Starting phenix.real_space_refine on Wed Mar 4 14:11:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nwl_12634/03_2026/7nwl_12634.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nwl_12634/03_2026/7nwl_12634.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7nwl_12634/03_2026/7nwl_12634.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nwl_12634/03_2026/7nwl_12634.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7nwl_12634/03_2026/7nwl_12634.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nwl_12634/03_2026/7nwl_12634.map" } resolution = 3.1 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= 0.002 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 Mn 7 7.51 5 S 59 5.16 5 C 8715 2.51 5 N 2291 2.21 5 O 2832 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13904 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 4583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4583 Classifications: {'peptide': 603} Link IDs: {'PTRANS': 39, 'TRANS': 563} Chain: "B" Number of atoms: 3430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3430 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 20, 'TRANS': 420} Chain: "C" Number of atoms: 2820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2820 Classifications: {'peptide': 368} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 34, 'TRANS': 333} Chain: "D" Number of atoms: 1362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1362 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 5, 'TRANS': 166} Chain: "E" Number of atoms: 1276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1276 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 153} Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.35, per 1000 atoms: 0.24 Number of scatterers: 13904 At special positions: 0 Unit cell: (173, 186.84, 168.848, 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) Mn 7 24.99 S 59 16.00 O 2832 8.00 N 2291 7.00 C 8715 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 58 " - pdb=" SG CYS A 67 " distance=2.03 Simple disulfide: pdb=" SG CYS A 115 " - pdb=" SG CYS A 135 " distance=2.03 Simple disulfide: pdb=" SG CYS A 151 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 472 " - pdb=" SG CYS A 481 " distance=2.83 Simple disulfide: pdb=" SG CYS A 487 " - pdb=" SG CYS A 543 " distance=2.03 Simple disulfide: pdb=" SG CYS B 7 " - pdb=" SG CYS B 25 " distance=2.05 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 444 " distance=2.03 Simple disulfide: pdb=" SG CYS B 18 " - pdb=" SG CYS B 44 " distance=2.04 Simple disulfide: pdb=" SG CYS B 28 " - pdb=" SG CYS B 55 " distance=2.25 Simple disulfide: pdb=" SG CYS B 187 " - pdb=" SG CYS B 193 " distance=2.03 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 281 " distance=2.03 Simple disulfide: pdb=" SG CYS B 381 " - pdb=" SG CYS B 395 " distance=2.03 Simple disulfide: pdb=" SG CYS B 415 " - pdb=" SG CYS B 442 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA I 3 " - " MAN I 4 " " BMA J 3 " - " MAN J 6 " ALPHA1-6 " BMA I 3 " - " MAN I 5 " " BMA J 3 " - " MAN J 4 " " BMA N 3 " - " MAN N 4 " BETA1-2 " MAN J 4 " - " NAG J 5 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG F 1 " - " ASN A 43 " " NAG G 1 " - " ASN A 141 " " NAG H 1 " - " ASN A 256 " " NAG I 1 " - " ASN A 266 " " NAG J 1 " - " ASN A 275 " " NAG K 1 " - " ASN A 568 " " NAG L 1 " - " ASN B 249 " " NAG M 1 " - " ASN B 343 " " NAG N 1 " - " ASN B 386 " " NAG O 1 " - " ASN B 397 " Time building additional restraints: 1.43 Conformation dependent library (CDL) restraints added in 469.0 milliseconds 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3194 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 33 sheets defined 15.5% alpha, 33.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 82 through 87 removed outlier: 3.598A pdb=" N SER A 87 " --> pdb=" O SER A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 189 Processing helix chain 'A' and resid 196 through 204 Processing helix chain 'A' and resid 223 through 227 Processing helix chain 'A' and resid 254 through 259 Processing helix chain 'B' and resid 7 through 11 removed outlier: 3.696A pdb=" N ASN B 11 " --> pdb=" O LEU B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 22 removed outlier: 3.911A pdb=" N CYS B 18 " --> pdb=" O SER B 14 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE B 19 " --> pdb=" O CYS B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 53 removed outlier: 3.745A pdb=" N LYS B 53 " --> pdb=" O ALA B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 84 Processing helix chain 'B' and resid 132 through 136 removed outlier: 3.501A pdb=" N LYS B 136 " --> pdb=" O TYR B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 157 removed outlier: 3.845A pdb=" N THR B 147 " --> pdb=" O LYS B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 185 removed outlier: 3.845A pdb=" N ARG B 184 " --> pdb=" O PRO B 180 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ASN B 185 " --> pdb=" O ALA B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 218 removed outlier: 3.724A pdb=" N PHE B 212 " --> pdb=" O LYS B 208 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL B 216 " --> pdb=" O PHE B 212 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY B 217 " --> pdb=" O ASN B 213 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS B 218 " --> pdb=" O GLU B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 241 removed outlier: 3.819A pdb=" N ALA B 234 " --> pdb=" O GLY B 230 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN B 237 " --> pdb=" O ASP B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 246 Processing helix chain 'B' and resid 298 through 310 Processing helix chain 'B' and resid 321 through 332 removed outlier: 4.152A pdb=" N GLU B 327 " --> pdb=" O PRO B 323 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU B 328 " --> pdb=" O VAL B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 357 removed outlier: 3.782A pdb=" N ILE B 348 " --> pdb=" O SER B 344 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE B 351 " --> pdb=" O VAL B 347 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER B 357 " --> pdb=" O ASP B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 385 removed outlier: 3.578A pdb=" N GLY B 384 " --> pdb=" O CYS B 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 1183 through 1185 No H-bonds generated for 'chain 'C' and resid 1183 through 1185' Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'D' and resid 114 through 123 removed outlier: 3.514A pdb=" N GLU D 118 " --> pdb=" O GLY D 114 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE D 119 " --> pdb=" O SER D 115 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N SER D 122 " --> pdb=" O GLU D 118 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N TRP D 123 " --> pdb=" O PHE D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 164 removed outlier: 3.592A pdb=" N LYS D 130 " --> pdb=" O GLU D 126 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG D 131 " --> pdb=" O ASP D 127 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU D 133 " --> pdb=" O GLN D 129 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA D 134 " --> pdb=" O LYS D 130 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU D 135 " --> pdb=" O ARG D 131 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASP D 136 " --> pdb=" O LEU D 132 " (cutoff:3.500A) Proline residue: D 137 - end of helix removed outlier: 3.511A pdb=" N LYS D 153 " --> pdb=" O LYS D 149 " (cutoff:3.500A) Proline residue: D 156 - end of helix Processing helix chain 'E' and resid 111 through 116 removed outlier: 3.837A pdb=" N LEU E 115 " --> pdb=" O ASP E 111 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS E 116 " --> pdb=" O TYR E 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 111 through 116' Processing helix chain 'E' and resid 119 through 159 removed outlier: 3.916A pdb=" N ASP E 131 " --> pdb=" O LEU E 127 " (cutoff:3.500A) Proline residue: E 132 - end of helix Proline residue: E 151 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 12 removed outlier: 6.704A pdb=" N ASP A 432 " --> pdb=" O GLY A 422 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLY A 422 " --> pdb=" O ASP A 432 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 22 through 26 removed outlier: 3.892A pdb=" N SER A 22 " --> pdb=" O GLY A 38 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N VAL A 55 " --> pdb=" O ILE A 70 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR A 68 " --> pdb=" O LEU A 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 104 through 108 removed outlier: 3.571A pdb=" N THR A 104 " --> pdb=" O CYS A 115 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N THR A 139 " --> pdb=" O ARG A 144 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ARG A 144 " --> pdb=" O THR A 139 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 121 through 122 removed outlier: 3.855A pdb=" N ASP A 130 " --> pdb=" O TRP A 121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 172 removed outlier: 3.995A pdb=" N SER A 169 " --> pdb=" O GLY A 181 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 234 through 238 removed outlier: 4.053A pdb=" N SER A 234 " --> pdb=" O GLY A 251 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N VAL A 262 " --> pdb=" O ASN A 275 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ASN A 275 " --> pdb=" O VAL A 262 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ILE A 264 " --> pdb=" O LEU A 273 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 289 through 292 Processing sheet with id=AA8, first strand: chain 'A' and resid 310 through 312 removed outlier: 3.611A pdb=" N GLN A 319 " --> pdb=" O ASP A 311 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 357 removed outlier: 3.907A pdb=" N SER A 354 " --> pdb=" O GLY A 372 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN A 400 " --> pdb=" O VAL A 386 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 519 through 521 removed outlier: 3.675A pdb=" N ARG A 544 " --> pdb=" O PHE A 486 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE A 486 " --> pdb=" O ARG A 544 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 464 through 465 removed outlier: 3.600A pdb=" N PHE A 465 " --> pdb=" O GLN A 599 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 27 through 28 removed outlier: 3.700A pdb=" N TRP B 27 " --> pdb=" O GLU B 61 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 98 through 102 removed outlier: 3.555A pdb=" N ILE B 437 " --> pdb=" O LEU B 99 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 109 through 116 Processing sheet with id=AB6, first strand: chain 'B' and resid 199 through 206 removed outlier: 3.709A pdb=" N VAL B 202 " --> pdb=" O PHE B 164 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N PHE B 164 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N SER B 204 " --> pdb=" O ILE B 162 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ILE B 162 " --> pdb=" O SER B 204 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N THR B 206 " --> pdb=" O PHE B 160 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N PHE B 160 " --> pdb=" O THR B 206 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE B 167 " --> pdb=" O MET B 129 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ARG B 252 " --> pdb=" O GLN B 312 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N ILE B 314 " --> pdb=" O ARG B 252 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU B 254 " --> pdb=" O ILE B 314 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ALA B 316 " --> pdb=" O LEU B 254 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N PHE B 256 " --> pdb=" O ALA B 316 " (cutoff:3.500A) removed outlier: 9.119A pdb=" N ALA B 336 " --> pdb=" O ILE B 311 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N THR B 313 " --> pdb=" O ALA B 336 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N GLY B 338 " --> pdb=" O THR B 313 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N PHE B 315 " --> pdb=" O GLY B 338 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 360 through 362 removed outlier: 5.899A pdb=" N SER B 360 " --> pdb=" O ASN B 397 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 1150 through 1152 removed outlier: 3.813A pdb=" N GLU C1152 " --> pdb=" O THR C1161 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N THR C1161 " --> pdb=" O GLU C1152 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU C1160 " --> pdb=" O PHE C1203 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 1190 through 1195 Processing sheet with id=AC1, first strand: chain 'C' and resid 1190 through 1195 Processing sheet with id=AC2, first strand: chain 'C' and resid 1240 through 1245 removed outlier: 4.990A pdb=" N ASP C1241 " --> pdb=" O ALA C1257 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA C1257 " --> pdb=" O ASP C1241 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG C1253 " --> pdb=" O THR C1245 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 1281 through 1285 removed outlier: 3.520A pdb=" N LEU C1268 " --> pdb=" O SER C1308 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 1281 through 1285 removed outlier: 3.520A pdb=" N LEU C1268 " --> pdb=" O SER C1308 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 1331 through 1336 removed outlier: 5.536A pdb=" N GLY C1332 " --> pdb=" O ILE C1348 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ILE C1348 " --> pdb=" O GLY C1332 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE C1382 " --> pdb=" O VAL C1345 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 1372 through 1376 Processing sheet with id=AC7, first strand: chain 'C' and resid 1372 through 1376 Processing sheet with id=AC8, first strand: chain 'C' and resid 1421 through 1428 removed outlier: 3.763A pdb=" N ARG C1421 " --> pdb=" O ASP C1438 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N LEU C1423 " --> pdb=" O SER C1436 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N SER C1436 " --> pdb=" O LEU C1423 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N VAL C1425 " --> pdb=" O LEU C1434 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LEU C1434 " --> pdb=" O VAL C1425 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 1461 through 1466 removed outlier: 3.638A pdb=" N ILE C1449 " --> pdb=" O PHE C1463 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N TYR C1446 " --> pdb=" O VAL C1490 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AD2, first strand: chain 'D' and resid 57 through 58 removed outlier: 5.251A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER D 35 " --> pdb=" O THR D 93 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N CYS D 92 " --> pdb=" O TRP D 103 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N TRP D 103 " --> pdb=" O CYS D 92 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ARG D 94 " --> pdb=" O ASP D 101 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY D 96 " --> pdb=" O ALA D 100B" (cutoff:3.500A) removed outlier: 7.825A pdb=" N ALA D 100B" --> pdb=" O GLY D 96 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 57 through 58 removed outlier: 5.251A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER D 35 " --> pdb=" O THR D 93 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL D 109 " --> pdb=" O ALA D 88 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 4 through 6 removed outlier: 3.519A pdb=" N SER E 65 " --> pdb=" O SER E 72 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.640A pdb=" N MET E 11 " --> pdb=" O ASP E 105 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU E 104 " --> pdb=" O ALA E 84 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA E 84 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.640A pdb=" N MET E 11 " --> pdb=" O ASP E 105 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU E 104 " --> pdb=" O ALA E 84 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA E 84 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR E 97 " --> pdb=" O GLN E 90 " (cutoff:3.500A) 515 hydrogen bonds defined for protein. 1344 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: 2.87 Time building geometry restraints manager: 1.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2473 1.32 - 1.45: 3663 1.45 - 1.57: 7978 1.57 - 1.69: 0 1.69 - 1.82: 85 Bond restraints: 14199 Sorted by residual: bond pdb=" CA PRO E 59 " pdb=" C PRO E 59 " ideal model delta sigma weight residual 1.514 1.536 -0.021 5.50e-03 3.31e+04 1.52e+01 bond pdb=" N VAL E 83 " pdb=" CA VAL E 83 " ideal model delta sigma weight residual 1.461 1.502 -0.042 1.08e-02 8.57e+03 1.50e+01 bond pdb=" N VAL A 321 " pdb=" CA VAL A 321 " ideal model delta sigma weight residual 1.456 1.493 -0.037 9.50e-03 1.11e+04 1.49e+01 bond pdb=" N ILE C1233 " pdb=" CA ILE C1233 " ideal model delta sigma weight residual 1.461 1.494 -0.033 9.10e-03 1.21e+04 1.32e+01 bond pdb=" N VAL C1465 " pdb=" CA VAL C1465 " ideal model delta sigma weight residual 1.462 1.495 -0.032 9.10e-03 1.21e+04 1.27e+01 ... (remaining 14194 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 14575 1.72 - 3.44: 4313 3.44 - 5.16: 370 5.16 - 6.88: 32 6.88 - 8.60: 7 Bond angle restraints: 19297 Sorted by residual: angle pdb=" CA GLY A 382 " pdb=" C GLY A 382 " pdb=" O GLY A 382 " ideal model delta sigma weight residual 122.37 117.89 4.48 7.30e-01 1.88e+00 3.77e+01 angle pdb=" CA GLY A 190 " pdb=" C GLY A 190 " pdb=" O GLY A 190 " ideal model delta sigma weight residual 122.23 118.25 3.98 6.90e-01 2.10e+00 3.33e+01 angle pdb=" CA GLY A 377 " pdb=" C GLY A 377 " pdb=" O GLY A 377 " ideal model delta sigma weight residual 122.22 118.57 3.65 6.50e-01 2.37e+00 3.15e+01 angle pdb=" CA GLY D 82A" pdb=" C GLY D 82A" pdb=" O GLY D 82A" ideal model delta sigma weight residual 121.47 116.51 4.96 9.00e-01 1.23e+00 3.04e+01 angle pdb=" N PRO A 117 " pdb=" CA PRO A 117 " pdb=" C PRO A 117 " ideal model delta sigma weight residual 113.40 120.29 -6.89 1.34e+00 5.57e-01 2.64e+01 ... (remaining 19292 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.75: 8601 21.75 - 43.50: 271 43.50 - 65.24: 43 65.24 - 86.99: 43 86.99 - 108.74: 30 Dihedral angle restraints: 8988 sinusoidal: 3978 harmonic: 5010 Sorted by residual: dihedral pdb=" CB CYS B 381 " pdb=" SG CYS B 381 " pdb=" SG CYS B 395 " pdb=" CB CYS B 395 " ideal model delta sinusoidal sigma weight residual -86.00 -175.10 89.10 1 1.00e+01 1.00e-02 9.45e+01 dihedral pdb=" CB CYS A 472 " pdb=" SG CYS A 472 " pdb=" SG CYS A 481 " pdb=" CB CYS A 481 " ideal model delta sinusoidal sigma weight residual 93.00 174.80 -81.80 1 1.00e+01 1.00e-02 8.23e+01 dihedral pdb=" CB CYS A 151 " pdb=" SG CYS A 151 " pdb=" SG CYS A 164 " pdb=" CB CYS A 164 " ideal model delta sinusoidal sigma weight residual -86.00 -28.05 -57.95 1 1.00e+01 1.00e-02 4.51e+01 ... (remaining 8985 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 1691 0.127 - 0.254: 535 0.254 - 0.382: 11 0.382 - 0.509: 1 0.509 - 0.636: 3 Chirality restraints: 2241 Sorted by residual: chirality pdb=" C1 MAN J 4 " pdb=" O6 BMA J 3 " pdb=" C2 MAN J 4 " pdb=" O5 MAN J 4 " both_signs ideal model delta sigma weight residual False 2.40 1.76 0.64 2.00e-02 2.50e+03 1.01e+03 chirality pdb=" C1 BMA J 3 " pdb=" O4 NAG J 2 " pdb=" C2 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.78 -0.62 2.00e-02 2.50e+03 9.52e+02 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-02 2.50e+03 3.06e+02 ... (remaining 2238 not shown) Planarity restraints: 2486 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 2 " -0.355 2.00e-02 2.50e+03 3.06e-01 1.17e+03 pdb=" C7 NAG F 2 " 0.084 2.00e-02 2.50e+03 pdb=" C8 NAG F 2 " -0.110 2.00e-02 2.50e+03 pdb=" N2 NAG F 2 " 0.545 2.00e-02 2.50e+03 pdb=" O7 NAG F 2 " -0.164 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 2 " -0.352 2.00e-02 2.50e+03 3.03e-01 1.15e+03 pdb=" C7 NAG H 2 " 0.085 2.00e-02 2.50e+03 pdb=" C8 NAG H 2 " -0.133 2.00e-02 2.50e+03 pdb=" N2 NAG H 2 " 0.540 2.00e-02 2.50e+03 pdb=" O7 NAG H 2 " -0.140 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG O 2 " -0.338 2.00e-02 2.50e+03 2.91e-01 1.06e+03 pdb=" C7 NAG O 2 " 0.084 2.00e-02 2.50e+03 pdb=" C8 NAG O 2 " -0.157 2.00e-02 2.50e+03 pdb=" N2 NAG O 2 " 0.515 2.00e-02 2.50e+03 pdb=" O7 NAG O 2 " -0.104 2.00e-02 2.50e+03 ... (remaining 2483 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 57 2.41 - 3.03: 8774 3.03 - 3.66: 19318 3.66 - 4.28: 28927 4.28 - 4.90: 49145 Nonbonded interactions: 106221 Sorted by model distance: nonbonded pdb=" OD1 ASN B 224 " pdb="MN MN B 803 " model vdw 1.790 2.320 nonbonded pdb=" O TYR A 430 " pdb="MN MN A1104 " model vdw 1.812 2.320 nonbonded pdb=" OD1 ASP A 247 " pdb="MN MN A1101 " model vdw 1.843 2.320 nonbonded pdb=" O LEU A 257 " pdb=" OG1 THR A 258 " model vdw 1.907 3.040 nonbonded pdb=" OD1 ASN A 428 " pdb="MN MN A1104 " model vdw 1.930 2.320 ... (remaining 106216 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'K' selection = chain 'M' } ncs_group { reference = chain 'H' selection = chain 'L' selection = chain 'O' } 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=0.50 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: 3.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.740 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6535 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 : 0.015 0.796 14247 Z= 1.081 Angle : 1.505 25.922 19426 Z= 1.114 Chirality : 0.110 0.636 2241 Planarity : 0.020 0.306 2476 Dihedral : 14.023 108.740 5749 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 40.17 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.90 % Favored : 98.04 % Rotamer: Outliers : 0.93 % Allowed : 6.87 % Favored : 92.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.19), residues: 1737 helix: 2.61 (0.38), residues: 196 sheet: 1.75 (0.22), residues: 536 loop : -0.40 (0.18), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1374 TYR 0.015 0.001 TYR A 208 PHE 0.016 0.001 PHE A 285 TRP 0.012 0.001 TRP C1164 HIS 0.004 0.001 HIS E 34 Details of bonding type rmsd covalent geometry : bond 0.01348 (14199) covalent geometry : angle 1.47510 (19297) SS BOND : bond 0.21324 ( 15) SS BOND : angle 3.81532 ( 30) hydrogen bonds : bond 0.27431 ( 463) hydrogen bonds : angle 9.46421 ( 1344) link_ALPHA1-3 : bond 0.00304 ( 2) link_ALPHA1-3 : angle 3.32366 ( 6) link_ALPHA1-6 : bond 0.01205 ( 3) link_ALPHA1-6 : angle 5.09949 ( 9) link_BETA1-2 : bond 0.00241 ( 1) link_BETA1-2 : angle 1.34176 ( 3) link_BETA1-4 : bond 0.00461 ( 17) link_BETA1-4 : angle 2.43172 ( 51) link_NAG-ASN : bond 0.01617 ( 10) link_NAG-ASN : angle 5.66558 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 205 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 91 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8274 (pt) REVERT: C 1262 ILE cc_start: 0.6493 (OUTLIER) cc_final: 0.6210 (mm) REVERT: D 119 PHE cc_start: 0.5956 (t80) cc_final: 0.5430 (t80) outliers start: 14 outliers final: 6 residues processed: 217 average time/residue: 0.1490 time to fit residues: 44.8761 Evaluate side-chains 100 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 568 ASN Chi-restraints excluded: chain B residue 33 PHE Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 121 TYR Chi-restraints excluded: chain B residue 440 TYR Chi-restraints excluded: chain C residue 1262 ILE Chi-restraints excluded: chain D residue 117 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN A 51 GLN A 191 GLN A 218 GLN A 329 GLN A 380 GLN A 510 GLN A 512 GLN B 201 ASN B 263 HIS B 286 ASN B 310 ASN ** B 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 383 ASN C1183 ASN C1198 GLN C1205 ASN C1296 ASN C1323 GLN C1457 ASN C1461 GLN D 76 ASN D 81 GLN E 136 GLN E 150 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.089232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.061389 restraints weight = 64096.880| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 5.25 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3675 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3675 r_free = 0.3675 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3675 r_free = 0.3675 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3675 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14247 Z= 0.215 Angle : 0.884 14.615 19426 Z= 0.419 Chirality : 0.054 0.427 2241 Planarity : 0.005 0.051 2476 Dihedral : 11.731 85.311 2581 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.20 % Allowed : 8.67 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.19), residues: 1737 helix: 1.95 (0.34), residues: 213 sheet: 1.43 (0.21), residues: 593 loop : -0.12 (0.19), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 71 TYR 0.027 0.002 TYR C1488 PHE 0.018 0.002 PHE B 264 TRP 0.012 0.002 TRP E 118 HIS 0.006 0.001 HIS B 282 Details of bonding type rmsd covalent geometry : bond 0.00485 (14199) covalent geometry : angle 0.85798 (19297) SS BOND : bond 0.00345 ( 15) SS BOND : angle 0.94487 ( 30) hydrogen bonds : bond 0.05295 ( 463) hydrogen bonds : angle 6.38512 ( 1344) link_ALPHA1-3 : bond 0.01067 ( 2) link_ALPHA1-3 : angle 3.47440 ( 6) link_ALPHA1-6 : bond 0.00982 ( 3) link_ALPHA1-6 : angle 1.84002 ( 9) link_BETA1-2 : bond 0.00635 ( 1) link_BETA1-2 : angle 2.41862 ( 3) link_BETA1-4 : bond 0.01037 ( 17) link_BETA1-4 : angle 3.28548 ( 51) link_NAG-ASN : bond 0.00454 ( 10) link_NAG-ASN : angle 3.13055 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 106 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 546 MET cc_start: 0.8395 (mmt) cc_final: 0.8146 (mmp) REVERT: E 5 THR cc_start: 0.8063 (OUTLIER) cc_final: 0.7682 (p) REVERT: E 78 MET cc_start: 0.6861 (mmt) cc_final: 0.6167 (mmt) outliers start: 33 outliers final: 16 residues processed: 134 average time/residue: 0.1387 time to fit residues: 26.4792 Evaluate side-chains 97 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain A residue 568 ASN Chi-restraints excluded: chain B residue 121 TYR Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 440 TYR Chi-restraints excluded: chain C residue 1450 THR Chi-restraints excluded: chain D residue 29 PHE Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 117 TYR Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 120 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 84 optimal weight: 1.9990 chunk 136 optimal weight: 0.8980 chunk 121 optimal weight: 10.0000 chunk 144 optimal weight: 2.9990 chunk 164 optimal weight: 0.9980 chunk 87 optimal weight: 0.5980 chunk 132 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 1 optimal weight: 0.0050 chunk 124 optimal weight: 0.7980 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 GLN ** A 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 286 ASN C1413 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.088356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.060532 restraints weight = 64368.824| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 5.14 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3654 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3654 r_free = 0.3654 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3654 r_free = 0.3654 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3654 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14247 Z= 0.150 Angle : 0.707 9.553 19426 Z= 0.340 Chirality : 0.048 0.259 2241 Planarity : 0.005 0.070 2476 Dihedral : 9.449 79.843 2575 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.80 % Allowed : 10.20 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.19), residues: 1737 helix: 1.93 (0.35), residues: 212 sheet: 1.35 (0.21), residues: 593 loop : 0.01 (0.19), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 66 TYR 0.022 0.002 TYR C1488 PHE 0.018 0.002 PHE B 33 TRP 0.022 0.002 TRP E 118 HIS 0.005 0.001 HIS D 102 Details of bonding type rmsd covalent geometry : bond 0.00331 (14199) covalent geometry : angle 0.68405 (19297) SS BOND : bond 0.00199 ( 15) SS BOND : angle 0.61881 ( 30) hydrogen bonds : bond 0.04484 ( 463) hydrogen bonds : angle 5.69409 ( 1344) link_ALPHA1-3 : bond 0.01071 ( 2) link_ALPHA1-3 : angle 3.17849 ( 6) link_ALPHA1-6 : bond 0.00893 ( 3) link_ALPHA1-6 : angle 1.72199 ( 9) link_BETA1-2 : bond 0.00511 ( 1) link_BETA1-2 : angle 1.08741 ( 3) link_BETA1-4 : bond 0.00705 ( 17) link_BETA1-4 : angle 2.83164 ( 51) link_NAG-ASN : bond 0.00278 ( 10) link_NAG-ASN : angle 2.45408 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 87 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 546 MET cc_start: 0.8486 (mmt) cc_final: 0.8175 (mmp) REVERT: B 38 MET cc_start: 0.5754 (mmm) cc_final: 0.4773 (ptm) REVERT: B 102 ARG cc_start: 0.7116 (OUTLIER) cc_final: 0.6841 (mtm110) REVERT: B 150 MET cc_start: 0.6793 (ttp) cc_final: 0.6586 (ttp) REVERT: D 20 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.7744 (mm) REVERT: E 5 THR cc_start: 0.8238 (OUTLIER) cc_final: 0.7989 (p) REVERT: E 82 ASP cc_start: 0.7893 (m-30) cc_final: 0.7293 (m-30) REVERT: E 85 THR cc_start: 0.8502 (OUTLIER) cc_final: 0.8196 (p) REVERT: E 108 ARG cc_start: 0.9353 (mtt180) cc_final: 0.9112 (mmm160) REVERT: E 148 LYS cc_start: 0.8735 (ptpt) cc_final: 0.8460 (ptpt) outliers start: 27 outliers final: 12 residues processed: 108 average time/residue: 0.1336 time to fit residues: 20.6249 Evaluate side-chains 94 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 121 TYR Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 440 TYR Chi-restraints excluded: chain C residue 1217 TYR Chi-restraints excluded: chain C residue 1398 VAL Chi-restraints excluded: chain C residue 1416 VAL Chi-restraints excluded: chain C residue 1450 THR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 85 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 128 optimal weight: 0.9980 chunk 158 optimal weight: 8.9990 chunk 26 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 chunk 164 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 chunk 166 optimal weight: 0.6980 chunk 68 optimal weight: 8.9990 chunk 86 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 chunk 129 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 494 HIS B 286 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.086753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.058730 restraints weight = 64474.589| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 5.05 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.4752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 14247 Z= 0.167 Angle : 0.734 24.933 19426 Z= 0.339 Chirality : 0.050 0.501 2241 Planarity : 0.004 0.048 2476 Dihedral : 8.625 76.670 2571 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.13 % Allowed : 10.73 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.19), residues: 1737 helix: 1.70 (0.35), residues: 213 sheet: 1.38 (0.21), residues: 580 loop : -0.12 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 71 TYR 0.019 0.001 TYR C1488 PHE 0.027 0.002 PHE A 569 TRP 0.021 0.001 TRP D 123 HIS 0.005 0.001 HIS B 301 Details of bonding type rmsd covalent geometry : bond 0.00363 (14199) covalent geometry : angle 0.67006 (19297) SS BOND : bond 0.00173 ( 15) SS BOND : angle 0.61741 ( 30) hydrogen bonds : bond 0.03995 ( 463) hydrogen bonds : angle 5.53071 ( 1344) link_ALPHA1-3 : bond 0.01162 ( 2) link_ALPHA1-3 : angle 3.15825 ( 6) link_ALPHA1-6 : bond 0.00813 ( 3) link_ALPHA1-6 : angle 1.82208 ( 9) link_BETA1-2 : bond 0.00076 ( 1) link_BETA1-2 : angle 1.37247 ( 3) link_BETA1-4 : bond 0.01096 ( 17) link_BETA1-4 : angle 2.96792 ( 51) link_NAG-ASN : bond 0.01198 ( 10) link_NAG-ASN : angle 6.44277 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 84 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 546 MET cc_start: 0.8481 (mmt) cc_final: 0.8177 (mmp) REVERT: B 38 MET cc_start: 0.5761 (mmm) cc_final: 0.4920 (ptm) REVERT: E 11 MET cc_start: 0.7771 (ppp) cc_final: 0.7530 (ppp) REVERT: E 82 ASP cc_start: 0.8265 (m-30) cc_final: 0.7866 (m-30) REVERT: E 105 ASP cc_start: 0.8850 (t0) cc_final: 0.7704 (m-30) REVERT: E 108 ARG cc_start: 0.9338 (mtt180) cc_final: 0.9085 (mmm160) REVERT: E 145 TYR cc_start: 0.7208 (m-80) cc_final: 0.6780 (m-80) outliers start: 32 outliers final: 15 residues processed: 107 average time/residue: 0.1401 time to fit residues: 21.4103 Evaluate side-chains 93 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain A residue 568 ASN Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 121 TYR Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 440 TYR Chi-restraints excluded: chain C residue 1398 VAL Chi-restraints excluded: chain C residue 1450 THR Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 3 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 121 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 169 optimal weight: 0.4980 chunk 80 optimal weight: 0.5980 chunk 146 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 98 optimal weight: 6.9990 chunk 62 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 286 ASN B 322 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.085157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.056907 restraints weight = 64617.850| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 5.23 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.5573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14247 Z= 0.180 Angle : 0.715 23.129 19426 Z= 0.342 Chirality : 0.050 0.571 2241 Planarity : 0.004 0.046 2476 Dihedral : 8.262 73.481 2569 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.67 % Allowed : 11.00 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.19), residues: 1737 helix: 1.51 (0.35), residues: 215 sheet: 1.21 (0.21), residues: 598 loop : -0.08 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 149 TYR 0.019 0.002 TYR C1488 PHE 0.017 0.002 PHE A 187 TRP 0.015 0.001 TRP D 123 HIS 0.005 0.001 HIS B 301 Details of bonding type rmsd covalent geometry : bond 0.00395 (14199) covalent geometry : angle 0.66523 (19297) SS BOND : bond 0.00173 ( 15) SS BOND : angle 0.58863 ( 30) hydrogen bonds : bond 0.04031 ( 463) hydrogen bonds : angle 5.47278 ( 1344) link_ALPHA1-3 : bond 0.01100 ( 2) link_ALPHA1-3 : angle 3.06539 ( 6) link_ALPHA1-6 : bond 0.00773 ( 3) link_ALPHA1-6 : angle 1.86151 ( 9) link_BETA1-2 : bond 0.00203 ( 1) link_BETA1-2 : angle 1.24959 ( 3) link_BETA1-4 : bond 0.00777 ( 17) link_BETA1-4 : angle 2.71327 ( 51) link_NAG-ASN : bond 0.01102 ( 10) link_NAG-ASN : angle 5.53382 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 86 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 TYR cc_start: 0.8937 (OUTLIER) cc_final: 0.8190 (t80) REVERT: A 546 MET cc_start: 0.8420 (mmt) cc_final: 0.8114 (mmp) REVERT: B 38 MET cc_start: 0.5586 (mmm) cc_final: 0.4892 (ptm) REVERT: B 135 MET cc_start: 0.8386 (mmm) cc_final: 0.8029 (mmt) REVERT: B 150 MET cc_start: 0.7088 (ttp) cc_final: 0.6831 (ttp) REVERT: B 287 MET cc_start: 0.8572 (mtp) cc_final: 0.8307 (mtt) REVERT: C 1354 ILE cc_start: 0.5561 (OUTLIER) cc_final: 0.5089 (tp) REVERT: D 82 MET cc_start: 0.7984 (mpp) cc_final: 0.7198 (mpp) REVERT: D 100 TYR cc_start: 0.8220 (OUTLIER) cc_final: 0.7564 (t80) REVERT: D 116 ASP cc_start: 0.7935 (t0) cc_final: 0.7693 (t0) REVERT: D 117 TYR cc_start: 0.7922 (t80) cc_final: 0.7643 (m-80) REVERT: D 118 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7227 (pm20) REVERT: E 11 MET cc_start: 0.7722 (ppp) cc_final: 0.7379 (ppp) REVERT: E 85 THR cc_start: 0.8757 (OUTLIER) cc_final: 0.8345 (p) REVERT: E 105 ASP cc_start: 0.8770 (t0) cc_final: 0.7717 (m-30) REVERT: E 108 ARG cc_start: 0.9366 (mtt180) cc_final: 0.9155 (mmm160) REVERT: E 159 LYS cc_start: 0.7863 (mmtt) cc_final: 0.7622 (mttm) outliers start: 40 outliers final: 21 residues processed: 118 average time/residue: 0.1318 time to fit residues: 22.8614 Evaluate side-chains 104 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 78 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain A residue 568 ASN Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 440 TYR Chi-restraints excluded: chain C residue 1354 ILE Chi-restraints excluded: chain C residue 1398 VAL Chi-restraints excluded: chain C residue 1416 VAL Chi-restraints excluded: chain C residue 1429 THR Chi-restraints excluded: chain C residue 1450 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 100 TYR Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain E residue 134 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 101 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 138 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 62 optimal weight: 0.0030 chunk 61 optimal weight: 2.9990 chunk 143 optimal weight: 6.9990 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 3.9990 overall best weight: 1.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 GLN B 286 ASN E 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.083484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.055386 restraints weight = 64581.052| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 5.03 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.6431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 14247 Z= 0.204 Angle : 0.729 19.962 19426 Z= 0.355 Chirality : 0.050 0.624 2241 Planarity : 0.005 0.042 2476 Dihedral : 8.305 72.711 2567 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.27 % Allowed : 12.00 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.19), residues: 1737 helix: 1.50 (0.36), residues: 214 sheet: 1.03 (0.20), residues: 613 loop : -0.15 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C1448 TYR 0.020 0.002 TYR C1488 PHE 0.021 0.002 PHE B 264 TRP 0.033 0.002 TRP D 123 HIS 0.005 0.001 HIS A 587 Details of bonding type rmsd covalent geometry : bond 0.00465 (14199) covalent geometry : angle 0.68493 (19297) SS BOND : bond 0.00230 ( 15) SS BOND : angle 0.61020 ( 30) hydrogen bonds : bond 0.04076 ( 463) hydrogen bonds : angle 5.54556 ( 1344) link_ALPHA1-3 : bond 0.01108 ( 2) link_ALPHA1-3 : angle 3.10605 ( 6) link_ALPHA1-6 : bond 0.00725 ( 3) link_ALPHA1-6 : angle 1.96691 ( 9) link_BETA1-2 : bond 0.00126 ( 1) link_BETA1-2 : angle 1.46405 ( 3) link_BETA1-4 : bond 0.00908 ( 17) link_BETA1-4 : angle 2.72812 ( 51) link_NAG-ASN : bond 0.00639 ( 10) link_NAG-ASN : angle 5.05642 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 81 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 TYR cc_start: 0.9018 (OUTLIER) cc_final: 0.7898 (t80) REVERT: A 546 MET cc_start: 0.8436 (mmt) cc_final: 0.8146 (mmp) REVERT: B 38 MET cc_start: 0.5814 (mmm) cc_final: 0.5101 (ptm) REVERT: B 77 ASN cc_start: 0.8550 (p0) cc_final: 0.8231 (t0) REVERT: B 287 MET cc_start: 0.8457 (mtp) cc_final: 0.8216 (mtt) REVERT: C 1354 ILE cc_start: 0.6106 (OUTLIER) cc_final: 0.5769 (tp) REVERT: D 0 MET cc_start: 0.6497 (tpt) cc_final: 0.5591 (tpt) REVERT: D 100 TYR cc_start: 0.8420 (OUTLIER) cc_final: 0.7247 (t80) REVERT: E 78 MET cc_start: 0.6058 (mmt) cc_final: 0.5827 (mmt) REVERT: E 85 THR cc_start: 0.9031 (OUTLIER) cc_final: 0.8579 (p) REVERT: E 105 ASP cc_start: 0.8753 (t0) cc_final: 0.7736 (m-30) REVERT: E 159 LYS cc_start: 0.7920 (mmtt) cc_final: 0.7690 (mttm) outliers start: 34 outliers final: 27 residues processed: 107 average time/residue: 0.1341 time to fit residues: 20.9442 Evaluate side-chains 106 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 75 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain A residue 568 ASN Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 440 TYR Chi-restraints excluded: chain C residue 1283 LEU Chi-restraints excluded: chain C residue 1339 THR Chi-restraints excluded: chain C residue 1354 ILE Chi-restraints excluded: chain C residue 1394 VAL Chi-restraints excluded: chain C residue 1398 VAL Chi-restraints excluded: chain C residue 1416 VAL Chi-restraints excluded: chain C residue 1429 THR Chi-restraints excluded: chain C residue 1450 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 100 TYR Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 139 MET Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 133 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 145 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 147 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 chunk 96 optimal weight: 0.3980 chunk 66 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 84 optimal weight: 0.9990 chunk 152 optimal weight: 5.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 286 ASN ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.083229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.055126 restraints weight = 64605.296| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 5.05 r_work: 0.3355 rms_B_bonded: 5.03 restraints_weight: 2.0000 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.6883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14247 Z= 0.179 Angle : 0.697 19.102 19426 Z= 0.338 Chirality : 0.049 0.718 2241 Planarity : 0.005 0.066 2476 Dihedral : 8.198 71.690 2567 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.33 % Allowed : 12.33 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.19), residues: 1737 helix: 1.47 (0.35), residues: 208 sheet: 0.94 (0.20), residues: 611 loop : -0.18 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 108 TYR 0.024 0.002 TYR E 145 PHE 0.018 0.002 PHE B 264 TRP 0.041 0.002 TRP D 123 HIS 0.004 0.001 HIS B 292 Details of bonding type rmsd covalent geometry : bond 0.00411 (14199) covalent geometry : angle 0.65411 (19297) SS BOND : bond 0.00207 ( 15) SS BOND : angle 0.54582 ( 30) hydrogen bonds : bond 0.03900 ( 463) hydrogen bonds : angle 5.45567 ( 1344) link_ALPHA1-3 : bond 0.01066 ( 2) link_ALPHA1-3 : angle 3.12598 ( 6) link_ALPHA1-6 : bond 0.00750 ( 3) link_ALPHA1-6 : angle 2.01266 ( 9) link_BETA1-2 : bond 0.00241 ( 1) link_BETA1-2 : angle 1.46670 ( 3) link_BETA1-4 : bond 0.00842 ( 17) link_BETA1-4 : angle 2.69285 ( 51) link_NAG-ASN : bond 0.00642 ( 10) link_NAG-ASN : angle 4.80989 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 78 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 TYR cc_start: 0.9015 (OUTLIER) cc_final: 0.7516 (t80) REVERT: A 546 MET cc_start: 0.8485 (mmt) cc_final: 0.8218 (mmp) REVERT: B 38 MET cc_start: 0.5891 (mmm) cc_final: 0.5150 (ptm) REVERT: B 77 ASN cc_start: 0.8737 (p0) cc_final: 0.8396 (t0) REVERT: B 236 MET cc_start: 0.8125 (OUTLIER) cc_final: 0.7809 (tpp) REVERT: C 1354 ILE cc_start: 0.6241 (OUTLIER) cc_final: 0.5902 (tp) REVERT: D 0 MET cc_start: 0.6506 (tpt) cc_final: 0.5498 (tpt) REVERT: D 82 MET cc_start: 0.8483 (OUTLIER) cc_final: 0.7672 (mpp) REVERT: D 100 TYR cc_start: 0.8442 (OUTLIER) cc_final: 0.7195 (t80) REVERT: E 11 MET cc_start: 0.7978 (ptp) cc_final: 0.7576 (mpp) REVERT: E 85 THR cc_start: 0.9139 (OUTLIER) cc_final: 0.8678 (p) REVERT: E 104 LEU cc_start: 0.9509 (tt) cc_final: 0.9190 (tp) REVERT: E 105 ASP cc_start: 0.8792 (t0) cc_final: 0.7892 (m-30) REVERT: E 116 LYS cc_start: 0.9146 (pttt) cc_final: 0.8923 (mmmt) REVERT: E 152 ILE cc_start: 0.8565 (OUTLIER) cc_final: 0.8345 (mt) REVERT: E 159 LYS cc_start: 0.8002 (mmtt) cc_final: 0.7776 (mttm) outliers start: 35 outliers final: 26 residues processed: 107 average time/residue: 0.1339 time to fit residues: 21.1585 Evaluate side-chains 108 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 75 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 568 ASN Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 236 MET Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 440 TYR Chi-restraints excluded: chain C residue 1339 THR Chi-restraints excluded: chain C residue 1354 ILE Chi-restraints excluded: chain C residue 1375 VAL Chi-restraints excluded: chain C residue 1398 VAL Chi-restraints excluded: chain C residue 1416 VAL Chi-restraints excluded: chain C residue 1429 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 100 TYR Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 139 MET Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain E residue 152 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 57 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 53 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 65 optimal weight: 5.9990 chunk 155 optimal weight: 4.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.083071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.054774 restraints weight = 64391.015| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 5.24 r_work: 0.3350 rms_B_bonded: 5.19 restraints_weight: 2.0000 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.7164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14247 Z= 0.165 Angle : 0.680 18.351 19426 Z= 0.329 Chirality : 0.049 0.767 2241 Planarity : 0.004 0.041 2476 Dihedral : 8.117 70.773 2567 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.33 % Allowed : 12.13 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.19), residues: 1737 helix: 1.42 (0.36), residues: 209 sheet: 0.97 (0.20), residues: 605 loop : -0.24 (0.20), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 540 TYR 0.028 0.002 TYR E 145 PHE 0.019 0.002 PHE B 264 TRP 0.045 0.002 TRP D 123 HIS 0.004 0.001 HIS A 587 Details of bonding type rmsd covalent geometry : bond 0.00377 (14199) covalent geometry : angle 0.63917 (19297) SS BOND : bond 0.00199 ( 15) SS BOND : angle 0.53418 ( 30) hydrogen bonds : bond 0.03743 ( 463) hydrogen bonds : angle 5.39018 ( 1344) link_ALPHA1-3 : bond 0.01039 ( 2) link_ALPHA1-3 : angle 3.07656 ( 6) link_ALPHA1-6 : bond 0.00783 ( 3) link_ALPHA1-6 : angle 2.03157 ( 9) link_BETA1-2 : bond 0.00267 ( 1) link_BETA1-2 : angle 1.50225 ( 3) link_BETA1-4 : bond 0.00815 ( 17) link_BETA1-4 : angle 2.65010 ( 51) link_NAG-ASN : bond 0.00559 ( 10) link_NAG-ASN : angle 4.62381 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 77 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 TYR cc_start: 0.9035 (OUTLIER) cc_final: 0.7342 (t80) REVERT: A 546 MET cc_start: 0.8438 (mmt) cc_final: 0.8159 (mmp) REVERT: B 38 MET cc_start: 0.6056 (mmm) cc_final: 0.5365 (ptm) REVERT: B 77 ASN cc_start: 0.8786 (p0) cc_final: 0.8469 (t0) REVERT: B 440 TYR cc_start: 0.8081 (m-80) cc_final: 0.7042 (m-10) REVERT: C 1354 ILE cc_start: 0.6392 (OUTLIER) cc_final: 0.6177 (tp) REVERT: D 0 MET cc_start: 0.6395 (tpt) cc_final: 0.5454 (tpt) REVERT: D 82 MET cc_start: 0.8608 (OUTLIER) cc_final: 0.7782 (mpp) REVERT: D 100 TYR cc_start: 0.8486 (OUTLIER) cc_final: 0.7225 (t80) REVERT: E 11 MET cc_start: 0.8148 (ptp) cc_final: 0.7554 (mpp) REVERT: E 78 MET cc_start: 0.6355 (mmt) cc_final: 0.5969 (mmt) REVERT: E 85 THR cc_start: 0.9189 (OUTLIER) cc_final: 0.8713 (p) REVERT: E 104 LEU cc_start: 0.9519 (tt) cc_final: 0.9219 (tp) REVERT: E 105 ASP cc_start: 0.8751 (t0) cc_final: 0.7937 (m-30) REVERT: E 116 LYS cc_start: 0.9152 (pttt) cc_final: 0.8927 (mmmt) outliers start: 35 outliers final: 27 residues processed: 108 average time/residue: 0.1315 time to fit residues: 20.8373 Evaluate side-chains 106 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 74 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 568 ASN Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain C residue 1339 THR Chi-restraints excluded: chain C residue 1354 ILE Chi-restraints excluded: chain C residue 1375 VAL Chi-restraints excluded: chain C residue 1394 VAL Chi-restraints excluded: chain C residue 1398 VAL Chi-restraints excluded: chain C residue 1416 VAL Chi-restraints excluded: chain C residue 1429 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 100 TYR Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 133 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 146 optimal weight: 0.0770 chunk 80 optimal weight: 1.9990 chunk 126 optimal weight: 4.9990 chunk 158 optimal weight: 0.8980 chunk 100 optimal weight: 6.9990 chunk 62 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 57 optimal weight: 0.0030 chunk 117 optimal weight: 0.4980 chunk 30 optimal weight: 1.9990 chunk 172 optimal weight: 5.9990 overall best weight: 0.4548 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.084005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.055847 restraints weight = 64396.604| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 5.15 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.7272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14247 Z= 0.115 Angle : 0.656 17.659 19426 Z= 0.312 Chirality : 0.049 0.836 2241 Planarity : 0.004 0.040 2476 Dihedral : 7.873 68.301 2565 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.67 % Allowed : 12.93 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.20), residues: 1737 helix: 1.44 (0.36), residues: 209 sheet: 1.04 (0.20), residues: 608 loop : -0.16 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 7 TYR 0.024 0.001 TYR E 145 PHE 0.015 0.001 PHE A 465 TRP 0.028 0.001 TRP D 123 HIS 0.004 0.001 HIS B 301 Details of bonding type rmsd covalent geometry : bond 0.00256 (14199) covalent geometry : angle 0.61605 (19297) SS BOND : bond 0.00163 ( 15) SS BOND : angle 0.47889 ( 30) hydrogen bonds : bond 0.03487 ( 463) hydrogen bonds : angle 5.20446 ( 1344) link_ALPHA1-3 : bond 0.01028 ( 2) link_ALPHA1-3 : angle 3.10367 ( 6) link_ALPHA1-6 : bond 0.00861 ( 3) link_ALPHA1-6 : angle 1.97803 ( 9) link_BETA1-2 : bond 0.00390 ( 1) link_BETA1-2 : angle 1.56691 ( 3) link_BETA1-4 : bond 0.00778 ( 17) link_BETA1-4 : angle 2.60923 ( 51) link_NAG-ASN : bond 0.00497 ( 10) link_NAG-ASN : angle 4.39456 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 74 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 TYR cc_start: 0.8893 (OUTLIER) cc_final: 0.7034 (t80) REVERT: A 546 MET cc_start: 0.8445 (mmt) cc_final: 0.8171 (mmp) REVERT: B 38 MET cc_start: 0.6028 (mmm) cc_final: 0.5403 (ptm) REVERT: B 77 ASN cc_start: 0.8615 (p0) cc_final: 0.8333 (t0) REVERT: B 440 TYR cc_start: 0.7928 (m-80) cc_final: 0.6916 (m-10) REVERT: D 0 MET cc_start: 0.6162 (tpt) cc_final: 0.5273 (tpt) REVERT: D 81 GLN cc_start: 0.7913 (tp40) cc_final: 0.7602 (tp40) REVERT: D 82 MET cc_start: 0.8468 (OUTLIER) cc_final: 0.7856 (mpp) REVERT: D 100 TYR cc_start: 0.8362 (OUTLIER) cc_final: 0.7025 (t80) REVERT: E 85 THR cc_start: 0.9182 (OUTLIER) cc_final: 0.8718 (p) REVERT: E 104 LEU cc_start: 0.9459 (tt) cc_final: 0.9133 (tp) REVERT: E 105 ASP cc_start: 0.8737 (t0) cc_final: 0.7885 (m-30) REVERT: E 113 GLU cc_start: 0.8663 (tm-30) cc_final: 0.8448 (tm-30) outliers start: 25 outliers final: 19 residues processed: 96 average time/residue: 0.1388 time to fit residues: 19.3364 Evaluate side-chains 90 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 67 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain A residue 568 ASN Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain C residue 1322 ARG Chi-restraints excluded: chain C residue 1339 THR Chi-restraints excluded: chain C residue 1375 VAL Chi-restraints excluded: chain C residue 1394 VAL Chi-restraints excluded: chain C residue 1398 VAL Chi-restraints excluded: chain C residue 1416 VAL Chi-restraints excluded: chain C residue 1429 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 100 TYR Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 133 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 94 optimal weight: 1.9990 chunk 121 optimal weight: 9.9990 chunk 154 optimal weight: 4.9990 chunk 146 optimal weight: 0.5980 chunk 156 optimal weight: 5.9990 chunk 79 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 65 optimal weight: 10.0000 chunk 132 optimal weight: 6.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 143 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.082950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.054693 restraints weight = 64315.933| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 5.27 r_work: 0.3351 rms_B_bonded: 5.24 restraints_weight: 2.0000 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.7582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14247 Z= 0.160 Angle : 0.694 17.326 19426 Z= 0.334 Chirality : 0.050 0.882 2241 Planarity : 0.004 0.039 2476 Dihedral : 8.024 67.981 2565 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.53 % Allowed : 13.20 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.20), residues: 1737 helix: 1.37 (0.36), residues: 210 sheet: 1.01 (0.20), residues: 604 loop : -0.24 (0.20), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 540 TYR 0.042 0.002 TYR E 145 PHE 0.018 0.001 PHE B 264 TRP 0.043 0.002 TRP D 123 HIS 0.006 0.001 HIS B 301 Details of bonding type rmsd covalent geometry : bond 0.00366 (14199) covalent geometry : angle 0.65841 (19297) SS BOND : bond 0.00184 ( 15) SS BOND : angle 0.50205 ( 30) hydrogen bonds : bond 0.03711 ( 463) hydrogen bonds : angle 5.30032 ( 1344) link_ALPHA1-3 : bond 0.00982 ( 2) link_ALPHA1-3 : angle 2.94497 ( 6) link_ALPHA1-6 : bond 0.00813 ( 3) link_ALPHA1-6 : angle 2.07746 ( 9) link_BETA1-2 : bond 0.00306 ( 1) link_BETA1-2 : angle 1.52865 ( 3) link_BETA1-4 : bond 0.00744 ( 17) link_BETA1-4 : angle 2.54149 ( 51) link_NAG-ASN : bond 0.00493 ( 10) link_NAG-ASN : angle 4.33625 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 70 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 TYR cc_start: 0.9055 (OUTLIER) cc_final: 0.7294 (t80) REVERT: A 310 MET cc_start: 0.7687 (mtt) cc_final: 0.7372 (mtt) REVERT: A 546 MET cc_start: 0.8447 (mmt) cc_final: 0.8178 (mmp) REVERT: B 38 MET cc_start: 0.6115 (mmm) cc_final: 0.5408 (ptm) REVERT: B 77 ASN cc_start: 0.8871 (p0) cc_final: 0.8424 (t0) REVERT: B 440 TYR cc_start: 0.7754 (m-80) cc_final: 0.6988 (m-10) REVERT: D 0 MET cc_start: 0.6313 (tpt) cc_final: 0.5414 (tpt) REVERT: D 100 TYR cc_start: 0.8531 (OUTLIER) cc_final: 0.7236 (t80) REVERT: E 85 THR cc_start: 0.9238 (OUTLIER) cc_final: 0.8753 (p) REVERT: E 104 LEU cc_start: 0.9514 (tt) cc_final: 0.9272 (tp) REVERT: E 105 ASP cc_start: 0.8784 (t0) cc_final: 0.7963 (m-30) REVERT: E 113 GLU cc_start: 0.8428 (tm-30) cc_final: 0.7951 (pt0) REVERT: E 114 PHE cc_start: 0.8547 (m-80) cc_final: 0.8299 (m-80) outliers start: 23 outliers final: 19 residues processed: 91 average time/residue: 0.1239 time to fit residues: 16.5326 Evaluate side-chains 90 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 68 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 568 ASN Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain C residue 1322 ARG Chi-restraints excluded: chain C residue 1339 THR Chi-restraints excluded: chain C residue 1375 VAL Chi-restraints excluded: chain C residue 1394 VAL Chi-restraints excluded: chain C residue 1398 VAL Chi-restraints excluded: chain C residue 1429 THR Chi-restraints excluded: chain C residue 1486 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 100 TYR Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 85 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 63 optimal weight: 9.9990 chunk 94 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 164 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 116 optimal weight: 7.9990 chunk 113 optimal weight: 0.9990 chunk 115 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 139 optimal weight: 0.6980 chunk 170 optimal weight: 0.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.082545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.054306 restraints weight = 64400.248| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 5.20 r_work: 0.3342 rms_B_bonded: 5.20 restraints_weight: 2.0000 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.7969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14247 Z= 0.163 Angle : 0.694 16.510 19426 Z= 0.336 Chirality : 0.051 0.959 2241 Planarity : 0.004 0.044 2476 Dihedral : 8.051 62.185 2565 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.53 % Allowed : 13.40 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.20), residues: 1737 helix: 1.43 (0.36), residues: 209 sheet: 0.91 (0.20), residues: 613 loop : -0.29 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 7 TYR 0.035 0.002 TYR D 150 PHE 0.019 0.001 PHE B 264 TRP 0.027 0.002 TRP D 123 HIS 0.005 0.001 HIS B 301 Details of bonding type rmsd covalent geometry : bond 0.00372 (14199) covalent geometry : angle 0.65927 (19297) SS BOND : bond 0.00193 ( 15) SS BOND : angle 0.52312 ( 30) hydrogen bonds : bond 0.03852 ( 463) hydrogen bonds : angle 5.27013 ( 1344) link_ALPHA1-3 : bond 0.00973 ( 2) link_ALPHA1-3 : angle 3.07314 ( 6) link_ALPHA1-6 : bond 0.00771 ( 3) link_ALPHA1-6 : angle 2.32497 ( 9) link_BETA1-2 : bond 0.00347 ( 1) link_BETA1-2 : angle 1.68976 ( 3) link_BETA1-4 : bond 0.00673 ( 17) link_BETA1-4 : angle 2.49292 ( 51) link_NAG-ASN : bond 0.00475 ( 10) link_NAG-ASN : angle 4.20463 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7608.59 seconds wall clock time: 129 minutes 38.07 seconds (7778.07 seconds total)