Starting phenix.real_space_refine on Tue Aug 26 17:24:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bxu_45012/08_2025/9bxu_45012.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bxu_45012/08_2025/9bxu_45012.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bxu_45012/08_2025/9bxu_45012.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bxu_45012/08_2025/9bxu_45012.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bxu_45012/08_2025/9bxu_45012.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bxu_45012/08_2025/9bxu_45012.map" } resolution = 3.0 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= 0.008 sd= 0.027 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: 6 Type Number sf(0) Gaussians P 13 5.49 5 Mg 5 5.21 5 S 140 5.16 5 C 24515 2.51 5 N 6557 2.21 5 O 7239 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38469 Number of models: 1 Model: "" Number of chains: 34 Chain: "8" Number of atoms: 247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 247 Classifications: {'peptide': 31} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 30} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 3543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3543 Classifications: {'peptide': 470} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 446} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "E" Number of atoms: 3532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3532 Classifications: {'peptide': 467} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 443} Chain: "F" Number of atoms: 3532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3532 Classifications: {'peptide': 467} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 443} Chain: "G" Number of atoms: 2093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2093 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 266} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "H" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 961 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain: "I" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 373 Classifications: {'peptide': 48} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 47} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "J" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 365 Classifications: {'peptide': 48} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 47} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "K" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "L" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 509 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 70} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "M" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "N" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 510 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 70} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "O" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 510 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 70} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "P" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "Q" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "R" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 510 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 70} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 1423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1423 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 177} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "T" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 587 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 75} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 46 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2, 'TRP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "U" Number of atoms: 301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 301 Classifications: {'peptide': 43} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 3, 'TRANS': 39} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 32 Chain: "V" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1710 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 7, 'TRANS': 204} Chain: "W" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 641 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 2, 'TRANS': 78} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'ARG:plan': 3, 'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "a" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1685 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 12, 'TRANS': 208} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "c" Number of atoms: 402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 402 Classifications: {'peptide': 69} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 43} Link IDs: {'PTRANS': 5, 'TRANS': 63} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 183 Unresolved non-hydrogen angles: 231 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PHE:plan': 6, 'TYR:plan': 2, 'ARG:plan': 2, 'ASP:plan': 5, 'GLU:plan': 5, 'GLN:plan1': 4, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 117 Chain: "d" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1160 Classifications: {'peptide': 153} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 10, 'TRANS': 142} Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 92 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 2, 'TRP:plan': 1, 'TYR:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 56 Chain: "i" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 303 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'TRANS': 41} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "k" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 145 Classifications: {'peptide': 29} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'TRANS': 28} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'UNK:plan-1': 29} Unresolved non-hydrogen planarities: 29 Chain: "A" Number of atoms: 3832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3832 Classifications: {'peptide': 507} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 489} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 3756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 3756 Classifications: {'peptide': 495} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 477} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 3635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3635 Classifications: {'peptide': 480} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 462} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.32, per 1000 atoms: 0.22 Number of scatterers: 38469 At special positions: 0 Unit cell: (138.03, 156.22, 254.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 140 16.00 P 13 15.00 Mg 5 11.99 O 7239 8.00 N 6557 7.00 C 24515 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=0, symmetry=0 Time building additional restraints: 2.70 Conformation dependent library (CDL) restraints added in 1.7 seconds Enol-peptide restraints added in 715.3 nanoseconds 10032 Ramachandran restraints generated. 5016 Oldfield, 0 Emsley, 5016 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9322 Finding SS restraints... Secondary structure from input PDB file: 217 helices and 24 sheets defined 58.8% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain '8' and resid 9 through 30 removed outlier: 3.548A pdb=" N ILE 8 13 " --> pdb=" O TRP 8 9 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N PHE 8 24 " --> pdb=" O LEU 8 20 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N GLN 8 25 " --> pdb=" O PHE 8 21 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASN 8 30 " --> pdb=" O LEU 8 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 183 removed outlier: 3.903A pdb=" N THR D 182 " --> pdb=" O GLY D 179 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU D 183 " --> pdb=" O PRO D 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 179 through 183' Processing helix chain 'D' and resid 214 through 218 removed outlier: 3.606A pdb=" N MET D 218 " --> pdb=" O PHE D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 236 Processing helix chain 'D' and resid 253 through 266 Processing helix chain 'D' and resid 281 through 295 removed outlier: 3.672A pdb=" N GLY D 285 " --> pdb=" O ARG D 281 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR D 289 " --> pdb=" O GLY D 285 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N HIS D 290 " --> pdb=" O ASN D 286 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU D 294 " --> pdb=" O HIS D 290 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER D 295 " --> pdb=" O GLU D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 322 removed outlier: 3.530A pdb=" N ARG D 321 " --> pdb=" O PRO D 317 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA D 322 " --> pdb=" O PRO D 318 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 317 through 322' Processing helix chain 'D' and resid 323 through 338 removed outlier: 3.616A pdb=" N VAL D 331 " --> pdb=" O THR D 327 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA D 332 " --> pdb=" O GLY D 328 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR D 334 " --> pdb=" O THR D 330 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE D 335 " --> pdb=" O VAL D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 356 Processing helix chain 'D' and resid 357 through 359 No H-bonds generated for 'chain 'D' and resid 357 through 359' Processing helix chain 'D' and resid 361 through 365 Processing helix chain 'D' and resid 369 through 373 Processing helix chain 'D' and resid 376 through 386 removed outlier: 3.592A pdb=" N MET D 384 " --> pdb=" O ASP D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 408 Processing helix chain 'D' and resid 411 through 416 removed outlier: 3.596A pdb=" N THR D 416 " --> pdb=" O PRO D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 421 removed outlier: 3.633A pdb=" N LEU D 421 " --> pdb=" O PHE D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 434 removed outlier: 3.698A pdb=" N ALA D 432 " --> pdb=" O SER D 428 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU D 434 " --> pdb=" O ALA D 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 456 Processing helix chain 'D' and resid 456 through 483 removed outlier: 3.753A pdb=" N TYR D 460 " --> pdb=" O GLY D 456 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LYS D 474 " --> pdb=" O LEU D 470 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N SER D 475 " --> pdb=" O GLN D 471 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU D 476 " --> pdb=" O ASP D 472 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN D 477 " --> pdb=" O TYR D 473 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASP D 478 " --> pdb=" O LYS D 474 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ILE D 479 " --> pdb=" O SER D 475 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA D 481 " --> pdb=" O GLN D 477 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE D 482 " --> pdb=" O ASP D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 484 through 488 removed outlier: 3.632A pdb=" N GLU D 487 " --> pdb=" O GLY D 484 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU D 488 " --> pdb=" O MET D 485 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 484 through 488' Processing helix chain 'D' and resid 489 through 506 removed outlier: 3.830A pdb=" N LEU D 506 " --> pdb=" O ILE D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 518 Processing helix chain 'D' and resid 525 through 539 removed outlier: 3.535A pdb=" N THR D 529 " --> pdb=" O PRO D 525 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE D 533 " --> pdb=" O THR D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 550 removed outlier: 3.627A pdb=" N ALA D 548 " --> pdb=" O PRO D 545 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR D 550 " --> pdb=" O GLN D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 569 removed outlier: 4.238A pdb=" N VAL D 559 " --> pdb=" O ILE D 555 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA D 560 " --> pdb=" O GLU D 556 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 218 removed outlier: 3.557A pdb=" N GLU E 217 " --> pdb=" O GLU E 214 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N MET E 218 " --> pdb=" O PHE E 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 214 through 218' Processing helix chain 'E' and resid 229 through 236 Processing helix chain 'E' and resid 253 through 269 removed outlier: 3.623A pdb=" N LEU E 257 " --> pdb=" O GLY E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 296 removed outlier: 3.620A pdb=" N ILE E 293 " --> pdb=" O TYR E 289 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLU E 294 " --> pdb=" O HIS E 290 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER E 295 " --> pdb=" O GLU E 291 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY E 296 " --> pdb=" O MET E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 322 Processing helix chain 'E' and resid 323 through 340 removed outlier: 3.617A pdb=" N VAL E 331 " --> pdb=" O THR E 327 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA E 332 " --> pdb=" O GLY E 328 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR E 334 " --> pdb=" O THR E 330 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE E 335 " --> pdb=" O VAL E 331 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU E 339 " --> pdb=" O PHE E 335 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 364 removed outlier: 4.000A pdb=" N PHE E 353 " --> pdb=" O ASN E 349 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR E 354 " --> pdb=" O ILE E 350 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL E 360 " --> pdb=" O ALA E 356 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER E 361 " --> pdb=" O GLY E 357 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA E 362 " --> pdb=" O SER E 358 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 373 Processing helix chain 'E' and resid 376 through 386 removed outlier: 3.576A pdb=" N MET E 381 " --> pdb=" O LEU E 377 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N MET E 384 " --> pdb=" O ASP E 380 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 408 removed outlier: 3.750A pdb=" N ASP E 407 " --> pdb=" O VAL E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 411 through 418 removed outlier: 3.539A pdb=" N THR E 416 " --> pdb=" O PRO E 412 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR E 417 " --> pdb=" O ALA E 413 " (cutoff:3.500A) Processing helix chain 'E' and resid 428 through 435 removed outlier: 3.888A pdb=" N ALA E 432 " --> pdb=" O SER E 428 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY E 435 " --> pdb=" O ILE E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 451 through 456 Processing helix chain 'E' and resid 457 through 480 removed outlier: 3.628A pdb=" N GLN E 467 " --> pdb=" O ALA E 463 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS E 474 " --> pdb=" O LEU E 470 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER E 475 " --> pdb=" O GLN E 471 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASP E 478 " --> pdb=" O LYS E 474 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ILE E 479 " --> pdb=" O SER E 475 " (cutoff:3.500A) Processing helix chain 'E' and resid 484 through 488 removed outlier: 3.628A pdb=" N GLU E 487 " --> pdb=" O GLY E 484 " (cutoff:3.500A) Processing helix chain 'E' and resid 489 through 506 removed outlier: 3.606A pdb=" N LYS E 493 " --> pdb=" O SER E 489 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU E 494 " --> pdb=" O GLU E 490 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER E 497 " --> pdb=" O LYS E 493 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG E 504 " --> pdb=" O ARG E 500 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU E 506 " --> pdb=" O ILE E 502 " (cutoff:3.500A) Processing helix chain 'E' and resid 513 through 518 removed outlier: 3.600A pdb=" N THR E 517 " --> pdb=" O ALA E 513 " (cutoff:3.500A) Processing helix chain 'E' and resid 525 through 539 Processing helix chain 'E' and resid 545 through 550 removed outlier: 3.530A pdb=" N TYR E 550 " --> pdb=" O GLN E 547 " (cutoff:3.500A) Processing helix chain 'E' and resid 554 through 565 removed outlier: 4.156A pdb=" N ALA E 558 " --> pdb=" O PRO E 554 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL E 559 " --> pdb=" O ILE E 555 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 218 removed outlier: 3.647A pdb=" N GLU F 217 " --> pdb=" O GLU F 214 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N MET F 218 " --> pdb=" O PHE F 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 214 through 218' Processing helix chain 'F' and resid 229 through 236 Processing helix chain 'F' and resid 253 through 266 removed outlier: 3.658A pdb=" N LEU F 257 " --> pdb=" O GLY F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 296 removed outlier: 3.775A pdb=" N GLY F 285 " --> pdb=" O ARG F 281 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 322 removed outlier: 3.589A pdb=" N ARG F 321 " --> pdb=" O PRO F 317 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 338 removed outlier: 3.598A pdb=" N THR F 327 " --> pdb=" O ARG F 323 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL F 331 " --> pdb=" O THR F 327 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE F 335 " --> pdb=" O VAL F 331 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG F 336 " --> pdb=" O ALA F 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 359 removed outlier: 4.027A pdb=" N THR F 354 " --> pdb=" O ILE F 350 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY F 357 " --> pdb=" O PHE F 353 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER F 358 " --> pdb=" O THR F 354 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU F 359 " --> pdb=" O GLN F 355 " (cutoff:3.500A) Processing helix chain 'F' and resid 378 through 386 removed outlier: 3.548A pdb=" N MET F 384 " --> pdb=" O ASP F 380 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 408 Processing helix chain 'F' and resid 417 through 421 removed outlier: 3.756A pdb=" N LEU F 421 " --> pdb=" O PHE F 418 " (cutoff:3.500A) Processing helix chain 'F' and resid 428 through 435 removed outlier: 3.532A pdb=" N ALA F 432 " --> pdb=" O SER F 428 " (cutoff:3.500A) Processing helix chain 'F' and resid 451 through 456 Processing helix chain 'F' and resid 456 through 475 removed outlier: 3.572A pdb=" N TYR F 460 " --> pdb=" O GLY F 456 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS F 474 " --> pdb=" O LEU F 470 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER F 475 " --> pdb=" O GLN F 471 " (cutoff:3.500A) Processing helix chain 'F' and resid 476 through 483 removed outlier: 3.613A pdb=" N ILE F 482 " --> pdb=" O ASP F 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 484 through 488 removed outlier: 3.673A pdb=" N GLU F 487 " --> pdb=" O GLY F 484 " (cutoff:3.500A) Processing helix chain 'F' and resid 489 through 506 removed outlier: 3.709A pdb=" N ARG F 504 " --> pdb=" O ARG F 500 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE F 505 " --> pdb=" O LYS F 501 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU F 506 " --> pdb=" O ILE F 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 513 through 517 removed outlier: 3.602A pdb=" N THR F 517 " --> pdb=" O GLU F 514 " (cutoff:3.500A) Processing helix chain 'F' and resid 525 through 538 Processing helix chain 'F' and resid 545 through 550 removed outlier: 3.840A pdb=" N PHE F 549 " --> pdb=" O GLU F 546 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N TYR F 550 " --> pdb=" O GLN F 547 " (cutoff:3.500A) Processing helix chain 'F' and resid 555 through 565 removed outlier: 3.882A pdb=" N VAL F 559 " --> pdb=" O ILE F 555 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA F 560 " --> pdb=" O GLU F 556 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 62 removed outlier: 3.519A pdb=" N ILE G 31 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE G 38 " --> pdb=" O ARG G 34 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASN G 40 " --> pdb=" O LYS G 36 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS G 43 " --> pdb=" O LYS G 39 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N MET G 50 " --> pdb=" O LYS G 46 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N VAL G 51 " --> pdb=" O SER G 47 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA G 52 " --> pdb=" O MET G 48 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG G 58 " --> pdb=" O ALA G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 74 removed outlier: 3.899A pdb=" N ALA G 66 " --> pdb=" O ASP G 62 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL G 68 " --> pdb=" O LYS G 64 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N TYR G 69 " --> pdb=" O PRO G 65 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU G 74 " --> pdb=" O GLY G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 80 Processing helix chain 'G' and resid 105 through 125 removed outlier: 3.548A pdb=" N SER G 109 " --> pdb=" O ALA G 105 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL G 110 " --> pdb=" O ILE G 106 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS G 115 " --> pdb=" O ALA G 111 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL G 118 " --> pdb=" O ILE G 114 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA G 119 " --> pdb=" O LYS G 115 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASN G 120 " --> pdb=" O SER G 116 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA G 124 " --> pdb=" O ASN G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 134 through 141 removed outlier: 3.601A pdb=" N ARG G 138 " --> pdb=" O GLY G 134 " (cutoff:3.500A) Processing helix chain 'G' and resid 162 through 175 removed outlier: 3.712A pdb=" N ALA G 166 " --> pdb=" O THR G 162 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASN G 175 " --> pdb=" O LEU G 171 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 211 Processing helix chain 'G' and resid 212 through 218 removed outlier: 3.920A pdb=" N ILE G 217 " --> pdb=" O SER G 214 " (cutoff:3.500A) Processing helix chain 'G' and resid 222 through 296 removed outlier: 3.807A pdb=" N ALA G 235 " --> pdb=" O GLU G 231 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N THR G 247 " --> pdb=" O LYS G 243 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER G 248 " --> pdb=" O GLU G 244 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N THR G 255 " --> pdb=" O SER G 251 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER G 261 " --> pdb=" O MET G 257 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASP G 269 " --> pdb=" O SER G 265 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LYS G 270 " --> pdb=" O GLU G 266 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR G 272 " --> pdb=" O ILE G 268 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU G 273 " --> pdb=" O ASP G 269 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE G 283 " --> pdb=" O ARG G 279 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU G 289 " --> pdb=" O LYS G 285 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILE G 290 " --> pdb=" O GLU G 286 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA G 296 " --> pdb=" O SER G 292 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 125 Processing helix chain 'H' and resid 126 through 144 removed outlier: 3.768A pdb=" N SER H 139 " --> pdb=" O GLU H 135 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU H 141 " --> pdb=" O ALA H 137 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LEU H 142 " --> pdb=" O GLN H 138 " (cutoff:3.500A) Processing helix chain 'H' and resid 146 through 164 Processing helix chain 'I' and resid 10 through 25 removed outlier: 3.567A pdb=" N ALA I 25 " --> pdb=" O ALA I 21 " (cutoff:3.500A) Processing helix chain 'I' and resid 32 through 38 removed outlier: 3.760A pdb=" N LYS I 36 " --> pdb=" O ALA I 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 38 through 43 removed outlier: 3.529A pdb=" N ASP J 42 " --> pdb=" O GLY J 38 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA J 43 " --> pdb=" O ALA J 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 38 through 43' Processing helix chain 'J' and resid 45 through 77 removed outlier: 3.780A pdb=" N LYS J 49 " --> pdb=" O GLY J 45 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP J 54 " --> pdb=" O LYS J 50 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU J 55 " --> pdb=" O GLU J 51 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG J 62 " --> pdb=" O TYR J 58 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ALA J 63 " --> pdb=" O PHE J 59 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ARG J 64 " --> pdb=" O ARG J 60 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLU J 65 " --> pdb=" O ALA J 61 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 15 Processing helix chain 'K' and resid 18 through 39 Processing helix chain 'K' and resid 42 through 73 removed outlier: 3.692A pdb=" N CYS K 64 " --> pdb=" O MET K 60 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 15 Processing helix chain 'L' and resid 18 through 39 removed outlier: 4.338A pdb=" N GLY L 22 " --> pdb=" O VAL L 18 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA L 23 " --> pdb=" O ALA L 19 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG L 38 " --> pdb=" O ILE L 34 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN L 39 " --> pdb=" O GLY L 35 " (cutoff:3.500A) Processing helix chain 'L' and resid 42 through 73 removed outlier: 3.736A pdb=" N PHE L 47 " --> pdb=" O LYS L 43 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N SER L 48 " --> pdb=" O GLN L 44 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TYR L 49 " --> pdb=" O GLN L 45 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 15 removed outlier: 3.628A pdb=" N THR M 15 " --> pdb=" O ALA M 11 " (cutoff:3.500A) Processing helix chain 'M' and resid 18 through 39 removed outlier: 4.155A pdb=" N GLY M 22 " --> pdb=" O VAL M 18 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA M 23 " --> pdb=" O ALA M 19 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE M 34 " --> pdb=" O GLY M 30 " (cutoff:3.500A) Processing helix chain 'M' and resid 42 through 58 removed outlier: 3.508A pdb=" N GLU M 58 " --> pdb=" O PHE M 54 " (cutoff:3.500A) Processing helix chain 'M' and resid 58 through 73 Processing helix chain 'N' and resid 3 through 15 Processing helix chain 'N' and resid 18 through 39 removed outlier: 3.570A pdb=" N ILE N 34 " --> pdb=" O GLY N 30 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASN N 39 " --> pdb=" O GLY N 35 " (cutoff:3.500A) Processing helix chain 'N' and resid 42 through 73 removed outlier: 4.279A pdb=" N PHE N 63 " --> pdb=" O ALA N 59 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N CYS N 64 " --> pdb=" O MET N 60 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N LEU N 65 " --> pdb=" O GLY N 61 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N MET N 66 " --> pdb=" O LEU N 62 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N VAL N 67 " --> pdb=" O PHE N 63 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA N 68 " --> pdb=" O CYS N 64 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 13 removed outlier: 3.799A pdb=" N ILE O 9 " --> pdb=" O ALA O 5 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY O 10 " --> pdb=" O ALA O 6 " (cutoff:3.500A) Processing helix chain 'O' and resid 16 through 38 removed outlier: 4.014A pdb=" N GLY O 20 " --> pdb=" O VAL O 16 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N SER O 21 " --> pdb=" O GLY O 17 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY O 22 " --> pdb=" O VAL O 18 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA O 23 " --> pdb=" O ALA O 19 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLY O 24 " --> pdb=" O GLY O 20 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE O 25 " --> pdb=" O SER O 21 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLY O 26 " --> pdb=" O GLY O 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG O 38 " --> pdb=" O ILE O 34 " (cutoff:3.500A) Processing helix chain 'O' and resid 42 through 73 removed outlier: 3.578A pdb=" N LEU O 46 " --> pdb=" O LEU O 42 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N CYS O 64 " --> pdb=" O MET O 60 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU O 72 " --> pdb=" O ALA O 68 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N PHE O 73 " --> pdb=" O PHE O 69 " (cutoff:3.500A) Processing helix chain 'P' and resid 3 through 7 Processing helix chain 'P' and resid 8 through 15 removed outlier: 3.578A pdb=" N THR P 15 " --> pdb=" O ALA P 11 " (cutoff:3.500A) Processing helix chain 'P' and resid 17 through 39 removed outlier: 4.469A pdb=" N SER P 21 " --> pdb=" O GLY P 17 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE P 29 " --> pdb=" O ILE P 25 " (cutoff:3.500A) Processing helix chain 'P' and resid 43 through 73 removed outlier: 4.051A pdb=" N PHE P 63 " --> pdb=" O ALA P 59 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N CYS P 64 " --> pdb=" O MET P 60 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LEU P 65 " --> pdb=" O GLY P 61 " (cutoff:3.500A) Processing helix chain 'Q' and resid 3 through 15 Processing helix chain 'Q' and resid 18 through 39 removed outlier: 4.056A pdb=" N GLY Q 26 " --> pdb=" O GLY Q 22 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N THR Q 27 " --> pdb=" O ALA Q 23 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL Q 28 " --> pdb=" O GLY Q 24 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG Q 38 " --> pdb=" O ILE Q 34 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN Q 39 " --> pdb=" O GLY Q 35 " (cutoff:3.500A) Processing helix chain 'Q' and resid 42 through 73 removed outlier: 3.839A pdb=" N LEU Q 46 " --> pdb=" O LEU Q 42 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N PHE Q 47 " --> pdb=" O LYS Q 43 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N SER Q 48 " --> pdb=" O GLN Q 44 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N TYR Q 49 " --> pdb=" O GLN Q 45 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N CYS Q 64 " --> pdb=" O MET Q 60 " (cutoff:3.500A) Processing helix chain 'R' and resid 3 through 15 removed outlier: 3.978A pdb=" N THR R 15 " --> pdb=" O ALA R 11 " (cutoff:3.500A) Processing helix chain 'R' and resid 18 through 38 removed outlier: 4.067A pdb=" N GLY R 22 " --> pdb=" O VAL R 18 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY R 26 " --> pdb=" O GLY R 22 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR R 27 " --> pdb=" O ALA R 23 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG R 38 " --> pdb=" O ILE R 34 " (cutoff:3.500A) Processing helix chain 'R' and resid 43 through 73 removed outlier: 4.478A pdb=" N VAL R 67 " --> pdb=" O PHE R 63 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ALA R 68 " --> pdb=" O CYS R 64 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N PHE R 69 " --> pdb=" O LEU R 65 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 28 Processing helix chain 'S' and resid 31 through 46 Processing helix chain 'S' and resid 48 through 56 Processing helix chain 'S' and resid 61 through 76 Processing helix chain 'S' and resid 81 through 93 Processing helix chain 'S' and resid 94 through 96 No H-bonds generated for 'chain 'S' and resid 94 through 96' Processing helix chain 'S' and resid 97 through 111 Processing helix chain 'S' and resid 112 through 114 No H-bonds generated for 'chain 'S' and resid 112 through 114' Processing helix chain 'S' and resid 127 through 143 Processing helix chain 'S' and resid 176 through 183 removed outlier: 4.030A pdb=" N GLN S 180 " --> pdb=" O LYS S 176 " (cutoff:3.500A) Processing helix chain 'T' and resid 17 through 36 removed outlier: 3.890A pdb=" N LYS T 24 " --> pdb=" O VAL T 20 " (cutoff:3.500A) Proline residue: T 25 - end of helix removed outlier: 3.898A pdb=" N PHE T 30 " --> pdb=" O ARG T 26 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N TRP T 31 " --> pdb=" O LEU T 27 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL T 36 " --> pdb=" O HIS T 32 " (cutoff:3.500A) Processing helix chain 'T' and resid 42 through 44 No H-bonds generated for 'chain 'T' and resid 42 through 44' Processing helix chain 'T' and resid 45 through 62 removed outlier: 3.582A pdb=" N SER T 59 " --> pdb=" O LYS T 55 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR T 62 " --> pdb=" O ASN T 58 " (cutoff:3.500A) Processing helix chain 'T' and resid 69 through 96 removed outlier: 3.743A pdb=" N ALA T 73 " --> pdb=" O THR T 69 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N TRP T 86 " --> pdb=" O GLU T 82 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N PHE T 87 " --> pdb=" O VAL T 83 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TYR T 88 " --> pdb=" O LEU T 84 " (cutoff:3.500A) Processing helix chain 'U' and resid 8 through 45 removed outlier: 3.867A pdb=" N TYR U 16 " --> pdb=" O LYS U 12 " (cutoff:3.500A) Proline residue: U 35 - end of helix removed outlier: 3.587A pdb=" N GLU U 38 " --> pdb=" O LYS U 34 " (cutoff:3.500A) Processing helix chain 'V' and resid 43 through 49 removed outlier: 3.510A pdb=" N LEU V 49 " --> pdb=" O PHE V 45 " (cutoff:3.500A) Processing helix chain 'V' and resid 49 through 54 Processing helix chain 'V' and resid 56 through 72 removed outlier: 4.010A pdb=" N VAL V 60 " --> pdb=" O THR V 56 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU V 61 " --> pdb=" O GLY V 57 " (cutoff:3.500A) Processing helix chain 'V' and resid 79 through 144 removed outlier: 3.933A pdb=" N SER V 83 " --> pdb=" O ALA V 79 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ALA V 100 " --> pdb=" O LYS V 96 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N SER V 101 " --> pdb=" O LYS V 97 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE V 102 " --> pdb=" O TYR V 98 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY V 103 " --> pdb=" O GLY V 99 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU V 109 " --> pdb=" O PHE V 105 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ASN V 110 " --> pdb=" O ALA V 106 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA V 140 " --> pdb=" O LYS V 136 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU V 141 " --> pdb=" O SER V 137 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL V 142 " --> pdb=" O GLN V 138 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN V 143 " --> pdb=" O GLN V 139 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LYS V 144 " --> pdb=" O ALA V 140 " (cutoff:3.500A) Processing helix chain 'V' and resid 146 through 209 removed outlier: 3.598A pdb=" N ASP V 150 " --> pdb=" O HIS V 146 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N THR V 163 " --> pdb=" O ALA V 159 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR V 164 " --> pdb=" O LEU V 160 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU V 166 " --> pdb=" O VAL V 162 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG V 167 " --> pdb=" O THR V 163 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU V 168 " --> pdb=" O TYR V 164 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG V 178 " --> pdb=" O GLU V 174 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU V 179 " --> pdb=" O ILE V 175 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N HIS V 182 " --> pdb=" O ARG V 178 " (cutoff:3.500A) Processing helix chain 'V' and resid 210 through 234 Processing helix chain 'W' and resid 116 through 123 Processing helix chain 'W' and resid 131 through 147 removed outlier: 3.542A pdb=" N PHE W 135 " --> pdb=" O ILE W 131 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR W 140 " --> pdb=" O GLN W 136 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS W 145 " --> pdb=" O ARG W 141 " (cutoff:3.500A) Processing helix chain 'W' and resid 154 through 172 removed outlier: 4.101A pdb=" N MET W 159 " --> pdb=" O ALA W 155 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N VAL W 160 " --> pdb=" O GLY W 156 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG W 171 " --> pdb=" O PHE W 167 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER W 172 " --> pdb=" O ASN W 168 " (cutoff:3.500A) Processing helix chain 'W' and resid 172 through 180 removed outlier: 3.526A pdb=" N GLU W 179 " --> pdb=" O GLU W 175 " (cutoff:3.500A) Processing helix chain 'a' and resid 4 through 8 removed outlier: 3.513A pdb=" N ALA a 7 " --> pdb=" O ASN a 4 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N SER a 8 " --> pdb=" O LEU a 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 4 through 8' Processing helix chain 'a' and resid 19 through 26 Processing helix chain 'a' and resid 27 through 29 No H-bonds generated for 'chain 'a' and resid 27 through 29' Processing helix chain 'a' and resid 40 through 58 removed outlier: 3.589A pdb=" N SER a 44 " --> pdb=" O ASN a 40 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLN a 46 " --> pdb=" O THR a 42 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLN a 56 " --> pdb=" O LEU a 52 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N MET a 57 " --> pdb=" O THR a 53 " (cutoff:3.500A) Processing helix chain 'a' and resid 64 through 67 Processing helix chain 'a' and resid 68 through 86 removed outlier: 3.652A pdb=" N GLY a 86 " --> pdb=" O THR a 82 " (cutoff:3.500A) Processing helix chain 'a' and resid 93 through 96 Processing helix chain 'a' and resid 97 through 120 removed outlier: 4.039A pdb=" N ASN a 101 " --> pdb=" O GLN a 97 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE a 106 " --> pdb=" O LEU a 102 " (cutoff:3.500A) Proline residue: a 107 - end of helix removed outlier: 3.577A pdb=" N PHE a 117 " --> pdb=" O VAL a 113 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG a 118 " --> pdb=" O PHE a 114 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR a 119 " --> pdb=" O THR a 115 " (cutoff:3.500A) Processing helix chain 'a' and resid 120 through 127 Processing helix chain 'a' and resid 137 through 151 removed outlier: 3.700A pdb=" N ILE a 143 " --> pdb=" O PRO a 139 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE a 144 " --> pdb=" O MET a 140 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR a 146 " --> pdb=" O VAL a 142 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE a 147 " --> pdb=" O ILE a 143 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE a 150 " --> pdb=" O THR a 146 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE a 151 " --> pdb=" O ILE a 147 " (cutoff:3.500A) Processing helix chain 'a' and resid 151 through 181 removed outlier: 4.356A pdb=" N LEU a 160 " --> pdb=" O LEU a 156 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE a 164 " --> pdb=" O LEU a 160 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N THR a 165 " --> pdb=" O THR a 161 " (cutoff:3.500A) Processing helix chain 'a' and resid 188 through 223 removed outlier: 3.944A pdb=" N LEU a 199 " --> pdb=" O ILE a 195 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N THR a 200 " --> pdb=" O LEU a 196 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ALA a 205 " --> pdb=" O ILE a 201 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N VAL a 206 " --> pdb=" O LEU a 202 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ALA a 207 " --> pdb=" O GLU a 203 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU a 208 " --> pdb=" O PHE a 204 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU a 216 " --> pdb=" O TYR a 212 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N HIS a 223 " --> pdb=" O SER a 219 " (cutoff:3.500A) Processing helix chain 'c' and resid 9 through 23 Processing helix chain 'c' and resid 34 through 51 Processing helix chain 'd' and resid 12 through 17 Processing helix chain 'd' and resid 24 through 45 Processing helix chain 'd' and resid 53 through 61 removed outlier: 3.534A pdb=" N TYR d 57 " --> pdb=" O ASP d 53 " (cutoff:3.500A) Processing helix chain 'd' and resid 64 through 75 removed outlier: 3.639A pdb=" N ASP d 69 " --> pdb=" O GLY d 65 " (cutoff:3.500A) Processing helix chain 'd' and resid 86 through 124 removed outlier: 3.723A pdb=" N GLU d 93 " --> pdb=" O LEU d 89 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU d 94 " --> pdb=" O VAL d 90 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLN d 95 " --> pdb=" O ASP d 91 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLU d 96 " --> pdb=" O ALA d 92 " (cutoff:3.500A) Processing helix chain 'd' and resid 132 through 140 Processing helix chain 'i' and resid 10 through 13 Processing helix chain 'i' and resid 14 through 21 Processing helix chain 'i' and resid 28 through 49 Processing helix chain 'k' and resid 8 through 29 removed outlier: 3.847A pdb=" N UNK k 13 " --> pdb=" O UNK k 9 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N UNK k 14 " --> pdb=" O UNK k 10 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N UNK k 15 " --> pdb=" O UNK k 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 60 removed outlier: 3.679A pdb=" N GLU A 57 " --> pdb=" O SER A 53 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG A 58 " --> pdb=" O ILE A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 125 removed outlier: 3.606A pdb=" N LEU A 124 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 198 removed outlier: 3.537A pdb=" N SER A 198 " --> pdb=" O LYS A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 229 removed outlier: 3.523A pdb=" N ILE A 221 " --> pdb=" O GLY A 217 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA A 222 " --> pdb=" O LYS A 218 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR A 225 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE A 226 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE A 227 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN A 228 " --> pdb=" O ASP A 224 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN A 229 " --> pdb=" O THR A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 234 removed outlier: 3.508A pdb=" N ASP A 234 " --> pdb=" O LYS A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 266 removed outlier: 3.684A pdb=" N VAL A 256 " --> pdb=" O LYS A 252 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA A 266 " --> pdb=" O ARG A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 270 No H-bonds generated for 'chain 'A' and resid 268 through 270' Processing helix chain 'A' and resid 282 through 302 removed outlier: 3.521A pdb=" N GLN A 286 " --> pdb=" O ALA A 282 " (cutoff:3.500A) Proline residue: A 290 - end of helix removed outlier: 3.760A pdb=" N TYR A 299 " --> pdb=" O SER A 295 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N PHE A 300 " --> pdb=" O MET A 296 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG A 301 " --> pdb=" O GLY A 297 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 328 removed outlier: 3.959A pdb=" N GLN A 317 " --> pdb=" O ASP A 313 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA A 318 " --> pdb=" O LEU A 314 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N MET A 324 " --> pdb=" O ALA A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 337 Processing helix chain 'A' and resid 341 through 349 removed outlier: 3.741A pdb=" N ARG A 347 " --> pdb=" O TYR A 343 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU A 348 " --> pdb=" O LEU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 360 Processing helix chain 'A' and resid 379 through 387 removed outlier: 3.508A pdb=" N SER A 387 " --> pdb=" O THR A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 removed outlier: 3.788A pdb=" N ALA A 420 " --> pdb=" O VAL A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 442 removed outlier: 3.796A pdb=" N GLN A 428 " --> pdb=" O ARG A 424 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N VAL A 429 " --> pdb=" O ALA A 425 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR A 432 " --> pdb=" O GLN A 428 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A 435 " --> pdb=" O GLY A 431 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR A 440 " --> pdb=" O GLU A 436 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLU A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 448 removed outlier: 3.981A pdb=" N GLN A 448 " --> pdb=" O ALA A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 471 removed outlier: 3.558A pdb=" N GLN A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU A 469 " --> pdb=" O VAL A 465 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU A 470 " --> pdb=" O ARG A 466 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU A 471 " --> pdb=" O LEU A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 493 removed outlier: 3.748A pdb=" N ALA A 490 " --> pdb=" O ALA A 486 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY A 491 " --> pdb=" O VAL A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 502 No H-bonds generated for 'chain 'A' and resid 500 through 502' Processing helix chain 'A' and resid 503 through 518 removed outlier: 3.505A pdb=" N SER A 513 " --> pdb=" O ASN A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 530 removed outlier: 4.125A pdb=" N LEU A 523 " --> pdb=" O HIS A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 552 removed outlier: 3.522A pdb=" N GLU A 542 " --> pdb=" O ALA A 538 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLU A 552 " --> pdb=" O LEU A 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 61 Processing helix chain 'C' and resid 193 through 198 removed outlier: 3.524A pdb=" N SER C 198 " --> pdb=" O LYS C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 229 removed outlier: 3.780A pdb=" N ILE C 221 " --> pdb=" O GLY C 217 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA C 222 " --> pdb=" O LYS C 218 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLN C 229 " --> pdb=" O THR C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 234 Processing helix chain 'C' and resid 237 through 241 removed outlier: 4.103A pdb=" N LYS C 240 " --> pdb=" O ASP C 237 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LYS C 241 " --> pdb=" O GLU C 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 237 through 241' Processing helix chain 'C' and resid 252 through 265 removed outlier: 3.606A pdb=" N VAL C 256 " --> pdb=" O LYS C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 267 No H-bonds generated for 'chain 'C' and resid 266 through 267' Processing helix chain 'C' and resid 268 through 270 No H-bonds generated for 'chain 'C' and resid 268 through 270' Processing helix chain 'C' and resid 282 through 302 Proline residue: C 290 - end of helix removed outlier: 3.535A pdb=" N MET C 296 " --> pdb=" O SER C 292 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N TYR C 299 " --> pdb=" O SER C 295 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N PHE C 300 " --> pdb=" O MET C 296 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG C 301 " --> pdb=" O GLY C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 327 removed outlier: 3.850A pdb=" N ALA C 318 " --> pdb=" O LEU C 314 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL C 319 " --> pdb=" O SER C 315 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA C 320 " --> pdb=" O LYS C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 337 Processing helix chain 'C' and resid 340 through 350 removed outlier: 3.752A pdb=" N HIS C 345 " --> pdb=" O VAL C 341 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG C 347 " --> pdb=" O TYR C 343 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LEU C 348 " --> pdb=" O LEU C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 387 removed outlier: 3.864A pdb=" N THR C 383 " --> pdb=" O ALA C 379 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN C 384 " --> pdb=" O TYR C 380 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER C 387 " --> pdb=" O THR C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 402 Processing helix chain 'C' and resid 423 through 442 removed outlier: 3.535A pdb=" N LYS C 427 " --> pdb=" O THR C 423 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN C 428 " --> pdb=" O ARG C 424 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL C 429 " --> pdb=" O ALA C 425 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N THR C 432 " --> pdb=" O GLN C 428 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N MET C 433 " --> pdb=" O VAL C 429 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU C 435 " --> pdb=" O GLY C 431 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU C 442 " --> pdb=" O ALA C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 471 removed outlier: 3.634A pdb=" N ARG C 466 " --> pdb=" O SER C 462 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU C 471 " --> pdb=" O LEU C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 493 removed outlier: 3.557A pdb=" N ARG C 493 " --> pdb=" O TYR C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 502 No H-bonds generated for 'chain 'C' and resid 500 through 502' Processing helix chain 'C' and resid 503 through 519 removed outlier: 3.558A pdb=" N PHE C 507 " --> pdb=" O LYS C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 530 removed outlier: 3.824A pdb=" N LEU C 523 " --> pdb=" O HIS C 519 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY C 524 " --> pdb=" O GLN C 520 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS C 525 " --> pdb=" O ALA C 521 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE C 526 " --> pdb=" O LEU C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 552 removed outlier: 3.503A pdb=" N LYS C 541 " --> pdb=" O ASP C 537 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU C 542 " --> pdb=" O ALA C 538 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU C 552 " --> pdb=" O LEU C 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 125 removed outlier: 4.159A pdb=" N LEU B 124 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE B 125 " --> pdb=" O ASP B 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 121 through 125' Processing helix chain 'B' and resid 193 through 200 Processing helix chain 'B' and resid 217 through 229 removed outlier: 3.933A pdb=" N ILE B 221 " --> pdb=" O GLY B 217 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA B 222 " --> pdb=" O LYS B 218 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLN B 229 " --> pdb=" O THR B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 234 Processing helix chain 'B' and resid 252 through 266 removed outlier: 3.578A pdb=" N ALA B 266 " --> pdb=" O ARG B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 302 removed outlier: 3.551A pdb=" N ALA B 289 " --> pdb=" O LEU B 285 " (cutoff:3.500A) Proline residue: B 290 - end of helix removed outlier: 4.273A pdb=" N PHE B 300 " --> pdb=" O MET B 296 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG B 301 " --> pdb=" O GLY B 297 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP B 302 " --> pdb=" O GLU B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 328 removed outlier: 4.007A pdb=" N GLN B 317 " --> pdb=" O ASP B 313 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU B 328 " --> pdb=" O MET B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 337 Processing helix chain 'B' and resid 340 through 349 removed outlier: 3.571A pdb=" N HIS B 345 " --> pdb=" O VAL B 341 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU B 348 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 360 Processing helix chain 'B' and resid 379 through 387 removed outlier: 3.615A pdb=" N THR B 383 " --> pdb=" O ALA B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 403 removed outlier: 3.817A pdb=" N PHE B 400 " --> pdb=" O GLU B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 445 removed outlier: 4.734A pdb=" N THR B 432 " --> pdb=" O GLN B 428 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N MET B 433 " --> pdb=" O VAL B 429 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ALA B 445 " --> pdb=" O ARG B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 471 removed outlier: 3.679A pdb=" N ARG B 466 " --> pdb=" O SER B 462 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU B 471 " --> pdb=" O LEU B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 493 Processing helix chain 'B' and resid 503 through 519 Processing helix chain 'B' and resid 520 through 530 Processing helix chain 'B' and resid 533 through 550 Processing sheet with id=AA1, first strand: chain 'D' and resid 102 through 109 removed outlier: 5.902A pdb=" N ILE D 105 " --> pdb=" O GLN D 116 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N GLN D 116 " --> pdb=" O ILE D 105 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA D 107 " --> pdb=" O ASP D 114 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N THR D 149 " --> pdb=" O HIS D 144 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N HIS D 144 " --> pdb=" O THR D 149 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ARG D 151 " --> pdb=" O ALA D 142 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 175 through 178 removed outlier: 3.574A pdb=" N VAL D 178 " --> pdb=" O GLN D 204 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLN D 204 " --> pdb=" O VAL D 178 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 186 through 187 removed outlier: 6.666A pdb=" N MET D 187 " --> pdb=" O TYR D 311 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N SER D 273 " --> pdb=" O ALA D 308 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N VAL D 310 " --> pdb=" O SER D 273 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N PHE D 275 " --> pdb=" O VAL D 310 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N GLY D 312 " --> pdb=" O PHE D 275 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N GLY D 277 " --> pdb=" O GLY D 312 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TYR D 272 " --> pdb=" O ASP D 342 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL D 278 " --> pdb=" O ASP D 348 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL D 343 " --> pdb=" O THR D 397 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N VAL D 399 " --> pdb=" O VAL D 343 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU D 345 " --> pdb=" O VAL D 399 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N ALA D 401 " --> pdb=" O LEU D 345 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ILE D 347 " --> pdb=" O ALA D 401 " (cutoff:3.500A) removed outlier: 8.982A pdb=" N TYR D 403 " --> pdb=" O ILE D 347 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ILE D 244 " --> pdb=" O GLN D 400 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N ILE D 402 " --> pdb=" O ILE D 244 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N LEU D 246 " --> pdb=" O ILE D 402 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR D 446 " --> pdb=" O THR D 424 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 224 through 225 removed outlier: 4.498A pdb=" N TYR D 238 " --> pdb=" O LEU D 225 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 102 through 109 removed outlier: 6.632A pdb=" N ASP E 114 " --> pdb=" O VAL E 106 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N VAL E 108 " --> pdb=" O VAL E 112 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N VAL E 112 " --> pdb=" O VAL E 108 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ARG E 151 " --> pdb=" O ALA E 142 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N GLY A 115 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ILE A 81 " --> pdb=" O ILE A 77 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ILE A 77 " --> pdb=" O ILE A 81 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ARG A 83 " --> pdb=" O LEU A 75 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 175 through 177 Processing sheet with id=AA7, first strand: chain 'E' and resid 186 through 187 removed outlier: 6.408A pdb=" N MET E 187 " --> pdb=" O TYR E 311 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N GLN E 313 " --> pdb=" O MET E 187 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N TYR E 272 " --> pdb=" O LEU E 344 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N PHE E 346 " --> pdb=" O TYR E 272 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL E 274 " --> pdb=" O PHE E 346 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA E 401 " --> pdb=" O ILE E 347 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LYS E 243 " --> pdb=" O ALA E 423 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N THR E 425 " --> pdb=" O LYS E 243 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N GLY E 245 " --> pdb=" O THR E 425 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 224 through 225 removed outlier: 4.479A pdb=" N TYR E 238 " --> pdb=" O LEU E 225 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 102 through 109 removed outlier: 6.700A pdb=" N ASP F 114 " --> pdb=" O VAL F 106 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N VAL F 108 " --> pdb=" O VAL F 112 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL F 112 " --> pdb=" O VAL F 108 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL F 113 " --> pdb=" O THR F 152 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N THR F 149 " --> pdb=" O HIS F 144 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N HIS F 144 " --> pdb=" O THR F 149 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ARG F 151 " --> pdb=" O ALA F 142 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 175 through 178 removed outlier: 3.606A pdb=" N VAL F 178 " --> pdb=" O GLN F 204 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLN F 204 " --> pdb=" O VAL F 178 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 186 through 187 removed outlier: 3.752A pdb=" N TYR F 311 " --> pdb=" O MET F 187 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR F 272 " --> pdb=" O ASP F 342 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL F 278 " --> pdb=" O ASP F 348 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE F 244 " --> pdb=" O GLN F 400 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N ILE F 402 " --> pdb=" O ILE F 244 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N LEU F 246 " --> pdb=" O ILE F 402 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 195 through 203 removed outlier: 6.553A pdb=" N SER G 195 " --> pdb=" O ARG G 191 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG G 191 " --> pdb=" O SER G 195 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY G 183 " --> pdb=" O ILE G 203 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N LEU G 92 " --> pdb=" O SER G 184 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N ILE G 186 " --> pdb=" O LEU G 92 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE G 94 " --> pdb=" O ILE G 186 " (cutoff:3.500A) removed outlier: 8.688A pdb=" N ASN G 188 " --> pdb=" O ILE G 94 " (cutoff:3.500A) removed outlier: 8.976A pdb=" N VAL G 96 " --> pdb=" O ASN G 188 " (cutoff:3.500A) removed outlier: 11.438A pdb=" N PHE G 190 " --> pdb=" O VAL G 96 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ILE G 93 " --> pdb=" O VAL G 131 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N VAL G 133 " --> pdb=" O ILE G 93 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N GLY G 95 " --> pdb=" O VAL G 133 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N ILE G 130 " --> pdb=" O LEU G 150 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N THR G 152 " --> pdb=" O ILE G 130 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N GLY G 132 " --> pdb=" O THR G 152 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N LYS G 154 " --> pdb=" O GLY G 132 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR G 152 " --> pdb=" O VAL I 45 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 39 through 43 removed outlier: 6.103A pdb=" N SER H 39 " --> pdb=" O VAL H 112 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N LEU H 114 " --> pdb=" O SER H 39 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N THR H 41 " --> pdb=" O LEU H 114 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ALA H 116 " --> pdb=" O THR H 41 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ALA H 43 " --> pdb=" O ALA H 116 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN H 78 " --> pdb=" O VAL H 104 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR H 76 " --> pdb=" O VAL H 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 69 through 70 removed outlier: 3.805A pdb=" N GLN H 57 " --> pdb=" O HIS H 88 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 149 through 154 removed outlier: 3.520A pdb=" N GLU S 151 " --> pdb=" O CYS S 118 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N GLU C 70 " --> pdb=" O ARG C 133 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ARG C 133 " --> pdb=" O GLU C 70 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N MET C 95 " --> pdb=" O THR C 134 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLU C 94 " --> pdb=" O SER C 106 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N GLY C 115 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE C 81 " --> pdb=" O ILE C 77 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ILE C 77 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ARG C 83 " --> pdb=" O LEU C 75 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'V' and resid 36 through 37 Processing sheet with id=AB8, first strand: chain 'A' and resid 139 through 141 Processing sheet with id=AB9, first strand: chain 'A' and resid 150 through 151 removed outlier: 3.893A pdb=" N ILE A 249 " --> pdb=" O ASP A 312 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR A 365 " --> pdb=" O ALA A 307 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE A 210 " --> pdb=" O ILE A 370 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 139 through 142 removed outlier: 4.222A pdb=" N THR C 168 " --> pdb=" O VAL C 142 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 150 through 151 removed outlier: 6.416A pdb=" N TYR C 243 " --> pdb=" O LEU C 308 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N ILE C 310 " --> pdb=" O TYR C 243 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ILE C 245 " --> pdb=" O ILE C 310 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N ASP C 312 " --> pdb=" O ILE C 245 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N VAL C 247 " --> pdb=" O ASP C 312 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR C 311 " --> pdb=" O LEU C 367 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE C 210 " --> pdb=" O ILE C 370 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU C 209 " --> pdb=" O ILE C 393 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN C 392 " --> pdb=" O VAL C 414 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 71 through 78 removed outlier: 6.833A pdb=" N ARG B 83 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ILE B 77 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N ILE B 81 " --> pdb=" O ILE B 77 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N GLY B 115 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLU B 94 " --> pdb=" O SER B 106 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N MET B 95 " --> pdb=" O THR B 134 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR B 134 " --> pdb=" O MET B 95 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 139 through 142 removed outlier: 3.904A pdb=" N THR B 168 " --> pdb=" O VAL B 142 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 150 through 151 removed outlier: 3.520A pdb=" N ALA B 307 " --> pdb=" O SER B 363 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 369 through 371 removed outlier: 6.368A pdb=" N ILE B 210 " --> pdb=" O ILE B 370 " (cutoff:3.500A) 2001 hydrogen bonds defined for protein. 5820 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: 6.93 Time building geometry restraints manager: 3.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10855 1.33 - 1.45: 5733 1.45 - 1.57: 22199 1.57 - 1.69: 20 1.69 - 1.81: 259 Bond restraints: 39066 Sorted by residual: bond pdb=" N VAL N 28 " pdb=" CA VAL N 28 " ideal model delta sigma weight residual 1.461 1.498 -0.037 1.17e-02 7.31e+03 1.01e+01 bond pdb=" N VAL P 28 " pdb=" CA VAL P 28 " ideal model delta sigma weight residual 1.460 1.497 -0.037 1.19e-02 7.06e+03 9.59e+00 bond pdb=" N VAL M 28 " pdb=" CA VAL M 28 " ideal model delta sigma weight residual 1.461 1.497 -0.036 1.17e-02 7.31e+03 9.39e+00 bond pdb=" N VAL L 28 " pdb=" CA VAL L 28 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.17e-02 7.31e+03 8.87e+00 bond pdb=" N ARG R 38 " pdb=" CA ARG R 38 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.15e-02 7.56e+03 8.58e+00 ... (remaining 39061 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 51486 1.49 - 2.98: 1200 2.98 - 4.47: 165 4.47 - 5.96: 48 5.96 - 7.45: 6 Bond angle restraints: 52905 Sorted by residual: angle pdb=" C GLN B 518 " pdb=" N HIS B 519 " pdb=" CA HIS B 519 " ideal model delta sigma weight residual 122.44 115.85 6.59 1.19e+00 7.06e-01 3.07e+01 angle pdb=" CA ILE L 33 " pdb=" C ILE L 33 " pdb=" O ILE L 33 " ideal model delta sigma weight residual 121.41 118.00 3.41 1.04e+00 9.25e-01 1.08e+01 angle pdb=" CA ILE P 33 " pdb=" C ILE P 33 " pdb=" O ILE P 33 " ideal model delta sigma weight residual 121.41 118.05 3.36 1.04e+00 9.25e-01 1.04e+01 angle pdb=" CA ILE M 33 " pdb=" C ILE M 33 " pdb=" O ILE M 33 " ideal model delta sigma weight residual 121.17 117.84 3.33 1.06e+00 8.90e-01 9.87e+00 angle pdb=" CA VAL S 66 " pdb=" C VAL S 66 " pdb=" O VAL S 66 " ideal model delta sigma weight residual 121.17 117.85 3.32 1.06e+00 8.90e-01 9.82e+00 ... (remaining 52900 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.53: 23316 33.53 - 67.05: 300 67.05 - 100.58: 8 100.58 - 134.10: 1 134.10 - 167.63: 1 Dihedral angle restraints: 23626 sinusoidal: 9075 harmonic: 14551 Sorted by residual: dihedral pdb=" C2' ADP D 601 " pdb=" C1' ADP D 601 " pdb=" N9 ADP D 601 " pdb=" C4 ADP D 601 " ideal model delta sinusoidal sigma weight residual 91.55 -100.83 -167.63 1 2.00e+01 2.50e-03 4.74e+01 dihedral pdb=" O2A ADP D 601 " pdb=" O3A ADP D 601 " pdb=" PA ADP D 601 " pdb=" PB ADP D 601 " ideal model delta sinusoidal sigma weight residual -60.00 49.43 -109.43 1 2.00e+01 2.50e-03 3.20e+01 dihedral pdb=" O1B ADP D 601 " pdb=" O3A ADP D 601 " pdb=" PB ADP D 601 " pdb=" PA ADP D 601 " ideal model delta sinusoidal sigma weight residual -60.00 33.64 -93.64 1 2.00e+01 2.50e-03 2.55e+01 ... (remaining 23623 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 4525 0.041 - 0.082: 1238 0.082 - 0.124: 413 0.124 - 0.165: 62 0.165 - 0.206: 14 Chirality restraints: 6252 Sorted by residual: chirality pdb=" CA ILE L 51 " pdb=" N ILE L 51 " pdb=" C ILE L 51 " pdb=" CB ILE L 51 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA LEU O 46 " pdb=" N LEU O 46 " pdb=" C LEU O 46 " pdb=" CB LEU O 46 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA ILE S 64 " pdb=" N ILE S 64 " pdb=" C ILE S 64 " pdb=" CB ILE S 64 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.57e-01 ... (remaining 6249 not shown) Planarity restraints: 6756 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS T 24 " -0.032 5.00e-02 4.00e+02 4.78e-02 3.66e+00 pdb=" N PRO T 25 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO T 25 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO T 25 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 411 " -0.031 5.00e-02 4.00e+02 4.75e-02 3.61e+00 pdb=" N PRO D 412 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO D 412 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 412 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG Q 38 " 0.169 9.50e-02 1.11e+02 7.58e-02 3.54e+00 pdb=" NE ARG Q 38 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG Q 38 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG Q 38 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG Q 38 " 0.005 2.00e-02 2.50e+03 ... (remaining 6753 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 194 2.58 - 3.16: 31567 3.16 - 3.74: 54899 3.74 - 4.32: 73388 4.32 - 4.90: 126516 Nonbonded interactions: 286564 Sorted by model distance: nonbonded pdb=" OG1 THR A 219 " pdb="MG MG A 602 " model vdw 2.003 2.170 nonbonded pdb=" O1B ADP D 601 " pdb="MG MG D 602 " model vdw 2.055 2.170 nonbonded pdb=" O2B ATP C 601 " pdb="MG MG C 602 " model vdw 2.147 2.170 nonbonded pdb=" OG SER C 517 " pdb=" OE1 GLN C 518 " model vdw 2.158 3.040 nonbonded pdb=" OG1 THR C 219 " pdb="MG MG C 602 " model vdw 2.161 2.170 ... (remaining 286559 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 65 through 68 or (resid 69 and (name N or name CA or name \ C or name O or name CB )) or resid 70 through 238 or (resid 239 and (name N or n \ ame CA or name C or name O or name CB )) or resid 240 through 445 or resid 454 t \ hrough 505 or (resid 506 and (name N or name CA or name C or name O or name CB ) \ ) or resid 507 through 550 or (resid 551 through 552 and (name N or name CA or n \ ame C or name O or name CB )) or resid 601 through 602)) selection = (chain 'B' and (resid 65 through 68 or (resid 69 and (name N or name CA or name \ C or name O or name CB )) or resid 70 through 238 or (resid 239 and (name N or n \ ame CA or name C or name O or name CB )) or resid 240 through 550 or (resid 551 \ through 552 and (name N or name CA or name C or name O or name CB )) or resid 60 \ 1 through 602)) selection = (chain 'C' and (resid 65 through 166 or (resid 167 and (name N or name CA or nam \ e C or name O or name CB )) or resid 168 through 237 or (resid 238 through 239 a \ nd (name N or name CA or name C or name O or name CB )) or resid 240 through 423 \ or (resid 424 through 425 and (name N or name CA or name C or name O or name CB \ )) or resid 426 through 445 or resid 454 through 499 or (resid 500 and (name N \ or name CA or name C or name O or name CB )) or resid 501 through 505 or (resid \ 506 and (name N or name CA or name C or name O or name CB )) or resid 507 throug \ h 552 or resid 601 through 602)) } ncs_group { reference = (chain 'D' and resid 100 through 566) selection = (chain 'E' and (resid 100 through 563 or (resid 564 and (name N or name CA or na \ me C or name O or name CB )) or resid 565 through 566)) selection = (chain 'F' and (resid 100 through 563 or (resid 564 and (name N or name CA or na \ me C or name O or name CB )) or resid 565 through 566)) } ncs_group { reference = (chain 'K' and (resid 2 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 or (resid 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 59 or (resid 60 and (name N or name C \ A or name C or name O or name CB )) or resid 61 through 65 or (resid 66 and (nam \ e N or name CA or name C or name O or name CB )) or resid 67 through 73)) selection = (chain 'L' and (resid 2 through 8 or (resid 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 59 or (resid 60 and (name N or name C \ A or name C or name O or name CB )) or resid 61 through 65 or (resid 66 and (nam \ e N or name CA or name C or name O or name CB )) or resid 67 through 73)) selection = (chain 'M' and (resid 2 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 or (resid 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 59 or (resid 60 and (name N or name C \ A or name C or name O or name CB )) or resid 61 through 65 or (resid 66 and (nam \ e N or name CA or name C or name O or name CB )) or resid 67 through 73)) selection = (chain 'N' and (resid 2 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 or (resid 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 65 or (resid 66 and (name N or name C \ A or name C or name O or name CB )) or resid 67 through 73)) selection = (chain 'O' and (resid 2 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 or (resid 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 59 or (resid 60 and (name N or name C \ A or name C or name O or name CB )) or resid 61 through 73)) selection = (chain 'P' and (resid 2 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 or (resid 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 59 or (resid 60 and (name N or name C \ A or name C or name O or name CB )) or resid 61 through 65 or (resid 66 and (nam \ e N or name CA or name C or name O or name CB )) or resid 67 through 73)) selection = (chain 'Q' and (resid 2 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 or (resid 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 59 or (resid 60 and (name N or name C \ A or name C or name O or name CB )) or resid 61 through 65 or (resid 66 and (nam \ e N or name CA or name C or name O or name CB )) or resid 67 through 73)) selection = (chain 'R' and (resid 2 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 59 or (resid 60 and (name N or name CA \ or name C or name O or name CB )) or resid 61 through 65 or (resid 66 and (name \ N or name CA or name C or name O or name CB )) or resid 67 through 73)) } 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=0.75 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: 8.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.580 Check model and map are aligned: 0.110 Set scattering table: 0.110 Process input model: 31.150 Find NCS groups from input model: 0.450 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:5.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 39066 Z= 0.216 Angle : 0.562 7.447 52905 Z= 0.340 Chirality : 0.044 0.206 6252 Planarity : 0.004 0.076 6756 Dihedral : 11.079 167.625 14304 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.79 % Favored : 97.19 % Rotamer: Outliers : 3.61 % Allowed : 5.99 % Favored : 90.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % 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 aren not related in a simple way. whole: 0.12 (0.12), residues: 5016 helix: 1.27 (0.11), residues: 2492 sheet: 0.13 (0.22), residues: 523 loop : -1.48 (0.13), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 352 TYR 0.013 0.001 TYR V 181 PHE 0.021 0.001 PHE a 114 TRP 0.013 0.001 TRP d 153 HIS 0.006 0.001 HIS T 32 Details of bonding type rmsd covalent geometry : bond 0.00374 (39066) covalent geometry : angle 0.56185 (52905) hydrogen bonds : bond 0.20273 ( 2001) hydrogen bonds : angle 6.09827 ( 5820) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10032 Ramachandran restraints generated. 5016 Oldfield, 0 Emsley, 5016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10032 Ramachandran restraints generated. 5016 Oldfield, 0 Emsley, 5016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1053 residues out of total 4096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 910 time to evaluate : 1.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 371 VAL cc_start: 0.8724 (m) cc_final: 0.8288 (t) REVERT: E 349 ASN cc_start: 0.8097 (OUTLIER) cc_final: 0.7659 (t0) REVERT: F 218 MET cc_start: 0.8972 (mmm) cc_final: 0.8645 (mmp) REVERT: G 218 TYR cc_start: 0.6669 (m-80) cc_final: 0.6460 (m-80) REVERT: H 155 ILE cc_start: 0.8709 (mm) cc_final: 0.8322 (mm) REVERT: I 44 ILE cc_start: 0.8595 (OUTLIER) cc_final: 0.8357 (mt) REVERT: O 18 VAL cc_start: 0.8784 (p) cc_final: 0.8399 (t) REVERT: O 36 TYR cc_start: 0.7563 (OUTLIER) cc_final: 0.5865 (p90) REVERT: Q 58 GLU cc_start: 0.7268 (pp20) cc_final: 0.7065 (pp20) REVERT: R 72 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8183 (tt) REVERT: V 48 PHE cc_start: 0.8213 (t80) cc_final: 0.7893 (t80) REVERT: V 86 SER cc_start: 0.8867 (t) cc_final: 0.8600 (m) REVERT: V 178 ARG cc_start: 0.8298 (mmt180) cc_final: 0.8034 (ptp-170) REVERT: W 183 LYS cc_start: 0.8192 (mttt) cc_final: 0.7624 (pttt) REVERT: d 152 TYR cc_start: 0.4815 (OUTLIER) cc_final: 0.4604 (p90) REVERT: A 296 MET cc_start: 0.9094 (mtt) cc_final: 0.8891 (mtt) REVERT: A 449 PHE cc_start: 0.8229 (OUTLIER) cc_final: 0.7853 (p90) outliers start: 143 outliers final: 51 residues processed: 1007 average time/residue: 0.6086 time to fit residues: 741.6739 Evaluate side-chains 681 residues out of total 4096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 624 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 5 ASP Chi-restraints excluded: chain 8 residue 28 ILE Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 369 SER Chi-restraints excluded: chain D residue 390 THR Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 349 ASN Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain M residue 33 ILE Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 71 ILE Chi-restraints excluded: chain O residue 9 ILE Chi-restraints excluded: chain O residue 36 TYR Chi-restraints excluded: chain P residue 18 VAL Chi-restraints excluded: chain P residue 54 PHE Chi-restraints excluded: chain R residue 72 LEU Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 11 ILE Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 171 VAL Chi-restraints excluded: chain V residue 224 ASP Chi-restraints excluded: chain a residue 33 THR Chi-restraints excluded: chain d residue 53 ASP Chi-restraints excluded: chain d residue 69 ASP Chi-restraints excluded: chain d residue 143 THR Chi-restraints excluded: chain d residue 146 ASP Chi-restraints excluded: chain d residue 152 TYR Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 449 PHE Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 542 GLU Chi-restraints excluded: chain B residue 397 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 432 optimal weight: 0.0020 chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 0.8980 chunk 455 optimal weight: 2.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 0.8980 chunk 494 optimal weight: 3.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 1.9990 overall best weight: 1.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 25 GLN D 116 GLN D 126 ASN D 131 GLN E 131 GLN E 313 GLN F 269 HIS F 341 GLN F 385 GLN F 459 HIS G 107 HIS G 230 GLN G 250 GLN H 73 HIS H 88 HIS I 6 GLN I 41 ASN K 39 ASN K 45 GLN ** R 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 10 GLN U 6 GLN ** V 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 4 ASN a 39 ASN a 61 HIS a 97 GLN a 168 HIS d 130 GLN i 28 ASN C 233 ASN C 251 GLN C 306 HIS C 373 GLN C 384 ASN C 484 GLN C 520 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.073247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.052278 restraints weight = 116901.822| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 2.46 r_work: 0.2790 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2670 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2670 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2670 r_free = 0.2670 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2670 r_free = 0.2670 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2670 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 39066 Z= 0.180 Angle : 0.645 9.901 52905 Z= 0.333 Chirality : 0.043 0.167 6252 Planarity : 0.004 0.052 6756 Dihedral : 7.243 166.891 5665 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.03 % Favored : 96.95 % Rotamer: Outliers : 4.17 % Allowed : 15.19 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % 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 aren not related in a simple way. whole: 0.37 (0.12), residues: 5016 helix: 1.47 (0.10), residues: 2549 sheet: 0.41 (0.23), residues: 528 loop : -1.51 (0.13), residues: 1939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG S 184 TYR 0.039 0.002 TYR O 49 PHE 0.021 0.001 PHE L 63 TRP 0.018 0.002 TRP d 153 HIS 0.005 0.001 HIS D 459 Details of bonding type rmsd covalent geometry : bond 0.00403 (39066) covalent geometry : angle 0.64470 (52905) hydrogen bonds : bond 0.07405 ( 2001) hydrogen bonds : angle 4.72251 ( 5820) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10032 Ramachandran restraints generated. 5016 Oldfield, 0 Emsley, 5016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10032 Ramachandran restraints generated. 5016 Oldfield, 0 Emsley, 5016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 840 residues out of total 4096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 675 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 16 MET cc_start: 0.8743 (tmm) cc_final: 0.8506 (tmm) REVERT: D 211 GLU cc_start: 0.8983 (OUTLIER) cc_final: 0.8628 (mt-10) REVERT: D 371 VAL cc_start: 0.8712 (m) cc_final: 0.8368 (t) REVERT: D 446 THR cc_start: 0.9115 (OUTLIER) cc_final: 0.8753 (p) REVERT: D 511 GLN cc_start: 0.8873 (tt0) cc_final: 0.8161 (tm-30) REVERT: E 349 ASN cc_start: 0.8904 (OUTLIER) cc_final: 0.8309 (t0) REVERT: E 478 ASP cc_start: 0.7900 (OUTLIER) cc_final: 0.7638 (p0) REVERT: H 47 GLN cc_start: 0.8580 (pm20) cc_final: 0.7998 (pm20) REVERT: H 136 LYS cc_start: 0.8586 (pttp) cc_final: 0.8301 (ptmt) REVERT: H 160 ASN cc_start: 0.7896 (OUTLIER) cc_final: 0.7676 (t0) REVERT: I 44 ILE cc_start: 0.9091 (OUTLIER) cc_final: 0.8741 (mp) REVERT: J 56 GLU cc_start: 0.8962 (tp30) cc_final: 0.8724 (tp30) REVERT: L 39 ASN cc_start: 0.8488 (m-40) cc_final: 0.7844 (t0) REVERT: L 66 MET cc_start: 0.8748 (ppp) cc_final: 0.8521 (ppp) REVERT: N 54 PHE cc_start: 0.8662 (t80) cc_final: 0.8273 (t80) REVERT: O 18 VAL cc_start: 0.8163 (p) cc_final: 0.7822 (t) REVERT: O 49 TYR cc_start: 0.7219 (m-80) cc_final: 0.6643 (m-80) REVERT: O 62 LEU cc_start: 0.7624 (OUTLIER) cc_final: 0.7333 (tm) REVERT: P 57 SER cc_start: 0.8565 (t) cc_final: 0.8352 (p) REVERT: Q 38 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.8498 (mtp-110) REVERT: Q 65 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8792 (tp) REVERT: R 62 LEU cc_start: 0.8802 (mm) cc_final: 0.8314 (mm) REVERT: R 63 PHE cc_start: 0.8703 (t80) cc_final: 0.8195 (t80) REVERT: R 72 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8417 (tt) REVERT: S 34 GLN cc_start: 0.8707 (tt0) cc_final: 0.7890 (tp-100) REVERT: S 38 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7324 (mt-10) REVERT: S 72 MET cc_start: 0.8596 (tmm) cc_final: 0.8376 (tmt) REVERT: S 78 PHE cc_start: 0.6691 (p90) cc_final: 0.6365 (p90) REVERT: S 159 MET cc_start: 0.7947 (mpp) cc_final: 0.7505 (mtt) REVERT: T 50 ILE cc_start: 0.8795 (mt) cc_final: 0.8467 (mt) REVERT: T 54 LYS cc_start: 0.9267 (mmtt) cc_final: 0.9032 (mmtt) REVERT: T 72 GLU cc_start: 0.8951 (OUTLIER) cc_final: 0.8728 (mp0) REVERT: U 12 LYS cc_start: 0.9035 (ttmm) cc_final: 0.8679 (tttm) REVERT: V 48 PHE cc_start: 0.8388 (t80) cc_final: 0.7967 (t80) REVERT: V 86 SER cc_start: 0.9198 (t) cc_final: 0.8979 (p) REVERT: V 130 ASP cc_start: 0.8628 (OUTLIER) cc_final: 0.8428 (p0) REVERT: V 158 MET cc_start: 0.8866 (ptm) cc_final: 0.8553 (ppp) REVERT: V 167 ARG cc_start: 0.8535 (ttt-90) cc_final: 0.8319 (ttt-90) REVERT: V 177 ASN cc_start: 0.8662 (t0) cc_final: 0.7903 (t0) REVERT: V 178 ARG cc_start: 0.9088 (mmt180) cc_final: 0.8181 (ptp-170) REVERT: V 190 ARG cc_start: 0.9190 (mtp-110) cc_final: 0.8827 (ptp-110) REVERT: V 218 ILE cc_start: 0.8552 (tp) cc_final: 0.8220 (pp) REVERT: W 120 TRP cc_start: 0.8682 (t60) cc_final: 0.8404 (t60) REVERT: W 123 MET cc_start: 0.7301 (tpp) cc_final: 0.6934 (tpp) REVERT: W 137 ARG cc_start: 0.6758 (OUTLIER) cc_final: 0.6262 (ptm160) REVERT: W 145 LYS cc_start: 0.9020 (tppt) cc_final: 0.8736 (tttm) REVERT: W 183 LYS cc_start: 0.7736 (mttt) cc_final: 0.6725 (pttt) REVERT: a 51 GLN cc_start: 0.9030 (tm-30) cc_final: 0.8791 (pp30) REVERT: a 71 MET cc_start: 0.7973 (OUTLIER) cc_final: 0.7055 (tpp) REVERT: a 100 MET cc_start: 0.8508 (ptm) cc_final: 0.8116 (ptp) REVERT: a 181 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8235 (tp) REVERT: a 221 TYR cc_start: 0.9456 (t80) cc_final: 0.9122 (t80) REVERT: a 222 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8687 (mm) REVERT: c 50 TYR cc_start: 0.7416 (t80) cc_final: 0.6648 (t80) REVERT: d 18 GLU cc_start: 0.8850 (mt-10) cc_final: 0.8625 (mp0) REVERT: d 125 ILE cc_start: 0.8286 (mm) cc_final: 0.8056 (mm) REVERT: d 130 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.8518 (mp10) REVERT: d 131 MET cc_start: 0.8435 (mmt) cc_final: 0.8202 (mmt) REVERT: A 296 MET cc_start: 0.9018 (mtt) cc_final: 0.8680 (mtt) REVERT: A 449 PHE cc_start: 0.8667 (OUTLIER) cc_final: 0.8122 (p90) REVERT: A 503 LYS cc_start: 0.9138 (OUTLIER) cc_final: 0.8761 (mtpt) REVERT: C 506 LYS cc_start: 0.9101 (mtpp) cc_final: 0.8785 (mppt) outliers start: 165 outliers final: 69 residues processed: 778 average time/residue: 0.5801 time to fit residues: 557.1279 Evaluate side-chains 684 residues out of total 4096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 596 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 28 ILE Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 446 THR Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 349 ASN Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 407 ASP Chi-restraints excluded: chain E residue 478 ASP Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 160 ASN Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain K residue 28 VAL Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 57 SER Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 47 PHE Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain M residue 33 ILE Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 66 MET Chi-restraints excluded: chain N residue 71 ILE Chi-restraints excluded: chain O residue 9 ILE Chi-restraints excluded: chain O residue 27 THR Chi-restraints excluded: chain O residue 34 ILE Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain P residue 2 ILE Chi-restraints excluded: chain P residue 32 LEU Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain Q residue 38 ARG Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 64 CYS Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain R residue 18 VAL Chi-restraints excluded: chain R residue 72 LEU Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 11 ILE Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 171 VAL Chi-restraints excluded: chain T residue 58 ASN Chi-restraints excluded: chain T residue 72 GLU Chi-restraints excluded: chain T residue 81 THR Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 130 ASP Chi-restraints excluded: chain W residue 119 SER Chi-restraints excluded: chain W residue 137 ARG Chi-restraints excluded: chain a residue 71 MET Chi-restraints excluded: chain a residue 141 LEU Chi-restraints excluded: chain a residue 181 LEU Chi-restraints excluded: chain a residue 222 LEU Chi-restraints excluded: chain d residue 14 VAL Chi-restraints excluded: chain d residue 130 GLN Chi-restraints excluded: chain d residue 143 THR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 449 PHE Chi-restraints excluded: chain A residue 503 LYS Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 417 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 458 optimal weight: 0.4980 chunk 267 optimal weight: 0.0980 chunk 72 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 340 optimal weight: 5.9990 chunk 289 optimal weight: 5.9990 chunk 403 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 34 optimal weight: 0.0670 chunk 332 optimal weight: 40.0000 chunk 320 optimal weight: 0.8980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 25 GLN E 453 ASN ** H 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 138 GLN H 154 GLN S 10 GLN V 154 ASN V 155 ASN a 4 ASN i 28 ASN C 509 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.074494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.053580 restraints weight = 116415.510| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 2.47 r_work: 0.2828 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2708 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2708 r_free = 0.2708 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2708 r_free = 0.2708 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2708 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 39066 Z= 0.130 Angle : 0.586 10.650 52905 Z= 0.297 Chirality : 0.041 0.175 6252 Planarity : 0.004 0.078 6756 Dihedral : 6.515 167.037 5635 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.51 % Favored : 97.47 % Rotamer: Outliers : 3.92 % Allowed : 16.22 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % 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 aren not related in a simple way. whole: 0.57 (0.12), residues: 5016 helix: 1.61 (0.10), residues: 2547 sheet: 0.68 (0.23), residues: 516 loop : -1.41 (0.13), residues: 1953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG W 124 TYR 0.040 0.001 TYR O 49 PHE 0.029 0.001 PHE K 54 TRP 0.022 0.001 TRP d 153 HIS 0.007 0.001 HIS H 88 Details of bonding type rmsd covalent geometry : bond 0.00258 (39066) covalent geometry : angle 0.58614 (52905) hydrogen bonds : bond 0.05991 ( 2001) hydrogen bonds : angle 4.34884 ( 5820) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10032 Ramachandran restraints generated. 5016 Oldfield, 0 Emsley, 5016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10032 Ramachandran restraints generated. 5016 Oldfield, 0 Emsley, 5016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 785 residues out of total 4096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 630 time to evaluate : 1.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 13 ILE cc_start: 0.8722 (mp) cc_final: 0.8507 (mp) REVERT: D 155 MET cc_start: 0.9176 (OUTLIER) cc_final: 0.8254 (mmt) REVERT: D 446 THR cc_start: 0.9049 (OUTLIER) cc_final: 0.8638 (p) REVERT: E 349 ASN cc_start: 0.8865 (OUTLIER) cc_final: 0.8236 (t0) REVERT: E 485 MET cc_start: 0.7153 (tpp) cc_final: 0.6724 (tmm) REVERT: F 258 ILE cc_start: 0.9202 (OUTLIER) cc_final: 0.8966 (tt) REVERT: H 47 GLN cc_start: 0.8457 (pm20) cc_final: 0.8187 (pm20) REVERT: H 56 ARG cc_start: 0.6073 (mmp-170) cc_final: 0.5801 (mmp-170) REVERT: H 59 ASP cc_start: 0.8464 (m-30) cc_final: 0.8231 (m-30) REVERT: H 67 PHE cc_start: 0.8369 (t80) cc_final: 0.8140 (t80) REVERT: H 96 LYS cc_start: 0.8005 (mtpt) cc_final: 0.7802 (pptt) REVERT: H 136 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8282 (ptmt) REVERT: I 44 ILE cc_start: 0.8888 (OUTLIER) cc_final: 0.8619 (mp) REVERT: J 56 GLU cc_start: 0.9012 (tp30) cc_final: 0.8792 (tp30) REVERT: K 25 ILE cc_start: 0.8284 (OUTLIER) cc_final: 0.8029 (mp) REVERT: K 31 SER cc_start: 0.9245 (m) cc_final: 0.8745 (t) REVERT: L 31 SER cc_start: 0.9149 (m) cc_final: 0.8827 (t) REVERT: L 42 LEU cc_start: 0.8344 (mp) cc_final: 0.8099 (mt) REVERT: L 66 MET cc_start: 0.8818 (OUTLIER) cc_final: 0.8560 (ppp) REVERT: M 47 PHE cc_start: 0.8581 (OUTLIER) cc_final: 0.8053 (t80) REVERT: O 49 TYR cc_start: 0.7249 (m-80) cc_final: 0.7047 (m-80) REVERT: O 62 LEU cc_start: 0.7605 (OUTLIER) cc_final: 0.7318 (tm) REVERT: P 57 SER cc_start: 0.8512 (t) cc_final: 0.8214 (p) REVERT: Q 65 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8607 (tp) REVERT: R 38 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.7859 (mtp180) REVERT: R 63 PHE cc_start: 0.8664 (t80) cc_final: 0.8358 (t80) REVERT: S 10 GLN cc_start: 0.8177 (tt0) cc_final: 0.7861 (tt0) REVERT: S 34 GLN cc_start: 0.8661 (tt0) cc_final: 0.8044 (tp-100) REVERT: S 41 ARG cc_start: 0.8219 (mtp85) cc_final: 0.7928 (mtp85) REVERT: S 77 LYS cc_start: 0.8466 (ttpp) cc_final: 0.8213 (ttpp) REVERT: S 159 MET cc_start: 0.8164 (mpp) cc_final: 0.7838 (mtm) REVERT: T 54 LYS cc_start: 0.9271 (mmtt) cc_final: 0.8993 (mmtt) REVERT: T 62 THR cc_start: 0.8440 (m) cc_final: 0.8075 (t) REVERT: T 89 VAL cc_start: 0.9447 (t) cc_final: 0.9246 (p) REVERT: U 10 LEU cc_start: 0.7820 (mp) cc_final: 0.7081 (tt) REVERT: U 12 LYS cc_start: 0.8964 (ttmm) cc_final: 0.8285 (ttmm) REVERT: V 48 PHE cc_start: 0.8375 (t80) cc_final: 0.7942 (t80) REVERT: V 130 ASP cc_start: 0.8628 (OUTLIER) cc_final: 0.8411 (p0) REVERT: V 153 ARG cc_start: 0.8685 (ptt90) cc_final: 0.8395 (ppt90) REVERT: V 158 MET cc_start: 0.8877 (ptm) cc_final: 0.8508 (ppp) REVERT: V 167 ARG cc_start: 0.8646 (ttt-90) cc_final: 0.8255 (ttt-90) REVERT: V 172 TYR cc_start: 0.8665 (t80) cc_final: 0.8438 (t80) REVERT: V 177 ASN cc_start: 0.8624 (t0) cc_final: 0.7955 (t0) REVERT: V 178 ARG cc_start: 0.9048 (mmt180) cc_final: 0.8075 (ptp-170) REVERT: V 204 HIS cc_start: 0.8943 (m90) cc_final: 0.8324 (m-70) REVERT: V 218 ILE cc_start: 0.8603 (tp) cc_final: 0.8273 (pp) REVERT: W 120 TRP cc_start: 0.8760 (t60) cc_final: 0.8530 (t60) REVERT: W 123 MET cc_start: 0.7274 (tpp) cc_final: 0.6803 (tpp) REVERT: W 145 LYS cc_start: 0.9024 (tppt) cc_final: 0.8802 (tttm) REVERT: W 181 LEU cc_start: 0.7436 (mp) cc_final: 0.7208 (mm) REVERT: W 183 LYS cc_start: 0.7787 (mttt) cc_final: 0.6811 (pttt) REVERT: a 17 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7839 (tm) REVERT: a 100 MET cc_start: 0.8421 (ptm) cc_final: 0.8162 (ptp) REVERT: a 120 LYS cc_start: 0.8573 (mtmt) cc_final: 0.8150 (pttp) REVERT: a 181 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8361 (tp) REVERT: a 222 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8609 (mm) REVERT: c 50 TYR cc_start: 0.7546 (t80) cc_final: 0.6931 (t80) REVERT: d 86 TYR cc_start: 0.5083 (t80) cc_final: 0.4841 (t80) REVERT: d 137 ASN cc_start: 0.8933 (OUTLIER) cc_final: 0.8315 (m110) REVERT: A 503 LYS cc_start: 0.9057 (OUTLIER) cc_final: 0.8657 (mtpt) REVERT: C 238 GLU cc_start: 0.8337 (mp0) cc_final: 0.7862 (tm-30) REVERT: C 506 LYS cc_start: 0.9084 (mtpp) cc_final: 0.8798 (mppt) REVERT: B 495 TYR cc_start: 0.8492 (m-10) cc_final: 0.8246 (m-10) outliers start: 155 outliers final: 58 residues processed: 721 average time/residue: 0.5914 time to fit residues: 525.3898 Evaluate side-chains 653 residues out of total 4096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 577 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 28 ILE Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 155 MET Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 216 MET Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 446 THR Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 349 ASN Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 360 VAL Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 136 LYS Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 57 SER Chi-restraints excluded: chain K residue 64 CYS Chi-restraints excluded: chain L residue 47 PHE Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 66 MET Chi-restraints excluded: chain M residue 28 VAL Chi-restraints excluded: chain M residue 47 PHE Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 71 ILE Chi-restraints excluded: chain O residue 9 ILE Chi-restraints excluded: chain O residue 45 GLN Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain Q residue 32 LEU Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain Q residue 67 VAL Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain R residue 38 ARG Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 11 ILE Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 171 VAL Chi-restraints excluded: chain V residue 26 VAL Chi-restraints excluded: chain V residue 130 ASP Chi-restraints excluded: chain W residue 119 SER Chi-restraints excluded: chain W residue 153 SER Chi-restraints excluded: chain a residue 17 LEU Chi-restraints excluded: chain a residue 141 LEU Chi-restraints excluded: chain a residue 181 LEU Chi-restraints excluded: chain a residue 193 PHE Chi-restraints excluded: chain a residue 222 LEU Chi-restraints excluded: chain c residue 10 LEU Chi-restraints excluded: chain d residue 137 ASN Chi-restraints excluded: chain d residue 143 THR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 503 LYS Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 417 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 5 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 464 optimal weight: 0.4980 chunk 71 optimal weight: 2.9990 chunk 450 optimal weight: 2.9990 chunk 497 optimal weight: 0.9990 chunk 63 optimal weight: 0.5980 chunk 111 optimal weight: 0.5980 chunk 268 optimal weight: 20.0000 chunk 446 optimal weight: 0.9980 chunk 136 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 25 GLN H 88 HIS H 154 GLN H 160 ASN Q 45 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.074451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.053535 restraints weight = 116169.885| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 2.44 r_work: 0.2827 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2710 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2710 r_free = 0.2710 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2710 r_free = 0.2710 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2710 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 39066 Z= 0.127 Angle : 0.570 9.550 52905 Z= 0.289 Chirality : 0.041 0.165 6252 Planarity : 0.004 0.063 6756 Dihedral : 6.222 165.956 5619 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.73 % Favored : 97.25 % Rotamer: Outliers : 3.74 % Allowed : 17.44 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % 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 aren not related in a simple way. whole: 0.66 (0.12), residues: 5016 helix: 1.69 (0.11), residues: 2554 sheet: 0.76 (0.23), residues: 499 loop : -1.39 (0.13), residues: 1963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG W 124 TYR 0.025 0.001 TYR I 3 PHE 0.034 0.001 PHE K 54 TRP 0.021 0.001 TRP d 153 HIS 0.007 0.001 HIS G 91 Details of bonding type rmsd covalent geometry : bond 0.00267 (39066) covalent geometry : angle 0.56988 (52905) hydrogen bonds : bond 0.05639 ( 2001) hydrogen bonds : angle 4.19004 ( 5820) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10032 Ramachandran restraints generated. 5016 Oldfield, 0 Emsley, 5016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10032 Ramachandran restraints generated. 5016 Oldfield, 0 Emsley, 5016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 753 residues out of total 4096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 605 time to evaluate : 1.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 13 ILE cc_start: 0.8729 (mp) cc_final: 0.8503 (mp) REVERT: 8 16 MET cc_start: 0.8673 (tmm) cc_final: 0.8469 (tmm) REVERT: D 371 VAL cc_start: 0.8880 (OUTLIER) cc_final: 0.8598 (t) REVERT: E 349 ASN cc_start: 0.8870 (OUTLIER) cc_final: 0.8225 (t0) REVERT: E 485 MET cc_start: 0.7151 (tpp) cc_final: 0.6752 (tmm) REVERT: F 109 ILE cc_start: 0.8988 (OUTLIER) cc_final: 0.8567 (mt) REVERT: F 258 ILE cc_start: 0.9165 (OUTLIER) cc_final: 0.8931 (tt) REVERT: H 47 GLN cc_start: 0.8441 (pm20) cc_final: 0.8142 (pm20) REVERT: H 67 PHE cc_start: 0.8368 (t80) cc_final: 0.8119 (t80) REVERT: H 136 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8201 (ptmt) REVERT: I 3 TYR cc_start: 0.7559 (p90) cc_final: 0.7156 (p90) REVERT: I 14 TYR cc_start: 0.8683 (t80) cc_final: 0.8479 (t80) REVERT: I 18 CYS cc_start: 0.8562 (m) cc_final: 0.8344 (m) REVERT: I 44 ILE cc_start: 0.8827 (OUTLIER) cc_final: 0.8572 (mp) REVERT: J 56 GLU cc_start: 0.9031 (tp30) cc_final: 0.8809 (tp30) REVERT: K 25 ILE cc_start: 0.8239 (OUTLIER) cc_final: 0.7977 (mp) REVERT: K 31 SER cc_start: 0.9264 (m) cc_final: 0.8769 (t) REVERT: L 31 SER cc_start: 0.9213 (m) cc_final: 0.8801 (t) REVERT: L 66 MET cc_start: 0.8803 (OUTLIER) cc_final: 0.8526 (ppp) REVERT: M 47 PHE cc_start: 0.8562 (OUTLIER) cc_final: 0.7994 (t80) REVERT: N 36 TYR cc_start: 0.8559 (t80) cc_final: 0.8323 (t80) REVERT: O 45 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.7878 (tt0) REVERT: O 60 MET cc_start: 0.7926 (tpp) cc_final: 0.7667 (tmt) REVERT: O 62 LEU cc_start: 0.7378 (OUTLIER) cc_final: 0.7168 (tm) REVERT: P 57 SER cc_start: 0.8581 (t) cc_final: 0.8308 (p) REVERT: Q 65 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8588 (tp) REVERT: R 38 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7825 (mtp180) REVERT: R 63 PHE cc_start: 0.8665 (t80) cc_final: 0.8345 (t80) REVERT: S 10 GLN cc_start: 0.8075 (tt0) cc_final: 0.7764 (tt0) REVERT: S 34 GLN cc_start: 0.8658 (tt0) cc_final: 0.8030 (tp-100) REVERT: S 159 MET cc_start: 0.8208 (mpp) cc_final: 0.7908 (mtm) REVERT: T 54 LYS cc_start: 0.9300 (mmtt) cc_final: 0.9070 (mmtt) REVERT: T 62 THR cc_start: 0.8509 (m) cc_final: 0.8188 (t) REVERT: U 12 LYS cc_start: 0.8952 (ttmm) cc_final: 0.8252 (ttmm) REVERT: V 48 PHE cc_start: 0.8372 (t80) cc_final: 0.7931 (t80) REVERT: V 130 ASP cc_start: 0.8608 (OUTLIER) cc_final: 0.8396 (p0) REVERT: V 158 MET cc_start: 0.8884 (ptm) cc_final: 0.8508 (ppp) REVERT: V 172 TYR cc_start: 0.8732 (t80) cc_final: 0.8517 (t80) REVERT: V 177 ASN cc_start: 0.8659 (t0) cc_final: 0.7915 (t0) REVERT: V 178 ARG cc_start: 0.9032 (mmt180) cc_final: 0.8024 (ptp-170) REVERT: V 204 HIS cc_start: 0.8968 (OUTLIER) cc_final: 0.8224 (m170) REVERT: V 218 ILE cc_start: 0.8584 (tp) cc_final: 0.8253 (pp) REVERT: W 120 TRP cc_start: 0.8760 (t60) cc_final: 0.8535 (t60) REVERT: W 123 MET cc_start: 0.7364 (tpp) cc_final: 0.6910 (tpp) REVERT: W 181 LEU cc_start: 0.7411 (mp) cc_final: 0.7176 (mm) REVERT: W 183 LYS cc_start: 0.7788 (mttt) cc_final: 0.6809 (pttt) REVERT: a 17 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7877 (tm) REVERT: a 100 MET cc_start: 0.8428 (ptm) cc_final: 0.8090 (ptp) REVERT: a 120 LYS cc_start: 0.8561 (mtmt) cc_final: 0.8171 (pttp) REVERT: a 222 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8553 (mm) REVERT: c 17 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.8132 (tp30) REVERT: c 50 TYR cc_start: 0.7560 (t80) cc_final: 0.6977 (t80) REVERT: d 45 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8957 (tm) REVERT: d 125 ILE cc_start: 0.8326 (mm) cc_final: 0.8019 (mm) REVERT: d 131 MET cc_start: 0.8421 (mmt) cc_final: 0.8218 (mmt) REVERT: d 137 ASN cc_start: 0.8903 (OUTLIER) cc_final: 0.8664 (m-40) REVERT: A 449 PHE cc_start: 0.8523 (OUTLIER) cc_final: 0.8042 (p90) REVERT: A 503 LYS cc_start: 0.9048 (OUTLIER) cc_final: 0.8647 (mtpt) REVERT: B 433 MET cc_start: 0.8594 (ttm) cc_final: 0.8377 (ttt) REVERT: B 495 TYR cc_start: 0.8498 (m-10) cc_final: 0.8240 (m-10) outliers start: 148 outliers final: 63 residues processed: 701 average time/residue: 0.6296 time to fit residues: 541.8331 Evaluate side-chains 656 residues out of total 4096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 571 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 28 ILE Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 349 ASN Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 407 ASP Chi-restraints excluded: chain E residue 479 ILE Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 360 VAL Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 136 LYS Chi-restraints excluded: chain H residue 161 GLU Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain K residue 28 VAL Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 57 SER Chi-restraints excluded: chain K residue 64 CYS Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 47 PHE Chi-restraints excluded: chain L residue 66 MET Chi-restraints excluded: chain M residue 47 PHE Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 71 ILE Chi-restraints excluded: chain O residue 9 ILE Chi-restraints excluded: chain O residue 45 GLN Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain Q residue 64 CYS Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain R residue 38 ARG Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 11 ILE Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 111 VAL Chi-restraints excluded: chain S residue 171 VAL Chi-restraints excluded: chain U residue 25 TYR Chi-restraints excluded: chain V residue 26 VAL Chi-restraints excluded: chain V residue 83 SER Chi-restraints excluded: chain V residue 130 ASP Chi-restraints excluded: chain V residue 204 HIS Chi-restraints excluded: chain V residue 224 ASP Chi-restraints excluded: chain W residue 119 SER Chi-restraints excluded: chain W residue 153 SER Chi-restraints excluded: chain a residue 17 LEU Chi-restraints excluded: chain a residue 141 LEU Chi-restraints excluded: chain a residue 222 LEU Chi-restraints excluded: chain c residue 12 VAL Chi-restraints excluded: chain c residue 17 GLU Chi-restraints excluded: chain d residue 45 LEU Chi-restraints excluded: chain d residue 137 ASN Chi-restraints excluded: chain d residue 143 THR Chi-restraints excluded: chain d residue 152 TYR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 449 PHE Chi-restraints excluded: chain A residue 503 LYS Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 520 GLN Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 417 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 319 optimal weight: 4.9990 chunk 206 optimal weight: 0.9980 chunk 213 optimal weight: 0.9990 chunk 296 optimal weight: 0.9990 chunk 220 optimal weight: 2.9990 chunk 495 optimal weight: 0.6980 chunk 369 optimal weight: 4.9990 chunk 242 optimal weight: 3.9990 chunk 158 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 496 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 30 ASN H 154 GLN J 73 HIS a 97 GLN B 458 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.073448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.052648 restraints weight = 116943.107| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 2.40 r_work: 0.2811 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2694 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2694 r_free = 0.2694 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2694 r_free = 0.2694 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2694 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 39066 Z= 0.145 Angle : 0.582 11.743 52905 Z= 0.297 Chirality : 0.042 0.172 6252 Planarity : 0.004 0.077 6756 Dihedral : 6.165 165.599 5615 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.83 % Favored : 97.15 % Rotamer: Outliers : 3.64 % Allowed : 18.27 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % 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 aren not related in a simple way. whole: 0.63 (0.12), residues: 5016 helix: 1.68 (0.11), residues: 2560 sheet: 0.70 (0.23), residues: 508 loop : -1.43 (0.13), residues: 1948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG V 199 TYR 0.019 0.001 TYR I 3 PHE 0.032 0.001 PHE K 54 TRP 0.018 0.001 TRP d 153 HIS 0.007 0.001 HIS G 91 Details of bonding type rmsd covalent geometry : bond 0.00333 (39066) covalent geometry : angle 0.58216 (52905) hydrogen bonds : bond 0.05733 ( 2001) hydrogen bonds : angle 4.17891 ( 5820) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10032 Ramachandran restraints generated. 5016 Oldfield, 0 Emsley, 5016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10032 Ramachandran restraints generated. 5016 Oldfield, 0 Emsley, 5016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 732 residues out of total 4096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 588 time to evaluate : 1.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 13 ILE cc_start: 0.8771 (mp) cc_final: 0.8541 (mp) REVERT: D 371 VAL cc_start: 0.8935 (OUTLIER) cc_final: 0.8606 (t) REVERT: E 349 ASN cc_start: 0.8855 (OUTLIER) cc_final: 0.8221 (t0) REVERT: E 485 MET cc_start: 0.7182 (tpp) cc_final: 0.6765 (tmm) REVERT: F 258 ILE cc_start: 0.9221 (OUTLIER) cc_final: 0.8976 (tt) REVERT: H 47 GLN cc_start: 0.8447 (pm20) cc_final: 0.7953 (pm20) REVERT: H 67 PHE cc_start: 0.8419 (t80) cc_final: 0.8190 (t80) REVERT: H 81 ARG cc_start: 0.8617 (ttm110) cc_final: 0.8219 (ptp-110) REVERT: H 136 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.8186 (ptmt) REVERT: H 154 GLN cc_start: 0.9142 (tt0) cc_final: 0.8920 (tp-100) REVERT: I 3 TYR cc_start: 0.7694 (p90) cc_final: 0.7158 (p90) REVERT: I 18 CYS cc_start: 0.8731 (m) cc_final: 0.8496 (m) REVERT: I 44 ILE cc_start: 0.8837 (OUTLIER) cc_final: 0.8565 (mp) REVERT: J 56 GLU cc_start: 0.9039 (tp30) cc_final: 0.8822 (tp30) REVERT: K 25 ILE cc_start: 0.8385 (OUTLIER) cc_final: 0.8095 (mp) REVERT: K 31 SER cc_start: 0.9267 (m) cc_final: 0.8787 (t) REVERT: K 47 PHE cc_start: 0.7350 (OUTLIER) cc_final: 0.7057 (t80) REVERT: L 31 SER cc_start: 0.9231 (m) cc_final: 0.8822 (t) REVERT: L 66 MET cc_start: 0.8807 (ppp) cc_final: 0.8523 (ppp) REVERT: M 34 ILE cc_start: 0.8672 (OUTLIER) cc_final: 0.8328 (tp) REVERT: M 47 PHE cc_start: 0.8583 (OUTLIER) cc_final: 0.7973 (t80) REVERT: O 49 TYR cc_start: 0.7186 (m-80) cc_final: 0.6768 (m-80) REVERT: P 57 SER cc_start: 0.8523 (t) cc_final: 0.8252 (p) REVERT: Q 65 LEU cc_start: 0.9086 (mt) cc_final: 0.8604 (tp) REVERT: R 38 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7800 (mtp180) REVERT: R 63 PHE cc_start: 0.8688 (t80) cc_final: 0.8389 (t80) REVERT: S 34 GLN cc_start: 0.8618 (tt0) cc_final: 0.7940 (tp-100) REVERT: S 41 ARG cc_start: 0.8392 (ttp80) cc_final: 0.8191 (ttt-90) REVERT: S 159 MET cc_start: 0.8253 (mpp) cc_final: 0.7923 (mtm) REVERT: T 54 LYS cc_start: 0.9327 (mmtt) cc_final: 0.9033 (mmtt) REVERT: T 62 THR cc_start: 0.8485 (m) cc_final: 0.8183 (t) REVERT: T 84 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8989 (pp) REVERT: U 10 LEU cc_start: 0.7654 (mp) cc_final: 0.7316 (pp) REVERT: U 12 LYS cc_start: 0.8933 (ttmm) cc_final: 0.8230 (ttmm) REVERT: U 19 LEU cc_start: 0.8720 (tt) cc_final: 0.8459 (pp) REVERT: V 48 PHE cc_start: 0.8389 (t80) cc_final: 0.7960 (t80) REVERT: V 130 ASP cc_start: 0.8597 (OUTLIER) cc_final: 0.8393 (p0) REVERT: V 155 ASN cc_start: 0.8431 (OUTLIER) cc_final: 0.8081 (p0) REVERT: V 158 MET cc_start: 0.8912 (ptm) cc_final: 0.8434 (ppp) REVERT: V 172 TYR cc_start: 0.8769 (t80) cc_final: 0.8566 (t80) REVERT: V 177 ASN cc_start: 0.8662 (t0) cc_final: 0.7932 (t0) REVERT: V 178 ARG cc_start: 0.9050 (mmt180) cc_final: 0.8092 (ptp90) REVERT: V 204 HIS cc_start: 0.8923 (OUTLIER) cc_final: 0.8460 (m170) REVERT: V 207 GLN cc_start: 0.9483 (tp-100) cc_final: 0.8930 (pt0) REVERT: V 218 ILE cc_start: 0.8557 (OUTLIER) cc_final: 0.8239 (pp) REVERT: W 123 MET cc_start: 0.7381 (tpp) cc_final: 0.6986 (tpp) REVERT: W 181 LEU cc_start: 0.7500 (mp) cc_final: 0.7248 (mm) REVERT: W 183 LYS cc_start: 0.7848 (mttt) cc_final: 0.6783 (pttt) REVERT: a 17 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7845 (tm) REVERT: a 97 GLN cc_start: 0.9055 (mm-40) cc_final: 0.8817 (mm110) REVERT: a 100 MET cc_start: 0.8469 (ptm) cc_final: 0.8246 (ptp) REVERT: a 119 TYR cc_start: 0.8143 (m-10) cc_final: 0.7837 (m-10) REVERT: a 120 LYS cc_start: 0.8556 (mtmt) cc_final: 0.8256 (pttp) REVERT: a 221 TYR cc_start: 0.9338 (t80) cc_final: 0.9034 (t80) REVERT: a 222 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8559 (mm) REVERT: c 50 TYR cc_start: 0.7543 (t80) cc_final: 0.6999 (t80) REVERT: d 45 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8935 (tm) REVERT: d 125 ILE cc_start: 0.8347 (mm) cc_final: 0.8030 (mm) REVERT: d 137 ASN cc_start: 0.8914 (OUTLIER) cc_final: 0.8688 (m-40) REVERT: A 110 GLU cc_start: 0.8921 (OUTLIER) cc_final: 0.8649 (mt-10) REVERT: A 449 PHE cc_start: 0.8566 (OUTLIER) cc_final: 0.8071 (p90) REVERT: A 503 LYS cc_start: 0.9091 (OUTLIER) cc_final: 0.8658 (mtpt) REVERT: C 238 GLU cc_start: 0.8199 (mp0) cc_final: 0.7859 (tm-30) REVERT: C 506 LYS cc_start: 0.9117 (mtpp) cc_final: 0.8830 (mppt) REVERT: B 433 MET cc_start: 0.8656 (ttm) cc_final: 0.8438 (ttt) REVERT: B 495 TYR cc_start: 0.8563 (m-10) cc_final: 0.8333 (m-10) outliers start: 144 outliers final: 80 residues processed: 675 average time/residue: 0.6088 time to fit residues: 506.6665 Evaluate side-chains 664 residues out of total 4096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 562 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 28 ILE Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 216 MET Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 338 GLN Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 204 GLN Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 349 ASN Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 407 ASP Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 360 VAL Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 136 LYS Chi-restraints excluded: chain H residue 161 GLU Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain J residue 74 HIS Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain K residue 28 VAL Chi-restraints excluded: chain K residue 47 PHE Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 64 CYS Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 47 PHE Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain M residue 47 PHE Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 71 ILE Chi-restraints excluded: chain O residue 9 ILE Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain O residue 45 GLN Chi-restraints excluded: chain P residue 2 ILE Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 47 PHE Chi-restraints excluded: chain Q residue 67 VAL Chi-restraints excluded: chain R residue 38 ARG Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 11 ILE Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 111 VAL Chi-restraints excluded: chain S residue 171 VAL Chi-restraints excluded: chain T residue 84 LEU Chi-restraints excluded: chain V residue 26 VAL Chi-restraints excluded: chain V residue 83 SER Chi-restraints excluded: chain V residue 130 ASP Chi-restraints excluded: chain V residue 155 ASN Chi-restraints excluded: chain V residue 204 HIS Chi-restraints excluded: chain V residue 218 ILE Chi-restraints excluded: chain W residue 110 LEU Chi-restraints excluded: chain W residue 119 SER Chi-restraints excluded: chain W residue 153 SER Chi-restraints excluded: chain a residue 17 LEU Chi-restraints excluded: chain a residue 33 THR Chi-restraints excluded: chain a residue 93 THR Chi-restraints excluded: chain a residue 141 LEU Chi-restraints excluded: chain a residue 222 LEU Chi-restraints excluded: chain c residue 12 VAL Chi-restraints excluded: chain d residue 14 VAL Chi-restraints excluded: chain d residue 19 ILE Chi-restraints excluded: chain d residue 45 LEU Chi-restraints excluded: chain d residue 137 ASN Chi-restraints excluded: chain d residue 143 THR Chi-restraints excluded: chain d residue 152 TYR Chi-restraints excluded: chain i residue 24 THR Chi-restraints excluded: chain i residue 31 LEU Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 449 PHE Chi-restraints excluded: chain A residue 503 LYS Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 520 GLN Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 417 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 274 optimal weight: 9.9990 chunk 35 optimal weight: 0.8980 chunk 388 optimal weight: 3.9990 chunk 108 optimal weight: 0.8980 chunk 436 optimal weight: 0.0050 chunk 72 optimal weight: 3.9990 chunk 264 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 493 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 481 optimal weight: 3.9990 overall best weight: 1.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 160 ASN S 10 GLN V 207 GLN A 475 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.073399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.052438 restraints weight = 118440.873| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 2.43 r_work: 0.2804 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2686 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2686 r_free = 0.2686 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2686 r_free = 0.2686 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2686 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 39066 Z= 0.146 Angle : 0.598 11.383 52905 Z= 0.302 Chirality : 0.042 0.189 6252 Planarity : 0.004 0.070 6756 Dihedral : 6.158 165.630 5615 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.95 % Favored : 97.01 % Rotamer: Outliers : 3.87 % Allowed : 18.90 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % 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 aren not related in a simple way. whole: 0.63 (0.12), residues: 5016 helix: 1.69 (0.11), residues: 2560 sheet: 0.69 (0.23), residues: 508 loop : -1.44 (0.13), residues: 1948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG V 199 TYR 0.018 0.001 TYR W 139 PHE 0.032 0.001 PHE U 20 TRP 0.026 0.002 TRP d 153 HIS 0.007 0.001 HIS G 91 Details of bonding type rmsd covalent geometry : bond 0.00337 (39066) covalent geometry : angle 0.59761 (52905) hydrogen bonds : bond 0.05688 ( 2001) hydrogen bonds : angle 4.15676 ( 5820) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10032 Ramachandran restraints generated. 5016 Oldfield, 0 Emsley, 5016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10032 Ramachandran restraints generated. 5016 Oldfield, 0 Emsley, 5016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 747 residues out of total 4096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 594 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 13 ILE cc_start: 0.8782 (mp) cc_final: 0.8547 (mp) REVERT: 8 16 MET cc_start: 0.8747 (tmm) cc_final: 0.8496 (tmm) REVERT: D 155 MET cc_start: 0.9175 (OUTLIER) cc_final: 0.8283 (mmt) REVERT: D 371 VAL cc_start: 0.8936 (OUTLIER) cc_final: 0.8663 (t) REVERT: E 349 ASN cc_start: 0.8848 (OUTLIER) cc_final: 0.8217 (t0) REVERT: E 485 MET cc_start: 0.7224 (tpp) cc_final: 0.6807 (tmm) REVERT: F 258 ILE cc_start: 0.9238 (OUTLIER) cc_final: 0.8989 (tt) REVERT: H 47 GLN cc_start: 0.8443 (pm20) cc_final: 0.7942 (pm20) REVERT: H 81 ARG cc_start: 0.8636 (ttm110) cc_final: 0.7941 (ptp-110) REVERT: H 154 GLN cc_start: 0.9208 (tt0) cc_final: 0.8927 (tp-100) REVERT: I 3 TYR cc_start: 0.7867 (p90) cc_final: 0.7209 (p90) REVERT: I 14 TYR cc_start: 0.8671 (t80) cc_final: 0.8423 (t80) REVERT: I 18 CYS cc_start: 0.8750 (m) cc_final: 0.8488 (m) REVERT: I 44 ILE cc_start: 0.8836 (OUTLIER) cc_final: 0.8554 (mp) REVERT: J 56 GLU cc_start: 0.9055 (tp30) cc_final: 0.8838 (tp30) REVERT: K 31 SER cc_start: 0.9263 (m) cc_final: 0.8828 (t) REVERT: K 47 PHE cc_start: 0.7399 (OUTLIER) cc_final: 0.7129 (t80) REVERT: K 63 PHE cc_start: 0.8101 (t80) cc_final: 0.7771 (t80) REVERT: K 66 MET cc_start: 0.7843 (pp-130) cc_final: 0.7081 (ppp) REVERT: L 31 SER cc_start: 0.9238 (m) cc_final: 0.8826 (t) REVERT: L 66 MET cc_start: 0.8828 (OUTLIER) cc_final: 0.8587 (ppp) REVERT: M 34 ILE cc_start: 0.8713 (OUTLIER) cc_final: 0.8432 (tp) REVERT: M 47 PHE cc_start: 0.8554 (OUTLIER) cc_final: 0.7943 (t80) REVERT: N 15 THR cc_start: 0.8619 (t) cc_final: 0.8313 (p) REVERT: O 49 TYR cc_start: 0.7102 (m-10) cc_final: 0.6797 (m-80) REVERT: P 57 SER cc_start: 0.8502 (t) cc_final: 0.8230 (p) REVERT: Q 65 LEU cc_start: 0.9077 (mt) cc_final: 0.8603 (tp) REVERT: R 63 PHE cc_start: 0.8684 (t80) cc_final: 0.8386 (t80) REVERT: S 10 GLN cc_start: 0.8125 (tt0) cc_final: 0.7775 (tt0) REVERT: S 34 GLN cc_start: 0.8614 (tt0) cc_final: 0.7913 (tp-100) REVERT: T 54 LYS cc_start: 0.9341 (mmtt) cc_final: 0.9084 (mmtt) REVERT: T 62 THR cc_start: 0.8462 (m) cc_final: 0.8160 (t) REVERT: T 84 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.8986 (pp) REVERT: T 88 TYR cc_start: 0.8375 (m-10) cc_final: 0.8101 (m-80) REVERT: U 10 LEU cc_start: 0.7633 (mp) cc_final: 0.7308 (pp) REVERT: U 12 LYS cc_start: 0.8910 (ttmm) cc_final: 0.8204 (ttmm) REVERT: U 19 LEU cc_start: 0.8707 (tt) cc_final: 0.8412 (pp) REVERT: V 48 PHE cc_start: 0.8362 (t80) cc_final: 0.7921 (t80) REVERT: V 130 ASP cc_start: 0.8616 (OUTLIER) cc_final: 0.8390 (p0) REVERT: V 155 ASN cc_start: 0.8460 (OUTLIER) cc_final: 0.8067 (p0) REVERT: V 158 MET cc_start: 0.8912 (ptm) cc_final: 0.8396 (ppp) REVERT: V 177 ASN cc_start: 0.8668 (t0) cc_final: 0.7941 (t0) REVERT: V 178 ARG cc_start: 0.9059 (mmt180) cc_final: 0.8082 (ptp90) REVERT: V 204 HIS cc_start: 0.8935 (OUTLIER) cc_final: 0.8395 (m170) REVERT: V 207 GLN cc_start: 0.9449 (tp40) cc_final: 0.8902 (pt0) REVERT: V 218 ILE cc_start: 0.8590 (OUTLIER) cc_final: 0.8236 (pp) REVERT: W 123 MET cc_start: 0.7131 (tpp) cc_final: 0.6817 (tpp) REVERT: W 183 LYS cc_start: 0.7829 (mttt) cc_final: 0.6738 (pttt) REVERT: a 17 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7853 (tm) REVERT: a 49 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.9026 (mp) REVERT: a 63 GLN cc_start: 0.9007 (tp-100) cc_final: 0.8748 (tp-100) REVERT: a 97 GLN cc_start: 0.9062 (mm-40) cc_final: 0.8836 (mm110) REVERT: a 100 MET cc_start: 0.8504 (ptm) cc_final: 0.8222 (ptp) REVERT: a 119 TYR cc_start: 0.8087 (m-10) cc_final: 0.7719 (m-10) REVERT: a 120 LYS cc_start: 0.8656 (mtmt) cc_final: 0.8365 (pttp) REVERT: a 222 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8596 (mm) REVERT: c 8 GLN cc_start: 0.6648 (OUTLIER) cc_final: 0.5841 (tp40) REVERT: c 50 TYR cc_start: 0.7521 (t80) cc_final: 0.6980 (t80) REVERT: d 45 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8935 (tm) REVERT: d 125 ILE cc_start: 0.8306 (OUTLIER) cc_final: 0.8055 (mm) REVERT: d 137 ASN cc_start: 0.8913 (OUTLIER) cc_final: 0.8686 (m-40) REVERT: A 449 PHE cc_start: 0.8581 (OUTLIER) cc_final: 0.8028 (p90) REVERT: A 503 LYS cc_start: 0.9107 (OUTLIER) cc_final: 0.8686 (mtpt) REVERT: C 417 VAL cc_start: 0.8408 (OUTLIER) cc_final: 0.8107 (p) REVERT: B 495 TYR cc_start: 0.8620 (m-10) cc_final: 0.8379 (m-10) outliers start: 153 outliers final: 91 residues processed: 688 average time/residue: 0.6630 time to fit residues: 563.9575 Evaluate side-chains 683 residues out of total 4096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 568 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 11 ILE Chi-restraints excluded: chain 8 residue 28 ILE Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 155 MET Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 216 MET Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 338 GLN Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 204 GLN Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 349 ASN Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 479 ILE Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 360 VAL Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 161 GLU Chi-restraints excluded: chain H residue 165 LYS Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain J residue 74 HIS Chi-restraints excluded: chain K residue 28 VAL Chi-restraints excluded: chain K residue 47 PHE Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 57 SER Chi-restraints excluded: chain K residue 64 CYS Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 47 PHE Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 66 MET Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain M residue 47 PHE Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 71 ILE Chi-restraints excluded: chain O residue 9 ILE Chi-restraints excluded: chain O residue 31 SER Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain O residue 45 GLN Chi-restraints excluded: chain P residue 2 ILE Chi-restraints excluded: chain P residue 32 LEU Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain Q residue 32 LEU Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 47 PHE Chi-restraints excluded: chain Q residue 64 CYS Chi-restraints excluded: chain R residue 66 MET Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 11 ILE Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 111 VAL Chi-restraints excluded: chain S residue 171 VAL Chi-restraints excluded: chain T residue 42 THR Chi-restraints excluded: chain T residue 84 LEU Chi-restraints excluded: chain V residue 26 VAL Chi-restraints excluded: chain V residue 83 SER Chi-restraints excluded: chain V residue 130 ASP Chi-restraints excluded: chain V residue 155 ASN Chi-restraints excluded: chain V residue 204 HIS Chi-restraints excluded: chain V residue 218 ILE Chi-restraints excluded: chain W residue 110 LEU Chi-restraints excluded: chain W residue 119 SER Chi-restraints excluded: chain W residue 153 SER Chi-restraints excluded: chain a residue 17 LEU Chi-restraints excluded: chain a residue 33 THR Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain a residue 85 LEU Chi-restraints excluded: chain a residue 93 THR Chi-restraints excluded: chain a residue 141 LEU Chi-restraints excluded: chain a residue 222 LEU Chi-restraints excluded: chain c residue 8 GLN Chi-restraints excluded: chain c residue 12 VAL Chi-restraints excluded: chain d residue 14 VAL Chi-restraints excluded: chain d residue 45 LEU Chi-restraints excluded: chain d residue 125 ILE Chi-restraints excluded: chain d residue 137 ASN Chi-restraints excluded: chain d residue 143 THR Chi-restraints excluded: chain i residue 24 THR Chi-restraints excluded: chain i residue 31 LEU Chi-restraints excluded: chain i residue 39 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 449 PHE Chi-restraints excluded: chain A residue 503 LYS Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 520 GLN Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 397 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 439 optimal weight: 2.9990 chunk 152 optimal weight: 10.0000 chunk 268 optimal weight: 10.0000 chunk 375 optimal weight: 1.9990 chunk 204 optimal weight: 10.0000 chunk 387 optimal weight: 0.9980 chunk 395 optimal weight: 0.9980 chunk 434 optimal weight: 5.9990 chunk 485 optimal weight: 0.4980 chunk 346 optimal weight: 4.9990 chunk 166 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 30 ASN d 130 GLN B 514 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.073190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.052195 restraints weight = 117075.663| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 2.43 r_work: 0.2791 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2672 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2672 r_free = 0.2672 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2672 r_free = 0.2672 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2672 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 39066 Z= 0.166 Angle : 0.615 11.823 52905 Z= 0.314 Chirality : 0.043 0.228 6252 Planarity : 0.004 0.086 6756 Dihedral : 6.238 165.783 5615 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.15 % Favored : 96.81 % Rotamer: Outliers : 3.84 % Allowed : 18.98 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % 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 aren not related in a simple way. whole: 0.56 (0.12), residues: 5016 helix: 1.64 (0.11), residues: 2559 sheet: 0.67 (0.23), residues: 506 loop : -1.49 (0.13), residues: 1951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG c 19 TYR 0.030 0.001 TYR a 221 PHE 0.033 0.002 PHE V 105 TRP 0.035 0.002 TRP d 153 HIS 0.007 0.001 HIS G 91 Details of bonding type rmsd covalent geometry : bond 0.00393 (39066) covalent geometry : angle 0.61486 (52905) hydrogen bonds : bond 0.05941 ( 2001) hydrogen bonds : angle 4.19698 ( 5820) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10032 Ramachandran restraints generated. 5016 Oldfield, 0 Emsley, 5016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10032 Ramachandran restraints generated. 5016 Oldfield, 0 Emsley, 5016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 736 residues out of total 4096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 584 time to evaluate : 1.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 13 ILE cc_start: 0.8713 (mp) cc_final: 0.8482 (mp) REVERT: 8 16 MET cc_start: 0.8738 (tmm) cc_final: 0.8504 (tmm) REVERT: D 155 MET cc_start: 0.9215 (OUTLIER) cc_final: 0.8328 (mmt) REVERT: D 371 VAL cc_start: 0.8879 (OUTLIER) cc_final: 0.8676 (t) REVERT: E 349 ASN cc_start: 0.8892 (OUTLIER) cc_final: 0.8263 (t0) REVERT: E 485 MET cc_start: 0.7288 (tpp) cc_final: 0.6788 (tmm) REVERT: F 258 ILE cc_start: 0.9173 (OUTLIER) cc_final: 0.8921 (tt) REVERT: H 47 GLN cc_start: 0.8396 (pm20) cc_final: 0.7882 (pm20) REVERT: H 81 ARG cc_start: 0.8653 (ttm110) cc_final: 0.7863 (ptp-110) REVERT: H 117 GLU cc_start: 0.8455 (tm-30) cc_final: 0.8249 (tm-30) REVERT: H 154 GLN cc_start: 0.9235 (tt0) cc_final: 0.8994 (tp-100) REVERT: H 160 ASN cc_start: 0.7920 (OUTLIER) cc_final: 0.7687 (t0) REVERT: I 3 TYR cc_start: 0.7911 (p90) cc_final: 0.7223 (p90) REVERT: I 14 TYR cc_start: 0.8728 (t80) cc_final: 0.8467 (t80) REVERT: I 18 CYS cc_start: 0.8690 (m) cc_final: 0.8445 (m) REVERT: I 43 LYS cc_start: 0.8771 (mmmm) cc_final: 0.8033 (mppt) REVERT: I 44 ILE cc_start: 0.8827 (OUTLIER) cc_final: 0.8526 (mp) REVERT: J 56 GLU cc_start: 0.8976 (tp30) cc_final: 0.8720 (tp30) REVERT: K 27 THR cc_start: 0.8970 (t) cc_final: 0.8681 (p) REVERT: K 31 SER cc_start: 0.9246 (m) cc_final: 0.8799 (t) REVERT: K 47 PHE cc_start: 0.7410 (OUTLIER) cc_final: 0.7132 (t80) REVERT: K 63 PHE cc_start: 0.8161 (t80) cc_final: 0.7810 (t80) REVERT: K 66 MET cc_start: 0.7877 (pp-130) cc_final: 0.7184 (ppp) REVERT: L 31 SER cc_start: 0.9237 (m) cc_final: 0.8797 (t) REVERT: L 66 MET cc_start: 0.8814 (ppp) cc_final: 0.8552 (ppp) REVERT: M 34 ILE cc_start: 0.8694 (OUTLIER) cc_final: 0.8436 (tp) REVERT: M 47 PHE cc_start: 0.8522 (OUTLIER) cc_final: 0.7929 (t80) REVERT: N 15 THR cc_start: 0.8650 (t) cc_final: 0.8227 (p) REVERT: O 49 TYR cc_start: 0.7108 (m-10) cc_final: 0.6900 (m-80) REVERT: P 57 SER cc_start: 0.8488 (t) cc_final: 0.8219 (p) REVERT: Q 65 LEU cc_start: 0.9055 (mt) cc_final: 0.8599 (tp) REVERT: R 63 PHE cc_start: 0.8680 (t80) cc_final: 0.8343 (t80) REVERT: S 10 GLN cc_start: 0.8025 (tt0) cc_final: 0.7717 (tt0) REVERT: S 34 GLN cc_start: 0.8619 (tt0) cc_final: 0.7882 (tp-100) REVERT: S 41 ARG cc_start: 0.8267 (mtp85) cc_final: 0.7967 (ttt-90) REVERT: T 54 LYS cc_start: 0.9340 (mmtt) cc_final: 0.9068 (mmtt) REVERT: T 62 THR cc_start: 0.8382 (m) cc_final: 0.8076 (t) REVERT: T 83 VAL cc_start: 0.8465 (p) cc_final: 0.8201 (t) REVERT: T 88 TYR cc_start: 0.8357 (m-10) cc_final: 0.8007 (m-80) REVERT: U 10 LEU cc_start: 0.7679 (mp) cc_final: 0.7376 (pp) REVERT: U 12 LYS cc_start: 0.8886 (ttmm) cc_final: 0.8202 (ttmm) REVERT: V 48 PHE cc_start: 0.8352 (t80) cc_final: 0.7852 (t80) REVERT: V 130 ASP cc_start: 0.8613 (OUTLIER) cc_final: 0.8412 (p0) REVERT: V 155 ASN cc_start: 0.8479 (OUTLIER) cc_final: 0.8140 (p0) REVERT: V 158 MET cc_start: 0.8888 (ptm) cc_final: 0.8409 (ppp) REVERT: V 172 TYR cc_start: 0.8658 (t80) cc_final: 0.8336 (t80) REVERT: V 177 ASN cc_start: 0.8647 (t0) cc_final: 0.7919 (t0) REVERT: V 178 ARG cc_start: 0.9038 (mmt180) cc_final: 0.8061 (ptp-170) REVERT: V 204 HIS cc_start: 0.8912 (OUTLIER) cc_final: 0.8370 (m170) REVERT: V 207 GLN cc_start: 0.9440 (tp40) cc_final: 0.8907 (pt0) REVERT: V 218 ILE cc_start: 0.8557 (OUTLIER) cc_final: 0.8205 (pp) REVERT: W 181 LEU cc_start: 0.7333 (mp) cc_final: 0.7101 (mm) REVERT: W 183 LYS cc_start: 0.7794 (mttt) cc_final: 0.6673 (pttt) REVERT: a 17 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7896 (tm) REVERT: a 49 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.9018 (mp) REVERT: a 63 GLN cc_start: 0.9017 (tp-100) cc_final: 0.8754 (tp-100) REVERT: a 97 GLN cc_start: 0.9097 (mm-40) cc_final: 0.8846 (mm110) REVERT: a 100 MET cc_start: 0.8485 (ptm) cc_final: 0.8221 (ptp) REVERT: a 120 LYS cc_start: 0.8694 (mtmt) cc_final: 0.8397 (pttp) REVERT: a 221 TYR cc_start: 0.9313 (t80) cc_final: 0.9052 (t80) REVERT: a 222 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8553 (mm) REVERT: c 50 TYR cc_start: 0.7472 (t80) cc_final: 0.6939 (t80) REVERT: d 45 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8721 (tm) REVERT: d 125 ILE cc_start: 0.8352 (OUTLIER) cc_final: 0.8023 (mm) REVERT: d 131 MET cc_start: 0.8447 (mmt) cc_final: 0.8137 (mmt) REVERT: d 137 ASN cc_start: 0.8899 (OUTLIER) cc_final: 0.8672 (m-40) REVERT: A 449 PHE cc_start: 0.8588 (OUTLIER) cc_final: 0.8022 (p90) REVERT: A 503 LYS cc_start: 0.9120 (OUTLIER) cc_final: 0.8738 (mtpt) REVERT: C 144 GLU cc_start: 0.8713 (pt0) cc_final: 0.8471 (tt0) REVERT: C 238 GLU cc_start: 0.8332 (mp0) cc_final: 0.7904 (tm-30) REVERT: B 70 GLU cc_start: 0.9192 (OUTLIER) cc_final: 0.8600 (mm-30) REVERT: B 495 TYR cc_start: 0.8647 (m-10) cc_final: 0.8396 (m-10) outliers start: 152 outliers final: 91 residues processed: 677 average time/residue: 0.7050 time to fit residues: 588.9930 Evaluate side-chains 675 residues out of total 4096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 562 time to evaluate : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 28 ILE Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 155 MET Chi-restraints excluded: chain D residue 216 MET Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 338 GLN Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 204 GLN Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 349 ASN Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 479 ILE Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 360 VAL Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 160 ASN Chi-restraints excluded: chain H residue 161 GLU Chi-restraints excluded: chain H residue 165 LYS Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain J residue 74 HIS Chi-restraints excluded: chain K residue 28 VAL Chi-restraints excluded: chain K residue 47 PHE Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 57 SER Chi-restraints excluded: chain K residue 64 CYS Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 47 PHE Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain M residue 47 PHE Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 71 ILE Chi-restraints excluded: chain O residue 9 ILE Chi-restraints excluded: chain O residue 31 SER Chi-restraints excluded: chain P residue 2 ILE Chi-restraints excluded: chain P residue 32 LEU Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain Q residue 32 LEU Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 47 PHE Chi-restraints excluded: chain Q residue 62 LEU Chi-restraints excluded: chain Q residue 64 CYS Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain R residue 66 MET Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 11 ILE Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 111 VAL Chi-restraints excluded: chain S residue 171 VAL Chi-restraints excluded: chain T residue 42 THR Chi-restraints excluded: chain V residue 26 VAL Chi-restraints excluded: chain V residue 83 SER Chi-restraints excluded: chain V residue 130 ASP Chi-restraints excluded: chain V residue 155 ASN Chi-restraints excluded: chain V residue 204 HIS Chi-restraints excluded: chain V residue 218 ILE Chi-restraints excluded: chain W residue 110 LEU Chi-restraints excluded: chain W residue 119 SER Chi-restraints excluded: chain W residue 153 SER Chi-restraints excluded: chain a residue 17 LEU Chi-restraints excluded: chain a residue 33 THR Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain a residue 93 THR Chi-restraints excluded: chain a residue 141 LEU Chi-restraints excluded: chain a residue 222 LEU Chi-restraints excluded: chain c residue 12 VAL Chi-restraints excluded: chain d residue 14 VAL Chi-restraints excluded: chain d residue 45 LEU Chi-restraints excluded: chain d residue 125 ILE Chi-restraints excluded: chain d residue 137 ASN Chi-restraints excluded: chain d residue 143 THR Chi-restraints excluded: chain i residue 24 THR Chi-restraints excluded: chain i residue 31 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 449 PHE Chi-restraints excluded: chain A residue 503 LYS Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 520 GLN Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 397 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 52 optimal weight: 0.6980 chunk 222 optimal weight: 6.9990 chunk 156 optimal weight: 0.9990 chunk 452 optimal weight: 1.9990 chunk 274 optimal weight: 7.9990 chunk 458 optimal weight: 4.9990 chunk 321 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 131 optimal weight: 0.8980 chunk 248 optimal weight: 0.0870 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.074206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.053059 restraints weight = 115965.404| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 2.46 r_work: 0.2822 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2701 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2701 r_free = 0.2701 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2701 r_free = 0.2701 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2701 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 39066 Z= 0.128 Angle : 0.620 15.194 52905 Z= 0.309 Chirality : 0.042 0.249 6252 Planarity : 0.004 0.077 6756 Dihedral : 6.078 166.399 5613 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.81 % Favored : 97.15 % Rotamer: Outliers : 3.23 % Allowed : 20.04 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % 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 aren not related in a simple way. whole: 0.66 (0.12), residues: 5016 helix: 1.69 (0.11), residues: 2559 sheet: 0.76 (0.23), residues: 507 loop : -1.41 (0.13), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG c 19 TYR 0.025 0.001 TYR a 221 PHE 0.030 0.001 PHE O 63 TRP 0.035 0.002 TRP W 120 HIS 0.007 0.001 HIS G 91 Details of bonding type rmsd covalent geometry : bond 0.00279 (39066) covalent geometry : angle 0.61961 (52905) hydrogen bonds : bond 0.05271 ( 2001) hydrogen bonds : angle 4.09965 ( 5820) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10032 Ramachandran restraints generated. 5016 Oldfield, 0 Emsley, 5016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10032 Ramachandran restraints generated. 5016 Oldfield, 0 Emsley, 5016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 713 residues out of total 4096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 585 time to evaluate : 1.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 13 ILE cc_start: 0.8700 (mp) cc_final: 0.8469 (mp) REVERT: E 349 ASN cc_start: 0.8850 (OUTLIER) cc_final: 0.8181 (t0) REVERT: E 485 MET cc_start: 0.7211 (tpp) cc_final: 0.6726 (tmm) REVERT: F 258 ILE cc_start: 0.9118 (OUTLIER) cc_final: 0.8904 (tt) REVERT: G 218 TYR cc_start: 0.7769 (m-80) cc_final: 0.7505 (m-80) REVERT: H 47 GLN cc_start: 0.8341 (pm20) cc_final: 0.7832 (pm20) REVERT: H 81 ARG cc_start: 0.8663 (ttm110) cc_final: 0.7808 (ptp-110) REVERT: H 165 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8337 (mmmm) REVERT: I 14 TYR cc_start: 0.8719 (t80) cc_final: 0.8388 (t80) REVERT: I 18 CYS cc_start: 0.8703 (m) cc_final: 0.8410 (m) REVERT: I 44 ILE cc_start: 0.8806 (OUTLIER) cc_final: 0.8544 (mp) REVERT: J 56 GLU cc_start: 0.9021 (tp30) cc_final: 0.8767 (tp30) REVERT: J 71 LYS cc_start: 0.8367 (ttpt) cc_final: 0.8159 (tttt) REVERT: K 27 THR cc_start: 0.8908 (t) cc_final: 0.8620 (p) REVERT: K 31 SER cc_start: 0.9241 (m) cc_final: 0.8790 (t) REVERT: K 47 PHE cc_start: 0.7324 (OUTLIER) cc_final: 0.7030 (t80) REVERT: K 63 PHE cc_start: 0.8124 (t80) cc_final: 0.7774 (t80) REVERT: K 66 MET cc_start: 0.7845 (pp-130) cc_final: 0.7144 (ppp) REVERT: L 31 SER cc_start: 0.9211 (m) cc_final: 0.8781 (t) REVERT: L 66 MET cc_start: 0.8805 (OUTLIER) cc_final: 0.8543 (ppp) REVERT: M 34 ILE cc_start: 0.8609 (OUTLIER) cc_final: 0.8406 (tp) REVERT: M 47 PHE cc_start: 0.8466 (OUTLIER) cc_final: 0.7870 (t80) REVERT: N 15 THR cc_start: 0.8525 (t) cc_final: 0.8139 (p) REVERT: O 45 GLN cc_start: 0.8725 (pm20) cc_final: 0.8491 (pm20) REVERT: O 49 TYR cc_start: 0.7093 (m-10) cc_final: 0.6782 (m-80) REVERT: P 57 SER cc_start: 0.8402 (t) cc_final: 0.8138 (p) REVERT: Q 65 LEU cc_start: 0.9035 (mt) cc_final: 0.8598 (tp) REVERT: R 63 PHE cc_start: 0.8663 (t80) cc_final: 0.8338 (t80) REVERT: S 10 GLN cc_start: 0.8048 (tt0) cc_final: 0.7830 (tt0) REVERT: S 34 GLN cc_start: 0.8626 (tt0) cc_final: 0.7932 (tp-100) REVERT: S 41 ARG cc_start: 0.8315 (mtp85) cc_final: 0.7966 (ttt-90) REVERT: S 109 MET cc_start: 0.8516 (mmm) cc_final: 0.7971 (tpt) REVERT: T 54 LYS cc_start: 0.9324 (mmtt) cc_final: 0.9046 (mmtt) REVERT: T 62 THR cc_start: 0.8371 (m) cc_final: 0.8073 (t) REVERT: T 82 GLU cc_start: 0.8469 (tm-30) cc_final: 0.8263 (tm-30) REVERT: T 83 VAL cc_start: 0.8436 (p) cc_final: 0.8142 (t) REVERT: T 84 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.9102 (tt) REVERT: T 85 MET cc_start: 0.9067 (mmm) cc_final: 0.8677 (tpp) REVERT: U 10 LEU cc_start: 0.7693 (mp) cc_final: 0.7378 (pp) REVERT: U 12 LYS cc_start: 0.8861 (ttmm) cc_final: 0.8164 (ttmm) REVERT: U 19 LEU cc_start: 0.8656 (tt) cc_final: 0.8364 (pp) REVERT: V 48 PHE cc_start: 0.8378 (t80) cc_final: 0.7933 (t80) REVERT: V 155 ASN cc_start: 0.8467 (OUTLIER) cc_final: 0.8167 (p0) REVERT: V 158 MET cc_start: 0.8866 (ptm) cc_final: 0.8461 (ppp) REVERT: V 172 TYR cc_start: 0.8662 (t80) cc_final: 0.8412 (t80) REVERT: V 177 ASN cc_start: 0.8624 (t0) cc_final: 0.7875 (t0) REVERT: V 178 ARG cc_start: 0.8998 (mmt180) cc_final: 0.8067 (ptp90) REVERT: V 204 HIS cc_start: 0.8898 (OUTLIER) cc_final: 0.8390 (m170) REVERT: V 207 GLN cc_start: 0.9386 (tp40) cc_final: 0.8932 (pt0) REVERT: W 123 MET cc_start: 0.8062 (tpp) cc_final: 0.7795 (tpp) REVERT: W 181 LEU cc_start: 0.7312 (mp) cc_final: 0.7066 (mm) REVERT: W 183 LYS cc_start: 0.7766 (mttt) cc_final: 0.6666 (pttt) REVERT: a 17 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7844 (tm) REVERT: a 25 MET cc_start: 0.9235 (mtp) cc_final: 0.8933 (mtm) REVERT: a 49 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.8997 (mp) REVERT: a 63 GLN cc_start: 0.8963 (tp-100) cc_final: 0.8700 (tp-100) REVERT: a 97 GLN cc_start: 0.9094 (mm-40) cc_final: 0.8848 (mm110) REVERT: a 100 MET cc_start: 0.8437 (ptm) cc_final: 0.8162 (ptp) REVERT: a 118 ARG cc_start: 0.7828 (tmm-80) cc_final: 0.7540 (tmm-80) REVERT: a 119 TYR cc_start: 0.8254 (m-10) cc_final: 0.7822 (m-10) REVERT: a 120 LYS cc_start: 0.8658 (mtmt) cc_final: 0.8360 (pttp) REVERT: a 221 TYR cc_start: 0.9310 (t80) cc_final: 0.9017 (t80) REVERT: a 222 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8486 (mm) REVERT: c 50 TYR cc_start: 0.7530 (t80) cc_final: 0.6993 (t80) REVERT: d 125 ILE cc_start: 0.8299 (OUTLIER) cc_final: 0.8080 (mm) REVERT: d 131 MET cc_start: 0.8422 (mmt) cc_final: 0.8095 (mmt) REVERT: d 137 ASN cc_start: 0.8892 (OUTLIER) cc_final: 0.8676 (m-40) REVERT: A 449 PHE cc_start: 0.8564 (OUTLIER) cc_final: 0.8018 (p90) REVERT: A 503 LYS cc_start: 0.9077 (OUTLIER) cc_final: 0.8659 (mtpt) REVERT: C 144 GLU cc_start: 0.8672 (pt0) cc_final: 0.8454 (tt0) REVERT: C 168 THR cc_start: 0.9014 (OUTLIER) cc_final: 0.8547 (p) REVERT: C 238 GLU cc_start: 0.8340 (mp0) cc_final: 0.7941 (tm-30) REVERT: C 417 VAL cc_start: 0.8319 (OUTLIER) cc_final: 0.8048 (p) REVERT: B 70 GLU cc_start: 0.9180 (OUTLIER) cc_final: 0.8602 (mm-30) REVERT: B 495 TYR cc_start: 0.8588 (m-10) cc_final: 0.8369 (m-10) outliers start: 128 outliers final: 76 residues processed: 661 average time/residue: 0.7254 time to fit residues: 588.2430 Evaluate side-chains 659 residues out of total 4096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 562 time to evaluate : 1.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 11 ILE Chi-restraints excluded: chain 8 residue 28 ILE Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 216 MET Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 204 GLN Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 349 ASN Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 520 LEU Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 360 VAL Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 161 GLU Chi-restraints excluded: chain H residue 165 LYS Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain J residue 74 HIS Chi-restraints excluded: chain K residue 28 VAL Chi-restraints excluded: chain K residue 47 PHE Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 57 SER Chi-restraints excluded: chain K residue 64 CYS Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 47 PHE Chi-restraints excluded: chain L residue 65 LEU Chi-restraints excluded: chain L residue 66 MET Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain M residue 47 PHE Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 71 ILE Chi-restraints excluded: chain O residue 9 ILE Chi-restraints excluded: chain P residue 2 ILE Chi-restraints excluded: chain P residue 32 LEU Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain Q residue 15 THR Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain Q residue 32 LEU Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain R residue 66 MET Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 11 ILE Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 111 VAL Chi-restraints excluded: chain S residue 171 VAL Chi-restraints excluded: chain T residue 42 THR Chi-restraints excluded: chain T residue 84 LEU Chi-restraints excluded: chain V residue 26 VAL Chi-restraints excluded: chain V residue 155 ASN Chi-restraints excluded: chain V residue 204 HIS Chi-restraints excluded: chain W residue 119 SER Chi-restraints excluded: chain W residue 153 SER Chi-restraints excluded: chain a residue 17 LEU Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain a residue 93 THR Chi-restraints excluded: chain a residue 141 LEU Chi-restraints excluded: chain a residue 216 LEU Chi-restraints excluded: chain a residue 222 LEU Chi-restraints excluded: chain c residue 12 VAL Chi-restraints excluded: chain d residue 14 VAL Chi-restraints excluded: chain d residue 125 ILE Chi-restraints excluded: chain d residue 137 ASN Chi-restraints excluded: chain d residue 143 THR Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 449 PHE Chi-restraints excluded: chain A residue 503 LYS Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 520 GLN Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 397 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 490 optimal weight: 1.9990 chunk 245 optimal weight: 8.9990 chunk 92 optimal weight: 2.9990 chunk 321 optimal weight: 0.9990 chunk 186 optimal weight: 9.9990 chunk 38 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 315 optimal weight: 0.9990 chunk 399 optimal weight: 0.9980 chunk 142 optimal weight: 3.9990 chunk 421 optimal weight: 0.6980 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 30 ASN H 160 ASN ** O 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 185 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.073974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.052933 restraints weight = 117019.823| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 2.44 r_work: 0.2816 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2695 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2695 r_free = 0.2695 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2695 r_free = 0.2695 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2695 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 39066 Z= 0.137 Angle : 0.632 17.986 52905 Z= 0.317 Chirality : 0.042 0.249 6252 Planarity : 0.004 0.075 6756 Dihedral : 6.037 165.925 5612 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.13 % Favored : 96.83 % Rotamer: Outliers : 2.88 % Allowed : 20.60 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % 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 aren not related in a simple way. whole: 0.66 (0.12), residues: 5016 helix: 1.71 (0.11), residues: 2543 sheet: 0.76 (0.23), residues: 507 loop : -1.42 (0.13), residues: 1966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG c 19 TYR 0.024 0.001 TYR a 221 PHE 0.040 0.001 PHE K 54 TRP 0.032 0.002 TRP W 120 HIS 0.007 0.001 HIS G 91 Details of bonding type rmsd covalent geometry : bond 0.00310 (39066) covalent geometry : angle 0.63193 (52905) hydrogen bonds : bond 0.05378 ( 2001) hydrogen bonds : angle 4.11710 ( 5820) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10032 Ramachandran restraints generated. 5016 Oldfield, 0 Emsley, 5016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10032 Ramachandran restraints generated. 5016 Oldfield, 0 Emsley, 5016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 4096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 572 time to evaluate : 1.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 349 ASN cc_start: 0.8858 (OUTLIER) cc_final: 0.8199 (t0) REVERT: E 485 MET cc_start: 0.7210 (tpp) cc_final: 0.6712 (tmm) REVERT: F 258 ILE cc_start: 0.9114 (OUTLIER) cc_final: 0.8904 (tt) REVERT: G 218 TYR cc_start: 0.7735 (m-80) cc_final: 0.7531 (m-80) REVERT: H 47 GLN cc_start: 0.8337 (pm20) cc_final: 0.7729 (pm20) REVERT: H 81 ARG cc_start: 0.8663 (ttm110) cc_final: 0.7807 (ptp-110) REVERT: I 14 TYR cc_start: 0.8703 (t80) cc_final: 0.8365 (t80) REVERT: I 18 CYS cc_start: 0.8648 (m) cc_final: 0.8383 (m) REVERT: I 43 LYS cc_start: 0.8703 (mmmm) cc_final: 0.7820 (mmpt) REVERT: I 44 ILE cc_start: 0.8815 (OUTLIER) cc_final: 0.8525 (mp) REVERT: J 56 GLU cc_start: 0.9000 (tp30) cc_final: 0.8745 (tp30) REVERT: J 71 LYS cc_start: 0.8342 (ttpt) cc_final: 0.8127 (tttt) REVERT: K 27 THR cc_start: 0.8899 (t) cc_final: 0.8622 (p) REVERT: K 31 SER cc_start: 0.9251 (m) cc_final: 0.8814 (t) REVERT: K 47 PHE cc_start: 0.7336 (OUTLIER) cc_final: 0.7075 (t80) REVERT: K 63 PHE cc_start: 0.8072 (t80) cc_final: 0.7676 (t80) REVERT: K 66 MET cc_start: 0.7939 (pp-130) cc_final: 0.7297 (ppp) REVERT: L 31 SER cc_start: 0.9215 (m) cc_final: 0.8773 (t) REVERT: L 66 MET cc_start: 0.8803 (OUTLIER) cc_final: 0.8542 (ppp) REVERT: M 34 ILE cc_start: 0.8617 (OUTLIER) cc_final: 0.8397 (tp) REVERT: M 47 PHE cc_start: 0.8492 (OUTLIER) cc_final: 0.7939 (t80) REVERT: O 45 GLN cc_start: 0.8612 (pm20) cc_final: 0.8379 (pm20) REVERT: O 49 TYR cc_start: 0.7124 (m-10) cc_final: 0.6802 (m-80) REVERT: P 57 SER cc_start: 0.8473 (t) cc_final: 0.8214 (p) REVERT: Q 65 LEU cc_start: 0.9025 (mt) cc_final: 0.8573 (tp) REVERT: R 63 PHE cc_start: 0.8659 (t80) cc_final: 0.8349 (t80) REVERT: S 10 GLN cc_start: 0.7925 (tt0) cc_final: 0.7695 (tt0) REVERT: S 34 GLN cc_start: 0.8629 (tt0) cc_final: 0.7938 (tp-100) REVERT: S 41 ARG cc_start: 0.8309 (mtp85) cc_final: 0.7949 (ttt-90) REVERT: S 109 MET cc_start: 0.8535 (mmm) cc_final: 0.8004 (tpt) REVERT: T 54 LYS cc_start: 0.9309 (mmtt) cc_final: 0.9035 (mmtt) REVERT: T 62 THR cc_start: 0.8351 (m) cc_final: 0.8053 (t) REVERT: T 69 THR cc_start: 0.8422 (m) cc_final: 0.8218 (p) REVERT: T 83 VAL cc_start: 0.8445 (p) cc_final: 0.8137 (t) REVERT: T 85 MET cc_start: 0.8910 (mmm) cc_final: 0.8613 (tpp) REVERT: T 88 TYR cc_start: 0.8354 (m-80) cc_final: 0.8104 (m-80) REVERT: U 10 LEU cc_start: 0.7628 (mp) cc_final: 0.7303 (pp) REVERT: U 12 LYS cc_start: 0.8859 (ttmm) cc_final: 0.8148 (ttmm) REVERT: V 48 PHE cc_start: 0.8407 (t80) cc_final: 0.7955 (t80) REVERT: V 155 ASN cc_start: 0.8428 (OUTLIER) cc_final: 0.8041 (p0) REVERT: V 158 MET cc_start: 0.8854 (ptm) cc_final: 0.8411 (ppp) REVERT: V 172 TYR cc_start: 0.8642 (t80) cc_final: 0.8386 (t80) REVERT: V 177 ASN cc_start: 0.8653 (t0) cc_final: 0.7897 (t0) REVERT: V 178 ARG cc_start: 0.8993 (mmt180) cc_final: 0.8084 (ptp-170) REVERT: V 196 HIS cc_start: 0.8508 (t70) cc_final: 0.8237 (t-90) REVERT: V 199 ARG cc_start: 0.8724 (ttp80) cc_final: 0.8336 (ttp80) REVERT: V 204 HIS cc_start: 0.8878 (OUTLIER) cc_final: 0.8403 (m170) REVERT: V 207 GLN cc_start: 0.9379 (tp40) cc_final: 0.8910 (pt0) REVERT: V 218 ILE cc_start: 0.8558 (tp) cc_final: 0.8158 (pp) REVERT: W 123 MET cc_start: 0.8075 (tpp) cc_final: 0.7816 (tpp) REVERT: W 183 LYS cc_start: 0.7807 (mttt) cc_final: 0.6669 (pttt) REVERT: a 17 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7856 (tm) REVERT: a 25 MET cc_start: 0.9238 (mtp) cc_final: 0.8932 (mtm) REVERT: a 49 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.9008 (mp) REVERT: a 63 GLN cc_start: 0.8971 (tp-100) cc_final: 0.8763 (tp-100) REVERT: a 97 GLN cc_start: 0.9099 (mm-40) cc_final: 0.8856 (mm110) REVERT: a 118 ARG cc_start: 0.7797 (tmm-80) cc_final: 0.7500 (tmm-80) REVERT: a 119 TYR cc_start: 0.8253 (m-10) cc_final: 0.7799 (m-10) REVERT: a 120 LYS cc_start: 0.8665 (mtmt) cc_final: 0.8380 (pttp) REVERT: a 221 TYR cc_start: 0.9349 (t80) cc_final: 0.9038 (t80) REVERT: a 222 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8490 (mm) REVERT: c 16 ARG cc_start: 0.9011 (tmm-80) cc_final: 0.8773 (tmm-80) REVERT: c 50 TYR cc_start: 0.7533 (t80) cc_final: 0.6971 (t80) REVERT: d 125 ILE cc_start: 0.8360 (OUTLIER) cc_final: 0.8077 (mm) REVERT: d 131 MET cc_start: 0.8407 (mmt) cc_final: 0.8156 (mmt) REVERT: d 137 ASN cc_start: 0.8887 (OUTLIER) cc_final: 0.8682 (m-40) REVERT: A 449 PHE cc_start: 0.8576 (OUTLIER) cc_final: 0.7960 (p90) REVERT: A 503 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8645 (mtpt) REVERT: C 168 THR cc_start: 0.9042 (OUTLIER) cc_final: 0.8622 (p) REVERT: C 238 GLU cc_start: 0.8316 (mp0) cc_final: 0.7950 (tm-30) REVERT: C 417 VAL cc_start: 0.8351 (OUTLIER) cc_final: 0.8070 (p) REVERT: B 70 GLU cc_start: 0.9185 (OUTLIER) cc_final: 0.8606 (mm-30) REVERT: B 495 TYR cc_start: 0.8619 (m-10) cc_final: 0.8405 (m-10) outliers start: 114 outliers final: 84 residues processed: 643 average time/residue: 0.7204 time to fit residues: 566.7347 Evaluate side-chains 662 residues out of total 4096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 559 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 11 ILE Chi-restraints excluded: chain 8 residue 28 ILE Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 216 MET Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 338 GLN Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 204 GLN Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 349 ASN Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain E residue 520 LEU Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 360 VAL Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 161 GLU Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain J residue 74 HIS Chi-restraints excluded: chain K residue 28 VAL Chi-restraints excluded: chain K residue 47 PHE Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 57 SER Chi-restraints excluded: chain K residue 64 CYS Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 47 PHE Chi-restraints excluded: chain L residue 66 MET Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain M residue 47 PHE Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 70 LEU Chi-restraints excluded: chain N residue 71 ILE Chi-restraints excluded: chain O residue 9 ILE Chi-restraints excluded: chain P residue 2 ILE Chi-restraints excluded: chain P residue 32 LEU Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain Q residue 32 LEU Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 47 PHE Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain R residue 66 MET Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 11 ILE Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 111 VAL Chi-restraints excluded: chain S residue 171 VAL Chi-restraints excluded: chain T residue 42 THR Chi-restraints excluded: chain V residue 26 VAL Chi-restraints excluded: chain V residue 83 SER Chi-restraints excluded: chain V residue 155 ASN Chi-restraints excluded: chain V residue 204 HIS Chi-restraints excluded: chain W residue 110 LEU Chi-restraints excluded: chain W residue 119 SER Chi-restraints excluded: chain W residue 153 SER Chi-restraints excluded: chain a residue 17 LEU Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain a residue 93 THR Chi-restraints excluded: chain a residue 141 LEU Chi-restraints excluded: chain a residue 216 LEU Chi-restraints excluded: chain a residue 222 LEU Chi-restraints excluded: chain c residue 12 VAL Chi-restraints excluded: chain d residue 14 VAL Chi-restraints excluded: chain d residue 125 ILE Chi-restraints excluded: chain d residue 137 ASN Chi-restraints excluded: chain d residue 143 THR Chi-restraints excluded: chain i residue 21 TYR Chi-restraints excluded: chain i residue 31 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 449 PHE Chi-restraints excluded: chain A residue 503 LYS Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 520 GLN Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 397 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 400 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 410 optimal weight: 0.9990 chunk 456 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 186 optimal weight: 8.9990 chunk 167 optimal weight: 0.7980 chunk 199 optimal weight: 0.9980 chunk 497 optimal weight: 0.9980 chunk 28 optimal weight: 0.4980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 185 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.074152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.053099 restraints weight = 116553.444| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 2.46 r_work: 0.2818 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2699 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2699 r_free = 0.2699 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2699 r_free = 0.2699 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2699 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 39066 Z= 0.135 Angle : 0.642 16.996 52905 Z= 0.322 Chirality : 0.042 0.264 6252 Planarity : 0.004 0.070 6756 Dihedral : 5.990 165.960 5612 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.95 % Favored : 97.01 % Rotamer: Outliers : 2.73 % Allowed : 21.10 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % 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 aren not related in a simple way. whole: 0.66 (0.12), residues: 5016 helix: 1.69 (0.11), residues: 2551 sheet: 0.76 (0.23), residues: 508 loop : -1.40 (0.13), residues: 1957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG c 19 TYR 0.023 0.001 TYR a 221 PHE 0.036 0.001 PHE O 63 TRP 0.032 0.002 TRP d 153 HIS 0.007 0.001 HIS G 91 Details of bonding type rmsd covalent geometry : bond 0.00304 (39066) covalent geometry : angle 0.64247 (52905) hydrogen bonds : bond 0.05271 ( 2001) hydrogen bonds : angle 4.10335 ( 5820) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10032 Ramachandran restraints generated. 5016 Oldfield, 0 Emsley, 5016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10032 Ramachandran restraints generated. 5016 Oldfield, 0 Emsley, 5016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 4096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 568 time to evaluate : 1.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 16 MET cc_start: 0.8653 (tmm) cc_final: 0.8408 (tmm) REVERT: E 349 ASN cc_start: 0.8868 (OUTLIER) cc_final: 0.8219 (t0) REVERT: E 485 MET cc_start: 0.7183 (tpp) cc_final: 0.6642 (tmm) REVERT: F 119 GLU cc_start: 0.8312 (pp20) cc_final: 0.7874 (pt0) REVERT: H 47 GLN cc_start: 0.8342 (pm20) cc_final: 0.7738 (pm20) REVERT: H 81 ARG cc_start: 0.8660 (ttm110) cc_final: 0.7803 (ptp-110) REVERT: I 14 TYR cc_start: 0.8720 (t80) cc_final: 0.8373 (t80) REVERT: I 18 CYS cc_start: 0.8713 (m) cc_final: 0.8420 (m) REVERT: I 36 LYS cc_start: 0.8093 (tmmt) cc_final: 0.7685 (mttt) REVERT: I 44 ILE cc_start: 0.8817 (OUTLIER) cc_final: 0.8560 (mp) REVERT: J 56 GLU cc_start: 0.9024 (tp30) cc_final: 0.8761 (tp30) REVERT: J 71 LYS cc_start: 0.8315 (ttpt) cc_final: 0.8102 (tttt) REVERT: K 27 THR cc_start: 0.8891 (t) cc_final: 0.8619 (p) REVERT: K 31 SER cc_start: 0.9258 (m) cc_final: 0.8825 (t) REVERT: K 47 PHE cc_start: 0.7268 (OUTLIER) cc_final: 0.6995 (t80) REVERT: K 63 PHE cc_start: 0.8081 (t80) cc_final: 0.7771 (t80) REVERT: K 66 MET cc_start: 0.7923 (pp-130) cc_final: 0.7302 (ppp) REVERT: L 31 SER cc_start: 0.9200 (m) cc_final: 0.8755 (t) REVERT: L 38 ARG cc_start: 0.8473 (mmm-85) cc_final: 0.8175 (tmm-80) REVERT: L 66 MET cc_start: 0.8794 (OUTLIER) cc_final: 0.8529 (ppp) REVERT: M 34 ILE cc_start: 0.8562 (OUTLIER) cc_final: 0.8346 (tp) REVERT: M 38 ARG cc_start: 0.7708 (tpp80) cc_final: 0.7093 (tpp80) REVERT: M 47 PHE cc_start: 0.8479 (OUTLIER) cc_final: 0.7936 (t80) REVERT: O 49 TYR cc_start: 0.7138 (m-10) cc_final: 0.6899 (m-80) REVERT: P 57 SER cc_start: 0.8399 (t) cc_final: 0.8134 (p) REVERT: Q 65 LEU cc_start: 0.9009 (mt) cc_final: 0.8578 (tp) REVERT: R 63 PHE cc_start: 0.8653 (t80) cc_final: 0.8336 (t80) REVERT: S 10 GLN cc_start: 0.7971 (tt0) cc_final: 0.7728 (tt0) REVERT: S 34 GLN cc_start: 0.8620 (tt0) cc_final: 0.7955 (tp-100) REVERT: S 41 ARG cc_start: 0.8313 (mtp85) cc_final: 0.7970 (ttt180) REVERT: S 109 MET cc_start: 0.8582 (mmm) cc_final: 0.8034 (tpt) REVERT: T 54 LYS cc_start: 0.9305 (mmtt) cc_final: 0.9048 (mmtt) REVERT: T 62 THR cc_start: 0.8359 (m) cc_final: 0.8063 (t) REVERT: T 83 VAL cc_start: 0.8423 (p) cc_final: 0.8109 (t) REVERT: U 10 LEU cc_start: 0.7614 (mp) cc_final: 0.7289 (pp) REVERT: U 12 LYS cc_start: 0.8849 (ttmm) cc_final: 0.8141 (ttmm) REVERT: V 48 PHE cc_start: 0.8411 (t80) cc_final: 0.7951 (t80) REVERT: V 155 ASN cc_start: 0.8453 (OUTLIER) cc_final: 0.8115 (p0) REVERT: V 158 MET cc_start: 0.8869 (ptm) cc_final: 0.8479 (ppp) REVERT: V 165 ARG cc_start: 0.8749 (mtm110) cc_final: 0.8453 (mtm180) REVERT: V 172 TYR cc_start: 0.8664 (t80) cc_final: 0.8422 (t80) REVERT: V 177 ASN cc_start: 0.8666 (t0) cc_final: 0.7855 (t0) REVERT: V 178 ARG cc_start: 0.8987 (mmt180) cc_final: 0.8056 (ptp90) REVERT: V 204 HIS cc_start: 0.8892 (OUTLIER) cc_final: 0.8451 (m170) REVERT: V 207 GLN cc_start: 0.9360 (tp40) cc_final: 0.8924 (pt0) REVERT: V 218 ILE cc_start: 0.8515 (tp) cc_final: 0.8163 (pp) REVERT: W 123 MET cc_start: 0.8110 (tpp) cc_final: 0.7909 (tpp) REVERT: W 183 LYS cc_start: 0.7797 (mttt) cc_final: 0.6625 (pttt) REVERT: a 17 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7856 (tm) REVERT: a 25 MET cc_start: 0.9245 (mtp) cc_final: 0.8945 (mtm) REVERT: a 49 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.9005 (mp) REVERT: a 57 MET cc_start: 0.8616 (mtp) cc_final: 0.8303 (ttm) REVERT: a 120 LYS cc_start: 0.8664 (mtmt) cc_final: 0.8386 (pttp) REVERT: a 131 GLN cc_start: 0.7633 (mm110) cc_final: 0.7430 (mp10) REVERT: a 221 TYR cc_start: 0.9351 (t80) cc_final: 0.8997 (t80) REVERT: a 222 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8467 (mm) REVERT: c 16 ARG cc_start: 0.9012 (tmm-80) cc_final: 0.8796 (tmm-80) REVERT: c 50 TYR cc_start: 0.7524 (t80) cc_final: 0.6940 (t80) REVERT: d 122 MET cc_start: 0.8807 (tpt) cc_final: 0.8462 (tmm) REVERT: d 125 ILE cc_start: 0.8366 (OUTLIER) cc_final: 0.7920 (mm) REVERT: d 131 MET cc_start: 0.8393 (mmt) cc_final: 0.8140 (mmt) REVERT: d 137 ASN cc_start: 0.8864 (OUTLIER) cc_final: 0.8662 (m-40) REVERT: A 449 PHE cc_start: 0.8551 (OUTLIER) cc_final: 0.7942 (p90) REVERT: C 168 THR cc_start: 0.9043 (OUTLIER) cc_final: 0.8629 (p) REVERT: C 238 GLU cc_start: 0.8334 (mp0) cc_final: 0.7951 (tm-30) REVERT: C 417 VAL cc_start: 0.8389 (OUTLIER) cc_final: 0.8120 (p) REVERT: B 495 TYR cc_start: 0.8636 (m-10) cc_final: 0.8423 (m-10) outliers start: 108 outliers final: 78 residues processed: 637 average time/residue: 0.7267 time to fit residues: 566.7001 Evaluate side-chains 653 residues out of total 4096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 559 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 11 ILE Chi-restraints excluded: chain 8 residue 28 ILE Chi-restraints excluded: chain D residue 216 MET Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 338 GLN Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 204 GLN Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 349 ASN Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain E residue 520 LEU Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 360 VAL Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 161 GLU Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain J residue 74 HIS Chi-restraints excluded: chain K residue 28 VAL Chi-restraints excluded: chain K residue 47 PHE Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 64 CYS Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 47 PHE Chi-restraints excluded: chain L residue 66 MET Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain M residue 47 PHE Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 71 ILE Chi-restraints excluded: chain O residue 9 ILE Chi-restraints excluded: chain P residue 2 ILE Chi-restraints excluded: chain P residue 32 LEU Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain Q residue 32 LEU Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain R residue 66 MET Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 11 ILE Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 111 VAL Chi-restraints excluded: chain S residue 171 VAL Chi-restraints excluded: chain T residue 42 THR Chi-restraints excluded: chain V residue 26 VAL Chi-restraints excluded: chain V residue 83 SER Chi-restraints excluded: chain V residue 155 ASN Chi-restraints excluded: chain V residue 204 HIS Chi-restraints excluded: chain W residue 110 LEU Chi-restraints excluded: chain W residue 119 SER Chi-restraints excluded: chain W residue 153 SER Chi-restraints excluded: chain a residue 17 LEU Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain a residue 93 THR Chi-restraints excluded: chain a residue 141 LEU Chi-restraints excluded: chain a residue 216 LEU Chi-restraints excluded: chain a residue 222 LEU Chi-restraints excluded: chain c residue 12 VAL Chi-restraints excluded: chain d residue 14 VAL Chi-restraints excluded: chain d residue 125 ILE Chi-restraints excluded: chain d residue 137 ASN Chi-restraints excluded: chain d residue 143 THR Chi-restraints excluded: chain i residue 31 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 449 PHE Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 520 GLN Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 397 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 54 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 145 optimal weight: 0.1980 chunk 117 optimal weight: 0.1980 chunk 183 optimal weight: 0.8980 chunk 382 optimal weight: 0.0470 chunk 90 optimal weight: 0.7980 chunk 123 optimal weight: 0.5980 chunk 83 optimal weight: 0.8980 chunk 233 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 overall best weight: 0.3678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 30 ASN H 160 ASN N 39 ASN O 44 GLN a 185 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.075380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.054256 restraints weight = 115567.366| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 2.49 r_work: 0.2853 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2734 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2734 r_free = 0.2734 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2734 r_free = 0.2734 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2734 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 39066 Z= 0.121 Angle : 0.634 19.088 52905 Z= 0.316 Chirality : 0.042 0.240 6252 Planarity : 0.004 0.071 6756 Dihedral : 5.805 165.684 5609 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.59 % Favored : 97.37 % Rotamer: Outliers : 2.48 % Allowed : 21.28 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % 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 aren not related in a simple way. whole: 0.77 (0.12), residues: 5016 helix: 1.75 (0.11), residues: 2553 sheet: 0.84 (0.23), residues: 509 loop : -1.30 (0.13), residues: 1954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG c 19 TYR 0.023 0.001 TYR W 139 PHE 0.043 0.001 PHE K 54 TRP 0.032 0.002 TRP d 153 HIS 0.007 0.001 HIS G 91 Details of bonding type rmsd covalent geometry : bond 0.00257 (39066) covalent geometry : angle 0.63450 (52905) hydrogen bonds : bond 0.04700 ( 2001) hydrogen bonds : angle 4.01888 ( 5820) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16683.46 seconds wall clock time: 283 minutes 56.52 seconds (17036.52 seconds total)