Starting phenix.real_space_refine on Mon Apr 6 00:23:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y7w_72668/04_2026/9y7w_72668.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y7w_72668/04_2026/9y7w_72668.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9y7w_72668/04_2026/9y7w_72668.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y7w_72668/04_2026/9y7w_72668.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9y7w_72668/04_2026/9y7w_72668.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y7w_72668/04_2026/9y7w_72668.map" } resolution = 3.19 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 90 5.16 5 C 9200 2.51 5 N 2308 2.21 5 O 2592 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14190 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2784 Classifications: {'peptide': 344} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 328} Chain breaks: 1 Chain: "B" Number of atoms: 2812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2812 Classifications: {'peptide': 347} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 331} Chain breaks: 1 Chain: "C" Number of atoms: 2804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2804 Classifications: {'peptide': 346} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 330} Chain breaks: 1 Chain: "D" Number of atoms: 2830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2830 Classifications: {'peptide': 349} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 333} Chain breaks: 1 Chain: "E" Number of atoms: 2795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2795 Classifications: {'peptide': 345} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 329} Chain breaks: 1 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.04, per 1000 atoms: 0.21 Number of scatterers: 14190 At special positions: 0 Unit cell: (94.08, 91.56, 133.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 90 16.00 O 2592 8.00 N 2308 7.00 C 9200 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 172 " - pdb=" SG CYS A 186 " distance=2.03 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 243 " distance=2.03 Simple disulfide: pdb=" SG CYS B 172 " - pdb=" SG CYS B 186 " distance=2.03 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 243 " distance=2.03 Simple disulfide: pdb=" SG CYS C 172 " - pdb=" SG CYS C 186 " distance=2.03 Simple disulfide: pdb=" SG CYS C 232 " - pdb=" SG CYS C 243 " distance=2.03 Simple disulfide: pdb=" SG CYS D 172 " - pdb=" SG CYS D 186 " distance=2.03 Simple disulfide: pdb=" SG CYS D 232 " - pdb=" SG CYS D 243 " distance=2.03 Simple disulfide: pdb=" SG CYS E 172 " - pdb=" SG CYS E 186 " distance=2.03 Simple disulfide: pdb=" SG CYS E 232 " - pdb=" SG CYS E 243 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.17 Conformation dependent library (CDL) restraints added in 520.1 milliseconds 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3322 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 23 sheets defined 42.3% alpha, 41.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 43 through 52 removed outlier: 4.176A pdb=" N PHE A 47 " --> pdb=" O SER A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 127 removed outlier: 3.504A pdb=" N LEU A 124 " --> pdb=" O PRO A 121 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASP A 125 " --> pdb=" O SER A 122 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER A 126 " --> pdb=" O MET A 123 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE A 127 " --> pdb=" O LEU A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 259 removed outlier: 3.653A pdb=" N ILE A 259 " --> pdb=" O GLY A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 273 removed outlier: 3.567A pdb=" N SER A 265 " --> pdb=" O MET A 261 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TRP A 273 " --> pdb=" O VAL A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 278 Processing helix chain 'A' and resid 282 through 304 Processing helix chain 'A' and resid 315 through 347 Processing helix chain 'A' and resid 413 through 450 Proline residue: A 427 - end of helix Processing helix chain 'B' and resid 43 through 52 Processing helix chain 'B' and resid 105 through 108 removed outlier: 3.532A pdb=" N ALA B 108 " --> pdb=" O SER B 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 105 through 108' Processing helix chain 'B' and resid 120 through 127 removed outlier: 3.869A pdb=" N LEU B 124 " --> pdb=" O PRO B 121 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ASP B 125 " --> pdb=" O SER B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 261 removed outlier: 3.600A pdb=" N ILE B 259 " --> pdb=" O GLY B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 275 removed outlier: 3.503A pdb=" N SER B 265 " --> pdb=" O MET B 261 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N SER B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 278 No H-bonds generated for 'chain 'B' and resid 276 through 278' Processing helix chain 'B' and resid 282 through 306 removed outlier: 3.745A pdb=" N ALA B 306 " --> pdb=" O SER B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 346 removed outlier: 4.291A pdb=" N TYR B 335 " --> pdb=" O ALA B 331 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA B 336 " --> pdb=" O LEU B 332 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LYS B 346 " --> pdb=" O SER B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 450 removed outlier: 3.767A pdb=" N ARG B 414 " --> pdb=" O LYS B 410 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA B 415 " --> pdb=" O PHE B 411 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS B 416 " --> pdb=" O VAL B 412 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP B 419 " --> pdb=" O ALA B 415 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA B 424 " --> pdb=" O THR B 420 " (cutoff:3.500A) Proline residue: B 427 - end of helix removed outlier: 3.869A pdb=" N ARG B 445 " --> pdb=" O TYR B 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 53 removed outlier: 3.565A pdb=" N ASP C 49 " --> pdb=" O SER C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 57 removed outlier: 4.190A pdb=" N GLY C 57 " --> pdb=" O ARG C 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 54 through 57' Processing helix chain 'C' and resid 105 through 108 Processing helix chain 'C' and resid 120 through 127 removed outlier: 4.438A pdb=" N ASP C 125 " --> pdb=" O SER C 122 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE C 127 " --> pdb=" O LEU C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 179 removed outlier: 4.549A pdb=" N ASN C 178 " --> pdb=" O ASP C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 261 Processing helix chain 'C' and resid 261 through 273 removed outlier: 3.815A pdb=" N TRP C 273 " --> pdb=" O VAL C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 278 removed outlier: 3.824A pdb=" N TRP C 277 " --> pdb=" O TRP C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 305 removed outlier: 3.852A pdb=" N ARG C 305 " --> pdb=" O SER C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 344 Processing helix chain 'C' and resid 345 through 347 No H-bonds generated for 'chain 'C' and resid 345 through 347' Processing helix chain 'C' and resid 411 through 424 Processing helix chain 'C' and resid 425 through 450 removed outlier: 4.113A pdb=" N ARG C 445 " --> pdb=" O TYR C 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 53 Processing helix chain 'D' and resid 54 through 57 removed outlier: 4.286A pdb=" N GLY D 57 " --> pdb=" O ARG D 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 54 through 57' Processing helix chain 'D' and resid 105 through 108 Processing helix chain 'D' and resid 120 through 127 removed outlier: 3.505A pdb=" N MET D 123 " --> pdb=" O ASP D 120 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASP D 125 " --> pdb=" O SER D 122 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE D 127 " --> pdb=" O LEU D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 261 removed outlier: 3.600A pdb=" N ILE D 259 " --> pdb=" O GLY D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 273 removed outlier: 3.562A pdb=" N SER D 265 " --> pdb=" O MET D 261 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TRP D 273 " --> pdb=" O VAL D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 278 Processing helix chain 'D' and resid 282 through 305 Processing helix chain 'D' and resid 315 through 344 Processing helix chain 'D' and resid 345 through 347 No H-bonds generated for 'chain 'D' and resid 345 through 347' Processing helix chain 'D' and resid 409 through 450 removed outlier: 3.573A pdb=" N ALA D 424 " --> pdb=" O THR D 420 " (cutoff:3.500A) Proline residue: D 427 - end of helix removed outlier: 3.994A pdb=" N ARG D 445 " --> pdb=" O TYR D 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 52 Processing helix chain 'E' and resid 105 through 108 Processing helix chain 'E' and resid 120 through 127 removed outlier: 3.610A pdb=" N MET E 123 " --> pdb=" O ASP E 120 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU E 124 " --> pdb=" O PRO E 121 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ASP E 125 " --> pdb=" O SER E 122 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE E 127 " --> pdb=" O LEU E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 179 removed outlier: 4.410A pdb=" N ASN E 178 " --> pdb=" O ASP E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 261 removed outlier: 3.525A pdb=" N ILE E 259 " --> pdb=" O GLY E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 273 Processing helix chain 'E' and resid 274 through 277 Processing helix chain 'E' and resid 282 through 305 Processing helix chain 'E' and resid 315 through 343 removed outlier: 3.810A pdb=" N LEU E 332 " --> pdb=" O VAL E 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 344 through 346 No H-bonds generated for 'chain 'E' and resid 344 through 346' Processing helix chain 'E' and resid 411 through 450 removed outlier: 3.512A pdb=" N ASP E 419 " --> pdb=" O ALA E 415 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA E 424 " --> pdb=" O THR E 420 " (cutoff:3.500A) Proline residue: E 427 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 116 through 119 removed outlier: 4.585A pdb=" N LEU A 152 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LYS A 159 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N ASP A 91 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N SER A 84 " --> pdb=" O ASP A 91 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N ARG A 93 " --> pdb=" O PHE A 82 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N PHE A 82 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ASN A 95 " --> pdb=" O ASN A 80 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ASN A 103 " --> pdb=" O ASN A 72 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASN A 72 " --> pdb=" O ASN A 103 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 137 through 141 removed outlier: 6.704A pdb=" N THR A 169 " --> pdb=" O LYS A 138 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ALA A 140 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N THR A 167 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N ASP A 91 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N SER A 84 " --> pdb=" O ASP A 91 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N ARG A 93 " --> pdb=" O PHE A 82 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N PHE A 82 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ASN A 95 " --> pdb=" O ASN A 80 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ASN A 103 " --> pdb=" O ASN A 72 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASN A 72 " --> pdb=" O ASN A 103 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 132 through 134 removed outlier: 5.317A pdb=" N THR A 242 " --> pdb=" O SER A 192 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N CYS A 243 " --> pdb=" O GLY A 230 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N GLY A 230 " --> pdb=" O CYS A 243 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLU A 245 " --> pdb=" O GLU A 228 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N GLU A 228 " --> pdb=" O GLU A 245 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N LYS A 247 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N GLU A 226 " --> pdb=" O LYS A 247 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N HIS A 249 " --> pdb=" O LYS A 224 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 132 through 134 removed outlier: 5.317A pdb=" N THR A 242 " --> pdb=" O SER A 192 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 116 through 119 removed outlier: 4.700A pdb=" N LEU B 152 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LYS B 159 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ASP B 91 " --> pdb=" O SER B 84 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N SER B 84 " --> pdb=" O ASP B 91 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N ARG B 93 " --> pdb=" O PHE B 82 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N PHE B 82 " --> pdb=" O ARG B 93 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ASN B 95 " --> pdb=" O ASN B 80 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ASN B 103 " --> pdb=" O ASN B 72 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N ASN B 72 " --> pdb=" O ASN B 103 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 137 through 141 removed outlier: 6.747A pdb=" N THR B 169 " --> pdb=" O LYS B 138 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ALA B 140 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N THR B 167 " --> pdb=" O ALA B 140 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ASP B 91 " --> pdb=" O SER B 84 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N SER B 84 " --> pdb=" O ASP B 91 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N ARG B 93 " --> pdb=" O PHE B 82 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N PHE B 82 " --> pdb=" O ARG B 93 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ASN B 95 " --> pdb=" O ASN B 80 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ASN B 103 " --> pdb=" O ASN B 72 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N ASN B 72 " --> pdb=" O ASN B 103 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 132 through 134 removed outlier: 4.795A pdb=" N HIS B 249 " --> pdb=" O GLU B 226 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N GLU B 226 " --> pdb=" O HIS B 249 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N GLU B 251 " --> pdb=" O LYS B 224 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N LYS B 224 " --> pdb=" O GLU B 251 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 234 through 236 Processing sheet with id=AA9, first strand: chain 'C' and resid 116 through 119 removed outlier: 4.613A pdb=" N LEU C 152 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N LYS C 159 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ASP C 91 " --> pdb=" O SER C 84 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N SER C 84 " --> pdb=" O ASP C 91 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N ARG C 93 " --> pdb=" O PHE C 82 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N PHE C 82 " --> pdb=" O ARG C 93 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ASN C 95 " --> pdb=" O ASN C 80 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ASN C 103 " --> pdb=" O ASN C 72 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ASN C 72 " --> pdb=" O ASN C 103 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N VAL C 71 " --> pdb=" O ILE C 201 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N GLU C 203 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N VAL C 73 " --> pdb=" O GLU C 203 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 137 through 141 removed outlier: 6.506A pdb=" N THR C 169 " --> pdb=" O LYS C 138 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA C 140 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N THR C 167 " --> pdb=" O ALA C 140 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ASP C 91 " --> pdb=" O SER C 84 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N SER C 84 " --> pdb=" O ASP C 91 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N ARG C 93 " --> pdb=" O PHE C 82 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N PHE C 82 " --> pdb=" O ARG C 93 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ASN C 95 " --> pdb=" O ASN C 80 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ASN C 103 " --> pdb=" O ASN C 72 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ASN C 72 " --> pdb=" O ASN C 103 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 132 through 134 Processing sheet with id=AB3, first strand: chain 'C' and resid 132 through 134 Processing sheet with id=AB4, first strand: chain 'C' and resid 234 through 235 Processing sheet with id=AB5, first strand: chain 'D' and resid 116 through 119 removed outlier: 3.541A pdb=" N ILE D 154 " --> pdb=" O LEU D 117 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LEU D 152 " --> pdb=" O LEU D 119 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LYS D 159 " --> pdb=" O SER D 155 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ASP D 91 " --> pdb=" O SER D 84 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N SER D 84 " --> pdb=" O ASP D 91 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N ARG D 93 " --> pdb=" O PHE D 82 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N PHE D 82 " --> pdb=" O ARG D 93 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ASN D 95 " --> pdb=" O ASN D 80 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N ASN D 103 " --> pdb=" O ASN D 72 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ASN D 72 " --> pdb=" O ASN D 103 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL D 71 " --> pdb=" O ILE D 201 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N GLU D 203 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N VAL D 73 " --> pdb=" O GLU D 203 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 137 through 141 removed outlier: 6.706A pdb=" N THR D 169 " --> pdb=" O LYS D 138 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ALA D 140 " --> pdb=" O THR D 167 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N THR D 167 " --> pdb=" O ALA D 140 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ASP D 91 " --> pdb=" O SER D 84 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N SER D 84 " --> pdb=" O ASP D 91 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N ARG D 93 " --> pdb=" O PHE D 82 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N PHE D 82 " --> pdb=" O ARG D 93 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ASN D 95 " --> pdb=" O ASN D 80 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N ASN D 103 " --> pdb=" O ASN D 72 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ASN D 72 " --> pdb=" O ASN D 103 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 132 through 134 Processing sheet with id=AB8, first strand: chain 'D' and resid 132 through 134 removed outlier: 3.574A pdb=" N GLY D 230 " --> pdb=" O GLU D 245 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 234 through 235 Processing sheet with id=AC1, first strand: chain 'E' and resid 116 through 119 removed outlier: 4.721A pdb=" N LEU E 152 " --> pdb=" O LEU E 119 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LYS E 159 " --> pdb=" O SER E 155 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ASP E 91 " --> pdb=" O SER E 84 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N SER E 84 " --> pdb=" O ASP E 91 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ARG E 93 " --> pdb=" O PHE E 82 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N PHE E 82 " --> pdb=" O ARG E 93 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ASN E 95 " --> pdb=" O ASN E 80 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE E 78 " --> pdb=" O PHE E 97 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ASN E 103 " --> pdb=" O ASN E 72 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ASN E 72 " --> pdb=" O ASN E 103 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N VAL E 71 " --> pdb=" O ILE E 201 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N GLU E 203 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N VAL E 73 " --> pdb=" O GLU E 203 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 137 through 141 removed outlier: 6.602A pdb=" N THR E 169 " --> pdb=" O LYS E 138 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ALA E 140 " --> pdb=" O THR E 167 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N THR E 167 " --> pdb=" O ALA E 140 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ASP E 91 " --> pdb=" O SER E 84 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N SER E 84 " --> pdb=" O ASP E 91 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ARG E 93 " --> pdb=" O PHE E 82 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N PHE E 82 " --> pdb=" O ARG E 93 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ASN E 95 " --> pdb=" O ASN E 80 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE E 78 " --> pdb=" O PHE E 97 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ASN E 103 " --> pdb=" O ASN E 72 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ASN E 72 " --> pdb=" O ASN E 103 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 132 through 133 Processing sheet with id=AC4, first strand: chain 'E' and resid 132 through 133 removed outlier: 3.538A pdb=" N GLU E 228 " --> pdb=" O LYS E 247 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 234 through 236 removed outlier: 3.550A pdb=" N LYS E 234 " --> pdb=" O PHE E 241 " (cutoff:3.500A) 862 hydrogen bonds defined for protein. 2505 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.44 Time building geometry restraints manager: 1.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4080 1.34 - 1.46: 3508 1.46 - 1.59: 6801 1.59 - 1.71: 0 1.71 - 1.84: 150 Bond restraints: 14539 Sorted by residual: bond pdb=" C PRO C 427 " pdb=" N LEU C 428 " ideal model delta sigma weight residual 1.335 1.287 0.048 1.36e-02 5.41e+03 1.24e+01 bond pdb=" N ILE C 77 " pdb=" CA ILE C 77 " ideal model delta sigma weight residual 1.456 1.494 -0.037 1.14e-02 7.69e+03 1.08e+01 bond pdb=" N ILE A 127 " pdb=" CA ILE A 127 " ideal model delta sigma weight residual 1.456 1.493 -0.036 1.14e-02 7.69e+03 1.02e+01 bond pdb=" N VAL C 212 " pdb=" CA VAL C 212 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.14e-02 7.69e+03 1.01e+01 bond pdb=" C LEU C 428 " pdb=" N ALA C 429 " ideal model delta sigma weight residual 1.334 1.374 -0.040 1.27e-02 6.20e+03 9.75e+00 ... (remaining 14534 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 18426 1.79 - 3.58: 1220 3.58 - 5.37: 55 5.37 - 7.16: 15 7.16 - 8.94: 3 Bond angle restraints: 19719 Sorted by residual: angle pdb=" CA MET A 181 " pdb=" C MET A 181 " pdb=" O MET A 181 " ideal model delta sigma weight residual 122.44 117.78 4.66 1.34e+00 5.57e-01 1.21e+01 angle pdb=" N ASN D 237 " pdb=" CA ASN D 237 " pdb=" C ASN D 237 " ideal model delta sigma weight residual 112.54 108.45 4.09 1.22e+00 6.72e-01 1.12e+01 angle pdb=" N PRO E 427 " pdb=" CA PRO E 427 " pdb=" C PRO E 427 " ideal model delta sigma weight residual 113.47 108.69 4.78 1.43e+00 4.89e-01 1.12e+01 angle pdb=" CA ALA E 282 " pdb=" C ALA E 282 " pdb=" O ALA E 282 " ideal model delta sigma weight residual 122.41 118.41 4.00 1.21e+00 6.83e-01 1.09e+01 angle pdb=" N ASN A 237 " pdb=" CA ASN A 237 " pdb=" C ASN A 237 " ideal model delta sigma weight residual 111.82 108.01 3.81 1.16e+00 7.43e-01 1.08e+01 ... (remaining 19714 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.37: 8205 22.37 - 44.73: 514 44.73 - 67.10: 58 67.10 - 89.46: 11 89.46 - 111.83: 4 Dihedral angle restraints: 8792 sinusoidal: 3674 harmonic: 5118 Sorted by residual: dihedral pdb=" CA GLU D 245 " pdb=" C GLU D 245 " pdb=" N VAL D 246 " pdb=" CA VAL D 246 " ideal model delta harmonic sigma weight residual 180.00 160.86 19.14 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" C3 NAG D 501 " pdb=" C1 NAG D 501 " pdb=" C2 NAG D 501 " pdb=" O5 NAG D 501 " ideal model delta sinusoidal sigma weight residual -55.55 56.28 -111.83 1 3.00e+01 1.11e-03 1.46e+01 dihedral pdb=" N2 NAG D 501 " pdb=" C1 NAG D 501 " pdb=" C2 NAG D 501 " pdb=" O5 NAG D 501 " ideal model delta sinusoidal sigma weight residual -178.19 -67.60 -110.59 1 3.00e+01 1.11e-03 1.44e+01 ... (remaining 8789 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1425 0.044 - 0.088: 442 0.088 - 0.132: 260 0.132 - 0.176: 92 0.176 - 0.220: 14 Chirality restraints: 2233 Sorted by residual: chirality pdb=" CA VAL A 449 " pdb=" N VAL A 449 " pdb=" C VAL A 449 " pdb=" CB VAL A 449 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA MET A 181 " pdb=" N MET A 181 " pdb=" C MET A 181 " pdb=" CB MET A 181 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA ILE E 435 " pdb=" N ILE E 435 " pdb=" C ILE E 435 " pdb=" CB ILE E 435 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.76e-01 ... (remaining 2230 not shown) Planarity restraints: 2453 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 343 " -0.267 9.50e-02 1.11e+02 1.20e-01 8.82e+00 pdb=" NE ARG B 343 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG B 343 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG B 343 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 343 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 252 " 0.249 9.50e-02 1.11e+02 1.12e-01 7.67e+00 pdb=" NE ARG A 252 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG A 252 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 252 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 252 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 99 " 0.193 9.50e-02 1.11e+02 8.66e-02 4.65e+00 pdb=" NE ARG E 99 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG E 99 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG E 99 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG E 99 " 0.006 2.00e-02 2.50e+03 ... (remaining 2450 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1161 2.75 - 3.29: 14212 3.29 - 3.82: 23562 3.82 - 4.36: 28636 4.36 - 4.90: 49324 Nonbonded interactions: 116895 Sorted by model distance: nonbonded pdb=" OE1 GLU A 203 " pdb=" OH TYR A 231 " model vdw 2.210 3.040 nonbonded pdb=" OG1 THR B 89 " pdb=" OD1 ASP B 91 " model vdw 2.257 3.040 nonbonded pdb=" OD2 ASP D 120 " pdb=" OG SER D 122 " model vdw 2.258 3.040 nonbonded pdb=" OG1 THR A 89 " pdb=" OD1 ASP A 91 " model vdw 2.264 3.040 nonbonded pdb=" OG1 THR B 196 " pdb=" OD1 ASN B 198 " model vdw 2.283 3.040 ... (remaining 116890 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 'A' and (resid 43 through 346 or resid 412 through 502)) selection = (chain 'B' and (resid 43 through 346 or resid 412 through 502)) selection = (chain 'C' and (resid 43 through 346 or resid 412 through 502)) selection = (chain 'D' and (resid 43 through 346 or resid 412 through 502)) selection = (chain 'E' and (resid 43 through 346 or resid 412 through 450 or resid 502 throu \ gh 503)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.790 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 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 : 0.006 0.061 14549 Z= 0.424 Angle : 0.836 8.944 19739 Z= 0.583 Chirality : 0.059 0.220 2233 Planarity : 0.006 0.120 2453 Dihedral : 14.027 111.831 5440 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.20), residues: 1711 helix: 0.47 (0.20), residues: 614 sheet: 0.22 (0.29), residues: 335 loop : -0.65 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 414 TYR 0.020 0.001 TYR E 441 PHE 0.016 0.001 PHE B 430 TRP 0.035 0.001 TRP B 273 HIS 0.012 0.001 HIS B 450 Details of bonding type rmsd covalent geometry : bond 0.00601 (14539) covalent geometry : angle 0.83134 (19719) SS BOND : bond 0.00244 ( 10) SS BOND : angle 2.82260 ( 20) hydrogen bonds : bond 0.17140 ( 727) hydrogen bonds : angle 7.17744 ( 2505) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 309 time to evaluate : 0.565 Fit side-chains revert: symmetry clash REVERT: A 46 ASP cc_start: 0.9024 (m-30) cc_final: 0.8808 (p0) REVERT: A 279 ASN cc_start: 0.7805 (t0) cc_final: 0.7585 (t0) REVERT: B 279 ASN cc_start: 0.7118 (t0) cc_final: 0.6819 (t0) REVERT: C 117 LEU cc_start: 0.8313 (mt) cc_final: 0.8023 (mt) REVERT: C 276 PHE cc_start: 0.8389 (m-80) cc_final: 0.8187 (m-80) REVERT: C 297 MET cc_start: 0.9280 (tpt) cc_final: 0.8863 (tpt) REVERT: C 321 MET cc_start: 0.9344 (mmt) cc_final: 0.9127 (mmt) REVERT: C 416 LYS cc_start: 0.8777 (mtpt) cc_final: 0.8512 (mmtm) REVERT: D 46 ASP cc_start: 0.8603 (m-30) cc_final: 0.8395 (m-30) REVERT: D 123 MET cc_start: 0.8173 (ppp) cc_final: 0.7965 (ppp) REVERT: D 334 GLU cc_start: 0.8628 (tm-30) cc_final: 0.8385 (tm-30) REVERT: D 339 ASN cc_start: 0.8736 (t0) cc_final: 0.8516 (t0) REVERT: E 260 GLN cc_start: 0.8843 (tp-100) cc_final: 0.8513 (tp-100) REVERT: E 297 MET cc_start: 0.9515 (tpt) cc_final: 0.9169 (tpt) REVERT: E 338 VAL cc_start: 0.8340 (t) cc_final: 0.8047 (t) outliers start: 0 outliers final: 0 residues processed: 309 average time/residue: 0.1050 time to fit residues: 49.3547 Evaluate side-chains 252 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 ASN A 253 GLN A 450 HIS B 95 ASN ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 GLN B 253 GLN B 279 ASN D 80 ASN D 95 ASN ** E 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.112237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.082665 restraints weight = 24022.111| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 2.81 r_work: 0.2819 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 14549 Z= 0.191 Angle : 0.583 8.118 19739 Z= 0.302 Chirality : 0.043 0.167 2233 Planarity : 0.004 0.030 2453 Dihedral : 5.180 75.843 2091 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.79 % Allowed : 7.30 % Favored : 90.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.76 (0.20), residues: 1711 helix: 1.74 (0.20), residues: 620 sheet: 0.44 (0.28), residues: 357 loop : -0.49 (0.22), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 93 TYR 0.023 0.001 TYR A 335 PHE 0.023 0.002 PHE A 47 TRP 0.023 0.001 TRP B 273 HIS 0.009 0.001 HIS D 345 Details of bonding type rmsd covalent geometry : bond 0.00442 (14539) covalent geometry : angle 0.58124 (19719) SS BOND : bond 0.00289 ( 10) SS BOND : angle 1.56399 ( 20) hydrogen bonds : bond 0.04719 ( 727) hydrogen bonds : angle 4.95379 ( 2505) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 265 time to evaluate : 0.583 Fit side-chains revert: symmetry clash REVERT: A 46 ASP cc_start: 0.8815 (m-30) cc_final: 0.8538 (m-30) REVERT: A 279 ASN cc_start: 0.7815 (t0) cc_final: 0.7559 (t0) REVERT: B 297 MET cc_start: 0.8796 (mmm) cc_final: 0.8527 (mmm) REVERT: B 430 PHE cc_start: 0.9507 (t80) cc_final: 0.9133 (t80) REVERT: C 280 MET cc_start: 0.7968 (tmm) cc_final: 0.7011 (mtm) REVERT: C 321 MET cc_start: 0.9414 (mmt) cc_final: 0.9166 (mmt) REVERT: C 416 LYS cc_start: 0.8875 (mtpt) cc_final: 0.8659 (pttt) REVERT: D 46 ASP cc_start: 0.8506 (m-30) cc_final: 0.8303 (m-30) REVERT: D 123 MET cc_start: 0.8157 (ppp) cc_final: 0.7816 (ppp) REVERT: E 260 GLN cc_start: 0.9041 (tp-100) cc_final: 0.8765 (tp-100) REVERT: E 297 MET cc_start: 0.9520 (tpt) cc_final: 0.9172 (tpt) REVERT: E 333 LEU cc_start: 0.9411 (mm) cc_final: 0.9167 (mm) REVERT: E 338 VAL cc_start: 0.8290 (t) cc_final: 0.8060 (t) outliers start: 28 outliers final: 16 residues processed: 278 average time/residue: 0.1101 time to fit residues: 46.4069 Evaluate side-chains 250 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 234 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain C residue 114 ASP Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 436 PHE Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain E residue 254 MET Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 325 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 24 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 11 optimal weight: 9.9990 chunk 81 optimal weight: 3.9990 chunk 103 optimal weight: 0.0010 chunk 26 optimal weight: 10.0000 chunk 149 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 162 optimal weight: 0.0020 chunk 23 optimal weight: 3.9990 overall best weight: 0.9196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN A 300 GLN ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN D 220 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.114850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.085642 restraints weight = 23881.362| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 2.75 r_work: 0.2851 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 14549 Z= 0.112 Angle : 0.524 10.089 19739 Z= 0.266 Chirality : 0.041 0.156 2233 Planarity : 0.003 0.029 2453 Dihedral : 4.514 70.750 2091 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.54 % Allowed : 10.12 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1711 helix: 2.07 (0.20), residues: 619 sheet: 0.69 (0.28), residues: 361 loop : -0.44 (0.22), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 414 TYR 0.025 0.001 TYR A 335 PHE 0.012 0.001 PHE B 276 TRP 0.018 0.001 TRP B 273 HIS 0.008 0.001 HIS D 345 Details of bonding type rmsd covalent geometry : bond 0.00247 (14539) covalent geometry : angle 0.52304 (19719) SS BOND : bond 0.00321 ( 10) SS BOND : angle 1.16017 ( 20) hydrogen bonds : bond 0.03916 ( 727) hydrogen bonds : angle 4.43411 ( 2505) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 267 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 ASP cc_start: 0.8831 (m-30) cc_final: 0.8506 (m-30) REVERT: A 307 SER cc_start: 0.9137 (OUTLIER) cc_final: 0.8860 (p) REVERT: B 430 PHE cc_start: 0.9511 (t80) cc_final: 0.8996 (t80) REVERT: B 434 ASN cc_start: 0.9131 (m-40) cc_final: 0.8904 (m-40) REVERT: C 280 MET cc_start: 0.8005 (tmm) cc_final: 0.7123 (mtm) REVERT: C 300 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.8016 (tt0) REVERT: D 345 HIS cc_start: 0.7771 (p-80) cc_final: 0.7371 (p-80) REVERT: E 50 LYS cc_start: 0.8397 (pttp) cc_final: 0.8130 (pttp) REVERT: E 131 ASP cc_start: 0.9255 (p0) cc_final: 0.8921 (p0) REVERT: E 260 GLN cc_start: 0.9008 (tp-100) cc_final: 0.8714 (tp-100) REVERT: E 333 LEU cc_start: 0.9379 (mm) cc_final: 0.9098 (mm) outliers start: 24 outliers final: 15 residues processed: 271 average time/residue: 0.1024 time to fit residues: 42.5101 Evaluate side-chains 267 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 250 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain C residue 114 ASP Chi-restraints excluded: chain C residue 300 GLN Chi-restraints excluded: chain C residue 436 PHE Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 332 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 163 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 151 optimal weight: 7.9990 chunk 133 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 140 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 139 optimal weight: 5.9990 chunk 72 optimal weight: 0.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 GLN ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN B 253 GLN D 345 HIS E 220 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.110610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.080575 restraints weight = 24128.558| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 2.84 r_work: 0.2816 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 14549 Z= 0.211 Angle : 0.572 9.614 19739 Z= 0.294 Chirality : 0.043 0.213 2233 Planarity : 0.003 0.029 2453 Dihedral : 4.544 61.699 2091 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.50 % Allowed : 12.04 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.01 (0.20), residues: 1711 helix: 2.10 (0.20), residues: 617 sheet: 0.62 (0.28), residues: 363 loop : -0.54 (0.22), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 414 TYR 0.025 0.002 TYR A 335 PHE 0.016 0.001 PHE B 82 TRP 0.012 0.001 TRP B 273 HIS 0.006 0.001 HIS D 345 Details of bonding type rmsd covalent geometry : bond 0.00495 (14539) covalent geometry : angle 0.57101 (19719) SS BOND : bond 0.00333 ( 10) SS BOND : angle 1.39695 ( 20) hydrogen bonds : bond 0.04239 ( 727) hydrogen bonds : angle 4.45359 ( 2505) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 264 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 ASP cc_start: 0.8811 (m-30) cc_final: 0.8507 (m-30) REVERT: A 47 PHE cc_start: 0.8847 (t80) cc_final: 0.8555 (t80) REVERT: A 279 ASN cc_start: 0.7913 (t0) cc_final: 0.7659 (t0) REVERT: A 307 SER cc_start: 0.9144 (OUTLIER) cc_final: 0.8875 (p) REVERT: B 430 PHE cc_start: 0.9522 (t80) cc_final: 0.9183 (t80) REVERT: C 280 MET cc_start: 0.8029 (tmm) cc_final: 0.7114 (mtm) REVERT: C 300 GLN cc_start: 0.8551 (OUTLIER) cc_final: 0.8165 (tt0) REVERT: C 416 LYS cc_start: 0.8828 (pttt) cc_final: 0.8488 (pttm) REVERT: D 343 ARG cc_start: 0.8411 (mmm160) cc_final: 0.8111 (mmm160) REVERT: D 345 HIS cc_start: 0.7893 (p90) cc_final: 0.7402 (p-80) REVERT: E 131 ASP cc_start: 0.9291 (p0) cc_final: 0.8960 (p0) REVERT: E 260 GLN cc_start: 0.9010 (tp-100) cc_final: 0.8747 (tp-100) REVERT: E 297 MET cc_start: 0.9443 (tpp) cc_final: 0.9047 (tpt) REVERT: E 333 LEU cc_start: 0.9425 (mm) cc_final: 0.9159 (mm) outliers start: 39 outliers final: 27 residues processed: 282 average time/residue: 0.1027 time to fit residues: 44.6585 Evaluate side-chains 270 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 241 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain C residue 114 ASP Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain C residue 300 GLN Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 436 PHE Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 435 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 100 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 97 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 158 optimal weight: 0.5980 chunk 70 optimal weight: 0.7980 chunk 142 optimal weight: 0.9980 chunk 67 optimal weight: 0.3980 chunk 140 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 GLN D 344 GLN E 220 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.114530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.084388 restraints weight = 23996.647| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 2.88 r_work: 0.2848 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 14549 Z= 0.106 Angle : 0.522 11.271 19739 Z= 0.264 Chirality : 0.041 0.177 2233 Planarity : 0.003 0.028 2453 Dihedral : 4.128 52.382 2091 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.99 % Allowed : 12.94 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.18 (0.20), residues: 1711 helix: 2.15 (0.20), residues: 619 sheet: 0.80 (0.28), residues: 368 loop : -0.40 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 414 TYR 0.024 0.001 TYR A 335 PHE 0.014 0.001 PHE A 47 TRP 0.017 0.001 TRP B 273 HIS 0.003 0.000 HIS A 446 Details of bonding type rmsd covalent geometry : bond 0.00237 (14539) covalent geometry : angle 0.52169 (19719) SS BOND : bond 0.00268 ( 10) SS BOND : angle 1.04759 ( 20) hydrogen bonds : bond 0.03643 ( 727) hydrogen bonds : angle 4.15187 ( 2505) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 263 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 ASP cc_start: 0.8770 (m-30) cc_final: 0.8455 (m-30) REVERT: A 47 PHE cc_start: 0.8842 (t80) cc_final: 0.8514 (t80) REVERT: A 231 TYR cc_start: 0.8806 (OUTLIER) cc_final: 0.7646 (t80) REVERT: A 279 ASN cc_start: 0.7923 (t0) cc_final: 0.7665 (t0) REVERT: A 307 SER cc_start: 0.9132 (OUTLIER) cc_final: 0.8876 (p) REVERT: B 430 PHE cc_start: 0.9525 (t80) cc_final: 0.8991 (t80) REVERT: C 280 MET cc_start: 0.7973 (tmm) cc_final: 0.7130 (mtm) REVERT: C 300 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.8122 (tt0) REVERT: C 416 LYS cc_start: 0.8773 (pttt) cc_final: 0.8472 (pttm) REVERT: D 343 ARG cc_start: 0.8356 (mmm160) cc_final: 0.7938 (mmm160) REVERT: D 345 HIS cc_start: 0.7824 (p90) cc_final: 0.7259 (p-80) REVERT: E 52 MET cc_start: 0.8879 (ptt) cc_final: 0.8649 (ptt) REVERT: E 131 ASP cc_start: 0.9293 (p0) cc_final: 0.8947 (p0) REVERT: E 253 GLN cc_start: 0.8553 (mm-40) cc_final: 0.8140 (mm-40) REVERT: E 260 GLN cc_start: 0.8972 (tp-100) cc_final: 0.8714 (tp-100) REVERT: E 333 LEU cc_start: 0.9370 (mm) cc_final: 0.9053 (mm) outliers start: 31 outliers final: 15 residues processed: 274 average time/residue: 0.1028 time to fit residues: 42.9370 Evaluate side-chains 265 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 247 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain C residue 114 ASP Chi-restraints excluded: chain C residue 300 GLN Chi-restraints excluded: chain C residue 436 PHE Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 325 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 112 optimal weight: 0.9990 chunk 105 optimal weight: 0.9980 chunk 141 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 chunk 169 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 121 optimal weight: 0.0000 chunk 165 optimal weight: 6.9990 chunk 161 optimal weight: 5.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN B 253 GLN D 300 GLN D 344 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.112973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.082947 restraints weight = 23856.620| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.87 r_work: 0.2825 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 14549 Z= 0.140 Angle : 0.527 8.523 19739 Z= 0.270 Chirality : 0.042 0.184 2233 Planarity : 0.003 0.029 2453 Dihedral : 4.082 44.346 2091 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.69 % Allowed : 13.32 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.16 (0.20), residues: 1711 helix: 2.17 (0.20), residues: 618 sheet: 0.79 (0.27), residues: 368 loop : -0.46 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 93 TYR 0.023 0.001 TYR A 335 PHE 0.014 0.001 PHE A 47 TRP 0.018 0.001 TRP B 273 HIS 0.003 0.000 HIS A 446 Details of bonding type rmsd covalent geometry : bond 0.00326 (14539) covalent geometry : angle 0.52634 (19719) SS BOND : bond 0.00306 ( 10) SS BOND : angle 1.16289 ( 20) hydrogen bonds : bond 0.03720 ( 727) hydrogen bonds : angle 4.17610 ( 2505) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 252 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 PHE cc_start: 0.8835 (t80) cc_final: 0.8517 (t80) REVERT: A 123 MET cc_start: 0.8903 (ttm) cc_final: 0.8626 (ttp) REVERT: A 231 TYR cc_start: 0.8884 (OUTLIER) cc_final: 0.7773 (t80) REVERT: A 279 ASN cc_start: 0.7959 (t0) cc_final: 0.7745 (t0) REVERT: A 307 SER cc_start: 0.9146 (OUTLIER) cc_final: 0.8891 (p) REVERT: B 131 ASP cc_start: 0.8751 (p0) cc_final: 0.8545 (p0) REVERT: B 414 ARG cc_start: 0.7848 (mmp80) cc_final: 0.7321 (mmm160) REVERT: B 430 PHE cc_start: 0.9543 (t80) cc_final: 0.9011 (t80) REVERT: C 280 MET cc_start: 0.7960 (tmm) cc_final: 0.7071 (mtm) REVERT: C 300 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.8134 (tt0) REVERT: C 416 LYS cc_start: 0.8778 (pttt) cc_final: 0.8455 (pttm) REVERT: D 343 ARG cc_start: 0.8337 (mmm160) cc_final: 0.7899 (mmm160) REVERT: D 345 HIS cc_start: 0.7880 (p90) cc_final: 0.7276 (p-80) REVERT: E 131 ASP cc_start: 0.9299 (p0) cc_final: 0.8962 (p0) REVERT: E 260 GLN cc_start: 0.9035 (tp-100) cc_final: 0.8775 (tp-100) REVERT: E 297 MET cc_start: 0.9469 (tpp) cc_final: 0.9022 (tpt) REVERT: E 333 LEU cc_start: 0.9367 (mm) cc_final: 0.9028 (mm) outliers start: 42 outliers final: 29 residues processed: 275 average time/residue: 0.1077 time to fit residues: 44.8870 Evaluate side-chains 275 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 243 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain C residue 114 ASP Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 232 CYS Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain C residue 300 GLN Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 436 PHE Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 300 GLN Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 188 MET Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 332 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 103 optimal weight: 9.9990 chunk 85 optimal weight: 2.9990 chunk 152 optimal weight: 5.9990 chunk 165 optimal weight: 8.9990 chunk 166 optimal weight: 8.9990 chunk 145 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 40 optimal weight: 0.1980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN D 300 GLN D 344 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.113603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.083806 restraints weight = 23790.883| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 2.85 r_work: 0.2853 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 14549 Z= 0.113 Angle : 0.535 14.426 19739 Z= 0.268 Chirality : 0.041 0.215 2233 Planarity : 0.003 0.028 2453 Dihedral : 3.927 36.945 2091 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.43 % Allowed : 14.35 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.20 (0.20), residues: 1711 helix: 2.17 (0.21), residues: 617 sheet: 0.88 (0.28), residues: 368 loop : -0.43 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 343 TYR 0.022 0.001 TYR A 335 PHE 0.015 0.001 PHE A 47 TRP 0.017 0.001 TRP B 273 HIS 0.003 0.000 HIS A 446 Details of bonding type rmsd covalent geometry : bond 0.00255 (14539) covalent geometry : angle 0.53385 (19719) SS BOND : bond 0.00264 ( 10) SS BOND : angle 1.03639 ( 20) hydrogen bonds : bond 0.03623 ( 727) hydrogen bonds : angle 4.10385 ( 2505) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 258 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 PHE cc_start: 0.8830 (t80) cc_final: 0.8519 (t80) REVERT: A 231 TYR cc_start: 0.8896 (OUTLIER) cc_final: 0.7784 (t80) REVERT: A 279 ASN cc_start: 0.8034 (t0) cc_final: 0.7808 (t0) REVERT: A 298 THR cc_start: 0.8704 (m) cc_final: 0.8448 (p) REVERT: A 307 SER cc_start: 0.9135 (OUTLIER) cc_final: 0.8885 (p) REVERT: B 131 ASP cc_start: 0.8730 (p0) cc_final: 0.8524 (p0) REVERT: B 430 PHE cc_start: 0.9534 (t80) cc_final: 0.8992 (t80) REVERT: C 280 MET cc_start: 0.7961 (tmm) cc_final: 0.7087 (mtm) REVERT: C 300 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.8153 (tt0) REVERT: C 416 LYS cc_start: 0.8790 (pttt) cc_final: 0.8466 (pttm) REVERT: D 343 ARG cc_start: 0.8296 (mmm160) cc_final: 0.7866 (mmm160) REVERT: D 345 HIS cc_start: 0.7870 (p90) cc_final: 0.7222 (p-80) REVERT: E 131 ASP cc_start: 0.9283 (p0) cc_final: 0.8939 (p0) REVERT: E 333 LEU cc_start: 0.9392 (mm) cc_final: 0.9033 (mm) outliers start: 38 outliers final: 24 residues processed: 276 average time/residue: 0.1001 time to fit residues: 42.4379 Evaluate side-chains 270 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 243 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 232 CYS Chi-restraints excluded: chain C residue 300 GLN Chi-restraints excluded: chain C residue 436 PHE Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain D residue 300 GLN Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 188 MET Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 332 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 71 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 98 optimal weight: 0.0170 chunk 94 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 119 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 chunk 158 optimal weight: 0.0040 chunk 105 optimal weight: 1.9990 chunk 135 optimal weight: 4.9990 chunk 118 optimal weight: 0.8980 overall best weight: 0.4830 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN D 300 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.114826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.085314 restraints weight = 23729.167| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.82 r_work: 0.2874 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 14549 Z= 0.101 Angle : 0.538 13.354 19739 Z= 0.268 Chirality : 0.042 0.288 2233 Planarity : 0.003 0.030 2453 Dihedral : 3.740 26.987 2091 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.79 % Allowed : 15.05 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.21 (0.20), residues: 1711 helix: 2.09 (0.21), residues: 625 sheet: 1.02 (0.28), residues: 367 loop : -0.45 (0.22), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 414 TYR 0.022 0.001 TYR A 335 PHE 0.014 0.001 PHE A 47 TRP 0.019 0.001 TRP B 273 HIS 0.003 0.000 HIS A 446 Details of bonding type rmsd covalent geometry : bond 0.00223 (14539) covalent geometry : angle 0.53702 (19719) SS BOND : bond 0.00278 ( 10) SS BOND : angle 0.94472 ( 20) hydrogen bonds : bond 0.03490 ( 727) hydrogen bonds : angle 4.02747 ( 2505) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 258 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 PHE cc_start: 0.8832 (t80) cc_final: 0.8501 (t80) REVERT: A 231 TYR cc_start: 0.8883 (OUTLIER) cc_final: 0.7811 (t80) REVERT: A 279 ASN cc_start: 0.8008 (t0) cc_final: 0.7793 (t0) REVERT: A 307 SER cc_start: 0.9128 (OUTLIER) cc_final: 0.8882 (p) REVERT: B 339 ASN cc_start: 0.8110 (m-40) cc_final: 0.7704 (m-40) REVERT: B 430 PHE cc_start: 0.9532 (t80) cc_final: 0.9022 (t80) REVERT: C 280 MET cc_start: 0.7900 (tmm) cc_final: 0.7105 (mtm) REVERT: C 300 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.8154 (tt0) REVERT: C 416 LYS cc_start: 0.8784 (pttt) cc_final: 0.8448 (ptpp) REVERT: D 123 MET cc_start: 0.8321 (ppp) cc_final: 0.8040 (ppp) REVERT: D 343 ARG cc_start: 0.8239 (mmm160) cc_final: 0.7974 (mmp80) REVERT: D 345 HIS cc_start: 0.7884 (p90) cc_final: 0.7445 (p-80) REVERT: E 46 ASP cc_start: 0.9102 (m-30) cc_final: 0.8719 (p0) REVERT: E 131 ASP cc_start: 0.9275 (p0) cc_final: 0.8927 (p0) REVERT: E 333 LEU cc_start: 0.9362 (mm) cc_final: 0.8973 (mm) outliers start: 28 outliers final: 18 residues processed: 274 average time/residue: 0.1054 time to fit residues: 43.8803 Evaluate side-chains 269 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 248 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 232 CYS Chi-restraints excluded: chain C residue 300 GLN Chi-restraints excluded: chain C residue 436 PHE Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain D residue 300 GLN Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 332 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 160 optimal weight: 0.6980 chunk 137 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 144 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 114 optimal weight: 6.9990 chunk 116 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 129 optimal weight: 5.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN B 300 GLN ** D 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.113784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.084170 restraints weight = 23956.260| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 2.83 r_work: 0.2861 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 14549 Z= 0.128 Angle : 0.559 11.098 19739 Z= 0.279 Chirality : 0.043 0.285 2233 Planarity : 0.003 0.029 2453 Dihedral : 3.797 26.340 2091 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.67 % Allowed : 15.82 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.19 (0.20), residues: 1711 helix: 2.11 (0.20), residues: 623 sheet: 1.00 (0.28), residues: 368 loop : -0.50 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 414 TYR 0.021 0.001 TYR A 335 PHE 0.014 0.001 PHE A 47 TRP 0.024 0.001 TRP B 273 HIS 0.002 0.000 HIS B 450 Details of bonding type rmsd covalent geometry : bond 0.00300 (14539) covalent geometry : angle 0.55653 (19719) SS BOND : bond 0.00324 ( 10) SS BOND : angle 1.82801 ( 20) hydrogen bonds : bond 0.03537 ( 727) hydrogen bonds : angle 4.09368 ( 2505) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 251 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 PHE cc_start: 0.8860 (t80) cc_final: 0.8487 (t80) REVERT: A 231 TYR cc_start: 0.8904 (OUTLIER) cc_final: 0.7921 (t80) REVERT: A 279 ASN cc_start: 0.8063 (t0) cc_final: 0.7829 (t0) REVERT: A 307 SER cc_start: 0.9132 (OUTLIER) cc_final: 0.8886 (p) REVERT: B 115 ASP cc_start: 0.8265 (m-30) cc_final: 0.7920 (t0) REVERT: B 339 ASN cc_start: 0.8169 (m-40) cc_final: 0.7788 (m-40) REVERT: B 430 PHE cc_start: 0.9536 (t80) cc_final: 0.9028 (t80) REVERT: C 280 MET cc_start: 0.7909 (tmm) cc_final: 0.7104 (mtm) REVERT: C 300 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.8199 (tt0) REVERT: C 416 LYS cc_start: 0.8800 (pttt) cc_final: 0.8491 (ptpp) REVERT: D 343 ARG cc_start: 0.8254 (mmm160) cc_final: 0.8006 (mmp80) REVERT: D 345 HIS cc_start: 0.7879 (p90) cc_final: 0.7509 (p-80) REVERT: E 131 ASP cc_start: 0.9287 (p0) cc_final: 0.8946 (p0) REVERT: E 333 LEU cc_start: 0.9379 (mm) cc_final: 0.9012 (mm) outliers start: 26 outliers final: 22 residues processed: 263 average time/residue: 0.1077 time to fit residues: 43.3032 Evaluate side-chains 277 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 252 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 232 CYS Chi-restraints excluded: chain C residue 300 GLN Chi-restraints excluded: chain C residue 436 PHE Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 188 MET Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 332 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 71 optimal weight: 0.9980 chunk 95 optimal weight: 6.9990 chunk 139 optimal weight: 1.9990 chunk 143 optimal weight: 0.0980 chunk 80 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 113 optimal weight: 6.9990 chunk 132 optimal weight: 9.9990 chunk 77 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN ** D 300 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 = 0.3481 r_free = 0.3481 target = 0.114587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.084521 restraints weight = 23776.324| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 2.87 r_work: 0.2851 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 14549 Z= 0.122 Angle : 0.566 12.703 19739 Z= 0.280 Chirality : 0.043 0.278 2233 Planarity : 0.003 0.031 2453 Dihedral : 3.775 22.810 2091 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.79 % Allowed : 16.02 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.22 (0.20), residues: 1711 helix: 2.18 (0.20), residues: 616 sheet: 0.99 (0.28), residues: 368 loop : -0.49 (0.22), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 417 TYR 0.021 0.001 TYR A 335 PHE 0.014 0.001 PHE A 47 TRP 0.028 0.001 TRP B 273 HIS 0.002 0.000 HIS B 450 Details of bonding type rmsd covalent geometry : bond 0.00283 (14539) covalent geometry : angle 0.56398 (19719) SS BOND : bond 0.00309 ( 10) SS BOND : angle 1.75042 ( 20) hydrogen bonds : bond 0.03546 ( 727) hydrogen bonds : angle 4.08887 ( 2505) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 251 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ASP cc_start: 0.8748 (m-30) cc_final: 0.8447 (m-30) REVERT: A 47 PHE cc_start: 0.8877 (t80) cc_final: 0.8557 (t80) REVERT: A 231 TYR cc_start: 0.8948 (OUTLIER) cc_final: 0.7992 (t80) REVERT: A 279 ASN cc_start: 0.8016 (t0) cc_final: 0.7783 (t0) REVERT: A 307 SER cc_start: 0.9146 (OUTLIER) cc_final: 0.8913 (p) REVERT: B 115 ASP cc_start: 0.8250 (m-30) cc_final: 0.7942 (t0) REVERT: B 339 ASN cc_start: 0.8149 (m-40) cc_final: 0.7742 (m-40) REVERT: B 430 PHE cc_start: 0.9497 (t80) cc_final: 0.9093 (t80) REVERT: C 280 MET cc_start: 0.7891 (tmm) cc_final: 0.7115 (mtm) REVERT: C 300 GLN cc_start: 0.8539 (OUTLIER) cc_final: 0.8242 (tt0) REVERT: C 416 LYS cc_start: 0.8767 (pttt) cc_final: 0.8461 (ptpp) REVERT: D 343 ARG cc_start: 0.8277 (mmm160) cc_final: 0.8016 (mmp80) REVERT: D 345 HIS cc_start: 0.7914 (p90) cc_final: 0.7542 (p-80) REVERT: E 131 ASP cc_start: 0.9296 (p0) cc_final: 0.8958 (p0) REVERT: E 333 LEU cc_start: 0.9353 (mm) cc_final: 0.8979 (mm) outliers start: 28 outliers final: 23 residues processed: 264 average time/residue: 0.0983 time to fit residues: 39.7909 Evaluate side-chains 270 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 244 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 232 CYS Chi-restraints excluded: chain C residue 300 GLN Chi-restraints excluded: chain C residue 436 PHE Chi-restraints excluded: chain D residue 52 MET Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 188 MET Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 332 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 149 optimal weight: 0.8980 chunk 14 optimal weight: 8.9990 chunk 88 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 84 optimal weight: 0.0970 chunk 136 optimal weight: 10.0000 chunk 101 optimal weight: 6.9990 chunk 169 optimal weight: 0.5980 chunk 75 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 chunk 156 optimal weight: 2.9990 overall best weight: 1.0780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN ** D 300 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 = 0.3484 r_free = 0.3484 target = 0.114768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.084714 restraints weight = 23792.924| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 2.87 r_work: 0.2854 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 14549 Z= 0.117 Angle : 0.559 11.556 19739 Z= 0.279 Chirality : 0.043 0.289 2233 Planarity : 0.003 0.032 2453 Dihedral : 3.735 21.172 2091 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.86 % Allowed : 16.53 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.29 (0.20), residues: 1711 helix: 2.26 (0.21), residues: 610 sheet: 1.01 (0.28), residues: 366 loop : -0.43 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 414 TYR 0.020 0.001 TYR A 335 PHE 0.014 0.001 PHE A 47 TRP 0.031 0.001 TRP B 273 HIS 0.002 0.000 HIS B 450 Details of bonding type rmsd covalent geometry : bond 0.00270 (14539) covalent geometry : angle 0.55680 (19719) SS BOND : bond 0.00303 ( 10) SS BOND : angle 1.65897 ( 20) hydrogen bonds : bond 0.03510 ( 727) hydrogen bonds : angle 4.07222 ( 2505) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2736.42 seconds wall clock time: 47 minutes 49.95 seconds (2869.95 seconds total)