Starting phenix.real_space_refine on Thu Jul 2 12:59:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vnq_65215/07_2026/9vnq_65215.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vnq_65215/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9vnq_65215/07_2026/9vnq_65215.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vnq_65215/07_2026/9vnq_65215.map" model { file = "/net/cci-nas-00/data/ceres_data/9vnq_65215/07_2026/9vnq_65215.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vnq_65215/07_2026/9vnq_65215.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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: 1.62, per 1000 atoms: 0.19 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: 0.67 Conformation dependent library (CDL) restraints added in 345.3 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: 1.02 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: 1.32 Time building geometry restraints manager: 0.91 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: 11977 1.99 - 3.98: 231 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: 4.340 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: 0.020 Extract box with map and model: 0.130 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 9.190 Find NCS groups from input model: 0.140 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:6.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.040 ------------------------------------------------------------------------------- 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 : 0.567 9.952 12211 Z= 0.436 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 0.56709 / 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 : 0.197 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: 0.5518 time to fit residues: 53.9609 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 : 0.335 ------------------------------------------------------------------------------- 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 = 0.163751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.127135 restraints weight = 9390.538| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.77 r_work: 0.3379 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.0504 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= 0.179 Angle : 0.562 8.617 12211 Z= 0.320 Chirality : 0.046 0.209 1381 Planarity : 0.004 0.051 1351 Dihedral : 22.763 174.216 1684 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.32 % Allowed : 25.83 % 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: 1.20 (0.27), residues: 895 helix: 2.92 (0.31), residues: 229 sheet: 0.18 (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 0.013 0.001 TYR B 81 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 0.00390 / 0.18 ( 8838) covalent geometry : angle 0.56193 / 0.32 (12211) hydrogen bonds : bond 0.03836 / 2.54 ( 404) hydrogen bonds : angle 4.55685 / 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 122 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 95 time to evaluate : 0.229 Fit side-chains REVERT: A 70 LYS cc_start: 0.7460 (ptmm) cc_final: 0.7048 (ttmt) REVERT: B 161 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7656 (mtt180) REVERT: B 241 LYS cc_start: 0.7360 (OUTLIER) cc_final: 0.6696 (mtmm) REVERT: B 243 GLU cc_start: 0.7251 (tt0) cc_final: 0.6814 (mm-30) REVERT: C 94 GLU cc_start: 0.7068 (mp0) cc_final: 0.6829 (mp0) REVERT: C 192 GLN cc_start: 0.8144 (mt0) cc_final: 0.7067 (tm-30) REVERT: C 217 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7321 (mp) REVERT: D 217 LEU cc_start: 0.7662 (OUTLIER) cc_final: 0.7431 (mp) outliers start: 27 outliers final: 10 residues processed: 113 average time/residue: 0.5081 time to fit residues: 60.9721 Evaluate side-chains 109 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.183 ------------------------------------------------------------------------------- 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 208 GLN 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 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: 5.9990 chunk 13 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 = 0.3926 r_free = 0.3926 target = 0.161578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.125146 restraints weight = 9292.324| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.76 r_work: 0.3350 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.0789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 8838 Z= 0.252 Angle : 0.622 8.706 12211 Z= 0.348 Chirality : 0.049 0.231 1381 Planarity : 0.005 0.053 1351 Dihedral : 23.065 177.564 1670 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 4.31 % Allowed : 24.97 % 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: 1.03 (0.27), residues: 895 helix: 2.64 (0.31), residues: 229 sheet: 0.21 (0.44), residues: 137 loop : -0.02 (0.25), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 188 TYR 0.012 0.002 TYR D 83 PHE 0.020 0.002 PHE C 28 TRP 0.009 0.002 TRP B 22 HIS 0.003 0.001 HIS C 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00585 / 0.25 ( 8838) covalent geometry : angle 0.62193 / 0.35 (12211) hydrogen bonds : bond 0.04324 / 2.85 ( 404) hydrogen bonds : angle 4.62324 / 3.17 ( 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 130 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 95 time to evaluate : 0.259 Fit side-chains REVERT: A 70 LYS cc_start: 0.7485 (ptmm) cc_final: 0.7104 (ttmt) REVERT: B 158 MET cc_start: 0.8499 (OUTLIER) cc_final: 0.7767 (ppp) REVERT: B 161 ARG cc_start: 0.7956 (OUTLIER) cc_final: 0.7668 (mtt180) REVERT: B 164 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.7770 (tp40) REVERT: B 241 LYS cc_start: 0.7390 (OUTLIER) cc_final: 0.6667 (mtmm) REVERT: B 243 GLU cc_start: 0.7151 (tt0) cc_final: 0.6803 (mp0) REVERT: C 94 GLU cc_start: 0.7085 (mp0) cc_final: 0.6814 (mp0) REVERT: C 138 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8451 (ttmm) REVERT: C 158 MET cc_start: 0.8282 (OUTLIER) cc_final: 0.7923 (ppp) REVERT: C 192 GLN cc_start: 0.8145 (mt0) cc_final: 0.7043 (tm-30) REVERT: C 217 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7458 (mp) REVERT: D 109 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7873 (tm-30) REVERT: D 158 MET cc_start: 0.8656 (OUTLIER) cc_final: 0.8241 (ppp) REVERT: D 217 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.7485 (mp) outliers start: 35 outliers final: 12 residues processed: 116 average time/residue: 0.5316 time to fit residues: 65.2173 Evaluate side-chains 115 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 158 MET 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 18 MET Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 68 CYS Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 119 ILE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 25 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 9 optimal weight: 0.1980 chunk 35 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 91 optimal weight: 7.9990 chunk 61 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 = 0.3940 r_free = 0.3940 target = 0.162813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.126242 restraints weight = 9441.006| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.77 r_work: 0.3374 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.0794 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= 0.179 Angle : 0.573 8.675 12211 Z= 0.323 Chirality : 0.046 0.218 1381 Planarity : 0.004 0.052 1351 Dihedral : 23.133 174.718 1668 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.44 % Allowed : 26.20 % 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: 1.13 (0.27), residues: 895 helix: 2.77 (0.31), residues: 229 sheet: -0.11 (0.42), residues: 152 loop : 0.16 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 188 TYR 0.011 0.001 TYR D 83 PHE 0.015 0.002 PHE C 28 TRP 0.009 0.002 TRP B 22 HIS 0.002 0.001 HIS A 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.18 ( 8838) covalent geometry : angle 0.57322 / 0.32 (12211) hydrogen bonds : bond 0.03649 / 2.42 ( 404) hydrogen bonds : angle 4.49358 / 3.07 ( 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 123 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 95 time to evaluate : 0.303 Fit side-chains revert: symmetry clash REVERT: A 70 LYS cc_start: 0.7476 (ptmm) cc_final: 0.7094 (ttmt) REVERT: B 161 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.7694 (mtt180) REVERT: B 241 LYS cc_start: 0.7418 (OUTLIER) cc_final: 0.6701 (mtmm) REVERT: B 243 GLU cc_start: 0.7122 (tt0) cc_final: 0.6781 (mp0) REVERT: C 138 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8432 (ttmm) REVERT: C 158 MET cc_start: 0.8274 (OUTLIER) cc_final: 0.7986 (ppp) REVERT: C 192 GLN cc_start: 0.8141 (mt0) cc_final: 0.7058 (tm-30) REVERT: C 217 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7407 (mp) REVERT: D 109 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7853 (tm-30) REVERT: D 158 MET cc_start: 0.8607 (OUTLIER) cc_final: 0.8221 (ppp) REVERT: D 217 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7482 (mp) REVERT: D 241 LYS cc_start: 0.8148 (OUTLIER) cc_final: 0.7895 (mttm) outliers start: 28 outliers final: 9 residues processed: 111 average time/residue: 0.5539 time to fit residues: 65.2458 Evaluate side-chains 114 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.302 ------------------------------------------------------------------------------- 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 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 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 119 ILE Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 241 LYS 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: 1.9990 chunk 58 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 88 optimal weight: 10.0000 chunk 3 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 chunk 42 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.3943 r_free = 0.3943 target = 0.163123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.126673 restraints weight = 9341.082| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 1.77 r_work: 0.3373 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.0788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8838 Z= 0.165 Angle : 0.561 8.879 12211 Z= 0.317 Chirality : 0.046 0.216 1381 Planarity : 0.004 0.051 1351 Dihedral : 23.142 174.134 1668 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 4.55 % Allowed : 24.97 % Favored : 70.48 % 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: 2.91 (0.31), residues: 229 sheet: -0.12 (0.42), residues: 152 loop : 0.17 (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 0.015 0.002 PHE C 28 TRP 0.009 0.002 TRP B 22 HIS 0.002 0.001 HIS C 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.17 ( 8838) covalent geometry : angle 0.56132 / 0.32 (12211) hydrogen bonds : bond 0.03521 / 2.34 ( 404) hydrogen bonds : angle 4.43229 / 3.03 ( 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 134 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 97 time to evaluate : 0.187 Fit side-chains REVERT: A 70 LYS cc_start: 0.7473 (ptmm) cc_final: 0.7094 (ttmt) REVERT: B 161 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.7684 (mtt180) REVERT: B 164 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.7703 (tp40) REVERT: B 241 LYS cc_start: 0.7403 (OUTLIER) cc_final: 0.6683 (mtmm) REVERT: B 243 GLU cc_start: 0.7151 (tt0) cc_final: 0.6813 (mp0) REVERT: C 138 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8435 (ttmm) REVERT: C 158 MET cc_start: 0.8304 (OUTLIER) cc_final: 0.8008 (ppp) REVERT: C 192 GLN cc_start: 0.8110 (mt0) cc_final: 0.7050 (tm-30) REVERT: C 217 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7401 (mp) REVERT: C 237 ARG cc_start: 0.8262 (tpp-160) cc_final: 0.8000 (tpp-160) REVERT: D 109 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7862 (tm-30) REVERT: D 158 MET cc_start: 0.8631 (OUTLIER) cc_final: 0.8223 (ppp) REVERT: D 241 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7894 (mttm) outliers start: 37 outliers final: 10 residues processed: 120 average time/residue: 0.5141 time to fit residues: 65.3564 Evaluate side-chains 116 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.312 ------------------------------------------------------------------------------- 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 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 119 ILE 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: 0.0270 chunk 58 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 52 optimal weight: 0.0870 chunk 33 optimal weight: 0.1980 chunk 46 optimal weight: 0.0670 chunk 22 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 overall best weight: 0.2154 ------------------------------------------------------------------------------- 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 = 0.3939 r_free = 0.3939 target = 0.162848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.125433 restraints weight = 9146.891| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 1.80 r_work: 0.3431 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.0731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8838 Z= 0.104 Angle : 0.515 8.874 12211 Z= 0.294 Chirality : 0.044 0.220 1381 Planarity : 0.004 0.047 1351 Dihedral : 23.051 169.511 1668 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.71 % Allowed : 26.81 % Favored : 70.48 % 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: 1.41 (0.27), residues: 895 helix: 3.36 (0.30), residues: 229 sheet: -0.23 (0.42), residues: 155 loop : 0.26 (0.26), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 144 TYR 0.012 0.001 TYR B 81 PHE 0.009 0.001 PHE C 28 TRP 0.007 0.001 TRP D 22 HIS 0.004 0.000 HIS C 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00182 / 0.10 ( 8838) covalent geometry : angle 0.51464 / 0.29 (12211) hydrogen bonds : bond 0.03007 / 1.98 ( 404) hydrogen bonds : angle 4.25843 / 2.89 ( 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 124 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.223 Fit side-chains REVERT: A 70 LYS cc_start: 0.7466 (ptmm) cc_final: 0.7058 (ttmt) REVERT: B 164 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.7751 (tp40) REVERT: B 243 GLU cc_start: 0.7239 (tt0) cc_final: 0.6843 (mp0) REVERT: C 192 GLN cc_start: 0.8057 (mt0) cc_final: 0.7043 (tm-30) REVERT: C 217 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7274 (mp) REVERT: D 158 MET cc_start: 0.8625 (OUTLIER) cc_final: 0.8256 (ppp) REVERT: D 241 LYS cc_start: 0.8059 (OUTLIER) cc_final: 0.7830 (mttm) outliers start: 22 outliers final: 5 residues processed: 113 average time/residue: 0.5000 time to fit residues: 60.1816 Evaluate side-chains 102 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 93 time to evaluate : 0.290 ------------------------------------------------------------------------------- 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 164 GLN Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 241 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 85 optimal weight: 0.7980 chunk 31 optimal weight: 0.1980 chunk 91 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 6 optimal weight: 0.0870 chunk 12 optimal weight: 0.6980 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: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 56 HIS ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.164005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.126659 restraints weight = 9202.304| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 1.80 r_work: 0.3417 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.0735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8838 Z= 0.117 Angle : 0.519 9.091 12211 Z= 0.295 Chirality : 0.044 0.212 1381 Planarity : 0.004 0.045 1351 Dihedral : 22.999 170.470 1668 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.34 % Allowed : 27.43 % Favored : 70.23 % 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: 1.50 (0.27), residues: 895 helix: 3.40 (0.30), residues: 229 sheet: -0.06 (0.42), residues: 152 loop : 0.29 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 148 TYR 0.011 0.001 TYR B 83 PHE 0.013 0.001 PHE C 28 TRP 0.007 0.001 TRP B 22 HIS 0.004 0.001 HIS B 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.12 ( 8838) covalent geometry : angle 0.51855 / 0.29 (12211) hydrogen bonds : bond 0.03015 / 2.01 ( 404) hydrogen bonds : angle 4.21744 / 2.86 ( 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: 19 poor density : 97 time to evaluate : 0.365 Fit side-chains REVERT: A 70 LYS cc_start: 0.7468 (ptmm) cc_final: 0.7058 (ttmt) REVERT: B 161 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.7600 (mtt180) REVERT: B 243 GLU cc_start: 0.7287 (tt0) cc_final: 0.6875 (mp0) REVERT: C 192 GLN cc_start: 0.8066 (mt0) cc_final: 0.7090 (tm-30) REVERT: C 217 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7314 (mp) REVERT: D 158 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.8267 (ppp) outliers start: 19 outliers final: 4 residues processed: 104 average time/residue: 0.5754 time to fit residues: 63.7303 Evaluate side-chains 102 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 95 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 C residue 213 LEU Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 158 MET 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: 3.9990 chunk 32 optimal weight: 0.6980 chunk 80 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 87 optimal weight: 0.7980 chunk 89 optimal weight: 9.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3921 r_free = 0.3921 target = 0.161251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.123784 restraints weight = 9120.397| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 1.79 r_work: 0.3409 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.0813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8838 Z= 0.132 Angle : 0.524 9.216 12211 Z= 0.297 Chirality : 0.044 0.213 1381 Planarity : 0.004 0.046 1351 Dihedral : 23.043 171.637 1666 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.71 % Allowed : 26.94 % 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: 1.48 (0.27), residues: 895 helix: 3.34 (0.30), residues: 229 sheet: -0.06 (0.42), residues: 152 loop : 0.29 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 237 TYR 0.011 0.001 TYR B 83 PHE 0.014 0.002 PHE C 28 TRP 0.007 0.002 TRP B 22 HIS 0.002 0.001 HIS B 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 ( 8838) covalent geometry : angle 0.52423 / 0.30 (12211) hydrogen bonds : bond 0.03102 / 2.08 ( 404) hydrogen bonds : angle 4.23315 / 2.87 ( 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: 22 poor density : 95 time to evaluate : 0.263 Fit side-chains REVERT: A 70 LYS cc_start: 0.7471 (ptmm) cc_final: 0.7062 (ttmt) REVERT: B 161 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.7619 (mtt180) REVERT: B 243 GLU cc_start: 0.7290 (tt0) cc_final: 0.6873 (mp0) REVERT: C 192 GLN cc_start: 0.8058 (mt0) cc_final: 0.7071 (tm-30) REVERT: C 217 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7302 (mp) REVERT: D 95 ASP cc_start: 0.7336 (m-30) cc_final: 0.7125 (t0) REVERT: D 97 LYS cc_start: 0.7963 (ttpp) cc_final: 0.7637 (mptt) REVERT: D 109 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7785 (tm-30) REVERT: D 158 MET cc_start: 0.8653 (OUTLIER) cc_final: 0.8261 (ppp) outliers start: 22 outliers final: 10 residues processed: 103 average time/residue: 0.4927 time to fit residues: 53.9999 Evaluate side-chains 109 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.195 ------------------------------------------------------------------------------- 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 134 ASP Chi-restraints excluded: chain B residue 161 ARG Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain C residue 97 LYS 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: 0.0980 chunk 79 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 68 optimal weight: 3.9990 chunk 88 optimal weight: 9.9990 chunk 46 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3954 r_free = 0.3954 target = 0.163746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.126094 restraints weight = 9051.653| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 1.81 r_work: 0.3409 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.0814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8838 Z= 0.125 Angle : 0.524 9.304 12211 Z= 0.297 Chirality : 0.044 0.212 1381 Planarity : 0.004 0.045 1351 Dihedral : 23.047 171.310 1666 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.85 % Allowed : 27.68 % Favored : 70.48 % 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: 1.48 (0.27), residues: 895 helix: 3.35 (0.30), residues: 229 sheet: -0.08 (0.42), residues: 152 loop : 0.30 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 237 TYR 0.011 0.001 TYR B 83 PHE 0.013 0.001 PHE C 28 TRP 0.007 0.001 TRP B 22 HIS 0.002 0.000 HIS A 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.13 ( 8838) covalent geometry : angle 0.52384 / 0.30 (12211) hydrogen bonds : bond 0.03012 / 2.02 ( 404) hydrogen bonds : angle 4.22297 / 2.86 ( 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 110 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.211 Fit side-chains REVERT: A 70 LYS cc_start: 0.7473 (ptmm) cc_final: 0.7064 (ttmt) REVERT: B 161 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.7606 (mtt180) REVERT: B 243 GLU cc_start: 0.7295 (tt0) cc_final: 0.6877 (mp0) REVERT: C 192 GLN cc_start: 0.8068 (mt0) cc_final: 0.7086 (tm-30) REVERT: C 217 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7338 (mp) REVERT: D 95 ASP cc_start: 0.7356 (m-30) cc_final: 0.7019 (t0) REVERT: D 97 LYS cc_start: 0.7916 (ttpp) cc_final: 0.7599 (mptt) REVERT: D 158 MET cc_start: 0.8643 (OUTLIER) cc_final: 0.8261 (ppp) outliers start: 15 outliers final: 9 residues processed: 101 average time/residue: 0.4968 time to fit residues: 53.2626 Evaluate side-chains 105 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.205 ------------------------------------------------------------------------------- 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 134 ASP Chi-restraints excluded: chain B residue 161 ARG Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain C residue 97 LYS 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 158 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 65 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 87 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.3958 r_free = 0.3958 target = 0.164447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.128341 restraints weight = 9275.459| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.73 r_work: 0.3394 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.0877 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= 0.160 Angle : 0.548 9.415 12211 Z= 0.308 Chirality : 0.045 0.214 1381 Planarity : 0.004 0.046 1351 Dihedral : 23.100 173.143 1666 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.48 % Allowed : 28.04 % Favored : 70.48 % 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: 1.39 (0.27), residues: 895 helix: 3.19 (0.31), residues: 229 sheet: -0.11 (0.43), residues: 151 loop : 0.27 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 237 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 B 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 ( 8838) covalent geometry : angle 0.54784 / 0.31 (12211) hydrogen bonds : bond 0.03284 / 2.20 ( 404) hydrogen bonds : angle 4.29431 / 2.92 ( 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 106 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.187 Fit side-chains REVERT: A 70 LYS cc_start: 0.7506 (ptmm) cc_final: 0.7103 (ttmt) REVERT: B 161 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7641 (mtt180) REVERT: B 243 GLU cc_start: 0.7272 (tt0) cc_final: 0.6893 (mp0) REVERT: C 192 GLN cc_start: 0.8073 (mt0) cc_final: 0.7100 (tm-30) REVERT: C 217 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7397 (mp) REVERT: D 97 LYS cc_start: 0.7996 (ttpp) cc_final: 0.7677 (mptt) REVERT: D 109 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7785 (tm-30) REVERT: D 158 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.8265 (ppp) outliers start: 12 outliers final: 7 residues processed: 99 average time/residue: 0.5174 time to fit residues: 54.4468 Evaluate side-chains 105 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.184 ------------------------------------------------------------------------------- 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 161 ARG Chi-restraints excluded: chain B residue 189 SER 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 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 57 optimal weight: 2.9990 chunk 90 optimal weight: 9.9990 chunk 5 optimal weight: 0.9980 chunk 16 optimal weight: 0.0010 chunk 32 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 91 optimal weight: 7.9990 chunk 9 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 overall best weight: 0.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 164 GLN B 232 GLN ** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.164626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.128486 restraints weight = 9202.803| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 1.75 r_work: 0.3399 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.0869 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= 0.145 Angle : 0.547 9.466 12211 Z= 0.307 Chirality : 0.045 0.214 1381 Planarity : 0.004 0.058 1351 Dihedral : 23.110 173.010 1666 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.72 % Allowed : 27.92 % 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: 1.41 (0.27), residues: 895 helix: 3.18 (0.30), residues: 229 sheet: 0.02 (0.42), residues: 159 loop : 0.26 (0.26), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 237 TYR 0.011 0.001 TYR B 83 PHE 0.015 0.002 PHE C 28 TRP 0.007 0.002 TRP B 22 HIS 0.003 0.001 HIS C 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.15 ( 8838) covalent geometry : angle 0.54735 / 0.31 (12211) hydrogen bonds : bond 0.03189 / 2.14 ( 404) hydrogen bonds : angle 4.29565 / 2.92 ( 1074) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2783.15 seconds wall clock time: 48 minutes 3.71 seconds (2883.71 seconds total)