Starting phenix.real_space_refine on Fri Aug 22 20:57:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iyw_35831/08_2025/8iyw_35831.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iyw_35831/08_2025/8iyw_35831.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8iyw_35831/08_2025/8iyw_35831.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iyw_35831/08_2025/8iyw_35831.map" model { file = "/net/cci-nas-00/data/ceres_data/8iyw_35831/08_2025/8iyw_35831.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iyw_35831/08_2025/8iyw_35831.cif" } resolution = 3.45 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= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 43 5.16 5 Cl 1 4.86 5 C 4980 2.51 5 N 1381 2.21 5 O 1444 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7849 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1475 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 4, 'TRANS': 197} Chain breaks: 2 Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 8, 'ASN:plan1': 3, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 76 Chain: "C" Number of atoms: 2393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2393 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 208 Unresolved non-hydrogen angles: 259 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 10, 'GLN:plan1': 3, 'ARG:plan': 8, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 119 Chain: "G" Number of atoms: 379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 379 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "H" Number of atoms: 1655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1655 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 8, 'ASP:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 67 Chain: "R" Number of atoms: 1930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 1930 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 120} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 280} Chain breaks: 1 Unresolved non-hydrogen bonds: 482 Unresolved non-hydrogen angles: 617 Unresolved non-hydrogen dihedrals: 411 Unresolved non-hydrogen chiralities: 46 Planarities with less than four sites: {'HIS:plan': 3, 'GLU:plan': 5, 'ASP:plan': 9, 'PHE:plan': 12, 'ARG:plan': 9, 'ASN:plan1': 6, 'TRP:plan': 4, 'GLN:plan1': 4, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 263 Chain: "R" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'OKL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.20, per 1000 atoms: 0.28 Number of scatterers: 7849 At special positions: 0 Unit cell: (87.8, 116.335, 132.797, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 43 16.00 O 1444 8.00 N 1381 7.00 C 4980 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 229 " distance=2.03 Simple disulfide: pdb=" SG CYS R 18 " - pdb=" SG CYS R 183 " distance=2.04 Simple disulfide: pdb=" SG CYS R 19 " - pdb=" SG CYS R 266 " distance=2.03 Simple disulfide: pdb=" SG CYS R 100 " - pdb=" SG CYS R 177 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.59 Conformation dependent library (CDL) restraints added in 487.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2090 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 14 sheets defined 37.9% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'B' and resid 8 through 31 Processing helix chain 'B' and resid 208 through 213 removed outlier: 4.074A pdb=" N TRP B 212 " --> pdb=" O GLU B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 219 removed outlier: 4.376A pdb=" N ASP B 218 " --> pdb=" O CYS B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 256 Processing helix chain 'B' and resid 271 through 280 removed outlier: 3.605A pdb=" N LYS B 280 " --> pdb=" O GLY B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 287 Processing helix chain 'B' and resid 296 through 310 Processing helix chain 'B' and resid 329 through 351 removed outlier: 4.463A pdb=" N GLN B 333 " --> pdb=" O THR B 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 26 removed outlier: 3.569A pdb=" N ALA C 26 " --> pdb=" O ARG C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 35 Processing helix chain 'G' and resid 9 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 4.144A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 53 through 56 Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.931A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 220 through 224 Processing helix chain 'R' and resid 24 through 55 Proline residue: R 31 - end of helix Processing helix chain 'R' and resid 60 through 89 Proline residue: R 81 - end of helix Processing helix chain 'R' and resid 96 through 130 Processing helix chain 'R' and resid 134 through 139 removed outlier: 3.690A pdb=" N ILE R 139 " --> pdb=" O LEU R 136 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 158 Processing helix chain 'R' and resid 160 through 165 removed outlier: 4.092A pdb=" N LYS R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 187 through 218 removed outlier: 3.624A pdb=" N PHE R 197 " --> pdb=" O PHE R 193 " (cutoff:3.500A) Proline residue: R 200 - end of helix Processing helix chain 'R' and resid 219 through 222 Processing helix chain 'R' and resid 223 through 262 removed outlier: 4.797A pdb=" N ALA R 237 " --> pdb=" O ILE R 233 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE R 238 " --> pdb=" O MET R 234 " (cutoff:3.500A) Proline residue: R 246 - end of helix removed outlier: 3.619A pdb=" N GLY R 262 " --> pdb=" O LEU R 258 " (cutoff:3.500A) Processing helix chain 'R' and resid 265 through 268 removed outlier: 3.806A pdb=" N VAL R 268 " --> pdb=" O ASN R 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 265 through 268' Processing helix chain 'R' and resid 269 through 281 removed outlier: 3.787A pdb=" N SER R 281 " --> pdb=" O PHE R 277 " (cutoff:3.500A) Processing helix chain 'R' and resid 281 through 290 Processing helix chain 'R' and resid 290 through 295 removed outlier: 4.099A pdb=" N TYR R 294 " --> pdb=" O ASP R 290 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 186 through 189 removed outlier: 6.314A pdb=" N VAL B 34 " --> pdb=" O ARG B 198 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N PHE B 200 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N LEU B 36 " --> pdb=" O PHE B 200 " (cutoff:3.500A) removed outlier: 9.864A pdb=" N ALA B 221 " --> pdb=" O ASP B 33 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N LYS B 35 " --> pdb=" O ALA B 221 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N ILE B 223 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LEU B 37 " --> pdb=" O ILE B 223 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N CYS B 225 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LEU B 39 " --> pdb=" O CYS B 225 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N ASP B 227 " --> pdb=" O LEU B 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 51 removed outlier: 3.776A pdb=" N LEU C 336 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 6.749A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N LEU C 79 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA C 92 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ILE C 81 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.957A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.737A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192 removed outlier: 3.654A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.448A pdb=" N CYS C 250 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N THR C 263 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU C 252 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN C 259 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 275 removed outlier: 6.316A pdb=" N GLY C 288 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA C 287 " --> pdb=" O ASN C 295 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N CYS C 294 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL C 307 " --> pdb=" O CYS C 294 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL C 296 " --> pdb=" O ALA C 305 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP C 303 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'H' and resid 10 through 12 removed outlier: 5.992A pdb=" N GLY H 10 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR H 59 " --> pdb=" O TYR H 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 140 through 141 Processing sheet with id=AB3, first strand: chain 'H' and resid 146 through 148 removed outlier: 5.862A pdb=" N LEU H 178 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N LEU H 187 " --> pdb=" O LEU H 178 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'R' and resid 11 through 13 Processing sheet with id=AB5, first strand: chain 'R' and resid 169 through 170 424 hydrogen bonds defined for protein. 1182 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.25 Time building geometry restraints manager: 0.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1407 1.33 - 1.45: 2209 1.45 - 1.58: 4347 1.58 - 1.71: 0 1.71 - 1.83: 55 Bond restraints: 8018 Sorted by residual: bond pdb=" C PHE R 282 " pdb=" N THR R 283 " ideal model delta sigma weight residual 1.335 1.218 0.117 1.38e-02 5.25e+03 7.15e+01 bond pdb=" C VAL R 88 " pdb=" N ARG R 89 " ideal model delta sigma weight residual 1.332 1.400 -0.068 1.52e-02 4.33e+03 2.02e+01 bond pdb=" CA ILE R 98 " pdb=" CB ILE R 98 " ideal model delta sigma weight residual 1.539 1.521 0.018 5.40e-03 3.43e+04 1.07e+01 bond pdb=" N ILE R 212 " pdb=" CA ILE R 212 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.33e-02 5.65e+03 7.98e+00 bond pdb=" N CYS B 287 " pdb=" CA CYS B 287 " ideal model delta sigma weight residual 1.456 1.493 -0.038 1.35e-02 5.49e+03 7.75e+00 ... (remaining 8013 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 10465 1.74 - 3.48: 385 3.48 - 5.22: 70 5.22 - 6.96: 21 6.96 - 8.69: 13 Bond angle restraints: 10954 Sorted by residual: angle pdb=" CA CYS R 177 " pdb=" C CYS R 177 " pdb=" O CYS R 177 " ideal model delta sigma weight residual 120.40 113.07 7.33 1.05e+00 9.07e-01 4.88e+01 angle pdb=" N TYR R 284 " pdb=" CA TYR R 284 " pdb=" C TYR R 284 " ideal model delta sigma weight residual 111.36 104.59 6.77 1.09e+00 8.42e-01 3.86e+01 angle pdb=" N LEU R 83 " pdb=" CA LEU R 83 " pdb=" C LEU R 83 " ideal model delta sigma weight residual 111.14 104.57 6.57 1.08e+00 8.57e-01 3.70e+01 angle pdb=" C PHE R 282 " pdb=" N THR R 283 " pdb=" CA THR R 283 " ideal model delta sigma weight residual 120.31 111.62 8.69 1.52e+00 4.33e-01 3.27e+01 angle pdb=" C ILE R 116 " pdb=" N PHE R 117 " pdb=" CA PHE R 117 " ideal model delta sigma weight residual 120.65 113.16 7.49 1.32e+00 5.74e-01 3.22e+01 ... (remaining 10949 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.42: 4453 23.42 - 46.83: 176 46.83 - 70.25: 18 70.25 - 93.67: 4 93.67 - 117.08: 1 Dihedral angle restraints: 4652 sinusoidal: 1421 harmonic: 3231 Sorted by residual: dihedral pdb=" CA GLN H 82 " pdb=" C GLN H 82 " pdb=" N MET H 83 " pdb=" CA MET H 83 " ideal model delta harmonic sigma weight residual -180.00 -159.40 -20.60 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA ALA B 7 " pdb=" C ALA B 7 " pdb=" N GLU B 8 " pdb=" CA GLU B 8 " ideal model delta harmonic sigma weight residual 180.00 159.63 20.37 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" C03 OKL R 401 " pdb=" C04 OKL R 401 " pdb=" C05 OKL R 401 " pdb=" N06 OKL R 401 " ideal model delta sinusoidal sigma weight residual 183.45 66.37 117.08 1 3.00e+01 1.11e-03 1.55e+01 ... (remaining 4649 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 962 0.050 - 0.100: 245 0.100 - 0.150: 66 0.150 - 0.200: 4 0.200 - 0.250: 4 Chirality restraints: 1281 Sorted by residual: chirality pdb=" CA HIS B 196 " pdb=" N HIS B 196 " pdb=" C HIS B 196 " pdb=" CB HIS B 196 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA PHE R 105 " pdb=" N PHE R 105 " pdb=" C PHE R 105 " pdb=" CB PHE R 105 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA HIS R 161 " pdb=" N HIS R 161 " pdb=" C HIS R 161 " pdb=" CB HIS R 161 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 1278 not shown) Planarity restraints: 1415 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C05 OKL R 401 " -0.012 2.00e-02 2.50e+03 4.04e-02 5.30e+01 pdb=" C07 OKL R 401 " -0.020 2.00e-02 2.50e+03 pdb=" C10 OKL R 401 " 0.006 2.00e-02 2.50e+03 pdb=" C12 OKL R 401 " 0.041 2.00e-02 2.50e+03 pdb=" C13 OKL R 401 " 0.053 2.00e-02 2.50e+03 pdb=" C15 OKL R 401 " 0.015 2.00e-02 2.50e+03 pdb=" N06 OKL R 401 " 0.018 2.00e-02 2.50e+03 pdb=" N09 OKL R 401 " -0.020 2.00e-02 2.50e+03 pdb=" N14 OKL R 401 " 0.054 2.00e-02 2.50e+03 pdb=" N16 OKL R 401 " 0.024 2.00e-02 2.50e+03 pdb=" O08 OKL R 401 " -0.041 2.00e-02 2.50e+03 pdb=" O11 OKL R 401 " -0.016 2.00e-02 2.50e+03 pdb="CL17 OKL R 401 " -0.099 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS R 177 " -0.018 2.00e-02 2.50e+03 3.82e-02 1.46e+01 pdb=" C CYS R 177 " 0.066 2.00e-02 2.50e+03 pdb=" O CYS R 177 " -0.025 2.00e-02 2.50e+03 pdb=" N SER R 178 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 210 " -0.014 2.00e-02 2.50e+03 2.87e-02 8.26e+00 pdb=" C LYS B 210 " 0.050 2.00e-02 2.50e+03 pdb=" O LYS B 210 " -0.019 2.00e-02 2.50e+03 pdb=" N LYS B 211 " -0.017 2.00e-02 2.50e+03 ... (remaining 1412 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1783 2.78 - 3.31: 7637 3.31 - 3.84: 12456 3.84 - 4.37: 14149 4.37 - 4.90: 25163 Nonbonded interactions: 61188 Sorted by model distance: nonbonded pdb=" O LYS B 193 " pdb=" ND2 ASN B 194 " model vdw 2.252 3.120 nonbonded pdb=" OG SER C 331 " pdb=" OD1 ASP C 333 " model vdw 2.260 3.040 nonbonded pdb=" O ARG R 228 " pdb=" OG1 THR R 231 " model vdw 2.278 3.040 nonbonded pdb=" NE ARG H 98 " pdb=" OD1 ASP H 109 " model vdw 2.295 3.120 nonbonded pdb=" O ASN R 17 " pdb=" ND2 ASN R 17 " model vdw 2.298 3.120 ... (remaining 61183 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.650 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: 0.020 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.130 Find NCS groups from input model: 0.040 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.117 8023 Z= 0.283 Angle : 0.837 8.695 10964 Z= 0.518 Chirality : 0.049 0.250 1281 Planarity : 0.005 0.047 1415 Dihedral : 12.733 117.085 2547 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.45 % Allowed : 11.76 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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 aren not related in a simple way. whole: 0.09 (0.25), residues: 1100 helix: 0.47 (0.27), residues: 353 sheet: 0.06 (0.32), residues: 250 loop : -0.09 (0.29), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 191 TYR 0.025 0.002 TYR R 284 PHE 0.017 0.002 PHE C 199 TRP 0.022 0.002 TRP R 152 HIS 0.006 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00456 ( 8018) covalent geometry : angle 0.83662 (10954) SS BOND : bond 0.00685 ( 5) SS BOND : angle 1.17701 ( 10) hydrogen bonds : bond 0.15971 ( 424) hydrogen bonds : angle 7.29997 ( 1182) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 131 time to evaluate : 0.303 Fit side-chains REVERT: R 216 ARG cc_start: 0.7355 (mtt180) cc_final: 0.7067 (mtt-85) outliers start: 10 outliers final: 3 residues processed: 136 average time/residue: 0.0958 time to fit residues: 17.7005 Evaluate side-chains 118 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 115 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain R residue 17 ASN Chi-restraints excluded: chain R residue 255 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.4980 chunk 33 optimal weight: 0.0170 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.2980 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 ASN ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN H 113 GLN R 112 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.176689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.132323 restraints weight = 9787.047| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 3.35 r_work: 0.3327 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8023 Z= 0.131 Angle : 0.575 6.680 10964 Z= 0.312 Chirality : 0.044 0.151 1281 Planarity : 0.004 0.037 1415 Dihedral : 6.942 147.993 1192 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.76 % Allowed : 13.06 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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 aren not related in a simple way. whole: 0.69 (0.26), residues: 1100 helix: 1.57 (0.28), residues: 360 sheet: 0.06 (0.31), residues: 249 loop : -0.05 (0.30), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 218 TYR 0.020 0.001 TYR R 269 PHE 0.024 0.001 PHE H 68 TRP 0.020 0.001 TRP C 169 HIS 0.006 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 8018) covalent geometry : angle 0.57503 (10954) SS BOND : bond 0.00379 ( 5) SS BOND : angle 0.75321 ( 10) hydrogen bonds : bond 0.04141 ( 424) hydrogen bonds : angle 5.17668 ( 1182) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.315 Fit side-chains revert: symmetry clash REVERT: G 44 HIS cc_start: 0.7959 (m-70) cc_final: 0.7563 (m-70) REVERT: G 48 ASP cc_start: 0.7672 (t0) cc_final: 0.7080 (t0) REVERT: R 198 PHE cc_start: 0.7979 (OUTLIER) cc_final: 0.7622 (m-10) REVERT: R 213 TRP cc_start: 0.8080 (t60) cc_final: 0.7856 (t60) REVERT: R 216 ARG cc_start: 0.7334 (mtt180) cc_final: 0.6924 (mtt-85) outliers start: 19 outliers final: 12 residues processed: 132 average time/residue: 0.0823 time to fit residues: 15.3549 Evaluate side-chains 125 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 198 PHE Chi-restraints excluded: chain R residue 255 PHE Chi-restraints excluded: chain R residue 269 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 96 optimal weight: 9.9990 chunk 55 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 26 optimal weight: 0.0970 chunk 17 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 87 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 ASN ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.172139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.116374 restraints weight = 9931.301| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.71 r_work: 0.3311 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8023 Z= 0.227 Angle : 0.613 6.533 10964 Z= 0.334 Chirality : 0.046 0.175 1281 Planarity : 0.004 0.037 1415 Dihedral : 6.813 138.948 1186 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 4.35 % Allowed : 13.06 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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 aren not related in a simple way. whole: 0.54 (0.26), residues: 1100 helix: 1.74 (0.28), residues: 369 sheet: -0.45 (0.29), residues: 265 loop : -0.15 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 38 TYR 0.018 0.002 TYR C 111 PHE 0.034 0.002 PHE H 68 TRP 0.016 0.002 TRP C 211 HIS 0.007 0.001 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00533 ( 8018) covalent geometry : angle 0.61266 (10954) SS BOND : bond 0.00410 ( 5) SS BOND : angle 0.78869 ( 10) hydrogen bonds : bond 0.03977 ( 424) hydrogen bonds : angle 4.96963 ( 1182) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 112 time to evaluate : 0.293 Fit side-chains revert: symmetry clash REVERT: B 290 GLU cc_start: 0.8242 (pm20) cc_final: 0.7868 (pm20) REVERT: G 44 HIS cc_start: 0.8162 (m-70) cc_final: 0.7779 (m-70) REVERT: G 48 ASP cc_start: 0.7793 (t0) cc_final: 0.7061 (t0) REVERT: H 140 MET cc_start: 0.9112 (mmm) cc_final: 0.8831 (mmt) REVERT: H 237 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8449 (mp) REVERT: R 198 PHE cc_start: 0.8078 (OUTLIER) cc_final: 0.7660 (m-10) REVERT: R 216 ARG cc_start: 0.7308 (mtt180) cc_final: 0.6949 (mtt-85) outliers start: 30 outliers final: 20 residues processed: 131 average time/residue: 0.0670 time to fit residues: 12.7122 Evaluate side-chains 127 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 161 SER Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 237 LEU Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 156 ILE Chi-restraints excluded: chain R residue 198 PHE Chi-restraints excluded: chain R residue 255 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 46 optimal weight: 3.9990 chunk 72 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 82 optimal weight: 8.9990 chunk 98 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 33 optimal weight: 0.0980 chunk 15 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 ASN ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 54 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.174203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.118502 restraints weight = 9959.135| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.72 r_work: 0.3338 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8023 Z= 0.143 Angle : 0.532 6.450 10964 Z= 0.287 Chirality : 0.043 0.154 1281 Planarity : 0.004 0.038 1415 Dihedral : 6.539 143.063 1186 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.92 % Allowed : 13.93 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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 aren not related in a simple way. whole: 0.72 (0.26), residues: 1100 helix: 2.13 (0.28), residues: 369 sheet: -0.42 (0.30), residues: 258 loop : -0.25 (0.30), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 218 TYR 0.019 0.001 TYR B 297 PHE 0.031 0.001 PHE H 68 TRP 0.020 0.001 TRP C 169 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 8018) covalent geometry : angle 0.53151 (10954) SS BOND : bond 0.00304 ( 5) SS BOND : angle 0.52359 ( 10) hydrogen bonds : bond 0.03385 ( 424) hydrogen bonds : angle 4.62289 ( 1182) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 114 time to evaluate : 0.187 Fit side-chains revert: symmetry clash REVERT: B 14 GLU cc_start: 0.8481 (tp30) cc_final: 0.8207 (tp30) REVERT: G 44 HIS cc_start: 0.8090 (m-70) cc_final: 0.7716 (m-70) REVERT: G 48 ASP cc_start: 0.7992 (t0) cc_final: 0.7205 (t0) REVERT: H 231 GLN cc_start: 0.8409 (pp30) cc_final: 0.8096 (pp30) REVERT: R 111 ARG cc_start: 0.5751 (mtm-85) cc_final: 0.5281 (mtm-85) REVERT: R 198 PHE cc_start: 0.8031 (OUTLIER) cc_final: 0.7643 (m-10) REVERT: R 216 ARG cc_start: 0.7301 (mtt180) cc_final: 0.6961 (mtt-85) outliers start: 27 outliers final: 18 residues processed: 133 average time/residue: 0.0726 time to fit residues: 13.7178 Evaluate side-chains 125 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 198 PHE Chi-restraints excluded: chain R residue 232 PHE Chi-restraints excluded: chain R residue 255 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 7 optimal weight: 0.1980 chunk 75 optimal weight: 0.9980 chunk 22 optimal weight: 9.9990 chunk 79 optimal weight: 0.9980 chunk 98 optimal weight: 9.9990 chunk 15 optimal weight: 0.0670 chunk 107 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 41 optimal weight: 0.4980 chunk 44 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 ASN ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.174954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.119215 restraints weight = 9968.291| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.74 r_work: 0.3347 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8023 Z= 0.124 Angle : 0.524 8.510 10964 Z= 0.279 Chirality : 0.042 0.177 1281 Planarity : 0.004 0.038 1415 Dihedral : 6.396 141.962 1186 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.92 % Allowed : 14.08 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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 aren not related in a simple way. whole: 0.82 (0.26), residues: 1100 helix: 2.31 (0.28), residues: 367 sheet: -0.45 (0.30), residues: 257 loop : -0.21 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 218 TYR 0.019 0.001 TYR B 297 PHE 0.031 0.001 PHE H 68 TRP 0.017 0.001 TRP C 169 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 8018) covalent geometry : angle 0.52435 (10954) SS BOND : bond 0.00306 ( 5) SS BOND : angle 0.52776 ( 10) hydrogen bonds : bond 0.03243 ( 424) hydrogen bonds : angle 4.51091 ( 1182) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 113 time to evaluate : 0.220 Fit side-chains revert: symmetry clash REVERT: B 290 GLU cc_start: 0.8296 (pm20) cc_final: 0.7896 (pm20) REVERT: G 44 HIS cc_start: 0.8134 (m-70) cc_final: 0.7776 (m-70) REVERT: G 48 ASP cc_start: 0.8030 (t0) cc_final: 0.7270 (t0) REVERT: H 140 MET cc_start: 0.8879 (mmm) cc_final: 0.8514 (mmt) REVERT: H 231 GLN cc_start: 0.8402 (pp30) cc_final: 0.7927 (pp30) REVERT: R 111 ARG cc_start: 0.5788 (mtm-85) cc_final: 0.5314 (mtm-85) REVERT: R 198 PHE cc_start: 0.8028 (OUTLIER) cc_final: 0.7692 (m-10) REVERT: R 216 ARG cc_start: 0.7300 (mtt180) cc_final: 0.6978 (mtt-85) outliers start: 27 outliers final: 21 residues processed: 131 average time/residue: 0.0744 time to fit residues: 13.7828 Evaluate side-chains 130 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 198 PHE Chi-restraints excluded: chain R residue 232 PHE Chi-restraints excluded: chain R residue 255 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 64 optimal weight: 0.2980 chunk 106 optimal weight: 0.0970 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 40 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 ASN ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.181273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.139776 restraints weight = 9784.734| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 2.84 r_work: 0.3480 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8023 Z= 0.124 Angle : 0.520 7.073 10964 Z= 0.277 Chirality : 0.042 0.182 1281 Planarity : 0.004 0.038 1415 Dihedral : 6.368 143.448 1186 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.92 % Allowed : 15.67 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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 aren not related in a simple way. whole: 0.84 (0.26), residues: 1100 helix: 2.40 (0.28), residues: 369 sheet: -0.52 (0.30), residues: 259 loop : -0.22 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 218 TYR 0.020 0.001 TYR B 297 PHE 0.027 0.001 PHE H 68 TRP 0.016 0.001 TRP C 169 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 8018) covalent geometry : angle 0.51979 (10954) SS BOND : bond 0.00291 ( 5) SS BOND : angle 0.50360 ( 10) hydrogen bonds : bond 0.03162 ( 424) hydrogen bonds : angle 4.43387 ( 1182) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 112 time to evaluate : 0.303 Fit side-chains revert: symmetry clash REVERT: B 14 GLU cc_start: 0.8549 (tp30) cc_final: 0.8299 (tp30) REVERT: G 44 HIS cc_start: 0.8144 (m-70) cc_final: 0.7817 (m-70) REVERT: G 48 ASP cc_start: 0.8006 (t0) cc_final: 0.7306 (t0) REVERT: H 106 SER cc_start: 0.9000 (t) cc_final: 0.8487 (p) REVERT: R 111 ARG cc_start: 0.5967 (mtm-85) cc_final: 0.5498 (mtm-85) REVERT: R 198 PHE cc_start: 0.8048 (OUTLIER) cc_final: 0.7707 (m-10) REVERT: R 216 ARG cc_start: 0.7483 (mtt180) cc_final: 0.7034 (mtt-85) outliers start: 27 outliers final: 23 residues processed: 130 average time/residue: 0.0701 time to fit residues: 12.9453 Evaluate side-chains 134 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 130 VAL Chi-restraints excluded: chain R residue 198 PHE Chi-restraints excluded: chain R residue 232 PHE Chi-restraints excluded: chain R residue 255 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 33 optimal weight: 0.6980 chunk 46 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 64 optimal weight: 0.0370 chunk 74 optimal weight: 0.4980 chunk 2 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 87 optimal weight: 6.9990 chunk 56 optimal weight: 0.0170 chunk 35 optimal weight: 0.9980 chunk 63 optimal weight: 0.5980 overall best weight: 0.3696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.175000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.131747 restraints weight = 9830.218| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 3.43 r_work: 0.3311 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8023 Z= 0.108 Angle : 0.515 9.351 10964 Z= 0.273 Chirality : 0.042 0.197 1281 Planarity : 0.004 0.038 1415 Dihedral : 6.281 144.212 1186 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.92 % Allowed : 15.53 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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 aren not related in a simple way. whole: 0.94 (0.26), residues: 1100 helix: 2.53 (0.28), residues: 369 sheet: -0.48 (0.30), residues: 257 loop : -0.20 (0.30), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 218 TYR 0.020 0.001 TYR B 297 PHE 0.021 0.001 PHE H 68 TRP 0.018 0.001 TRP C 169 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 8018) covalent geometry : angle 0.51474 (10954) SS BOND : bond 0.00279 ( 5) SS BOND : angle 0.48244 ( 10) hydrogen bonds : bond 0.03043 ( 424) hydrogen bonds : angle 4.34863 ( 1182) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: B 14 GLU cc_start: 0.8355 (tp30) cc_final: 0.8045 (tp30) REVERT: B 38 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7717 (tt) REVERT: B 290 GLU cc_start: 0.8320 (pm20) cc_final: 0.7903 (pm20) REVERT: C 339 TRP cc_start: 0.7638 (m-10) cc_final: 0.7396 (m-10) REVERT: G 44 HIS cc_start: 0.7964 (m-70) cc_final: 0.7635 (m-70) REVERT: G 48 ASP cc_start: 0.8293 (t0) cc_final: 0.7472 (t0) REVERT: H 106 SER cc_start: 0.9224 (t) cc_final: 0.8683 (p) REVERT: H 231 GLN cc_start: 0.8496 (pp30) cc_final: 0.8029 (pp30) REVERT: R 111 ARG cc_start: 0.5572 (mtm-85) cc_final: 0.5149 (mtm-85) REVERT: R 216 ARG cc_start: 0.7238 (mtt180) cc_final: 0.6822 (mtt-85) outliers start: 27 outliers final: 21 residues processed: 139 average time/residue: 0.0727 time to fit residues: 14.7293 Evaluate side-chains 137 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 130 VAL Chi-restraints excluded: chain R residue 255 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 86 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 63 optimal weight: 0.0970 chunk 33 optimal weight: 0.0570 chunk 100 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 69 optimal weight: 0.0470 chunk 0 optimal weight: 5.9990 chunk 5 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.174282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.130998 restraints weight = 9891.998| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 3.44 r_work: 0.3308 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8023 Z= 0.127 Angle : 0.520 6.342 10964 Z= 0.277 Chirality : 0.042 0.165 1281 Planarity : 0.004 0.038 1415 Dihedral : 6.299 144.250 1186 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.77 % Allowed : 15.82 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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 aren not related in a simple way. whole: 0.93 (0.26), residues: 1100 helix: 2.60 (0.28), residues: 369 sheet: -0.57 (0.31), residues: 255 loop : -0.22 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 218 TYR 0.021 0.001 TYR B 297 PHE 0.028 0.001 PHE H 68 TRP 0.014 0.001 TRP C 169 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 8018) covalent geometry : angle 0.51977 (10954) SS BOND : bond 0.00300 ( 5) SS BOND : angle 0.56814 ( 10) hydrogen bonds : bond 0.03120 ( 424) hydrogen bonds : angle 4.36821 ( 1182) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 117 time to evaluate : 0.312 Fit side-chains revert: symmetry clash REVERT: B 14 GLU cc_start: 0.8336 (tp30) cc_final: 0.8071 (tp30) REVERT: B 38 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7685 (tt) REVERT: B 290 GLU cc_start: 0.8420 (pm20) cc_final: 0.8004 (pm20) REVERT: C 339 TRP cc_start: 0.7628 (m-10) cc_final: 0.7339 (m-10) REVERT: G 44 HIS cc_start: 0.7922 (m-70) cc_final: 0.7640 (m-70) REVERT: G 48 ASP cc_start: 0.8275 (t0) cc_final: 0.7405 (t0) REVERT: H 68 PHE cc_start: 0.5789 (OUTLIER) cc_final: 0.4191 (m-10) REVERT: H 106 SER cc_start: 0.9265 (t) cc_final: 0.8949 (t) REVERT: R 63 ARG cc_start: 0.6389 (mmt180) cc_final: 0.6110 (mmt180) REVERT: R 111 ARG cc_start: 0.5535 (mtm-85) cc_final: 0.5111 (mtm-85) REVERT: R 216 ARG cc_start: 0.7167 (mtt180) cc_final: 0.6756 (mtt-85) outliers start: 26 outliers final: 20 residues processed: 135 average time/residue: 0.0903 time to fit residues: 16.9756 Evaluate side-chains 135 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 130 VAL Chi-restraints excluded: chain R residue 255 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 91 optimal weight: 0.7980 chunk 50 optimal weight: 0.0570 chunk 80 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 chunk 72 optimal weight: 7.9990 chunk 26 optimal weight: 0.6980 chunk 105 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 60 optimal weight: 0.5980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.174420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.130756 restraints weight = 9804.296| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 3.29 r_work: 0.3330 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8023 Z= 0.126 Angle : 0.523 10.064 10964 Z= 0.278 Chirality : 0.042 0.165 1281 Planarity : 0.004 0.038 1415 Dihedral : 6.250 144.174 1186 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.19 % Allowed : 16.98 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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 aren not related in a simple way. whole: 0.92 (0.26), residues: 1100 helix: 2.62 (0.28), residues: 369 sheet: -0.69 (0.30), residues: 258 loop : -0.18 (0.30), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 218 TYR 0.020 0.001 TYR B 297 PHE 0.023 0.001 PHE H 68 TRP 0.015 0.001 TRP C 169 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 8018) covalent geometry : angle 0.52324 (10954) SS BOND : bond 0.00287 ( 5) SS BOND : angle 0.50651 ( 10) hydrogen bonds : bond 0.03054 ( 424) hydrogen bonds : angle 4.32711 ( 1182) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 117 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: B 14 GLU cc_start: 0.8347 (tp30) cc_final: 0.8088 (tp30) REVERT: B 38 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7677 (tt) REVERT: B 331 ASN cc_start: 0.7588 (m-40) cc_final: 0.7278 (p0) REVERT: C 339 TRP cc_start: 0.7598 (m-10) cc_final: 0.7386 (m-10) REVERT: G 44 HIS cc_start: 0.7940 (m-70) cc_final: 0.7650 (m-70) REVERT: G 48 ASP cc_start: 0.8278 (t0) cc_final: 0.7428 (t0) REVERT: H 68 PHE cc_start: 0.5455 (OUTLIER) cc_final: 0.3982 (m-10) REVERT: H 106 SER cc_start: 0.9235 (t) cc_final: 0.8904 (t) REVERT: H 231 GLN cc_start: 0.8488 (pp30) cc_final: 0.7966 (pp30) REVERT: R 63 ARG cc_start: 0.6513 (mmt180) cc_final: 0.6243 (mmt180) REVERT: R 111 ARG cc_start: 0.5773 (mtm-85) cc_final: 0.5320 (mtm-85) outliers start: 22 outliers final: 19 residues processed: 131 average time/residue: 0.0930 time to fit residues: 16.7626 Evaluate side-chains 135 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 164 SER Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 130 VAL Chi-restraints excluded: chain R residue 255 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 45 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 68 optimal weight: 0.0870 chunk 0 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 81 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 43 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.174389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.119909 restraints weight = 9853.129| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.73 r_work: 0.3359 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8023 Z= 0.124 Angle : 0.531 10.065 10964 Z= 0.280 Chirality : 0.042 0.160 1281 Planarity : 0.004 0.037 1415 Dihedral : 6.209 144.688 1186 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.63 % Allowed : 16.84 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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 aren not related in a simple way. whole: 0.94 (0.26), residues: 1100 helix: 2.67 (0.28), residues: 369 sheet: -0.73 (0.30), residues: 258 loop : -0.17 (0.30), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 218 TYR 0.020 0.001 TYR B 297 PHE 0.021 0.001 PHE H 68 TRP 0.015 0.001 TRP C 169 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 8018) covalent geometry : angle 0.53136 (10954) SS BOND : bond 0.00344 ( 5) SS BOND : angle 0.61562 ( 10) hydrogen bonds : bond 0.03025 ( 424) hydrogen bonds : angle 4.27943 ( 1182) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 114 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: B 14 GLU cc_start: 0.8479 (tp30) cc_final: 0.8181 (tp30) REVERT: B 38 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7749 (tt) REVERT: B 290 GLU cc_start: 0.8532 (pm20) cc_final: 0.8175 (pm20) REVERT: B 322 HIS cc_start: 0.7015 (OUTLIER) cc_final: 0.6569 (m90) REVERT: G 44 HIS cc_start: 0.8010 (m-70) cc_final: 0.7762 (m-70) REVERT: G 48 ASP cc_start: 0.8270 (t0) cc_final: 0.7561 (t0) REVERT: H 68 PHE cc_start: 0.5385 (OUTLIER) cc_final: 0.4038 (m-10) REVERT: H 106 SER cc_start: 0.9135 (t) cc_final: 0.8790 (t) REVERT: R 63 ARG cc_start: 0.6668 (mmt180) cc_final: 0.6399 (mmt180) REVERT: R 111 ARG cc_start: 0.5900 (mtm-85) cc_final: 0.5438 (mtm-85) outliers start: 25 outliers final: 20 residues processed: 131 average time/residue: 0.0991 time to fit residues: 17.3657 Evaluate side-chains 135 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 322 HIS Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 164 SER Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 130 VAL Chi-restraints excluded: chain R residue 255 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 45 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 104 optimal weight: 0.7980 chunk 74 optimal weight: 0.0270 chunk 92 optimal weight: 0.7980 chunk 75 optimal weight: 0.0670 chunk 43 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 7 optimal weight: 0.0030 chunk 12 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.175899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.121673 restraints weight = 9780.104| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.72 r_work: 0.3371 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8023 Z= 0.107 Angle : 0.524 10.074 10964 Z= 0.275 Chirality : 0.042 0.157 1281 Planarity : 0.004 0.038 1415 Dihedral : 6.103 144.930 1186 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.05 % Allowed : 18.14 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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 aren not related in a simple way. whole: 1.09 (0.26), residues: 1100 helix: 2.74 (0.28), residues: 369 sheet: -0.51 (0.30), residues: 251 loop : -0.14 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 218 TYR 0.020 0.001 TYR B 297 PHE 0.016 0.001 PHE H 68 TRP 0.018 0.001 TRP C 169 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 8018) covalent geometry : angle 0.52376 (10954) SS BOND : bond 0.00339 ( 5) SS BOND : angle 0.63730 ( 10) hydrogen bonds : bond 0.02879 ( 424) hydrogen bonds : angle 4.21777 ( 1182) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2071.11 seconds wall clock time: 36 minutes 12.96 seconds (2172.96 seconds total)