Starting phenix.real_space_refine on Sat Aug 23 08:40:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f2b_28812/08_2025/8f2b_28812.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f2b_28812/08_2025/8f2b_28812.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8f2b_28812/08_2025/8f2b_28812.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f2b_28812/08_2025/8f2b_28812.map" model { file = "/net/cci-nas-00/data/ceres_data/8f2b_28812/08_2025/8f2b_28812.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f2b_28812/08_2025/8f2b_28812.cif" } resolution = 2.0 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 74 5.16 5 C 6643 2.51 5 N 1740 2.21 5 O 1902 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 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: 10360 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1876 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2606 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 420 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "E" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 817 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 109} Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 139 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 3, 'ASP:plan': 3, 'TYR:plan': 1, 'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 58 Chain: "P" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 277 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 3025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 3025 Classifications: {'peptide': 369} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 16, 'TRANS': 352} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 3, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "P" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'D6M': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'D6M:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 308 Unusual residues: {'NAG': 3, 'P42': 1, 'PLM': 8, 'Y01': 2} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "R" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Time building chain proxies: 2.56, per 1000 atoms: 0.25 Number of scatterers: 10360 At special positions: 0 Unit cell: (111.15, 99.45, 149.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 74 16.00 P 1 15.00 O 1902 8.00 N 1740 7.00 C 6643 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS E 28 " - pdb=" SG CYS E 82 " distance=2.03 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 72 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 104 " distance=2.03 Simple disulfide: pdb=" SG CYS P 2 " - pdb=" SG CYS P 7 " distance=2.03 Simple disulfide: pdb=" SG CYS R 55 " - pdb=" SG CYS R 81 " distance=2.03 Simple disulfide: pdb=" SG CYS R 72 " - pdb=" SG CYS R 112 " distance=2.03 Simple disulfide: pdb=" SG CYS R 95 " - pdb=" SG CYS R 134 " distance=2.03 Simple disulfide: pdb=" SG CYS R 219 " - pdb=" SG CYS R 289 " 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=2, symmetry=0 Links applied NAG-ASN " NAG R 501 " - " ASN R 73 " " NAG R 502 " - " ASN R 125 " " NAG R 503 " - " ASN R 130 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.16 Conformation dependent library (CDL) restraints added in 427.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2396 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 14 sheets defined 45.1% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 11 through 40 Processing helix chain 'A' and resid 52 through 59 Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.618A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 279 Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.547A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.802A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 3 through 26 removed outlier: 3.615A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.608A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.585A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.529A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 51 removed outlier: 3.895A pdb=" N GLU E 35 " --> pdb=" O THR E 31 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG E 36 " --> pdb=" O GLY E 32 " (cutoff:3.500A) Proline residue: E 38 - end of helix removed outlier: 3.549A pdb=" N MET E 47 " --> pdb=" O ALA E 43 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLY E 49 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL E 51 " --> pdb=" O MET E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 61 Processing helix chain 'E' and resid 62 through 80 removed outlier: 3.668A pdb=" N MET E 75 " --> pdb=" O ASN E 71 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA E 77 " --> pdb=" O THR E 73 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASN E 78 " --> pdb=" O GLU E 74 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL E 80 " --> pdb=" O GLU E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 100 removed outlier: 3.788A pdb=" N PHE E 92 " --> pdb=" O LEU E 88 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN E 99 " --> pdb=" O GLY E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 141 Proline residue: E 121 - end of helix Proline residue: E 126 - end of helix Processing helix chain 'P' and resid 4 through 6 No H-bonds generated for 'chain 'P' and resid 4 through 6' Processing helix chain 'P' and resid 7 through 19 Processing helix chain 'R' and resid 42 through 62 Processing helix chain 'R' and resid 131 through 135 removed outlier: 3.551A pdb=" N ASN R 135 " --> pdb=" O THR R 132 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 173 removed outlier: 3.533A pdb=" N VAL R 147 " --> pdb=" O LYS R 143 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR R 150 " --> pdb=" O TYR R 146 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 177 Processing helix chain 'R' and resid 178 through 204 Processing helix chain 'R' and resid 208 through 215 removed outlier: 3.613A pdb=" N VAL R 212 " --> pdb=" O ASN R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 216 through 249 removed outlier: 3.614A pdb=" N LYS R 220 " --> pdb=" O PRO R 216 " (cutoff:3.500A) Processing helix chain 'R' and resid 259 through 268 Processing helix chain 'R' and resid 270 through 282 Processing helix chain 'R' and resid 287 through 291 Processing helix chain 'R' and resid 295 through 297 No H-bonds generated for 'chain 'R' and resid 295 through 297' Processing helix chain 'R' and resid 298 through 330 Proline residue: R 304 - end of helix Processing helix chain 'R' and resid 333 through 353 Proline residue: R 350 - end of helix Processing helix chain 'R' and resid 354 through 359 Processing helix chain 'R' and resid 365 through 382 Processing helix chain 'R' and resid 382 through 392 Processing helix chain 'R' and resid 395 through 409 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 4.404A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.550A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.416A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.570A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.797A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.631A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.159A 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: 6.772A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.624A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.887A 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: 6.350A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.836A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 71 through 72 Processing sheet with id=AB3, first strand: chain 'R' and resid 75 through 76 Processing sheet with id=AB4, first strand: chain 'R' and resid 90 through 94 Processing sheet with id=AB5, first strand: chain 'R' and resid 120 through 121 removed outlier: 3.580A pdb=" N ARG R 126 " --> pdb=" O HIS R 121 " (cutoff:3.500A) 512 hydrogen bonds defined for protein. 1446 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: 1.76 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1642 1.31 - 1.44: 2930 1.44 - 1.56: 5884 1.56 - 1.69: 2 1.69 - 1.81: 104 Bond restraints: 10562 Sorted by residual: bond pdb=" C02 D6M P 101 " pdb=" N03 D6M P 101 " ideal model delta sigma weight residual 1.339 1.451 -0.112 2.00e-02 2.50e+03 3.14e+01 bond pdb=" C LYS P 21 " pdb=" O LYS P 21 " ideal model delta sigma weight residual 1.234 1.187 0.046 1.44e-02 4.82e+03 1.04e+01 bond pdb=" N VAL E 79 " pdb=" CA VAL E 79 " ideal model delta sigma weight residual 1.461 1.498 -0.038 1.19e-02 7.06e+03 9.98e+00 bond pdb=" C07 D6M P 101 " pdb=" O08 D6M P 101 " ideal model delta sigma weight residual 1.247 1.185 0.062 2.00e-02 2.50e+03 9.65e+00 bond pdb=" N VAL E 80 " pdb=" CA VAL E 80 " ideal model delta sigma weight residual 1.462 1.493 -0.031 1.17e-02 7.31e+03 7.19e+00 ... (remaining 10557 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 13865 1.41 - 2.82: 340 2.82 - 4.23: 61 4.23 - 5.65: 18 5.65 - 7.06: 2 Bond angle restraints: 14286 Sorted by residual: angle pdb=" N GLU E 76 " pdb=" CA GLU E 76 " pdb=" C GLU E 76 " ideal model delta sigma weight residual 111.07 106.17 4.90 1.07e+00 8.73e-01 2.10e+01 angle pdb=" CA TRP E 84 " pdb=" C TRP E 84 " pdb=" N PRO E 85 " ideal model delta sigma weight residual 118.23 121.65 -3.42 9.20e-01 1.18e+00 1.38e+01 angle pdb=" N GLU R 255 " pdb=" CA GLU R 255 " pdb=" C GLU R 255 " ideal model delta sigma weight residual 113.97 109.43 4.54 1.28e+00 6.10e-01 1.26e+01 angle pdb=" N VAL E 80 " pdb=" CA VAL E 80 " pdb=" C VAL E 80 " ideal model delta sigma weight residual 113.07 108.79 4.28 1.36e+00 5.41e-01 9.88e+00 angle pdb=" C ASN E 29 " pdb=" CA ASN E 29 " pdb=" CB ASN E 29 " ideal model delta sigma weight residual 110.19 105.06 5.13 1.64e+00 3.72e-01 9.78e+00 ... (remaining 14281 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.30: 6094 24.30 - 48.60: 286 48.60 - 72.90: 57 72.90 - 97.20: 7 97.20 - 121.50: 4 Dihedral angle restraints: 6448 sinusoidal: 2739 harmonic: 3709 Sorted by residual: dihedral pdb=" CB CYS E 40 " pdb=" SG CYS E 40 " pdb=" SG CYS E 72 " pdb=" CB CYS E 72 " ideal model delta sinusoidal sigma weight residual 93.00 141.79 -48.79 1 1.00e+01 1.00e-02 3.28e+01 dihedral pdb=" CB CYS R 95 " pdb=" SG CYS R 95 " pdb=" SG CYS R 134 " pdb=" CB CYS R 134 " ideal model delta sinusoidal sigma weight residual 93.00 131.10 -38.10 1 1.00e+01 1.00e-02 2.05e+01 dihedral pdb=" CAI P42 R 512 " pdb=" CAJ P42 R 512 " pdb=" CAK P42 R 512 " pdb=" CAL P42 R 512 " ideal model delta sinusoidal sigma weight residual 179.92 58.42 121.50 1 3.00e+01 1.11e-03 1.62e+01 ... (remaining 6445 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1270 0.050 - 0.100: 251 0.100 - 0.150: 47 0.150 - 0.200: 6 0.200 - 0.250: 3 Chirality restraints: 1577 Sorted by residual: chirality pdb=" CA TYR E 83 " pdb=" N TYR E 83 " pdb=" C TYR E 83 " pdb=" CB TYR E 83 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CB VAL E 79 " pdb=" CA VAL E 79 " pdb=" CG1 VAL E 79 " pdb=" CG2 VAL E 79 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA ASN E 29 " pdb=" N ASN E 29 " pdb=" C ASN E 29 " pdb=" CB ASN E 29 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 1574 not shown) Planarity restraints: 1796 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.026 5.00e-02 4.00e+02 3.93e-02 2.48e+00 pdb=" N PRO B 236 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 37 " -0.023 5.00e-02 4.00e+02 3.43e-02 1.88e+00 pdb=" N PRO E 38 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO E 38 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO E 38 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 54 " 0.022 5.00e-02 4.00e+02 3.34e-02 1.79e+00 pdb=" N PRO G 55 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO G 55 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO G 55 " 0.019 5.00e-02 4.00e+02 ... (remaining 1793 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2808 2.80 - 3.33: 9321 3.33 - 3.85: 17500 3.85 - 4.38: 21502 4.38 - 4.90: 35815 Nonbonded interactions: 86946 Sorted by model distance: nonbonded pdb=" O SER A 352 " pdb=" OG SER A 352 " model vdw 2.278 3.040 nonbonded pdb=" O SER P 20 " pdb=" OG SER P 20 " model vdw 2.295 3.040 nonbonded pdb=" OE1 GLN R 227 " pdb=" O HOH R 601 " model vdw 2.303 3.040 nonbonded pdb=" OD2 ASP R 373 " pdb=" O HOH R 602 " model vdw 2.305 3.040 nonbonded pdb=" OE1 GLU R 240 " pdb=" O HOH R 603 " model vdw 2.312 3.040 ... (remaining 86941 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.110 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: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.550 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:6.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 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 0.112 10577 Z= 0.242 Angle : 0.593 18.592 14315 Z= 0.332 Chirality : 0.043 0.250 1577 Planarity : 0.003 0.039 1793 Dihedral : 14.226 121.499 4022 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 1.32 % Allowed : 12.56 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -2.02 (0.20), residues: 1255 helix: -1.84 (0.17), residues: 504 sheet: -0.17 (0.31), residues: 234 loop : -1.17 (0.25), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 129 TYR 0.015 0.001 TYR E 83 PHE 0.010 0.001 PHE B 151 TRP 0.009 0.001 TRP A 234 HIS 0.002 0.001 HIS A 387 Details of bonding type rmsd covalent geometry : bond 0.00398 (10562) covalent geometry : angle 0.55359 (14286) SS BOND : bond 0.00187 ( 10) SS BOND : angle 0.78561 ( 20) hydrogen bonds : bond 0.23008 ( 512) hydrogen bonds : angle 7.86310 ( 1446) Misc. bond : bond 0.07616 ( 2) link_NAG-ASN : bond 0.00766 ( 3) link_NAG-ASN : angle 8.41622 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 204 time to evaluate : 0.409 Fit side-chains revert: symmetry clash REVERT: A 60 MET cc_start: 0.4201 (mmp) cc_final: 0.3710 (mpp) REVERT: R 261 TRP cc_start: 0.5889 (m100) cc_final: 0.5634 (m100) REVERT: R 327 MET cc_start: 0.7279 (mtm) cc_final: 0.6728 (mmm) REVERT: R 374 TYR cc_start: 0.6131 (m-80) cc_final: 0.5923 (m-80) outliers start: 14 outliers final: 1 residues processed: 215 average time/residue: 0.7476 time to fit residues: 170.5107 Evaluate side-chains 156 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 155 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 59 GLN A 294 GLN B 13 GLN B 155 ASN ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 GLN N 13 GLN R 93 GLN R 179 GLN R 186 ASN R 223 HIS R 257 GLN R 318 ASN R 408 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.220813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.187885 restraints weight = 8267.178| |-----------------------------------------------------------------------------| r_work (start): 0.4070 rms_B_bonded: 0.80 r_work: 0.3830 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3762 rms_B_bonded: 2.29 restraints_weight: 0.2500 r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10577 Z= 0.147 Angle : 0.604 16.169 14315 Z= 0.317 Chirality : 0.042 0.140 1577 Planarity : 0.005 0.039 1793 Dihedral : 10.019 150.667 1774 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.46 % Allowed : 13.69 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.31 (0.23), residues: 1255 helix: 1.00 (0.22), residues: 509 sheet: 0.15 (0.32), residues: 244 loop : -0.48 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 219 TYR 0.013 0.001 TYR R 191 PHE 0.011 0.002 PHE A 222 TRP 0.015 0.002 TRP B 339 HIS 0.007 0.001 HIS B 266 Details of bonding type rmsd covalent geometry : bond 0.00300 (10562) covalent geometry : angle 0.57880 (14286) SS BOND : bond 0.00231 ( 10) SS BOND : angle 0.87839 ( 20) hydrogen bonds : bond 0.05552 ( 512) hydrogen bonds : angle 4.92950 ( 1446) Misc. bond : bond 0.00283 ( 2) link_NAG-ASN : bond 0.00902 ( 3) link_NAG-ASN : angle 6.80864 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 0.421 Fit side-chains REVERT: A 60 MET cc_start: 0.4488 (mmp) cc_final: 0.3974 (mpp) REVERT: B 96 ARG cc_start: 0.7702 (OUTLIER) cc_final: 0.7166 (mtm-85) REVERT: G 21 MET cc_start: 0.6856 (tpp) cc_final: 0.6627 (mmp) REVERT: N 3 GLN cc_start: 0.7892 (OUTLIER) cc_final: 0.7634 (tt0) REVERT: N 34 MET cc_start: 0.8862 (mmm) cc_final: 0.8351 (mmm) REVERT: N 105 ARG cc_start: 0.6324 (mtm-85) cc_final: 0.5894 (ttm110) REVERT: R 141 LYS cc_start: 0.5026 (mmtt) cc_final: 0.4694 (tttt) REVERT: R 261 TRP cc_start: 0.6237 (m100) cc_final: 0.5877 (m100) REVERT: R 361 TRP cc_start: 0.6773 (t-100) cc_final: 0.6311 (t-100) REVERT: R 374 TYR cc_start: 0.6091 (m-80) cc_final: 0.5850 (m-80) outliers start: 26 outliers final: 6 residues processed: 163 average time/residue: 0.7850 time to fit residues: 135.5902 Evaluate side-chains 143 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 135 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain R residue 91 SER Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 337 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 65 optimal weight: 0.9980 chunk 91 optimal weight: 30.0000 chunk 42 optimal weight: 3.9990 chunk 114 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 48 optimal weight: 0.5980 chunk 56 optimal weight: 4.9990 chunk 13 optimal weight: 0.3980 chunk 72 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 83 optimal weight: 10.0000 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 35 GLN B 13 GLN B 268 ASN N 5 GLN N 13 GLN P 10 GLN P 14 ASN R 179 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.221101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.190623 restraints weight = 8204.814| |-----------------------------------------------------------------------------| r_work (start): 0.4097 rms_B_bonded: 0.78 r_work: 0.3851 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3796 rms_B_bonded: 2.11 restraints_weight: 0.2500 r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10577 Z= 0.126 Angle : 0.550 14.482 14315 Z= 0.287 Chirality : 0.041 0.143 1577 Planarity : 0.004 0.042 1793 Dihedral : 9.447 146.092 1772 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.74 % Allowed : 14.64 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.04 (0.24), residues: 1255 helix: 1.80 (0.22), residues: 509 sheet: 0.23 (0.32), residues: 251 loop : -0.14 (0.29), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 219 TYR 0.010 0.001 TYR R 191 PHE 0.011 0.001 PHE B 151 TRP 0.017 0.002 TRP A 234 HIS 0.005 0.001 HIS B 266 Details of bonding type rmsd covalent geometry : bond 0.00252 (10562) covalent geometry : angle 0.52699 (14286) SS BOND : bond 0.00238 ( 10) SS BOND : angle 0.78161 ( 20) hydrogen bonds : bond 0.04914 ( 512) hydrogen bonds : angle 4.68220 ( 1446) Misc. bond : bond 0.00039 ( 2) link_NAG-ASN : bond 0.00795 ( 3) link_NAG-ASN : angle 6.26496 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 141 time to evaluate : 0.416 Fit side-chains REVERT: A 60 MET cc_start: 0.4553 (mmp) cc_final: 0.4013 (mpp) REVERT: N 3 GLN cc_start: 0.7906 (OUTLIER) cc_final: 0.7637 (tt0) REVERT: N 105 ARG cc_start: 0.6270 (mtm-85) cc_final: 0.5855 (ttm110) REVERT: R 141 LYS cc_start: 0.5047 (mmtt) cc_final: 0.4817 (tttt) REVERT: R 261 TRP cc_start: 0.6142 (m100) cc_final: 0.5823 (m100) REVERT: R 361 TRP cc_start: 0.6768 (t-100) cc_final: 0.6256 (t-100) REVERT: R 374 TYR cc_start: 0.6083 (m-80) cc_final: 0.5814 (m-80) outliers start: 29 outliers final: 9 residues processed: 155 average time/residue: 0.8129 time to fit residues: 133.0313 Evaluate side-chains 146 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 136 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 127 SER Chi-restraints excluded: chain P residue 10 GLN Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 330 THR Chi-restraints excluded: chain R residue 339 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 81 optimal weight: 10.0000 chunk 1 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 68 optimal weight: 8.9990 chunk 38 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 35 GLN B 13 GLN B 268 ASN N 5 GLN N 13 GLN P 10 GLN R 179 GLN R 223 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.220675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.189626 restraints weight = 8230.804| |-----------------------------------------------------------------------------| r_work (start): 0.4084 rms_B_bonded: 0.77 r_work: 0.3831 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3770 rms_B_bonded: 2.19 restraints_weight: 0.2500 r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10577 Z= 0.129 Angle : 0.556 13.508 14315 Z= 0.290 Chirality : 0.041 0.141 1577 Planarity : 0.004 0.043 1793 Dihedral : 9.330 135.855 1772 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.27 % Allowed : 15.49 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.22 (0.24), residues: 1255 helix: 2.01 (0.23), residues: 510 sheet: 0.18 (0.31), residues: 253 loop : -0.04 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 219 TYR 0.009 0.001 TYR A 339 PHE 0.011 0.001 PHE B 151 TRP 0.017 0.002 TRP A 234 HIS 0.005 0.001 HIS B 266 Details of bonding type rmsd covalent geometry : bond 0.00267 (10562) covalent geometry : angle 0.53604 (14286) SS BOND : bond 0.00234 ( 10) SS BOND : angle 0.88602 ( 20) hydrogen bonds : bond 0.04756 ( 512) hydrogen bonds : angle 4.63645 ( 1446) Misc. bond : bond 0.00015 ( 2) link_NAG-ASN : bond 0.00755 ( 3) link_NAG-ASN : angle 5.88144 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 140 time to evaluate : 0.358 Fit side-chains REVERT: A 60 MET cc_start: 0.4623 (mmp) cc_final: 0.4031 (mpp) REVERT: B 96 ARG cc_start: 0.7685 (OUTLIER) cc_final: 0.7168 (mtm-85) REVERT: N 3 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7670 (tt0) REVERT: R 141 LYS cc_start: 0.5147 (mmtt) cc_final: 0.4918 (tttt) REVERT: R 198 ILE cc_start: 0.6156 (mt) cc_final: 0.5903 (mm) REVERT: R 229 MET cc_start: 0.6982 (tpp) cc_final: 0.6758 (tpp) REVERT: R 261 TRP cc_start: 0.6186 (m100) cc_final: 0.5874 (m100) REVERT: R 343 LYS cc_start: 0.6537 (tttp) cc_final: 0.6243 (ttmt) REVERT: R 361 TRP cc_start: 0.6746 (t-100) cc_final: 0.6253 (t-100) REVERT: R 374 TYR cc_start: 0.6138 (m-80) cc_final: 0.5910 (m-80) outliers start: 24 outliers final: 12 residues processed: 151 average time/residue: 0.7688 time to fit residues: 122.7271 Evaluate side-chains 149 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 135 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 127 SER Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain R residue 201 HIS Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 330 THR Chi-restraints excluded: chain R residue 337 MET Chi-restraints excluded: chain R residue 339 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 71 optimal weight: 0.7980 chunk 116 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 117 optimal weight: 6.9990 chunk 16 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 35 GLN B 13 GLN B 268 ASN N 1 GLN N 5 GLN N 13 GLN R 179 GLN R 383 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.220406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.189405 restraints weight = 8163.519| |-----------------------------------------------------------------------------| r_work (start): 0.4081 rms_B_bonded: 0.78 r_work: 0.3853 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.3789 rms_B_bonded: 2.19 restraints_weight: 0.2500 r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10577 Z= 0.135 Angle : 0.569 12.509 14315 Z= 0.297 Chirality : 0.042 0.155 1577 Planarity : 0.004 0.044 1793 Dihedral : 9.520 134.344 1772 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.08 % Allowed : 15.86 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.16 (0.24), residues: 1255 helix: 1.93 (0.22), residues: 518 sheet: 0.16 (0.32), residues: 244 loop : -0.06 (0.30), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 96 TYR 0.014 0.002 TYR R 338 PHE 0.012 0.001 PHE B 151 TRP 0.018 0.002 TRP A 234 HIS 0.006 0.001 HIS B 266 Details of bonding type rmsd covalent geometry : bond 0.00281 (10562) covalent geometry : angle 0.55251 (14286) SS BOND : bond 0.00265 ( 10) SS BOND : angle 0.81701 ( 20) hydrogen bonds : bond 0.04763 ( 512) hydrogen bonds : angle 4.65785 ( 1446) Misc. bond : bond 0.00016 ( 2) link_NAG-ASN : bond 0.00691 ( 3) link_NAG-ASN : angle 5.43701 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 0.411 Fit side-chains revert: symmetry clash REVERT: A 60 MET cc_start: 0.4538 (mmp) cc_final: 0.3946 (mpp) REVERT: N 3 GLN cc_start: 0.7888 (OUTLIER) cc_final: 0.7639 (tt0) REVERT: R 198 ILE cc_start: 0.6190 (mt) cc_final: 0.5954 (mm) REVERT: R 361 TRP cc_start: 0.6763 (t-100) cc_final: 0.6311 (t-100) outliers start: 22 outliers final: 13 residues processed: 144 average time/residue: 0.7383 time to fit residues: 112.5332 Evaluate side-chains 145 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 127 SER Chi-restraints excluded: chain R residue 133 MET Chi-restraints excluded: chain R residue 201 HIS Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 258 ARG Chi-restraints excluded: chain R residue 330 THR Chi-restraints excluded: chain R residue 337 MET Chi-restraints excluded: chain R residue 339 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 116 optimal weight: 0.2980 chunk 91 optimal weight: 0.0670 chunk 37 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 62 optimal weight: 10.0000 chunk 58 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 overall best weight: 0.8520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 35 GLN B 13 GLN ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 1 GLN N 5 GLN N 13 GLN R 179 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.221934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.191032 restraints weight = 8302.388| |-----------------------------------------------------------------------------| r_work (start): 0.4099 rms_B_bonded: 0.79 r_work: 0.3854 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3793 rms_B_bonded: 2.26 restraints_weight: 0.2500 r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10577 Z= 0.106 Angle : 0.510 11.663 14315 Z= 0.266 Chirality : 0.040 0.137 1577 Planarity : 0.004 0.045 1793 Dihedral : 8.886 125.504 1772 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.08 % Allowed : 15.49 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.38 (0.24), residues: 1255 helix: 2.21 (0.23), residues: 518 sheet: 0.26 (0.33), residues: 233 loop : -0.06 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 219 TYR 0.017 0.001 TYR R 338 PHE 0.010 0.001 PHE B 151 TRP 0.018 0.001 TRP A 234 HIS 0.006 0.001 HIS B 266 Details of bonding type rmsd covalent geometry : bond 0.00213 (10562) covalent geometry : angle 0.49411 (14286) SS BOND : bond 0.00202 ( 10) SS BOND : angle 0.60755 ( 20) hydrogen bonds : bond 0.04179 ( 512) hydrogen bonds : angle 4.41671 ( 1446) Misc. bond : bond 0.00011 ( 2) link_NAG-ASN : bond 0.00708 ( 3) link_NAG-ASN : angle 5.08936 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 139 time to evaluate : 0.281 Fit side-chains revert: symmetry clash REVERT: A 60 MET cc_start: 0.4467 (mmp) cc_final: 0.3895 (mpp) REVERT: N 3 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7686 (tt0) REVERT: R 198 ILE cc_start: 0.6203 (mt) cc_final: 0.5984 (mm) REVERT: R 293 VAL cc_start: 0.6848 (m) cc_final: 0.6497 (p) REVERT: R 361 TRP cc_start: 0.6772 (t-100) cc_final: 0.6316 (t-100) REVERT: R 374 TYR cc_start: 0.6047 (m-80) cc_final: 0.5807 (m-80) outliers start: 22 outliers final: 8 residues processed: 150 average time/residue: 0.7020 time to fit residues: 111.3150 Evaluate side-chains 142 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 133 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain R residue 109 THR Chi-restraints excluded: chain R residue 201 HIS Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 258 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 58 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 23 optimal weight: 9.9990 chunk 55 optimal weight: 0.5980 chunk 111 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 35 GLN B 13 GLN ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 1 GLN N 5 GLN N 13 GLN R 179 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.221200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.190642 restraints weight = 8116.600| |-----------------------------------------------------------------------------| r_work (start): 0.4094 rms_B_bonded: 0.71 r_work: 0.3818 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3754 rms_B_bonded: 2.12 restraints_weight: 0.2500 r_work: 0.3605 rms_B_bonded: 4.97 restraints_weight: 0.1250 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10577 Z= 0.119 Angle : 0.544 10.812 14315 Z= 0.283 Chirality : 0.041 0.138 1577 Planarity : 0.004 0.045 1793 Dihedral : 8.983 125.266 1772 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.89 % Allowed : 16.05 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.41 (0.24), residues: 1255 helix: 2.17 (0.22), residues: 519 sheet: 0.31 (0.32), residues: 233 loop : -0.00 (0.29), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 105 TYR 0.026 0.001 TYR R 338 PHE 0.010 0.001 PHE B 151 TRP 0.016 0.002 TRP A 234 HIS 0.005 0.001 HIS B 266 Details of bonding type rmsd covalent geometry : bond 0.00245 (10562) covalent geometry : angle 0.53005 (14286) SS BOND : bond 0.00176 ( 10) SS BOND : angle 0.93081 ( 20) hydrogen bonds : bond 0.04384 ( 512) hydrogen bonds : angle 4.49454 ( 1446) Misc. bond : bond 0.00008 ( 2) link_NAG-ASN : bond 0.00629 ( 3) link_NAG-ASN : angle 4.78302 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 137 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: A 60 MET cc_start: 0.4687 (mmp) cc_final: 0.3889 (mpp) REVERT: R 198 ILE cc_start: 0.6308 (mt) cc_final: 0.6078 (mm) REVERT: R 261 TRP cc_start: 0.6557 (m100) cc_final: 0.6304 (m100) REVERT: R 361 TRP cc_start: 0.6764 (t-100) cc_final: 0.6311 (t-100) REVERT: R 374 TYR cc_start: 0.6229 (m-80) cc_final: 0.5928 (m-80) outliers start: 20 outliers final: 11 residues processed: 146 average time/residue: 0.7957 time to fit residues: 122.9378 Evaluate side-chains 141 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 130 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain R residue 109 THR Chi-restraints excluded: chain R residue 201 HIS Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 258 ARG Chi-restraints excluded: chain R residue 337 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 41 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 88 optimal weight: 9.9990 chunk 2 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 109 optimal weight: 20.0000 chunk 17 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN B 13 GLN B 268 ASN N 1 GLN N 5 GLN N 13 GLN N 82 GLN N 84 ASN R 179 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.219065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.188917 restraints weight = 8073.476| |-----------------------------------------------------------------------------| r_work (start): 0.4077 rms_B_bonded: 0.74 r_work: 0.3825 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3768 rms_B_bonded: 2.06 restraints_weight: 0.2500 r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10577 Z= 0.173 Angle : 0.632 9.845 14315 Z= 0.328 Chirality : 0.044 0.148 1577 Planarity : 0.005 0.049 1793 Dihedral : 10.116 130.523 1772 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.46 % Allowed : 15.68 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.08 (0.24), residues: 1255 helix: 1.76 (0.22), residues: 527 sheet: 0.13 (0.32), residues: 244 loop : -0.03 (0.30), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 96 TYR 0.025 0.002 TYR R 338 PHE 0.013 0.002 PHE B 151 TRP 0.018 0.002 TRP A 234 HIS 0.006 0.001 HIS B 266 Details of bonding type rmsd covalent geometry : bond 0.00372 (10562) covalent geometry : angle 0.62099 (14286) SS BOND : bond 0.00283 ( 10) SS BOND : angle 1.23388 ( 20) hydrogen bonds : bond 0.05259 ( 512) hydrogen bonds : angle 4.82494 ( 1446) Misc. bond : bond 0.00010 ( 2) link_NAG-ASN : bond 0.00608 ( 3) link_NAG-ASN : angle 4.51414 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 0.409 Fit side-chains revert: symmetry clash REVERT: A 60 MET cc_start: 0.4612 (mmp) cc_final: 0.3977 (mpp) REVERT: B 59 TYR cc_start: 0.8603 (OUTLIER) cc_final: 0.8359 (m-80) REVERT: R 198 ILE cc_start: 0.6195 (mt) cc_final: 0.5940 (mm) REVERT: R 361 TRP cc_start: 0.6745 (t-100) cc_final: 0.6346 (t-100) outliers start: 26 outliers final: 15 residues processed: 145 average time/residue: 0.8469 time to fit residues: 130.1906 Evaluate side-chains 142 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 127 SER Chi-restraints excluded: chain R residue 109 THR Chi-restraints excluded: chain R residue 153 ILE Chi-restraints excluded: chain R residue 201 HIS Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 258 ARG Chi-restraints excluded: chain R residue 323 LEU Chi-restraints excluded: chain R residue 330 THR Chi-restraints excluded: chain R residue 337 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 63 optimal weight: 10.0000 chunk 48 optimal weight: 7.9990 chunk 82 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 102 optimal weight: 0.1980 chunk 84 optimal weight: 9.9990 chunk 69 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN B 13 GLN B 16 ASN B 88 ASN B 268 ASN N 5 GLN N 13 GLN R 179 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.221128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.190246 restraints weight = 8229.696| |-----------------------------------------------------------------------------| r_work (start): 0.4092 rms_B_bonded: 0.78 r_work: 0.3863 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3802 rms_B_bonded: 2.24 restraints_weight: 0.2500 r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10577 Z= 0.115 Angle : 0.542 9.456 14315 Z= 0.281 Chirality : 0.041 0.146 1577 Planarity : 0.004 0.047 1793 Dihedral : 9.390 125.006 1772 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.42 % Allowed : 16.43 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.31 (0.24), residues: 1255 helix: 2.01 (0.22), residues: 528 sheet: 0.31 (0.33), residues: 233 loop : -0.02 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 219 TYR 0.023 0.001 TYR R 338 PHE 0.011 0.001 PHE B 151 TRP 0.018 0.002 TRP A 234 HIS 0.005 0.001 HIS B 266 Details of bonding type rmsd covalent geometry : bond 0.00236 (10562) covalent geometry : angle 0.53115 (14286) SS BOND : bond 0.00198 ( 10) SS BOND : angle 0.86024 ( 20) hydrogen bonds : bond 0.04304 ( 512) hydrogen bonds : angle 4.51634 ( 1446) Misc. bond : bond 0.00007 ( 2) link_NAG-ASN : bond 0.00544 ( 3) link_NAG-ASN : angle 4.30365 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 0.420 Fit side-chains revert: symmetry clash REVERT: A 60 MET cc_start: 0.4445 (mmp) cc_final: 0.3855 (mpp) REVERT: B 59 TYR cc_start: 0.8630 (OUTLIER) cc_final: 0.8426 (m-80) REVERT: R 261 TRP cc_start: 0.6381 (m100) cc_final: 0.6138 (m100) REVERT: R 293 VAL cc_start: 0.6802 (m) cc_final: 0.6511 (p) REVERT: R 361 TRP cc_start: 0.6698 (t-100) cc_final: 0.6308 (t-100) outliers start: 15 outliers final: 10 residues processed: 141 average time/residue: 0.7878 time to fit residues: 117.8327 Evaluate side-chains 142 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 131 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain R residue 109 THR Chi-restraints excluded: chain R residue 153 ILE Chi-restraints excluded: chain R residue 201 HIS Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 258 ARG Chi-restraints excluded: chain R residue 337 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 49 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 chunk 59 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 91 optimal weight: 0.0060 chunk 109 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 54 optimal weight: 0.3980 overall best weight: 1.2400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN B 13 GLN B 16 ASN B 268 ASN N 1 GLN N 5 GLN N 13 GLN R 179 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.220984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.190837 restraints weight = 8097.904| |-----------------------------------------------------------------------------| r_work (start): 0.4098 rms_B_bonded: 0.75 r_work: 0.3853 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3790 rms_B_bonded: 2.22 restraints_weight: 0.2500 r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10577 Z= 0.118 Angle : 0.542 9.135 14315 Z= 0.281 Chirality : 0.041 0.138 1577 Planarity : 0.004 0.048 1793 Dihedral : 9.325 126.484 1772 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.42 % Allowed : 16.62 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.35 (0.24), residues: 1255 helix: 2.10 (0.22), residues: 527 sheet: 0.23 (0.33), residues: 235 loop : -0.01 (0.29), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 219 TYR 0.021 0.001 TYR R 338 PHE 0.011 0.001 PHE B 151 TRP 0.017 0.002 TRP A 234 HIS 0.006 0.001 HIS B 266 Details of bonding type rmsd covalent geometry : bond 0.00245 (10562) covalent geometry : angle 0.53121 (14286) SS BOND : bond 0.00176 ( 10) SS BOND : angle 0.91061 ( 20) hydrogen bonds : bond 0.04363 ( 512) hydrogen bonds : angle 4.51006 ( 1446) Misc. bond : bond 0.00005 ( 2) link_NAG-ASN : bond 0.00517 ( 3) link_NAG-ASN : angle 4.20306 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 0.409 Fit side-chains revert: symmetry clash REVERT: A 60 MET cc_start: 0.4470 (mmp) cc_final: 0.3919 (mpp) REVERT: B 59 TYR cc_start: 0.8608 (OUTLIER) cc_final: 0.8399 (m-80) REVERT: R 261 TRP cc_start: 0.6372 (m100) cc_final: 0.6134 (m100) REVERT: R 293 VAL cc_start: 0.6830 (m) cc_final: 0.6524 (p) REVERT: R 361 TRP cc_start: 0.6670 (t-100) cc_final: 0.6309 (t-100) outliers start: 15 outliers final: 11 residues processed: 138 average time/residue: 0.8242 time to fit residues: 120.6314 Evaluate side-chains 142 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain R residue 109 THR Chi-restraints excluded: chain R residue 201 HIS Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 258 ARG Chi-restraints excluded: chain R residue 323 LEU Chi-restraints excluded: chain R residue 337 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 43 optimal weight: 0.7980 chunk 69 optimal weight: 8.9990 chunk 107 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 28 optimal weight: 0.3980 chunk 15 optimal weight: 4.9990 chunk 83 optimal weight: 7.9990 chunk 4 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 chunk 23 optimal weight: 20.0000 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN B 13 GLN B 16 ASN ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 1 GLN N 5 GLN N 13 GLN P 10 GLN R 179 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.220324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.190358 restraints weight = 8170.114| |-----------------------------------------------------------------------------| r_work (start): 0.4092 rms_B_bonded: 0.75 r_work: 0.3837 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3777 rms_B_bonded: 2.15 restraints_weight: 0.2500 r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10577 Z= 0.132 Angle : 0.579 10.163 14315 Z= 0.299 Chirality : 0.042 0.165 1577 Planarity : 0.004 0.052 1793 Dihedral : 9.589 125.779 1772 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.51 % Allowed : 16.43 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.28 (0.24), residues: 1255 helix: 1.98 (0.22), residues: 528 sheet: 0.28 (0.33), residues: 233 loop : -0.03 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 219 TYR 0.021 0.002 TYR R 338 PHE 0.011 0.001 PHE B 151 TRP 0.016 0.002 TRP A 234 HIS 0.006 0.001 HIS B 266 Details of bonding type rmsd covalent geometry : bond 0.00278 (10562) covalent geometry : angle 0.56883 (14286) SS BOND : bond 0.00214 ( 10) SS BOND : angle 0.98523 ( 20) hydrogen bonds : bond 0.04582 ( 512) hydrogen bonds : angle 4.61907 ( 1446) Misc. bond : bond 0.00003 ( 2) link_NAG-ASN : bond 0.00518 ( 3) link_NAG-ASN : angle 4.10601 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6029.22 seconds wall clock time: 103 minutes 2.96 seconds (6182.96 seconds total)