Starting phenix.real_space_refine on Wed Feb 4 11:17:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cbo_16547/02_2026/8cbo_16547.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cbo_16547/02_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 { model { file = "/net/cci-nas-00/data/ceres_data/8cbo_16547/02_2026/8cbo_16547.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cbo_16547/02_2026/8cbo_16547.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8cbo_16547/02_2026/8cbo_16547.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cbo_16547/02_2026/8cbo_16547.map" } 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-2.0-5952/lib/python3.9/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: 2.32, per 1000 atoms: 0.22 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: 0.70 Conformation dependent library (CDL) restraints added in 352.3 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: 0.91 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: 1.12 Time building geometry restraints manager: 0.92 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: 2.840 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: 0.030 Set scattering table: 0.040 Process input model: 9.450 Find NCS groups from input model: 0.100 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 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= 0.239 Angle : 0.607 7.357 15052 Z= 0.316 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 covalent geometry : bond 0.00459 (10881) covalent geometry : angle 0.60722 (15052) hydrogen bonds : bond 0.12938 ( 479) hydrogen bonds : angle 6.17393 ( 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 : 0.445 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: 0.1436 time to fit residues: 46.8309 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 : 0.358 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 90 ASN ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 ASN E 203 GLN E 222 ASN ** E 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 263 GLN E 355 GLN ** E 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.092930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.066909 restraints weight = 27812.306| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.86 r_work: 0.3063 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10881 Z= 0.124 Angle : 0.553 6.565 15052 Z= 0.280 Chirality : 0.041 0.181 1793 Planarity : 0.004 0.042 1729 Dihedral : 16.346 161.840 2384 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.83 % Allowed : 9.70 % Favored : 89.47 % 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: 1.17 (0.26), residues: 1221 helix: 2.36 (0.23), residues: 550 sheet: -1.16 (0.40), residues: 179 loop : -0.24 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 235 TYR 0.013 0.001 TYR A 168 PHE 0.014 0.002 PHE D 126 TRP 0.008 0.001 TRP E 233 HIS 0.003 0.000 HIS E 303 Details of bonding type rmsd covalent geometry : bond 0.00282 (10881) covalent geometry : angle 0.55254 (15052) hydrogen bonds : bond 0.03622 ( 479) hydrogen bonds : angle 5.00281 ( 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 198 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 190 time to evaluate : 0.391 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: symmetry clash REVERT: A 28 GLU cc_start: 0.9073 (mt-10) cc_final: 0.8758 (mt-10) REVERT: A 70 ASP cc_start: 0.9126 (m-30) cc_final: 0.8736 (m-30) REVERT: A 249 GLU cc_start: 0.8327 (tp30) cc_final: 0.8012 (tp30) REVERT: B 99 LYS cc_start: 0.9490 (mtpt) cc_final: 0.9061 (mptt) REVERT: B 194 MET cc_start: 0.8536 (mmm) cc_final: 0.8207 (tpt) REVERT: B 203 THR cc_start: 0.9112 (OUTLIER) cc_final: 0.8831 (p) REVERT: C 119 ASP cc_start: 0.9089 (m-30) cc_final: 0.8880 (m-30) REVERT: C 147 ARG cc_start: 0.8787 (mtt90) cc_final: 0.8226 (ttm-80) REVERT: D 69 LYS cc_start: 0.9183 (tppt) cc_final: 0.8983 (tppt) REVERT: D 81 LYS cc_start: 0.9610 (tppt) cc_final: 0.9370 (tppt) outliers start: 8 outliers final: 5 residues processed: 194 average time/residue: 0.1226 time to fit residues: 32.3990 Evaluate side-chains 153 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 147 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 203 THR 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: 6.9990 chunk 92 optimal weight: 0.0670 chunk 79 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 29 optimal weight: 7.9990 chunk 73 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 69 optimal weight: 0.5980 chunk 30 optimal weight: 7.9990 overall best weight: 1.3322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 260 GLN ** 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 = 0.3739 r_free = 0.3739 target = 0.090940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.065122 restraints weight = 28354.831| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.87 r_work: 0.3028 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.2677 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= 0.137 Angle : 0.528 6.853 15052 Z= 0.267 Chirality : 0.040 0.140 1793 Planarity : 0.004 0.039 1729 Dihedral : 16.045 158.931 2383 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.15 % Allowed : 12.62 % Favored : 86.24 % 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: 1.38 (0.26), residues: 1221 helix: 2.63 (0.23), residues: 549 sheet: -1.03 (0.36), residues: 203 loop : -0.21 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 84 TYR 0.008 0.001 TYR E 214 PHE 0.016 0.001 PHE D 159 TRP 0.005 0.001 TRP E 193 HIS 0.003 0.001 HIS E 303 Details of bonding type rmsd covalent geometry : bond 0.00315 (10881) covalent geometry : angle 0.52774 (15052) hydrogen bonds : bond 0.03439 ( 479) hydrogen bonds : angle 4.85761 ( 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 182 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 171 time to evaluate : 0.339 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: 0.9105 (m-30) cc_final: 0.8824 (m-30) REVERT: A 104 LYS cc_start: 0.9230 (mmtm) cc_final: 0.8647 (mmtm) REVERT: A 160 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.8298 (pm20) REVERT: B 99 LYS cc_start: 0.9572 (mtpt) cc_final: 0.9088 (mptt) REVERT: B 203 THR cc_start: 0.9125 (OUTLIER) cc_final: 0.8831 (p) REVERT: B 229 ASP cc_start: 0.8892 (t0) cc_final: 0.8678 (t0) REVERT: C 81 LYS cc_start: 0.9423 (tppp) cc_final: 0.9037 (tppp) REVERT: C 86 ASP cc_start: 0.8869 (m-30) cc_final: 0.8657 (m-30) REVERT: C 119 ASP cc_start: 0.9152 (m-30) cc_final: 0.8904 (m-30) REVERT: C 147 ARG cc_start: 0.8793 (mtt90) cc_final: 0.8522 (mtt90) REVERT: D 70 ASP cc_start: 0.9104 (m-30) cc_final: 0.8765 (t0) REVERT: D 81 LYS cc_start: 0.9606 (tppt) cc_final: 0.9353 (tppt) REVERT: D 242 GLU cc_start: 0.8940 (mt-10) cc_final: 0.8686 (mm-30) REVERT: D 252 ARG cc_start: 0.9139 (mtp85) cc_final: 0.8914 (mtp-110) REVERT: D 254 ASP cc_start: 0.8858 (p0) cc_final: 0.8510 (p0) REVERT: E 187 MET cc_start: 0.9129 (mtp) cc_final: 0.8830 (mtt) outliers start: 11 outliers final: 2 residues processed: 177 average time/residue: 0.1368 time to fit residues: 32.2158 Evaluate side-chains 146 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 142 time to evaluate : 0.373 ------------------------------------------------------------------------------- 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 203 THR 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: 8.9990 chunk 108 optimal weight: 0.9990 chunk 72 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 152 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.089866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.063738 restraints weight = 28286.594| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.96 r_work: 0.2986 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.2996 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= 0.119 Angle : 0.523 6.790 15052 Z= 0.262 Chirality : 0.039 0.134 1793 Planarity : 0.004 0.041 1729 Dihedral : 15.908 158.992 2383 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % 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: 1.54 (0.25), residues: 1221 helix: 2.78 (0.23), residues: 548 sheet: -0.90 (0.38), residues: 189 loop : -0.20 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 84 TYR 0.019 0.001 TYR A 168 PHE 0.018 0.001 PHE E 179 TRP 0.008 0.001 TRP E 183 HIS 0.002 0.001 HIS E 255 Details of bonding type rmsd covalent geometry : bond 0.00276 (10881) covalent geometry : angle 0.52348 (15052) hydrogen bonds : bond 0.03127 ( 479) hydrogen bonds : angle 4.64883 ( 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 183 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 171 time to evaluate : 0.464 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 28 GLU cc_start: 0.9103 (mt-10) cc_final: 0.8783 (mt-10) REVERT: A 70 ASP cc_start: 0.9169 (m-30) cc_final: 0.8825 (m-30) REVERT: A 104 LYS cc_start: 0.9218 (mmtm) cc_final: 0.8558 (mmtm) REVERT: A 160 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8243 (pm20) REVERT: A 185 ASP cc_start: 0.8538 (m-30) cc_final: 0.8217 (m-30) REVERT: A 249 GLU cc_start: 0.8518 (tp30) cc_final: 0.8112 (tp30) REVERT: B 99 LYS cc_start: 0.9586 (mtpt) cc_final: 0.9084 (mptt) REVERT: B 194 MET cc_start: 0.8751 (mmm) cc_final: 0.8305 (tpt) REVERT: B 203 THR cc_start: 0.9086 (OUTLIER) cc_final: 0.8773 (p) REVERT: C 28 GLU cc_start: 0.8778 (mt-10) cc_final: 0.8550 (mt-10) REVERT: C 140 GLU cc_start: 0.8655 (tp30) cc_final: 0.8451 (tm-30) REVERT: D 70 ASP cc_start: 0.9119 (m-30) cc_final: 0.8778 (t0) REVERT: D 242 GLU cc_start: 0.8993 (mt-10) cc_final: 0.8736 (mm-30) REVERT: D 252 ARG cc_start: 0.9121 (mtp85) cc_final: 0.8734 (mtp-110) REVERT: D 254 ASP cc_start: 0.8903 (p0) cc_final: 0.8635 (p0) REVERT: E 219 GLU cc_start: 0.9096 (mp0) cc_final: 0.8395 (pt0) outliers start: 12 outliers final: 6 residues processed: 177 average time/residue: 0.1328 time to fit residues: 31.7583 Evaluate side-chains 147 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 139 time to evaluate : 0.383 ------------------------------------------------------------------------------- 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 B residue 203 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 112 optimal weight: 7.9990 chunk 80 optimal weight: 7.9990 chunk 51 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 102 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 chunk 11 optimal weight: 0.9990 chunk 92 optimal weight: 4.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3723 r_free = 0.3723 target = 0.089440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.063463 restraints weight = 28488.085| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.83 r_work: 0.3010 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10881 Z= 0.158 Angle : 0.546 7.195 15052 Z= 0.273 Chirality : 0.039 0.127 1793 Planarity : 0.004 0.040 1729 Dihedral : 15.925 159.429 2383 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.94 % Allowed : 14.18 % Favored : 84.88 % 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: 1.58 (0.25), residues: 1221 helix: 2.81 (0.23), residues: 548 sheet: -0.82 (0.38), residues: 185 loop : -0.21 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 84 TYR 0.006 0.001 TYR D 168 PHE 0.018 0.001 PHE E 179 TRP 0.011 0.001 TRP E 183 HIS 0.002 0.001 HIS A 109 Details of bonding type rmsd covalent geometry : bond 0.00362 (10881) covalent geometry : angle 0.54635 (15052) hydrogen bonds : bond 0.03283 ( 479) hydrogen bonds : angle 4.68744 ( 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: 9 poor density : 160 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ASP cc_start: 0.9140 (m-30) cc_final: 0.8792 (m-30) REVERT: A 104 LYS cc_start: 0.9217 (mmtm) cc_final: 0.8660 (mmtm) REVERT: A 185 ASP cc_start: 0.8518 (m-30) cc_final: 0.8219 (m-30) REVERT: B 99 LYS cc_start: 0.9627 (mtpt) cc_final: 0.9111 (mptt) REVERT: B 203 THR cc_start: 0.9184 (OUTLIER) cc_final: 0.8885 (p) REVERT: C 28 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8532 (mt-10) REVERT: C 211 GLU cc_start: 0.8506 (mp0) cc_final: 0.8296 (mp0) REVERT: C 249 GLU cc_start: 0.8428 (tp30) cc_final: 0.7730 (tp30) REVERT: D 70 ASP cc_start: 0.9087 (m-30) cc_final: 0.8766 (t0) REVERT: D 242 GLU cc_start: 0.8958 (mt-10) cc_final: 0.8721 (mm-30) REVERT: D 254 ASP cc_start: 0.8864 (p0) cc_final: 0.8494 (p0) REVERT: E 384 PHE cc_start: 0.7856 (m-80) cc_final: 0.7110 (m-80) outliers start: 9 outliers final: 7 residues processed: 165 average time/residue: 0.1373 time to fit residues: 30.3391 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 : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain B residue 203 THR 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 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: 7.9990 chunk 28 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 11 optimal weight: 0.4980 chunk 125 optimal weight: 40.0000 chunk 15 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 152 ASN ** E 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 366 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.088592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.063432 restraints weight = 28638.992| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.86 r_work: 0.2999 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10881 Z= 0.166 Angle : 0.565 7.240 15052 Z= 0.282 Chirality : 0.039 0.133 1793 Planarity : 0.004 0.040 1729 Dihedral : 15.926 159.280 2383 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.36 % Allowed : 14.39 % Favored : 84.25 % 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: 1.56 (0.25), residues: 1221 helix: 2.79 (0.23), residues: 549 sheet: -0.77 (0.38), residues: 183 loop : -0.27 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 84 TYR 0.014 0.001 TYR A 168 PHE 0.019 0.001 PHE E 179 TRP 0.010 0.001 TRP E 183 HIS 0.002 0.001 HIS C 109 Details of bonding type rmsd covalent geometry : bond 0.00381 (10881) covalent geometry : angle 0.56479 (15052) hydrogen bonds : bond 0.03253 ( 479) hydrogen bonds : angle 4.64608 ( 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 174 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 161 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.9027 (mt-10) cc_final: 0.8773 (mt-10) REVERT: A 70 ASP cc_start: 0.9188 (m-30) cc_final: 0.8850 (m-30) REVERT: A 104 LYS cc_start: 0.9273 (mmtm) cc_final: 0.8704 (mmtm) REVERT: A 185 ASP cc_start: 0.8523 (m-30) cc_final: 0.8221 (m-30) REVERT: A 249 GLU cc_start: 0.8631 (tp30) cc_final: 0.8339 (tp30) REVERT: B 99 LYS cc_start: 0.9642 (mtpt) cc_final: 0.9081 (mptt) REVERT: C 28 GLU cc_start: 0.8788 (mt-10) cc_final: 0.8547 (mt-10) REVERT: C 211 GLU cc_start: 0.8466 (mp0) cc_final: 0.8263 (pm20) REVERT: C 249 GLU cc_start: 0.8308 (tp30) cc_final: 0.7613 (tp30) REVERT: D 70 ASP cc_start: 0.9094 (m-30) cc_final: 0.8760 (t0) REVERT: D 242 GLU cc_start: 0.8976 (mt-10) cc_final: 0.8726 (mm-30) REVERT: E 219 GLU cc_start: 0.9060 (mp0) cc_final: 0.8323 (pt0) REVERT: E 384 PHE cc_start: 0.7855 (m-80) cc_final: 0.7080 (m-80) outliers start: 13 outliers final: 9 residues processed: 167 average time/residue: 0.1364 time to fit residues: 30.6061 Evaluate side-chains 136 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 127 time to evaluate : 0.392 ------------------------------------------------------------------------------- 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 B residue 203 THR 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 274 THR Chi-restraints excluded: chain E residue 291 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 39 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 88 optimal weight: 10.0000 chunk 61 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 2 optimal weight: 0.3980 chunk 5 optimal weight: 1.9990 chunk 27 optimal weight: 9.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 366 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.089309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.063655 restraints weight = 28232.266| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.82 r_work: 0.3013 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.3463 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= 0.143 Angle : 0.562 7.770 15052 Z= 0.281 Chirality : 0.039 0.142 1793 Planarity : 0.004 0.040 1729 Dihedral : 15.865 159.055 2383 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.25 % Allowed : 14.91 % 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: 1.56 (0.25), residues: 1221 helix: 2.74 (0.23), residues: 549 sheet: -0.77 (0.38), residues: 183 loop : -0.19 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 84 TYR 0.006 0.001 TYR D 168 PHE 0.018 0.001 PHE E 179 TRP 0.007 0.001 TRP E 183 HIS 0.002 0.001 HIS A 109 Details of bonding type rmsd covalent geometry : bond 0.00331 (10881) covalent geometry : angle 0.56224 (15052) hydrogen bonds : bond 0.03128 ( 479) hydrogen bonds : angle 4.61343 ( 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 158 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 146 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.9041 (mt-10) cc_final: 0.8766 (mt-10) REVERT: A 70 ASP cc_start: 0.9153 (m-30) cc_final: 0.8823 (m-30) REVERT: A 104 LYS cc_start: 0.9242 (mmtm) cc_final: 0.8648 (mmtm) REVERT: A 147 ARG cc_start: 0.9243 (mtt90) cc_final: 0.9005 (ttm-80) REVERT: A 185 ASP cc_start: 0.8525 (m-30) cc_final: 0.8265 (m-30) REVERT: A 249 GLU cc_start: 0.8590 (tp30) cc_final: 0.8313 (tp30) REVERT: B 203 THR cc_start: 0.9181 (OUTLIER) cc_final: 0.8885 (p) REVERT: C 53 LYS cc_start: 0.9475 (ttpp) cc_final: 0.8921 (pttm) REVERT: C 211 GLU cc_start: 0.8458 (mp0) cc_final: 0.8232 (mp0) REVERT: D 70 ASP cc_start: 0.9090 (m-30) cc_final: 0.8754 (t0) REVERT: D 242 GLU cc_start: 0.8946 (mt-10) cc_final: 0.8669 (mm-30) REVERT: E 219 GLU cc_start: 0.9071 (mp0) cc_final: 0.8438 (pt0) REVERT: E 384 PHE cc_start: 0.7819 (m-80) cc_final: 0.7069 (m-80) outliers start: 12 outliers final: 7 residues processed: 153 average time/residue: 0.1244 time to fit residues: 25.9049 Evaluate side-chains 137 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 129 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 252 ARG Chi-restraints excluded: chain B residue 203 THR 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 291 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 49 optimal weight: 7.9990 chunk 21 optimal weight: 0.7980 chunk 101 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 61 optimal weight: 7.9990 chunk 47 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 97 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 152 ASN ** E 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 366 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.089754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.063939 restraints weight = 28304.037| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.85 r_work: 0.3027 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.3585 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= 0.128 Angle : 0.553 8.165 15052 Z= 0.277 Chirality : 0.039 0.150 1793 Planarity : 0.004 0.040 1729 Dihedral : 15.729 159.053 2383 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.04 % Allowed : 15.02 % Favored : 83.94 % 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: 1.59 (0.25), residues: 1221 helix: 2.74 (0.23), residues: 549 sheet: -0.74 (0.38), residues: 183 loop : -0.15 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 84 TYR 0.021 0.001 TYR A 168 PHE 0.018 0.001 PHE E 179 TRP 0.007 0.001 TRP E 233 HIS 0.002 0.000 HIS E 242 Details of bonding type rmsd covalent geometry : bond 0.00302 (10881) covalent geometry : angle 0.55339 (15052) hydrogen bonds : bond 0.03015 ( 479) hydrogen bonds : angle 4.53060 ( 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 152 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 142 time to evaluate : 0.327 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: 0.9036 (mt-10) cc_final: 0.8754 (mt-10) REVERT: A 70 ASP cc_start: 0.9131 (m-30) cc_final: 0.8792 (m-30) REVERT: A 104 LYS cc_start: 0.9218 (mmtm) cc_final: 0.8623 (mmtm) REVERT: A 147 ARG cc_start: 0.9266 (mtt90) cc_final: 0.8931 (ttm-80) REVERT: A 185 ASP cc_start: 0.8519 (m-30) cc_final: 0.8285 (m-30) REVERT: B 203 THR cc_start: 0.9172 (OUTLIER) cc_final: 0.8875 (p) REVERT: C 53 LYS cc_start: 0.9478 (ttpp) cc_final: 0.8881 (pttm) REVERT: C 147 ARG cc_start: 0.8928 (mtt90) cc_final: 0.8495 (ttm-80) REVERT: C 211 GLU cc_start: 0.8455 (mp0) cc_final: 0.8230 (mp0) REVERT: D 70 ASP cc_start: 0.9067 (m-30) cc_final: 0.8753 (m-30) REVERT: D 242 GLU cc_start: 0.8941 (mt-10) cc_final: 0.8684 (mm-30) REVERT: E 384 PHE cc_start: 0.7813 (m-80) cc_final: 0.7085 (m-80) outliers start: 10 outliers final: 7 residues processed: 148 average time/residue: 0.1133 time to fit residues: 23.1205 Evaluate side-chains 137 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 129 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 252 ARG Chi-restraints excluded: chain B residue 203 THR 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 291 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 98 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 chunk 52 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 93 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 47 optimal weight: 0.3980 chunk 28 optimal weight: 7.9990 chunk 49 optimal weight: 7.9990 chunk 125 optimal weight: 40.0000 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 152 ASN ** E 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 366 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.090022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.064193 restraints weight = 28243.966| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.86 r_work: 0.3036 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.3721 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= 0.125 Angle : 0.568 8.522 15052 Z= 0.284 Chirality : 0.039 0.152 1793 Planarity : 0.004 0.041 1729 Dihedral : 15.628 159.141 2383 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.15 % Allowed : 15.95 % 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: 1.62 (0.25), residues: 1221 helix: 2.74 (0.23), residues: 549 sheet: -0.67 (0.39), residues: 183 loop : -0.12 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 84 TYR 0.006 0.001 TYR D 168 PHE 0.018 0.001 PHE E 179 TRP 0.008 0.001 TRP E 233 HIS 0.001 0.000 HIS E 242 Details of bonding type rmsd covalent geometry : bond 0.00295 (10881) covalent geometry : angle 0.56782 (15052) hydrogen bonds : bond 0.02966 ( 479) hydrogen bonds : angle 4.51056 ( 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 158 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 147 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.9045 (mt-10) cc_final: 0.8776 (mt-10) REVERT: A 52 LYS cc_start: 0.9337 (mmtm) cc_final: 0.9128 (mmtm) REVERT: A 70 ASP cc_start: 0.9151 (m-30) cc_final: 0.8814 (m-30) REVERT: A 104 LYS cc_start: 0.9214 (mmtm) cc_final: 0.8618 (mmtm) REVERT: A 147 ARG cc_start: 0.9259 (mtt90) cc_final: 0.9029 (ttm-80) REVERT: A 185 ASP cc_start: 0.8503 (m-30) cc_final: 0.8291 (m-30) REVERT: A 249 GLU cc_start: 0.8562 (tp30) cc_final: 0.8311 (tp30) REVERT: B 113 ASP cc_start: 0.8997 (m-30) cc_final: 0.8712 (t0) REVERT: B 203 THR cc_start: 0.9168 (OUTLIER) cc_final: 0.8870 (p) REVERT: C 53 LYS cc_start: 0.9473 (ttpp) cc_final: 0.8871 (pttm) REVERT: C 147 ARG cc_start: 0.8917 (mtt90) cc_final: 0.8495 (ttm-80) REVERT: C 211 GLU cc_start: 0.8502 (mp0) cc_final: 0.8275 (mp0) REVERT: D 70 ASP cc_start: 0.9087 (m-30) cc_final: 0.8784 (m-30) REVERT: D 242 GLU cc_start: 0.8935 (mt-10) cc_final: 0.8681 (mm-30) REVERT: E 384 PHE cc_start: 0.7821 (m-80) cc_final: 0.7127 (m-80) outliers start: 11 outliers final: 9 residues processed: 154 average time/residue: 0.1075 time to fit residues: 22.8323 Evaluate side-chains 147 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 137 time to evaluate : 0.290 ------------------------------------------------------------------------------- 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 A residue 252 ARG Chi-restraints excluded: chain B residue 203 THR 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 254 LEU Chi-restraints excluded: chain E residue 291 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 9 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 108 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3688 r_free = 0.3688 target = 0.091401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.063927 restraints weight = 29305.469| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 3.07 r_work: 0.3031 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.3818 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= 0.123 Angle : 0.590 8.819 15052 Z= 0.294 Chirality : 0.039 0.151 1793 Planarity : 0.004 0.041 1729 Dihedral : 15.558 159.187 2383 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % 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: 1.62 (0.25), residues: 1221 helix: 2.72 (0.23), residues: 549 sheet: -0.68 (0.38), residues: 183 loop : -0.09 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 84 TYR 0.021 0.001 TYR A 168 PHE 0.017 0.001 PHE E 179 TRP 0.008 0.001 TRP E 233 HIS 0.001 0.000 HIS E 242 Details of bonding type rmsd covalent geometry : bond 0.00296 (10881) covalent geometry : angle 0.59048 (15052) hydrogen bonds : bond 0.02926 ( 479) hydrogen bonds : angle 4.44245 ( 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 151 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 141 time to evaluate : 0.389 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: 0.9014 (mt-10) cc_final: 0.8775 (mt-10) REVERT: A 52 LYS cc_start: 0.9352 (mmtm) cc_final: 0.9146 (mmtm) REVERT: A 70 ASP cc_start: 0.9147 (m-30) cc_final: 0.8818 (m-30) REVERT: A 104 LYS cc_start: 0.9238 (mmtm) cc_final: 0.8654 (mmtm) REVERT: A 147 ARG cc_start: 0.9292 (mtt90) cc_final: 0.8919 (ttm-80) REVERT: A 249 GLU cc_start: 0.8582 (tp30) cc_final: 0.8320 (tp30) REVERT: B 113 ASP cc_start: 0.9036 (m-30) cc_final: 0.8748 (t0) REVERT: B 203 THR cc_start: 0.9142 (OUTLIER) cc_final: 0.8838 (p) REVERT: C 53 LYS cc_start: 0.9479 (ttpp) cc_final: 0.8871 (pttm) REVERT: C 147 ARG cc_start: 0.8917 (mtt90) cc_final: 0.8484 (ttm-80) REVERT: C 211 GLU cc_start: 0.8522 (mp0) cc_final: 0.8302 (mp0) REVERT: D 70 ASP cc_start: 0.9112 (m-30) cc_final: 0.8831 (m-30) REVERT: D 242 GLU cc_start: 0.8985 (mt-10) cc_final: 0.8732 (mm-30) REVERT: E 298 MET cc_start: 0.8493 (ttp) cc_final: 0.8268 (ppp) REVERT: E 384 PHE cc_start: 0.7803 (m-80) cc_final: 0.7082 (m-80) outliers start: 10 outliers final: 9 residues processed: 147 average time/residue: 0.1112 time to fit residues: 22.6189 Evaluate side-chains 149 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 139 time to evaluate : 0.393 ------------------------------------------------------------------------------- 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 A residue 252 ARG Chi-restraints excluded: chain B residue 203 THR 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 254 LEU Chi-restraints excluded: chain E residue 291 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 55 optimal weight: 10.0000 chunk 96 optimal weight: 0.7980 chunk 28 optimal weight: 0.0470 chunk 16 optimal weight: 0.9990 chunk 124 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 79 optimal weight: 0.5980 chunk 119 optimal weight: 6.9990 chunk 69 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 226 GLN ** 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 = 0.3702 r_free = 0.3702 target = 0.092160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.064878 restraints weight = 29441.126| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 3.06 r_work: 0.3051 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.3963 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= 0.114 Angle : 0.578 8.889 15052 Z= 0.287 Chirality : 0.039 0.148 1793 Planarity : 0.004 0.040 1729 Dihedral : 15.437 159.184 2383 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.04 % Allowed : 15.95 % Favored : 83.00 % 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: 1.65 (0.25), residues: 1221 helix: 2.72 (0.23), residues: 549 sheet: -0.63 (0.39), residues: 183 loop : -0.06 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 84 TYR 0.007 0.001 TYR D 168 PHE 0.016 0.001 PHE E 179 TRP 0.009 0.001 TRP E 233 HIS 0.001 0.000 HIS E 242 Details of bonding type rmsd covalent geometry : bond 0.00274 (10881) covalent geometry : angle 0.57754 (15052) hydrogen bonds : bond 0.02815 ( 479) hydrogen bonds : angle 4.39842 ( 1337) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2562.43 seconds wall clock time: 44 minutes 55.80 seconds (2695.80 seconds total)