Starting phenix.real_space_refine on Fri Jul 3 12:32:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7nwl_12634/07_2026/7nwl_12634.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nwl_12634/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7nwl_12634/07_2026/7nwl_12634.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7nwl_12634/07_2026/7nwl_12634.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7nwl_12634/07_2026/7nwl_12634.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nwl_12634/07_2026/7nwl_12634.map" model { file = "/net/cci-nas-00/data/ceres_data/7nwl_12634/07_2026/7nwl_12634.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nwl_12634/07_2026/7nwl_12634.cif" } 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-6108/lib/python3.11/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 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 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 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 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 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 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 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 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 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 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: 3.56, per 1000 atoms: 0.26 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: 1.59 Conformation dependent library (CDL) restraints added in 753.2 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: 0.48 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: 3.03 Time building geometry restraints manager: 2.05 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 - 17.82: 7919 17.82 - 35.64: 340 35.64 - 53.46: 42 53.46 - 71.28: 16 71.28 - 89.10: 2 Dihedral angle restraints: 8319 sinusoidal: 3309 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 8316 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: 4.270 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: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 15.330 Find NCS groups from input model: 0.090 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:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6585 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 : 9.428 70.845 5080 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/Z covalent geometry : bond 0.01348 / 1.03 (14199) covalent geometry : angle 1.47510 / 1.11 (19297) SS BOND : bond 0.21324 / 10.45 ( 15) SS BOND : angle 3.81532 / 2.25 ( 30) hydrogen bonds : bond 0.27431 / 18.95 ( 463) hydrogen bonds : angle 9.46421 / 6.74 ( 1344) link_ALPHA1-3 : bond 0.00304 / 0.15 ( 2) link_ALPHA1-3 : angle 3.32366 / 1.98 ( 6) link_ALPHA1-6 : bond 0.01205 / 0.57 ( 3) link_ALPHA1-6 : angle 5.09949 / 3.00 ( 9) link_BETA1-2 : bond 0.00241 / 0.13 ( 1) link_BETA1-2 : angle 1.34176 / 1.06 ( 3) link_BETA1-4 : bond 0.00461 / 0.28 ( 17) link_BETA1-4 : angle 2.43172 / 1.73 ( 51) link_NAG-ASN : bond 0.01617 / 0.70 ( 10) link_NAG-ASN : angle 5.66558 / 3.71 ( 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 : 0.575 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: 0.1471 time to fit residues: 44.5876 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 : 0.549 ------------------------------------------------------------------------------- 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... 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 143 GLN E 150 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.089614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.061746 restraints weight = 64056.894| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 5.23 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3682 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3682 r_free = 0.3682 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3682 r_free = 0.3682 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3682 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.3066 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= 0.218 Angle : 0.854 14.658 19426 Z= 0.409 Chirality : 0.053 0.455 2241 Planarity : 0.005 0.048 2476 Dihedral : 4.847 54.071 1912 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.07 % Allowed : 8.80 % 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: 1.07 (0.20), residues: 1737 helix: 2.06 (0.34), residues: 213 sheet: 1.49 (0.21), residues: 594 loop : -0.11 (0.19), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 71 TYR 0.026 0.002 TYR C1488 PHE 0.020 0.002 PHE B 264 TRP 0.012 0.002 TRP E 118 HIS 0.005 0.001 HIS B 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.22 (14199) covalent geometry : angle 0.83252 / 0.40 (19297) SS BOND : bond 0.00561 / 0.31 ( 15) SS BOND : angle 0.90733 / 0.61 ( 30) hydrogen bonds : bond 0.05561 / 3.73 ( 463) hydrogen bonds : angle 6.50275 / 4.60 ( 1344) link_ALPHA1-3 : bond 0.00743 / 0.37 ( 2) link_ALPHA1-3 : angle 2.62395 / 1.65 ( 6) link_ALPHA1-6 : bond 0.01247 / 0.60 ( 3) link_ALPHA1-6 : angle 1.56802 / 1.01 ( 9) link_BETA1-2 : bond 0.00430 / 0.23 ( 1) link_BETA1-2 : angle 2.04155 / 1.51 ( 3) link_BETA1-4 : bond 0.01065 / 0.61 ( 17) link_BETA1-4 : angle 2.87316 / 1.89 ( 51) link_NAG-ASN : bond 0.00585 / 0.25 ( 10) link_NAG-ASN : angle 3.08403 / 2.06 ( 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 137 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 106 time to evaluate : 0.544 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 546 MET cc_start: 0.8397 (mmt) cc_final: 0.8163 (mmp) REVERT: D 20 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8265 (mm) REVERT: D 110 THR cc_start: 0.8623 (p) cc_final: 0.8409 (t) REVERT: E 5 THR cc_start: 0.8135 (OUTLIER) cc_final: 0.7820 (p) REVERT: E 78 MET cc_start: 0.6853 (mmt) cc_final: 0.6349 (mmt) REVERT: E 113 GLU cc_start: 0.8384 (pt0) cc_final: 0.8183 (tm-30) outliers start: 31 outliers final: 15 residues processed: 132 average time/residue: 0.1379 time to fit residues: 26.2425 Evaluate side-chains 93 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 0.645 ------------------------------------------------------------------------------- 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 20 LEU Chi-restraints excluded: chain D residue 29 PHE Chi-restraints excluded: chain D residue 109 VAL 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: 0.9990 chunk 136 optimal weight: 0.0870 chunk 121 optimal weight: 5.9990 chunk 144 optimal weight: 0.7980 chunk 164 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 132 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 124 optimal weight: 0.7980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 216 GLN ** A 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1413 GLN D 141 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.088367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.060580 restraints weight = 64454.087| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 5.15 r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3657 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3657 r_free = 0.3657 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3657 r_free = 0.3657 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3657 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14247 Z= 0.153 Angle : 0.701 9.496 19426 Z= 0.341 Chirality : 0.048 0.255 2241 Planarity : 0.005 0.074 2476 Dihedral : 4.435 48.906 1904 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.93 % Allowed : 10.27 % Favored : 87.80 % 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 (0.20), residues: 1737 helix: 1.82 (0.35), residues: 212 sheet: 1.36 (0.21), residues: 591 loop : -0.03 (0.19), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C1322 TYR 0.025 0.002 TYR C1488 PHE 0.015 0.002 PHE B 33 TRP 0.017 0.001 TRP E 118 HIS 0.005 0.001 HIS D 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (14199) covalent geometry : angle 0.68221 / 0.34 (19297) SS BOND : bond 0.00232 / 0.15 ( 15) SS BOND : angle 0.70944 / 0.45 ( 30) hydrogen bonds : bond 0.04462 / 2.99 ( 463) hydrogen bonds : angle 5.76059 / 4.07 ( 1344) link_ALPHA1-3 : bond 0.00624 / 0.33 ( 2) link_ALPHA1-3 : angle 2.62731 / 1.74 ( 6) link_ALPHA1-6 : bond 0.00661 / 0.33 ( 3) link_ALPHA1-6 : angle 1.50687 / 0.98 ( 9) link_BETA1-2 : bond 0.00240 / 0.13 ( 1) link_BETA1-2 : angle 1.02418 / 0.62 ( 3) link_BETA1-4 : bond 0.00792 / 0.52 ( 17) link_BETA1-4 : angle 2.43228 / 1.55 ( 51) link_NAG-ASN : bond 0.00268 / 0.12 ( 10) link_NAG-ASN : angle 2.50651 / 1.67 ( 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 116 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 87 time to evaluate : 0.551 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: A 546 MET cc_start: 0.8369 (mmt) cc_final: 0.8059 (mmp) REVERT: B 38 MET cc_start: 0.5696 (mmm) cc_final: 0.4805 (ptm) REVERT: D 20 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8424 (mm) REVERT: D 117 TYR cc_start: 0.8514 (t80) cc_final: 0.8241 (m-80) REVERT: E 78 MET cc_start: 0.6344 (mmp) cc_final: 0.6111 (mmt) REVERT: E 148 LYS cc_start: 0.8753 (ptpt) cc_final: 0.8508 (ptpt) REVERT: E 159 LYS cc_start: 0.7733 (mmtt) cc_final: 0.7258 (mttm) outliers start: 29 outliers final: 16 residues processed: 106 average time/residue: 0.1318 time to fit residues: 20.5486 Evaluate side-chains 92 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 499 ILE 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 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 118 GLU Chi-restraints excluded: chain D residue 150 TYR Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 5 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 128 optimal weight: 0.5980 chunk 158 optimal weight: 0.0270 chunk 26 optimal weight: 0.6980 chunk 62 optimal weight: 8.9990 chunk 164 optimal weight: 4.9990 chunk 105 optimal weight: 0.7980 chunk 166 optimal weight: 0.8980 chunk 68 optimal weight: 9.9990 chunk 86 optimal weight: 0.0770 chunk 48 optimal weight: 10.0000 chunk 129 optimal weight: 2.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 494 HIS B 286 ASN ** B 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.088059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.060510 restraints weight = 64291.506| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 4.79 r_work: 0.3519 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.4505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 14247 Z= 0.132 Angle : 0.685 19.821 19426 Z= 0.317 Chirality : 0.048 0.412 2241 Planarity : 0.004 0.045 2476 Dihedral : 4.190 48.197 1902 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.93 % Allowed : 10.87 % Favored : 87.20 % 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: 1.02 (0.19), residues: 1737 helix: 1.72 (0.35), residues: 213 sheet: 1.37 (0.21), residues: 585 loop : 0.03 (0.19), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C1322 TYR 0.021 0.001 TYR E 145 PHE 0.012 0.001 PHE A 569 TRP 0.018 0.001 TRP D 123 HIS 0.006 0.001 HIS B 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (14199) covalent geometry : angle 0.63231 / 0.30 (19297) SS BOND : bond 0.00155 / 0.10 ( 15) SS BOND : angle 0.57152 / 0.36 ( 30) hydrogen bonds : bond 0.03832 / 2.54 ( 463) hydrogen bonds : angle 5.43116 / 3.84 ( 1344) link_ALPHA1-3 : bond 0.00660 / 0.35 ( 2) link_ALPHA1-3 : angle 2.53210 / 1.65 ( 6) link_ALPHA1-6 : bond 0.00640 / 0.32 ( 3) link_ALPHA1-6 : angle 1.49915 / 1.00 ( 9) link_BETA1-2 : bond 0.00176 / 0.09 ( 1) link_BETA1-2 : angle 1.29209 / 0.77 ( 3) link_BETA1-4 : bond 0.01524 / 0.65 ( 17) link_BETA1-4 : angle 2.81409 / 1.95 ( 51) link_NAG-ASN : bond 0.00432 / 0.19 ( 10) link_NAG-ASN : angle 5.57303 / 3.09 ( 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 107 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 78 time to evaluate : 0.534 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: B 38 MET cc_start: 0.5757 (mmm) cc_final: 0.4886 (ptm) REVERT: D 20 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8730 (mm) REVERT: D 100 MET cc_start: 0.8891 (mtm) cc_final: 0.8262 (mtm) REVERT: E 78 MET cc_start: 0.5998 (mmp) cc_final: 0.5536 (mmt) REVERT: E 85 THR cc_start: 0.8473 (OUTLIER) cc_final: 0.8270 (p) REVERT: E 105 ASP cc_start: 0.8895 (t0) cc_final: 0.7903 (m-30) REVERT: E 159 LYS cc_start: 0.7764 (mmtt) cc_final: 0.7464 (mttm) outliers start: 29 outliers final: 17 residues processed: 99 average time/residue: 0.1381 time to fit residues: 19.7239 Evaluate side-chains 92 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 262 VAL 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 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 1217 TYR 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 D residue 150 TYR Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 85 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 121 optimal weight: 10.0000 chunk 134 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 169 optimal weight: 6.9990 chunk 80 optimal weight: 0.7980 chunk 146 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 62 optimal weight: 9.9990 chunk 39 optimal weight: 0.0020 overall best weight: 0.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 322 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.086277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.058167 restraints weight = 64626.301| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 5.14 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.5176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14247 Z= 0.161 Angle : 0.700 22.812 19426 Z= 0.334 Chirality : 0.047 0.497 2241 Planarity : 0.004 0.049 2476 Dihedral : 4.298 49.116 1902 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.40 % Allowed : 11.27 % 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: 0.88 (0.19), residues: 1737 helix: 1.50 (0.35), residues: 214 sheet: 1.29 (0.21), residues: 587 loop : -0.05 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 7 TYR 0.019 0.002 TYR C1488 PHE 0.017 0.002 PHE B 264 TRP 0.017 0.001 TRP E 118 HIS 0.004 0.001 HIS B 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (14199) covalent geometry : angle 0.65105 / 0.32 (19297) SS BOND : bond 0.00186 / 0.12 ( 15) SS BOND : angle 0.56773 / 0.36 ( 30) hydrogen bonds : bond 0.03878 / 2.61 ( 463) hydrogen bonds : angle 5.41830 / 3.83 ( 1344) link_ALPHA1-3 : bond 0.00606 / 0.32 ( 2) link_ALPHA1-3 : angle 2.46805 / 1.64 ( 6) link_ALPHA1-6 : bond 0.00531 / 0.26 ( 3) link_ALPHA1-6 : angle 1.62533 / 1.06 ( 9) link_BETA1-2 : bond 0.00136 / 0.07 ( 1) link_BETA1-2 : angle 1.27355 / 0.75 ( 3) link_BETA1-4 : bond 0.00877 / 0.45 ( 17) link_BETA1-4 : angle 2.54799 / 1.73 ( 51) link_NAG-ASN : bond 0.00699 / 0.31 ( 10) link_NAG-ASN : angle 5.54950 / 3.39 ( 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 115 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 79 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 546 MET cc_start: 0.8840 (mmm) cc_final: 0.8638 (mmp) REVERT: B 38 MET cc_start: 0.5664 (mmm) cc_final: 0.4927 (ptm) REVERT: B 135 MET cc_start: 0.8432 (mmm) cc_final: 0.8116 (mmt) REVERT: B 287 MET cc_start: 0.8440 (mtp) cc_final: 0.8209 (mtt) REVERT: C 1354 ILE cc_start: 0.5325 (OUTLIER) cc_final: 0.4850 (tp) REVERT: D 20 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8685 (mm) REVERT: D 100 TYR cc_start: 0.8027 (OUTLIER) cc_final: 0.7813 (t80) REVERT: D 117 TYR cc_start: 0.8430 (t80) cc_final: 0.8142 (m-80) REVERT: E 78 MET cc_start: 0.6721 (mmp) cc_final: 0.6276 (mmt) REVERT: E 85 THR cc_start: 0.8672 (OUTLIER) cc_final: 0.8306 (p) REVERT: E 105 ASP cc_start: 0.8877 (t0) cc_final: 0.7814 (m-30) REVERT: E 159 LYS cc_start: 0.7742 (mmtt) cc_final: 0.7438 (mttm) outliers start: 36 outliers final: 21 residues processed: 109 average time/residue: 0.1313 time to fit residues: 21.2229 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 : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 286 ASN Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 440 TYR Chi-restraints excluded: chain C residue 1217 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 20 LEU 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 101 optimal weight: 0.6980 chunk 127 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 138 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 62 optimal weight: 10.0000 chunk 61 optimal weight: 4.9990 chunk 143 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 GLN E 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.083272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.054782 restraints weight = 64643.393| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 5.31 r_work: 0.3350 rms_B_bonded: 5.24 restraints_weight: 2.0000 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.6520 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= 0.223 Angle : 0.771 19.771 19426 Z= 0.380 Chirality : 0.050 0.600 2241 Planarity : 0.005 0.042 2476 Dihedral : 4.635 32.446 1898 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.40 % Allowed : 12.07 % 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: 0.63 (0.20), residues: 1737 helix: 1.28 (0.36), residues: 211 sheet: 1.07 (0.21), residues: 604 loop : -0.18 (0.20), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 7 TYR 0.024 0.002 TYR A 284 PHE 0.026 0.002 PHE B 264 TRP 0.034 0.002 TRP D 123 HIS 0.006 0.001 HIS A 587 Details of bonding type rmsd/Z covalent geometry : bond 0.00513 / 0.22 (14199) covalent geometry : angle 0.73237 / 0.37 (19297) SS BOND : bond 0.00250 / 0.15 ( 15) SS BOND : angle 0.68222 / 0.46 ( 30) hydrogen bonds : bond 0.04440 / 2.99 ( 463) hydrogen bonds : angle 5.69596 / 4.05 ( 1344) link_ALPHA1-3 : bond 0.00560 / 0.29 ( 2) link_ALPHA1-3 : angle 2.51714 / 1.66 ( 6) link_ALPHA1-6 : bond 0.00428 / 0.22 ( 3) link_ALPHA1-6 : angle 1.70456 / 1.10 ( 9) link_BETA1-2 : bond 0.00067 / 0.04 ( 1) link_BETA1-2 : angle 1.56586 / 0.94 ( 3) link_BETA1-4 : bond 0.00705 / 0.35 ( 17) link_BETA1-4 : angle 2.67578 / 1.83 ( 51) link_NAG-ASN : bond 0.00660 / 0.32 ( 10) link_NAG-ASN : angle 5.03322 / 3.14 ( 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 110 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 74 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 TYR cc_start: 0.8998 (OUTLIER) cc_final: 0.8054 (t80) REVERT: B 38 MET cc_start: 0.5902 (mmm) cc_final: 0.5147 (ptm) REVERT: B 77 ASN cc_start: 0.8759 (p0) cc_final: 0.8345 (t0) REVERT: B 236 MET cc_start: 0.8158 (tpp) cc_final: 0.7918 (tpp) REVERT: C 1354 ILE cc_start: 0.6105 (OUTLIER) cc_final: 0.5748 (tp) REVERT: D 0 MET cc_start: 0.6914 (tpt) cc_final: 0.5800 (tpt) REVERT: D 20 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8535 (mm) REVERT: D 100 TYR cc_start: 0.8507 (OUTLIER) cc_final: 0.7402 (t80) REVERT: D 117 TYR cc_start: 0.8139 (t80) cc_final: 0.7798 (m-80) REVERT: D 150 TYR cc_start: 0.7379 (m-80) cc_final: 0.7101 (m-10) REVERT: E 78 MET cc_start: 0.6463 (mmp) cc_final: 0.6093 (mmt) REVERT: E 85 THR cc_start: 0.9059 (OUTLIER) cc_final: 0.8598 (p) REVERT: E 105 ASP cc_start: 0.8914 (t0) cc_final: 0.7855 (m-30) REVERT: E 134 MET cc_start: 0.8436 (OUTLIER) cc_final: 0.8212 (mpp) REVERT: E 159 LYS cc_start: 0.7903 (mmtt) cc_final: 0.7671 (mttm) outliers start: 36 outliers final: 23 residues processed: 104 average time/residue: 0.1145 time to fit residues: 17.7598 Evaluate side-chains 97 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 68 time to evaluate : 0.337 ------------------------------------------------------------------------------- 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 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 244 LEU Chi-restraints excluded: chain B residue 273 ILE 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 1394 VAL Chi-restraints excluded: chain C residue 1398 VAL Chi-restraints excluded: chain C residue 1429 THR Chi-restraints excluded: chain C residue 1450 THR Chi-restraints excluded: chain D residue 20 LEU 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 E residue 3 VAL Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 134 MET Chi-restraints excluded: chain E residue 147 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 145 optimal weight: 3.9990 chunk 140 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 147 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 152 optimal weight: 9.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 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 = 0.4275 r_free = 0.4275 target = 0.082958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.054782 restraints weight = 64673.304| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 4.94 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.7036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 14247 Z= 0.198 Angle : 0.703 18.731 19426 Z= 0.343 Chirality : 0.049 0.698 2241 Planarity : 0.005 0.074 2476 Dihedral : 4.472 30.949 1898 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.27 % Allowed : 12.27 % Favored : 85.47 % 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: 0.55 (0.20), residues: 1737 helix: 1.36 (0.35), residues: 209 sheet: 0.87 (0.20), residues: 617 loop : -0.18 (0.20), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 7 TYR 0.020 0.002 TYR C1488 PHE 0.021 0.002 PHE B 264 TRP 0.030 0.002 TRP D 123 HIS 0.003 0.001 HIS B 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.20 (14199) covalent geometry : angle 0.66461 / 0.34 (19297) SS BOND : bond 0.00237 / 0.15 ( 15) SS BOND : angle 0.58580 / 0.41 ( 30) hydrogen bonds : bond 0.04097 / 2.77 ( 463) hydrogen bonds : angle 5.53058 / 3.94 ( 1344) link_ALPHA1-3 : bond 0.00561 / 0.29 ( 2) link_ALPHA1-3 : angle 2.57164 / 1.70 ( 6) link_ALPHA1-6 : bond 0.00470 / 0.24 ( 3) link_ALPHA1-6 : angle 1.72055 / 1.11 ( 9) link_BETA1-2 : bond 0.00197 / 0.10 ( 1) link_BETA1-2 : angle 1.56562 / 0.96 ( 3) link_BETA1-4 : bond 0.00759 / 0.42 ( 17) link_BETA1-4 : angle 2.54335 / 1.70 ( 51) link_NAG-ASN : bond 0.00598 / 0.27 ( 10) link_NAG-ASN : angle 4.74184 / 3.01 ( 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 103 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 69 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 TYR cc_start: 0.8958 (OUTLIER) cc_final: 0.7284 (t80) REVERT: B 38 MET cc_start: 0.6072 (mmm) cc_final: 0.5429 (ptm) REVERT: B 77 ASN cc_start: 0.8729 (p0) cc_final: 0.8247 (t0) REVERT: B 440 TYR cc_start: 0.7896 (OUTLIER) cc_final: 0.6914 (m-10) REVERT: C 1354 ILE cc_start: 0.6473 (OUTLIER) cc_final: 0.6146 (tp) REVERT: D 0 MET cc_start: 0.6842 (tpt) cc_final: 0.5654 (tpt) REVERT: D 20 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8311 (mm) REVERT: D 100 TYR cc_start: 0.8538 (OUTLIER) cc_final: 0.7260 (t80) REVERT: D 117 TYR cc_start: 0.7962 (t80) cc_final: 0.7431 (m-80) REVERT: D 150 TYR cc_start: 0.7241 (m-80) cc_final: 0.6969 (m-10) REVERT: E 11 MET cc_start: 0.8618 (mpp) cc_final: 0.8357 (mpp) REVERT: E 78 MET cc_start: 0.6910 (mmp) cc_final: 0.6462 (mmt) REVERT: E 85 THR cc_start: 0.9247 (OUTLIER) cc_final: 0.8772 (p) REVERT: E 159 LYS cc_start: 0.8137 (mmtt) cc_final: 0.7785 (mttm) outliers start: 34 outliers final: 23 residues processed: 96 average time/residue: 0.1159 time to fit residues: 16.5229 Evaluate side-chains 97 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 68 time to evaluate : 0.514 ------------------------------------------------------------------------------- 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 548 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 273 ILE Chi-restraints excluded: chain B residue 274 VAL 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 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 20 LEU 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 139 MET Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 147 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 57 optimal weight: 0.0170 chunk 74 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 53 optimal weight: 7.9990 chunk 41 optimal weight: 0.8980 chunk 132 optimal weight: 0.4980 chunk 26 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 65 optimal weight: 5.9990 chunk 155 optimal weight: 4.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4295 r_free = 0.4295 target = 0.083867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.055682 restraints weight = 63966.111| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 5.21 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.7177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14247 Z= 0.123 Angle : 0.648 17.749 19426 Z= 0.311 Chirality : 0.048 0.760 2241 Planarity : 0.004 0.040 2476 Dihedral : 4.158 30.612 1898 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.53 % Allowed : 12.87 % Favored : 85.60 % 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: 0.71 (0.20), residues: 1737 helix: 1.59 (0.36), residues: 211 sheet: 1.03 (0.20), residues: 609 loop : -0.14 (0.20), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 7 TYR 0.016 0.001 TYR C1217 PHE 0.012 0.001 PHE B 264 TRP 0.019 0.001 TRP E 118 HIS 0.005 0.001 HIS B 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (14199) covalent geometry : angle 0.60894 / 0.30 (19297) SS BOND : bond 0.00178 / 0.11 ( 15) SS BOND : angle 0.49259 / 0.33 ( 30) hydrogen bonds : bond 0.03529 / 2.35 ( 463) hydrogen bonds : angle 5.26108 / 3.74 ( 1344) link_ALPHA1-3 : bond 0.00553 / 0.29 ( 2) link_ALPHA1-3 : angle 2.56586 / 1.69 ( 6) link_ALPHA1-6 : bond 0.00564 / 0.28 ( 3) link_ALPHA1-6 : angle 1.62298 / 1.06 ( 9) link_BETA1-2 : bond 0.00372 / 0.20 ( 1) link_BETA1-2 : angle 1.62003 / 0.97 ( 3) link_BETA1-4 : bond 0.00765 / 0.43 ( 17) link_BETA1-4 : angle 2.52151 / 1.70 ( 51) link_NAG-ASN : bond 0.00520 / 0.23 ( 10) link_NAG-ASN : angle 4.46000 / 2.85 ( 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 90 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 67 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 TYR cc_start: 0.8915 (OUTLIER) cc_final: 0.7131 (t80) REVERT: A 310 MET cc_start: 0.8186 (mtp) cc_final: 0.7853 (mtt) REVERT: B 38 MET cc_start: 0.6029 (mmm) cc_final: 0.5407 (ptm) REVERT: B 77 ASN cc_start: 0.8664 (p0) cc_final: 0.8325 (t0) REVERT: B 135 MET cc_start: 0.8438 (mmm) cc_final: 0.8199 (mmm) REVERT: B 440 TYR cc_start: 0.7975 (OUTLIER) cc_final: 0.6914 (m-10) REVERT: D 0 MET cc_start: 0.6524 (tpt) cc_final: 0.5396 (tpt) REVERT: D 100 TYR cc_start: 0.8478 (OUTLIER) cc_final: 0.7198 (t80) REVERT: E 78 MET cc_start: 0.6984 (mmp) cc_final: 0.6539 (mmt) REVERT: E 85 THR cc_start: 0.9206 (OUTLIER) cc_final: 0.8740 (p) REVERT: E 104 LEU cc_start: 0.9425 (tt) cc_final: 0.9184 (tp) REVERT: E 105 ASP cc_start: 0.8796 (t0) cc_final: 0.7903 (m-30) REVERT: E 150 GLN cc_start: 0.8721 (tp40) cc_final: 0.8147 (tt0) REVERT: E 159 LYS cc_start: 0.8157 (mmtt) cc_final: 0.7943 (mttm) outliers start: 23 outliers final: 16 residues processed: 87 average time/residue: 0.1104 time to fit residues: 14.3723 Evaluate side-chains 87 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 67 time to evaluate : 0.321 ------------------------------------------------------------------------------- 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 198 SER Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 274 VAL 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 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 146 optimal weight: 0.0670 chunk 80 optimal weight: 0.7980 chunk 126 optimal weight: 0.8980 chunk 158 optimal weight: 0.3980 chunk 100 optimal weight: 6.9990 chunk 62 optimal weight: 20.0000 chunk 81 optimal weight: 0.0050 chunk 57 optimal weight: 0.0060 chunk 117 optimal weight: 0.0770 chunk 30 optimal weight: 1.9990 chunk 172 optimal weight: 4.9990 overall best weight: 0.1106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 GLN A 531 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.085095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.057363 restraints weight = 64148.445| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 5.01 r_work: 0.3432 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.7236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14247 Z= 0.105 Angle : 0.634 16.799 19426 Z= 0.303 Chirality : 0.048 0.835 2241 Planarity : 0.004 0.040 2476 Dihedral : 3.884 29.850 1898 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.20 % Allowed : 13.20 % Favored : 85.60 % 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: 0.87 (0.20), residues: 1737 helix: 1.72 (0.36), residues: 209 sheet: 1.19 (0.21), residues: 609 loop : -0.06 (0.20), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 7 TYR 0.016 0.001 TYR D 150 PHE 0.015 0.001 PHE A 465 TRP 0.021 0.001 TRP D 123 HIS 0.003 0.000 HIS B 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (14199) covalent geometry : angle 0.59785 / 0.30 (19297) SS BOND : bond 0.00156 / 0.11 ( 15) SS BOND : angle 0.47211 / 0.29 ( 30) hydrogen bonds : bond 0.03087 / 2.05 ( 463) hydrogen bonds : angle 4.98812 / 3.56 ( 1344) link_ALPHA1-3 : bond 0.00589 / 0.31 ( 2) link_ALPHA1-3 : angle 2.54560 / 1.67 ( 6) link_ALPHA1-6 : bond 0.00654 / 0.32 ( 3) link_ALPHA1-6 : angle 1.55400 / 1.02 ( 9) link_BETA1-2 : bond 0.00496 / 0.26 ( 1) link_BETA1-2 : angle 1.66135 / 0.98 ( 3) link_BETA1-4 : bond 0.00776 / 0.46 ( 17) link_BETA1-4 : angle 2.48046 / 1.67 ( 51) link_NAG-ASN : bond 0.00512 / 0.23 ( 10) link_NAG-ASN : angle 4.19092 / 2.70 ( 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 89 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 0.523 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: A 310 MET cc_start: 0.8186 (mtp) cc_final: 0.7897 (mtt) REVERT: B 38 MET cc_start: 0.6036 (mmm) cc_final: 0.5382 (ptm) REVERT: B 77 ASN cc_start: 0.8722 (p0) cc_final: 0.8378 (t0) REVERT: B 284 GLU cc_start: 0.8996 (tm-30) cc_final: 0.8738 (tm-30) REVERT: B 440 TYR cc_start: 0.8020 (m-80) cc_final: 0.6945 (m-10) REVERT: D 0 MET cc_start: 0.6605 (tpt) cc_final: 0.5526 (tpt) REVERT: D 82 MET cc_start: 0.7909 (mpp) cc_final: 0.6987 (mpp) REVERT: D 100 TYR cc_start: 0.8478 (OUTLIER) cc_final: 0.7159 (t80) REVERT: E 78 MET cc_start: 0.6711 (mmp) cc_final: 0.6346 (mmt) REVERT: E 85 THR cc_start: 0.9120 (OUTLIER) cc_final: 0.8674 (p) REVERT: E 105 ASP cc_start: 0.8831 (t0) cc_final: 0.8004 (m-30) REVERT: E 150 GLN cc_start: 0.8732 (tp40) cc_final: 0.8107 (tt0) REVERT: E 159 LYS cc_start: 0.8205 (mmtt) cc_final: 0.7951 (mttm) outliers start: 18 outliers final: 14 residues processed: 86 average time/residue: 0.1339 time to fit residues: 16.6543 Evaluate side-chains 83 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE 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 273 ILE Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain C residue 1283 LEU Chi-restraints excluded: chain C residue 1339 THR 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 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 139 MET 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 94 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 chunk 154 optimal weight: 8.9990 chunk 146 optimal weight: 0.4980 chunk 156 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 65 optimal weight: 8.9990 chunk 132 optimal weight: 0.3980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 136 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.083821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.055860 restraints weight = 64197.622| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 5.20 r_work: 0.3388 rms_B_bonded: 5.14 restraints_weight: 2.0000 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.7457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14247 Z= 0.131 Angle : 0.652 15.983 19426 Z= 0.312 Chirality : 0.051 1.118 2241 Planarity : 0.004 0.054 2476 Dihedral : 3.919 25.569 1896 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.27 % Allowed : 13.00 % 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: 0.82 (0.20), residues: 1737 helix: 1.77 (0.36), residues: 210 sheet: 1.14 (0.21), residues: 606 loop : -0.11 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 7 TYR 0.015 0.001 TYR A 284 PHE 0.012 0.001 PHE B 264 TRP 0.025 0.001 TRP D 123 HIS 0.005 0.001 HIS B 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (14199) covalent geometry : angle 0.61745 / 0.30 (19297) SS BOND : bond 0.00174 / 0.11 ( 15) SS BOND : angle 0.50327 / 0.32 ( 30) hydrogen bonds : bond 0.03489 / 2.32 ( 463) hydrogen bonds : angle 5.01240 / 3.55 ( 1344) link_ALPHA1-3 : bond 0.00535 / 0.28 ( 2) link_ALPHA1-3 : angle 2.43611 / 1.61 ( 6) link_ALPHA1-6 : bond 0.00555 / 0.28 ( 3) link_ALPHA1-6 : angle 1.62944 / 1.07 ( 9) link_BETA1-2 : bond 0.00287 / 0.15 ( 1) link_BETA1-2 : angle 1.55408 / 0.93 ( 3) link_BETA1-4 : bond 0.00699 / 0.41 ( 17) link_BETA1-4 : angle 2.35746 / 1.56 ( 51) link_NAG-ASN : bond 0.00372 / 0.17 ( 10) link_NAG-ASN : angle 4.28499 / 2.76 ( 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 89 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 70 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 TYR cc_start: 0.9002 (OUTLIER) cc_final: 0.7287 (t80) REVERT: A 583 ARG cc_start: 0.8769 (mtt180) cc_final: 0.8420 (mtp180) REVERT: B 38 MET cc_start: 0.6097 (mmm) cc_final: 0.5410 (ptm) REVERT: B 77 ASN cc_start: 0.8841 (p0) cc_final: 0.8380 (t0) REVERT: B 284 GLU cc_start: 0.8967 (tm-30) cc_final: 0.8710 (tm-30) REVERT: B 440 TYR cc_start: 0.7984 (m-80) cc_final: 0.6925 (m-10) REVERT: D 0 MET cc_start: 0.6552 (tpt) cc_final: 0.5500 (tpt) REVERT: D 80 LEU cc_start: 0.9118 (tp) cc_final: 0.8472 (tp) REVERT: D 82 MET cc_start: 0.7635 (mpp) cc_final: 0.7009 (mpp) REVERT: D 100 TYR cc_start: 0.8529 (OUTLIER) cc_final: 0.7276 (t80) REVERT: E 78 MET cc_start: 0.6831 (mmp) cc_final: 0.6387 (mmt) REVERT: E 85 THR cc_start: 0.9176 (OUTLIER) cc_final: 0.8695 (p) REVERT: E 105 ASP cc_start: 0.8895 (t0) cc_final: 0.8023 (m-30) REVERT: E 159 LYS cc_start: 0.8169 (mmtt) cc_final: 0.7936 (mttm) outliers start: 19 outliers final: 16 residues processed: 86 average time/residue: 0.1167 time to fit residues: 14.9658 Evaluate side-chains 87 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 68 time to evaluate : 0.575 ------------------------------------------------------------------------------- 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 244 LEU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain C residue 1339 THR 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 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 139 MET Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 136 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 63 optimal weight: 0.8980 chunk 94 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 164 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 116 optimal weight: 6.9990 chunk 113 optimal weight: 0.8980 chunk 115 optimal weight: 6.9990 chunk 32 optimal weight: 0.7980 chunk 139 optimal weight: 2.9990 chunk 170 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.083274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.055483 restraints weight = 64298.515| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 5.02 r_work: 0.3371 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.7643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14247 Z= 0.145 Angle : 0.662 14.969 19426 Z= 0.318 Chirality : 0.051 1.150 2241 Planarity : 0.004 0.047 2476 Dihedral : 3.976 25.977 1896 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.27 % Allowed : 13.13 % Favored : 85.60 % 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: 0.75 (0.20), residues: 1737 helix: 1.81 (0.36), residues: 210 sheet: 0.98 (0.20), residues: 616 loop : -0.10 (0.20), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 7 TYR 0.024 0.001 TYR E 71 PHE 0.016 0.001 PHE B 264 TRP 0.028 0.001 TRP E 118 HIS 0.004 0.001 HIS B 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (14199) covalent geometry : angle 0.62964 / 0.31 (19297) SS BOND : bond 0.00188 / 0.12 ( 15) SS BOND : angle 0.50828 / 0.33 ( 30) hydrogen bonds : bond 0.03556 / 2.37 ( 463) hydrogen bonds : angle 5.02395 / 3.56 ( 1344) link_ALPHA1-3 : bond 0.00514 / 0.27 ( 2) link_ALPHA1-3 : angle 2.45212 / 1.63 ( 6) link_ALPHA1-6 : bond 0.00532 / 0.27 ( 3) link_ALPHA1-6 : angle 1.65816 / 1.08 ( 9) link_BETA1-2 : bond 0.00261 / 0.14 ( 1) link_BETA1-2 : angle 1.55997 / 0.94 ( 3) link_BETA1-4 : bond 0.00632 / 0.39 ( 17) link_BETA1-4 : angle 2.38132 / 1.58 ( 51) link_NAG-ASN : bond 0.00383 / 0.18 ( 10) link_NAG-ASN : angle 4.05451 / 2.61 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7026.92 seconds wall clock time: 120 minutes 1.31 seconds (7201.31 seconds total)