Starting phenix.real_space_refine on Sat Jul 4 03:03:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8b0i_15784/07_2026/8b0i_15784.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b0i_15784/07_2026/8b0i_15784.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8b0i_15784/07_2026/8b0i_15784.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8b0i_15784/07_2026/8b0i_15784.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8b0i_15784/07_2026/8b0i_15784.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b0i_15784/07_2026/8b0i_15784.map" model { file = "/net/cci-nas-00/data/ceres_data/8b0i_15784/07_2026/8b0i_15784.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b0i_15784/07_2026/8b0i_15784.cif" } resolution = 4.28 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= 0.007 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: 6 Type Number sf(0) Gaussians P 103 5.49 5 S 20 5.16 5 C 5767 2.51 5 N 1701 2.21 5 O 2214 1.98 5 H 7831 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17636 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 3560 Classifications: {'peptide': 270} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 255} Chain breaks: 1 Unresolved non-hydrogen bonds: 285 Unresolved non-hydrogen angles: 354 Unresolved non-hydrogen dihedrals: 237 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ARG:plan': 15, 'TYR:plan': 2, 'GLU:plan': 8, 'ASP:plan': 4, 'PHE:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 2, 'GLN:plan1': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 180 Chain: "B" Number of atoms: 3825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 3825 Classifications: {'peptide': 281} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 15, 'TRANS': 265} Chain breaks: 1 Unresolved non-hydrogen bonds: 276 Unresolved non-hydrogen angles: 346 Unresolved non-hydrogen dihedrals: 234 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ARG:plan': 14, 'TYR:plan': 4, 'ASN:plan1': 5, 'ASP:plan': 4, 'GLU:plan': 4, 'PHE:plan': 5, 'GLN:plan1': 3, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 198 Chain: "D" Number of atoms: 3763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 3763 Classifications: {'peptide': 282} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 15, 'TRANS': 266} Unresolved non-hydrogen bonds: 275 Unresolved non-hydrogen angles: 342 Unresolved non-hydrogen dihedrals: 227 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'ARG:plan': 13, 'PHE:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 2, 'GLU:plan': 7, 'GLN:plan1': 2, 'HIS:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 163 Chain: "C" Number of atoms: 3298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 3298 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 14, 'TRANS': 227} Chain breaks: 4 Unresolved non-hydrogen bonds: 211 Unresolved non-hydrogen angles: 254 Unresolved non-hydrogen dihedrals: 183 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ARG:plan': 12, 'GLU:plan': 5, 'ASN:plan1': 1, 'PHE:plan': 2, 'HIS:plan': 2, 'ASP:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 117 Chain: "K" Number of atoms: 3190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 3190 Classifications: {'RNA': 103} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 27, 'rna3p_pur': 36, 'rna3p_pyr': 31} Link IDs: {'rna2p': 36, 'rna3p': 66} Chain breaks: 5 Time building chain proxies: 3.35, per 1000 atoms: 0.19 Number of scatterers: 17636 At special positions: 0 Unit cell: (93.888, 107.58, 142.788, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 20 16.00 P 103 15.00 O 2214 8.00 N 1701 7.00 C 5767 6.00 H 7831 1.00 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: 1.70 Conformation dependent library (CDL) restraints added in 644.3 milliseconds 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2058 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 10 sheets defined 49.2% alpha, 8.5% beta 6 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 2.84 Creating SS restraints... Processing helix chain 'A' and resid 13 through 24 Processing helix chain 'A' and resid 36 through 48 Processing helix chain 'A' and resid 63 through 74 Processing helix chain 'A' and resid 88 through 96 removed outlier: 3.723A pdb=" N TYR A 96 " --> pdb=" O LEU A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 129 removed outlier: 3.939A pdb=" N GLU A 119 " --> pdb=" O ALA A 115 " (cutoff:3.500A) Proline residue: A 125 - end of helix Processing helix chain 'A' and resid 140 through 153 Processing helix chain 'A' and resid 188 through 192 removed outlier: 3.762A pdb=" N TRP A 191 " --> pdb=" O ASN A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 212 Processing helix chain 'A' and resid 212 through 235 removed outlier: 3.728A pdb=" N HIS A 216 " --> pdb=" O HIS A 212 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR A 220 " --> pdb=" O HIS A 216 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TRP A 229 " --> pdb=" O TYR A 225 " (cutoff:3.500A) Proline residue: A 231 - end of helix removed outlier: 3.962A pdb=" N THR A 235 " --> pdb=" O PRO A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 268 removed outlier: 4.089A pdb=" N TYR A 256 " --> pdb=" O HIS A 252 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ILE A 257 " --> pdb=" O ARG A 253 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TYR A 264 " --> pdb=" O GLN A 260 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE A 265 " --> pdb=" O LEU A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 281 removed outlier: 3.977A pdb=" N LYS A 281 " --> pdb=" O ARG A 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 25 Processing helix chain 'B' and resid 36 through 41 removed outlier: 3.859A pdb=" N LEU B 40 " --> pdb=" O LEU B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 47 Processing helix chain 'B' and resid 64 through 73 Processing helix chain 'B' and resid 88 through 99 Processing helix chain 'B' and resid 111 through 123 removed outlier: 3.677A pdb=" N ASP B 121 " --> pdb=" O ASP B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 129 Processing helix chain 'B' and resid 140 through 155 removed outlier: 3.681A pdb=" N GLU B 146 " --> pdb=" O HIS B 142 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET B 147 " --> pdb=" O GLU B 143 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS B 155 " --> pdb=" O ARG B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 212 removed outlier: 4.102A pdb=" N HIS B 212 " --> pdb=" O PHE B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 235 removed outlier: 3.919A pdb=" N TRP B 229 " --> pdb=" O TYR B 225 " (cutoff:3.500A) Proline residue: B 231 - end of helix removed outlier: 4.053A pdb=" N THR B 235 " --> pdb=" O PRO B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 269 Processing helix chain 'D' and resid 13 through 25 removed outlier: 4.157A pdb=" N ALA D 17 " --> pdb=" O GLY D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 35 No H-bonds generated for 'chain 'D' and resid 33 through 35' Processing helix chain 'D' and resid 36 through 46 removed outlier: 4.142A pdb=" N ASP D 46 " --> pdb=" O ARG D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 72 Processing helix chain 'D' and resid 88 through 99 Processing helix chain 'D' and resid 111 through 130 removed outlier: 3.776A pdb=" N ALA D 115 " --> pdb=" O SER D 111 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ILE D 116 " --> pdb=" O LEU D 112 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ASP D 117 " --> pdb=" O GLU D 113 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASP D 121 " --> pdb=" O ASP D 117 " (cutoff:3.500A) Proline residue: D 125 - end of helix Processing helix chain 'D' and resid 140 through 148 removed outlier: 3.820A pdb=" N ALA D 145 " --> pdb=" O VAL D 141 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU D 146 " --> pdb=" O HIS D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 151 No H-bonds generated for 'chain 'D' and resid 149 through 151' Processing helix chain 'D' and resid 188 through 192 Processing helix chain 'D' and resid 205 through 212 Processing helix chain 'D' and resid 212 through 228 removed outlier: 3.668A pdb=" N LEU D 228 " --> pdb=" O SER D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 235 removed outlier: 3.737A pdb=" N THR D 235 " --> pdb=" O PRO D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 269 removed outlier: 5.922A pdb=" N TYR D 256 " --> pdb=" O HIS D 252 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ILE D 257 " --> pdb=" O ARG D 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 25 removed outlier: 3.621A pdb=" N GLU C 22 " --> pdb=" O LEU C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 48 removed outlier: 4.172A pdb=" N ASP C 39 " --> pdb=" O VAL C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 74 Processing helix chain 'C' and resid 125 through 130 removed outlier: 3.663A pdb=" N ARG C 129 " --> pdb=" O PRO C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 145 Processing helix chain 'C' and resid 148 through 152 Processing helix chain 'C' and resid 188 through 192 Processing helix chain 'C' and resid 202 through 212 removed outlier: 3.544A pdb=" N PHE C 208 " --> pdb=" O PRO C 204 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG C 211 " --> pdb=" O ALA C 207 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N HIS C 212 " --> pdb=" O PHE C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 235 removed outlier: 3.708A pdb=" N HIS C 216 " --> pdb=" O HIS C 212 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TRP C 229 " --> pdb=" O TYR C 225 " (cutoff:3.500A) Proline residue: C 231 - end of helix Processing helix chain 'C' and resid 251 through 269 removed outlier: 4.497A pdb=" N TYR C 256 " --> pdb=" O HIS C 252 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N ILE C 257 " --> pdb=" O ARG C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 281 removed outlier: 4.259A pdb=" N LYS C 281 " --> pdb=" O THR C 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 278 through 281' Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7 removed outlier: 6.997A pdb=" N LEU A 3 " --> pdb=" O GLN A 81 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N LEU A 83 " --> pdb=" O LEU A 3 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ILE A 5 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU A 132 " --> pdb=" O LEU A 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 164 through 168 removed outlier: 6.190A pdb=" N GLU A 165 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N CYS A 247 " --> pdb=" O GLU A 165 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N PHE A 167 " --> pdb=" O CYS A 247 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 180 through 181 removed outlier: 3.668A pdb=" N VAL A 180 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL B 180 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N TYR B 179 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N GLY B 246 " --> pdb=" O TYR B 179 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N PHE B 181 " --> pdb=" O GLY B 246 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N PHE B 167 " --> pdb=" O CYS B 247 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.633A pdb=" N ASP B 86 " --> pdb=" O VAL B 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 161 through 163 removed outlier: 5.583A pdb=" N THR B 161 " --> pdb=" O LEU B 241 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'D' and resid 5 through 6 removed outlier: 6.755A pdb=" N ILE D 5 " --> pdb=" O LEU D 83 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N LEU D 85 " --> pdb=" O ILE D 5 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 27 through 30 removed outlier: 5.493A pdb=" N TYR D 27 " --> pdb=" O ALA D 52 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N SER D 54 " --> pdb=" O TYR D 27 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N VAL D 29 " --> pdb=" O SER D 54 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 272 through 274 removed outlier: 3.537A pdb=" N ILE D 245 " --> pdb=" O GLU D 165 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N TYR D 179 " --> pdb=" O ALA D 244 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N GLY D 246 " --> pdb=" O TYR D 179 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N PHE D 181 " --> pdb=" O GLY D 246 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL D 180 " --> pdb=" O VAL C 180 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 27 through 30 removed outlier: 6.678A pdb=" N TYR C 27 " --> pdb=" O ALA C 52 " (cutoff:3.500A) removed outlier: 8.893A pdb=" N SER C 54 " --> pdb=" O TYR C 27 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N VAL C 29 " --> pdb=" O SER C 54 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 244 through 246 removed outlier: 7.874A pdb=" N ILE C 245 " --> pdb=" O VAL C 163 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N GLU C 165 " --> pdb=" O ILE C 245 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N MET C 162 " --> pdb=" O GLN C 273 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N ARG C 275 " --> pdb=" O MET C 162 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N PHE C 164 " --> pdb=" O ARG C 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 314 hydrogen bonds defined for protein. 912 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 13 hydrogen bonds 22 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 27 stacking parallelities Total time for adding SS restraints: 4.07 Time building geometry restraints manager: 2.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 7379 1.03 - 1.23: 791 1.23 - 1.42: 4059 1.42 - 1.62: 5727 1.62 - 1.81: 64 Bond restraints: 18020 Sorted by residual: bond pdb=" N2 G K 115 " pdb=" H21 G K 115 " ideal model delta sigma weight residual 0.860 1.049 -0.189 2.00e-02 2.50e+03 8.91e+01 bond pdb=" N3 U K 32 " pdb=" H3 U K 32 " ideal model delta sigma weight residual 0.860 1.040 -0.180 2.00e-02 2.50e+03 8.12e+01 bond pdb=" N3 U K 70 " pdb=" H3 U K 70 " ideal model delta sigma weight residual 0.860 1.040 -0.180 2.00e-02 2.50e+03 8.12e+01 bond pdb=" N3 U K 69 " pdb=" H3 U K 69 " ideal model delta sigma weight residual 0.860 1.040 -0.180 2.00e-02 2.50e+03 8.10e+01 bond pdb=" N1 G K 135 " pdb=" H1 G K 135 " ideal model delta sigma weight residual 0.860 1.040 -0.180 2.00e-02 2.50e+03 8.08e+01 ... (remaining 18015 not shown) Histogram of bond angle deviations from ideal: 0.00 - 21.76: 32283 21.76 - 43.51: 5 43.51 - 65.27: 0 65.27 - 87.02: 0 87.02 - 108.78: 5 Bond angle restraints: 32293 Sorted by residual: angle pdb=" H5' G K 73 " pdb=" C5' G K 73 " pdb="H5'' G K 73 " ideal model delta sigma weight residual 109.00 0.22 108.78 3.00e+00 1.11e-01 1.31e+03 angle pdb=" H5' U K 84 " pdb=" C5' U K 84 " pdb="H5'' U K 84 " ideal model delta sigma weight residual 109.00 0.53 108.47 3.00e+00 1.11e-01 1.31e+03 angle pdb=" H5' A K 45 " pdb=" C5' A K 45 " pdb="H5'' A K 45 " ideal model delta sigma weight residual 109.00 0.85 108.15 3.00e+00 1.11e-01 1.30e+03 angle pdb=" H5' A K 129 " pdb=" C5' A K 129 " pdb="H5'' A K 129 " ideal model delta sigma weight residual 109.00 0.96 108.04 3.00e+00 1.11e-01 1.30e+03 angle pdb=" O5' G K 123 " pdb=" C5' G K 123 " pdb="H5'' G K 123 " ideal model delta sigma weight residual 109.00 21.92 87.08 3.00e+00 1.11e-01 8.43e+02 ... (remaining 32288 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 7901 35.99 - 71.99: 402 71.99 - 107.98: 87 107.98 - 143.98: 5 143.98 - 179.97: 37 Dihedral angle restraints: 8432 sinusoidal: 4922 harmonic: 3510 Sorted by residual: dihedral pdb=" O4' U K 138 " pdb=" C1' U K 138 " pdb=" N1 U K 138 " pdb=" C2 U K 138 " ideal model delta sinusoidal sigma weight residual 200.00 43.52 156.48 1 1.50e+01 4.44e-03 8.18e+01 dihedral pdb=" O4' U K 84 " pdb=" C1' U K 84 " pdb=" N1 U K 84 " pdb=" C2 U K 84 " ideal model delta sinusoidal sigma weight residual 200.00 50.85 149.15 1 1.50e+01 4.44e-03 7.93e+01 dihedral pdb=" O4' C K 85 " pdb=" C1' C K 85 " pdb=" N1 C K 85 " pdb=" C2 C K 85 " ideal model delta sinusoidal sigma weight residual 200.00 51.23 148.77 1 1.50e+01 4.44e-03 7.92e+01 ... (remaining 8429 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.129: 1374 0.129 - 0.257: 380 0.257 - 0.386: 29 0.386 - 0.514: 4 0.514 - 0.643: 1 Chirality restraints: 1788 Sorted by residual: chirality pdb=" C3' U K 36 " pdb=" C4' U K 36 " pdb=" O3' U K 36 " pdb=" C2' U K 36 " both_signs ideal model delta sigma weight residual False -2.74 -2.10 -0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" C3' G K 37 " pdb=" C4' G K 37 " pdb=" O3' G K 37 " pdb=" C2' G K 37 " both_signs ideal model delta sigma weight residual False -2.74 -2.24 -0.50 2.00e-01 2.50e+01 6.34e+00 chirality pdb=" C3' A K 53 " pdb=" C4' A K 53 " pdb=" O3' A K 53 " pdb=" C2' A K 53 " both_signs ideal model delta sigma weight residual False -2.74 -2.27 -0.47 2.00e-01 2.50e+01 5.56e+00 ... (remaining 1785 not shown) Planarity restraints: 2593 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 59 " -0.240 2.00e-02 2.50e+03 3.52e-01 1.86e+03 pdb=" CG ASN A 59 " 0.018 2.00e-02 2.50e+03 pdb=" OD1 ASN A 59 " 0.228 2.00e-02 2.50e+03 pdb=" ND2 ASN A 59 " 0.006 2.00e-02 2.50e+03 pdb="HD21 ASN A 59 " -0.569 2.00e-02 2.50e+03 pdb="HD22 ASN A 59 " 0.557 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 271 " -0.238 2.00e-02 2.50e+03 3.07e-01 1.41e+03 pdb=" CG ASN B 271 " 0.023 2.00e-02 2.50e+03 pdb=" OD1 ASN B 271 " 0.228 2.00e-02 2.50e+03 pdb=" ND2 ASN B 271 " 0.002 2.00e-02 2.50e+03 pdb="HD21 ASN B 271 " -0.485 2.00e-02 2.50e+03 pdb="HD22 ASN B 271 " 0.470 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 69 " -0.191 2.00e-02 2.50e+03 2.22e-01 7.36e+02 pdb=" CD GLN C 69 " 0.013 2.00e-02 2.50e+03 pdb=" OE1 GLN C 69 " 0.186 2.00e-02 2.50e+03 pdb=" NE2 GLN C 69 " -0.004 2.00e-02 2.50e+03 pdb="HE21 GLN C 69 " 0.333 2.00e-02 2.50e+03 pdb="HE22 GLN C 69 " -0.336 2.00e-02 2.50e+03 ... (remaining 2590 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 1155 2.23 - 2.82: 34628 2.82 - 3.42: 44190 3.42 - 4.01: 55099 4.01 - 4.60: 81309 Nonbonded interactions: 216381 Sorted by model distance: nonbonded pdb=" O SER D 114 " pdb=" HG SER D 114 " model vdw 1.640 2.450 nonbonded pdb=" H3 MET A 1 " pdb=" O ALA A 77 " model vdw 1.647 2.450 nonbonded pdb=" O TYR B 96 " pdb=" HG1 THR B 99 " model vdw 1.665 2.450 nonbonded pdb=" O GLN A 221 " pdb=" HG SER A 224 " model vdw 1.696 2.450 nonbonded pdb=" H8 A K 23 " pdb=" H2 A K 54 " model vdw 1.706 2.100 ... (remaining 216376 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 or (resid 3 through 4 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 5 through 6 or resid 13 or \ (resid 14 and (name N or name CA or name C or name O or name CB or name H or nam \ e HA )) or resid 15 through 18 or (resid 19 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 20 through 21 or (resid 22 an \ d (name N or name CA or name C or name O or name CB or name H or name HA )) or r \ esid 23 or (resid 24 and (name N or name CA or name C or name O or name CB or na \ me H or name HA )) or resid 25 or (resid 26 through 29 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 30 or (resid 31 th \ rough 32 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 33 or (resid 34 and (name N or name CA or name C or name O or na \ me CB or name H or name HA )) or resid 35 or (resid 36 through 37 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 38 thro \ ugh 41 or (resid 42 and (name N or name CA or name C or name O or name CB or nam \ e H or name HA )) or resid 43 or (resid 44 and (name N or name CA or name C or n \ ame O or name CB or name H or name HA )) or resid 45 or (resid 46 through 49 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or re \ sid 50 through 55 or (resid 56 and (name N or name CA or name C or name O or nam \ e CB or name H or name HA )) or resid 57 through 58 or (resid 59 through 60 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or res \ id 61 or resid 63 through 65 or (resid 66 through 69 and (name N or name CA or n \ ame C or name O or name CB or name H or name HA )) or resid 70 through 73 or (re \ sid 74 and (name N or name CA or name C or name O or name CB or name H or name H \ A )) or resid 75 through 77 or (resid 78 and (name N or name CA or name C or nam \ e O or name CB or name H or name HA )) or resid 79 through 80 or (resid 81 throu \ gh 84 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 86 through 87 or (resid 88 through 91 and (name N or name CA or nam \ e C or name O or name CB or name H or name HA )) or resid 92 or resid 124 throug \ h 128 or (resid 129 and (name N or name CA or name C or name O or name CB or nam \ e H or name HA )) or resid 130 through 132 or (resid 133 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 134 through 141 \ or (resid 142 through 144 and (name N or name CA or name C or name O or name CB \ or name H or name HA )) or resid 145 or resid 147 through 150 or (resid 151 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or res \ id 152 through 156 or (resid 157 through 158 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 159 or (resid 160 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 161 \ through 162 or (resid 163 through 165 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 166 or (resid 167 and (name N or n \ ame CA or name C or name O or name CB or name H or name HA )) or resid 168 throu \ gh 169 or (resid 170 and (name N or name CA or name C or name O or name CB or na \ me CG or name CD or name CE or name H or name HA or name HB2 or name HB3 or name \ HG2 or name HG3 or name HD2 or name HD3)) or resid 171 through 172 or (resid 17 \ 3 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 174 through 177 or (resid 178 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 179 through 181 or (resid 182 thro \ ugh 186 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 187 through 194 or (resid 195 through 196 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 197 through 200 \ or (resid 201 through 203 and (name N or name CA or name C or name O or name CB \ or name H or name HA )) or resid 204 through 214 or (resid 215 and (name N or na \ me CA or name C or name O or name CB or name H or name HA )) or resid 216 throug \ h 217 or (resid 218 and (name N or name CA or name C or name O or name CB or nam \ e H or name HA )) or resid 219 through 221 or (resid 222 through 223 and (name N \ or name CA or name C or name O or name CB or name H or name HA )) or resid 224 \ through 227 or (resid 228 through 230 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 231 through 234 or (resid 235 throu \ gh 238 and (name N or name CA or name C or name O or name CB or name H or name H \ A )) or resid 239 through 240 or (resid 241 through 242 and (name N or name CA o \ r name C or name O or name CB or name H or name HA )) or resid 243 through 252 o \ r (resid 253 through 257 and (name N or name CA or name C or name O or name CB o \ r name H or name HA )) or resid 258 through 260 or (resid 261 and (name N or nam \ e CA or name C or name O or name CB or name H or name HA )) or resid 262 through \ 263 or (resid 264 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 265 or (resid 266 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 267 through 269 or (resid 270 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) o \ r resid 271 through 275 or (resid 276 through 280 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 281 through 282)) selection = (chain 'B' and (resid 2 or (resid 3 through 4 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 5 through 6 or resid 13 or \ (resid 14 and (name N or name CA or name C or name O or name CB or name H or nam \ e HA )) or resid 15 through 17 or (resid 18 through 19 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 20 or (resid 21 th \ rough 22 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 23 through 25 or (resid 26 through 29 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 30 through 48 or (r \ esid 49 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 50 through 64 or (resid 65 through 69 and (name N or name CA or n \ ame C or name O or name CB or name H or name HA )) or resid 70 through 73 or (re \ sid 74 and (name N or name CA or name C or name O or name CB or name H or name H \ A )) or resid 75 through 84 or (resid 86 and (name N or name CA or name C or nam \ e O or name CB or name H or name HA )) or resid 87 through 88 or (resid 89 throu \ gh 91 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 92 or (resid 124 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 125 or (resid 126 through 127 and (name N o \ r name CA or name C or name O or name CB or name H or name HA )) or resid 128 th \ rough 132 or (resid 133 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or resid 134 through 135 or (resid 136 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 137 or (resi \ d 138 through 139 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 140 through 141 or (resid 142 through 144 and (name N o \ r name CA or name C or name O or name CB or name H or name HA )) or resid 145 or \ resid 147 through 148 or (resid 149 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 150 or (resid 151 and (name N or nam \ e CA or name C or name O or name CB or name H or name HA )) or resid 152 or (res \ id 153 and (name N or name CA or name C or name O or name CB or name H or name H \ A )) or (resid 154 and (name N or name CA or name C or name O or name H )) or (r \ esid 155 through 158 and (name N or name CA or name C or name O or name CB or na \ me H or name HA )) or resid 159 or (resid 160 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 161 through 169 or (resid 1 \ 70 and (name N or name CA or name C or name O or name CB or name CG or name CD o \ r name CE or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 o \ r name HD2 or name HD3)) or resid 171 through 172 or (resid 173 and (name N or n \ ame CA or name C or name O or name CB or name H or name HA )) or resid 174 throu \ gh 181 or (resid 182 through 186 and (name N or name CA or name C or name O or n \ ame CB or name H or name HA )) or resid 187 or (resid 188 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 189 or (resid 1 \ 90 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 191 or (resid 192 and (name N or name CA or name C or name O or name C \ B or name H or name HA )) or resid 193 or (resid 194 through 196 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 197 or ( \ resid 198 through 199 and (name N or name CA or name C or name O or name CB or n \ ame H or name HA )) or resid 200 or (resid 201 through 203 and (name N or name C \ A or name C or name O or name CB or name H or name HA )) or resid 204 through 20 \ 7 or (resid 208 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 209 through 210 or (resid 211 and (name N or name CA or n \ ame C or name O or name CB or name H or name HA )) or resid 212 through 213 or ( \ resid 214 through 215 and (name N or name CA or name C or name O or name CB or n \ ame H or name HA )) or resid 216 through 217 or (resid 218 and (name N or name C \ A or name C or name O or name CB or name H or name HA )) or resid 219 through 22 \ 7 or (resid 228 through 230 and (name N or name CA or name C or name O or name C \ B or name H or name HA )) or resid 231 through 234 or (resid 235 through 238 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or re \ sid 239 through 240 or (resid 241 through 242 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 243 through 253 or (resid 2 \ 54 through 257 and (name N or name CA or name C or name O or name CB or name H o \ r name HA )) or resid 258 through 259 or (resid 260 through 261 and (name N or n \ ame CA or name C or name O or name CB or name H or name HA )) or resid 262 throu \ gh 269 or (resid 270 and (name N or name CA or name C or name O or name CB or na \ me H or name HA )) or resid 271 through 274 or (resid 275 through 280 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 281 \ through 282)) selection = (chain 'C' and (resid 2 or (resid 3 through 4 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 5 through 17 or (resid 18 t \ hrough 19 and (name N or name CA or name C or name O or name CB or name H or nam \ e HA )) or resid 20 or (resid 21 through 22 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 23 through 25 or (resid 26 th \ rough 29 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 30 or (resid 31 through 32 and (name N or name CA or name C or n \ ame O or name CB or name H or name HA )) or resid 33 or (resid 34 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 35 thro \ ugh 36 or (resid 37 and (name N or name CA or name C or name O or name CB or nam \ e H or name HA )) or resid 38 through 39 or (resid 40 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 41 or (resid 42 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or re \ sid 43 through 45 or (resid 46 through 49 and (name N or name CA or name C or na \ me O or name CB or name H or name HA )) or resid 50 through 55 or (resid 56 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or res \ id 57 or (resid 58 through 60 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 61 or resid 63 through 65 or (resid 66 thro \ ugh 69 and (name N or name CA or name C or name O or name CB or name H or name H \ A )) or resid 70 through 73 or (resid 74 and (name N or name CA or name C or nam \ e O or name CB or name H or name HA )) or resid 75 through 77 or (resid 78 and ( \ name N or name CA or name C or name O or name CB or name H or name HA )) or resi \ d 79 through 80 or (resid 81 through 86 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 87 or (resid 88 through 91 and (n \ ame N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 92 or (resid 124 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 125 or (resid 126 through 127 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 128 or (resid 129 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 130 through 135 or (resid 136 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 137 through 142 or (resid 143 throug \ h 144 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 145 through 152 or (resid 153 and (name N or name CA or name C or n \ ame O or name CB or name H or name HA )) or resid 154 through 162 or (resid 163 \ through 165 and (name N or name CA or name C or name O or name CB or name H or n \ ame HA )) or resid 166 or (resid 167 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 168 through 177 or (resid 178 and (n \ ame N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 179 through 181 or (resid 182 through 186 and (name N or name CA or name C or n \ ame O or name CB or name H or name HA )) or resid 187 or (resid 188 and (name N \ or name CA or name C or name O or name CB or name H or name HA )) or resid 189 o \ r (resid 190 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 191 or (resid 192 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 193 or (resid 194 through 196 and ( \ name N or name CA or name C or name O or name CB or name H or name HA )) or resi \ d 197 through 198 or (resid 199 and (name N or name CA or name C or name O or na \ me CB or name H or name HA )) or resid 200 or (resid 201 through 203 and (name N \ or name CA or name C or name O or name CB or name H or name HA )) or resid 204 \ through 207 or (resid 208 and (name N or name CA or name C or name O or name CB \ or name H or name HA )) or resid 209 through 210 or (resid 211 and (name N or na \ me CA or name C or name O or name CB or name H or name HA )) or resid 212 throug \ h 213 or (resid 214 through 215 and (name N or name CA or name C or name O or na \ me CB or name H or name HA )) or resid 216 through 217 or (resid 218 and (name N \ or name CA or name C or name O or name CB or name H or name HA )) or resid 219 \ through 220 or (resid 221 through 223 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 224 through 227 or (resid 228 throu \ gh 230 and (name N or name CA or name C or name O or name CB or name H or name H \ A )) or resid 231 or (resid 232 and (name N or name CA or name C or name O or na \ me CB or name H or name HA )) or resid 233 through 234 or (resid 235 through 238 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) o \ r resid 239 through 254 or (resid 255 through 257 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 258 through 259 or (res \ id 260 through 261 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 262 through 263 or (resid 264 and (name N or name CA o \ r name C or name O or name CB or name H or name HA )) or resid 265 through 272 o \ r (resid 273 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 274 or (resid 275 through 280 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 281 through 282)) selection = (chain 'D' and (resid 2 through 3 or (resid 4 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 5 through 6 or resid 13 or \ (resid 14 and (name N or name CA or name C or name O or name CB or name H or nam \ e HA )) or resid 15 through 17 or (resid 18 through 19 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 20 or (resid 21 th \ rough 22 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 23 or (resid 24 and (name N or name CA or name C or name O or na \ me CB or name H or name HA )) or resid 25 through 30 or (resid 31 through 32 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or re \ sid 33 or (resid 34 and (name N or name CA or name C or name O or name CB or nam \ e H or name HA )) or resid 35 or (resid 36 through 37 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 38 through 41 or (r \ esid 42 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 43 through 45 or (resid 46 through 49 and (name N or name CA or n \ ame C or name O or name CB or name H or name HA )) or resid 50 through 55 or (re \ sid 56 and (name N or name CA or name C or name O or name CB or name H or name H \ A )) or resid 57 or (resid 58 through 60 and (name N or name CA or name C or nam \ e O or name CB or name H or name HA )) or resid 61 or resid 63 through 66 or (re \ sid 67 through 69 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 70 through 77 or (resid 78 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 79 through 81 or (res \ id 82 through 84 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or (resid 86 and (name N or name CA or name C or name O or name C \ B or name H or name HA )) or resid 87 or (resid 88 through 91 and (name N or nam \ e CA or name C or name O or name CB or name H or name HA )) or resid 92 or (resi \ d 124 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 125 through 126 or (resid 127 and (name N or name CA or name C or n \ ame O or name CB or name H or name HA )) or resid 128 through 132 or (resid 133 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 134 through 135 or (resid 136 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 137 or (resid 138 through 139 and (n \ ame N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 140 through 141 or (resid 142 through 144 and (name N or name CA or name C or n \ ame O or name CB or name H or name HA )) or resid 145 or (resid 147 and (name N \ or name CA or name C or name O or name CB or name H or name HA )) or resid 148 o \ r (resid 149 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 150 or (resid 151 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 152 through 157 or (resid 158 and ( \ name N or name CA or name C or name O or name CB or name H or name HA )) or resi \ d 159 or (resid 160 and (name N or name CA or name C or name O or name CB or nam \ e H or name HA )) or resid 161 or (resid 162 through 165 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 166 or (resid 16 \ 7 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 168 through 169 or (resid 170 and (name N or name CA or name C or name \ O or name CB or name CG or name CD or name CE or name H or name HA or name HB2 o \ r name HB3 or name HG2 or name HG3 or name HD2 or name HD3)) or resid 171 throug \ h 172 or (resid 173 and (name N or name CA or name C or name O or name CB or nam \ e H or name HA )) or resid 174 through 177 or (resid 178 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 179 through 183 \ or (resid 184 through 186 and (name N or name CA or name C or name O or name CB \ or name H or name HA )) or resid 187 or (resid 188 and (name N or name CA or nam \ e C or name O or name CB or name H or name HA )) or resid 189 or (resid 190 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or res \ id 191 or (resid 192 and (name N or name CA or name C or name O or name CB or na \ me H or name HA )) or resid 193 or (resid 194 through 196 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 197 or (resid 1 \ 98 through 199 and (name N or name CA or name C or name O or name CB or name H o \ r name HA )) or resid 200 through 220 or (resid 221 through 223 and (name N or n \ ame CA or name C or name O or name CB or name H or name HA )) or resid 224 throu \ gh 228 or (resid 229 through 230 and (name N or name CA or name C or name O or n \ ame CB or name H or name HA )) or resid 231 through 235 or (resid 236 through 23 \ 8 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 239 through 240 or (resid 241 through 242 and (name N or name CA or nam \ e C or name O or name CB or name H or name HA )) or resid 243 through 246 or (re \ sid 247 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 248 through 251 or (resid 252 through 257 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 258 through 259 \ or (resid 260 through 261 and (name N or name CA or name C or name O or name CB \ or name H or name HA )) or resid 262 through 263 or (resid 264 and (name N or na \ me CA or name C or name O or name CB or name H or name HA )) or resid 265 throug \ h 267 or (resid 268 and (name N or name CA or name C or name O or name CB or nam \ e H or name HA )) or resid 269 or (resid 270 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 271 through 272 or (resid 27 \ 3 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 274 through 275 or (resid 276 through 280 and (name N or name CA or nam \ e C or name O or name CB or name H or name HA )) or resid 281 through 282)) } 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 group one per residue 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: 8.650 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: 0.130 Extract box with map and model: 0.380 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 20.000 Find NCS groups from input model: 0.300 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:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6104 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 : 0.012 0.087 10189 Z= 0.893 Angle : 1.979 13.684 14374 Z= 1.480 Chirality : 0.108 0.643 1788 Planarity : 0.011 0.076 1512 Dihedral : 22.564 179.381 3864 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.14 % Allowed : 6.17 % Favored : 93.69 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.25), residues: 1055 helix: -0.52 (0.24), residues: 431 sheet: -1.70 (0.37), residues: 175 loop : -1.20 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 89 TYR 0.042 0.004 TYR A 256 PHE 0.034 0.003 PHE B 218 TRP 0.037 0.004 TRP B 229 HIS 0.013 0.003 HIS D 276 Details of bonding type rmsd/Z covalent geometry : bond 0.01203 / 0.89 (10189) covalent geometry : angle 1.97931 / 1.48 (14374) hydrogen bonds : bond 0.25338 / 17.32 ( 327) hydrogen bonds : angle 11.08099 / 7.83 ( 934) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue ILE 93 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue ILE 116 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LEU 279 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue TYR 256 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue ILE 49 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue ILE 66 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue VAL 255 is missing expected H atoms. Skipping. Residue TYR 256 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue SER 254 is missing expected H atoms. Skipping. Residue ILE 257 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Evaluate side-chains 418 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 417 time to evaluate : 0.455 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: 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 69 GLN cc_start: 0.9685 (tt0) cc_final: 0.9295 (tp-100) REVERT: A 73 ASN cc_start: 0.8993 (m-40) cc_final: 0.8282 (m-40) REVERT: A 112 LEU cc_start: 0.9174 (mp) cc_final: 0.8862 (tp) REVERT: A 210 ASP cc_start: 0.9403 (p0) cc_final: 0.9149 (p0) REVERT: A 212 HIS cc_start: 0.8830 (m-70) cc_final: 0.8205 (m-70) REVERT: A 266 ARG cc_start: 0.9490 (tpp-160) cc_final: 0.9229 (ttm-80) REVERT: A 276 HIS cc_start: 0.8602 (p-80) cc_final: 0.8372 (p-80) REVERT: B 91 THR cc_start: 0.9541 (m) cc_final: 0.9059 (t) REVERT: B 98 ASP cc_start: 0.9350 (m-30) cc_final: 0.9037 (m-30) REVERT: B 112 LEU cc_start: 0.9524 (tp) cc_final: 0.9261 (tp) REVERT: B 148 LEU cc_start: 0.9560 (mt) cc_final: 0.9239 (mt) REVERT: B 171 HIS cc_start: 0.8851 (m-70) cc_final: 0.8376 (t-90) REVERT: B 186 LEU cc_start: 0.8875 (mt) cc_final: 0.8640 (mt) REVERT: D 107 SER cc_start: 0.9733 (t) cc_final: 0.9447 (p) REVERT: D 149 ARG cc_start: 0.9478 (tpp-160) cc_final: 0.8990 (tpt90) REVERT: D 263 ASP cc_start: 0.9008 (m-30) cc_final: 0.8763 (m-30) REVERT: C 212 HIS cc_start: 0.8669 (m-70) cc_final: 0.8413 (m90) outliers start: 1 outliers final: 1 residues processed: 417 average time/residue: 0.2274 time to fit residues: 126.8308 Evaluate side-chains 306 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 305 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 212 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.090746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.069045 restraints weight = 132071.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.072022 restraints weight = 76097.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.074169 restraints weight = 51235.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.075684 restraints weight = 38359.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.076655 restraints weight = 31132.504| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3467 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3467 r_free = 0.3467 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3466 r_free = 0.3466 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.3466 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.4024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10189 Z= 0.145 Angle : 0.697 6.850 14374 Z= 0.369 Chirality : 0.042 0.224 1788 Planarity : 0.005 0.079 1512 Dihedral : 24.828 176.492 2352 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.26), residues: 1055 helix: 0.14 (0.23), residues: 457 sheet: -1.53 (0.33), residues: 209 loop : -0.77 (0.33), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 149 TYR 0.011 0.001 TYR B 220 PHE 0.012 0.001 PHE D 67 TRP 0.012 0.002 TRP B 229 HIS 0.005 0.001 HIS D 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.15 (10189) covalent geometry : angle 0.69689 / 0.37 (14374) hydrogen bonds : bond 0.05596 / 3.90 ( 327) hydrogen bonds : angle 6.63151 / 4.71 ( 934) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue ILE 93 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue ILE 116 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LEU 279 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue TYR 256 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue ILE 49 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue ILE 66 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue VAL 255 is missing expected H atoms. Skipping. Residue TYR 256 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue SER 254 is missing expected H atoms. Skipping. Residue ILE 257 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Evaluate side-chains 365 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 365 time to evaluate : 0.476 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash revert: symmetry clash REVERT: A 26 PHE cc_start: 0.9466 (m-80) cc_final: 0.9190 (m-80) REVERT: A 69 GLN cc_start: 0.9778 (tt0) cc_final: 0.9516 (tp-100) REVERT: A 112 LEU cc_start: 0.8873 (mp) cc_final: 0.8440 (tp) REVERT: A 146 GLU cc_start: 0.9378 (tp30) cc_final: 0.8841 (tp30) REVERT: A 191 TRP cc_start: 0.9279 (m-10) cc_final: 0.8767 (m-10) REVERT: A 265 PHE cc_start: 0.9612 (m-80) cc_final: 0.9250 (m-80) REVERT: A 272 VAL cc_start: 0.6969 (p) cc_final: 0.6518 (p) REVERT: A 276 HIS cc_start: 0.8774 (p-80) cc_final: 0.8486 (p-80) REVERT: B 26 PHE cc_start: 0.9359 (m-80) cc_final: 0.9058 (m-10) REVERT: B 91 THR cc_start: 0.9312 (m) cc_final: 0.8923 (t) REVERT: B 98 ASP cc_start: 0.9269 (m-30) cc_final: 0.9006 (m-30) REVERT: B 112 LEU cc_start: 0.9422 (tp) cc_final: 0.9218 (tp) REVERT: B 171 HIS cc_start: 0.8813 (m-70) cc_final: 0.8158 (t-90) REVERT: B 220 TYR cc_start: 0.8967 (m-80) cc_final: 0.8607 (m-80) REVERT: B 271 ASN cc_start: 0.9477 (t0) cc_final: 0.8959 (t0) REVERT: D 113 GLU cc_start: 0.9061 (tp30) cc_final: 0.8820 (tp30) REVERT: D 149 ARG cc_start: 0.9635 (tpp-160) cc_final: 0.9012 (tpt90) REVERT: D 169 PHE cc_start: 0.8142 (m-80) cc_final: 0.7722 (m-80) REVERT: D 220 TYR cc_start: 0.9350 (t80) cc_final: 0.8895 (t80) REVERT: C 227 GLU cc_start: 0.9595 (tp30) cc_final: 0.9370 (tp30) REVERT: C 230 LEU cc_start: 0.9680 (tp) cc_final: 0.9363 (tp) outliers start: 0 outliers final: 0 residues processed: 365 average time/residue: 0.2473 time to fit residues: 118.9550 Evaluate side-chains 298 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 298 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 14 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 9 optimal weight: 20.0000 chunk 26 optimal weight: 9.9990 chunk 46 optimal weight: 8.9990 chunk 96 optimal weight: 0.0370 chunk 55 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 overall best weight: 3.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 GLN D 171 HIS D 217 ASN C 73 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.083712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.061647 restraints weight = 134066.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.064337 restraints weight = 76507.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.066297 restraints weight = 51384.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.067686 restraints weight = 38536.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.068596 restraints weight = 31314.142| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3320 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3320 r_free = 0.3320 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3319 r_free = 0.3319 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3319 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.5430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10189 Z= 0.241 Angle : 0.700 7.149 14374 Z= 0.383 Chirality : 0.040 0.235 1788 Planarity : 0.005 0.067 1512 Dihedral : 24.932 179.050 2352 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.25), residues: 1055 helix: -0.03 (0.23), residues: 468 sheet: -1.46 (0.34), residues: 194 loop : -0.87 (0.33), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 127 TYR 0.016 0.002 TYR C 225 PHE 0.015 0.002 PHE D 84 TRP 0.015 0.002 TRP B 229 HIS 0.007 0.002 HIS B 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.24 (10189) covalent geometry : angle 0.70010 / 0.38 (14374) hydrogen bonds : bond 0.05592 / 3.97 ( 327) hydrogen bonds : angle 6.46228 / 4.61 ( 934) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue ILE 93 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue ILE 116 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LEU 279 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue TYR 256 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue ILE 49 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue ILE 66 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue VAL 255 is missing expected H atoms. Skipping. Residue TYR 256 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue SER 254 is missing expected H atoms. Skipping. Residue ILE 257 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Evaluate side-chains 331 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 331 time to evaluate : 0.487 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 CYS cc_start: 0.8619 (p) cc_final: 0.8080 (p) REVERT: A 69 GLN cc_start: 0.9807 (tt0) cc_final: 0.9576 (tp-100) REVERT: A 112 LEU cc_start: 0.8962 (mp) cc_final: 0.8495 (tp) REVERT: A 146 GLU cc_start: 0.9422 (tp30) cc_final: 0.8966 (tp30) REVERT: A 178 ASP cc_start: 0.8844 (p0) cc_final: 0.8532 (p0) REVERT: A 264 TYR cc_start: 0.9474 (t80) cc_final: 0.9220 (t80) REVERT: A 265 PHE cc_start: 0.9732 (m-80) cc_final: 0.9437 (m-80) REVERT: B 4 MET cc_start: 0.9023 (tpt) cc_final: 0.8812 (tpp) REVERT: B 18 LEU cc_start: 0.9549 (tp) cc_final: 0.9187 (tp) REVERT: B 91 THR cc_start: 0.9400 (m) cc_final: 0.9016 (t) REVERT: B 98 ASP cc_start: 0.9359 (m-30) cc_final: 0.9091 (m-30) REVERT: B 171 HIS cc_start: 0.9068 (m-70) cc_final: 0.8439 (t-90) REVERT: B 220 TYR cc_start: 0.9033 (m-80) cc_final: 0.8637 (m-80) REVERT: B 234 GLU cc_start: 0.9274 (mt-10) cc_final: 0.9014 (mt-10) REVERT: B 236 ASN cc_start: 0.8537 (t0) cc_final: 0.8279 (t0) REVERT: D 92 LEU cc_start: 0.9201 (mm) cc_final: 0.8890 (mm) REVERT: D 94 ARG cc_start: 0.9432 (ttp80) cc_final: 0.9080 (tpp80) REVERT: D 149 ARG cc_start: 0.9656 (tpp-160) cc_final: 0.9009 (tpt90) REVERT: D 162 MET cc_start: 0.9184 (pmm) cc_final: 0.8957 (pmm) REVERT: C 71 MET cc_start: 0.9007 (mmp) cc_final: 0.8793 (mmm) REVERT: C 165 GLU cc_start: 0.8494 (mp0) cc_final: 0.8136 (mp0) REVERT: C 169 PHE cc_start: 0.8936 (m-80) cc_final: 0.8555 (m-80) outliers start: 0 outliers final: 0 residues processed: 331 average time/residue: 0.2371 time to fit residues: 104.5563 Evaluate side-chains 270 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 93 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 112 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 chunk 115 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.083083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.060988 restraints weight = 132447.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.063663 restraints weight = 75770.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.065623 restraints weight = 50980.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.067028 restraints weight = 38188.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.068054 restraints weight = 31085.988| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3311 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3311 r_free = 0.3311 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3311 r_free = 0.3311 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3311 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.5984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10189 Z= 0.194 Angle : 0.625 7.069 14374 Z= 0.337 Chirality : 0.039 0.215 1788 Planarity : 0.004 0.066 1512 Dihedral : 24.665 179.487 2352 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.26), residues: 1055 helix: 0.12 (0.24), residues: 467 sheet: -1.25 (0.35), residues: 194 loop : -0.77 (0.33), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 151 TYR 0.013 0.002 TYR A 179 PHE 0.014 0.002 PHE C 167 TRP 0.011 0.001 TRP B 229 HIS 0.007 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.19 (10189) covalent geometry : angle 0.62491 / 0.34 (14374) hydrogen bonds : bond 0.04671 / 3.33 ( 327) hydrogen bonds : angle 6.25795 / 4.48 ( 934) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue ILE 93 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue ILE 116 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LEU 279 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue TYR 256 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue ILE 49 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue ILE 66 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue VAL 255 is missing expected H atoms. Skipping. Residue TYR 256 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue SER 254 is missing expected H atoms. Skipping. Residue ILE 257 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Evaluate side-chains 311 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 311 time to evaluate : 0.538 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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 69 GLN cc_start: 0.9815 (tt0) cc_final: 0.9586 (tp-100) REVERT: A 146 GLU cc_start: 0.9458 (tp30) cc_final: 0.9030 (tp30) REVERT: A 178 ASP cc_start: 0.8895 (p0) cc_final: 0.8583 (p0) REVERT: A 264 TYR cc_start: 0.9462 (t80) cc_final: 0.9157 (t80) REVERT: B 18 LEU cc_start: 0.9488 (tp) cc_final: 0.9273 (tp) REVERT: B 91 THR cc_start: 0.9451 (m) cc_final: 0.9072 (t) REVERT: B 151 ARG cc_start: 0.9322 (mmt-90) cc_final: 0.8633 (tpp-160) REVERT: B 171 HIS cc_start: 0.9175 (m-70) cc_final: 0.8523 (t-90) REVERT: B 220 TYR cc_start: 0.9065 (m-80) cc_final: 0.8650 (m-80) REVERT: B 236 ASN cc_start: 0.8596 (t0) cc_final: 0.8228 (t0) REVERT: D 94 ARG cc_start: 0.9492 (ttp80) cc_final: 0.9198 (tpp80) REVERT: D 149 ARG cc_start: 0.9667 (tpp-160) cc_final: 0.9010 (tpt90) REVERT: D 220 TYR cc_start: 0.9353 (t80) cc_final: 0.8892 (t80) REVERT: C 165 GLU cc_start: 0.8543 (mp0) cc_final: 0.8341 (mp0) REVERT: C 169 PHE cc_start: 0.8899 (m-80) cc_final: 0.8628 (m-80) outliers start: 0 outliers final: 0 residues processed: 311 average time/residue: 0.2320 time to fit residues: 96.7523 Evaluate side-chains 274 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 274 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 35 optimal weight: 10.0000 chunk 80 optimal weight: 0.6980 chunk 116 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 83 optimal weight: 10.0000 chunk 59 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 113 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 HIS D 276 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.081554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.059050 restraints weight = 126280.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.061671 restraints weight = 71926.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.063607 restraints weight = 48611.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.065042 restraints weight = 36502.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.065993 restraints weight = 29648.169| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3287 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3287 r_free = 0.3287 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3287 r_free = 0.3287 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3287 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.6573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10189 Z= 0.185 Angle : 0.611 6.934 14374 Z= 0.329 Chirality : 0.039 0.196 1788 Planarity : 0.004 0.064 1512 Dihedral : 24.523 178.295 2352 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.26), residues: 1055 helix: 0.16 (0.24), residues: 469 sheet: -1.32 (0.35), residues: 199 loop : -0.71 (0.34), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 127 TYR 0.017 0.002 TYR A 179 PHE 0.013 0.002 PHE C 167 TRP 0.011 0.001 TRP B 229 HIS 0.010 0.002 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.19 (10189) covalent geometry : angle 0.61077 / 0.33 (14374) hydrogen bonds : bond 0.04440 / 3.17 ( 327) hydrogen bonds : angle 6.08111 / 4.36 ( 934) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue ILE 93 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue ILE 116 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LEU 279 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue TYR 256 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue ILE 49 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue ILE 66 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue VAL 255 is missing expected H atoms. Skipping. Residue TYR 256 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue SER 254 is missing expected H atoms. Skipping. Residue ILE 257 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Evaluate side-chains 314 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 314 time to evaluate : 0.456 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 GLN cc_start: 0.9819 (tt0) cc_final: 0.9600 (tp-100) REVERT: A 146 GLU cc_start: 0.9472 (tp30) cc_final: 0.9067 (tp30) REVERT: A 178 ASP cc_start: 0.8951 (p0) cc_final: 0.8481 (p0) REVERT: A 264 TYR cc_start: 0.9469 (t80) cc_final: 0.9103 (t80) REVERT: B 4 MET cc_start: 0.9071 (tpt) cc_final: 0.8846 (tpt) REVERT: B 18 LEU cc_start: 0.9535 (tp) cc_final: 0.9274 (tp) REVERT: B 26 PHE cc_start: 0.9363 (m-80) cc_final: 0.8900 (m-80) REVERT: B 91 THR cc_start: 0.9444 (m) cc_final: 0.9015 (t) REVERT: B 146 GLU cc_start: 0.8817 (mp0) cc_final: 0.8612 (mp0) REVERT: B 171 HIS cc_start: 0.9233 (m-70) cc_final: 0.8609 (t70) REVERT: D 58 ARG cc_start: 0.9141 (mtp180) cc_final: 0.8927 (ttp80) REVERT: D 123 LEU cc_start: 0.9219 (mt) cc_final: 0.8980 (mp) REVERT: D 149 ARG cc_start: 0.9640 (tpp-160) cc_final: 0.9208 (mmm160) REVERT: D 162 MET cc_start: 0.9253 (pmm) cc_final: 0.8962 (pmm) REVERT: D 220 TYR cc_start: 0.9310 (t80) cc_final: 0.8823 (t80) REVERT: C 71 MET cc_start: 0.9104 (mmp) cc_final: 0.8871 (mmm) REVERT: C 165 GLU cc_start: 0.8701 (mp0) cc_final: 0.8310 (mp0) REVERT: C 169 PHE cc_start: 0.8886 (m-80) cc_final: 0.8650 (m-80) REVERT: C 259 GLU cc_start: 0.9224 (tp30) cc_final: 0.8858 (tp30) outliers start: 0 outliers final: 0 residues processed: 314 average time/residue: 0.2376 time to fit residues: 99.3953 Evaluate side-chains 272 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 272 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 107 optimal weight: 9.9990 chunk 92 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 chunk 115 optimal weight: 7.9990 chunk 35 optimal weight: 9.9990 chunk 54 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 114 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 142 HIS ** A 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 HIS ** 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 = 0.3575 r_free = 0.3575 target = 0.079882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.058324 restraints weight = 138244.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.060881 restraints weight = 79238.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.062688 restraints weight = 53932.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.063992 restraints weight = 41030.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.064715 restraints weight = 33823.069| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3243 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3243 r_free = 0.3243 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3244 r_free = 0.3244 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3244 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.7190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10189 Z= 0.228 Angle : 0.645 6.986 14374 Z= 0.349 Chirality : 0.039 0.213 1788 Planarity : 0.005 0.062 1512 Dihedral : 24.596 178.973 2352 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.26), residues: 1055 helix: -0.12 (0.23), residues: 469 sheet: -1.48 (0.36), residues: 194 loop : -0.78 (0.34), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 127 TYR 0.016 0.002 TYR D 179 PHE 0.022 0.002 PHE C 218 TRP 0.013 0.002 TRP B 229 HIS 0.013 0.002 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.23 (10189) covalent geometry : angle 0.64538 / 0.35 (14374) hydrogen bonds : bond 0.04641 / 3.33 ( 327) hydrogen bonds : angle 6.25110 / 4.47 ( 934) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue ILE 93 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue ILE 116 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LEU 279 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue TYR 256 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue ILE 49 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue ILE 66 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue VAL 255 is missing expected H atoms. Skipping. Residue TYR 256 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue SER 254 is missing expected H atoms. Skipping. Residue ILE 257 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Evaluate side-chains 300 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 0.451 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash revert: symmetry clash REVERT: A 69 GLN cc_start: 0.9830 (tt0) cc_final: 0.9620 (tp-100) REVERT: A 146 GLU cc_start: 0.9493 (tp30) cc_final: 0.9105 (tp30) REVERT: A 264 TYR cc_start: 0.9484 (t80) cc_final: 0.9118 (t80) REVERT: B 18 LEU cc_start: 0.9550 (tp) cc_final: 0.9305 (tp) REVERT: B 26 PHE cc_start: 0.9397 (m-80) cc_final: 0.8765 (m-80) REVERT: B 92 LEU cc_start: 0.9524 (mt) cc_final: 0.9310 (mt) REVERT: B 171 HIS cc_start: 0.9324 (m-70) cc_final: 0.9087 (m-70) REVERT: B 173 ILE cc_start: 0.9555 (pt) cc_final: 0.9329 (mm) REVERT: B 220 TYR cc_start: 0.9068 (m-80) cc_final: 0.8649 (m-80) REVERT: B 259 GLU cc_start: 0.9342 (tm-30) cc_final: 0.9131 (tm-30) REVERT: D 149 ARG cc_start: 0.9643 (tpp-160) cc_final: 0.9226 (mmm160) REVERT: D 162 MET cc_start: 0.9232 (pmm) cc_final: 0.9002 (pmm) REVERT: D 178 ASP cc_start: 0.7926 (m-30) cc_final: 0.7476 (m-30) REVERT: D 220 TYR cc_start: 0.9281 (t80) cc_final: 0.8808 (t80) REVERT: D 242 THR cc_start: 0.7689 (p) cc_final: 0.7027 (p) REVERT: C 71 MET cc_start: 0.9228 (mmp) cc_final: 0.8973 (mmm) REVERT: C 259 GLU cc_start: 0.9186 (tp30) cc_final: 0.8811 (tp30) REVERT: C 265 PHE cc_start: 0.9749 (m-80) cc_final: 0.9385 (m-80) outliers start: 0 outliers final: 0 residues processed: 300 average time/residue: 0.2303 time to fit residues: 92.5763 Evaluate side-chains 264 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 90 optimal weight: 9.9990 chunk 15 optimal weight: 4.9990 chunk 45 optimal weight: 0.0770 chunk 81 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 50 optimal weight: 6.9990 chunk 73 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 110 optimal weight: 8.9990 chunk 30 optimal weight: 8.9990 chunk 115 optimal weight: 7.9990 overall best weight: 4.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 276 HIS C 190 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.078490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.057718 restraints weight = 144222.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.060193 restraints weight = 82407.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.061996 restraints weight = 55994.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.063282 restraints weight = 42504.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.064170 restraints weight = 35009.469| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.7759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 10189 Z= 0.275 Angle : 0.695 6.928 14374 Z= 0.378 Chirality : 0.040 0.221 1788 Planarity : 0.006 0.107 1512 Dihedral : 24.715 179.968 2352 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 19.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.26), residues: 1055 helix: -0.60 (0.23), residues: 466 sheet: -1.72 (0.36), residues: 191 loop : -0.97 (0.34), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 58 TYR 0.023 0.002 TYR C 225 PHE 0.017 0.002 PHE C 265 TRP 0.015 0.002 TRP B 229 HIS 0.016 0.002 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.28 (10189) covalent geometry : angle 0.69505 / 0.38 (14374) hydrogen bonds : bond 0.05269 / 3.83 ( 327) hydrogen bonds : angle 6.59273 / 4.74 ( 934) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue ILE 93 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue ILE 116 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LEU 279 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue TYR 256 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue ILE 49 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue ILE 66 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue VAL 255 is missing expected H atoms. Skipping. Residue TYR 256 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue SER 254 is missing expected H atoms. Skipping. Residue ILE 257 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Evaluate side-chains 292 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 292 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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 22 GLU cc_start: 0.9450 (mp0) cc_final: 0.9242 (mp0) REVERT: A 69 GLN cc_start: 0.9827 (tt0) cc_final: 0.9621 (tp-100) REVERT: A 119 GLU cc_start: 0.8737 (mp0) cc_final: 0.8515 (mp0) REVERT: A 146 GLU cc_start: 0.9477 (tp30) cc_final: 0.9098 (tp30) REVERT: B 4 MET cc_start: 0.9363 (mmm) cc_final: 0.9125 (tpp) REVERT: B 26 PHE cc_start: 0.9308 (m-80) cc_final: 0.8773 (m-80) REVERT: B 155 LYS cc_start: 0.8258 (pptt) cc_final: 0.7945 (ptmm) REVERT: B 171 HIS cc_start: 0.9350 (m-70) cc_final: 0.8908 (m-70) REVERT: B 173 ILE cc_start: 0.9558 (pt) cc_final: 0.9187 (mm) REVERT: B 259 GLU cc_start: 0.9347 (tm-30) cc_final: 0.9104 (tm-30) REVERT: D 149 ARG cc_start: 0.9650 (tpp-160) cc_final: 0.9250 (mmm160) REVERT: D 178 ASP cc_start: 0.7924 (m-30) cc_final: 0.7471 (m-30) REVERT: D 220 TYR cc_start: 0.9248 (t80) cc_final: 0.8806 (t80) REVERT: D 242 THR cc_start: 0.7647 (p) cc_final: 0.6975 (p) REVERT: C 58 ARG cc_start: 0.8447 (ttt180) cc_final: 0.8224 (ttt180) REVERT: C 71 MET cc_start: 0.9252 (mmp) cc_final: 0.9007 (mmm) REVERT: C 259 GLU cc_start: 0.9200 (tp30) cc_final: 0.8852 (tp30) REVERT: C 265 PHE cc_start: 0.9767 (m-80) cc_final: 0.9381 (m-80) outliers start: 0 outliers final: 0 residues processed: 292 average time/residue: 0.2348 time to fit residues: 91.5760 Evaluate side-chains 270 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 48 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 110 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 79 optimal weight: 6.9990 chunk 94 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.081608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.059282 restraints weight = 125737.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.061938 restraints weight = 71387.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.063900 restraints weight = 48228.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.065264 restraints weight = 36359.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.066271 restraints weight = 29698.053| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.7902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10189 Z= 0.127 Angle : 0.567 6.782 14374 Z= 0.300 Chirality : 0.038 0.184 1788 Planarity : 0.005 0.062 1512 Dihedral : 24.190 178.136 2352 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.27), residues: 1055 helix: 0.31 (0.24), residues: 470 sheet: -1.52 (0.37), residues: 190 loop : -0.60 (0.35), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 58 TYR 0.016 0.001 TYR C 256 PHE 0.010 0.001 PHE C 265 TRP 0.011 0.001 TRP B 229 HIS 0.007 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.13 (10189) covalent geometry : angle 0.56651 / 0.30 (14374) hydrogen bonds : bond 0.03927 / 2.83 ( 327) hydrogen bonds : angle 5.86068 / 4.21 ( 934) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue ILE 93 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue ILE 116 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LEU 279 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue TYR 256 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue ILE 49 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue ILE 66 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue VAL 255 is missing expected H atoms. Skipping. Residue TYR 256 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue SER 254 is missing expected H atoms. Skipping. Residue ILE 257 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Evaluate side-chains 303 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 303 time to evaluate : 0.525 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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 69 GLN cc_start: 0.9833 (tt0) cc_final: 0.9608 (tp-100) REVERT: A 119 GLU cc_start: 0.8776 (mp0) cc_final: 0.8567 (mp0) REVERT: A 146 GLU cc_start: 0.9500 (tp30) cc_final: 0.9145 (tp30) REVERT: B 4 MET cc_start: 0.9379 (mmm) cc_final: 0.9091 (tpp) REVERT: B 18 LEU cc_start: 0.9552 (tp) cc_final: 0.9325 (tp) REVERT: B 26 PHE cc_start: 0.9303 (m-80) cc_final: 0.8792 (m-80) REVERT: B 155 LYS cc_start: 0.8193 (pptt) cc_final: 0.7889 (ptmm) REVERT: B 171 HIS cc_start: 0.9325 (m-70) cc_final: 0.8852 (m-70) REVERT: B 173 ILE cc_start: 0.9525 (pt) cc_final: 0.9257 (mm) REVERT: D 149 ARG cc_start: 0.9627 (tpp-160) cc_final: 0.9206 (mmm160) REVERT: D 162 MET cc_start: 0.9239 (pmm) cc_final: 0.8883 (pmm) REVERT: D 178 ASP cc_start: 0.7932 (m-30) cc_final: 0.7618 (m-30) REVERT: D 220 TYR cc_start: 0.9271 (t80) cc_final: 0.8819 (t80) REVERT: D 242 THR cc_start: 0.7748 (p) cc_final: 0.7110 (p) REVERT: C 71 MET cc_start: 0.9177 (mmp) cc_final: 0.8922 (mmm) REVERT: C 165 GLU cc_start: 0.8698 (mp0) cc_final: 0.8126 (mp0) REVERT: C 259 GLU cc_start: 0.9170 (tp30) cc_final: 0.8778 (tp30) REVERT: C 265 PHE cc_start: 0.9730 (m-80) cc_final: 0.9377 (m-80) outliers start: 0 outliers final: 0 residues processed: 303 average time/residue: 0.2271 time to fit residues: 92.3191 Evaluate side-chains 271 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 11 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 92 optimal weight: 10.0000 chunk 63 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 47 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 142 HIS ** 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 = 0.3561 r_free = 0.3561 target = 0.078682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.057391 restraints weight = 139987.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.059902 restraints weight = 79702.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.061716 restraints weight = 54114.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.062943 restraints weight = 41175.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.063804 restraints weight = 34088.270| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.8216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10189 Z= 0.194 Angle : 0.610 6.799 14374 Z= 0.326 Chirality : 0.038 0.199 1788 Planarity : 0.005 0.068 1512 Dihedral : 24.294 178.199 2352 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.27), residues: 1055 helix: 0.12 (0.24), residues: 464 sheet: -1.51 (0.37), residues: 191 loop : -0.75 (0.34), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 268 TYR 0.015 0.002 TYR C 225 PHE 0.018 0.001 PHE C 218 TRP 0.012 0.001 TRP B 229 HIS 0.011 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.19 (10189) covalent geometry : angle 0.60996 / 0.33 (14374) hydrogen bonds : bond 0.04375 / 3.20 ( 327) hydrogen bonds : angle 6.02658 / 4.33 ( 934) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue ILE 93 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue ILE 116 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LEU 279 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue TYR 256 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue ILE 49 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue ILE 66 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue VAL 255 is missing expected H atoms. Skipping. Residue TYR 256 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue SER 254 is missing expected H atoms. Skipping. Residue ILE 257 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Evaluate side-chains 293 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 293 time to evaluate : 0.468 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: 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 69 GLN cc_start: 0.9829 (tt0) cc_final: 0.9603 (tp-100) REVERT: A 119 GLU cc_start: 0.8769 (mp0) cc_final: 0.8560 (mp0) REVERT: A 146 GLU cc_start: 0.9499 (tp30) cc_final: 0.9138 (tp30) REVERT: B 18 LEU cc_start: 0.9585 (tp) cc_final: 0.9359 (tp) REVERT: B 26 PHE cc_start: 0.9329 (m-80) cc_final: 0.8196 (m-80) REVERT: B 146 GLU cc_start: 0.9134 (mp0) cc_final: 0.8814 (mp0) REVERT: B 171 HIS cc_start: 0.9362 (m-70) cc_final: 0.8868 (m-70) REVERT: B 173 ILE cc_start: 0.9578 (pt) cc_final: 0.9280 (mm) REVERT: D 122 LEU cc_start: 0.9552 (mm) cc_final: 0.9267 (tt) REVERT: D 162 MET cc_start: 0.9221 (pmm) cc_final: 0.8973 (pmm) REVERT: D 178 ASP cc_start: 0.7835 (m-30) cc_final: 0.7453 (m-30) REVERT: D 220 TYR cc_start: 0.9232 (t80) cc_final: 0.8806 (t80) REVERT: D 242 THR cc_start: 0.7678 (p) cc_final: 0.7076 (p) REVERT: C 58 ARG cc_start: 0.8780 (ptm160) cc_final: 0.8544 (ptp-170) REVERT: C 71 MET cc_start: 0.9202 (mmp) cc_final: 0.8945 (mmm) REVERT: C 169 PHE cc_start: 0.8866 (m-80) cc_final: 0.8650 (m-80) REVERT: C 259 GLU cc_start: 0.9157 (tp30) cc_final: 0.8801 (tp30) REVERT: C 265 PHE cc_start: 0.9734 (m-80) cc_final: 0.9375 (m-80) outliers start: 0 outliers final: 0 residues processed: 293 average time/residue: 0.2184 time to fit residues: 87.0163 Evaluate side-chains 261 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 261 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 64 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 111 optimal weight: 8.9990 chunk 100 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 30 optimal weight: 6.9990 chunk 90 optimal weight: 0.9980 chunk 43 optimal weight: 10.0000 chunk 3 optimal weight: 0.0980 chunk 58 optimal weight: 0.2980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 190 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.082173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.060138 restraints weight = 130266.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.062841 restraints weight = 73184.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.064792 restraints weight = 49283.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.066124 restraints weight = 37175.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.067150 restraints weight = 30540.853| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.8275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10189 Z= 0.107 Angle : 0.550 6.677 14374 Z= 0.287 Chirality : 0.038 0.157 1788 Planarity : 0.004 0.062 1512 Dihedral : 23.815 179.104 2352 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.27), residues: 1055 helix: 0.77 (0.25), residues: 474 sheet: -1.36 (0.37), residues: 193 loop : -0.45 (0.35), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 151 TYR 0.014 0.001 TYR A 220 PHE 0.010 0.001 PHE D 265 TRP 0.013 0.001 TRP B 229 HIS 0.004 0.001 HIS D 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.11 (10189) covalent geometry : angle 0.54997 / 0.29 (14374) hydrogen bonds : bond 0.03562 / 2.58 ( 327) hydrogen bonds : angle 5.46706 / 3.94 ( 934) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue ILE 93 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue ILE 116 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LEU 279 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue TYR 256 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue ILE 49 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue ILE 66 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue VAL 255 is missing expected H atoms. Skipping. Residue TYR 256 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue SER 254 is missing expected H atoms. Skipping. Residue ILE 257 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Evaluate side-chains 305 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 305 time to evaluate : 0.478 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 GLN cc_start: 0.9833 (tt0) cc_final: 0.9628 (tp-100) REVERT: A 112 LEU cc_start: 0.8841 (mp) cc_final: 0.8378 (tp) REVERT: A 119 GLU cc_start: 0.8741 (mp0) cc_final: 0.8541 (mp0) REVERT: A 146 GLU cc_start: 0.9489 (tp30) cc_final: 0.9149 (tp30) REVERT: B 26 PHE cc_start: 0.9294 (m-80) cc_final: 0.8822 (m-80) REVERT: B 146 GLU cc_start: 0.9024 (mp0) cc_final: 0.8679 (mp0) REVERT: B 171 HIS cc_start: 0.9331 (m-70) cc_final: 0.8797 (m-70) REVERT: B 186 LEU cc_start: 0.9266 (mt) cc_final: 0.9036 (mt) REVERT: D 122 LEU cc_start: 0.9544 (mm) cc_final: 0.9284 (tt) REVERT: D 162 MET cc_start: 0.9269 (pmm) cc_final: 0.9026 (pmm) REVERT: C 71 MET cc_start: 0.9128 (mmp) cc_final: 0.8860 (mmm) REVERT: C 165 GLU cc_start: 0.8718 (mp0) cc_final: 0.8310 (mp0) REVERT: C 259 GLU cc_start: 0.9158 (tp30) cc_final: 0.8772 (tp30) outliers start: 0 outliers final: 0 residues processed: 305 average time/residue: 0.2125 time to fit residues: 88.6575 Evaluate side-chains 268 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 95 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 chunk 100 optimal weight: 0.6980 chunk 51 optimal weight: 7.9990 chunk 3 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 18 optimal weight: 0.0870 chunk 14 optimal weight: 8.9990 chunk 87 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 276 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.082322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.060189 restraints weight = 129029.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.062887 restraints weight = 72457.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.064887 restraints weight = 48700.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.066221 restraints weight = 36548.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.067218 restraints weight = 29921.813| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.8405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10189 Z= 0.099 Angle : 0.536 6.658 14374 Z= 0.278 Chirality : 0.037 0.148 1788 Planarity : 0.004 0.062 1512 Dihedral : 23.668 179.061 2352 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.28), residues: 1055 helix: 1.06 (0.25), residues: 480 sheet: -1.11 (0.37), residues: 193 loop : -0.37 (0.35), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 268 TYR 0.010 0.001 TYR A 220 PHE 0.011 0.001 PHE D 265 TRP 0.010 0.001 TRP B 229 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.10 (10189) covalent geometry : angle 0.53550 / 0.28 (14374) hydrogen bonds : bond 0.03451 / 2.52 ( 327) hydrogen bonds : angle 5.31818 / 3.83 ( 934) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4033.25 seconds wall clock time: 69 minutes 32.18 seconds (4172.18 seconds total)