Starting phenix.real_space_refine on Thu Jul 2 21:33:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cbo_16547/07_2026/8cbo_16547.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cbo_16547/07_2026/8cbo_16547.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cbo_16547/07_2026/8cbo_16547.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cbo_16547/07_2026/8cbo_16547.map" model { file = "/net/cci-nas-00/data/ceres_data/8cbo_16547/07_2026/8cbo_16547.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cbo_16547/07_2026/8cbo_16547.cif" } resolution = 3.2 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= 0.002 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 66 5.49 5 S 44 5.16 5 C 6431 2.51 5 N 1856 2.21 5 O 2177 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 10574 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1848 Classifications: {'peptide': 255} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 241} Chain: "B" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1848 Classifications: {'peptide': 255} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 241} Chain: "C" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1848 Classifications: {'peptide': 255} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 241} Chain: "D" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1848 Classifications: {'peptide': 255} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 241} Chain: "E" Number of atoms: 1747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1747 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 7, 'TRANS': 203} Chain: "T" Number of atoms: 1233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 1233 Classifications: {'RNA': 58} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 5, 'rna3p_pur': 23, 'rna3p_pyr': 22} Link IDs: {'rna2p': 13, 'rna3p': 44} Chain breaks: 2 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Time building chain proxies: 2.44, per 1000 atoms: 0.23 Number of scatterers: 10574 At special positions: 0 Unit cell: (95.436, 87.483, 133.755, 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 44 16.00 P 66 15.00 O 2177 8.00 N 1856 7.00 C 6431 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: 0.83 Conformation dependent library (CDL) restraints added in 246.6 milliseconds 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2196 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 9 sheets defined 51.5% alpha, 10.4% beta 14 base pairs and 25 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 20 through 34 Processing helix chain 'A' and resid 42 through 45 Processing helix chain 'A' and resid 46 through 55 removed outlier: 4.180A pdb=" N GLN A 50 " --> pdb=" O GLY A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 83 Processing helix chain 'A' and resid 110 through 138 removed outlier: 3.529A pdb=" N PHE A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N MET A 123 " --> pdb=" O ASP A 119 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLY A 124 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY A 134 " --> pdb=" O ARG A 130 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLU A 135 " --> pdb=" O LEU A 131 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN A 138 " --> pdb=" O GLY A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 161 Processing helix chain 'A' and resid 165 through 186 removed outlier: 4.457A pdb=" N LEU A 180 " --> pdb=" O VAL A 176 " (cutoff:3.500A) Proline residue: A 181 - end of helix Processing helix chain 'A' and resid 203 through 208 removed outlier: 4.122A pdb=" N SER A 208 " --> pdb=" O LEU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 220 Processing helix chain 'A' and resid 229 through 243 removed outlier: 3.573A pdb=" N TYR A 233 " --> pdb=" O ASP A 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 33 Processing helix chain 'B' and resid 46 through 55 removed outlier: 4.126A pdb=" N GLN B 50 " --> pdb=" O GLY B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 83 Processing helix chain 'B' and resid 110 through 139 removed outlier: 3.797A pdb=" N MET B 123 " --> pdb=" O ASP B 119 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY B 124 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLY B 134 " --> pdb=" O ARG B 130 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLU B 135 " --> pdb=" O LEU B 131 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN B 139 " --> pdb=" O GLU B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 159 Processing helix chain 'B' and resid 165 through 186 removed outlier: 4.583A pdb=" N LEU B 180 " --> pdb=" O VAL B 176 " (cutoff:3.500A) Proline residue: B 181 - end of helix Processing helix chain 'B' and resid 203 through 208 removed outlier: 4.067A pdb=" N SER B 208 " --> pdb=" O LEU B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 221 Processing helix chain 'B' and resid 229 through 243 removed outlier: 3.524A pdb=" N TYR B 233 " --> pdb=" O ASP B 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 33 Processing helix chain 'C' and resid 42 through 45 Processing helix chain 'C' and resid 46 through 55 removed outlier: 3.867A pdb=" N GLN C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 83 Processing helix chain 'C' and resid 110 through 122 removed outlier: 3.661A pdb=" N PHE C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 137 Processing helix chain 'C' and resid 156 through 161 Processing helix chain 'C' and resid 165 through 186 removed outlier: 4.576A pdb=" N LEU C 180 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Proline residue: C 181 - end of helix Processing helix chain 'C' and resid 210 through 221 removed outlier: 3.642A pdb=" N VAL C 221 " --> pdb=" O LEU C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 243 Processing helix chain 'D' and resid 21 through 33 Processing helix chain 'D' and resid 46 through 55 removed outlier: 3.622A pdb=" N GLN D 50 " --> pdb=" O GLY D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 83 Processing helix chain 'D' and resid 110 through 138 removed outlier: 3.570A pdb=" N PHE D 114 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N MET D 123 " --> pdb=" O ASP D 119 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY D 124 " --> pdb=" O VAL D 120 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLN D 138 " --> pdb=" O GLY D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 159 Processing helix chain 'D' and resid 165 through 187 removed outlier: 4.511A pdb=" N LEU D 180 " --> pdb=" O VAL D 176 " (cutoff:3.500A) Proline residue: D 181 - end of helix Processing helix chain 'D' and resid 203 through 208 removed outlier: 3.556A pdb=" N SER D 208 " --> pdb=" O PRO D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 221 Processing helix chain 'D' and resid 229 through 243 Processing helix chain 'E' and resid 182 through 202 removed outlier: 3.707A pdb=" N GLN E 200 " --> pdb=" O ALA E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 236 Processing helix chain 'E' and resid 252 through 263 Processing helix chain 'E' and resid 264 through 268 removed outlier: 3.976A pdb=" N ASP E 267 " --> pdb=" O GLU E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 281 Processing helix chain 'E' and resid 283 through 285 No H-bonds generated for 'chain 'E' and resid 283 through 285' Processing helix chain 'E' and resid 320 through 329 Processing helix chain 'E' and resid 337 through 342 removed outlier: 3.577A pdb=" N TYR E 341 " --> pdb=" O PRO E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 352 through 364 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 374 through 376 No H-bonds generated for 'chain 'E' and resid 374 through 376' Processing helix chain 'E' and resid 377 through 381 Processing sheet with id=AA1, first strand: chain 'A' and resid 58 through 60 removed outlier: 6.837A pdb=" N ALA A 13 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N LEU A 40 " --> pdb=" O ALA A 13 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE A 15 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ALA A 88 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N THR A 153 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N ASN A 90 " --> pdb=" O THR A 153 " (cutoff:3.500A) removed outlier: 9.131A pdb=" N ILE A 251 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N THR A 195 " --> pdb=" O ILE A 251 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 102 Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62 removed outlier: 6.290A pdb=" N ALA B 37 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N ALA B 61 " --> pdb=" O ALA B 37 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N LEU B 39 " --> pdb=" O ALA B 61 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ALA B 13 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N LEU B 40 " --> pdb=" O ALA B 13 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE B 15 " --> pdb=" O LEU B 40 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N GLY B 148 " --> pdb=" O ARG B 192 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N MET B 194 " --> pdb=" O GLY B 148 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ILE B 150 " --> pdb=" O MET B 194 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N ILE B 196 " --> pdb=" O ILE B 150 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ASN B 152 " --> pdb=" O ILE B 196 " (cutoff:3.500A) removed outlier: 8.946A pdb=" N ILE B 251 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N THR B 195 " --> pdb=" O ILE B 251 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 101 through 102 Processing sheet with id=AA5, first strand: chain 'C' and resid 58 through 62 removed outlier: 6.315A pdb=" N ALA C 37 " --> pdb=" O VAL C 59 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ALA C 61 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU C 39 " --> pdb=" O ALA C 61 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL C 12 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N VAL C 89 " --> pdb=" O VAL C 12 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL C 14 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ALA C 88 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N THR C 153 " --> pdb=" O ALA C 88 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N ASN C 90 " --> pdb=" O THR C 153 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE C 196 " --> pdb=" O ASN C 152 " (cutoff:3.500A) removed outlier: 9.090A pdb=" N ILE C 251 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N THR C 195 " --> pdb=" O ILE C 251 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 Processing sheet with id=AA7, first strand: chain 'D' and resid 58 through 60 removed outlier: 6.435A pdb=" N ALA D 37 " --> pdb=" O VAL D 59 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ALA D 13 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N LEU D 40 " --> pdb=" O ALA D 13 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE D 15 " --> pdb=" O LEU D 40 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N VAL D 12 " --> pdb=" O VAL D 87 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N VAL D 89 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL D 14 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ALA D 88 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N THR D 153 " --> pdb=" O ALA D 88 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N ASN D 90 " --> pdb=" O THR D 153 " (cutoff:3.500A) removed outlier: 9.147A pdb=" N ILE D 251 " --> pdb=" O VAL D 193 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N THR D 195 " --> pdb=" O ILE D 251 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 101 through 102 Processing sheet with id=AA9, first strand: chain 'E' and resid 272 through 274 removed outlier: 6.313A pdb=" N LEU E 205 " --> pdb=" O TYR E 244 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N CYS E 246 " --> pdb=" O LEU E 205 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N PHE E 207 " --> pdb=" O CYS E 246 " (cutoff:3.500A) removed outlier: 8.535A pdb=" N ILE E 309 " --> pdb=" O PRO E 204 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL E 206 " --> pdb=" O ILE E 309 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE E 288 " --> pdb=" O VAL E 308 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA E 332 " --> pdb=" O ILE E 287 " (cutoff:3.500A) 445 hydrogen bonds defined for protein. 1269 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 34 hydrogen bonds 68 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 25 stacking parallelities Total time for adding SS restraints: 1.38 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2285 1.33 - 1.45: 2455 1.45 - 1.57: 5939 1.57 - 1.69: 129 1.69 - 1.81: 73 Bond restraints: 10881 Sorted by residual: bond pdb=" C GLY E 320 " pdb=" N THR E 321 " ideal model delta sigma weight residual 1.332 1.418 -0.086 1.40e-02 5.10e+03 3.78e+01 bond pdb=" C GLY B 202 " pdb=" N THR B 203 " ideal model delta sigma weight residual 1.327 1.272 0.054 1.19e-02 7.06e+03 2.09e+01 bond pdb=" CA SER E 322 " pdb=" CB SER E 322 " ideal model delta sigma weight residual 1.529 1.458 0.072 1.58e-02 4.01e+03 2.06e+01 bond pdb=" O3 NAD A 301 " pdb=" PA NAD A 301 " ideal model delta sigma weight residual 1.653 1.578 0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" O3 NAD B 301 " pdb=" PA NAD B 301 " ideal model delta sigma weight residual 1.653 1.580 0.073 2.00e-02 2.50e+03 1.35e+01 ... (remaining 10876 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 14593 1.47 - 2.94: 314 2.94 - 4.41: 115 4.41 - 5.89: 24 5.89 - 7.36: 6 Bond angle restraints: 15052 Sorted by residual: angle pdb=" CA THR B 203 " pdb=" C THR B 203 " pdb=" N PRO B 204 " ideal model delta sigma weight residual 117.68 122.78 -5.10 7.10e-01 1.98e+00 5.15e+01 angle pdb=" C GLN E 221 " pdb=" N ASN E 222 " pdb=" CA ASN E 222 " ideal model delta sigma weight residual 120.44 113.47 6.97 1.30e+00 5.92e-01 2.88e+01 angle pdb=" C TYR E 211 " pdb=" CA TYR E 211 " pdb=" CB TYR E 211 " ideal model delta sigma weight residual 111.06 103.70 7.36 1.55e+00 4.16e-01 2.25e+01 angle pdb=" CA THR B 203 " pdb=" C THR B 203 " pdb=" O THR B 203 " ideal model delta sigma weight residual 120.71 116.77 3.94 8.70e-01 1.32e+00 2.05e+01 angle pdb=" CA GLY E 320 " pdb=" C GLY E 320 " pdb=" N THR E 321 " ideal model delta sigma weight residual 118.42 112.91 5.51 1.26e+00 6.30e-01 1.91e+01 ... (remaining 15047 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.53: 6376 33.53 - 67.05: 281 67.05 - 100.58: 27 100.58 - 134.11: 0 134.11 - 167.63: 1 Dihedral angle restraints: 6685 sinusoidal: 3244 harmonic: 3441 Sorted by residual: dihedral pdb=" O4' A T 14 " pdb=" C1' A T 14 " pdb=" N9 A T 14 " pdb=" C4 A T 14 " ideal model delta sinusoidal sigma weight residual -78.00 -16.71 -61.29 1 1.70e+01 3.46e-03 1.73e+01 dihedral pdb=" O4' G T 30 " pdb=" C1' G T 30 " pdb=" N9 G T 30 " pdb=" C4 G T 30 " ideal model delta sinusoidal sigma weight residual -106.00 -164.50 58.50 1 1.70e+01 3.46e-03 1.59e+01 dihedral pdb=" C4' A T 7 " pdb=" C3' A T 7 " pdb=" O3' A T 7 " pdb=" P U T 8 " ideal model delta sinusoidal sigma weight residual -140.00 27.63 -167.63 1 3.50e+01 8.16e-04 1.55e+01 ... (remaining 6682 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1553 0.054 - 0.107: 171 0.107 - 0.161: 65 0.161 - 0.215: 3 0.215 - 0.268: 1 Chirality restraints: 1793 Sorted by residual: chirality pdb=" CA TYR E 211 " pdb=" N TYR E 211 " pdb=" C TYR E 211 " pdb=" CB TYR E 211 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" C2' SAH E 401 " pdb=" C1' SAH E 401 " pdb=" C3' SAH E 401 " pdb=" O2' SAH E 401 " both_signs ideal model delta sigma weight residual False -2.53 -2.72 0.19 2.00e-01 2.50e+01 8.97e-01 chirality pdb=" C1D NAD C 301 " pdb=" C2D NAD C 301 " pdb=" N1N NAD C 301 " pdb=" O4D NAD C 301 " both_signs ideal model delta sigma weight residual False 2.41 2.59 -0.17 2.00e-01 2.50e+01 7.45e-01 ... (remaining 1790 not shown) Planarity restraints: 1729 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1D NAD D 301 " 0.044 2.00e-02 2.50e+03 2.69e-02 1.45e+01 pdb=" C2N NAD D 301 " -0.035 2.00e-02 2.50e+03 pdb=" C3N NAD D 301 " -0.005 2.00e-02 2.50e+03 pdb=" C4N NAD D 301 " 0.009 2.00e-02 2.50e+03 pdb=" C5N NAD D 301 " 0.005 2.00e-02 2.50e+03 pdb=" C6N NAD D 301 " 0.003 2.00e-02 2.50e+03 pdb=" C7N NAD D 301 " 0.022 2.00e-02 2.50e+03 pdb=" N1N NAD D 301 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY E 320 " 0.018 2.00e-02 2.50e+03 3.64e-02 1.33e+01 pdb=" C GLY E 320 " -0.063 2.00e-02 2.50e+03 pdb=" O GLY E 320 " 0.025 2.00e-02 2.50e+03 pdb=" N THR E 321 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D NAD B 301 " -0.027 2.00e-02 2.50e+03 1.56e-02 4.87e+00 pdb=" C2N NAD B 301 " 0.009 2.00e-02 2.50e+03 pdb=" C3N NAD B 301 " 0.003 2.00e-02 2.50e+03 pdb=" C4N NAD B 301 " -0.012 2.00e-02 2.50e+03 pdb=" C5N NAD B 301 " -0.011 2.00e-02 2.50e+03 pdb=" C6N NAD B 301 " 0.017 2.00e-02 2.50e+03 pdb=" C7N NAD B 301 " -0.003 2.00e-02 2.50e+03 pdb=" N1N NAD B 301 " 0.024 2.00e-02 2.50e+03 ... (remaining 1726 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1281 2.74 - 3.28: 10605 3.28 - 3.82: 18984 3.82 - 4.36: 23797 4.36 - 4.90: 39164 Nonbonded interactions: 93831 Sorted by model distance: nonbonded pdb=" OG1 THR C 153 " pdb=" OH TYR C 233 " model vdw 2.203 3.040 nonbonded pdb=" NH1 ARG C 184 " pdb=" O GLY D 161 " model vdw 2.212 3.120 nonbonded pdb=" OG1 THR A 179 " pdb=" OG1 THR A 195 " model vdw 2.212 3.040 nonbonded pdb=" O PHE D 216 " pdb=" OG SER D 219 " model vdw 2.248 3.040 nonbonded pdb=" OH TYR E 211 " pdb=" OH TYR E 289 " model vdw 2.260 3.040 ... (remaining 93826 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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=0.00 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: 2.980 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: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 9.510 Find NCS groups from input model: 0.100 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:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 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 : 0.005 0.086 10881 Z= 0.247 Angle : 0.607 7.357 15052 Z= 0.345 Chirality : 0.041 0.268 1793 Planarity : 0.004 0.038 1729 Dihedral : 17.263 167.633 4489 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.21 % Allowed : 0.73 % Favored : 99.06 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 6.78 % 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: 0.61 (0.25), residues: 1221 helix: 1.89 (0.23), residues: 550 sheet: -1.26 (0.37), residues: 201 loop : -0.54 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 147 TYR 0.019 0.002 TYR E 289 PHE 0.017 0.001 PHE D 245 TRP 0.006 0.001 TRP E 193 HIS 0.002 0.001 HIS A 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.25 (10881) covalent geometry : angle 0.60722 / 0.35 (15052) hydrogen bonds : bond 0.12938 / 8.69 ( 479) hydrogen bonds : angle 6.17393 / 4.45 ( 1337) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 247 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 317 MET cc_start: 0.7399 (mmm) cc_final: 0.6929 (mmt) REVERT: E 344 TRP cc_start: 0.6673 (t-100) cc_final: 0.6315 (t-100) REVERT: E 354 ASP cc_start: 0.7278 (p0) cc_final: 0.6769 (p0) outliers start: 2 outliers final: 1 residues processed: 248 average time/residue: 0.1137 time to fit residues: 37.4980 Evaluate side-chains 137 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 136 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 321 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.0030 chunk 33 optimal weight: 7.9990 chunk 123 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 ASN D 90 ASN E 203 GLN E 222 ASN ** E 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 263 GLN ** E 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.091842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.065481 restraints weight = 27422.894| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.90 r_work: 0.2997 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10881 Z= 0.143 Angle : 0.609 7.272 15052 Z= 0.313 Chirality : 0.042 0.230 1793 Planarity : 0.005 0.046 1729 Dihedral : 16.753 165.916 2384 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.04 % Allowed : 9.80 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % 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: 0.99 (0.25), residues: 1221 helix: 2.20 (0.23), residues: 549 sheet: -1.15 (0.39), residues: 179 loop : -0.34 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 236 TYR 0.015 0.002 TYR C 233 PHE 0.016 0.002 PHE E 241 TRP 0.006 0.001 TRP E 183 HIS 0.003 0.001 HIS E 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (10881) covalent geometry : angle 0.60878 / 0.31 (15052) hydrogen bonds : bond 0.04433 / 2.96 ( 479) hydrogen bonds : angle 5.22641 / 3.80 ( 1337) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 175 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.9064 (mt-10) cc_final: 0.8753 (mt-10) REVERT: A 70 ASP cc_start: 0.9134 (m-30) cc_final: 0.8817 (m-30) REVERT: A 142 ASP cc_start: 0.9161 (t0) cc_final: 0.8959 (t0) REVERT: A 249 GLU cc_start: 0.8166 (tp30) cc_final: 0.7908 (tp30) REVERT: A 254 ASP cc_start: 0.8873 (p0) cc_final: 0.8658 (p0) REVERT: C 86 ASP cc_start: 0.8638 (m-30) cc_final: 0.8422 (m-30) REVERT: C 119 ASP cc_start: 0.9112 (m-30) cc_final: 0.8836 (m-30) REVERT: C 254 ASP cc_start: 0.8950 (p0) cc_final: 0.8694 (p0) REVERT: D 81 LYS cc_start: 0.9628 (tppt) cc_final: 0.9390 (tppt) REVERT: D 254 ASP cc_start: 0.8756 (p0) cc_final: 0.8201 (p0) REVERT: E 211 TYR cc_start: 0.8137 (m-10) cc_final: 0.7896 (m-10) REVERT: E 275 GLU cc_start: 0.8450 (mm-30) cc_final: 0.8172 (mm-30) REVERT: E 317 MET cc_start: 0.7961 (mmm) cc_final: 0.7702 (mmt) outliers start: 10 outliers final: 3 residues processed: 180 average time/residue: 0.0818 time to fit residues: 21.0998 Evaluate side-chains 147 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 144 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain D residue 178 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 89 optimal weight: 3.9990 chunk 92 optimal weight: 0.0170 chunk 79 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 chunk 87 optimal weight: 0.9980 chunk 108 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 30 optimal weight: 10.0000 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 152 ASN ** E 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 365 ASN ** 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 = 0.3756 r_free = 0.3756 target = 0.092360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.066790 restraints weight = 28106.842| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.84 r_work: 0.3053 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10881 Z= 0.122 Angle : 0.546 7.706 15052 Z= 0.283 Chirality : 0.041 0.175 1793 Planarity : 0.004 0.041 1729 Dihedral : 16.542 163.537 2383 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.36 % Allowed : 11.57 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % 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: 1.18 (0.25), residues: 1221 helix: 2.38 (0.23), residues: 548 sheet: -1.15 (0.39), residues: 179 loop : -0.24 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 235 TYR 0.016 0.001 TYR A 168 PHE 0.015 0.001 PHE D 159 TRP 0.008 0.001 TRP E 183 HIS 0.008 0.001 HIS E 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (10881) covalent geometry : angle 0.54553 / 0.28 (15052) hydrogen bonds : bond 0.03943 / 2.64 ( 479) hydrogen bonds : angle 5.05634 / 3.71 ( 1337) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 163 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ASP cc_start: 0.9117 (m-30) cc_final: 0.8778 (m-30) REVERT: B 99 LYS cc_start: 0.9494 (mtpt) cc_final: 0.9074 (mptt) REVERT: B 194 MET cc_start: 0.8549 (mmm) cc_final: 0.8292 (tpt) REVERT: C 86 ASP cc_start: 0.8694 (m-30) cc_final: 0.8401 (m-30) REVERT: C 119 ASP cc_start: 0.9142 (m-30) cc_final: 0.8874 (m-30) REVERT: C 147 ARG cc_start: 0.8679 (mtt90) cc_final: 0.8340 (ttm-80) REVERT: C 249 GLU cc_start: 0.8296 (tp30) cc_final: 0.7149 (tp30) REVERT: D 70 ASP cc_start: 0.9026 (m-30) cc_final: 0.8665 (t0) REVERT: D 249 GLU cc_start: 0.8377 (tp30) cc_final: 0.7705 (tp30) REVERT: E 187 MET cc_start: 0.9127 (mtp) cc_final: 0.8870 (mtp) REVERT: E 317 MET cc_start: 0.7959 (mmm) cc_final: 0.7693 (mmt) outliers start: 13 outliers final: 5 residues processed: 171 average time/residue: 0.0917 time to fit residues: 21.7001 Evaluate side-chains 137 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 132 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 178 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 123 optimal weight: 10.0000 chunk 14 optimal weight: 0.9990 chunk 108 optimal weight: 0.7980 chunk 72 optimal weight: 8.9990 chunk 7 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 355 GLN ** E 365 ASN ** 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 = 0.3669 r_free = 0.3669 target = 0.090285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.064238 restraints weight = 28002.671| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.85 r_work: 0.2971 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10881 Z= 0.153 Angle : 0.556 7.099 15052 Z= 0.286 Chirality : 0.040 0.150 1793 Planarity : 0.004 0.049 1729 Dihedral : 16.410 162.039 2383 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.63 % Allowed : 14.08 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % 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 (0.25), residues: 1221 helix: 2.43 (0.23), residues: 548 sheet: -1.15 (0.39), residues: 179 loop : -0.22 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 84 TYR 0.014 0.001 TYR A 168 PHE 0.019 0.001 PHE B 82 TRP 0.010 0.001 TRP E 183 HIS 0.004 0.001 HIS E 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (10881) covalent geometry : angle 0.55644 / 0.29 (15052) hydrogen bonds : bond 0.03818 / 2.56 ( 479) hydrogen bonds : angle 5.00448 / 3.68 ( 1337) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 150 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ASP cc_start: 0.9169 (m-30) cc_final: 0.8886 (m-30) REVERT: A 242 GLU cc_start: 0.8896 (mt-10) cc_final: 0.8635 (mt-10) REVERT: A 249 GLU cc_start: 0.8428 (tp30) cc_final: 0.8227 (tp30) REVERT: B 194 MET cc_start: 0.8525 (mmm) cc_final: 0.8190 (tpt) REVERT: C 28 GLU cc_start: 0.8807 (mt-10) cc_final: 0.8576 (mt-10) REVERT: C 86 ASP cc_start: 0.8723 (m-30) cc_final: 0.8383 (m-30) REVERT: C 119 ASP cc_start: 0.9136 (m-30) cc_final: 0.8845 (m-30) REVERT: C 147 ARG cc_start: 0.8773 (mtt90) cc_final: 0.8393 (ttm-80) REVERT: C 249 GLU cc_start: 0.8081 (tp30) cc_final: 0.7231 (tp30) REVERT: D 70 ASP cc_start: 0.9143 (m-30) cc_final: 0.8774 (t0) REVERT: D 123 MET cc_start: 0.9004 (ttp) cc_final: 0.8788 (tmm) REVERT: E 187 MET cc_start: 0.9097 (mtp) cc_final: 0.8866 (mtp) REVERT: E 275 GLU cc_start: 0.8435 (mm-30) cc_final: 0.8128 (mm-30) REVERT: E 317 MET cc_start: 0.7948 (mmm) cc_final: 0.7745 (mmp) outliers start: 6 outliers final: 5 residues processed: 151 average time/residue: 0.0840 time to fit residues: 17.8886 Evaluate side-chains 139 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 134 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain D residue 178 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 112 optimal weight: 7.9990 chunk 80 optimal weight: 10.0000 chunk 51 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 58 optimal weight: 8.9990 chunk 34 optimal weight: 6.9990 chunk 102 optimal weight: 0.9990 chunk 74 optimal weight: 7.9990 chunk 25 optimal weight: 10.0000 chunk 11 optimal weight: 0.7980 chunk 92 optimal weight: 4.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.089953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.064305 restraints weight = 28358.560| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.84 r_work: 0.3004 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10881 Z= 0.178 Angle : 0.554 7.120 15052 Z= 0.285 Chirality : 0.040 0.140 1793 Planarity : 0.004 0.044 1729 Dihedral : 16.317 160.867 2383 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.25 % Allowed : 13.24 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % 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: 1.24 (0.25), residues: 1221 helix: 2.53 (0.23), residues: 548 sheet: -1.11 (0.38), residues: 183 loop : -0.34 (0.29), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 84 TYR 0.014 0.001 TYR A 168 PHE 0.013 0.001 PHE D 159 TRP 0.011 0.001 TRP E 183 HIS 0.004 0.001 HIS E 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.18 (10881) covalent geometry : angle 0.55419 / 0.28 (15052) hydrogen bonds : bond 0.03739 / 2.52 ( 479) hydrogen bonds : angle 4.96374 / 3.65 ( 1337) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 148 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.9074 (mt-10) cc_final: 0.8726 (mt-10) REVERT: A 70 ASP cc_start: 0.9142 (m-30) cc_final: 0.8808 (m-30) REVERT: A 104 LYS cc_start: 0.9245 (mmtm) cc_final: 0.8616 (mmtm) REVERT: A 142 ASP cc_start: 0.9073 (t70) cc_final: 0.8647 (p0) REVERT: A 242 GLU cc_start: 0.8883 (mt-10) cc_final: 0.8614 (mt-10) REVERT: C 28 GLU cc_start: 0.8800 (mt-10) cc_final: 0.8549 (mt-10) REVERT: C 86 ASP cc_start: 0.8800 (m-30) cc_final: 0.8437 (m-30) REVERT: C 119 ASP cc_start: 0.9160 (m-30) cc_final: 0.8879 (m-30) REVERT: C 147 ARG cc_start: 0.8803 (mtt90) cc_final: 0.8495 (ttm-80) REVERT: C 249 GLU cc_start: 0.8165 (tp30) cc_final: 0.7147 (tp30) REVERT: D 70 ASP cc_start: 0.9087 (m-30) cc_final: 0.8731 (t0) REVERT: E 187 MET cc_start: 0.9145 (mtp) cc_final: 0.8872 (mtp) REVERT: E 384 PHE cc_start: 0.8072 (m-80) cc_final: 0.7860 (m-80) outliers start: 12 outliers final: 9 residues processed: 155 average time/residue: 0.0872 time to fit residues: 19.3527 Evaluate side-chains 144 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 135 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 297 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 120 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 47 optimal weight: 0.3980 chunk 11 optimal weight: 0.8980 chunk 125 optimal weight: 50.0000 chunk 15 optimal weight: 0.0670 chunk 49 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 chunk 118 optimal weight: 0.9980 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 350 ASN ** E 365 ASN ** 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 = 0.3684 r_free = 0.3684 target = 0.092479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.064609 restraints weight = 29512.131| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.99 r_work: 0.3029 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10881 Z= 0.115 Angle : 0.550 8.171 15052 Z= 0.281 Chirality : 0.040 0.165 1793 Planarity : 0.004 0.045 1729 Dihedral : 16.164 159.778 2383 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.15 % Allowed : 13.56 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % 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: 1.34 (0.25), residues: 1221 helix: 2.56 (0.23), residues: 549 sheet: -1.06 (0.37), residues: 183 loop : -0.21 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 328 TYR 0.012 0.001 TYR A 168 PHE 0.012 0.001 PHE D 159 TRP 0.008 0.001 TRP E 183 HIS 0.004 0.001 HIS E 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (10881) covalent geometry : angle 0.55000 / 0.28 (15052) hydrogen bonds : bond 0.03519 / 2.37 ( 479) hydrogen bonds : angle 4.84136 / 3.56 ( 1337) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 152 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ASP cc_start: 0.9155 (m-30) cc_final: 0.8822 (m-30) REVERT: A 104 LYS cc_start: 0.9212 (mmtm) cc_final: 0.8635 (mmtm) REVERT: A 242 GLU cc_start: 0.8886 (mt-10) cc_final: 0.8596 (mt-10) REVERT: A 249 GLU cc_start: 0.8511 (tp30) cc_final: 0.8152 (tt0) REVERT: C 28 GLU cc_start: 0.8814 (mt-10) cc_final: 0.8541 (mt-10) REVERT: C 81 LYS cc_start: 0.9385 (mmmm) cc_final: 0.9169 (tppt) REVERT: C 86 ASP cc_start: 0.8839 (m-30) cc_final: 0.8480 (m-30) REVERT: C 119 ASP cc_start: 0.9142 (m-30) cc_final: 0.8860 (m-30) REVERT: C 147 ARG cc_start: 0.8832 (mtt90) cc_final: 0.8499 (ttm-80) REVERT: C 249 GLU cc_start: 0.8122 (tp30) cc_final: 0.7281 (tp30) REVERT: D 70 ASP cc_start: 0.9078 (m-30) cc_final: 0.8710 (t0) outliers start: 11 outliers final: 8 residues processed: 156 average time/residue: 0.1029 time to fit residues: 22.9048 Evaluate side-chains 150 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 142 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 297 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 39 optimal weight: 7.9990 chunk 91 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 chunk 88 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 41 optimal weight: 0.7980 chunk 73 optimal weight: 6.9990 chunk 2 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 27 optimal weight: 10.0000 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.089383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.063489 restraints weight = 28268.502| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.79 r_work: 0.2998 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10881 Z= 0.193 Angle : 0.583 7.581 15052 Z= 0.298 Chirality : 0.040 0.161 1793 Planarity : 0.004 0.044 1729 Dihedral : 16.148 159.708 2383 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.04 % Allowed : 15.33 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % 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 (0.25), residues: 1221 helix: 2.66 (0.23), residues: 549 sheet: -1.11 (0.37), residues: 185 loop : -0.20 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 84 TYR 0.016 0.001 TYR A 168 PHE 0.015 0.002 PHE E 179 TRP 0.013 0.001 TRP E 183 HIS 0.005 0.001 HIS E 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.19 (10881) covalent geometry : angle 0.58275 / 0.30 (15052) hydrogen bonds : bond 0.03655 / 2.47 ( 479) hydrogen bonds : angle 4.90257 / 3.60 ( 1337) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 140 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.9067 (mt-10) cc_final: 0.8752 (mt-10) REVERT: A 70 ASP cc_start: 0.9151 (m-30) cc_final: 0.8803 (m-30) REVERT: A 104 LYS cc_start: 0.9230 (mmtm) cc_final: 0.8684 (mmtm) REVERT: A 232 GLU cc_start: 0.8934 (OUTLIER) cc_final: 0.8623 (mm-30) REVERT: A 242 GLU cc_start: 0.8880 (mt-10) cc_final: 0.8589 (mt-10) REVERT: C 28 GLU cc_start: 0.8800 (mt-10) cc_final: 0.8529 (mt-10) REVERT: C 81 LYS cc_start: 0.9385 (mmmm) cc_final: 0.9180 (tppt) REVERT: C 86 ASP cc_start: 0.8840 (m-30) cc_final: 0.8471 (m-30) REVERT: C 119 ASP cc_start: 0.9158 (m-30) cc_final: 0.8874 (m-30) REVERT: C 147 ARG cc_start: 0.8823 (mtt90) cc_final: 0.8335 (ttm-80) REVERT: C 249 GLU cc_start: 0.8148 (tp30) cc_final: 0.7309 (tp30) REVERT: D 70 ASP cc_start: 0.9095 (m-30) cc_final: 0.8744 (t0) REVERT: D 254 ASP cc_start: 0.8696 (p0) cc_final: 0.8399 (p0) REVERT: E 215 MET cc_start: 0.8113 (mtm) cc_final: 0.7768 (mtm) REVERT: E 219 GLU cc_start: 0.9069 (mp0) cc_final: 0.8400 (pt0) outliers start: 10 outliers final: 8 residues processed: 145 average time/residue: 0.1017 time to fit residues: 21.2619 Evaluate side-chains 141 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 132 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain D residue 259 MET Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 297 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 49 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 chunk 101 optimal weight: 0.6980 chunk 82 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 97 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.089339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.063054 restraints weight = 27996.443| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.90 r_work: 0.2963 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10881 Z= 0.130 Angle : 0.569 8.291 15052 Z= 0.291 Chirality : 0.040 0.137 1793 Planarity : 0.004 0.045 1729 Dihedral : 16.079 159.265 2383 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.94 % Allowed : 15.85 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % 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: 1.46 (0.25), residues: 1221 helix: 2.68 (0.23), residues: 549 sheet: -1.08 (0.38), residues: 185 loop : -0.14 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 328 TYR 0.014 0.001 TYR A 168 PHE 0.014 0.001 PHE E 179 TRP 0.007 0.001 TRP E 183 HIS 0.004 0.001 HIS E 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (10881) covalent geometry : angle 0.56856 / 0.29 (15052) hydrogen bonds : bond 0.03487 / 2.35 ( 479) hydrogen bonds : angle 4.78119 / 3.51 ( 1337) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 144 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.9049 (mt-10) cc_final: 0.8707 (mt-10) REVERT: A 70 ASP cc_start: 0.9197 (m-30) cc_final: 0.8901 (m-30) REVERT: A 104 LYS cc_start: 0.9279 (mmtm) cc_final: 0.8681 (mmtm) REVERT: A 232 GLU cc_start: 0.9026 (OUTLIER) cc_final: 0.8699 (mm-30) REVERT: A 242 GLU cc_start: 0.8950 (mt-10) cc_final: 0.8642 (mt-10) REVERT: A 249 GLU cc_start: 0.8588 (tp30) cc_final: 0.8386 (tp30) REVERT: C 28 GLU cc_start: 0.8836 (mt-10) cc_final: 0.8540 (mt-10) REVERT: C 81 LYS cc_start: 0.9399 (mmmm) cc_final: 0.9147 (tppp) REVERT: C 86 ASP cc_start: 0.8793 (m-30) cc_final: 0.8415 (m-30) REVERT: C 119 ASP cc_start: 0.9163 (m-30) cc_final: 0.8886 (m-30) REVERT: C 147 ARG cc_start: 0.8864 (mtt90) cc_final: 0.8304 (ttm-80) REVERT: C 249 GLU cc_start: 0.8061 (tp30) cc_final: 0.7182 (tp30) REVERT: D 70 ASP cc_start: 0.9166 (m-30) cc_final: 0.8811 (t0) REVERT: D 254 ASP cc_start: 0.8751 (p0) cc_final: 0.8453 (p0) REVERT: E 370 GLN cc_start: 0.8487 (mm110) cc_final: 0.8105 (mm-40) REVERT: E 384 PHE cc_start: 0.7627 (m-80) cc_final: 0.6789 (m-80) outliers start: 9 outliers final: 8 residues processed: 148 average time/residue: 0.1052 time to fit residues: 22.2443 Evaluate side-chains 149 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 140 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain D residue 259 MET Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 297 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 98 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 chunk 27 optimal weight: 8.9990 chunk 93 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 125 optimal weight: 50.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 152 ASN ** E 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 365 ASN ** 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 = 0.3710 r_free = 0.3710 target = 0.088990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.063989 restraints weight = 28028.816| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.73 r_work: 0.3013 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10881 Z= 0.165 Angle : 0.592 8.580 15052 Z= 0.303 Chirality : 0.040 0.141 1793 Planarity : 0.004 0.044 1729 Dihedral : 16.058 159.269 2383 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.15 % Allowed : 15.64 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % 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: 1.46 (0.25), residues: 1221 helix: 2.68 (0.23), residues: 549 sheet: -1.06 (0.38), residues: 185 loop : -0.15 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 328 TYR 0.008 0.001 TYR E 244 PHE 0.014 0.001 PHE E 179 TRP 0.010 0.001 TRP E 183 HIS 0.004 0.001 HIS E 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 (10881) covalent geometry : angle 0.59162 / 0.30 (15052) hydrogen bonds : bond 0.03498 / 2.36 ( 479) hydrogen bonds : angle 4.81772 / 3.53 ( 1337) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 146 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.9067 (mt-10) cc_final: 0.8741 (mt-10) REVERT: A 70 ASP cc_start: 0.9240 (m-30) cc_final: 0.8928 (m-30) REVERT: A 104 LYS cc_start: 0.9235 (mmtm) cc_final: 0.8662 (mmtm) REVERT: A 232 GLU cc_start: 0.8958 (OUTLIER) cc_final: 0.8641 (mm-30) REVERT: A 242 GLU cc_start: 0.8911 (mt-10) cc_final: 0.8613 (mt-10) REVERT: C 28 GLU cc_start: 0.8824 (mt-10) cc_final: 0.8543 (mt-10) REVERT: C 81 LYS cc_start: 0.9373 (mmmm) cc_final: 0.9139 (tppp) REVERT: C 86 ASP cc_start: 0.8811 (m-30) cc_final: 0.8482 (m-30) REVERT: C 147 ARG cc_start: 0.8862 (mtt90) cc_final: 0.8372 (ttm-80) REVERT: C 249 GLU cc_start: 0.8137 (tp30) cc_final: 0.7310 (tp30) REVERT: D 70 ASP cc_start: 0.9096 (m-30) cc_final: 0.8729 (t0) REVERT: E 370 GLN cc_start: 0.8515 (mm110) cc_final: 0.8149 (mm-40) REVERT: E 384 PHE cc_start: 0.7650 (m-80) cc_final: 0.6865 (m-80) outliers start: 11 outliers final: 8 residues processed: 152 average time/residue: 0.1005 time to fit residues: 21.6212 Evaluate side-chains 148 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 139 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain D residue 259 MET Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 297 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 9 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 110 optimal weight: 0.2980 chunk 19 optimal weight: 0.5980 chunk 85 optimal weight: 9.9990 chunk 81 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 152 ASN E 237 ASN E 365 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.091587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.063922 restraints weight = 29355.374| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 3.00 r_work: 0.3023 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10881 Z= 0.130 Angle : 0.596 8.790 15052 Z= 0.306 Chirality : 0.040 0.135 1793 Planarity : 0.004 0.045 1729 Dihedral : 16.008 159.016 2383 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.04 % Allowed : 16.16 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % 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: 1.43 (0.25), residues: 1221 helix: 2.59 (0.23), residues: 549 sheet: -0.97 (0.38), residues: 185 loop : -0.14 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 328 TYR 0.007 0.001 TYR E 244 PHE 0.014 0.001 PHE E 179 TRP 0.007 0.001 TRP E 233 HIS 0.003 0.001 HIS E 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (10881) covalent geometry : angle 0.59638 / 0.31 (15052) hydrogen bonds : bond 0.03425 / 2.31 ( 479) hydrogen bonds : angle 4.69395 / 3.45 ( 1337) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 151 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.9074 (mt-10) cc_final: 0.8761 (mt-10) REVERT: A 70 ASP cc_start: 0.9229 (m-30) cc_final: 0.8919 (m-30) REVERT: A 104 LYS cc_start: 0.9218 (mmtm) cc_final: 0.8632 (mmtm) REVERT: A 185 ASP cc_start: 0.8565 (m-30) cc_final: 0.8267 (m-30) REVERT: A 211 GLU cc_start: 0.8335 (mp0) cc_final: 0.8119 (mp0) REVERT: A 232 GLU cc_start: 0.8946 (OUTLIER) cc_final: 0.8671 (mm-30) REVERT: A 242 GLU cc_start: 0.8908 (mt-10) cc_final: 0.8614 (mt-10) REVERT: C 28 GLU cc_start: 0.8833 (mt-10) cc_final: 0.8554 (mt-10) REVERT: C 81 LYS cc_start: 0.9354 (mmmm) cc_final: 0.9144 (tppp) REVERT: C 86 ASP cc_start: 0.8814 (m-30) cc_final: 0.8479 (m-30) REVERT: C 147 ARG cc_start: 0.8904 (mtt90) cc_final: 0.8446 (ttm-80) REVERT: C 249 GLU cc_start: 0.8152 (tp30) cc_final: 0.7372 (tp30) REVERT: D 70 ASP cc_start: 0.9099 (m-30) cc_final: 0.8756 (m-30) REVERT: E 215 MET cc_start: 0.7892 (mtm) cc_final: 0.7460 (mtm) REVERT: E 219 GLU cc_start: 0.9112 (mp0) cc_final: 0.8401 (pt0) REVERT: E 370 GLN cc_start: 0.8542 (mm110) cc_final: 0.8195 (mm-40) REVERT: E 384 PHE cc_start: 0.7621 (m-80) cc_final: 0.6837 (m-80) outliers start: 10 outliers final: 9 residues processed: 156 average time/residue: 0.0928 time to fit residues: 20.4964 Evaluate side-chains 148 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 138 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain D residue 259 MET Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 297 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 55 optimal weight: 5.9990 chunk 96 optimal weight: 0.9980 chunk 28 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 124 optimal weight: 20.0000 chunk 7 optimal weight: 6.9990 chunk 79 optimal weight: 8.9990 chunk 119 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 71 optimal weight: 0.1980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 152 ASN E 366 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.091462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.063891 restraints weight = 29590.310| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.99 r_work: 0.3018 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.173 10881 Z= 0.211 Angle : 0.855 59.200 15052 Z= 0.495 Chirality : 0.042 0.435 1793 Planarity : 0.004 0.045 1729 Dihedral : 16.024 159.012 2383 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.94 % Allowed : 16.58 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 1.40 (0.25), residues: 1221 helix: 2.58 (0.23), residues: 549 sheet: -1.04 (0.38), residues: 185 loop : -0.14 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 328 TYR 0.005 0.001 TYR D 168 PHE 0.018 0.001 PHE E 179 TRP 0.006 0.001 TRP E 233 HIS 0.003 0.001 HIS E 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.21 (10881) covalent geometry : angle 0.85528 / 0.50 (15052) hydrogen bonds : bond 0.03572 / 2.37 ( 479) hydrogen bonds : angle 4.71444 / 3.45 ( 1337) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2158.58 seconds wall clock time: 37 minutes 59.32 seconds (2279.32 seconds total)