final: 10 residues processed: 115 average time/residue: 0.5271 time to fit residues: 64.5879 Evaluate side-chains 108 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 161 ARG Chi-restraints excluded: chain B residue 241 LYS Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 217 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 21 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 chunk 24 optimal weight: 0.0970 chunk 83 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 GLN ** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.163231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.125663 restraints weight = 9111.697| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 1.80 r_work: 0.3403 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.0535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8838 Z= 0.128 Angle : 0.535 8.473 12211 Z= 0.305 Chirality : 0.045 0.225 1381 Planarity : 0.004 0.047 1351 Dihedral : 22.848 173.676 1672 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.32 % Allowed : 25.58 % Favored : 71.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.27), residues: 895 helix: 3.11 (0.31), residues: 229 sheet: 0.23 (0.46), residues: 128 loop : 0.07 (0.25), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 148 TYR 0.011 0.001 TYR B 83 PHE 0.013 0.001 PHE C 28 TRP 0.007 0.002 TRP B 22 HIS 0.002 0.000 HIS B 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.13 ( 8838) covalent geometry : angle 0.53494 / 0.30 (12211) hydrogen bonds : bond 0.03391 / 2.25 ( 404) hydrogen bonds : angle 4.42197 / 3.01 ( 1074) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 93 time to evaluate : 0.191 Fit side-chains REVERT: A 70 LYS cc_start: 0.7436 (ptmm) cc_final: 0.7018 (ttmt) REVERT: B 161 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7660 (mtt180) REVERT: B 241 LYS cc_start: 0.7305 (OUTLIER) cc_final: 0.6626 (mtmm) REVERT: B 243 GLU cc_start: 0.7246 (tt0) cc_final: 0.6855 (mp0) REVERT: C 94 GLU cc_start: 0.7057 (mp0) cc_final: 0.6790 (mp0) REVERT: C 158 MET cc_start: 0.8254 (OUTLIER) cc_final: 0.8004 (ppp) REVERT: C 192 GLN cc_start: 0.8113 (mt0) cc_final: 0.7032 (tm-30) REVERT: C 217 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7298 (mp) REVERT: D 158 MET cc_start: 0.8663 (OUTLIER) cc_final: 0.8270 (ppp) REVERT: D 217 LEU cc_start: 0.7636 (OUTLIER) cc_final: 0.7423 (mp) REVERT: D 241 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7851 (mttm) outliers start: 27 outliers final: 10 residues processed: 109 average time/residue: 0.5358 time to fit residues: 62.1990 Evaluate side-chains 108 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 161 ARG Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 241 LYS Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 70 LYS Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 241 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 25 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 91 optimal weight: 8.9990 chunk 61 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 232 GLN ** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.161873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.125284 restraints weight = 9438.099| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.77 r_work: 0.3353 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.0836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8838 Z= 0.237 Angle : 0.613 8.541 12211 Z= 0.340 Chirality : 0.048 0.246 1381 Planarity : 0.005 0.051 1351 Dihedral : 23.066 177.940 1670 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.81 % Allowed : 25.58 % Favored : 70.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.27), residues: 895 helix: 2.75 (0.31), residues: 229 sheet: -0.06 (0.41), residues: 161 loop : 0.15 (0.26), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 148 TYR 0.012 0.002 TYR A 83 PHE 0.021 0.002 PHE C 28 TRP 0.008 0.002 TRP B 22 HIS 0.003 0.001 HIS B 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.24 ( 8838) covalent geometry : angle 0.61256 / 0.34 (12211) hydrogen bonds : bond 0.04108 / 2.71 ( 404) hydrogen bonds : angle 4.56899 / 3.13 ( 1074) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 93 time to evaluate : 0.285 Fit side-chains REVERT: A 70 LYS cc_start: 0.7479 (ptmm) cc_final: 0.7097 (ttmt) REVERT: B 161 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.7689 (mtt180) REVERT: B 164 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.7766 (tp40) REVERT: B 241 LYS cc_start: 0.7384 (OUTLIER) cc_final: 0.6667 (mtmm) REVERT: B 243 GLU cc_start: 0.7186 (tt0) cc_final: 0.6837 (mp0) REVERT: C 94 GLU cc_start: 0.7102 (mp0) cc_final: 0.6889 (mp0) REVERT: C 138 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8450 (ttmm) REVERT: C 158 MET cc_start: 0.8302 (OUTLIER) cc_final: 0.7958 (ppp) REVERT: C 192 GLN cc_start: 0.8154 (mt0) cc_final: 0.7058 (tm-30) REVERT: C 217 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7453 (mp) REVERT: C 237 ARG cc_start: 0.8071 (tpp80) cc_final: 0.7862 (tpp-160) REVERT: D 109 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7855 (tm-30) REVERT: D 158 MET cc_start: 0.8637 (OUTLIER) cc_final: 0.8246 (ppp) REVERT: D 217 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7481 (mp) outliers start: 31 outliers final: 13 residues processed: 108 average time/residue: 0.5301 time to fit residues: 60.9186 Evaluate side-chains 113 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 161 ARG Chi-restraints excluded: chain B residue 164 GLN Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 241 LYS Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 217 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 70 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 chunk 3 optimal weight: 4.9990 chunk 80 optimal weight: 0.8980 chunk 78 optimal weight: 0.0980 chunk 42 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 232 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.161726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.124217 restraints weight = 9194.979| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 1.80 r_work: 0.3379 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.0741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8838 Z= 0.146 Angle : 0.555 8.781 12211 Z= 0.312 Chirality : 0.045 0.232 1381 Planarity : 0.004 0.050 1351 Dihedral : 23.080 174.559 1670 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 4.18 % Allowed : 25.09 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.27), residues: 895 helix: 2.96 (0.31), residues: 229 sheet: -0.13 (0.42), residues: 152 loop : 0.19 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 148 TYR 0.011 0.001 TYR B 83 PHE 0.014 0.002 PHE C 28 TRP 0.008 0.002 TRP B 22 HIS 0.002 0.001 HIS A 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.15 ( 8838) covalent geometry : angle 0.55520 / 0.31 (12211) hydrogen bonds : bond 0.03412 / 2.27 ( 404) hydrogen bonds : angle 4.41443 / 3.01 ( 1074) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 93 time to evaluate : 0.186 Fit side-chains REVERT: A 70 LYS cc_start: 0.7463 (ptmm) cc_final: 0.7075 (ttmt) REVERT: B 161 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.7686 (mtt180) REVERT: B 164 GLN cc_start: 0.8778 (OUTLIER) cc_final: 0.7711 (tp40) REVERT: B 241 LYS cc_start: 0.7376 (OUTLIER) cc_final: 0.6660 (mtmm) REVERT: B 243 GLU cc_start: 0.7190 (tt0) cc_final: 0.6830 (mp0) REVERT: C 138 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8413 (ttmm) REVERT: C 158 MET cc_start: 0.8309 (OUTLIER) cc_final: 0.8050 (ppp) REVERT: C 192 GLN cc_start: 0.8123 (mt0) cc_final: 0.7049 (tm-30) REVERT: C 217 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7387 (mp) REVERT: D 109 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7813 (tm-30) REVERT: D 158 MET cc_start: 0.8619 (OUTLIER) cc_final: 0.8226 (ppp) REVERT: D 241 LYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7880 (mttm) outliers start: 34 outliers final: 10 residues processed: 113 average time/residue: 0.4948 time to fit residues: 59.4805 Evaluate side-chains 112 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 161 ARG Chi-restraints excluded: chain B residue 164 GLN Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 241 LYS Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 241 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 42 optimal weight: 0.1980 chunk 58 optimal weight: 2.9990 chunk 50 optimal weight: 0.0000 chunk 77 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.163280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.126092 restraints weight = 9136.994| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 1.79 r_work: 0.3403 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.0721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8838 Z= 0.120 Angle : 0.531 8.930 12211 Z= 0.300 Chirality : 0.045 0.229 1381 Planarity : 0.004 0.048 1351 Dihedral : 23.015 172.718 1670 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.20 % Allowed : 25.83 % Favored : 70.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.27), residues: 895 helix: 3.19 (0.30), residues: 229 sheet: -0.09 (0.42), residues: 152 loop : 0.22 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 148 TYR 0.012 0.001 TYR B 81 PHE 0.012 0.001 PHE C 28 TRP 0.008 0.002 TRP B 22 HIS 0.001 0.000 HIS A 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.12 ( 8838) covalent geometry : angle 0.53053 / 0.30 (12211) hydrogen bonds : bond 0.03143 / 2.09 ( 404) hydrogen bonds : angle 4.30760 / 2.93 ( 1074) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 96 time to evaluate : 0.312 Fit side-chains REVERT: A 70 LYS cc_start: 0.7466 (ptmm) cc_final: 0.7068 (ttmt) REVERT: B 161 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.7669 (mtt180) REVERT: B 164 GLN cc_start: 0.8765 (OUTLIER) cc_final: 0.7769 (tp40) REVERT: B 243 GLU cc_start: 0.7279 (tt0) cc_final: 0.6869 (mp0) REVERT: C 51 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8185 (mt) REVERT: C 138 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8421 (ttmm) REVERT: C 158 MET cc_start: 0.8266 (OUTLIER) cc_final: 0.7973 (ppp) REVERT: C 192 GLN cc_start: 0.8080 (mt0) cc_final: 0.7040 (tm-30) REVERT: C 217 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7349 (mp) REVERT: C 237 ARG cc_start: 0.8252 (tpp-160) cc_final: 0.7906 (tpp-160) REVERT: D 109 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7831 (tm-30) REVERT: D 158 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.8219 (ppp) outliers start: 26 outliers final: 6 residues processed: 110 average time/residue: 0.5645 time to fit residues: 65.9001 Evaluate side-chains 106 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 161 ARG Chi-restraints excluded: chain B residue 164 GLN Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 158 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 85 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 91 optimal weight: 8.9990 chunk 30 optimal weight: 0.6980 chunk 36 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 12 optimal weight: 0.3980 chunk 89 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 232 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.161818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.124085 restraints weight = 9234.863| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 1.82 r_work: 0.3378 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.0795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8838 Z= 0.164 Angle : 0.562 9.221 12211 Z= 0.314 Chirality : 0.046 0.233 1381 Planarity : 0.004 0.047 1351 Dihedral : 23.037 174.471 1668 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.08 % Allowed : 25.95 % Favored : 70.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.27), residues: 895 helix: 3.08 (0.30), residues: 229 sheet: -0.09 (0.42), residues: 157 loop : 0.23 (0.26), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 148 TYR 0.011 0.001 TYR A 83 PHE 0.017 0.002 PHE C 28 TRP 0.008 0.002 TRP B 22 HIS 0.003 0.001 HIS C 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 ( 8838) covalent geometry : angle 0.56244 / 0.31 (12211) hydrogen bonds : bond 0.03448 / 2.31 ( 404) hydrogen bonds : angle 4.36239 / 2.98 ( 1074) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 91 time to evaluate : 0.316 Fit side-chains REVERT: A 70 LYS cc_start: 0.7480 (ptmm) cc_final: 0.7088 (ttmt) REVERT: B 134 ASP cc_start: 0.7696 (m-30) cc_final: 0.6901 (OUTLIER) REVERT: B 161 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.7653 (mtt180) REVERT: B 164 GLN cc_start: 0.8771 (OUTLIER) cc_final: 0.7785 (tp40) REVERT: B 241 LYS cc_start: 0.7382 (OUTLIER) cc_final: 0.6658 (mtmm) REVERT: B 243 GLU cc_start: 0.7262 (tt0) cc_final: 0.6880 (mp0) REVERT: C 138 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8433 (ttmm) REVERT: C 158 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.7985 (ppp) REVERT: C 192 GLN cc_start: 0.8141 (mt0) cc_final: 0.7081 (tm-30) REVERT: C 217 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7382 (mp) REVERT: C 237 ARG cc_start: 0.8268 (tpp-160) cc_final: 0.8040 (tpp-160) REVERT: D 109 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7833 (tm-30) REVERT: D 158 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.8243 (ppp) outliers start: 25 outliers final: 11 residues processed: 103 average time/residue: 0.5354 time to fit residues: 58.6603 Evaluate side-chains 110 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 161 ARG Chi-restraints excluded: chain B residue 164 GLN Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 241 LYS Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 168 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 9 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 89 optimal weight: 9.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 232 GLN ** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.162332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.124788 restraints weight = 9109.036| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.81 r_work: 0.3389 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.0797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8838 Z= 0.142 Angle : 0.556 9.202 12211 Z= 0.309 Chirality : 0.045 0.231 1381 Planarity : 0.004 0.047 1351 Dihedral : 23.045 174.062 1668 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.83 % Allowed : 25.95 % Favored : 71.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.27), residues: 895 helix: 3.14 (0.30), residues: 229 sheet: -0.10 (0.42), residues: 157 loop : 0.24 (0.26), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 148 TYR 0.011 0.001 TYR B 83 PHE 0.015 0.002 PHE C 28 TRP 0.007 0.002 TRP C 22 HIS 0.002 0.001 HIS A 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 ( 8838) covalent geometry : angle 0.55579 / 0.31 (12211) hydrogen bonds : bond 0.03294 / 2.23 ( 404) hydrogen bonds : angle 4.34202 / 2.96 ( 1074) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 0.310 Fit side-chains REVERT: A 70 LYS cc_start: 0.7478 (ptmm) cc_final: 0.7083 (ttmt) REVERT: B 134 ASP cc_start: 0.7687 (m-30) cc_final: 0.6913 (OUTLIER) REVERT: B 161 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7661 (mtt180) REVERT: B 164 GLN cc_start: 0.8777 (OUTLIER) cc_final: 0.7807 (tp40) REVERT: B 241 LYS cc_start: 0.7366 (OUTLIER) cc_final: 0.6647 (mtmm) REVERT: B 243 GLU cc_start: 0.7269 (tt0) cc_final: 0.6876 (mp0) REVERT: C 51 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8140 (mt) REVERT: C 138 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8429 (ttmm) REVERT: C 158 MET cc_start: 0.8303 (OUTLIER) cc_final: 0.7957 (ppp) REVERT: C 192 GLN cc_start: 0.8109 (mt0) cc_final: 0.7065 (tm-30) REVERT: C 217 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7372 (mp) REVERT: D 109 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7834 (tm-30) REVERT: D 158 MET cc_start: 0.8619 (OUTLIER) cc_final: 0.8234 (ppp) outliers start: 23 outliers final: 10 residues processed: 103 average time/residue: 0.5810 time to fit residues: 63.4814 Evaluate side-chains 112 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 161 ARG Chi-restraints excluded: chain B residue 164 GLN Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 241 LYS Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 158 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 14 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 88 optimal weight: 9.9990 chunk 46 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 232 GLN ** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.161743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.124151 restraints weight = 9079.796| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 1.80 r_work: 0.3378 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.0839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8838 Z= 0.164 Angle : 0.571 9.425 12211 Z= 0.317 Chirality : 0.046 0.235 1381 Planarity : 0.004 0.047 1351 Dihedral : 23.078 174.708 1668 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.08 % Allowed : 25.83 % Favored : 71.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.27), residues: 895 helix: 3.05 (0.30), residues: 229 sheet: -0.13 (0.42), residues: 152 loop : 0.20 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 148 TYR 0.011 0.001 TYR B 83 PHE 0.016 0.002 PHE C 28 TRP 0.007 0.002 TRP B 22 HIS 0.002 0.001 HIS C 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 ( 8838) covalent geometry : angle 0.57116 / 0.32 (12211) hydrogen bonds : bond 0.03440 / 2.33 ( 404) hydrogen bonds : angle 4.37055 / 2.98 ( 1074) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 94 time to evaluate : 0.328 Fit side-chains REVERT: A 70 LYS cc_start: 0.7479 (ptmm) cc_final: 0.7089 (ttmt) REVERT: B 134 ASP cc_start: 0.7706 (m-30) cc_final: 0.6922 (OUTLIER) REVERT: B 161 ARG cc_start: 0.7956 (OUTLIER) cc_final: 0.7682 (mtt180) REVERT: B 164 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.7797 (tp40) REVERT: B 241 LYS cc_start: 0.7386 (OUTLIER) cc_final: 0.6661 (mtmm) REVERT: B 243 GLU cc_start: 0.7234 (tt0) cc_final: 0.6865 (mp0) REVERT: C 138 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8436 (ttmm) REVERT: C 158 MET cc_start: 0.8331 (OUTLIER) cc_final: 0.7992 (ppp) REVERT: C 192 GLN cc_start: 0.8127 (mt0) cc_final: 0.7067 (tm-30) REVERT: C 217 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7397 (mp) REVERT: C 237 ARG cc_start: 0.8093 (tpp-160) cc_final: 0.7797 (ttp-170) REVERT: D 97 LYS cc_start: 0.7844 (mmtt) cc_final: 0.7563 (tppt) REVERT: D 109 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7842 (tm-30) REVERT: D 158 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.8240 (ppp) outliers start: 25 outliers final: 11 residues processed: 107 average time/residue: 0.5786 time to fit residues: 65.8152 Evaluate side-chains 109 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 161 ARG Chi-restraints excluded: chain B residue 164 GLN Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 241 LYS Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 158 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 65 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 22 optimal weight: 0.5980 chunk 46 optimal weight: 0.3980 chunk 23 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 232 GLN ** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.161989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.124314 restraints weight = 9115.596| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.81 r_work: 0.3382 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.0860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8838 Z= 0.151 Angle : 0.567 9.576 12211 Z= 0.314 Chirality : 0.046 0.234 1381 Planarity : 0.004 0.047 1351 Dihedral : 23.080 174.537 1668 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.34 % Allowed : 26.57 % Favored : 71.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.27), residues: 895 helix: 3.08 (0.30), residues: 229 sheet: -0.14 (0.42), residues: 152 loop : 0.20 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 148 TYR 0.013 0.001 TYR B 81 PHE 0.015 0.002 PHE C 28 TRP 0.007 0.002 TRP B 22 HIS 0.002 0.001 HIS A 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 ( 8838) covalent geometry : angle 0.56733 / 0.31 (12211) hydrogen bonds : bond 0.03362 / 2.29 ( 404) hydrogen bonds : angle 4.36108 / 2.97 ( 1074) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.272 Fit side-chains REVERT: A 70 LYS cc_start: 0.7480 (ptmm) cc_final: 0.7089 (ttmt) REVERT: B 134 ASP cc_start: 0.7719 (m-30) cc_final: 0.6920 (OUTLIER) REVERT: B 161 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.7667 (mtt180) REVERT: B 164 GLN cc_start: 0.8777 (OUTLIER) cc_final: 0.7806 (tp40) REVERT: B 241 LYS cc_start: 0.7392 (OUTLIER) cc_final: 0.6667 (mtmm) REVERT: B 243 GLU cc_start: 0.7272 (tt0) cc_final: 0.6885 (mp0) REVERT: C 138 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8429 (ttmm) REVERT: C 158 MET cc_start: 0.8321 (OUTLIER) cc_final: 0.7981 (ppp) REVERT: C 192 GLN cc_start: 0.8120 (mt0) cc_final: 0.7064 (tm-30) REVERT: C 217 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7409 (mp) REVERT: D 97 LYS cc_start: 0.7847 (mmtt) cc_final: 0.7645 (ttpp) REVERT: D 109 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7844 (tm-30) REVERT: D 158 MET cc_start: 0.8631 (OUTLIER) cc_final: 0.8243 (ppp) REVERT: D 217 LEU cc_start: 0.7607 (OUTLIER) cc_final: 0.7320 (mp) outliers start: 19 outliers final: 11 residues processed: 99 average time/residue: 0.6089 time to fit residues: 64.0139 Evaluate side-chains 111 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 161 ARG Chi-restraints excluded: chain B residue 164 GLN Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 241 LYS Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 217 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 57 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 chunk 16 optimal weight: 0.0670 chunk 32 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 91 optimal weight: 8.9990 chunk 9 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 232 GLN ** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.158434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.120720 restraints weight = 9102.294| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.79 r_work: 0.3364 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.0939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8838 Z= 0.194 Angle : 0.598 9.674 12211 Z= 0.330 Chirality : 0.047 0.242 1381 Planarity : 0.004 0.049 1351 Dihedral : 23.159 176.456 1668 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.58 % Allowed : 26.45 % Favored : 70.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.27), residues: 895 helix: 2.90 (0.30), residues: 229 sheet: -0.07 (0.41), residues: 161 loop : 0.16 (0.26), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 188 TYR 0.011 0.001 TYR A 83 PHE 0.018 0.002 PHE C 28 TRP 0.008 0.002 TRP B 22 HIS 0.002 0.001 HIS B 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.19 ( 8838) covalent geometry : angle 0.59759 / 0.33 (12211) hydrogen bonds : bond 0.03722 / 2.51 ( 404) hydrogen bonds : angle 4.44521 / 3.04 ( 1074) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2885.75 seconds wall clock time: 49 minutes 47.66 seconds (2987.66 seconds total)