Starting phenix.real_space_refine on Wed Aug 5 15:10:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cbo_16547/08_2026/8cbo_16547.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cbo_16547/08_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_16547/08_2026/8cbo_16547.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cbo_16547/08_2026/8cbo_16547.map" model { file = "/net/cci-nas-00/data/ceres_data/8cbo_16547/08_2026/8cbo_16547.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cbo_16547/08_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-2.2rc3-6140/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: 2.72, per 1000 atoms: 0.26 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: 0.86 Conformation dependent library (CDL) restraints added in 279.2 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: 1.25 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: 1.81 Time building geometry restraints manager: 1.16 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: 14442 1.47 - 2.94: 465 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: 1494 0.054 - 0.107: 227 0.107 - 0.161: 68 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: 2.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 11.590 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.610 ------------------------------------------------------------------------------- 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= 0.250 Angle : 0.641 7.357 15052 Z= 0.393 Chirality : 0.045 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 0.00462 / 0.25 (10881) covalent geometry : angle 0.64131 / 0.39 (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 : 0.285 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: 0.6931 (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: 0.6773 (p0) outliers start: 2 outliers final: 1 residues processed: 248 average time/residue: 0.1357 time to fit residues: 44.7342 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 : 0.383 ------------------------------------------------------------------------------- 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: 4.9990 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: 20.0000 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 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.091805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.065394 restraints weight = 27466.687| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.89 r_work: 0.2993 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10881 Z= 0.144 Angle : 0.602 7.064 15052 Z= 0.310 Chirality : 0.042 0.219 1793 Planarity : 0.005 0.045 1729 Dihedral : 16.726 167.582 2384 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % 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: 0.94 (0.25), residues: 1221 helix: 2.20 (0.23), residues: 550 sheet: -1.21 (0.36), residues: 203 loop : -0.36 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 236 TYR 0.014 0.002 TYR A 168 PHE 0.015 0.002 PHE E 241 TRP 0.006 0.001 TRP E 183 HIS 0.004 0.001 HIS E 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (10881) covalent geometry : angle 0.60159 / 0.31 (15052) hydrogen bonds : bond 0.04622 / 3.09 ( 479) hydrogen bonds : angle 5.27431 / 3.84 ( 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 184 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 174 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.9070 (mt-10) cc_final: 0.8755 (mt-10) REVERT: A 70 ASP cc_start: 0.9119 (m-30) cc_final: 0.8839 (m-30) REVERT: A 249 GLU cc_start: 0.8249 (tp30) cc_final: 0.7983 (tp30) REVERT: A 254 ASP cc_start: 0.8867 (p0) cc_final: 0.8647 (p0) REVERT: C 86 ASP cc_start: 0.8628 (m-30) cc_final: 0.8418 (m-30) REVERT: C 119 ASP cc_start: 0.9113 (m-30) cc_final: 0.8826 (m-30) REVERT: C 254 ASP cc_start: 0.8927 (p0) cc_final: 0.8691 (p0) REVERT: D 81 LYS cc_start: 0.9626 (tppt) cc_final: 0.9384 (tppt) REVERT: D 242 GLU cc_start: 0.8932 (OUTLIER) cc_final: 0.8728 (mm-30) REVERT: E 211 TYR cc_start: 0.8111 (m-10) cc_final: 0.7903 (m-10) REVERT: E 275 GLU cc_start: 0.8432 (mm-30) cc_final: 0.8149 (mm-30) REVERT: E 317 MET cc_start: 0.7935 (mmm) cc_final: 0.7679 (mmt) REVERT: E 344 TRP cc_start: 0.6639 (t-100) cc_final: 0.6437 (t-100) outliers start: 10 outliers final: 3 residues processed: 179 average time/residue: 0.0938 time to fit residues: 23.8555 Evaluate side-chains 147 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 143 time to evaluate : 0.245 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain D residue 242 GLU 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: 0.0970 chunk 79 optimal weight: 5.9990 chunk 12 optimal weight: 0.0970 chunk 87 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 9 optimal weight: 0.0000 chunk 69 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 152 ASN D 243 ASN ** E 237 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.092803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.067236 restraints weight = 28016.533| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.84 r_work: 0.3062 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.2199 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= 0.117 Angle : 0.550 7.756 15052 Z= 0.285 Chirality : 0.041 0.188 1793 Planarity : 0.004 0.041 1729 Dihedral : 16.468 165.456 2383 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.25 % Allowed : 10.95 % Favored : 87.80 % 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: 1.14 (0.25), residues: 1221 helix: 2.32 (0.23), residues: 549 sheet: -1.14 (0.39), residues: 179 loop : -0.25 (0.29), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 235 TYR 0.017 0.001 TYR A 168 PHE 0.015 0.001 PHE D 159 TRP 0.008 0.001 TRP E 183 HIS 0.007 0.001 HIS E 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (10881) covalent geometry : angle 0.54980 / 0.28 (15052) hydrogen bonds : bond 0.03934 / 2.62 ( 479) hydrogen bonds : angle 5.05495 / 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 179 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 167 time to evaluate : 0.244 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: 0.9107 (m-30) cc_final: 0.8842 (m-30) REVERT: B 99 LYS cc_start: 0.9491 (mtpt) cc_final: 0.9079 (mptt) REVERT: B 194 MET cc_start: 0.8532 (mmm) cc_final: 0.8270 (tpt) REVERT: C 86 ASP cc_start: 0.8697 (m-30) cc_final: 0.8386 (m-30) REVERT: C 119 ASP cc_start: 0.9131 (m-30) cc_final: 0.8881 (m-30) REVERT: C 147 ARG cc_start: 0.8675 (mtt90) cc_final: 0.8354 (ttm-80) REVERT: C 232 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7848 (mt-10) REVERT: C 249 GLU cc_start: 0.8302 (tp30) cc_final: 0.7173 (tp30) REVERT: D 70 ASP cc_start: 0.9025 (m-30) cc_final: 0.8665 (t0) REVERT: E 187 MET cc_start: 0.9099 (mtp) cc_final: 0.8842 (mtp) REVERT: E 317 MET cc_start: 0.7951 (mmm) cc_final: 0.7719 (mmt) outliers start: 12 outliers final: 5 residues processed: 175 average time/residue: 0.1080 time to fit residues: 26.5893 Evaluate side-chains 138 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 133 time to evaluate : 0.341 ------------------------------------------------------------------------------- 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: 20.0000 chunk 14 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 72 optimal weight: 0.0870 chunk 7 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 42 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 chunk 15 optimal weight: 0.7980 overall best weight: 0.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 152 ASN D 243 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.092475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.066249 restraints weight = 28182.817| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.81 r_work: 0.3052 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10881 Z= 0.129 Angle : 0.553 7.797 15052 Z= 0.284 Chirality : 0.040 0.149 1793 Planarity : 0.004 0.053 1729 Dihedral : 16.304 163.701 2383 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.25 % Allowed : 12.72 % Favored : 86.03 % 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: 1.22 (0.25), residues: 1221 helix: 2.43 (0.23), residues: 548 sheet: -1.19 (0.39), residues: 179 loop : -0.21 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 84 TYR 0.011 0.001 TYR E 244 PHE 0.020 0.001 PHE B 82 TRP 0.010 0.001 TRP E 183 HIS 0.003 0.001 HIS E 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (10881) covalent geometry : angle 0.55315 / 0.28 (15052) hydrogen bonds : bond 0.03737 / 2.50 ( 479) hydrogen bonds : angle 4.97514 / 3.65 ( 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 168 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 156 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ASP cc_start: 0.9147 (m-30) cc_final: 0.8860 (m-30) REVERT: A 104 LYS cc_start: 0.9215 (mmtm) cc_final: 0.8814 (mmtm) REVERT: A 242 GLU cc_start: 0.8832 (mt-10) cc_final: 0.8565 (mt-10) REVERT: B 194 MET cc_start: 0.8566 (mmm) cc_final: 0.8253 (tpt) REVERT: C 28 GLU cc_start: 0.8745 (mt-10) cc_final: 0.8542 (mt-10) REVERT: C 86 ASP cc_start: 0.8770 (m-30) cc_final: 0.8415 (m-30) REVERT: C 119 ASP cc_start: 0.9111 (m-30) cc_final: 0.8850 (m-30) REVERT: C 147 ARG cc_start: 0.8770 (mtt90) cc_final: 0.8400 (ttm-80) REVERT: C 249 GLU cc_start: 0.8145 (tp30) cc_final: 0.7338 (tp30) REVERT: D 70 ASP cc_start: 0.9055 (m-30) cc_final: 0.8685 (t0) REVERT: D 123 MET cc_start: 0.8971 (ttp) cc_final: 0.8759 (tmm) REVERT: D 160 GLU cc_start: 0.8967 (mp0) cc_final: 0.8766 (mp0) REVERT: D 242 GLU cc_start: 0.8886 (mt-10) cc_final: 0.8671 (mm-30) REVERT: E 275 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8195 (mm-30) outliers start: 12 outliers final: 8 residues processed: 161 average time/residue: 0.1183 time to fit residues: 26.1234 Evaluate side-chains 139 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 131 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 178 MET 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 152 ASN 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: 0.9980 chunk 65 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 34 optimal weight: 0.1980 chunk 102 optimal weight: 0.5980 chunk 74 optimal weight: 0.4980 chunk 25 optimal weight: 10.0000 chunk 11 optimal weight: 8.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 152 ASN D 243 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.093131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.065281 restraints weight = 29398.735| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 3.02 r_work: 0.3035 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.2593 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= 0.127 Angle : 0.540 7.089 15052 Z= 0.278 Chirality : 0.040 0.139 1793 Planarity : 0.004 0.044 1729 Dihedral : 16.195 162.717 2383 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.36 % Allowed : 13.03 % Favored : 85.61 % 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: 1.28 (0.25), residues: 1221 helix: 2.52 (0.23), residues: 548 sheet: -1.05 (0.37), residues: 191 loop : -0.27 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 84 TYR 0.009 0.001 TYR E 244 PHE 0.013 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 0.00291 / 0.13 (10881) covalent geometry : angle 0.53987 / 0.28 (15052) hydrogen bonds : bond 0.03600 / 2.41 ( 479) hydrogen bonds : angle 4.87989 / 3.58 ( 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 169 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 156 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ASP cc_start: 0.9145 (m-30) cc_final: 0.8825 (m-30) REVERT: A 242 GLU cc_start: 0.8886 (mt-10) cc_final: 0.8628 (mt-10) REVERT: B 99 LYS cc_start: 0.9533 (mtpt) cc_final: 0.9097 (mptt) REVERT: B 194 MET cc_start: 0.8611 (mmm) cc_final: 0.8306 (tpt) REVERT: B 229 ASP cc_start: 0.8771 (t0) cc_final: 0.8558 (t0) REVERT: C 28 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8518 (mt-10) REVERT: C 81 LYS cc_start: 0.9366 (mmmm) cc_final: 0.9155 (tppt) REVERT: C 86 ASP cc_start: 0.8824 (m-30) cc_final: 0.8486 (m-30) REVERT: C 119 ASP cc_start: 0.9126 (m-30) cc_final: 0.8863 (m-30) REVERT: C 147 ARG cc_start: 0.8805 (mtt90) cc_final: 0.8455 (ttm-80) REVERT: D 70 ASP cc_start: 0.9069 (m-30) cc_final: 0.8704 (t0) REVERT: D 242 GLU cc_start: 0.8941 (mt-10) cc_final: 0.8721 (mm-30) REVERT: E 384 PHE cc_start: 0.8055 (m-80) cc_final: 0.7820 (m-80) outliers start: 13 outliers final: 7 residues processed: 161 average time/residue: 0.1001 time to fit residues: 22.5391 Evaluate side-chains 145 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 138 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LYS 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 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: 0.8980 chunk 28 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 11 optimal weight: 0.0970 chunk 125 optimal weight: 50.0000 chunk 15 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 58 optimal weight: 10.0000 chunk 118 optimal weight: 2.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 243 ASN E 237 ASN E 350 ASN E 365 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.093440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.065590 restraints weight = 29403.746| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 3.00 r_work: 0.3054 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10881 Z= 0.120 Angle : 0.558 8.266 15052 Z= 0.285 Chirality : 0.040 0.145 1793 Planarity : 0.004 0.045 1729 Dihedral : 16.089 162.004 2383 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.15 % Allowed : 14.29 % Favored : 84.57 % 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: 1.37 (0.25), residues: 1221 helix: 2.56 (0.23), residues: 549 sheet: -1.03 (0.40), residues: 163 loop : -0.22 (0.28), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 256 TYR 0.007 0.001 TYR D 168 PHE 0.015 0.001 PHE A 82 TRP 0.008 0.001 TRP E 183 HIS 0.003 0.001 HIS E 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (10881) covalent geometry : angle 0.55760 / 0.29 (15052) hydrogen bonds : bond 0.03591 / 2.40 ( 479) hydrogen bonds : angle 4.83535 / 3.54 ( 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 162 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 151 time to evaluate : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.9063 (mt-10) cc_final: 0.8739 (mt-10) REVERT: A 70 ASP cc_start: 0.9161 (m-30) cc_final: 0.8846 (m-30) REVERT: A 84 ARG cc_start: 0.8383 (mmm-85) cc_final: 0.8112 (mmm-85) REVERT: A 86 ASP cc_start: 0.8003 (m-30) cc_final: 0.7678 (m-30) REVERT: A 104 LYS cc_start: 0.9176 (mmtm) cc_final: 0.8601 (mmtm) REVERT: A 185 ASP cc_start: 0.8619 (m-30) cc_final: 0.8349 (m-30) REVERT: A 194 MET cc_start: 0.9013 (mmm) cc_final: 0.8553 (tpp) REVERT: A 242 GLU cc_start: 0.8867 (mt-10) cc_final: 0.8585 (mt-10) REVERT: A 252 ARG cc_start: 0.8793 (mtp-110) cc_final: 0.8485 (ptm-80) REVERT: A 254 ASP cc_start: 0.8687 (p0) cc_final: 0.8279 (p0) REVERT: B 194 MET cc_start: 0.8631 (mmm) cc_final: 0.8319 (tpt) REVERT: C 28 GLU cc_start: 0.8742 (mt-10) cc_final: 0.8491 (mt-10) REVERT: C 86 ASP cc_start: 0.8839 (m-30) cc_final: 0.8474 (m-30) REVERT: C 119 ASP cc_start: 0.9132 (m-30) cc_final: 0.8882 (m-30) REVERT: C 147 ARG cc_start: 0.8813 (mtt90) cc_final: 0.8480 (ttm-80) REVERT: C 249 GLU cc_start: 0.8151 (tp30) cc_final: 0.7543 (tp30) REVERT: D 70 ASP cc_start: 0.9071 (m-30) cc_final: 0.8703 (t0) REVERT: D 242 GLU cc_start: 0.8899 (mt-10) cc_final: 0.8676 (mm-30) REVERT: E 298 MET cc_start: 0.9008 (ttt) cc_final: 0.8766 (ttt) outliers start: 11 outliers final: 6 residues processed: 154 average time/residue: 0.0905 time to fit residues: 19.7484 Evaluate side-chains 145 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 139 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LYS 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 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: 8.9990 chunk 81 optimal weight: 5.9990 chunk 88 optimal weight: 0.0370 chunk 61 optimal weight: 0.9990 chunk 97 optimal weight: 6.9990 chunk 41 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 2 optimal weight: 9.9990 chunk 5 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 overall best weight: 1.2062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 243 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.091619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.065645 restraints weight = 28023.659| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.80 r_work: 0.3052 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10881 Z= 0.137 Angle : 0.555 7.711 15052 Z= 0.285 Chirality : 0.040 0.131 1793 Planarity : 0.004 0.043 1729 Dihedral : 16.035 161.707 2383 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.04 % Allowed : 14.91 % Favored : 84.05 % 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: 1.42 (0.25), residues: 1221 helix: 2.60 (0.23), residues: 549 sheet: -1.05 (0.40), residues: 163 loop : -0.18 (0.28), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 84 TYR 0.009 0.001 TYR E 244 PHE 0.012 0.001 PHE D 159 TRP 0.009 0.001 TRP E 183 HIS 0.003 0.001 HIS E 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (10881) covalent geometry : angle 0.55490 / 0.28 (15052) hydrogen bonds : bond 0.03510 / 2.35 ( 479) hydrogen bonds : angle 4.79601 / 3.53 ( 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 159 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 149 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.9046 (mt-10) cc_final: 0.8717 (mt-10) REVERT: A 70 ASP cc_start: 0.9165 (m-30) cc_final: 0.8875 (m-30) REVERT: A 104 LYS cc_start: 0.9170 (mmtm) cc_final: 0.8573 (mmtm) REVERT: A 185 ASP cc_start: 0.8571 (m-30) cc_final: 0.8290 (m-30) REVERT: A 242 GLU cc_start: 0.8850 (mt-10) cc_final: 0.8565 (mt-10) REVERT: A 249 GLU cc_start: 0.8145 (tp30) cc_final: 0.7809 (tt0) REVERT: C 28 GLU cc_start: 0.8740 (mt-10) cc_final: 0.8482 (mt-10) REVERT: C 86 ASP cc_start: 0.8841 (m-30) cc_final: 0.8472 (m-30) REVERT: C 119 ASP cc_start: 0.9150 (m-30) cc_final: 0.8870 (m-30) REVERT: C 147 ARG cc_start: 0.8813 (mtt90) cc_final: 0.8467 (ttm-80) REVERT: C 249 GLU cc_start: 0.8120 (tp30) cc_final: 0.7523 (tp30) REVERT: C 259 MET cc_start: 0.9242 (mmm) cc_final: 0.8997 (mmm) REVERT: D 70 ASP cc_start: 0.9063 (m-30) cc_final: 0.8697 (t0) REVERT: D 123 MET cc_start: 0.8911 (ttp) cc_final: 0.8325 (tmm) REVERT: D 242 GLU cc_start: 0.8897 (mt-10) cc_final: 0.8668 (mm-30) REVERT: E 229 GLU cc_start: 0.8661 (tt0) cc_final: 0.8377 (tt0) REVERT: E 298 MET cc_start: 0.8988 (ttt) cc_final: 0.8778 (ttt) outliers start: 10 outliers final: 7 residues processed: 153 average time/residue: 0.0870 time to fit residues: 18.9007 Evaluate side-chains 137 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 130 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 49 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 101 optimal weight: 0.7980 chunk 82 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 28 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 47 optimal weight: 0.0020 chunk 51 optimal weight: 0.8980 chunk 97 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 243 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.093457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.065433 restraints weight = 29170.004| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 3.01 r_work: 0.3057 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10881 Z= 0.118 Angle : 0.577 9.000 15052 Z= 0.296 Chirality : 0.039 0.135 1793 Planarity : 0.004 0.044 1729 Dihedral : 15.952 161.295 2383 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.15 % Allowed : 16.06 % 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: 1.42 (0.25), residues: 1221 helix: 2.61 (0.23), residues: 549 sheet: -1.03 (0.38), residues: 183 loop : -0.16 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 84 TYR 0.008 0.001 TYR E 244 PHE 0.024 0.001 PHE A 82 TRP 0.006 0.001 TRP E 183 HIS 0.003 0.001 HIS E 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (10881) covalent geometry : angle 0.57660 / 0.30 (15052) hydrogen bonds : bond 0.03424 / 2.29 ( 479) hydrogen bonds : angle 4.75015 / 3.48 ( 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 160 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 149 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.9054 (mt-10) cc_final: 0.8726 (mt-10) REVERT: A 70 ASP cc_start: 0.9182 (m-30) cc_final: 0.8858 (m-30) REVERT: A 104 LYS cc_start: 0.9168 (mmtm) cc_final: 0.8576 (mmtm) REVERT: A 185 ASP cc_start: 0.8575 (m-30) cc_final: 0.8299 (m-30) REVERT: A 242 GLU cc_start: 0.8883 (mt-10) cc_final: 0.8611 (mt-10) REVERT: A 249 GLU cc_start: 0.8080 (tp30) cc_final: 0.7772 (tt0) REVERT: A 252 ARG cc_start: 0.8773 (mtp-110) cc_final: 0.8464 (ptm-80) REVERT: A 254 ASP cc_start: 0.8599 (p0) cc_final: 0.8273 (p0) REVERT: C 28 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8495 (mt-10) REVERT: C 86 ASP cc_start: 0.8834 (m-30) cc_final: 0.8461 (m-30) REVERT: C 119 ASP cc_start: 0.9139 (m-30) cc_final: 0.8873 (m-30) REVERT: C 147 ARG cc_start: 0.8830 (mtt90) cc_final: 0.8363 (ttm-80) REVERT: D 70 ASP cc_start: 0.9084 (m-30) cc_final: 0.8723 (m-30) REVERT: D 242 GLU cc_start: 0.8923 (mt-10) cc_final: 0.8703 (mm-30) REVERT: E 209 MET cc_start: 0.8059 (mpp) cc_final: 0.7848 (mmm) REVERT: E 384 PHE cc_start: 0.7653 (m-80) cc_final: 0.6931 (m-80) outliers start: 11 outliers final: 7 residues processed: 153 average time/residue: 0.0936 time to fit residues: 20.6330 Evaluate side-chains 146 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 139 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 93 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 28 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 125 optimal weight: 50.0000 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 263 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.088017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.062025 restraints weight = 28095.610| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.85 r_work: 0.2935 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 10881 Z= 0.209 Angle : 0.605 8.138 15052 Z= 0.309 Chirality : 0.040 0.173 1793 Planarity : 0.004 0.042 1729 Dihedral : 16.029 161.733 2383 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.83 % Allowed : 15.33 % Favored : 83.84 % 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: 2.70 (0.23), residues: 549 sheet: -1.06 (0.38), residues: 183 loop : -0.24 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 256 TYR 0.007 0.001 TYR A 101 PHE 0.020 0.002 PHE A 82 TRP 0.015 0.002 TRP E 183 HIS 0.004 0.001 HIS E 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.21 (10881) covalent geometry : angle 0.60486 / 0.31 (15052) hydrogen bonds : bond 0.03628 / 2.44 ( 479) hydrogen bonds : angle 4.81517 / 3.54 ( 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 139 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 131 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ASP cc_start: 0.9190 (m-30) cc_final: 0.8878 (m-30) REVERT: A 81 LYS cc_start: 0.9485 (tptp) cc_final: 0.9267 (tptp) REVERT: A 104 LYS cc_start: 0.9316 (mmtm) cc_final: 0.8728 (mmtm) REVERT: A 185 ASP cc_start: 0.8538 (m-30) cc_final: 0.8262 (m-30) REVERT: C 28 GLU cc_start: 0.8813 (mt-10) cc_final: 0.8532 (mt-10) REVERT: C 86 ASP cc_start: 0.8792 (m-30) cc_final: 0.8425 (m-30) REVERT: C 119 ASP cc_start: 0.9195 (m-30) cc_final: 0.8872 (m-30) REVERT: C 147 ARG cc_start: 0.8837 (mtt90) cc_final: 0.8293 (ttm-80) REVERT: C 249 GLU cc_start: 0.8139 (tp30) cc_final: 0.7297 (tp30) REVERT: D 70 ASP cc_start: 0.9194 (m-30) cc_final: 0.8844 (m-30) REVERT: D 242 GLU cc_start: 0.8973 (mt-10) cc_final: 0.8722 (mm-30) REVERT: E 370 GLN cc_start: 0.8484 (mm110) cc_final: 0.8115 (mm-40) REVERT: E 384 PHE cc_start: 0.7638 (m-80) cc_final: 0.6779 (m-80) outliers start: 8 outliers final: 8 residues processed: 135 average time/residue: 0.0953 time to fit residues: 18.5113 Evaluate side-chains 136 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 128 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 0.7980 chunk 13 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 19 optimal weight: 0.2980 chunk 85 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 112 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.090109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.063591 restraints weight = 27970.667| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.92 r_work: 0.2958 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10881 Z= 0.126 Angle : 0.594 9.306 15052 Z= 0.306 Chirality : 0.040 0.136 1793 Planarity : 0.004 0.044 1729 Dihedral : 15.964 161.275 2383 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.94 % Allowed : 15.75 % Favored : 83.32 % 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: 2.66 (0.23), residues: 549 sheet: -1.05 (0.41), residues: 163 loop : -0.19 (0.28), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 256 TYR 0.014 0.001 TYR A 168 PHE 0.016 0.001 PHE A 82 TRP 0.008 0.001 TRP E 233 HIS 0.003 0.001 HIS E 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (10881) covalent geometry : angle 0.59390 / 0.31 (15052) hydrogen bonds : bond 0.03421 / 2.29 ( 479) hydrogen bonds : angle 4.72586 / 3.47 ( 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 157 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 148 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.9046 (mt-10) cc_final: 0.8703 (mt-10) REVERT: A 70 ASP cc_start: 0.9186 (m-30) cc_final: 0.8844 (m-30) REVERT: A 104 LYS cc_start: 0.9277 (mmtm) cc_final: 0.8645 (mmtm) REVERT: A 185 ASP cc_start: 0.8541 (m-30) cc_final: 0.8263 (m-30) REVERT: A 194 MET cc_start: 0.9038 (mmm) cc_final: 0.8583 (tpp) REVERT: A 242 GLU cc_start: 0.8941 (mt-10) cc_final: 0.8642 (mt-10) REVERT: A 249 GLU cc_start: 0.8191 (tp30) cc_final: 0.7427 (tt0) REVERT: C 28 GLU cc_start: 0.8795 (mt-10) cc_final: 0.8507 (mt-10) REVERT: C 86 ASP cc_start: 0.8788 (m-30) cc_final: 0.8437 (m-30) REVERT: C 140 GLU cc_start: 0.8764 (tm-30) cc_final: 0.8545 (tm-30) REVERT: C 147 ARG cc_start: 0.8875 (mtt90) cc_final: 0.8352 (ttm-80) REVERT: D 70 ASP cc_start: 0.9190 (m-30) cc_final: 0.8849 (m-30) REVERT: D 242 GLU cc_start: 0.9002 (mt-10) cc_final: 0.8753 (mm-30) REVERT: E 370 GLN cc_start: 0.8525 (mm110) cc_final: 0.8162 (mm-40) REVERT: E 384 PHE cc_start: 0.7643 (m-80) cc_final: 0.6799 (m-80) outliers start: 9 outliers final: 8 residues processed: 151 average time/residue: 0.0933 time to fit residues: 19.6917 Evaluate side-chains 143 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 135 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 0.1980 chunk 96 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 16 optimal weight: 7.9990 chunk 124 optimal weight: 20.0000 chunk 7 optimal weight: 6.9990 chunk 79 optimal weight: 8.9990 chunk 119 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 chunk 71 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 366 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.091706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.064635 restraints weight = 29509.656| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.95 r_work: 0.3035 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10881 Z= 0.136 Angle : 0.596 8.989 15052 Z= 0.307 Chirality : 0.040 0.147 1793 Planarity : 0.004 0.047 1729 Dihedral : 15.929 161.294 2383 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.83 % Allowed : 16.27 % Favored : 82.90 % 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: 1.44 (0.25), residues: 1221 helix: 2.62 (0.23), residues: 549 sheet: -0.96 (0.39), residues: 183 loop : -0.16 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 256 TYR 0.007 0.001 TYR A 101 PHE 0.017 0.001 PHE A 82 TRP 0.010 0.001 TRP E 344 HIS 0.003 0.001 HIS E 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (10881) covalent geometry : angle 0.59619 / 0.31 (15052) hydrogen bonds : bond 0.03376 / 2.24 ( 479) hydrogen bonds : angle 4.71747 / 3.46 ( 1337) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2193.91 seconds wall clock time: 38 minutes 26.54 seconds (2306.54 seconds total)