Starting phenix.real_space_refine on Mon Oct 26 21:02:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/29kn_57241/10_2026/29kn_57241.cif Found real_map, /net/cci-nas-00/data/ceres_data/29kn_57241/10_2026/29kn_57241.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/29kn_57241/10_2026/29kn_57241.map" default_real_map = "/net/cci-nas-00/data/ceres_data/29kn_57241/10_2026/29kn_57241.map" model { file = "/net/cci-nas-00/data/ceres_data/29kn_57241/10_2026/29kn_57241.cif" } default_model = "/net/cci-nas-00/data/ceres_data/29kn_57241/10_2026/29kn_57241.cif" } resolution = 3.37 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= 0.004 sd= 1.055 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 74 5.16 5 C 13374 2.51 5 N 4010 2.21 5 O 4170 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21636 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2400 Classifications: {'peptide': 322} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 10, 'TRANS': 311} Chain breaks: 2 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 62 Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "B" Number of atoms: 2794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 2794 Classifications: {'peptide': 406} Incomplete info: {'truncation_to_alanine': 105} Link IDs: {'PTRANS': 10, 'TRANS': 395} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 357 Unresolved non-hydrogen angles: 445 Unresolved non-hydrogen dihedrals: 283 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLU:plan': 15, 'GLN:plan1': 6, 'ASP:plan': 10, 'ARG:plan': 6, 'TYR:plan': 2, 'PHE:plan': 3} Unresolved non-hydrogen planarities: 176 Chain: "C" Number of atoms: 2780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 2780 Classifications: {'peptide': 407} Incomplete info: {'truncation_to_alanine': 107} Link IDs: {'PTRANS': 10, 'TRANS': 396} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 376 Unresolved non-hydrogen angles: 464 Unresolved non-hydrogen dihedrals: 296 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'ARG:plan': 7, 'GLU:plan': 24, 'ASP:plan': 9, 'GLN:plan1': 6, 'TYR:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 201 Chain: "D" Number of atoms: 2758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 2758 Classifications: {'peptide': 403} Incomplete info: {'truncation_to_alanine': 104} Link IDs: {'PTRANS': 10, 'TRANS': 392} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 370 Unresolved non-hydrogen angles: 456 Unresolved non-hydrogen dihedrals: 294 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'ARG:plan': 7, 'ASP:plan': 10, 'GLU:plan': 22, 'GLN:plan1': 6, 'TYR:plan': 1, 'PHE:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 201 Chain: "E" Number of atoms: 2637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 2637 Classifications: {'peptide': 388} Incomplete info: {'truncation_to_alanine': 109} Link IDs: {'PTRANS': 10, 'TRANS': 377} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 389 Unresolved non-hydrogen angles: 479 Unresolved non-hydrogen dihedrals: 311 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLU:plan': 23, 'GLN:plan1': 8, 'ASP:plan': 10, 'ARG:plan': 6, 'TYR:plan': 2, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 210 Chain: "F" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 2900 Classifications: {'peptide': 419} Incomplete info: {'truncation_to_alanine': 101} Link IDs: {'PTRANS': 11, 'TRANS': 407} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 352 Unresolved non-hydrogen angles: 434 Unresolved non-hydrogen dihedrals: 278 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLU:plan': 20, 'ARG:plan': 6, 'ASP:plan': 10, 'GLN:plan1': 6, 'TYR:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 183 Chain: "G" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 707 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 3, 'TRANS': 104} Chain breaks: 2 Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 183 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 3, 'ARG:plan': 6, 'HIS:plan': 2, 'GLN:plan1': 5, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 108 Chain: "H" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 914 Classifications: {'peptide': 184} Incomplete info: {'truncation_to_alanine': 165} Link IDs: {'PTRANS': 9, 'TRANS': 174} Chain breaks: 1 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 620 Unresolved non-hydrogen angles: 785 Unresolved non-hydrogen dihedrals: 529 Unresolved non-hydrogen chiralities: 49 Planarities with less than four sites: {'TRP:plan': 4, 'GLU:plan': 14, 'ARG:plan': 11, 'GLN:plan1': 9, 'ASP:plan': 11, 'HIS:plan': 3, 'TYR:plan': 7, 'PHE:plan': 5, 'ASN:plan1': 5} Unresolved non-hydrogen planarities: 325 Chain: "I" Number of atoms: 894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 894 Classifications: {'peptide': 180} Incomplete info: {'truncation_to_alanine': 163} Link IDs: {'PTRANS': 8, 'TRANS': 171} Chain breaks: 1 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 617 Unresolved non-hydrogen angles: 781 Unresolved non-hydrogen dihedrals: 528 Unresolved non-hydrogen chiralities: 48 Planarities with less than four sites: {'TRP:plan': 4, 'GLU:plan': 13, 'ARG:plan': 11, 'GLN:plan1': 9, 'ASP:plan': 11, 'HIS:plan': 4, 'TYR:plan': 7, 'PHE:plan': 5, 'ASN:plan1': 5} Unresolved non-hydrogen planarities: 326 Chain: "J" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 951 Classifications: {'peptide': 192} Incomplete info: {'truncation_to_alanine': 169} Link IDs: {'PTRANS': 10, 'TRANS': 181} Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 632 Unresolved non-hydrogen angles: 801 Unresolved non-hydrogen dihedrals: 538 Unresolved non-hydrogen chiralities: 51 Planarities with less than four sites: {'TRP:plan': 4, 'GLU:plan': 14, 'ARG:plan': 11, 'GLN:plan1': 9, 'ASP:plan': 11, 'HIS:plan': 3, 'TYR:plan': 7, 'PHE:plan': 5, 'ASN:plan1': 6} Unresolved non-hydrogen planarities: 328 Chain: "K" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 889 Classifications: {'peptide': 179} Incomplete info: {'truncation_to_alanine': 162} Link IDs: {'PTRANS': 9, 'TRANS': 169} Chain breaks: 1 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 612 Unresolved non-hydrogen angles: 775 Unresolved non-hydrogen dihedrals: 523 Unresolved non-hydrogen chiralities: 47 Planarities with less than four sites: {'TRP:plan': 4, 'GLU:plan': 14, 'ARG:plan': 11, 'GLN:plan1': 9, 'ASP:plan': 11, 'HIS:plan': 3, 'TYR:plan': 7, 'PHE:plan': 5, 'ASN:plan1': 5} Unresolved non-hydrogen planarities: 325 Chain: "L" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 904 Classifications: {'peptide': 182} Incomplete info: {'truncation_to_alanine': 164} Link IDs: {'PTRANS': 9, 'TRANS': 172} Chain breaks: 1 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 618 Unresolved non-hydrogen angles: 782 Unresolved non-hydrogen dihedrals: 528 Unresolved non-hydrogen chiralities: 48 Planarities with less than four sites: {'TRP:plan': 4, 'GLU:plan': 14, 'ARG:plan': 11, 'GLN:plan1': 9, 'ASP:plan': 11, 'HIS:plan': 3, 'TYR:plan': 7, 'PHE:plan': 5, 'ASN:plan1': 5} Unresolved non-hydrogen planarities: 325 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" C1' ADP A 501 " occ=0.76 ... (25 atoms not shown) pdb=" PB ADP A 501 " occ=0.76 residue: pdb=" C1' ADP C 501 " occ=0.76 ... (25 atoms not shown) pdb=" PB ADP C 501 " occ=0.76 residue: pdb=" C1' ADP D 501 " occ=0.76 ... (25 atoms not shown) pdb=" PB ADP D 501 " occ=0.76 residue: pdb=" C1' ADP F 501 " occ=0.76 ... (25 atoms not shown) pdb=" PB ADP F 501 " occ=0.76 Time building chain proxies: 5.17, per 1000 atoms: 0.24 Number of scatterers: 21636 At special positions: 0 Unit cell: (171.68, 158.36, 131.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 74 16.00 P 8 15.00 O 4170 8.00 N 4010 7.00 C 13374 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.83 Conformation dependent library (CDL) restraints added in 1.3 seconds 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6296 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 44 sheets defined 42.1% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 42 through 58 Processing helix chain 'A' and resid 75 through 88 removed outlier: 3.707A pdb=" N ALA A 84 " --> pdb=" O ALA A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 101 No H-bonds generated for 'chain 'A' and resid 99 through 101' Processing helix chain 'A' and resid 107 through 118 Processing helix chain 'A' and resid 240 through 247 removed outlier: 3.851A pdb=" N ASP A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 289 Processing helix chain 'A' and resid 303 through 307 Processing helix chain 'A' and resid 308 through 320 removed outlier: 3.584A pdb=" N GLU A 320 " --> pdb=" O HIS A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 350 Processing helix chain 'A' and resid 351 through 356 removed outlier: 3.652A pdb=" N ASP A 356 " --> pdb=" O LEU A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 383 removed outlier: 3.933A pdb=" N GLN A 373 " --> pdb=" O GLN A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 401 Processing helix chain 'A' and resid 402 through 408 Processing helix chain 'A' and resid 409 through 421 removed outlier: 3.964A pdb=" N ALA A 413 " --> pdb=" O LEU A 409 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU A 415 " --> pdb=" O THR A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 437 Processing helix chain 'A' and resid 439 through 451 Processing helix chain 'B' and resid 49 through 66 Processing helix chain 'B' and resid 82 through 95 removed outlier: 3.521A pdb=" N GLY B 95 " --> pdb=" O ALA B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 109 Processing helix chain 'B' and resid 114 through 126 Processing helix chain 'B' and resid 175 through 185 Processing helix chain 'B' and resid 210 through 217 removed outlier: 5.181A pdb=" N ARG B 213 " --> pdb=" O THR B 210 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ASP B 216 " --> pdb=" O ARG B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 250 Processing helix chain 'B' and resid 269 through 287 Processing helix chain 'B' and resid 300 through 304 Processing helix chain 'B' and resid 305 through 316 Processing helix chain 'B' and resid 347 through 352 Processing helix chain 'B' and resid 363 through 379 Processing helix chain 'B' and resid 383 through 397 Processing helix chain 'B' and resid 398 through 416 removed outlier: 3.602A pdb=" N ALA B 402 " --> pdb=" O SER B 398 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N THR B 407 " --> pdb=" O ILE B 403 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA B 408 " --> pdb=" O GLN B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 431 Processing helix chain 'B' and resid 435 through 450 removed outlier: 3.666A pdb=" N TYR B 446 " --> pdb=" O TYR B 442 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ALA B 449 " --> pdb=" O GLU B 445 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE B 450 " --> pdb=" O TYR B 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 21 removed outlier: 3.592A pdb=" N ARG C 21 " --> pdb=" O ARG C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 66 Processing helix chain 'C' and resid 82 through 95 removed outlier: 3.656A pdb=" N GLY C 95 " --> pdb=" O ALA C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 108 removed outlier: 3.675A pdb=" N ILE C 108 " --> pdb=" O GLY C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 126 removed outlier: 3.892A pdb=" N SER C 126 " --> pdb=" O ALA C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 185 Processing helix chain 'C' and resid 210 through 212 No H-bonds generated for 'chain 'C' and resid 210 through 212' Processing helix chain 'C' and resid 244 through 251 Processing helix chain 'C' and resid 258 through 263 removed outlier: 4.329A pdb=" N GLY C 263 " --> pdb=" O ALA C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 286 removed outlier: 3.868A pdb=" N GLU C 285 " --> pdb=" O ALA C 281 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLU C 286 " --> pdb=" O GLU C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 304 Processing helix chain 'C' and resid 305 through 317 removed outlier: 3.745A pdb=" N GLU C 317 " --> pdb=" O ASN C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 352 Processing helix chain 'C' and resid 363 through 379 Processing helix chain 'C' and resid 383 through 397 Processing helix chain 'C' and resid 398 through 416 removed outlier: 3.564A pdb=" N ALA C 402 " --> pdb=" O SER C 398 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N THR C 407 " --> pdb=" O ILE C 403 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA C 408 " --> pdb=" O GLN C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 433 Processing helix chain 'C' and resid 435 through 443 removed outlier: 3.987A pdb=" N MET C 443 " --> pdb=" O SER C 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 66 Processing helix chain 'D' and resid 82 through 95 Processing helix chain 'D' and resid 114 through 125 Processing helix chain 'D' and resid 175 through 185 Processing helix chain 'D' and resid 210 through 212 No H-bonds generated for 'chain 'D' and resid 210 through 212' Processing helix chain 'D' and resid 244 through 252 Processing helix chain 'D' and resid 258 through 262 Processing helix chain 'D' and resid 269 through 287 Processing helix chain 'D' and resid 300 through 304 Processing helix chain 'D' and resid 305 through 317 removed outlier: 3.848A pdb=" N GLU D 317 " --> pdb=" O ASN D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 352 Processing helix chain 'D' and resid 363 through 378 removed outlier: 3.838A pdb=" N GLN D 369 " --> pdb=" O LYS D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 397 Processing helix chain 'D' and resid 398 through 416 removed outlier: 3.784A pdb=" N ALA D 402 " --> pdb=" O SER D 398 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU D 405 " --> pdb=" O TYR D 401 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ILE D 406 " --> pdb=" O ALA D 402 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N THR D 407 " --> pdb=" O ILE D 403 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ALA D 408 " --> pdb=" O GLN D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 433 removed outlier: 3.604A pdb=" N VAL D 429 " --> pdb=" O ASP D 425 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N TYR D 430 " --> pdb=" O ILE D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 444 removed outlier: 3.504A pdb=" N MET D 443 " --> pdb=" O SER D 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 66 Processing helix chain 'E' and resid 82 through 94 Processing helix chain 'E' and resid 114 through 125 Processing helix chain 'E' and resid 175 through 185 Processing helix chain 'E' and resid 210 through 212 No H-bonds generated for 'chain 'E' and resid 210 through 212' Processing helix chain 'E' and resid 244 through 252 Processing helix chain 'E' and resid 269 through 287 Processing helix chain 'E' and resid 300 through 304 Processing helix chain 'E' and resid 305 through 316 Processing helix chain 'E' and resid 347 through 352 Processing helix chain 'E' and resid 365 through 378 removed outlier: 3.566A pdb=" N GLU E 376 " --> pdb=" O ARG E 372 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU E 378 " --> pdb=" O ARG E 374 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 397 Processing helix chain 'E' and resid 398 through 416 removed outlier: 3.653A pdb=" N ALA E 402 " --> pdb=" O SER E 398 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE E 406 " --> pdb=" O ALA E 402 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N THR E 407 " --> pdb=" O ILE E 403 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ALA E 408 " --> pdb=" O GLN E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 422 through 433 Processing helix chain 'E' and resid 435 through 447 removed outlier: 3.728A pdb=" N MET E 443 " --> pdb=" O SER E 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 17 through 23 Processing helix chain 'F' and resid 49 through 66 Processing helix chain 'F' and resid 82 through 95 removed outlier: 3.509A pdb=" N ALA F 87 " --> pdb=" O LYS F 83 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY F 95 " --> pdb=" O ALA F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 109 Processing helix chain 'F' and resid 114 through 125 Processing helix chain 'F' and resid 175 through 185 Processing helix chain 'F' and resid 210 through 212 No H-bonds generated for 'chain 'F' and resid 210 through 212' Processing helix chain 'F' and resid 243 through 251 removed outlier: 3.505A pdb=" N ILE F 247 " --> pdb=" O SER F 243 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 262 Processing helix chain 'F' and resid 269 through 287 Processing helix chain 'F' and resid 300 through 304 Processing helix chain 'F' and resid 305 through 316 Processing helix chain 'F' and resid 347 through 352 Processing helix chain 'F' and resid 363 through 379 removed outlier: 3.970A pdb=" N GLN F 369 " --> pdb=" O LYS F 365 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 397 Processing helix chain 'F' and resid 398 through 416 removed outlier: 4.089A pdb=" N THR F 407 " --> pdb=" O ILE F 403 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA F 408 " --> pdb=" O GLN F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 422 through 433 Processing helix chain 'F' and resid 435 through 443 Processing helix chain 'G' and resid 101 through 112 Processing helix chain 'G' and resid 117 through 126 Processing helix chain 'G' and resid 128 through 135 removed outlier: 4.260A pdb=" N GLY G 132 " --> pdb=" O GLY G 128 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 153 removed outlier: 4.639A pdb=" N GLU G 146 " --> pdb=" O GLY G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 162 through 172 removed outlier: 3.961A pdb=" N ILE G 166 " --> pdb=" O ALA G 162 " (cutoff:3.500A) Processing helix chain 'G' and resid 175 through 182 Processing helix chain 'G' and resid 184 through 197 removed outlier: 3.805A pdb=" N GLY G 193 " --> pdb=" O GLU G 189 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N PHE G 195 " --> pdb=" O CYS G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 230 through 241 Processing helix chain 'H' and resid 3 through 13 Processing helix chain 'H' and resid 112 through 114 No H-bonds generated for 'chain 'H' and resid 112 through 114' Processing helix chain 'H' and resid 142 through 148 Processing helix chain 'H' and resid 153 through 155 No H-bonds generated for 'chain 'H' and resid 153 through 155' Processing helix chain 'H' and resid 173 through 190 removed outlier: 3.596A pdb=" N LYS H 189 " --> pdb=" O LYS H 185 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 13 Processing helix chain 'I' and resid 112 through 114 No H-bonds generated for 'chain 'I' and resid 112 through 114' Processing helix chain 'I' and resid 142 through 148 Processing helix chain 'I' and resid 153 through 155 No H-bonds generated for 'chain 'I' and resid 153 through 155' Processing helix chain 'I' and resid 173 through 190 removed outlier: 3.596A pdb=" N LYS I 189 " --> pdb=" O LYS I 185 " (cutoff:3.500A) Processing helix chain 'J' and resid 3 through 13 Processing helix chain 'J' and resid 112 through 114 No H-bonds generated for 'chain 'J' and resid 112 through 114' Processing helix chain 'J' and resid 142 through 148 Processing helix chain 'J' and resid 153 through 155 No H-bonds generated for 'chain 'J' and resid 153 through 155' Processing helix chain 'J' and resid 173 through 190 removed outlier: 3.596A pdb=" N LYS J 189 " --> pdb=" O LYS J 185 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 13 Processing helix chain 'K' and resid 112 through 114 No H-bonds generated for 'chain 'K' and resid 112 through 114' Processing helix chain 'K' and resid 142 through 148 Processing helix chain 'K' and resid 153 through 155 No H-bonds generated for 'chain 'K' and resid 153 through 155' Processing helix chain 'K' and resid 173 through 190 removed outlier: 3.597A pdb=" N LYS K 189 " --> pdb=" O LYS K 185 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 13 Processing helix chain 'L' and resid 112 through 114 No H-bonds generated for 'chain 'L' and resid 112 through 114' Processing helix chain 'L' and resid 142 through 148 Processing helix chain 'L' and resid 153 through 155 No H-bonds generated for 'chain 'L' and resid 153 through 155' Processing helix chain 'L' and resid 173 through 190 removed outlier: 3.597A pdb=" N LYS L 189 " --> pdb=" O LYS L 185 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 36 Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 97 removed outlier: 6.566A pdb=" N CYS A 94 " --> pdb=" O PHE A 300 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N ASP A 302 " --> pdb=" O CYS A 94 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N MET A 96 " --> pdb=" O ASP A 302 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LEU A 299 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N ALA A 330 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL A 301 " --> pdb=" O ALA A 330 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL A 66 " --> pdb=" O PHE A 329 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N SER A 331 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU A 68 " --> pdb=" O SER A 331 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ALA A 65 " --> pdb=" O MET A 359 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N ILE A 361 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU A 67 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ILE A 360 " --> pdb=" O LEU B 434 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 238 through 239 Processing sheet with id=AA4, first strand: chain 'A' and resid 336 through 337 Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 104 Processing sheet with id=AA6, first strand: chain 'B' and resid 127 through 129 Processing sheet with id=AA7, first strand: chain 'B' and resid 224 through 225 removed outlier: 5.827A pdb=" N VAL B 225 " --> pdb=" O LEU B 205 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ARG B 207 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ILE B 202 " --> pdb=" O ASP B 196 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N ASP B 196 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N LYS B 204 " --> pdb=" O THR B 194 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N THR B 194 " --> pdb=" O LYS B 204 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY B 206 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ASP B 191 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N THR B 162 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ILE B 145 " --> pdb=" O LYS B 160 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LYS B 160 " --> pdb=" O ILE B 145 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ILE B 147 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N VAL B 158 " --> pdb=" O ILE B 147 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLY B 159 " --> pdb=" O LEU B 174 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 332 through 334 Processing sheet with id=AA9, first strand: chain 'C' and resid 42 through 43 Processing sheet with id=AB1, first strand: chain 'C' and resid 100 through 103 removed outlier: 3.761A pdb=" N ILE C 325 " --> pdb=" O LEU C 296 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA C 327 " --> pdb=" O ILE C 298 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ALA C 72 " --> pdb=" O LEU C 355 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N VAL C 357 " --> pdb=" O ALA C 72 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU C 74 " --> pdb=" O VAL C 357 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 240 through 243 removed outlier: 3.641A pdb=" N VAL C 242 " --> pdb=" O VAL C 129 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY C 128 " --> pdb=" O ILE C 292 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU C 290 " --> pdb=" O ARG C 130 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 224 through 225 removed outlier: 5.826A pdb=" N VAL C 225 " --> pdb=" O LEU C 205 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ARG C 207 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N LYS C 204 " --> pdb=" O THR C 194 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N THR C 194 " --> pdb=" O LYS C 204 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY C 206 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ASP C 191 " --> pdb=" O VAL C 142 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ILE C 137 " --> pdb=" O LYS C 234 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LYS C 234 " --> pdb=" O ILE C 137 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 224 through 225 removed outlier: 5.826A pdb=" N VAL C 225 " --> pdb=" O LEU C 205 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ARG C 207 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N LYS C 204 " --> pdb=" O THR C 194 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N THR C 194 " --> pdb=" O LYS C 204 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY C 206 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ASP C 191 " --> pdb=" O VAL C 142 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N THR C 162 " --> pdb=" O VAL C 143 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ILE C 145 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LYS C 160 " --> pdb=" O ILE C 145 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 332 through 334 Processing sheet with id=AB6, first strand: chain 'C' and resid 381 through 382 removed outlier: 7.578A pdb=" N GLU C 381 " --> pdb=" O VAL C 421 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'D' and resid 42 through 43 Processing sheet with id=AB8, first strand: chain 'D' and resid 100 through 104 removed outlier: 6.252A pdb=" N THR D 101 " --> pdb=" O PHE D 297 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N ASP D 299 " --> pdb=" O THR D 101 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ILE D 103 " --> pdb=" O ASP D 299 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU D 296 " --> pdb=" O ILE D 325 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N ALA D 327 " --> pdb=" O LEU D 296 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ILE D 298 " --> pdb=" O ALA D 327 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL D 73 " --> pdb=" O MET D 326 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N THR D 328 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ILE D 75 " --> pdb=" O THR D 328 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ALA D 72 " --> pdb=" O LEU D 355 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N VAL D 357 " --> pdb=" O ALA D 72 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N LEU D 74 " --> pdb=" O VAL D 357 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'D' and resid 224 through 225 removed outlier: 5.826A pdb=" N VAL D 225 " --> pdb=" O LEU D 205 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N ARG D 207 " --> pdb=" O VAL D 225 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ILE D 202 " --> pdb=" O ASP D 196 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N ASP D 196 " --> pdb=" O ILE D 202 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N LYS D 204 " --> pdb=" O THR D 194 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N THR D 194 " --> pdb=" O LYS D 204 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY D 206 " --> pdb=" O VAL D 192 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ASP D 191 " --> pdb=" O VAL D 142 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 233 through 243 removed outlier: 3.943A pdb=" N LYS D 236 " --> pdb=" O THR D 135 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N THR D 135 " --> pdb=" O LYS D 236 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL D 238 " --> pdb=" O GLU D 133 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N THR D 162 " --> pdb=" O VAL D 143 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ILE D 145 " --> pdb=" O LYS D 160 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LYS D 160 " --> pdb=" O ILE D 145 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 332 through 334 Processing sheet with id=AC3, first strand: chain 'E' and resid 100 through 104 removed outlier: 6.453A pdb=" N THR E 101 " --> pdb=" O PHE E 297 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ASP E 299 " --> pdb=" O THR E 101 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ILE E 103 " --> pdb=" O ASP E 299 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N ALA E 72 " --> pdb=" O LEU E 355 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N VAL E 357 " --> pdb=" O ALA E 72 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LEU E 74 " --> pdb=" O VAL E 357 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 224 through 225 removed outlier: 5.825A pdb=" N VAL E 225 " --> pdb=" O LEU E 205 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ARG E 207 " --> pdb=" O VAL E 225 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ILE E 202 " --> pdb=" O ASP E 196 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N ASP E 196 " --> pdb=" O ILE E 202 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N LYS E 204 " --> pdb=" O THR E 194 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N THR E 194 " --> pdb=" O LYS E 204 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY E 206 " --> pdb=" O VAL E 192 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ASP E 191 " --> pdb=" O VAL E 142 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 233 through 243 removed outlier: 3.531A pdb=" N GLU E 133 " --> pdb=" O VAL E 238 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL E 242 " --> pdb=" O VAL E 129 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N THR E 162 " --> pdb=" O VAL E 143 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ILE E 145 " --> pdb=" O LYS E 160 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LYS E 160 " --> pdb=" O ILE E 145 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ILE E 147 " --> pdb=" O VAL E 158 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL E 158 " --> pdb=" O ILE E 147 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY E 159 " --> pdb=" O LEU E 174 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 332 through 334 Processing sheet with id=AC7, first strand: chain 'F' and resid 42 through 43 Processing sheet with id=AC8, first strand: chain 'F' and resid 100 through 104 removed outlier: 6.482A pdb=" N THR F 101 " --> pdb=" O PHE F 297 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ASP F 299 " --> pdb=" O THR F 101 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ILE F 103 " --> pdb=" O ASP F 299 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LEU F 296 " --> pdb=" O ILE F 325 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N ALA F 327 " --> pdb=" O LEU F 296 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE F 298 " --> pdb=" O ALA F 327 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL F 73 " --> pdb=" O MET F 326 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N THR F 328 " --> pdb=" O VAL F 73 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE F 75 " --> pdb=" O THR F 328 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N ALA F 72 " --> pdb=" O LEU F 355 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N VAL F 357 " --> pdb=" O ALA F 72 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU F 74 " --> pdb=" O VAL F 357 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'F' and resid 224 through 225 removed outlier: 5.826A pdb=" N VAL F 225 " --> pdb=" O LEU F 205 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N ARG F 207 " --> pdb=" O VAL F 225 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ILE F 202 " --> pdb=" O ASP F 196 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ASP F 196 " --> pdb=" O ILE F 202 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N LYS F 204 " --> pdb=" O THR F 194 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N THR F 194 " --> pdb=" O LYS F 204 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY F 206 " --> pdb=" O VAL F 192 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ASP F 191 " --> pdb=" O VAL F 142 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 233 through 242 removed outlier: 3.535A pdb=" N LYS F 236 " --> pdb=" O THR F 135 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR F 135 " --> pdb=" O LYS F 236 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU F 133 " --> pdb=" O VAL F 238 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N THR F 162 " --> pdb=" O VAL F 143 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ILE F 145 " --> pdb=" O LYS F 160 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LYS F 160 " --> pdb=" O ILE F 145 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 332 through 334 Processing sheet with id=AD3, first strand: chain 'H' and resid 65 through 68 removed outlier: 6.275A pdb=" N ARG H 50 " --> pdb=" O GLU H 67 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLU H 39 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ARG H 50 " --> pdb=" O ALA H 37 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ALA H 37 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N TRP H 52 " --> pdb=" O GLU H 35 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N GLU H 35 " --> pdb=" O TRP H 52 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 92 through 95 Processing sheet with id=AD5, first strand: chain 'H' and resid 116 through 121 Processing sheet with id=AD6, first strand: chain 'I' and resid 65 through 68 removed outlier: 6.275A pdb=" N ARG I 50 " --> pdb=" O GLU I 67 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLU I 39 " --> pdb=" O LEU I 48 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ARG I 50 " --> pdb=" O ALA I 37 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ALA I 37 " --> pdb=" O ARG I 50 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N TRP I 52 " --> pdb=" O GLU I 35 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N GLU I 35 " --> pdb=" O TRP I 52 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 92 through 95 Processing sheet with id=AD8, first strand: chain 'I' and resid 116 through 121 Processing sheet with id=AD9, first strand: chain 'J' and resid 65 through 68 removed outlier: 6.275A pdb=" N ARG J 50 " --> pdb=" O GLU J 67 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLU J 39 " --> pdb=" O LEU J 48 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ARG J 50 " --> pdb=" O ALA J 37 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ALA J 37 " --> pdb=" O ARG J 50 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N TRP J 52 " --> pdb=" O GLU J 35 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N GLU J 35 " --> pdb=" O TRP J 52 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 92 through 95 Processing sheet with id=AE2, first strand: chain 'J' and resid 116 through 121 Processing sheet with id=AE3, first strand: chain 'K' and resid 14 through 20 removed outlier: 6.846A pdb=" N GLU K 35 " --> pdb=" O TRP K 52 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N TRP K 52 " --> pdb=" O GLU K 35 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ALA K 37 " --> pdb=" O ARG K 50 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ARG K 50 " --> pdb=" O ALA K 37 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLU K 39 " --> pdb=" O LEU K 48 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ARG K 50 " --> pdb=" O GLU K 67 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 92 through 95 Processing sheet with id=AE5, first strand: chain 'K' and resid 116 through 121 Processing sheet with id=AE6, first strand: chain 'L' and resid 65 through 68 removed outlier: 6.275A pdb=" N ARG L 50 " --> pdb=" O GLU L 67 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLU L 39 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ARG L 50 " --> pdb=" O ALA L 37 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ALA L 37 " --> pdb=" O ARG L 50 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N TRP L 52 " --> pdb=" O GLU L 35 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N GLU L 35 " --> pdb=" O TRP L 52 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 92 through 95 Processing sheet with id=AE8, first strand: chain 'L' and resid 116 through 121 1268 hydrogen bonds defined for protein. 3615 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: 4.80 Time building geometry restraints manager: 2.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 3825 1.28 - 1.41: 4728 1.41 - 1.55: 13083 1.55 - 1.68: 47 1.68 - 1.82: 131 Bond restraints: 21814 Sorted by residual: bond pdb=" C ILE D 393 " pdb=" O ILE D 393 " ideal model delta sigma weight residual 1.237 1.142 0.095 1.17e-02 7.31e+03 6.58e+01 bond pdb=" C THR A 239 " pdb=" O THR A 239 " ideal model delta sigma weight residual 1.234 1.141 0.093 1.22e-02 6.72e+03 5.82e+01 bond pdb=" C GLN B 121 " pdb=" O GLN B 121 " ideal model delta sigma weight residual 1.237 1.155 0.082 1.17e-02 7.31e+03 4.89e+01 bond pdb=" C ILE A 323 " pdb=" O ILE A 323 " ideal model delta sigma weight residual 1.237 1.171 0.066 9.80e-03 1.04e+04 4.48e+01 bond pdb=" C ARG B 124 " pdb=" O ARG B 124 " ideal model delta sigma weight residual 1.237 1.159 0.078 1.17e-02 7.31e+03 4.45e+01 ... (remaining 21809 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.25: 28880 3.25 - 6.50: 833 6.50 - 9.74: 82 9.74 - 12.99: 18 12.99 - 16.24: 4 Bond angle restraints: 29817 Sorted by residual: angle pdb=" C GLU D 136 " pdb=" N ILE D 137 " pdb=" CA ILE D 137 " ideal model delta sigma weight residual 123.19 110.38 12.81 1.24e+00 6.50e-01 1.07e+02 angle pdb=" CA THR D 391 " pdb=" CB THR D 391 " pdb=" OG1 THR D 391 " ideal model delta sigma weight residual 109.60 94.43 15.17 1.50e+00 4.44e-01 1.02e+02 angle pdb=" C THR E 391 " pdb=" CA THR E 391 " pdb=" CB THR E 391 " ideal model delta sigma weight residual 110.88 95.17 15.71 1.57e+00 4.06e-01 1.00e+02 angle pdb=" C ASP B 248 " pdb=" CA ASP B 248 " pdb=" CB ASP B 248 " ideal model delta sigma weight residual 110.85 94.61 16.24 1.70e+00 3.46e-01 9.13e+01 angle pdb=" CA HIS A 20 " pdb=" CB HIS A 20 " pdb=" CG HIS A 20 " ideal model delta sigma weight residual 113.80 104.37 9.43 1.00e+00 1.00e+00 8.90e+01 ... (remaining 29812 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.18: 12744 33.18 - 66.35: 310 66.35 - 99.53: 22 99.53 - 132.70: 5 132.70 - 165.88: 1 Dihedral angle restraints: 13082 sinusoidal: 3405 harmonic: 9677 Sorted by residual: dihedral pdb=" C ASP B 248 " pdb=" N ASP B 248 " pdb=" CA ASP B 248 " pdb=" CB ASP B 248 " ideal model delta harmonic sigma weight residual -122.60 -104.33 -18.27 0 2.50e+00 1.60e-01 5.34e+01 dihedral pdb=" C THR E 391 " pdb=" N THR E 391 " pdb=" CA THR E 391 " pdb=" CB THR E 391 " ideal model delta harmonic sigma weight residual -122.00 -104.50 -17.50 0 2.50e+00 1.60e-01 4.90e+01 dihedral pdb=" C5' ADP C 501 " pdb=" O5' ADP C 501 " pdb=" PA ADP C 501 " pdb=" O2A ADP C 501 " ideal model delta sinusoidal sigma weight residual -60.00 105.88 -165.88 1 2.00e+01 2.50e-03 4.73e+01 ... (remaining 13079 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.124: 3407 0.124 - 0.247: 333 0.247 - 0.371: 40 0.371 - 0.495: 11 0.495 - 0.618: 1 Chirality restraints: 3792 Sorted by residual: chirality pdb=" CA ARG B 53 " pdb=" N ARG B 53 " pdb=" C ARG B 53 " pdb=" CB ARG B 53 " both_signs ideal model delta sigma weight residual False 2.51 1.89 0.62 2.00e-01 2.50e+01 9.55e+00 chirality pdb=" CA VAL D 421 " pdb=" N VAL D 421 " pdb=" C VAL D 421 " pdb=" CB VAL D 421 " both_signs ideal model delta sigma weight residual False 2.44 2.93 -0.49 2.00e-01 2.50e+01 5.89e+00 chirality pdb=" CA GLU F 364 " pdb=" N GLU F 364 " pdb=" C GLU F 364 " pdb=" CB GLU F 364 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.92e+00 ... (remaining 3789 not shown) Planarity restraints: 3946 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 242 " -0.026 2.00e-02 2.50e+03 5.57e-02 3.10e+01 pdb=" C VAL B 242 " 0.096 2.00e-02 2.50e+03 pdb=" O VAL B 242 " -0.037 2.00e-02 2.50e+03 pdb=" N SER B 243 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP D 385 " 0.026 2.00e-02 2.50e+03 5.56e-02 3.09e+01 pdb=" C ASP D 385 " -0.096 2.00e-02 2.50e+03 pdb=" O ASP D 385 " 0.038 2.00e-02 2.50e+03 pdb=" N ALA D 386 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP D 435 " 0.026 2.00e-02 2.50e+03 5.39e-02 2.91e+01 pdb=" C ASP D 435 " -0.093 2.00e-02 2.50e+03 pdb=" O ASP D 435 " 0.035 2.00e-02 2.50e+03 pdb=" N GLU D 436 " 0.032 2.00e-02 2.50e+03 ... (remaining 3943 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.11: 30 2.11 - 2.81: 5831 2.81 - 3.51: 30220 3.51 - 4.20: 43388 4.20 - 4.90: 78700 Nonbonded interactions: 158169 Sorted by model distance: nonbonded pdb=" CD1 TYR G 120 " pdb=" O ALA G 150 " model vdw 1.417 3.340 nonbonded pdb=" NH2 ARG A 117 " pdb=" OD2 ASP A 244 " model vdw 1.531 3.120 nonbonded pdb=" O GLU D 420 " pdb=" NE2 GLN D 422 " model vdw 1.578 3.120 nonbonded pdb=" CD2 LEU F 371 " pdb=" CD2 LEU F 390 " model vdw 1.620 3.880 nonbonded pdb=" CG2 ILE F 13 " pdb=" CA THR F 199 " model vdw 1.625 3.890 ... (remaining 158164 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 'B' and (resid 45 through 111 or (resid 112 and (name N or name CA or nam \ e C or name O or name CB )) or resid 113 through 147 or resid 159 through 212 or \ resid 223 through 239 or (resid 240 and (name N or name CA or name C or name O \ or name CB )) or resid 241 through 245 or (resid 246 and (name N or name CA or n \ ame C or name O or name CB )) or resid 247 through 259 or (resid 260 and (name N \ or name CA or name C or name O or name CB )) or resid 261 through 270 or (resid \ 271 and (name N or name CA or name C or name O or name CB )) or resid 272 throu \ gh 273 or (resid 274 through 275 and (name N or name CA or name C or name O or n \ ame CB )) or resid 276 through 278 or (resid 279 and (name N or name CA or name \ C or name O or name CB )) or resid 280 through 281 or (resid 282 and (name N or \ name CA or name C or name O or name CB )) or resid 283 through 289 or (resid 290 \ and (name N or name CA or name C or name O or name CB )) or resid 291 through 3 \ 16 or (resid 317 and (name N or name CA or name C or name O or name CB )) or res \ id 318 or (resid 319 and (name N or name CA or name C or name O or name CB )) or \ resid 320 through 348 or (resid 349 and (name N or name CA or name C or name O \ or name CB )) or resid 350 through 363 or (resid 364 through 366 and (name N or \ name CA or name C or name O or name CB )) or resid 367 through 375 or (resid 376 \ through 379 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 80 or (resid 381 and (name N or name CA or name C or name O or name CB )) or res \ id 382 through 383 or (resid 384 and (name N or name CA or name C or name O or n \ ame CB )) or resid 385 through 391 or (resid 392 and (name N or name CA or name \ C or name O or name CB )) or resid 393 through 395 or (resid 396 and (name N or \ name CA or name C or name O or name CB )) or resid 397 through 399 or (resid 400 \ and (name N or name CA or name C or name O or name CB )) or resid 401 through 4 \ 14 or (resid 415 through 417 and (name N or name CA or name C or name O or name \ CB )) or resid 418 through 419 or (resid 420 and (name N or name CA or name C or \ name O or name CB )) or resid 421 through 426 or (resid 427 and (name N or name \ CA or name C or name O or name CB )) or resid 428 through 435 or (resid 436 and \ (name N or name CA or name C or name O or name CB )) or resid 437 through 440 o \ r (resid 441 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 42 through 443)) selection = (chain 'C' and (resid 45 through 111 or (resid 112 and (name N or name CA or nam \ e C or name O or name CB )) or resid 113 through 212 or resid 223 through 239 or \ (resid 240 and (name N or name CA or name C or name O or name CB )) or resid 24 \ 1 through 264 or (resid 265 and (name N or name CA or name C or name O or name C \ B )) or resid 266 through 274 or (resid 275 and (name N or name CA or name C or \ name O or name CB )) or resid 276 through 278 or (resid 279 and (name N or name \ CA or name C or name O or name CB )) or resid 280 through 284 or (resid 285 thro \ ugh 286 and (name N or name CA or name C or name O or name CB )) or (resid 287 t \ hrough 290 and (name N or name CA or name C or name O or name CB )) or resid 291 \ through 348 or (resid 349 and (name N or name CA or name C or name O or name CB \ )) or resid 350 through 363 or (resid 364 through 366 and (name N or name CA or \ name C or name O or name CB )) or resid 367 through 376 or (resid 377 through 3 \ 79 and (name N or name CA or name C or name O or name CB )) or resid 380 or (res \ id 381 and (name N or name CA or name C or name O or name CB )) or resid 382 thr \ ough 399 or (resid 400 and (name N or name CA or name C or name O or name CB )) \ or resid 401 through 415 or (resid 416 through 417 and (name N or name CA or nam \ e C or name O or name CB )) or resid 418 through 419 or (resid 420 and (name N o \ r name CA or name C or name O or name CB )) or resid 421 through 426 or (resid 4 \ 27 and (name N or name CA or name C or name O or name CB )) or resid 428 through \ 443)) selection = (chain 'D' and (resid 45 through 147 or resid 159 through 212 or resid 223 throu \ gh 253 or (resid 254 through 255 and (name N or name CA or name C or name O or n \ ame CB )) or resid 256 through 259 or (resid 260 and (name N or name CA or name \ C or name O or name CB )) or resid 261 through 264 or (resid 265 and (name N or \ name CA or name C or name O or name CB )) or resid 266 or (resid 267 and (name N \ or name CA or name C or name O or name CB )) or resid 268 or (resid 269 and (na \ me N or name CA or name C or name O or name CB )) or resid 270 or (resid 271 and \ (name N or name CA or name C or name O or name CB )) or resid 272 through 274 o \ r (resid 275 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 76 through 278 or (resid 279 and (name N or name CA or name C or name O or name \ CB )) or resid 280 through 281 or (resid 282 and (name N or name CA or name C or \ name O or name CB )) or resid 283 through 284 or (resid 285 through 286 and (na \ me N or name CA or name C or name O or name CB )) or resid 287 or (resid 288 thr \ ough 290 and (name N or name CA or name C or name O or name CB )) or resid 291 t \ hrough 316 or (resid 317 and (name N or name CA or name C or name O or name CB ) \ ) or resid 318 or (resid 319 and (name N or name CA or name C or name O or name \ CB )) or resid 320 through 348 or (resid 349 and (name N or name CA or name C or \ name O or name CB )) or resid 350 through 365 or (resid 366 and (name N or name \ CA or name C or name O or name CB )) or resid 367 through 380 or (resid 381 and \ (name N or name CA or name C or name O or name CB )) or resid 382 through 383 o \ r (resid 384 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 85 through 391 or (resid 392 and (name N or name CA or name C or name O or name \ CB )) or resid 393 through 395 or (resid 396 and (name N or name CA or name C or \ name O or name CB )) or resid 397 through 399 or (resid 400 and (name N or name \ CA or name C or name O or name CB )) or resid 401 through 419 or (resid 420 and \ (name N or name CA or name C or name O or name CB )) or resid 421 through 443)) \ selection = (chain 'E' and (resid 45 through 111 or (resid 112 and (name N or name CA or nam \ e C or name O or name CB )) or resid 113 through 147 or resid 159 through 212 or \ (resid 223 through 238 and (name N or name CA or name C or name O or name CB )) \ or resid 239 or (resid 240 and (name N or name CA or name C or name O or name C \ B )) or resid 241 through 253 or (resid 254 through 255 and (name N or name CA o \ r name C or name O or name CB )) or resid 256 through 259 or (resid 260 and (nam \ e N or name CA or name C or name O or name CB )) or resid 261 through 264 or (re \ sid 265 and (name N or name CA or name C or name O or name CB )) or resid 266 th \ rough 268 or (resid 269 and (name N or name CA or name C or name O or name CB )) \ or resid 270 through 281 or (resid 282 and (name N or name CA or name C or name \ O or name CB )) or resid 283 through 285 or (resid 286 and (name N or name CA o \ r name C or name O or name CB )) or resid 287 through 299 or (resid 300 and (nam \ e N or name CA or name C or name O or name CB )) or resid 301 through 316 or (re \ sid 317 and (name N or name CA or name C or name O or name CB )) or resid 318 th \ rough 363 or (resid 364 through 366 and (name N or name CA or name C or name O o \ r name CB )) or resid 367 through 378 or (resid 379 and (name N or name CA or na \ me C or name O or name CB )) or resid 380 through 383 or (resid 384 and (name N \ or name CA or name C or name O or name CB )) or resid 385 through 391 or (resid \ 392 and (name N or name CA or name C or name O or name CB )) or resid 393 throug \ h 395 or (resid 396 and (name N or name CA or name C or name O or name CB )) or \ resid 397 through 399 or (resid 400 and (name N or name CA or name C or name O o \ r name CB )) or resid 401 through 415 or (resid 416 through 417 and (name N or n \ ame CA or name C or name O or name CB )) or resid 418 through 426 or (resid 427 \ and (name N or name CA or name C or name O or name CB )) or resid 428 through 43 \ 5 or (resid 436 and (name N or name CA or name C or name O or name CB )) or resi \ d 437 through 443)) selection = (chain 'F' and (resid 45 through 111 or (resid 112 and (name N or name CA or nam \ e C or name O or name CB )) or resid 113 through 212 or resid 223 through 239 or \ (resid 240 and (name N or name CA or name C or name O or name CB )) or resid 24 \ 1 through 252 or (resid 253 through 255 and (name N or name CA or name C or name \ O or name CB )) or resid 256 through 259 or (resid 260 and (name N or name CA o \ r name C or name O or name CB )) or resid 261 through 264 or (resid 265 and (nam \ e N or name CA or name C or name O or name CB )) or resid 266 through 268 or (re \ sid 269 and (name N or name CA or name C or name O or name CB )) or resid 270 th \ rough 274 or (resid 275 and (name N or name CA or name C or name O or name CB )) \ or resid 276 through 278 or (resid 279 and (name N or name CA or name C or name \ O or name CB )) or resid 280 through 281 or (resid 282 and (name N or name CA o \ r name C or name O or name CB )) or resid 283 through 285 or (resid 286 and (nam \ e N or name CA or name C or name O or name CB )) or (resid 287 through 290 and ( \ name N or name CA or name C or name O or name CB )) or resid 291 through 316 or \ (resid 317 and (name N or name CA or name C or name O or name CB )) or resid 318 \ through 363 or (resid 364 through 366 and (name N or name CA or name C or name \ O or name CB )) or resid 367 through 375 or (resid 376 through 379 and (name N o \ r name CA or name C or name O or name CB )) or resid 380 through 383 or (resid 3 \ 84 and (name N or name CA or name C or name O or name CB )) or resid 385 through \ 391 or (resid 392 and (name N or name CA or name C or name O or name CB )) or r \ esid 393 through 415 or (resid 416 through 417 and (name N or name CA or name C \ or name O or name CB )) or resid 418 through 419 or (resid 420 and (name N or na \ me CA or name C or name O or name CB )) or resid 421 through 426 or (resid 427 a \ nd (name N or name CA or name C or name O or name CB )) or resid 428 through 435 \ or (resid 436 and (name N or name CA or name C or name O or name CB )) or resid \ 437 through 443)) } ncs_group { reference = (chain 'H' and (resid 4 through 71 or resid 83 through 190)) selection = (chain 'I' and resid 4 through 190) selection = (chain 'J' and (resid 4 through 71 or resid 83 through 190)) selection = (chain 'K' and (resid 4 through 71 or resid 83 through 190)) selection = (chain 'L' and (resid 4 through 71 or resid 83 through 190)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.76 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: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.270 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.290 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 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 : 0.013 0.822 21818 Z= 1.114 Angle : 1.322 16.241 29817 Z= 0.904 Chirality : 0.079 0.618 3792 Planarity : 0.007 0.077 3946 Dihedral : 15.191 165.878 6786 Min Nonbonded Distance : 1.417 Molprobity Statistics. All-atom Clashscore : 24.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 4.02 % Allowed : 24.60 % Favored : 71.38 % Cbeta Deviations : 0.73 % Peptide Plane: Cis-proline : 0.00 % 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: 0.42 (0.14), residues: 3314 helix: 0.98 (0.15), residues: 1313 sheet: -0.02 (0.17), residues: 809 loop : -0.11 (0.18), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 124 TYR 0.042 0.002 TYR E 362 PHE 0.028 0.002 PHE B 100 TRP 0.006 0.001 TRP E 283 HIS 0.022 0.002 HIS A 20 Details of bonding type rmsd/Z covalent geometry : bond 0.00899 / 0.64 (21814) covalent geometry : angle 1.32189 / 0.90 (29817) hydrogen bonds : bond 0.16333 / 11.45 ( 1262) hydrogen bonds : angle 6.36086 / 4.63 ( 3615) Misc. bond : bond 0.67155 / 33.51 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 248 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 THR cc_start: 0.9223 (OUTLIER) cc_final: 0.8788 (t) REVERT: B 307 GLU cc_start: 0.9167 (mt-10) cc_final: 0.8939 (mm-30) REVERT: B 320 MET cc_start: 0.8959 (mmt) cc_final: 0.8701 (mmm) REVERT: B 338 THR cc_start: 0.8092 (m) cc_final: 0.7662 (p) REVERT: B 354 LEU cc_start: 0.9609 (mp) cc_final: 0.9396 (mm) REVERT: C 46 MET cc_start: 0.9066 (tpp) cc_final: 0.8855 (mmm) REVERT: C 265 THR cc_start: 0.9714 (p) cc_final: 0.9384 (t) REVERT: C 334 ARG cc_start: 0.8937 (ttt180) cc_final: 0.8469 (ttt90) REVERT: C 387 TYR cc_start: 0.8720 (m-80) cc_final: 0.8514 (m-80) REVERT: D 88 MET cc_start: 0.9516 (ttt) cc_final: 0.9107 (tmm) REVERT: D 108 ILE cc_start: 0.9587 (mt) cc_final: 0.8953 (tp) REVERT: D 113 MET cc_start: 0.9110 (mtm) cc_final: 0.8707 (mtm) REVERT: D 123 PHE cc_start: 0.9626 (m-80) cc_final: 0.9347 (m-80) REVERT: D 257 PHE cc_start: 0.6556 (p90) cc_final: 0.6300 (p90) REVERT: D 340 TYR cc_start: 0.8906 (m-80) cc_final: 0.8337 (m-80) REVERT: D 354 LEU cc_start: 0.9630 (mp) cc_final: 0.9299 (mm) REVERT: E 121 GLN cc_start: 0.9563 (mt0) cc_final: 0.9011 (mm-40) REVERT: E 248 ASP cc_start: 0.8835 (m-30) cc_final: 0.8300 (m-30) REVERT: E 299 ASP cc_start: 0.9068 (t0) cc_final: 0.8179 (t0) REVERT: E 300 GLU cc_start: 0.8870 (pt0) cc_final: 0.8325 (pm20) REVERT: E 301 VAL cc_start: 0.9596 (p) cc_final: 0.9273 (p) REVERT: E 303 MET cc_start: 0.9626 (mmm) cc_final: 0.9007 (mpp) REVERT: E 375 CYS cc_start: 0.8822 (OUTLIER) cc_final: 0.7690 (m) REVERT: E 422 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.8409 (mm110) REVERT: F 106 SER cc_start: 0.9615 (m) cc_final: 0.9329 (p) REVERT: F 248 ASP cc_start: 0.9014 (t0) cc_final: 0.8748 (t0) REVERT: F 346 ILE cc_start: 0.9753 (mt) cc_final: 0.9532 (mm) REVERT: G 168 CYS cc_start: 0.9663 (t) cc_final: 0.9438 (p) REVERT: G 172 SER cc_start: 0.9371 (t) cc_final: 0.9157 (p) outliers start: 60 outliers final: 16 residues processed: 297 average time/residue: 0.1412 time to fit residues: 65.7024 Evaluate side-chains 194 residues out of total 2894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 175 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 366 ASP Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain E residue 375 CYS Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 422 GLN Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain F residue 13 ILE Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain F residue 393 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 298] chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.2980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 50.0000 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 50.0000 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 20.0000 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 236 GLN A 247 ASN A 429 HIS B 251 ASN B 441 GLN ** C 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 GLN C 251 ASN D 302 HIS E 121 GLN F 41 GLN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.082925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.063607 restraints weight = 140709.734| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 5.02 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3037 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3034 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 21818 Z= 0.189 Angle : 0.614 12.707 29817 Z= 0.311 Chirality : 0.044 0.233 3792 Planarity : 0.004 0.036 3946 Dihedral : 7.297 162.301 3588 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 4.56 % Allowed : 24.06 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.14), residues: 3314 helix: 1.71 (0.14), residues: 1339 sheet: 0.37 (0.17), residues: 817 loop : 0.38 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 117 TYR 0.024 0.002 TYR G 120 PHE 0.016 0.002 PHE D 109 TRP 0.037 0.002 TRP D 283 HIS 0.008 0.001 HIS C 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.19 (21814) covalent geometry : angle 0.61438 / 0.31 (29817) hydrogen bonds : bond 0.03156 / 2.17 ( 1262) hydrogen bonds : angle 4.03726 / 2.95 ( 3615) Misc. bond : bond 0.00423 / 0.21 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 175 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 60 LEU cc_start: 0.9471 (OUTLIER) cc_final: 0.9255 (tt) REVERT: B 90 MET cc_start: 0.9475 (ttm) cc_final: 0.9001 (tpp) REVERT: B 354 LEU cc_start: 0.9612 (mp) cc_final: 0.9398 (mm) REVERT: B 415 LYS cc_start: 0.9514 (tttp) cc_final: 0.9246 (tttm) REVERT: B 446 TYR cc_start: 0.9289 (t80) cc_final: 0.9086 (t80) REVERT: C 38 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8218 (mm-30) REVERT: C 46 MET cc_start: 0.9060 (tpp) cc_final: 0.8857 (mmm) REVERT: C 248 ASP cc_start: 0.8800 (m-30) cc_final: 0.8541 (m-30) REVERT: C 265 THR cc_start: 0.9710 (p) cc_final: 0.9354 (t) REVERT: C 334 ARG cc_start: 0.8889 (ttt180) cc_final: 0.8676 (ptm-80) REVERT: C 425 ASP cc_start: 0.9192 (OUTLIER) cc_final: 0.8646 (m-30) REVERT: D 88 MET cc_start: 0.9289 (ttt) cc_final: 0.8998 (tmm) REVERT: D 90 MET cc_start: 0.9274 (OUTLIER) cc_final: 0.8927 (tpp) REVERT: D 108 ILE cc_start: 0.9662 (mt) cc_final: 0.9313 (tp) REVERT: D 115 LYS cc_start: 0.9216 (mmmt) cc_final: 0.8891 (mmtt) REVERT: D 310 SER cc_start: 0.9652 (OUTLIER) cc_final: 0.9290 (p) REVERT: D 354 LEU cc_start: 0.9645 (mp) cc_final: 0.9309 (mm) REVERT: D 375 CYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8720 (t) REVERT: E 90 MET cc_start: 0.9437 (mmm) cc_final: 0.8947 (mpp) REVERT: E 113 MET cc_start: 0.7884 (mmm) cc_final: 0.7552 (mmm) REVERT: E 121 GLN cc_start: 0.9569 (mt0) cc_final: 0.8782 (mm-40) REVERT: E 248 ASP cc_start: 0.8791 (m-30) cc_final: 0.8270 (m-30) REVERT: E 299 ASP cc_start: 0.9221 (t0) cc_final: 0.8624 (t0) REVERT: E 300 GLU cc_start: 0.9069 (pt0) cc_final: 0.8467 (pm20) REVERT: E 303 MET cc_start: 0.9486 (mmm) cc_final: 0.9180 (tpp) REVERT: E 422 GLN cc_start: 0.9066 (OUTLIER) cc_final: 0.8710 (mm-40) REVERT: F 53 ARG cc_start: 0.9576 (OUTLIER) cc_final: 0.9336 (mtp180) REVERT: F 248 ASP cc_start: 0.8944 (t0) cc_final: 0.8701 (t0) REVERT: F 320 MET cc_start: 0.9165 (ppp) cc_final: 0.8926 (ppp) REVERT: F 425 ASP cc_start: 0.9204 (OUTLIER) cc_final: 0.8779 (m-30) outliers start: 68 outliers final: 20 residues processed: 233 average time/residue: 0.1267 time to fit residues: 47.9547 Evaluate side-chains 191 residues out of total 2894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 162 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain C residue 38 GLU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 257 PHE Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 310 SER Chi-restraints excluded: chain D residue 342 SER Chi-restraints excluded: chain D residue 375 CYS Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 265 THR Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 422 GLN Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 53 ARG Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 425 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: [27, 222, 307, 286, 96, 260, 103, 3, 15, 314, 124] chunk 27 optimal weight: 4.9990 chunk 222 optimal weight: 1.9990 chunk 307 optimal weight: 8.9990 chunk 286 optimal weight: 50.0000 chunk 96 optimal weight: 0.7980 chunk 260 optimal weight: 50.0000 chunk 103 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 314 optimal weight: 50.0000 chunk 124 optimal weight: 50.0000 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 HIS F 49 GLN F 313 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.067523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.047471 restraints weight = 109829.945| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 5.25 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2974 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2973 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 21818 Z= 0.206 Angle : 0.577 9.078 29817 Z= 0.291 Chirality : 0.043 0.174 3792 Planarity : 0.004 0.047 3946 Dihedral : 6.991 162.835 3566 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 4.42 % Allowed : 23.46 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.73 (0.15), residues: 3314 helix: 2.03 (0.15), residues: 1345 sheet: 0.65 (0.17), residues: 825 loop : 0.61 (0.19), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 53 TYR 0.023 0.001 TYR E 442 PHE 0.009 0.002 PHE D 109 TRP 0.014 0.001 TRP D 283 HIS 0.008 0.001 HIS A 20 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.21 (21814) covalent geometry : angle 0.57655 / 0.29 (29817) hydrogen bonds : bond 0.03156 / 2.17 ( 1262) hydrogen bonds : angle 3.87125 / 2.79 ( 3615) Misc. bond : bond 0.00279 / 0.14 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 160 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 ASP cc_start: 0.9289 (t0) cc_final: 0.9046 (t0) REVERT: A 431 GLU cc_start: 0.9044 (OUTLIER) cc_final: 0.8639 (mm-30) REVERT: A 436 LEU cc_start: 0.9649 (OUTLIER) cc_final: 0.9447 (mt) REVERT: B 240 HIS cc_start: 0.8884 (OUTLIER) cc_final: 0.7227 (p90) REVERT: C 248 ASP cc_start: 0.8896 (m-30) cc_final: 0.8656 (m-30) REVERT: C 265 THR cc_start: 0.9729 (p) cc_final: 0.9387 (t) REVERT: C 334 ARG cc_start: 0.8885 (ttt180) cc_final: 0.8664 (ptm-80) REVERT: D 90 MET cc_start: 0.9197 (OUTLIER) cc_final: 0.8719 (tpp) REVERT: D 283 TRP cc_start: 0.9260 (m-10) cc_final: 0.8710 (m-90) REVERT: D 310 SER cc_start: 0.9572 (OUTLIER) cc_final: 0.9229 (p) REVERT: D 354 LEU cc_start: 0.9640 (mp) cc_final: 0.9323 (mm) REVERT: E 248 ASP cc_start: 0.8884 (m-30) cc_final: 0.8524 (m-30) REVERT: E 299 ASP cc_start: 0.9349 (t0) cc_final: 0.9066 (t70) REVERT: E 300 GLU cc_start: 0.9187 (pt0) cc_final: 0.8914 (pt0) REVERT: E 303 MET cc_start: 0.9490 (mmm) cc_final: 0.9148 (tpp) REVERT: E 422 GLN cc_start: 0.9161 (OUTLIER) cc_final: 0.8765 (mm-40) REVERT: F 326 MET cc_start: 0.9190 (mpp) cc_final: 0.8807 (mpp) REVERT: F 354 LEU cc_start: 0.9578 (OUTLIER) cc_final: 0.9352 (mt) outliers start: 66 outliers final: 31 residues processed: 219 average time/residue: 0.1319 time to fit residues: 45.8136 Evaluate side-chains 184 residues out of total 2894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 146 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 431 GLU Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 310 SER Chi-restraints excluded: chain D residue 342 SER Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 265 THR Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 422 GLN Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 348 ILE Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain G residue 137 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: [157, 233, 146, 275, 310, 280, 121, 78, 86, 268, 297] chunk 157 optimal weight: 0.0170 chunk 233 optimal weight: 20.0000 chunk 146 optimal weight: 4.9990 chunk 275 optimal weight: 1.9990 chunk 310 optimal weight: 30.0000 chunk 280 optimal weight: 50.0000 chunk 121 optimal weight: 0.6980 chunk 78 optimal weight: 4.9990 chunk 86 optimal weight: 30.0000 chunk 268 optimal weight: 9.9990 chunk 297 optimal weight: 50.0000 overall best weight: 2.5424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 335 ASN ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.067483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.047529 restraints weight = 110607.143| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 5.18 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2983 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2983 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 21818 Z= 0.164 Angle : 0.529 9.485 29817 Z= 0.264 Chirality : 0.042 0.187 3792 Planarity : 0.003 0.035 3946 Dihedral : 6.796 164.937 3565 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 3.62 % Allowed : 24.93 % Favored : 71.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.98 (0.15), residues: 3314 helix: 2.19 (0.15), residues: 1347 sheet: 0.78 (0.17), residues: 832 loop : 0.82 (0.19), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 107 TYR 0.010 0.001 TYR E 442 PHE 0.014 0.001 PHE D 257 TRP 0.011 0.001 TRP D 283 HIS 0.005 0.001 HIS A 20 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (21814) covalent geometry : angle 0.52896 / 0.26 (29817) hydrogen bonds : bond 0.02611 / 1.80 ( 1262) hydrogen bonds : angle 3.64957 / 2.63 ( 3615) Misc. bond : bond 0.00237 / 0.12 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 153 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 302 ASP cc_start: 0.9330 (t0) cc_final: 0.9085 (t0) REVERT: B 240 HIS cc_start: 0.8982 (OUTLIER) cc_final: 0.7070 (p90) REVERT: C 67 LYS cc_start: 0.9750 (mmmm) cc_final: 0.9382 (mptt) REVERT: C 248 ASP cc_start: 0.8923 (m-30) cc_final: 0.8669 (m-30) REVERT: C 265 THR cc_start: 0.9750 (p) cc_final: 0.9424 (t) REVERT: C 334 ARG cc_start: 0.8901 (ttt180) cc_final: 0.8663 (ptm-80) REVERT: C 425 ASP cc_start: 0.9177 (OUTLIER) cc_final: 0.8762 (m-30) REVERT: D 90 MET cc_start: 0.9306 (OUTLIER) cc_final: 0.9072 (tpp) REVERT: D 283 TRP cc_start: 0.9169 (m-10) cc_final: 0.8620 (m-90) REVERT: D 310 SER cc_start: 0.9593 (OUTLIER) cc_final: 0.9268 (p) REVERT: D 354 LEU cc_start: 0.9629 (mp) cc_final: 0.9269 (mm) REVERT: E 248 ASP cc_start: 0.8880 (m-30) cc_final: 0.8557 (m-30) REVERT: E 299 ASP cc_start: 0.9424 (t0) cc_final: 0.9135 (t70) REVERT: E 300 GLU cc_start: 0.9195 (pt0) cc_final: 0.8956 (pt0) REVERT: E 303 MET cc_start: 0.9494 (mmm) cc_final: 0.9162 (tpp) REVERT: E 305 ASP cc_start: 0.8884 (p0) cc_final: 0.8541 (p0) REVERT: E 320 MET cc_start: 0.9139 (mmp) cc_final: 0.8938 (mmm) REVERT: E 422 GLN cc_start: 0.9206 (OUTLIER) cc_final: 0.8867 (mm110) REVERT: F 326 MET cc_start: 0.9282 (mpp) cc_final: 0.8884 (mpp) REVERT: F 338 THR cc_start: 0.8647 (OUTLIER) cc_final: 0.8414 (p) REVERT: F 354 LEU cc_start: 0.9564 (OUTLIER) cc_final: 0.9348 (mt) REVERT: G 195 PHE cc_start: 0.7657 (m-80) cc_final: 0.7432 (m-80) outliers start: 54 outliers final: 30 residues processed: 202 average time/residue: 0.1285 time to fit residues: 41.9746 Evaluate side-chains 186 residues out of total 2894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 149 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 335 ASN Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 115 LYS Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 366 ASP Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 310 SER Chi-restraints excluded: chain D residue 342 SER Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 265 THR Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 422 GLN Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 338 THR Chi-restraints excluded: chain F residue 354 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: [309, 240, 328, 127, 71, 285, 48, 283, 301, 126, 167] chunk 309 optimal weight: 6.9990 chunk 240 optimal weight: 5.9990 chunk 328 optimal weight: 5.9990 chunk 127 optimal weight: 50.0000 chunk 71 optimal weight: 2.9990 chunk 285 optimal weight: 50.0000 chunk 48 optimal weight: 50.0000 chunk 283 optimal weight: 0.6980 chunk 301 optimal weight: 50.0000 chunk 126 optimal weight: 7.9990 chunk 167 optimal weight: 0.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.066044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.046035 restraints weight = 110717.275| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 5.19 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2946 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2946 r_free = 0.2946 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2946 r_free = 0.2946 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.2946 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 21818 Z= 0.211 Angle : 0.563 10.312 29817 Z= 0.281 Chirality : 0.042 0.153 3792 Planarity : 0.003 0.041 3946 Dihedral : 6.788 158.549 3565 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 4.09 % Allowed : 25.20 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.01 (0.15), residues: 3314 helix: 2.22 (0.15), residues: 1346 sheet: 0.74 (0.18), residues: 833 loop : 0.87 (0.20), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 333 TYR 0.023 0.001 TYR E 442 PHE 0.028 0.002 PHE B 257 TRP 0.005 0.001 TRP D 283 HIS 0.007 0.001 HIS A 20 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.21 (21814) covalent geometry : angle 0.56251 / 0.28 (29817) hydrogen bonds : bond 0.02907 / 1.99 ( 1262) hydrogen bonds : angle 3.80531 / 2.72 ( 3615) Misc. bond : bond 0.00233 / 0.12 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 154 time to evaluate : 0.827 Fit side-chains REVERT: A 310 GLU cc_start: 0.9282 (mm-30) cc_final: 0.9039 (mm-30) REVERT: A 364 MET cc_start: 0.8844 (mmt) cc_final: 0.8643 (mmt) REVERT: A 394 LEU cc_start: 0.9720 (OUTLIER) cc_final: 0.9359 (tt) REVERT: B 240 HIS cc_start: 0.9113 (OUTLIER) cc_final: 0.7321 (p90) REVERT: B 320 MET cc_start: 0.9075 (mmm) cc_final: 0.8836 (mmm) REVERT: C 67 LYS cc_start: 0.9728 (mmmm) cc_final: 0.9493 (mmmm) REVERT: C 248 ASP cc_start: 0.8910 (m-30) cc_final: 0.8665 (m-30) REVERT: C 265 THR cc_start: 0.9740 (p) cc_final: 0.9437 (t) REVERT: C 320 MET cc_start: 0.8429 (mtm) cc_final: 0.8226 (pmm) REVERT: C 334 ARG cc_start: 0.8917 (ttt180) cc_final: 0.8669 (ptm-80) REVERT: D 88 MET cc_start: 0.9102 (tmm) cc_final: 0.8464 (tmm) REVERT: D 90 MET cc_start: 0.9298 (OUTLIER) cc_final: 0.8828 (tpp) REVERT: D 283 TRP cc_start: 0.9268 (m-10) cc_final: 0.8746 (m-90) REVERT: D 310 SER cc_start: 0.9618 (OUTLIER) cc_final: 0.9311 (p) REVERT: D 334 ARG cc_start: 0.9127 (ttt180) cc_final: 0.8921 (ptm-80) REVERT: D 354 LEU cc_start: 0.9656 (mp) cc_final: 0.9297 (mm) REVERT: E 113 MET cc_start: 0.7846 (mmm) cc_final: 0.7596 (mmm) REVERT: E 248 ASP cc_start: 0.8864 (m-30) cc_final: 0.8532 (m-30) REVERT: E 299 ASP cc_start: 0.9336 (t0) cc_final: 0.9067 (t70) REVERT: E 300 GLU cc_start: 0.9202 (pt0) cc_final: 0.8960 (pt0) REVERT: E 303 MET cc_start: 0.9491 (mmm) cc_final: 0.9011 (tpp) REVERT: E 422 GLN cc_start: 0.9206 (OUTLIER) cc_final: 0.8791 (mm-40) REVERT: F 354 LEU cc_start: 0.9549 (OUTLIER) cc_final: 0.9280 (mt) REVERT: G 110 ARG cc_start: 0.9516 (tpp80) cc_final: 0.9207 (tpp80) outliers start: 61 outliers final: 36 residues processed: 207 average time/residue: 0.1279 time to fit residues: 43.2778 Evaluate side-chains 185 residues out of total 2894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 143 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 335 ASN Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 366 ASP Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 310 SER Chi-restraints excluded: chain D residue 342 SER Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 265 THR Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 422 GLN Chi-restraints excluded: chain F residue 113 MET Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 348 ILE Chi-restraints excluded: chain F residue 354 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: [69, 115, 292, 2, 76, 178, 306, 74, 179, 211, 1] chunk 69 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 chunk 292 optimal weight: 7.9990 chunk 2 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 chunk 178 optimal weight: 0.7980 chunk 306 optimal weight: 50.0000 chunk 74 optimal weight: 10.0000 chunk 179 optimal weight: 4.9990 chunk 211 optimal weight: 9.9990 chunk 1 optimal weight: 3.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 335 ASN ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.067076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.047347 restraints weight = 109873.919| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 5.19 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2968 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2968 r_free = 0.2968 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2968 r_free = 0.2968 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (10 function evaluations) r_final: 0.2968 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.4317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 21818 Z= 0.112 Angle : 0.496 9.574 29817 Z= 0.245 Chirality : 0.042 0.155 3792 Planarity : 0.003 0.037 3946 Dihedral : 6.498 162.890 3565 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 3.42 % Allowed : 26.41 % Favored : 70.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.22 (0.15), residues: 3314 helix: 2.44 (0.15), residues: 1347 sheet: 0.88 (0.18), residues: 815 loop : 0.90 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 107 TYR 0.013 0.001 TYR E 442 PHE 0.019 0.001 PHE G 195 TRP 0.007 0.001 TRP D 283 HIS 0.004 0.001 HIS A 20 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (21814) covalent geometry : angle 0.49613 / 0.24 (29817) hydrogen bonds : bond 0.02348 / 1.60 ( 1262) hydrogen bonds : angle 3.40398 / 2.45 ( 3615) Misc. bond : bond 0.00182 / 0.09 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 156 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 310 GLU cc_start: 0.9292 (mm-30) cc_final: 0.9065 (mm-30) REVERT: B 320 MET cc_start: 0.8983 (mmm) cc_final: 0.8642 (mmm) REVERT: C 38 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8516 (mm-30) REVERT: C 248 ASP cc_start: 0.8924 (m-30) cc_final: 0.8657 (m-30) REVERT: C 265 THR cc_start: 0.9697 (p) cc_final: 0.9425 (t) REVERT: C 334 ARG cc_start: 0.8892 (ttt180) cc_final: 0.8591 (ptm-80) REVERT: C 382 MET cc_start: 0.8457 (ptp) cc_final: 0.8213 (ptm) REVERT: D 90 MET cc_start: 0.9267 (OUTLIER) cc_final: 0.8775 (tpp) REVERT: D 107 GLU cc_start: 0.9156 (tt0) cc_final: 0.8944 (tm-30) REVERT: D 283 TRP cc_start: 0.9283 (m-10) cc_final: 0.8772 (m-90) REVERT: D 303 MET cc_start: 0.9647 (tpp) cc_final: 0.9375 (mmt) REVERT: D 310 SER cc_start: 0.9610 (OUTLIER) cc_final: 0.9307 (p) REVERT: D 340 TYR cc_start: 0.8934 (m-80) cc_final: 0.8728 (m-80) REVERT: D 354 LEU cc_start: 0.9628 (mp) cc_final: 0.9216 (mm) REVERT: E 113 MET cc_start: 0.7826 (mmm) cc_final: 0.7603 (mmm) REVERT: E 299 ASP cc_start: 0.9426 (t0) cc_final: 0.9167 (t70) REVERT: E 300 GLU cc_start: 0.9168 (pt0) cc_final: 0.8963 (pt0) REVERT: E 303 MET cc_start: 0.9443 (mmm) cc_final: 0.9132 (tpp) REVERT: E 422 GLN cc_start: 0.9227 (OUTLIER) cc_final: 0.8874 (mm110) REVERT: F 88 MET cc_start: 0.9390 (tpp) cc_final: 0.9150 (tpp) REVERT: F 326 MET cc_start: 0.9284 (mpp) cc_final: 0.8908 (mpp) REVERT: F 340 TYR cc_start: 0.9247 (m-80) cc_final: 0.8760 (m-10) outliers start: 51 outliers final: 33 residues processed: 203 average time/residue: 0.1269 time to fit residues: 41.8564 Evaluate side-chains 185 residues out of total 2894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 148 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 335 ASN Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain C residue 38 GLU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 113 MET Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 310 SER Chi-restraints excluded: chain D residue 342 SER Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 265 THR Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 422 GLN Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 370 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: [138, 36, 297, 89, 68, 70, 146, 319, 93, 191, 16] chunk 138 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 chunk 297 optimal weight: 50.0000 chunk 89 optimal weight: 50.0000 chunk 68 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 chunk 146 optimal weight: 4.9990 chunk 319 optimal weight: 40.0000 chunk 93 optimal weight: 0.5980 chunk 191 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 335 ASN ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.066516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.046644 restraints weight = 111173.715| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 5.13 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2963 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2963 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.4488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21818 Z= 0.139 Angle : 0.519 11.696 29817 Z= 0.253 Chirality : 0.041 0.153 3792 Planarity : 0.003 0.041 3946 Dihedral : 6.408 165.202 3565 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 3.49 % Allowed : 26.68 % Favored : 69.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.25 (0.15), residues: 3314 helix: 2.45 (0.15), residues: 1348 sheet: 0.95 (0.18), residues: 806 loop : 0.88 (0.19), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 107 TYR 0.023 0.001 TYR E 442 PHE 0.019 0.001 PHE G 195 TRP 0.005 0.001 TRP D 283 HIS 0.005 0.001 HIS A 20 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (21814) covalent geometry : angle 0.51945 / 0.25 (29817) hydrogen bonds : bond 0.02449 / 1.68 ( 1262) hydrogen bonds : angle 3.42215 / 2.46 ( 3615) Misc. bond : bond 0.00179 / 0.09 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 152 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 GLU cc_start: 0.9310 (mm-30) cc_final: 0.9052 (mm-30) REVERT: B 320 MET cc_start: 0.9008 (mmm) cc_final: 0.8609 (mmm) REVERT: C 248 ASP cc_start: 0.8920 (m-30) cc_final: 0.8648 (m-30) REVERT: C 265 THR cc_start: 0.9722 (p) cc_final: 0.9470 (t) REVERT: D 90 MET cc_start: 0.9303 (OUTLIER) cc_final: 0.8821 (tpp) REVERT: D 107 GLU cc_start: 0.9173 (tt0) cc_final: 0.8934 (tm-30) REVERT: D 283 TRP cc_start: 0.9290 (m-10) cc_final: 0.8799 (m-90) REVERT: D 310 SER cc_start: 0.9598 (OUTLIER) cc_final: 0.9300 (p) REVERT: D 352 ASP cc_start: 0.8788 (m-30) cc_final: 0.8560 (t0) REVERT: D 354 LEU cc_start: 0.9603 (mp) cc_final: 0.9259 (mm) REVERT: E 67 LYS cc_start: 0.9459 (mptt) cc_final: 0.9248 (mptt) REVERT: E 113 MET cc_start: 0.7767 (mmm) cc_final: 0.7520 (mmm) REVERT: E 248 ASP cc_start: 0.8866 (m-30) cc_final: 0.8629 (m-30) REVERT: E 299 ASP cc_start: 0.9478 (t0) cc_final: 0.9204 (t70) REVERT: E 303 MET cc_start: 0.9446 (mmm) cc_final: 0.9136 (tpp) REVERT: E 422 GLN cc_start: 0.9203 (OUTLIER) cc_final: 0.8826 (mm110) REVERT: F 88 MET cc_start: 0.9406 (tpp) cc_final: 0.9162 (tpp) REVERT: F 326 MET cc_start: 0.9305 (mpp) cc_final: 0.8897 (mpp) REVERT: F 340 TYR cc_start: 0.9247 (m-80) cc_final: 0.8758 (m-10) outliers start: 52 outliers final: 35 residues processed: 199 average time/residue: 0.1338 time to fit residues: 42.9534 Evaluate side-chains 187 residues out of total 2894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 149 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 366 ASP Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 113 MET Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 310 SER Chi-restraints excluded: chain D residue 342 SER Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 265 THR Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 422 GLN Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 404 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: [233, 24, 114, 172, 141, 231, 61, 55, 116, 288, 43] chunk 233 optimal weight: 9.9990 chunk 24 optimal weight: 0.8980 chunk 114 optimal weight: 6.9990 chunk 172 optimal weight: 0.0570 chunk 141 optimal weight: 2.9990 chunk 231 optimal weight: 10.0000 chunk 61 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 288 optimal weight: 50.0000 chunk 43 optimal weight: 50.0000 overall best weight: 1.5904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.066606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.046729 restraints weight = 110115.139| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 5.22 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2967 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2967 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.4621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21818 Z= 0.115 Angle : 0.514 12.022 29817 Z= 0.249 Chirality : 0.041 0.155 3792 Planarity : 0.003 0.050 3946 Dihedral : 6.315 162.405 3565 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 3.15 % Allowed : 27.01 % Favored : 69.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.28 (0.15), residues: 3314 helix: 2.49 (0.15), residues: 1347 sheet: 0.99 (0.18), residues: 804 loop : 0.85 (0.19), residues: 1163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 107 TYR 0.016 0.001 TYR E 442 PHE 0.019 0.001 PHE G 195 TRP 0.005 0.000 TRP D 283 HIS 0.004 0.001 HIS B 302 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (21814) covalent geometry : angle 0.51384 / 0.25 (29817) hydrogen bonds : bond 0.02295 / 1.57 ( 1262) hydrogen bonds : angle 3.31620 / 2.38 ( 3615) Misc. bond : bond 0.00161 / 0.08 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 153 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 240 HIS cc_start: 0.9167 (OUTLIER) cc_final: 0.7520 (p90) REVERT: B 320 MET cc_start: 0.8983 (mmm) cc_final: 0.8553 (mmm) REVERT: B 348 ILE cc_start: 0.9625 (pt) cc_final: 0.9406 (tp) REVERT: C 248 ASP cc_start: 0.8930 (m-30) cc_final: 0.8665 (m-30) REVERT: C 265 THR cc_start: 0.9723 (p) cc_final: 0.9470 (t) REVERT: D 90 MET cc_start: 0.9208 (OUTLIER) cc_final: 0.8698 (tpp) REVERT: D 107 GLU cc_start: 0.9173 (tt0) cc_final: 0.8926 (tm-30) REVERT: D 310 SER cc_start: 0.9611 (OUTLIER) cc_final: 0.9306 (p) REVERT: D 354 LEU cc_start: 0.9588 (mp) cc_final: 0.9210 (mm) REVERT: E 113 MET cc_start: 0.7799 (mmm) cc_final: 0.7555 (mmm) REVERT: E 248 ASP cc_start: 0.8849 (m-30) cc_final: 0.8592 (m-30) REVERT: E 299 ASP cc_start: 0.9410 (t0) cc_final: 0.9160 (t70) REVERT: E 303 MET cc_start: 0.9477 (mmm) cc_final: 0.9105 (tpp) REVERT: E 422 GLN cc_start: 0.9205 (OUTLIER) cc_final: 0.8831 (mm110) REVERT: F 88 MET cc_start: 0.9391 (tpp) cc_final: 0.9134 (tpp) REVERT: F 326 MET cc_start: 0.9313 (mpp) cc_final: 0.8926 (mpp) REVERT: F 340 TYR cc_start: 0.9224 (m-80) cc_final: 0.8690 (m-10) outliers start: 47 outliers final: 33 residues processed: 196 average time/residue: 0.1282 time to fit residues: 40.8711 Evaluate side-chains 187 residues out of total 2894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 150 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 310 SER Chi-restraints excluded: chain D residue 342 SER Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 265 THR Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 422 GLN Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 404 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: [5, 76, 203, 107, 234, 327, 210, 116, 318, 243, 188] chunk 5 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 203 optimal weight: 50.0000 chunk 107 optimal weight: 2.9990 chunk 234 optimal weight: 0.0070 chunk 327 optimal weight: 40.0000 chunk 210 optimal weight: 0.0070 chunk 116 optimal weight: 4.9990 chunk 318 optimal weight: 50.0000 chunk 243 optimal weight: 50.0000 chunk 188 optimal weight: 0.7980 overall best weight: 0.7620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 408 GLN ** D 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.067182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.047304 restraints weight = 109945.687| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 5.21 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2990 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.4720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 21818 Z= 0.088 Angle : 0.529 12.865 29817 Z= 0.251 Chirality : 0.041 0.155 3792 Planarity : 0.003 0.045 3946 Dihedral : 6.135 157.999 3565 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.61 % Allowed : 27.55 % Favored : 69.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.24 (0.15), residues: 3314 helix: 2.47 (0.15), residues: 1349 sheet: 1.01 (0.18), residues: 806 loop : 0.78 (0.19), residues: 1159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 107 TYR 0.027 0.001 TYR E 442 PHE 0.020 0.001 PHE G 195 TRP 0.005 0.000 TRP D 283 HIS 0.003 0.001 HIS B 302 Details of bonding type rmsd/Z covalent geometry : bond 0.00197 / 0.09 (21814) covalent geometry : angle 0.52858 / 0.25 (29817) hydrogen bonds : bond 0.02113 / 1.43 ( 1262) hydrogen bonds : angle 3.16567 / 2.28 ( 3615) Misc. bond : bond 0.00141 / 0.07 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 162 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 LYS cc_start: 0.9498 (mttt) cc_final: 0.9158 (mtpt) REVERT: B 240 HIS cc_start: 0.9238 (OUTLIER) cc_final: 0.7643 (p90) REVERT: B 320 MET cc_start: 0.8967 (mmm) cc_final: 0.8493 (mmm) REVERT: B 348 ILE cc_start: 0.9630 (pt) cc_final: 0.9134 (tp) REVERT: B 352 ASP cc_start: 0.8969 (t0) cc_final: 0.8732 (p0) REVERT: C 248 ASP cc_start: 0.9020 (m-30) cc_final: 0.8773 (m-30) REVERT: C 265 THR cc_start: 0.9723 (p) cc_final: 0.9476 (t) REVERT: D 90 MET cc_start: 0.9205 (OUTLIER) cc_final: 0.8746 (tpp) REVERT: D 107 GLU cc_start: 0.9142 (tt0) cc_final: 0.8834 (tm-30) REVERT: D 310 SER cc_start: 0.9604 (OUTLIER) cc_final: 0.9138 (p) REVERT: D 340 TYR cc_start: 0.8881 (m-80) cc_final: 0.8605 (m-80) REVERT: E 248 ASP cc_start: 0.8833 (m-30) cc_final: 0.8480 (m-30) REVERT: E 299 ASP cc_start: 0.9473 (t0) cc_final: 0.9246 (t70) REVERT: E 300 GLU cc_start: 0.9248 (pt0) cc_final: 0.8760 (pp20) REVERT: E 303 MET cc_start: 0.9459 (mmm) cc_final: 0.8921 (tpp) REVERT: E 320 MET cc_start: 0.9351 (mmm) cc_final: 0.8990 (mmm) REVERT: E 422 GLN cc_start: 0.9210 (OUTLIER) cc_final: 0.8848 (mm110) REVERT: F 67 LYS cc_start: 0.9684 (mmmm) cc_final: 0.9368 (mmtp) REVERT: F 88 MET cc_start: 0.9361 (tpp) cc_final: 0.9097 (tpp) REVERT: F 340 TYR cc_start: 0.9193 (m-80) cc_final: 0.8673 (m-10) REVERT: G 172 SER cc_start: 0.9323 (t) cc_final: 0.9069 (p) outliers start: 39 outliers final: 32 residues processed: 196 average time/residue: 0.1360 time to fit residues: 42.7699 Evaluate side-chains 189 residues out of total 2894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 153 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 115 LYS Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 444 LYS Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 310 SER Chi-restraints excluded: chain D residue 342 SER Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 265 THR Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 422 GLN Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 404 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: [115, 247, 316, 217, 27, 262, 328, 315, 174, 232, 305] chunk 115 optimal weight: 4.9990 chunk 247 optimal weight: 50.0000 chunk 316 optimal weight: 10.0000 chunk 217 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 262 optimal weight: 7.9990 chunk 328 optimal weight: 10.0000 chunk 315 optimal weight: 40.0000 chunk 174 optimal weight: 5.9990 chunk 232 optimal weight: 7.9990 chunk 305 optimal weight: 50.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.064733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.044766 restraints weight = 115625.340| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 5.15 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2916 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2916 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.5011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 21818 Z= 0.277 Angle : 0.633 10.427 29817 Z= 0.313 Chirality : 0.043 0.176 3792 Planarity : 0.003 0.044 3946 Dihedral : 6.461 156.023 3565 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.68 % Allowed : 27.48 % Favored : 69.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.05 (0.15), residues: 3314 helix: 2.28 (0.15), residues: 1346 sheet: 0.86 (0.18), residues: 801 loop : 0.76 (0.19), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 314 TYR 0.029 0.002 TYR C 387 PHE 0.018 0.002 PHE G 195 TRP 0.006 0.001 TRP F 283 HIS 0.008 0.001 HIS A 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00594 / 0.28 (21814) covalent geometry : angle 0.63348 / 0.31 (29817) hydrogen bonds : bond 0.03076 / 2.13 ( 1262) hydrogen bonds : angle 3.87705 / 2.77 ( 3615) Misc. bond : bond 0.00222 / 0.11 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 149 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 240 HIS cc_start: 0.9168 (OUTLIER) cc_final: 0.7622 (p90) REVERT: B 320 MET cc_start: 0.9106 (mmm) cc_final: 0.8828 (mmm) REVERT: B 348 ILE cc_start: 0.9642 (pt) cc_final: 0.9416 (tp) REVERT: C 248 ASP cc_start: 0.9000 (m-30) cc_final: 0.8774 (m-30) REVERT: C 265 THR cc_start: 0.9734 (p) cc_final: 0.9407 (t) REVERT: D 90 MET cc_start: 0.9299 (OUTLIER) cc_final: 0.8834 (tpp) REVERT: D 107 GLU cc_start: 0.9269 (tt0) cc_final: 0.9000 (tm-30) REVERT: D 115 LYS cc_start: 0.9089 (mmmt) cc_final: 0.8818 (mmmt) REVERT: D 310 SER cc_start: 0.9561 (OUTLIER) cc_final: 0.9302 (p) REVERT: E 248 ASP cc_start: 0.8935 (m-30) cc_final: 0.8714 (m-30) REVERT: E 299 ASP cc_start: 0.9408 (t0) cc_final: 0.9181 (t70) REVERT: E 300 GLU cc_start: 0.9200 (pt0) cc_final: 0.8751 (pp20) REVERT: E 303 MET cc_start: 0.9452 (mmm) cc_final: 0.8948 (tpp) REVERT: E 422 GLN cc_start: 0.9214 (OUTLIER) cc_final: 0.8875 (mm110) REVERT: G 110 ARG cc_start: 0.9421 (tpp80) cc_final: 0.9095 (tpp80) REVERT: G 172 SER cc_start: 0.9361 (t) cc_final: 0.9078 (p) outliers start: 40 outliers final: 32 residues processed: 184 average time/residue: 0.1330 time to fit residues: 39.7260 Evaluate side-chains 182 residues out of total 2894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 146 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 115 LYS Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 444 LYS Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 366 ASP Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 310 SER Chi-restraints excluded: chain D residue 342 SER Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 265 THR Chi-restraints excluded: chain E residue 326 MET Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 422 GLN Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 370 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: [98, 54, 189, 64, 110, 230, 307, 321, 240, 175, 258] chunk 98 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 189 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 110 optimal weight: 0.2980 chunk 230 optimal weight: 0.7980 chunk 307 optimal weight: 0.9990 chunk 321 optimal weight: 0.9980 chunk 240 optimal weight: 20.0000 chunk 175 optimal weight: 0.0980 chunk 258 optimal weight: 40.0000 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.066688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.046854 restraints weight = 110946.103| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 5.18 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2976 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2976 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.5033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 21818 Z= 0.091 Angle : 0.554 12.780 29817 Z= 0.263 Chirality : 0.042 0.175 3792 Planarity : 0.003 0.049 3946 Dihedral : 6.124 155.905 3565 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.01 % Allowed : 28.35 % Favored : 69.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.17 (0.15), residues: 3314 helix: 2.42 (0.15), residues: 1349 sheet: 0.95 (0.18), residues: 806 loop : 0.75 (0.19), residues: 1159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 314 TYR 0.024 0.001 TYR E 442 PHE 0.021 0.001 PHE G 195 TRP 0.006 0.000 TRP D 283 HIS 0.004 0.001 HIS B 302 Details of bonding type rmsd/Z covalent geometry : bond 0.00203 / 0.09 (21814) covalent geometry : angle 0.55440 / 0.26 (29817) hydrogen bonds : bond 0.02225 / 1.52 ( 1262) hydrogen bonds : angle 3.28108 / 2.36 ( 3615) Misc. bond : bond 0.00147 / 0.08 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4042.99 seconds wall clock time: 69 minutes 55.60 seconds (4195.60 seconds total)