Starting phenix.real_space_refine on Mon Jun 9 19:57:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f2b_28812/06_2025/8f2b_28812.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f2b_28812/06_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_28812/06_2025/8f2b_28812.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f2b_28812/06_2025/8f2b_28812.map" model { file = "/net/cci-nas-00/data/ceres_data/8f2b_28812/06_2025/8f2b_28812.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f2b_28812/06_2025/8f2b_28812.cif" } resolution = 2.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP: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: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 4, 'ARG:plan': 3} 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, 'ASP:plan': 1, 'GLU:plan': 2} 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: 6.37, per 1000 atoms: 0.61 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: 3.12 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.01 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: 3.26 Time building geometry restraints manager: 3.63 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: 2.320 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: 0.470 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 26.650 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 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:13.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.230 ------------------------------------------------------------------------------- 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 : 5.13 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.009 0.001 TRP A 234 HIS 0.002 0.001 HIS A 387 PHE 0.010 0.001 PHE B 151 TYR 0.015 0.001 TYR E 83 ARG 0.005 0.000 ARG B 129 Details of bonding type rmsd link_NAG-ASN : bond 0.00766 ( 3) link_NAG-ASN : angle 8.41622 ( 9) hydrogen bonds : bond 0.23008 ( 512) hydrogen bonds : angle 7.86310 ( 1446) SS BOND : bond 0.00187 ( 10) SS BOND : angle 0.78561 ( 20) covalent geometry : bond 0.00398 (10562) covalent geometry : angle 0.55359 (14286) Misc. bond : bond 0.07616 ( 2) *********************** 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 : 1.073 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: 1.4530 time to fit residues: 332.0920 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 : 1.134 ------------------------------------------------------------------------------- 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 103 optimal weight: 0.9990 chunk 92 optimal weight: 9.9990 chunk 51 optimal weight: 9.9990 chunk 31 optimal weight: 4.9990 chunk 62 optimal weight: 10.0000 chunk 49 optimal weight: 7.9990 chunk 95 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 58 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 N 82 GLN N 84 ASN P 14 ASN 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: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.218993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.188097 restraints weight = 8029.086| |-----------------------------------------------------------------------------| r_work (start): 0.4068 rms_B_bonded: 0.77 r_work: 0.3830 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3753 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10577 Z= 0.223 Angle : 0.722 16.268 14315 Z= 0.379 Chirality : 0.047 0.158 1577 Planarity : 0.006 0.040 1793 Dihedral : 11.108 175.149 1774 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.12 % Allowed : 13.31 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.23), residues: 1255 helix: 0.82 (0.22), residues: 503 sheet: 0.10 (0.32), residues: 253 loop : -0.33 (0.29), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 211 HIS 0.008 0.002 HIS B 266 PHE 0.016 0.003 PHE A 222 TYR 0.014 0.002 TYR R 146 ARG 0.008 0.001 ARG B 251 Details of bonding type rmsd link_NAG-ASN : bond 0.00898 ( 3) link_NAG-ASN : angle 6.80011 ( 9) hydrogen bonds : bond 0.06408 ( 512) hydrogen bonds : angle 5.24636 ( 1446) SS BOND : bond 0.00438 ( 10) SS BOND : angle 1.09420 ( 20) covalent geometry : bond 0.00479 (10562) covalent geometry : angle 0.70105 (14286) Misc. bond : bond 0.00326 ( 2) *********************** 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 194 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 161 time to evaluate : 1.034 Fit side-chains REVERT: A 60 MET cc_start: 0.4520 (mmp) cc_final: 0.4086 (mpp) REVERT: B 59 TYR cc_start: 0.8604 (OUTLIER) cc_final: 0.8370 (m-80) REVERT: B 96 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.7308 (mtm-85) REVERT: N 3 GLN cc_start: 0.7904 (OUTLIER) cc_final: 0.7651 (tt0) REVERT: N 34 MET cc_start: 0.8882 (mmm) cc_final: 0.8390 (mmm) REVERT: R 141 LYS cc_start: 0.5114 (mmtt) cc_final: 0.4809 (tttt) REVERT: R 261 TRP cc_start: 0.6242 (m100) cc_final: 0.5921 (m100) REVERT: R 343 LYS cc_start: 0.6518 (tttp) cc_final: 0.6281 (ttmt) REVERT: R 361 TRP cc_start: 0.6825 (t-100) cc_final: 0.6300 (t-100) REVERT: R 374 TYR cc_start: 0.6181 (m-80) cc_final: 0.5910 (m-80) outliers start: 33 outliers final: 10 residues processed: 179 average time/residue: 1.5785 time to fit residues: 298.9933 Evaluate side-chains 147 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 134 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 96 ARG 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 91 SER Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 337 MET Chi-restraints excluded: chain R residue 339 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 21 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 chunk 87 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 20 optimal weight: 7.9990 chunk 65 optimal weight: 7.9990 chunk 8 optimal weight: 3.9990 chunk 93 optimal weight: 0.0470 chunk 4 optimal weight: 0.9980 chunk 100 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.0080 ------------------------------------------------------------------------------- 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 88 ASN B 268 ASN N 5 GLN N 13 GLN P 10 GLN R 179 GLN R 223 HIS R 383 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.221544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.190759 restraints weight = 8259.001| |-----------------------------------------------------------------------------| r_work (start): 0.4097 rms_B_bonded: 0.75 r_work: 0.3816 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3752 rms_B_bonded: 2.25 restraints_weight: 0.2500 r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10577 Z= 0.116 Angle : 0.538 14.461 14315 Z= 0.280 Chirality : 0.041 0.142 1577 Planarity : 0.004 0.043 1793 Dihedral : 9.543 138.898 1772 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.46 % Allowed : 15.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.24), residues: 1255 helix: 1.76 (0.23), residues: 508 sheet: 0.15 (0.32), residues: 252 loop : -0.12 (0.29), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 234 HIS 0.004 0.001 HIS B 266 PHE 0.012 0.001 PHE A 212 TYR 0.010 0.001 TYR R 191 ARG 0.005 0.000 ARG B 219 Details of bonding type rmsd link_NAG-ASN : bond 0.00768 ( 3) link_NAG-ASN : angle 6.29303 ( 9) hydrogen bonds : bond 0.04677 ( 512) hydrogen bonds : angle 4.61791 ( 1446) SS BOND : bond 0.00263 ( 10) SS BOND : angle 0.68766 ( 20) covalent geometry : bond 0.00232 (10562) covalent geometry : angle 0.51460 (14286) Misc. bond : bond 0.00035 ( 2) *********************** 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 171 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 145 time to evaluate : 0.968 Fit side-chains REVERT: A 60 MET cc_start: 0.4552 (mmp) cc_final: 0.3950 (mpp) REVERT: A 352 SER cc_start: 0.6440 (OUTLIER) cc_final: 0.6060 (p) REVERT: B 59 TYR cc_start: 0.8636 (OUTLIER) cc_final: 0.8419 (m-80) REVERT: G 21 MET cc_start: 0.6856 (tpp) cc_final: 0.6626 (mmp) REVERT: N 3 GLN cc_start: 0.7960 (OUTLIER) cc_final: 0.7686 (tt0) REVERT: R 141 LYS cc_start: 0.5104 (mmtt) cc_final: 0.4800 (tttt) REVERT: R 198 ILE cc_start: 0.6203 (mt) cc_final: 0.5929 (mm) REVERT: R 261 TRP cc_start: 0.6218 (m100) cc_final: 0.5895 (m100) REVERT: R 343 LYS cc_start: 0.6538 (tttp) cc_final: 0.6241 (ttmt) REVERT: R 361 TRP cc_start: 0.6734 (t-100) cc_final: 0.6228 (t-100) REVERT: R 374 TYR cc_start: 0.6150 (m-80) cc_final: 0.5866 (m-80) outliers start: 26 outliers final: 6 residues processed: 154 average time/residue: 1.5623 time to fit residues: 255.5269 Evaluate side-chains 147 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 138 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain R residue 250 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 91 optimal weight: 10.0000 chunk 67 optimal weight: 0.5980 chunk 114 optimal weight: 4.9990 chunk 71 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 73 optimal weight: 8.9990 chunk 18 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 90 optimal weight: 9.9990 chunk 75 optimal weight: 7.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 GLN N 13 GLN R 179 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.219693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.188744 restraints weight = 8091.427| |-----------------------------------------------------------------------------| r_work (start): 0.4073 rms_B_bonded: 0.75 r_work: 0.3821 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3752 rms_B_bonded: 2.25 restraints_weight: 0.2500 r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.3093 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= 0.153 Angle : 0.596 13.393 14315 Z= 0.311 Chirality : 0.043 0.145 1577 Planarity : 0.004 0.043 1793 Dihedral : 9.989 139.299 1772 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.64 % Allowed : 14.83 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.24), residues: 1255 helix: 1.70 (0.22), residues: 523 sheet: 0.11 (0.32), residues: 250 loop : -0.10 (0.30), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 234 HIS 0.006 0.001 HIS B 266 PHE 0.011 0.002 PHE B 151 TYR 0.010 0.002 TYR R 146 ARG 0.006 0.001 ARG P 11 Details of bonding type rmsd link_NAG-ASN : bond 0.00731 ( 3) link_NAG-ASN : angle 5.83352 ( 9) hydrogen bonds : bond 0.05120 ( 512) hydrogen bonds : angle 4.78136 ( 1446) SS BOND : bond 0.00317 ( 10) SS BOND : angle 0.84532 ( 20) covalent geometry : bond 0.00321 (10562) covalent geometry : angle 0.57758 (14286) Misc. bond : bond 0.00022 ( 2) *********************** 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 161 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 133 time to evaluate : 1.134 Fit side-chains REVERT: A 60 MET cc_start: 0.4629 (mmp) cc_final: 0.4000 (mpp) REVERT: B 59 TYR cc_start: 0.8650 (OUTLIER) cc_final: 0.8411 (m-80) REVERT: B 96 ARG cc_start: 0.7721 (OUTLIER) cc_final: 0.7207 (mtm-85) REVERT: N 3 GLN cc_start: 0.7931 (OUTLIER) cc_final: 0.7672 (tt0) REVERT: R 198 ILE cc_start: 0.6114 (mt) cc_final: 0.5891 (mm) REVERT: R 229 MET cc_start: 0.7015 (tpp) cc_final: 0.6777 (tpp) REVERT: R 361 TRP cc_start: 0.6753 (t-100) cc_final: 0.6269 (t-100) outliers start: 28 outliers final: 15 residues processed: 143 average time/residue: 1.5757 time to fit residues: 239.4121 Evaluate side-chains 151 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 59 TYR 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 P residue 4 THR Chi-restraints excluded: chain R residue 133 MET Chi-restraints excluded: chain R residue 196 MET 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 89 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 118 optimal weight: 0.5980 chunk 68 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 30 optimal weight: 0.1980 chunk 14 optimal weight: 0.8980 chunk 13 optimal weight: 0.4980 chunk 58 optimal weight: 5.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- 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 ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.220890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.190458 restraints weight = 8118.386| |-----------------------------------------------------------------------------| r_work (start): 0.4092 rms_B_bonded: 0.74 r_work: 0.3850 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3784 rms_B_bonded: 2.25 restraints_weight: 0.2500 r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.3202 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= 0.117 Angle : 0.534 12.617 14315 Z= 0.278 Chirality : 0.041 0.139 1577 Planarity : 0.004 0.045 1793 Dihedral : 9.576 129.714 1772 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.36 % Allowed : 15.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.24), residues: 1255 helix: 2.01 (0.22), residues: 523 sheet: 0.12 (0.32), residues: 246 loop : -0.05 (0.30), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 234 HIS 0.004 0.001 HIS B 266 PHE 0.011 0.001 PHE B 151 TYR 0.010 0.001 TYR R 191 ARG 0.005 0.000 ARG B 219 Details of bonding type rmsd link_NAG-ASN : bond 0.00684 ( 3) link_NAG-ASN : angle 5.49160 ( 9) hydrogen bonds : bond 0.04456 ( 512) hydrogen bonds : angle 4.52088 ( 1446) SS BOND : bond 0.00194 ( 10) SS BOND : angle 0.81925 ( 20) covalent geometry : bond 0.00239 (10562) covalent geometry : angle 0.51529 (14286) Misc. bond : bond 0.00009 ( 2) *********************** 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 163 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 1.049 Fit side-chains REVERT: A 60 MET cc_start: 0.4469 (mmp) cc_final: 0.3857 (mpp) REVERT: B 59 TYR cc_start: 0.8653 (OUTLIER) cc_final: 0.8411 (m-80) REVERT: N 3 GLN cc_start: 0.7920 (OUTLIER) cc_final: 0.7672 (tt0) REVERT: R 198 ILE cc_start: 0.6193 (mt) cc_final: 0.5947 (mm) REVERT: R 261 TRP cc_start: 0.6332 (m100) cc_final: 0.6080 (m100) REVERT: R 361 TRP cc_start: 0.6736 (t-100) cc_final: 0.6300 (t-100) REVERT: R 374 TYR cc_start: 0.6018 (m-80) cc_final: 0.5812 (m-80) outliers start: 25 outliers final: 10 residues processed: 149 average time/residue: 1.6044 time to fit residues: 253.1226 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 : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 127 SER Chi-restraints excluded: chain R residue 109 THR 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 339 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 119 optimal weight: 0.8980 chunk 93 optimal weight: 8.9990 chunk 28 optimal weight: 7.9990 chunk 43 optimal weight: 0.9980 chunk 116 optimal weight: 6.9990 chunk 1 optimal weight: 0.6980 chunk 50 optimal weight: 0.4980 chunk 15 optimal weight: 0.0040 overall best weight: 0.6192 ------------------------------------------------------------------------------- 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 ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.222486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.191557 restraints weight = 8198.659| |-----------------------------------------------------------------------------| r_work (start): 0.4106 rms_B_bonded: 0.75 r_work: 0.3874 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3813 rms_B_bonded: 2.17 restraints_weight: 0.2500 r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10577 Z= 0.102 Angle : 0.501 11.820 14315 Z= 0.260 Chirality : 0.040 0.136 1577 Planarity : 0.004 0.080 1793 Dihedral : 8.958 121.410 1772 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.61 % Allowed : 16.15 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.24), residues: 1255 helix: 2.26 (0.23), residues: 525 sheet: 0.23 (0.32), residues: 242 loop : 0.05 (0.30), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 234 HIS 0.005 0.001 HIS B 266 PHE 0.010 0.001 PHE A 212 TYR 0.017 0.001 TYR R 338 ARG 0.006 0.000 ARG B 219 Details of bonding type rmsd link_NAG-ASN : bond 0.00707 ( 3) link_NAG-ASN : angle 5.14739 ( 9) hydrogen bonds : bond 0.03978 ( 512) hydrogen bonds : angle 4.31849 ( 1446) SS BOND : bond 0.00166 ( 10) SS BOND : angle 0.62538 ( 20) covalent geometry : bond 0.00203 (10562) covalent geometry : angle 0.48394 (14286) Misc. bond : bond 0.00007 ( 2) *********************** 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 154 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 137 time to evaluate : 1.046 Fit side-chains REVERT: A 60 MET cc_start: 0.4386 (mmp) cc_final: 0.3827 (mpp) REVERT: B 59 TYR cc_start: 0.8626 (OUTLIER) cc_final: 0.8419 (m-80) REVERT: R 198 ILE cc_start: 0.6199 (mt) cc_final: 0.5957 (mm) REVERT: R 261 TRP cc_start: 0.6301 (m100) cc_final: 0.6066 (m100) REVERT: R 293 VAL cc_start: 0.6855 (m) cc_final: 0.6488 (p) REVERT: R 361 TRP cc_start: 0.6710 (t-100) cc_final: 0.6312 (t-100) outliers start: 17 outliers final: 7 residues processed: 142 average time/residue: 1.5871 time to fit residues: 238.7337 Evaluate side-chains 138 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 130 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain R residue 109 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 62 optimal weight: 7.9990 chunk 64 optimal weight: 5.9990 chunk 115 optimal weight: 0.1980 chunk 87 optimal weight: 0.9990 chunk 104 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 70 optimal weight: 0.1980 chunk 116 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 77 optimal weight: 6.9990 chunk 100 optimal weight: 1.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** N 1 GLN N 5 GLN N 13 GLN R 179 GLN R 226 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.220377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.189368 restraints weight = 8183.420| |-----------------------------------------------------------------------------| r_work (start): 0.4080 rms_B_bonded: 0.74 r_work: 0.3839 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3772 rms_B_bonded: 2.25 restraints_weight: 0.2500 r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.3412 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= 0.131 Angle : 0.558 10.885 14315 Z= 0.291 Chirality : 0.042 0.140 1577 Planarity : 0.004 0.047 1793 Dihedral : 9.590 129.633 1772 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.93 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.24), residues: 1255 helix: 2.09 (0.22), residues: 529 sheet: 0.15 (0.32), residues: 245 loop : 0.03 (0.30), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 234 HIS 0.007 0.001 HIS B 266 PHE 0.010 0.001 PHE A 212 TYR 0.018 0.002 TYR R 338 ARG 0.006 0.001 ARG P 11 Details of bonding type rmsd link_NAG-ASN : bond 0.00640 ( 3) link_NAG-ASN : angle 4.82273 ( 9) hydrogen bonds : bond 0.04613 ( 512) hydrogen bonds : angle 4.56301 ( 1446) SS BOND : bond 0.00125 ( 10) SS BOND : angle 1.19798 ( 20) covalent geometry : bond 0.00272 (10562) covalent geometry : angle 0.54294 (14286) Misc. bond : bond 0.00013 ( 2) *********************** 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 149 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 134 time to evaluate : 1.135 Fit side-chains REVERT: A 60 MET cc_start: 0.4528 (mmp) cc_final: 0.3933 (mpp) REVERT: R 198 ILE cc_start: 0.6173 (mt) cc_final: 0.5954 (mm) REVERT: R 261 TRP cc_start: 0.6287 (m100) cc_final: 0.6046 (m100) REVERT: R 361 TRP cc_start: 0.6705 (t-100) cc_final: 0.6288 (t-100) outliers start: 15 outliers final: 7 residues processed: 141 average time/residue: 1.5511 time to fit residues: 231.6629 Evaluate side-chains 135 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 128 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 217 MET 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 330 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 30 optimal weight: 0.4980 chunk 83 optimal weight: 9.9990 chunk 70 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 102 optimal weight: 0.0370 chunk 66 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 25 optimal weight: 0.4980 chunk 118 optimal weight: 0.2980 chunk 32 optimal weight: 0.9990 overall best weight: 0.4658 ------------------------------------------------------------------------------- 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 5 GLN N 13 GLN R 179 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.222860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.192381 restraints weight = 8241.744| |-----------------------------------------------------------------------------| r_work (start): 0.4114 rms_B_bonded: 0.75 r_work: 0.3833 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3767 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10577 Z= 0.097 Angle : 0.489 10.237 14315 Z= 0.255 Chirality : 0.040 0.135 1577 Planarity : 0.004 0.062 1793 Dihedral : 8.742 117.311 1772 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.04 % Allowed : 16.71 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.24), residues: 1255 helix: 2.37 (0.23), residues: 525 sheet: 0.27 (0.33), residues: 234 loop : 0.06 (0.30), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 234 HIS 0.004 0.001 HIS B 266 PHE 0.010 0.001 PHE A 212 TYR 0.022 0.001 TYR R 65 ARG 0.006 0.000 ARG B 219 Details of bonding type rmsd link_NAG-ASN : bond 0.00583 ( 3) link_NAG-ASN : angle 4.57750 ( 9) hydrogen bonds : bond 0.03819 ( 512) hydrogen bonds : angle 4.25147 ( 1446) SS BOND : bond 0.00140 ( 10) SS BOND : angle 0.76595 ( 20) covalent geometry : bond 0.00195 (10562) covalent geometry : angle 0.47532 (14286) Misc. bond : bond 0.00003 ( 2) *********************** 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 139 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 128 time to evaluate : 1.185 Fit side-chains REVERT: A 60 MET cc_start: 0.4459 (mmp) cc_final: 0.3847 (mpp) REVERT: R 198 ILE cc_start: 0.6249 (mt) cc_final: 0.6012 (mm) REVERT: R 261 TRP cc_start: 0.6247 (m100) cc_final: 0.6015 (m100) REVERT: R 293 VAL cc_start: 0.6801 (m) cc_final: 0.6481 (p) REVERT: R 361 TRP cc_start: 0.6672 (t-100) cc_final: 0.6242 (t-100) outliers start: 11 outliers final: 5 residues processed: 134 average time/residue: 1.5641 time to fit residues: 222.6608 Evaluate side-chains 131 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 126 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain R residue 109 THR Chi-restraints excluded: chain R residue 250 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 0 optimal weight: 20.0000 chunk 109 optimal weight: 7.9990 chunk 75 optimal weight: 5.9990 chunk 79 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 55 optimal weight: 7.9990 chunk 72 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 88 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 88 ASN ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 1 GLN N 5 GLN N 13 GLN R 144 ASN R 179 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.217745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.189666 restraints weight = 8115.697| |-----------------------------------------------------------------------------| r_work (start): 0.4084 rms_B_bonded: 0.69 r_work: 0.3808 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.3733 rms_B_bonded: 2.10 restraints_weight: 0.2500 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 10577 Z= 0.243 Angle : 0.752 9.823 14315 Z= 0.391 Chirality : 0.049 0.192 1577 Planarity : 0.006 0.055 1793 Dihedral : 11.125 132.887 1772 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.89 % Allowed : 15.11 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.24), residues: 1255 helix: 1.47 (0.22), residues: 526 sheet: 0.12 (0.32), residues: 245 loop : -0.13 (0.30), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP E 56 HIS 0.008 0.002 HIS B 266 PHE 0.018 0.003 PHE B 151 TYR 0.023 0.003 TYR R 65 ARG 0.011 0.001 ARG P 11 Details of bonding type rmsd link_NAG-ASN : bond 0.00707 ( 3) link_NAG-ASN : angle 4.61942 ( 9) hydrogen bonds : bond 0.05950 ( 512) hydrogen bonds : angle 5.08306 ( 1446) SS BOND : bond 0.00415 ( 10) SS BOND : angle 1.55669 ( 20) covalent geometry : bond 0.00531 (10562) covalent geometry : angle 0.74173 (14286) Misc. bond : bond 0.00023 ( 2) *********************** 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 146 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 1.316 Fit side-chains REVERT: A 60 MET cc_start: 0.4616 (mmp) cc_final: 0.4057 (mpp) REVERT: B 59 TYR cc_start: 0.8639 (OUTLIER) cc_final: 0.8399 (m-80) REVERT: R 198 ILE cc_start: 0.6159 (mt) cc_final: 0.5956 (mm) REVERT: R 261 TRP cc_start: 0.6344 (m100) cc_final: 0.6111 (m100) REVERT: R 361 TRP cc_start: 0.6751 (t-100) cc_final: 0.6347 (t-100) outliers start: 20 outliers final: 12 residues processed: 137 average time/residue: 1.6332 time to fit residues: 237.4125 Evaluate side-chains 137 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS 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 P residue 4 THR 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 271 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 78 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 84 optimal weight: 9.9990 chunk 74 optimal weight: 0.0570 chunk 110 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 115 optimal weight: 0.0870 chunk 45 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 overall best weight: 0.7478 ------------------------------------------------------------------------------- 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 88 ASN B 268 ASN 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 = 0.4406 r_free = 0.4406 target = 0.221281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.191996 restraints weight = 8180.384| |-----------------------------------------------------------------------------| r_work (start): 0.4110 rms_B_bonded: 0.76 r_work: 0.3863 rms_B_bonded: 1.55 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: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10577 Z= 0.110 Angle : 0.530 9.254 14315 Z= 0.277 Chirality : 0.041 0.147 1577 Planarity : 0.004 0.054 1793 Dihedral : 9.712 122.331 1772 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.66 % Allowed : 16.62 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.24), residues: 1255 helix: 2.05 (0.22), residues: 528 sheet: 0.27 (0.33), residues: 235 loop : 0.01 (0.30), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 234 HIS 0.005 0.001 HIS B 266 PHE 0.011 0.001 PHE A 212 TYR 0.019 0.001 TYR R 338 ARG 0.012 0.001 ARG B 96 Details of bonding type rmsd link_NAG-ASN : bond 0.00522 ( 3) link_NAG-ASN : angle 4.20273 ( 9) hydrogen bonds : bond 0.04192 ( 512) hydrogen bonds : angle 4.49612 ( 1446) SS BOND : bond 0.00151 ( 10) SS BOND : angle 0.82081 ( 20) covalent geometry : bond 0.00223 (10562) covalent geometry : angle 0.51916 (14286) Misc. bond : bond 0.00009 ( 2) ********************** 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 133 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 126 time to evaluate : 1.208 Fit side-chains REVERT: A 60 MET cc_start: 0.4420 (mmp) cc_final: 0.3818 (mpp) REVERT: B 59 TYR cc_start: 0.8607 (OUTLIER) cc_final: 0.8384 (m-80) REVERT: R 198 ILE cc_start: 0.6174 (mt) cc_final: 0.5943 (mm) REVERT: R 258 ARG cc_start: 0.5561 (ptp90) cc_final: 0.5298 (ptp-170) REVERT: R 261 TRP cc_start: 0.6275 (m100) cc_final: 0.6044 (m100) REVERT: R 361 TRP cc_start: 0.6758 (t-100) cc_final: 0.6386 (t-100) outliers start: 7 outliers final: 4 residues processed: 130 average time/residue: 1.6782 time to fit residues: 231.0053 Evaluate side-chains 126 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 121 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain R residue 109 THR Chi-restraints excluded: chain R residue 250 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 84 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 90 optimal weight: 0.0570 chunk 17 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 52 optimal weight: 10.0000 chunk 78 optimal weight: 0.4980 chunk 69 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 overall best weight: 0.9102 ------------------------------------------------------------------------------- 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 ** N 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 GLN N 13 GLN R 179 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.221292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.190605 restraints weight = 8185.900| |-----------------------------------------------------------------------------| r_work (start): 0.4094 rms_B_bonded: 0.74 r_work: 0.3823 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3758 rms_B_bonded: 2.28 restraints_weight: 0.2500 r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.3692 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= 0.110 Angle : 0.527 10.939 14315 Z= 0.272 Chirality : 0.041 0.149 1577 Planarity : 0.004 0.051 1793 Dihedral : 9.244 120.550 1772 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.94 % Allowed : 16.62 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.24), residues: 1255 helix: 2.18 (0.23), residues: 529 sheet: 0.28 (0.33), residues: 235 loop : 0.02 (0.30), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 234 HIS 0.002 0.001 HIS R 302 PHE 0.010 0.001 PHE A 212 TYR 0.022 0.001 TYR R 338 ARG 0.006 0.000 ARG B 219 Details of bonding type rmsd link_NAG-ASN : bond 0.00500 ( 3) link_NAG-ASN : angle 4.09916 ( 9) hydrogen bonds : bond 0.04155 ( 512) hydrogen bonds : angle 4.41959 ( 1446) SS BOND : bond 0.00152 ( 10) SS BOND : angle 0.85451 ( 20) covalent geometry : bond 0.00223 (10562) covalent geometry : angle 0.51636 (14286) Misc. bond : bond 0.00004 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11837.67 seconds wall clock time: 201 minutes 44.75 seconds (12104.75 seconds total)