Starting phenix.real_space_refine on Wed Feb 4 05:23:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jid_61502/02_2026/9jid_61502.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jid_61502/02_2026/9jid_61502.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jid_61502/02_2026/9jid_61502.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jid_61502/02_2026/9jid_61502.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jid_61502/02_2026/9jid_61502.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jid_61502/02_2026/9jid_61502.map" } resolution = 2.78 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= 0.020 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: 4 Type Number sf(0) Gaussians S 65 5.16 5 C 5613 2.51 5 N 1501 2.21 5 O 1605 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8784 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2288 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 10, 'TRANS': 278} Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 3, 'ARG:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "C" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1710 Classifications: {'peptide': 216} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 10} Link IDs: {'PTRANS': 2, 'TRANS': 213} Chain breaks: 2 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 2577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2577 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "G" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 431 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1769 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'NIO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.58, per 1000 atoms: 0.18 Number of scatterers: 8784 At special positions: 0 Unit cell: (89.25, 122.4, 129.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 65 16.00 O 1605 8.00 N 1501 7.00 C 5613 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 18 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS A 19 " - pdb=" SG CYS A 266 " distance=2.03 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 177 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " 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: 0.47 Conformation dependent library (CDL) restraints added in 375.2 milliseconds 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2114 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 13 sheets defined 35.7% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 24 through 53 Proline residue: A 31 - end of helix Processing helix chain 'A' and resid 60 through 79 Processing helix chain 'A' and resid 80 through 84 Processing helix chain 'A' and resid 96 through 130 removed outlier: 3.646A pdb=" N ARG A 128 " --> pdb=" O ASP A 124 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL A 129 " --> pdb=" O ARG A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 138 Processing helix chain 'A' and resid 140 through 160 Processing helix chain 'A' and resid 160 through 165 removed outlier: 3.843A pdb=" N LYS A 164 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS A 165 " --> pdb=" O HIS A 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 160 through 165' Processing helix chain 'A' and resid 187 through 218 removed outlier: 3.508A pdb=" N ALA A 191 " --> pdb=" O ARG A 187 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE A 197 " --> pdb=" O PHE A 193 " (cutoff:3.500A) Proline residue: A 200 - end of helix Processing helix chain 'A' and resid 223 through 261 removed outlier: 4.098A pdb=" N LYS A 227 " --> pdb=" O HIS A 223 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG A 228 " --> pdb=" O ALA A 224 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A 236 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA A 237 " --> pdb=" O ILE A 233 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A 245 " --> pdb=" O VAL A 241 " (cutoff:3.500A) Proline residue: A 246 - end of helix Processing helix chain 'A' and resid 265 through 270 Processing helix chain 'A' and resid 271 through 295 removed outlier: 4.045A pdb=" N PHE A 282 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR A 283 " --> pdb=" O THR A 279 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N TYR A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N SER A 287 " --> pdb=" O THR A 283 " (cutoff:3.500A) Proline residue: A 291 - end of helix Processing helix chain 'C' and resid 6 through 31 removed outlier: 3.511A pdb=" N LYS C 10 " --> pdb=" O SER C 6 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA C 11 " --> pdb=" O ALA C 7 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA C 12 " --> pdb=" O GLU C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 53 removed outlier: 3.576A pdb=" N MET C 53 " --> pdb=" O ILE C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 216 removed outlier: 4.181A pdb=" N ILE C 212 " --> pdb=" O LYS C 209 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N HIS C 213 " --> pdb=" O LYS C 210 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE C 215 " --> pdb=" O ILE C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 230 No H-bonds generated for 'chain 'C' and resid 228 through 230' Processing helix chain 'C' and resid 242 through 255 Processing helix chain 'C' and resid 270 through 281 removed outlier: 3.978A pdb=" N GLU C 276 " --> pdb=" O ASP C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 301 removed outlier: 4.324A pdb=" N ALA C 301 " --> pdb=" O GLU C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 310 removed outlier: 3.536A pdb=" N PHE C 307 " --> pdb=" O ILE C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 351 Processing helix chain 'B' and resid 5 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.607A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.572A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.899A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 185 through 190 removed outlier: 6.902A pdb=" N LYS C 35 " --> pdb=" O ALA C 220 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N ILE C 222 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU C 37 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N CYS C 224 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N LEU C 39 " --> pdb=" O CYS C 224 " (cutoff:3.500A) removed outlier: 9.067A pdb=" N ALA C 226 " --> pdb=" O LEU C 39 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ILE C 221 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N PHE C 267 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N PHE C 223 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N ASN C 269 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N VAL C 225 " --> pdb=" O ASN C 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.538A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.695A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.765A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.858A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.733A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.659A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.468A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.528A pdb=" N GLY S 10 " --> pdb=" O THR S 116 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR S 118 " --> pdb=" O GLY S 10 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL S 97 " --> pdb=" O HIS S 35 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.528A pdb=" N GLY S 10 " --> pdb=" O THR S 116 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR S 118 " --> pdb=" O GLY S 10 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 143 through 148 Processing sheet with id=AB4, first strand: chain 'S' and resid 182 through 183 removed outlier: 6.487A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N THR S 226 " --> pdb=" O GLN S 219 " (cutoff:3.500A) 396 hydrogen bonds defined for protein. 1095 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: 1.50 Time building geometry restraints manager: 0.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2774 1.34 - 1.46: 1582 1.46 - 1.58: 4532 1.58 - 1.70: 0 1.70 - 1.82: 93 Bond restraints: 8981 Sorted by residual: bond pdb=" N VAL A 88 " pdb=" CA VAL A 88 " ideal model delta sigma weight residual 1.458 1.395 0.063 1.76e-02 3.23e+03 1.29e+01 bond pdb=" N GLN A 112 " pdb=" CA GLN A 112 " ideal model delta sigma weight residual 1.459 1.418 0.041 1.25e-02 6.40e+03 1.07e+01 bond pdb=" C GLN A 112 " pdb=" N GLY A 113 " ideal model delta sigma weight residual 1.334 1.371 -0.037 1.21e-02 6.83e+03 9.50e+00 bond pdb=" CA VAL A 88 " pdb=" C VAL A 88 " ideal model delta sigma weight residual 1.526 1.490 0.036 1.19e-02 7.06e+03 9.22e+00 bond pdb=" N PRO C 288 " pdb=" CA PRO C 288 " ideal model delta sigma weight residual 1.466 1.435 0.032 1.21e-02 6.83e+03 6.93e+00 ... (remaining 8976 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 11923 2.02 - 4.04: 207 4.04 - 6.06: 31 6.06 - 8.07: 8 8.07 - 10.09: 3 Bond angle restraints: 12172 Sorted by residual: angle pdb=" N ARG A 89 " pdb=" CA ARG A 89 " pdb=" C ARG A 89 " ideal model delta sigma weight residual 111.39 106.30 5.09 1.38e+00 5.25e-01 1.36e+01 angle pdb=" N ILE A 77 " pdb=" CA ILE A 77 " pdb=" CB ILE A 77 " ideal model delta sigma weight residual 110.58 116.11 -5.53 1.50e+00 4.44e-01 1.36e+01 angle pdb=" N TYR A 86 " pdb=" CA TYR A 86 " pdb=" C TYR A 86 " ideal model delta sigma weight residual 110.80 103.12 7.68 2.13e+00 2.20e-01 1.30e+01 angle pdb=" C TYR A 87 " pdb=" N VAL A 88 " pdb=" CA VAL A 88 " ideal model delta sigma weight residual 120.34 114.71 5.63 1.58e+00 4.01e-01 1.27e+01 angle pdb=" C ARG B 8 " pdb=" N GLN B 9 " pdb=" CA GLN B 9 " ideal model delta sigma weight residual 121.14 114.93 6.21 1.75e+00 3.27e-01 1.26e+01 ... (remaining 12167 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 4686 17.70 - 35.40: 483 35.40 - 53.10: 99 53.10 - 70.80: 13 70.80 - 88.51: 4 Dihedral angle restraints: 5285 sinusoidal: 2012 harmonic: 3273 Sorted by residual: dihedral pdb=" CB CYS A 19 " pdb=" SG CYS A 19 " pdb=" SG CYS A 266 " pdb=" CB CYS A 266 " ideal model delta sinusoidal sigma weight residual 93.00 153.51 -60.51 1 1.00e+01 1.00e-02 4.87e+01 dihedral pdb=" CA ARG A 22 " pdb=" C ARG A 22 " pdb=" N ASP A 23 " pdb=" CA ASP A 23 " ideal model delta harmonic sigma weight residual -180.00 -158.57 -21.43 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA THR S 91 " pdb=" C THR S 91 " pdb=" N ALA S 92 " pdb=" CA ALA S 92 " ideal model delta harmonic sigma weight residual -180.00 -162.67 -17.33 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 5282 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 943 0.040 - 0.081: 319 0.081 - 0.121: 98 0.121 - 0.161: 12 0.161 - 0.202: 2 Chirality restraints: 1374 Sorted by residual: chirality pdb=" CB ILE A 78 " pdb=" CA ILE A 78 " pdb=" CG1 ILE A 78 " pdb=" CG2 ILE A 78 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA GLN A 112 " pdb=" N GLN A 112 " pdb=" C GLN A 112 " pdb=" CB GLN A 112 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.95e-01 chirality pdb=" CA TYR S 223 " pdb=" N TYR S 223 " pdb=" C TYR S 223 " pdb=" CB TYR S 223 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.12e-01 ... (remaining 1371 not shown) Planarity restraints: 1540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR S 138 " -0.061 5.00e-02 4.00e+02 9.24e-02 1.37e+01 pdb=" N PRO S 139 " 0.160 5.00e-02 4.00e+02 pdb=" CA PRO S 139 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO S 139 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 79 " -0.015 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C CYS A 79 " 0.055 2.00e-02 2.50e+03 pdb=" O CYS A 79 " -0.021 2.00e-02 2.50e+03 pdb=" N LEU A 80 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 298 " -0.047 5.00e-02 4.00e+02 7.06e-02 7.98e+00 pdb=" N PRO A 299 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO A 299 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 299 " -0.039 5.00e-02 4.00e+02 ... (remaining 1537 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 121 2.64 - 3.21: 7940 3.21 - 3.77: 12644 3.77 - 4.34: 18035 4.34 - 4.90: 30918 Nonbonded interactions: 69658 Sorted by model distance: nonbonded pdb=" OG SER G 57 " pdb=" OE1 GLU G 58 " model vdw 2.076 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.100 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.164 3.040 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.169 3.040 nonbonded pdb=" O LEU A 280 " pdb=" OG1 THR A 283 " model vdw 2.194 3.040 ... (remaining 69653 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: 2.370 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.470 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:7.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 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 : 0.004 0.063 8986 Z= 0.207 Angle : 0.674 10.092 12182 Z= 0.388 Chirality : 0.044 0.202 1374 Planarity : 0.005 0.092 1540 Dihedral : 14.548 88.505 3156 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.48 % Favored : 94.25 % Rotamer: Outliers : 0.43 % Allowed : 13.48 % Favored : 86.10 % 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: -0.53 (0.25), residues: 1113 helix: 1.29 (0.28), residues: 360 sheet: -0.51 (0.32), residues: 266 loop : -1.53 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 63 TYR 0.014 0.001 TYR S 223 PHE 0.020 0.001 PHE A 107 TRP 0.017 0.001 TRP A 188 HIS 0.005 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 8981) covalent geometry : angle 0.67379 (12172) SS BOND : bond 0.00345 ( 5) SS BOND : angle 0.65685 ( 10) hydrogen bonds : bond 0.19788 ( 393) hydrogen bonds : angle 6.66709 ( 1095) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 150 time to evaluate : 0.221 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: A 106 MET cc_start: 0.6831 (mmm) cc_final: 0.6561 (mmm) REVERT: A 241 VAL cc_start: 0.8562 (OUTLIER) cc_final: 0.8336 (m) outliers start: 4 outliers final: 4 residues processed: 153 average time/residue: 0.5502 time to fit residues: 89.1709 Evaluate side-chains 147 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 142 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 TYR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain G residue 48 ASP Chi-restraints excluded: chain S residue 189 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 0.3980 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS C 22 ASN B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.132544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.091552 restraints weight = 12557.858| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 3.02 r_work: 0.2937 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8986 Z= 0.151 Angle : 0.605 10.252 12182 Z= 0.320 Chirality : 0.044 0.166 1374 Planarity : 0.005 0.068 1540 Dihedral : 4.782 47.090 1227 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.75 % Favored : 94.07 % Rotamer: Outliers : 2.57 % Allowed : 16.04 % Favored : 81.39 % 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: -0.10 (0.26), residues: 1113 helix: 1.78 (0.28), residues: 357 sheet: -0.13 (0.32), residues: 276 loop : -1.49 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 19 TYR 0.024 0.002 TYR C 230 PHE 0.013 0.001 PHE C 189 TRP 0.013 0.001 TRP S 47 HIS 0.005 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 8981) covalent geometry : angle 0.60488 (12172) SS BOND : bond 0.00594 ( 5) SS BOND : angle 0.84713 ( 10) hydrogen bonds : bond 0.05114 ( 393) hydrogen bonds : angle 4.88950 ( 1095) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 151 time to evaluate : 0.332 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: A 192 MET cc_start: 0.5614 (mmt) cc_final: 0.4892 (mpt) REVERT: A 241 VAL cc_start: 0.8499 (t) cc_final: 0.8152 (m) REVERT: C 52 GLN cc_start: 0.7612 (mp10) cc_final: 0.7308 (mp10) REVERT: B 258 ASP cc_start: 0.8302 (t0) cc_final: 0.8018 (t0) REVERT: G 21 MET cc_start: 0.8501 (OUTLIER) cc_final: 0.8091 (tmt) REVERT: G 58 GLU cc_start: 0.8311 (pm20) cc_final: 0.8050 (pm20) REVERT: S 3 GLN cc_start: 0.8084 (tt0) cc_final: 0.7737 (mm-40) REVERT: S 222 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7703 (mt-10) outliers start: 24 outliers final: 9 residues processed: 163 average time/residue: 0.5401 time to fit residues: 93.5662 Evaluate side-chains 150 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 140 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 TYR Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 138 THR Chi-restraints excluded: chain S residue 162 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 2 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 77 optimal weight: 0.3980 chunk 46 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS C 22 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.133544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.092478 restraints weight = 12490.488| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 3.02 r_work: 0.2946 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8986 Z= 0.129 Angle : 0.561 9.585 12182 Z= 0.297 Chirality : 0.043 0.150 1374 Planarity : 0.004 0.060 1540 Dihedral : 4.208 31.170 1220 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.84 % Favored : 93.98 % Rotamer: Outliers : 2.57 % Allowed : 18.18 % Favored : 79.25 % 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: 0.09 (0.26), residues: 1113 helix: 2.01 (0.28), residues: 352 sheet: -0.03 (0.32), residues: 276 loop : -1.39 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 19 TYR 0.016 0.001 TYR C 296 PHE 0.017 0.001 PHE A 21 TRP 0.011 0.001 TRP B 339 HIS 0.006 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 8981) covalent geometry : angle 0.56121 (12172) SS BOND : bond 0.00458 ( 5) SS BOND : angle 0.81126 ( 10) hydrogen bonds : bond 0.04516 ( 393) hydrogen bonds : angle 4.49079 ( 1095) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 150 time to evaluate : 0.295 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: A 241 VAL cc_start: 0.8439 (t) cc_final: 0.8096 (m) REVERT: G 48 ASP cc_start: 0.8494 (t0) cc_final: 0.8186 (t0) REVERT: G 58 GLU cc_start: 0.8313 (pm20) cc_final: 0.7993 (pm20) REVERT: S 3 GLN cc_start: 0.8066 (tt0) cc_final: 0.7635 (mm110) REVERT: S 222 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7643 (mt-10) outliers start: 24 outliers final: 11 residues processed: 164 average time/residue: 0.5366 time to fit residues: 93.5823 Evaluate side-chains 144 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 133 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 TRP Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 138 THR Chi-restraints excluded: chain S residue 162 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 54 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 100 optimal weight: 0.0980 chunk 75 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS C 22 ASN B 268 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.133084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.092051 restraints weight = 12762.348| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 3.04 r_work: 0.2945 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8986 Z= 0.138 Angle : 0.570 10.372 12182 Z= 0.302 Chirality : 0.044 0.157 1374 Planarity : 0.004 0.058 1540 Dihedral : 4.080 27.272 1218 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.57 % Favored : 94.34 % Rotamer: Outliers : 2.89 % Allowed : 18.72 % Favored : 78.40 % 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: 0.14 (0.26), residues: 1113 helix: 2.05 (0.28), residues: 352 sheet: 0.03 (0.32), residues: 276 loop : -1.38 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 19 TYR 0.015 0.001 TYR S 178 PHE 0.013 0.001 PHE C 189 TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 8981) covalent geometry : angle 0.56940 (12172) SS BOND : bond 0.00495 ( 5) SS BOND : angle 0.81489 ( 10) hydrogen bonds : bond 0.04408 ( 393) hydrogen bonds : angle 4.37420 ( 1095) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 140 time to evaluate : 0.396 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: A 106 MET cc_start: 0.7465 (mmm) cc_final: 0.7172 (mmm) REVERT: A 241 VAL cc_start: 0.8387 (t) cc_final: 0.8039 (m) REVERT: G 20 LYS cc_start: 0.8490 (mttp) cc_final: 0.8270 (mtmm) REVERT: G 48 ASP cc_start: 0.8452 (t0) cc_final: 0.8156 (t0) REVERT: G 58 GLU cc_start: 0.8321 (pm20) cc_final: 0.7999 (pm20) REVERT: S 3 GLN cc_start: 0.8078 (tt0) cc_final: 0.7664 (mm110) REVERT: S 19 LYS cc_start: 0.8733 (ttmt) cc_final: 0.8496 (ttmp) REVERT: S 76 LYS cc_start: 0.8966 (mtmm) cc_final: 0.8671 (mptt) outliers start: 27 outliers final: 17 residues processed: 160 average time/residue: 0.5140 time to fit residues: 87.3954 Evaluate side-chains 155 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 138 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 TRP Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 162 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 6.9990 chunk 56 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 27 optimal weight: 8.9990 chunk 2 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 109 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS C 22 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.132536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.091456 restraints weight = 12683.689| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 3.04 r_work: 0.2937 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8986 Z= 0.149 Angle : 0.588 10.463 12182 Z= 0.309 Chirality : 0.044 0.175 1374 Planarity : 0.004 0.057 1540 Dihedral : 4.087 27.539 1218 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.39 % Favored : 94.52 % Rotamer: Outliers : 2.99 % Allowed : 19.89 % Favored : 77.11 % 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: 0.13 (0.26), residues: 1113 helix: 2.12 (0.28), residues: 345 sheet: 0.05 (0.31), residues: 276 loop : -1.42 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 19 TYR 0.016 0.001 TYR S 178 PHE 0.017 0.001 PHE A 21 TRP 0.011 0.001 TRP B 82 HIS 0.005 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 8981) covalent geometry : angle 0.58809 (12172) SS BOND : bond 0.00523 ( 5) SS BOND : angle 0.86422 ( 10) hydrogen bonds : bond 0.04438 ( 393) hydrogen bonds : angle 4.36949 ( 1095) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 0.370 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: A 241 VAL cc_start: 0.8388 (t) cc_final: 0.8043 (m) REVERT: C 52 GLN cc_start: 0.7634 (mp10) cc_final: 0.7341 (mp10) REVERT: G 48 ASP cc_start: 0.8503 (t0) cc_final: 0.8193 (t0) REVERT: G 58 GLU cc_start: 0.8343 (pm20) cc_final: 0.8000 (pm20) REVERT: S 3 GLN cc_start: 0.8071 (tt0) cc_final: 0.7657 (mm110) REVERT: S 76 LYS cc_start: 0.8952 (mtmm) cc_final: 0.8650 (mptt) REVERT: S 87 ARG cc_start: 0.8125 (ptp90) cc_final: 0.7703 (ptp90) outliers start: 28 outliers final: 15 residues processed: 159 average time/residue: 0.5791 time to fit residues: 97.7098 Evaluate side-chains 152 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 162 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 90 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 109 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 86 optimal weight: 0.0670 chunk 75 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 overall best weight: 1.1324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN A 223 HIS C 22 ASN B 268 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.132619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.091607 restraints weight = 12633.652| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 3.03 r_work: 0.2937 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8986 Z= 0.151 Angle : 0.585 10.907 12182 Z= 0.310 Chirality : 0.044 0.184 1374 Planarity : 0.004 0.056 1540 Dihedral : 4.085 27.843 1218 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.57 % Favored : 94.34 % Rotamer: Outliers : 3.21 % Allowed : 19.89 % Favored : 76.90 % 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: 0.16 (0.26), residues: 1113 helix: 2.14 (0.28), residues: 345 sheet: 0.07 (0.31), residues: 276 loop : -1.41 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 242 TYR 0.017 0.001 TYR A 294 PHE 0.012 0.001 PHE C 189 TRP 0.012 0.001 TRP B 82 HIS 0.005 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 8981) covalent geometry : angle 0.58471 (12172) SS BOND : bond 0.00523 ( 5) SS BOND : angle 0.83901 ( 10) hydrogen bonds : bond 0.04421 ( 393) hydrogen bonds : angle 4.32812 ( 1095) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 143 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: A 106 MET cc_start: 0.7482 (mmm) cc_final: 0.7249 (mmm) REVERT: A 241 VAL cc_start: 0.8380 (t) cc_final: 0.8033 (m) REVERT: B 146 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8323 (mp) REVERT: B 258 ASP cc_start: 0.8499 (t0) cc_final: 0.8206 (t0) REVERT: G 48 ASP cc_start: 0.8528 (t0) cc_final: 0.8235 (t0) REVERT: G 58 GLU cc_start: 0.8361 (pm20) cc_final: 0.8002 (pm20) REVERT: S 3 GLN cc_start: 0.8048 (tt0) cc_final: 0.7643 (mm110) REVERT: S 76 LYS cc_start: 0.8931 (mtmm) cc_final: 0.8632 (mptt) outliers start: 30 outliers final: 19 residues processed: 163 average time/residue: 0.5521 time to fit residues: 95.8151 Evaluate side-chains 158 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 TRP Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 162 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 96 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 109 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 45 optimal weight: 0.0470 chunk 93 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 chunk 4 optimal weight: 6.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS A 253 HIS C 22 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.134176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.092906 restraints weight = 12613.581| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 3.04 r_work: 0.2960 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8986 Z= 0.122 Angle : 0.579 11.715 12182 Z= 0.302 Chirality : 0.043 0.163 1374 Planarity : 0.004 0.055 1540 Dihedral : 3.999 29.488 1218 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.21 % Favored : 94.70 % Rotamer: Outliers : 2.89 % Allowed : 21.28 % Favored : 75.83 % 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: 0.27 (0.26), residues: 1113 helix: 2.20 (0.28), residues: 346 sheet: 0.16 (0.31), residues: 275 loop : -1.33 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 19 TYR 0.034 0.001 TYR C 230 PHE 0.021 0.001 PHE A 38 TRP 0.010 0.001 TRP A 188 HIS 0.003 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 8981) covalent geometry : angle 0.57918 (12172) SS BOND : bond 0.00436 ( 5) SS BOND : angle 0.73212 ( 10) hydrogen bonds : bond 0.04074 ( 393) hydrogen bonds : angle 4.26968 ( 1095) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 142 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: A 76 LEU cc_start: 0.5832 (OUTLIER) cc_final: 0.5409 (tt) REVERT: A 106 MET cc_start: 0.7426 (mmm) cc_final: 0.7174 (mmm) REVERT: A 241 VAL cc_start: 0.8364 (t) cc_final: 0.8020 (m) REVERT: C 52 GLN cc_start: 0.7640 (mp10) cc_final: 0.7316 (mp10) REVERT: B 36 ASN cc_start: 0.8959 (m-40) cc_final: 0.8339 (p0) REVERT: B 146 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8321 (mp) REVERT: B 258 ASP cc_start: 0.8466 (t0) cc_final: 0.8176 (t0) REVERT: G 20 LYS cc_start: 0.8542 (mtmm) cc_final: 0.8340 (mttp) REVERT: G 48 ASP cc_start: 0.8412 (t0) cc_final: 0.8146 (t0) REVERT: G 58 GLU cc_start: 0.8337 (pm20) cc_final: 0.7966 (pm20) REVERT: S 3 GLN cc_start: 0.8018 (tt0) cc_final: 0.7625 (mm110) REVERT: S 43 LYS cc_start: 0.8439 (mptp) cc_final: 0.8231 (mppt) REVERT: S 76 LYS cc_start: 0.8918 (mtmm) cc_final: 0.8613 (mptt) REVERT: S 87 ARG cc_start: 0.8013 (ptp90) cc_final: 0.7667 (ptp90) outliers start: 27 outliers final: 16 residues processed: 160 average time/residue: 0.5920 time to fit residues: 100.5132 Evaluate side-chains 158 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 TRP Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 162 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 15 optimal weight: 20.0000 chunk 33 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 97 optimal weight: 0.0870 chunk 92 optimal weight: 0.0370 chunk 38 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 94 optimal weight: 0.0270 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS A 253 HIS C 22 ASN B 268 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.135616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.094367 restraints weight = 12543.178| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 3.04 r_work: 0.2990 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8986 Z= 0.111 Angle : 0.572 11.558 12182 Z= 0.298 Chirality : 0.042 0.161 1374 Planarity : 0.004 0.054 1540 Dihedral : 3.885 29.061 1218 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.76 % Favored : 95.15 % Rotamer: Outliers : 2.03 % Allowed : 22.03 % Favored : 75.94 % 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: 0.36 (0.26), residues: 1113 helix: 2.25 (0.28), residues: 346 sheet: 0.22 (0.31), residues: 275 loop : -1.27 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 19 TYR 0.015 0.001 TYR S 178 PHE 0.011 0.001 PHE C 189 TRP 0.012 0.001 TRP A 188 HIS 0.003 0.000 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 8981) covalent geometry : angle 0.57154 (12172) SS BOND : bond 0.00374 ( 5) SS BOND : angle 0.67560 ( 10) hydrogen bonds : bond 0.03861 ( 393) hydrogen bonds : angle 4.13756 ( 1095) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 140 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: A 106 MET cc_start: 0.7358 (mmm) cc_final: 0.7127 (mmm) REVERT: A 241 VAL cc_start: 0.8484 (t) cc_final: 0.8167 (m) REVERT: C 52 GLN cc_start: 0.7551 (mp10) cc_final: 0.7243 (mp10) REVERT: C 242 ARG cc_start: 0.8216 (mtt90) cc_final: 0.7965 (mtt90) REVERT: B 36 ASN cc_start: 0.8973 (m-40) cc_final: 0.8357 (p0) REVERT: B 258 ASP cc_start: 0.8429 (t0) cc_final: 0.8125 (t0) REVERT: G 20 LYS cc_start: 0.8525 (mtmm) cc_final: 0.8253 (mtmm) REVERT: G 58 GLU cc_start: 0.8256 (pm20) cc_final: 0.7954 (pm20) REVERT: S 3 GLN cc_start: 0.8015 (tt0) cc_final: 0.7637 (mm110) REVERT: S 43 LYS cc_start: 0.8517 (mptp) cc_final: 0.8280 (mppt) REVERT: S 76 LYS cc_start: 0.8921 (mtmm) cc_final: 0.8622 (mptt) REVERT: S 87 ARG cc_start: 0.7967 (ptp90) cc_final: 0.7576 (ptp90) outliers start: 19 outliers final: 14 residues processed: 154 average time/residue: 0.5583 time to fit residues: 91.1256 Evaluate side-chains 151 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 137 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 162 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 42 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 78 optimal weight: 0.7980 chunk 73 optimal weight: 0.0050 chunk 60 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 overall best weight: 1.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS C 22 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.133501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.092177 restraints weight = 12555.752| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 3.03 r_work: 0.2949 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 8986 Z= 0.155 Angle : 0.623 15.713 12182 Z= 0.321 Chirality : 0.044 0.213 1374 Planarity : 0.004 0.055 1540 Dihedral : 3.994 27.751 1218 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.48 % Favored : 94.43 % Rotamer: Outliers : 2.03 % Allowed : 22.46 % Favored : 75.51 % 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: 0.29 (0.26), residues: 1113 helix: 2.18 (0.28), residues: 345 sheet: 0.16 (0.31), residues: 276 loop : -1.27 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 19 TYR 0.035 0.002 TYR C 230 PHE 0.024 0.001 PHE A 38 TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS C 213 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 8981) covalent geometry : angle 0.62257 (12172) SS BOND : bond 0.00525 ( 5) SS BOND : angle 0.83467 ( 10) hydrogen bonds : bond 0.04288 ( 393) hydrogen bonds : angle 4.22842 ( 1095) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 140 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: A 106 MET cc_start: 0.7459 (mmm) cc_final: 0.7210 (mmm) REVERT: A 195 LEU cc_start: 0.7547 (tt) cc_final: 0.7237 (tp) REVERT: A 241 VAL cc_start: 0.8497 (t) cc_final: 0.8165 (m) REVERT: B 36 ASN cc_start: 0.9007 (m-40) cc_final: 0.8384 (p0) REVERT: B 146 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8333 (mp) REVERT: B 258 ASP cc_start: 0.8465 (t0) cc_final: 0.8176 (t0) REVERT: G 48 ASP cc_start: 0.8681 (t0) cc_final: 0.8331 (t0) REVERT: G 58 GLU cc_start: 0.8299 (pm20) cc_final: 0.7898 (pm20) REVERT: S 3 GLN cc_start: 0.8051 (tt0) cc_final: 0.7656 (mm110) REVERT: S 76 LYS cc_start: 0.8918 (mtmm) cc_final: 0.8623 (mptt) REVERT: S 87 ARG cc_start: 0.8049 (ptp90) cc_final: 0.7733 (ptp90) outliers start: 19 outliers final: 14 residues processed: 155 average time/residue: 0.5566 time to fit residues: 91.7148 Evaluate side-chains 150 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 135 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 162 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 38 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 106 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 102 optimal weight: 0.0980 chunk 1 optimal weight: 9.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS A 253 HIS C 22 ASN B 268 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.134053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.092832 restraints weight = 12508.387| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 3.02 r_work: 0.2961 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 8986 Z= 0.140 Angle : 0.620 13.621 12182 Z= 0.322 Chirality : 0.044 0.227 1374 Planarity : 0.004 0.055 1540 Dihedral : 3.988 27.224 1218 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.21 % Favored : 94.70 % Rotamer: Outliers : 1.71 % Allowed : 22.89 % Favored : 75.40 % 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: 0.27 (0.26), residues: 1113 helix: 2.08 (0.28), residues: 351 sheet: 0.18 (0.31), residues: 275 loop : -1.27 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 19 TYR 0.016 0.001 TYR A 294 PHE 0.016 0.001 PHE A 21 TRP 0.013 0.001 TRP A 188 HIS 0.003 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 8981) covalent geometry : angle 0.61986 (12172) SS BOND : bond 0.00601 ( 5) SS BOND : angle 0.85568 ( 10) hydrogen bonds : bond 0.04202 ( 393) hydrogen bonds : angle 4.27733 ( 1095) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 0.420 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: A 195 LEU cc_start: 0.7530 (tt) cc_final: 0.7219 (tp) REVERT: A 241 VAL cc_start: 0.8484 (t) cc_final: 0.8159 (m) REVERT: C 52 GLN cc_start: 0.7537 (mp10) cc_final: 0.7250 (mp-120) REVERT: B 36 ASN cc_start: 0.9005 (m-40) cc_final: 0.8397 (p0) REVERT: B 146 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8282 (mp) REVERT: B 258 ASP cc_start: 0.8437 (t0) cc_final: 0.8140 (t0) REVERT: G 48 ASP cc_start: 0.8619 (t0) cc_final: 0.8306 (t0) REVERT: G 58 GLU cc_start: 0.8326 (pm20) cc_final: 0.7971 (pm20) REVERT: S 3 GLN cc_start: 0.8038 (tt0) cc_final: 0.7649 (mm110) REVERT: S 76 LYS cc_start: 0.8923 (mtmm) cc_final: 0.8631 (mptt) REVERT: S 87 ARG cc_start: 0.8038 (ptp90) cc_final: 0.7734 (ptp90) outliers start: 16 outliers final: 15 residues processed: 151 average time/residue: 0.5467 time to fit residues: 87.8866 Evaluate side-chains 154 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 138 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 162 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 9 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS C 22 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.133368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.092171 restraints weight = 12491.176| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 3.01 r_work: 0.2970 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 8986 Z= 0.156 Angle : 0.634 13.101 12182 Z= 0.330 Chirality : 0.045 0.221 1374 Planarity : 0.004 0.055 1540 Dihedral : 4.060 27.362 1218 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.57 % Favored : 94.34 % Rotamer: Outliers : 2.03 % Allowed : 22.78 % Favored : 75.19 % 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: 0.18 (0.26), residues: 1113 helix: 1.86 (0.28), residues: 358 sheet: 0.16 (0.31), residues: 274 loop : -1.27 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 19 TYR 0.043 0.002 TYR C 230 PHE 0.027 0.001 PHE A 38 TRP 0.013 0.001 TRP A 188 HIS 0.003 0.001 HIS C 213 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 8981) covalent geometry : angle 0.63412 (12172) SS BOND : bond 0.00536 ( 5) SS BOND : angle 0.88604 ( 10) hydrogen bonds : bond 0.04336 ( 393) hydrogen bonds : angle 4.29895 ( 1095) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3063.89 seconds wall clock time: 52 minutes 57.35 seconds (3177.35 seconds total)