Starting phenix.real_space_refine on Wed May 6 12:52:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w2s_65578/05_2026/9w2s_65578.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w2s_65578/05_2026/9w2s_65578.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9w2s_65578/05_2026/9w2s_65578.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w2s_65578/05_2026/9w2s_65578.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9w2s_65578/05_2026/9w2s_65578.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w2s_65578/05_2026/9w2s_65578.map" } resolution = 4.0 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= -0.000 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 147 5.16 5 C 24941 2.51 5 N 6675 2.21 5 O 7353 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 245 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39116 Number of models: 1 Model: "" Number of chains: 29 Chain: "8" Number of atoms: 294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 294 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 34} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3710 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 17, 'TRANS': 468} Chain: "A" Number of atoms: 3820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3820 Classifications: {'peptide': 501} Link IDs: {'PTRANS': 17, 'TRANS': 483} Chain: "B" Number of atoms: 3870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 3870 Classifications: {'peptide': 508} Link IDs: {'PTRANS': 17, 'TRANS': 490} Chain: "F" Number of atoms: 3539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3539 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 23, 'TRANS': 443} Chain: "D" Number of atoms: 3558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3558 Classifications: {'peptide': 469} Link IDs: {'PTRANS': 23, 'TRANS': 445} Chain: "E" Number of atoms: 3539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3539 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 23, 'TRANS': 443} Chain: "G" Number of atoms: 2115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2115 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 5, 'TRANS': 266} Chain: "H" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 971 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "I" Number of atoms: 369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 369 Classifications: {'peptide': 47} Link IDs: {'TRANS': 46} Chain: "J" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 370 Classifications: {'peptide': 47} Link IDs: {'TRANS': 46} Chain: "K" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 529 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 523 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 538 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 529 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 538 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 520 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 7 Chain: "Q" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 529 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'M3L:plan-1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "R" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 538 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "S" Number of atoms: 1438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1438 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 8, 'TRANS': 178} Chain: "a" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1690 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 12, 'TRANS': 210} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "b" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1603 Classifications: {'peptide': 205} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 5, 'TRANS': 199} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 1, 'PHE:plan': 2, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 36 Chain: "d" Number of atoms: 1249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1249 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 11, 'TRANS': 143} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "e" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 410 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 2, 'TRANS': 52} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 1, 'TYR:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "f" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 632 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 78} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 3, 'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "g" Number of atoms: 551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 551 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 5, 'TRANS': 73} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 1, 'PHE:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 43 Chain: "h" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 514 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 5, 'TRANS': 56} Chain: "j" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 378 Classifications: {'peptide': 46} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 43} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 252 Classifications: {'peptide': 35} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 34} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 9.39, per 1000 atoms: 0.24 Number of scatterers: 39116 At special positions: 0 Unit cell: (154.053, 194.747, 222.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 147 16.00 O 7353 8.00 N 6675 7.00 C 24941 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: 3.74 Conformation dependent library (CDL) restraints added in 1.9 seconds 10146 Ramachandran restraints generated. 5073 Oldfield, 0 Emsley, 5073 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9420 Finding SS restraints... Secondary structure from input PDB file: 242 helices and 29 sheets defined 61.1% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain '8' and resid 5 through 9 Processing helix chain '8' and resid 10 through 22 Processing helix chain '8' and resid 24 through 30 Processing helix chain 'C' and resid 150 through 157 Processing helix chain 'C' and resid 171 through 174 Processing helix chain 'C' and resid 175 through 186 removed outlier: 4.407A pdb=" N ALA C 179 " --> pdb=" O LYS C 175 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ILE C 184 " --> pdb=" O ILE C 180 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 191 Processing helix chain 'C' and resid 209 through 224 Processing helix chain 'C' and resid 225 through 227 No H-bonds generated for 'chain 'C' and resid 225 through 227' Processing helix chain 'C' and resid 239 through 260 removed outlier: 3.595A pdb=" N GLN C 243 " --> pdb=" O ALA C 239 " (cutoff:3.500A) Proline residue: C 247 - end of helix Processing helix chain 'C' and resid 270 through 285 removed outlier: 3.631A pdb=" N GLN C 274 " --> pdb=" O ASP C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 294 Processing helix chain 'C' and resid 295 through 296 No H-bonds generated for 'chain 'C' and resid 295 through 296' Processing helix chain 'C' and resid 297 through 307 Processing helix chain 'C' and resid 313 through 317 Processing helix chain 'C' and resid 336 through 344 removed outlier: 3.836A pdb=" N SER C 344 " --> pdb=" O THR C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 358 Processing helix chain 'C' and resid 374 through 378 removed outlier: 3.505A pdb=" N ALA C 377 " --> pdb=" O VAL C 374 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA C 378 " --> pdb=" O GLY C 375 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 374 through 378' Processing helix chain 'C' and resid 380 through 400 removed outlier: 4.381A pdb=" N VAL C 386 " --> pdb=" O ALA C 382 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N GLY C 388 " --> pdb=" O LYS C 384 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N THR C 389 " --> pdb=" O GLN C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 405 removed outlier: 3.923A pdb=" N ALA C 404 " --> pdb=" O ALA C 401 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLN C 405 " --> pdb=" O ALA C 402 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 401 through 405' Processing helix chain 'C' and resid 411 through 428 Processing helix chain 'C' and resid 437 through 450 Processing helix chain 'C' and resid 460 through 476 Processing helix chain 'C' and resid 476 through 487 Processing helix chain 'C' and resid 490 through 507 Processing helix chain 'A' and resid 9 through 18 removed outlier: 3.626A pdb=" N GLU A 13 " --> pdb=" O SER A 9 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU A 14 " --> pdb=" O SER A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 82 removed outlier: 4.461A pdb=" N LEU A 81 " --> pdb=" O ASN A 78 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE A 82 " --> pdb=" O ASP A 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 78 through 82' Processing helix chain 'A' and resid 100 through 104 Processing helix chain 'A' and resid 150 through 156 Processing helix chain 'A' and resid 174 through 186 removed outlier: 3.835A pdb=" N ALA A 179 " --> pdb=" O LYS A 175 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 192 Processing helix chain 'A' and resid 209 through 224 Processing helix chain 'A' and resid 225 through 227 No H-bonds generated for 'chain 'A' and resid 225 through 227' Processing helix chain 'A' and resid 239 through 260 Proline residue: A 247 - end of helix removed outlier: 3.826A pdb=" N GLY A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 285 removed outlier: 3.565A pdb=" N GLN A 274 " --> pdb=" O ASP A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 294 Processing helix chain 'A' and resid 295 through 296 No H-bonds generated for 'chain 'A' and resid 295 through 296' Processing helix chain 'A' and resid 297 through 307 Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 336 through 344 Processing helix chain 'A' and resid 353 through 359 Processing helix chain 'A' and resid 380 through 400 removed outlier: 3.777A pdb=" N VAL A 386 " --> pdb=" O ALA A 382 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N THR A 389 " --> pdb=" O GLN A 385 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LEU A 392 " --> pdb=" O GLY A 388 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU A 393 " --> pdb=" O THR A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 406 removed outlier: 3.843A pdb=" N GLN A 405 " --> pdb=" O ALA A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 428 Processing helix chain 'A' and resid 437 through 451 Processing helix chain 'A' and resid 452 through 456 removed outlier: 3.757A pdb=" N LYS A 455 " --> pdb=" O TYR A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 476 Processing helix chain 'A' and resid 476 through 486 Processing helix chain 'A' and resid 490 through 508 Processing helix chain 'B' and resid 8 through 17 Processing helix chain 'B' and resid 18 through 23 removed outlier: 4.275A pdb=" N THR B 21 " --> pdb=" O GLY B 18 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL B 23 " --> pdb=" O ASP B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 82 removed outlier: 3.511A pdb=" N LEU B 81 " --> pdb=" O ASN B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 104 removed outlier: 3.744A pdb=" N LEU B 103 " --> pdb=" O GLY B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 157 Processing helix chain 'B' and resid 176 through 191 removed outlier: 3.501A pdb=" N GLN B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LYS B 187 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ARG B 188 " --> pdb=" O ILE B 184 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE B 189 " --> pdb=" O ASN B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 222 removed outlier: 3.590A pdb=" N THR B 221 " --> pdb=" O VAL B 217 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP B 222 " --> pdb=" O LYS B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 227 removed outlier: 5.628A pdb=" N MET B 226 " --> pdb=" O ALA B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 260 removed outlier: 3.512A pdb=" N GLN B 243 " --> pdb=" O ALA B 239 " (cutoff:3.500A) Proline residue: B 247 - end of helix removed outlier: 3.587A pdb=" N ASN B 260 " --> pdb=" O TYR B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 285 removed outlier: 3.702A pdb=" N GLN B 274 " --> pdb=" O ASP B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 294 Processing helix chain 'B' and resid 295 through 296 No H-bonds generated for 'chain 'B' and resid 295 through 296' Processing helix chain 'B' and resid 297 through 307 removed outlier: 3.512A pdb=" N LEU B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 317 Processing helix chain 'B' and resid 336 through 344 Processing helix chain 'B' and resid 353 through 359 Processing helix chain 'B' and resid 374 through 379 removed outlier: 4.392A pdb=" N ALA B 378 " --> pdb=" O VAL B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 402 removed outlier: 4.227A pdb=" N THR B 389 " --> pdb=" O GLN B 385 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET B 390 " --> pdb=" O VAL B 386 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU B 392 " --> pdb=" O GLY B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 429 Processing helix chain 'B' and resid 437 through 450 Processing helix chain 'B' and resid 460 through 476 Processing helix chain 'B' and resid 476 through 487 Processing helix chain 'B' and resid 490 through 509 removed outlier: 3.520A pdb=" N ALA B 495 " --> pdb=" O GLU B 491 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU B 509 " --> pdb=" O LEU B 505 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'F' and resid 137 through 144 Processing helix chain 'F' and resid 162 through 175 removed outlier: 4.235A pdb=" N LYS F 175 " --> pdb=" O ASN F 171 " (cutoff:3.500A) Processing helix chain 'F' and resid 189 through 203 Processing helix chain 'F' and resid 225 through 230 Processing helix chain 'F' and resid 231 through 246 Processing helix chain 'F' and resid 258 through 272 removed outlier: 3.699A pdb=" N THR F 262 " --> pdb=" O ILE F 258 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA F 270 " --> pdb=" O SER F 266 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N LEU F 271 " --> pdb=" O GLU F 267 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU F 272 " --> pdb=" O VAL F 268 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 295 removed outlier: 4.075A pdb=" N ARG F 295 " --> pdb=" O THR F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 316 Processing helix chain 'F' and resid 319 through 324 Processing helix chain 'F' and resid 325 through 329 Processing helix chain 'F' and resid 336 through 341 Processing helix chain 'F' and resid 359 through 364 Processing helix chain 'F' and resid 364 through 392 removed outlier: 4.402A pdb=" N ASP F 386 " --> pdb=" O LYS F 382 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N ILE F 387 " --> pdb=" O SER F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 414 Processing helix chain 'F' and resid 421 through 426 removed outlier: 3.603A pdb=" N THR F 425 " --> pdb=" O ALA F 421 " (cutoff:3.500A) Processing helix chain 'F' and resid 433 through 446 Processing helix chain 'F' and resid 453 through 458 Processing helix chain 'F' and resid 462 through 474 Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'D' and resid 122 through 126 Processing helix chain 'D' and resid 137 through 144 Processing helix chain 'D' and resid 162 through 174 removed outlier: 3.757A pdb=" N ILE D 166 " --> pdb=" O LYS D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 204 Processing helix chain 'D' and resid 225 through 230 Processing helix chain 'D' and resid 231 through 248 removed outlier: 3.553A pdb=" N GLU D 247 " --> pdb=" O PHE D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 270 removed outlier: 4.117A pdb=" N THR D 262 " --> pdb=" O ILE D 258 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ALA D 270 " --> pdb=" O SER D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 273 No H-bonds generated for 'chain 'D' and resid 271 through 273' Processing helix chain 'D' and resid 284 through 295 removed outlier: 3.819A pdb=" N MET D 292 " --> pdb=" O ASP D 288 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARG D 295 " --> pdb=" O THR D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 316 Processing helix chain 'D' and resid 319 through 326 Processing helix chain 'D' and resid 327 through 329 No H-bonds generated for 'chain 'D' and resid 327 through 329' Processing helix chain 'D' and resid 336 through 342 removed outlier: 3.534A pdb=" N LEU D 342 " --> pdb=" O ALA D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 364 Processing helix chain 'D' and resid 364 through 392 removed outlier: 3.951A pdb=" N ASP D 386 " --> pdb=" O LYS D 382 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ILE D 387 " --> pdb=" O SER D 383 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE D 390 " --> pdb=" O ASP D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 396 Processing helix chain 'D' and resid 397 through 414 Processing helix chain 'D' and resid 421 through 426 Processing helix chain 'D' and resid 433 through 447 Processing helix chain 'D' and resid 453 through 458 removed outlier: 4.089A pdb=" N PHE D 457 " --> pdb=" O PRO D 453 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR D 458 " --> pdb=" O GLU D 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 453 through 458' Processing helix chain 'D' and resid 462 through 477 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 137 through 144 Processing helix chain 'E' and resid 161 through 178 Processing helix chain 'E' and resid 189 through 204 removed outlier: 3.927A pdb=" N HIS E 198 " --> pdb=" O ASN E 194 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU E 199 " --> pdb=" O ASP E 195 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N MET E 200 " --> pdb=" O LEU E 196 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE E 201 " --> pdb=" O TYR E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 230 removed outlier: 3.571A pdb=" N ARG E 229 " --> pdb=" O PRO E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 231 through 248 removed outlier: 3.745A pdb=" N THR E 235 " --> pdb=" O ARG E 231 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY E 236 " --> pdb=" O VAL E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 272 Processing helix chain 'E' and resid 284 through 295 removed outlier: 3.999A pdb=" N ARG E 295 " --> pdb=" O THR E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 316 removed outlier: 3.540A pdb=" N ASP E 315 " --> pdb=" O VAL E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 327 removed outlier: 3.667A pdb=" N ALA E 327 " --> pdb=" O ALA E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 342 Processing helix chain 'E' and resid 359 through 364 Processing helix chain 'E' and resid 364 through 391 removed outlier: 4.145A pdb=" N ASP E 386 " --> pdb=" O LYS E 382 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ILE E 387 " --> pdb=" O SER E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 397 through 415 removed outlier: 3.804A pdb=" N SER E 415 " --> pdb=" O GLN E 411 " (cutoff:3.500A) Processing helix chain 'E' and resid 418 through 420 No H-bonds generated for 'chain 'E' and resid 418 through 420' Processing helix chain 'E' and resid 421 through 426 Processing helix chain 'E' and resid 433 through 446 Processing helix chain 'E' and resid 453 through 457 Processing helix chain 'E' and resid 462 through 475 removed outlier: 3.928A pdb=" N GLU E 475 " --> pdb=" O ASP E 471 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 55 removed outlier: 3.656A pdb=" N ILE G 6 " --> pdb=" O THR G 2 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS G 21 " --> pdb=" O GLN G 17 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N VAL G 26 " --> pdb=" O SER G 22 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU G 37 " --> pdb=" O ARG G 33 " (cutoff:3.500A) Proline residue: G 40 - end of helix removed outlier: 4.723A pdb=" N VAL G 43 " --> pdb=" O LYS G 39 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TYR G 44 " --> pdb=" O PRO G 40 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER G 48 " --> pdb=" O TYR G 44 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LEU G 51 " --> pdb=" O GLY G 47 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N TYR G 52 " --> pdb=" O SER G 48 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU G 53 " --> pdb=" O LEU G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 100 Processing helix chain 'G' and resid 109 through 121 removed outlier: 3.675A pdb=" N ARG G 113 " --> pdb=" O GLY G 109 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ARG G 118 " --> pdb=" O SER G 114 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N THR G 119 " --> pdb=" O ILE G 115 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER G 121 " --> pdb=" O HIS G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 151 Processing helix chain 'G' and resid 180 through 185 Processing helix chain 'G' and resid 188 through 193 Processing helix chain 'G' and resid 197 through 272 removed outlier: 4.312A pdb=" N ASP G 244 " --> pdb=" O SER G 240 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N LYS G 245 " --> pdb=" O GLU G 241 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU G 246 " --> pdb=" O MET G 242 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU G 272 " --> pdb=" O GLY G 268 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 103 Processing helix chain 'H' and resid 104 through 119 Processing helix chain 'H' and resid 120 through 122 No H-bonds generated for 'chain 'H' and resid 120 through 122' Processing helix chain 'H' and resid 124 through 146 Processing helix chain 'I' and resid 2 through 8 Processing helix chain 'I' and resid 10 through 24 Processing helix chain 'I' and resid 27 through 36 removed outlier: 4.163A pdb=" N LYS I 36 " --> pdb=" O ALA I 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 13 through 19 Processing helix chain 'J' and resid 20 through 50 removed outlier: 3.961A pdb=" N ALA J 36 " --> pdb=" O ARG J 32 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG J 37 " --> pdb=" O TYR J 33 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU J 50 " --> pdb=" O LYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 51 through 53 No H-bonds generated for 'chain 'J' and resid 51 through 53' Processing helix chain 'K' and resid 2 through 16 removed outlier: 4.033A pdb=" N VAL K 16 " --> pdb=" O GLY K 12 " (cutoff:3.500A) Processing helix chain 'K' and resid 18 through 39 removed outlier: 3.715A pdb=" N GLY K 22 " --> pdb=" O VAL K 18 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY K 26 " --> pdb=" O GLY K 22 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER K 31 " --> pdb=" O THR K 27 " (cutoff:3.500A) Processing helix chain 'K' and resid 42 through 73 removed outlier: 3.808A pdb=" N ALA K 59 " --> pdb=" O ALA K 55 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N MET K 60 " --> pdb=" O LEU K 56 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY K 61 " --> pdb=" O SER K 57 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE K 63 " --> pdb=" O ALA K 59 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N CYS K 64 " --> pdb=" O MET K 60 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU K 65 " --> pdb=" O GLY K 61 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 15 Processing helix chain 'L' and resid 16 through 18 No H-bonds generated for 'chain 'L' and resid 16 through 18' Processing helix chain 'L' and resid 19 through 39 removed outlier: 4.061A pdb=" N ALA L 23 " --> pdb=" O ALA L 19 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLY L 24 " --> pdb=" O GLY L 20 " (cutoff:3.500A) Processing helix chain 'L' and resid 42 through 58 removed outlier: 3.634A pdb=" N LEU L 46 " --> pdb=" O LEU L 42 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE L 47 " --> pdb=" O M3L L 43 " (cutoff:3.500A) Processing helix chain 'L' and resid 58 through 73 removed outlier: 3.835A pdb=" N LEU L 62 " --> pdb=" O GLU L 58 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 15 Processing helix chain 'M' and resid 17 through 39 removed outlier: 4.483A pdb=" N SER M 21 " --> pdb=" O GLY M 17 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY M 26 " --> pdb=" O GLY M 22 " (cutoff:3.500A) Processing helix chain 'M' and resid 42 through 73 removed outlier: 4.072A pdb=" N ALA M 59 " --> pdb=" O ALA M 55 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N MET M 60 " --> pdb=" O LEU M 56 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLY M 61 " --> pdb=" O SER M 57 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA M 68 " --> pdb=" O CYS M 64 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE M 69 " --> pdb=" O LEU M 65 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 15 removed outlier: 3.769A pdb=" N GLY N 10 " --> pdb=" O ALA N 6 " (cutoff:3.500A) Processing helix chain 'N' and resid 18 through 39 Processing helix chain 'N' and resid 42 through 67 removed outlier: 4.445A pdb=" N MET N 60 " --> pdb=" O LEU N 56 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLY N 61 " --> pdb=" O SER N 57 " (cutoff:3.500A) Processing helix chain 'N' and resid 68 through 73 Processing helix chain 'O' and resid 2 through 8 removed outlier: 3.727A pdb=" N LYS O 7 " --> pdb=" O ASP O 3 " (cutoff:3.500A) Processing helix chain 'O' and resid 9 through 15 Processing helix chain 'O' and resid 17 through 39 removed outlier: 3.827A pdb=" N SER O 21 " --> pdb=" O GLY O 17 " (cutoff:3.500A) Processing helix chain 'O' and resid 42 through 59 removed outlier: 3.759A pdb=" N LEU O 46 " --> pdb=" O LEU O 42 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N PHE O 47 " --> pdb=" O M3L O 43 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N SER O 48 " --> pdb=" O GLN O 44 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N TYR O 49 " --> pdb=" O GLN O 45 " (cutoff:3.500A) Processing helix chain 'O' and resid 61 through 73 removed outlier: 3.986A pdb=" N LEU O 65 " --> pdb=" O GLY O 61 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 16 removed outlier: 3.910A pdb=" N ALA P 6 " --> pdb=" O ILE P 2 " (cutoff:3.500A) Processing helix chain 'P' and resid 17 through 39 Processing helix chain 'P' and resid 42 through 74 removed outlier: 4.683A pdb=" N CYS P 64 " --> pdb=" O MET P 60 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU P 65 " --> pdb=" O GLY P 61 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LEU P 72 " --> pdb=" O ALA P 68 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N PHE P 73 " --> pdb=" O PHE P 69 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 8 removed outlier: 4.194A pdb=" N ALA Q 5 " --> pdb=" O ILE Q 2 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA Q 6 " --> pdb=" O ASP Q 3 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N LYS Q 7 " --> pdb=" O THR Q 4 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N PHE Q 8 " --> pdb=" O ALA Q 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 2 through 8' Processing helix chain 'Q' and resid 9 through 15 Processing helix chain 'Q' and resid 15 through 39 removed outlier: 3.633A pdb=" N ALA Q 19 " --> pdb=" O THR Q 15 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ALA Q 23 " --> pdb=" O ALA Q 19 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLY Q 24 " --> pdb=" O GLY Q 20 " (cutoff:3.500A) Processing helix chain 'Q' and resid 42 through 74 removed outlier: 3.802A pdb=" N MET Q 60 " --> pdb=" O LEU Q 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 14 Processing helix chain 'R' and resid 17 through 39 removed outlier: 4.037A pdb=" N SER R 21 " --> pdb=" O GLY R 17 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY R 22 " --> pdb=" O VAL R 18 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA R 23 " --> pdb=" O ALA R 19 " (cutoff:3.500A) Processing helix chain 'R' and resid 42 through 74 removed outlier: 4.126A pdb=" N SER R 48 " --> pdb=" O GLN R 44 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N VAL R 67 " --> pdb=" O PHE R 63 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ALA R 68 " --> pdb=" O CYS R 64 " (cutoff:3.500A) removed outlier: 4.147A 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 57 Processing helix chain 'S' and resid 61 through 77 Processing helix chain 'S' and resid 79 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 114 Processing helix chain 'S' and resid 127 through 142 removed outlier: 3.900A pdb=" N SER S 140 " --> pdb=" O THR S 136 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N PHE S 141 " --> pdb=" O VAL S 137 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU S 142 " --> pdb=" O LEU S 138 " (cutoff:3.500A) Processing helix chain 'S' and resid 174 through 186 removed outlier: 3.837A pdb=" N LYS S 178 " --> pdb=" O SER S 174 " (cutoff:3.500A) Processing helix chain 'a' and resid 3 through 10 removed outlier: 4.900A pdb=" N SER a 8 " --> pdb=" O LEU a 5 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE a 10 " --> pdb=" O THR a 7 " (cutoff:3.500A) Processing helix chain 'a' and resid 19 through 23 removed outlier: 4.179A pdb=" N LEU a 22 " --> pdb=" O LEU a 19 " (cutoff:3.500A) Processing helix chain 'a' and resid 26 through 31 removed outlier: 4.064A pdb=" N LEU a 30 " --> pdb=" O PHE a 26 " (cutoff:3.500A) Processing helix chain 'a' and resid 40 through 59 removed outlier: 3.755A pdb=" N LYS a 55 " --> pdb=" O GLN a 51 " (cutoff:3.500A) Processing helix chain 'a' and resid 62 through 86 removed outlier: 3.531A pdb=" N TRP a 68 " --> pdb=" O LYS a 64 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N LEU a 70 " --> pdb=" O GLN a 66 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N MET a 71 " --> pdb=" O THR a 67 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU a 77 " --> pdb=" O MET a 73 " (cutoff:3.500A) removed outlier: 4.108A 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 104 Processing helix chain 'a' and resid 105 through 116 removed outlier: 3.630A pdb=" N TRP a 109 " --> pdb=" O ALA a 105 " (cutoff:3.500A) Processing helix chain 'a' and resid 121 through 127 removed outlier: 3.807A pdb=" N HIS a 127 " --> pdb=" O ALA a 123 " (cutoff:3.500A) Processing helix chain 'a' and resid 138 through 181 removed outlier: 4.042A pdb=" N ILE a 144 " --> pdb=" O MET a 140 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE a 150 " --> pdb=" O THR a 146 " (cutoff:3.500A) Proline residue: a 153 - end of helix removed outlier: 3.958A pdb=" N ARG a 159 " --> pdb=" O ALA a 155 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N HIS a 168 " --> pdb=" O ILE a 164 " (cutoff:3.500A) Processing helix chain 'a' and resid 182 through 184 No H-bonds generated for 'chain 'a' and resid 182 through 184' Processing helix chain 'a' and resid 185 through 225 removed outlier: 3.810A pdb=" N ALA a 189 " --> pdb=" O SER a 185 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU a 198 " --> pdb=" O THR a 194 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LEU a 199 " --> pdb=" O ILE a 195 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N THR a 200 " --> pdb=" O LEU a 196 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ILE a 201 " --> pdb=" O ILE a 197 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU a 202 " --> pdb=" O LEU a 198 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA a 211 " --> pdb=" O ALA a 207 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU a 220 " --> pdb=" O LEU a 216 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N TYR a 221 " --> pdb=" O LEU a 217 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU a 222 " --> pdb=" O VAL a 218 " (cutoff:3.500A) Processing helix chain 'b' and resid 14 through 16 No H-bonds generated for 'chain 'b' and resid 14 through 16' Processing helix chain 'b' and resid 19 through 30 Proline residue: b 27 - end of helix Processing helix chain 'b' and resid 31 through 38 Processing helix chain 'b' and resid 42 through 48 removed outlier: 4.034A pdb=" N LEU b 46 " --> pdb=" O ILE b 42 " (cutoff:3.500A) Processing helix chain 'b' and resid 55 through 116 removed outlier: 4.417A pdb=" N SER b 59 " --> pdb=" O PRO b 55 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ALA b 76 " --> pdb=" O LYS b 72 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N SER b 77 " --> pdb=" O LYS b 73 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LEU b 93 " --> pdb=" O LYS b 89 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLU b 94 " --> pdb=" O ILE b 90 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N GLU b 95 " --> pdb=" O ALA b 91 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N VAL b 96 " --> pdb=" O GLN b 92 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE b 104 " --> pdb=" O SER b 100 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLN b 105 " --> pdb=" O ILE b 101 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE b 108 " --> pdb=" O ILE b 104 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ASP b 109 " --> pdb=" O GLN b 105 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N MET b 110 " --> pdb=" O ASP b 106 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU b 111 " --> pdb=" O ALA b 107 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN b 114 " --> pdb=" O MET b 110 " (cutoff:3.500A) Processing helix chain 'b' and resid 117 through 121 removed outlier: 3.930A pdb=" N LYS b 120 " --> pdb=" O LEU b 117 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG b 121 " --> pdb=" O VAL b 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 117 through 121' Processing helix chain 'b' and resid 122 through 185 removed outlier: 3.813A pdb=" N ILE b 132 " --> pdb=" O GLN b 128 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N HIS b 145 " --> pdb=" O ARG b 141 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU b 155 " --> pdb=" O VAL b 151 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N HIS b 158 " --> pdb=" O ARG b 154 " (cutoff:3.500A) Processing helix chain 'b' and resid 189 through 209 removed outlier: 4.053A pdb=" N ALA b 199 " --> pdb=" O ALA b 195 " (cutoff:3.500A) Processing helix chain 'd' and resid 11 through 13 No H-bonds generated for 'chain 'd' and resid 11 through 13' Processing helix chain 'd' and resid 14 through 19 removed outlier: 4.331A pdb=" N ILE d 18 " --> pdb=" O ALA d 14 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE d 19 " --> pdb=" O PHE d 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 14 through 19' Processing helix chain 'd' and resid 20 through 25 removed outlier: 6.257A pdb=" N ALA d 25 " --> pdb=" O ASN d 22 " (cutoff:3.500A) Processing helix chain 'd' and resid 26 through 42 removed outlier: 4.023A pdb=" N LEU d 30 " --> pdb=" O VAL d 26 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LYS d 31 " --> pdb=" O ALA d 27 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA d 42 " --> pdb=" O THR d 38 " (cutoff:3.500A) Processing helix chain 'd' and resid 52 through 60 Processing helix chain 'd' and resid 64 through 76 Processing helix chain 'd' and resid 84 through 89 removed outlier: 3.576A pdb=" N GLN d 88 " --> pdb=" O TYR d 85 " (cutoff:3.500A) Processing helix chain 'd' and resid 90 through 101 removed outlier: 4.410A pdb=" N ASP d 96 " --> pdb=" O GLU d 92 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LYS d 98 " --> pdb=" O LYS d 94 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N SER d 99 " --> pdb=" O GLU d 95 " (cutoff:3.500A) Processing helix chain 'd' and resid 103 through 123 Processing helix chain 'd' and resid 131 through 139 Processing helix chain 'd' and resid 140 through 143 Processing helix chain 'e' and resid 7 through 38 removed outlier: 3.904A pdb=" N GLY e 13 " --> pdb=" O LEU e 9 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU e 18 " --> pdb=" O ARG e 14 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N PHE e 19 " --> pdb=" O TYR e 15 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LEU e 20 " --> pdb=" O SER e 16 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY e 21 " --> pdb=" O ALA e 17 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN e 30 " --> pdb=" O ALA e 26 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N LYS e 33 " --> pdb=" O TYR e 29 " (cutoff:3.500A) Proline residue: e 34 - end of helix Processing helix chain 'e' and resid 39 through 45 removed outlier: 4.079A pdb=" N ALA e 43 " --> pdb=" O GLU e 39 " (cutoff:3.500A) Processing helix chain 'e' and resid 46 through 57 removed outlier: 4.273A pdb=" N ARG e 50 " --> pdb=" O GLU e 46 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARG e 55 " --> pdb=" O ASP e 51 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE e 56 " --> pdb=" O GLU e 52 " (cutoff:3.500A) Processing helix chain 'f' and resid 10 through 14 removed outlier: 3.774A pdb=" N VAL f 14 " --> pdb=" O LEU f 11 " (cutoff:3.500A) Processing helix chain 'f' and resid 18 through 22 Processing helix chain 'f' and resid 29 through 49 removed outlier: 3.824A pdb=" N ARG f 39 " --> pdb=" O GLY f 35 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N GLY f 40 " --> pdb=" O ALA f 36 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N TYR f 41 " --> pdb=" O PHE f 37 " (cutoff:3.500A) Processing helix chain 'f' and resid 59 through 65 Processing helix chain 'f' and resid 67 through 74 removed outlier: 4.156A pdb=" N TYR f 71 " --> pdb=" O VAL f 67 " (cutoff:3.500A) Processing helix chain 'f' and resid 74 through 80 removed outlier: 3.946A pdb=" N HIS f 80 " --> pdb=" O LYS f 76 " (cutoff:3.500A) Processing helix chain 'g' and resid 21 through 37 removed outlier: 4.081A pdb=" N ARG g 25 " --> pdb=" O TYR g 21 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL g 35 " --> pdb=" O TYR g 31 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLU g 36 " --> pdb=" O TYR g 32 " (cutoff:3.500A) Processing helix chain 'g' and resid 43 through 53 Processing helix chain 'g' and resid 55 through 60 Processing helix chain 'g' and resid 68 through 76 Processing helix chain 'g' and resid 77 through 79 No H-bonds generated for 'chain 'g' and resid 77 through 79' Processing helix chain 'g' and resid 80 through 94 removed outlier: 4.031A pdb=" N TRP g 85 " --> pdb=" O GLU g 81 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N PHE g 86 " --> pdb=" O VAL g 82 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N TYR g 87 " --> pdb=" O TRP g 83 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL g 88 " --> pdb=" O MET g 84 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE g 92 " --> pdb=" O VAL g 88 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LYS g 94 " --> pdb=" O GLU g 90 " (cutoff:3.500A) Processing helix chain 'h' and resid 9 through 24 Processing helix chain 'h' and resid 32 through 51 removed outlier: 3.635A pdb=" N GLN h 36 " --> pdb=" O GLY h 32 " (cutoff:3.500A) Processing helix chain 'j' and resid 6 through 21 Proline residue: j 12 - end of helix Proline residue: j 15 - end of helix removed outlier: 3.582A pdb=" N TYR j 21 " --> pdb=" O TYR j 17 " (cutoff:3.500A) Processing helix chain 'j' and resid 21 through 28 removed outlier: 3.532A pdb=" N TRP j 25 " --> pdb=" O TYR j 21 " (cutoff:3.500A) Processing helix chain 'j' and resid 29 through 49 removed outlier: 4.466A pdb=" N TYR j 33 " --> pdb=" O GLY j 29 " (cutoff:3.500A) Processing helix chain 'k' and resid 13 through 18 Processing helix chain 'k' and resid 22 through 35 Processing helix chain 'k' and resid 38 through 45 Processing sheet with id=AA1, first strand: chain 'C' and resid 28 through 35 removed outlier: 3.557A pdb=" N ARG C 30 " --> pdb=" O HIS C 42 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ARG C 40 " --> pdb=" O LEU C 32 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ILE C 34 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE C 38 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL C 71 " --> pdb=" O VAL C 41 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N GLY C 72 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL C 53 " --> pdb=" O GLY C 61 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 96 through 99 removed outlier: 3.927A pdb=" N ALA C 125 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 107 through 108 removed outlier: 6.722A pdb=" N VAL C 108 " --> pdb=" O SER C 233 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N THR C 235 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N CYS C 201 " --> pdb=" O ILE C 230 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N VAL C 232 " --> pdb=" O CYS C 201 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N TYR C 203 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ALA C 234 " --> pdb=" O TYR C 203 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N ALA C 205 " --> pdb=" O ALA C 234 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA C 264 " --> pdb=" O SER C 320 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 145 through 146 removed outlier: 4.242A pdb=" N ILE C 159 " --> pdb=" O MET C 146 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 326 through 328 removed outlier: 6.572A pdb=" N ILE C 167 " --> pdb=" O ILE C 327 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 25 through 26 removed outlier: 3.629A pdb=" N VAL S 164 " --> pdb=" O VAL S 171 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 28 through 35 removed outlier: 5.689A pdb=" N VAL A 31 " --> pdb=" O HIS A 42 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N HIS A 42 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N GLY A 72 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU A 64 " --> pdb=" O GLY A 72 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 96 through 99 removed outlier: 3.999A pdb=" N ALA A 125 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 107 through 108 removed outlier: 6.655A pdb=" N VAL A 108 " --> pdb=" O SER A 233 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N CYS A 201 " --> pdb=" O ILE A 230 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N VAL A 232 " --> pdb=" O CYS A 201 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N TYR A 203 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N ALA A 234 " --> pdb=" O TYR A 203 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ALA A 205 " --> pdb=" O ALA A 234 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N TYR A 200 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ILE A 267 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE A 202 " --> pdb=" O ILE A 267 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 326 through 328 removed outlier: 6.361A pdb=" N ILE A 167 " --> pdb=" O ILE A 327 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LEU A 166 " --> pdb=" O GLY A 348 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN A 349 " --> pdb=" O VAL A 371 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 60 through 66 removed outlier: 3.745A pdb=" N SER B 63 " --> pdb=" O GLU B 51 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N GLU B 51 " --> pdb=" O SER B 63 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N ALA B 93 " --> pdb=" O MET B 52 " (cutoff:3.500A) removed outlier: 8.490A pdb=" N GLU B 54 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N THR B 91 " --> pdb=" O GLU B 54 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ARG B 40 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ILE B 34 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ILE B 38 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N GLY B 72 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ALA F 35 " --> pdb=" O SER F 78 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ASN F 34 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N VAL F 49 " --> pdb=" O ILE F 61 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE F 61 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N THR F 57 " --> pdb=" O LEU F 53 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N GLN F 24 " --> pdb=" O ILE F 13 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N ILE F 13 " --> pdb=" O GLN F 24 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 96 through 99 removed outlier: 3.859A pdb=" N ALA B 125 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 107 through 108 removed outlier: 3.547A pdb=" N GLY B 169 " --> pdb=" O ILE B 327 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 145 through 146 removed outlier: 4.634A pdb=" N ILE B 159 " --> pdb=" O MET B 146 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 83 through 86 removed outlier: 4.052A pdb=" N GLN F 112 " --> pdb=" O VAL F 86 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 94 through 95 removed outlier: 6.424A pdb=" N MET F 95 " --> pdb=" O TYR F 219 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N SER F 181 " --> pdb=" O ALA F 216 " (cutoff:3.500A) removed outlier: 8.884A pdb=" N VAL F 218 " --> pdb=" O SER F 181 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N PHE F 183 " --> pdb=" O VAL F 218 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N GLY F 220 " --> pdb=" O PHE F 183 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N GLY F 185 " --> pdb=" O GLY F 220 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N TYR F 180 " --> pdb=" O LEU F 252 " (cutoff:3.500A) removed outlier: 8.675A pdb=" N PHE F 254 " --> pdb=" O TYR F 180 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL F 182 " --> pdb=" O PHE F 254 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY F 156 " --> pdb=" O ILE F 310 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 132 through 133 removed outlier: 4.226A pdb=" N TYR F 146 " --> pdb=" O LEU F 133 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 10 through 17 removed outlier: 5.817A pdb=" N ILE D 13 " --> pdb=" O GLN D 24 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N GLN D 24 " --> pdb=" O ILE D 13 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA D 15 " --> pdb=" O ASP D 22 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N THR D 57 " --> pdb=" O HIS D 52 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N HIS D 52 " --> pdb=" O THR D 57 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ARG D 59 " --> pdb=" O ALA D 50 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU D 48 " --> pdb=" O ILE D 61 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 83 through 86 removed outlier: 4.394A pdb=" N GLN D 112 " --> pdb=" O VAL D 86 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 94 through 95 removed outlier: 6.589A pdb=" N TYR D 180 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N PHE D 254 " --> pdb=" O TYR D 180 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL D 182 " --> pdb=" O PHE D 254 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA D 331 " --> pdb=" O LYS D 151 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR D 333 " --> pdb=" O GLY D 153 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 132 through 133 removed outlier: 4.120A pdb=" N TYR D 146 " --> pdb=" O LEU D 133 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 10 through 17 removed outlier: 5.748A pdb=" N ILE E 13 " --> pdb=" O GLN E 24 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N GLN E 24 " --> pdb=" O ILE E 13 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA E 15 " --> pdb=" O ASP E 22 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL E 23 " --> pdb=" O VAL E 58 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N THR E 57 " --> pdb=" O HIS E 52 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N HIS E 52 " --> pdb=" O THR E 57 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ARG E 59 " --> pdb=" O ALA E 50 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 83 through 85 Processing sheet with id=AC6, first strand: chain 'E' and resid 94 through 95 removed outlier: 3.626A pdb=" N TYR E 219 " --> pdb=" O MET E 95 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N TYR E 180 " --> pdb=" O LEU E 252 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N PHE E 254 " --> pdb=" O TYR E 180 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL E 182 " --> pdb=" O PHE E 254 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N VAL E 251 " --> pdb=" O THR E 305 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N VAL E 307 " --> pdb=" O VAL E 251 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU E 253 " --> pdb=" O VAL E 307 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N ALA E 309 " --> pdb=" O LEU E 253 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N ILE E 255 " --> pdb=" O ALA E 309 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LYS E 151 " --> pdb=" O ALA E 331 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N THR E 333 " --> pdb=" O LYS E 151 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N GLY E 153 " --> pdb=" O THR E 333 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 132 through 133 removed outlier: 4.277A pdb=" N TYR E 146 " --> pdb=" O LEU E 133 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 171 through 179 removed outlier: 6.360A pdb=" N LEU G 67 " --> pdb=" O SER G 159 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ILE G 161 " --> pdb=" O LEU G 67 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ILE G 69 " --> pdb=" O ILE G 161 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N ASN G 163 " --> pdb=" O ILE G 69 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N HIS G 66 " --> pdb=" O LYS G 104 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N ILE G 106 " --> pdb=" O HIS G 66 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ILE G 68 " --> pdb=" O ILE G 106 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N VAL G 108 " --> pdb=" O ILE G 68 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N GLY G 70 " --> pdb=" O VAL G 108 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N PHE G 124 " --> pdb=" O VAL G 103 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ILE G 105 " --> pdb=" O PHE G 124 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N VAL G 126 " --> pdb=" O ILE G 105 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR G 127 " --> pdb=" O VAL I 45 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS I 43 " --> pdb=" O LYS G 129 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 26 through 31 removed outlier: 4.787A pdb=" N PHE H 18 " --> pdb=" O SER H 30 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL H 90 " --> pdb=" O SER H 17 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ALA H 94 " --> pdb=" O ALA H 21 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 45 through 47 removed outlier: 3.700A pdb=" N VAL H 36 " --> pdb=" O ILE H 47 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'b' and resid 12 through 13 2221 hydrogen bonds defined for protein. 6426 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: 9.73 Time building geometry restraints manager: 4.99 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: 10155 1.33 - 1.46: 7408 1.46 - 1.58: 21894 1.58 - 1.70: 0 1.70 - 1.82: 273 Bond restraints: 39730 Sorted by residual: bond pdb=" N ILE g 49 " pdb=" CA ILE g 49 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.18e+00 bond pdb=" CZ ARG b 143 " pdb=" NH2 ARG b 143 " ideal model delta sigma weight residual 1.330 1.291 0.039 1.30e-02 5.92e+03 9.09e+00 bond pdb=" CZ ARG b 141 " pdb=" NH2 ARG b 141 " ideal model delta sigma weight residual 1.330 1.291 0.039 1.30e-02 5.92e+03 9.00e+00 bond pdb=" CZ ARG D 229 " pdb=" NH2 ARG D 229 " ideal model delta sigma weight residual 1.330 1.293 0.037 1.30e-02 5.92e+03 8.13e+00 bond pdb=" CZ ARG C 164 " pdb=" NH2 ARG C 164 " ideal model delta sigma weight residual 1.330 1.293 0.037 1.30e-02 5.92e+03 8.07e+00 ... (remaining 39725 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.07: 52891 3.07 - 6.13: 712 6.13 - 9.20: 89 9.20 - 12.26: 23 12.26 - 15.33: 7 Bond angle restraints: 53722 Sorted by residual: angle pdb=" C GLN C 172 " pdb=" N THR C 173 " pdb=" CA THR C 173 " ideal model delta sigma weight residual 120.38 129.53 -9.15 1.37e+00 5.33e-01 4.46e+01 angle pdb=" CA MET I 35 " pdb=" CB MET I 35 " pdb=" CG MET I 35 " ideal model delta sigma weight residual 114.10 124.06 -9.96 2.00e+00 2.50e-01 2.48e+01 angle pdb=" C ALA K 23 " pdb=" N GLY K 24 " pdb=" CA GLY K 24 " ideal model delta sigma weight residual 119.98 125.43 -5.45 1.11e+00 8.12e-01 2.41e+01 angle pdb=" C LYS d 120 " pdb=" N MET d 121 " pdb=" CA MET d 121 " ideal model delta sigma weight residual 122.38 113.65 8.73 1.81e+00 3.05e-01 2.33e+01 angle pdb=" CB HIS J 49 " pdb=" CG HIS J 49 " pdb=" CD2 HIS J 49 " ideal model delta sigma weight residual 131.20 124.97 6.23 1.30e+00 5.92e-01 2.29e+01 ... (remaining 53717 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 21393 17.99 - 35.97: 2076 35.97 - 53.96: 455 53.96 - 71.94: 107 71.94 - 89.93: 34 Dihedral angle restraints: 24065 sinusoidal: 9356 harmonic: 14709 Sorted by residual: dihedral pdb=" CA ASP B 224 " pdb=" C ASP B 224 " pdb=" N ALA B 225 " pdb=" CA ALA B 225 " ideal model delta harmonic sigma weight residual -180.00 -152.86 -27.14 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CA MET A 436 " pdb=" C MET A 436 " pdb=" N ALA A 437 " pdb=" CA ALA A 437 " ideal model delta harmonic sigma weight residual -180.00 -156.12 -23.88 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" CA ILE B 361 " pdb=" C ILE B 361 " pdb=" N ARG B 362 " pdb=" CA ARG B 362 " ideal model delta harmonic sigma weight residual -180.00 -157.22 -22.78 0 5.00e+00 4.00e-02 2.08e+01 ... (remaining 24062 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 5494 0.077 - 0.155: 718 0.155 - 0.232: 42 0.232 - 0.309: 13 0.309 - 0.387: 3 Chirality restraints: 6270 Sorted by residual: chirality pdb=" CG LEU F 237 " pdb=" CB LEU F 237 " pdb=" CD1 LEU F 237 " pdb=" CD2 LEU F 237 " both_signs ideal model delta sigma weight residual False -2.59 -2.20 -0.39 2.00e-01 2.50e+01 3.74e+00 chirality pdb=" CG LEU A 284 " pdb=" CB LEU A 284 " pdb=" CD1 LEU A 284 " pdb=" CD2 LEU A 284 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.40e+00 chirality pdb=" CG LEU K 62 " pdb=" CB LEU K 62 " pdb=" CD1 LEU K 62 " pdb=" CD2 LEU K 62 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.55e+00 ... (remaining 6267 not shown) Planarity restraints: 6893 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR d 85 " -0.112 2.00e-02 2.50e+03 6.31e-02 7.95e+01 pdb=" CG TYR d 85 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR d 85 " 0.045 2.00e-02 2.50e+03 pdb=" CD2 TYR d 85 " 0.053 2.00e-02 2.50e+03 pdb=" CE1 TYR d 85 " 0.041 2.00e-02 2.50e+03 pdb=" CE2 TYR d 85 " 0.036 2.00e-02 2.50e+03 pdb=" CZ TYR d 85 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR d 85 " -0.101 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 433 " 0.085 2.00e-02 2.50e+03 4.40e-02 3.86e+01 pdb=" CG TYR B 433 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR B 433 " -0.038 2.00e-02 2.50e+03 pdb=" CD2 TYR B 433 " -0.034 2.00e-02 2.50e+03 pdb=" CE1 TYR B 433 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR B 433 " -0.020 2.00e-02 2.50e+03 pdb=" CZ TYR B 433 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 433 " 0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 219 " 0.069 2.00e-02 2.50e+03 4.25e-02 3.62e+01 pdb=" CG TYR D 219 " -0.004 2.00e-02 2.50e+03 pdb=" CD1 TYR D 219 " -0.034 2.00e-02 2.50e+03 pdb=" CD2 TYR D 219 " -0.033 2.00e-02 2.50e+03 pdb=" CE1 TYR D 219 " -0.032 2.00e-02 2.50e+03 pdb=" CE2 TYR D 219 " -0.031 2.00e-02 2.50e+03 pdb=" CZ TYR D 219 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR D 219 " 0.074 2.00e-02 2.50e+03 ... (remaining 6890 not shown) Histogram of nonbonded interaction distances: 1.09 - 1.85: 1 1.85 - 2.62: 45 2.62 - 3.38: 57920 3.38 - 4.14: 94733 4.14 - 4.90: 167456 Nonbonded interactions: 320155 Sorted by model distance: nonbonded pdb=" O VAL B 422 " pdb=" OE1 GLU B 426 " model vdw 1.093 3.040 nonbonded pdb=" CG2 THR H 40 " pdb=" O VAL H 57 " model vdw 2.108 3.460 nonbonded pdb=" OE1 GLU C 67 " pdb=" ND2 ASN C 70 " model vdw 2.133 3.120 nonbonded pdb=" CZ ARG B 362 " pdb=" NE2 GLN B 432 " model vdw 2.134 3.350 nonbonded pdb=" O VAL B 422 " pdb=" CD GLU B 426 " model vdw 2.153 3.270 ... (remaining 320150 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 23 through 508) selection = (chain 'B' and resid 23 through 508) selection = chain 'C' } ncs_group { reference = (chain 'D' and resid 9 through 475) selection = chain 'E' selection = chain 'F' } ncs_group { reference = (chain 'K' and (resid 1 through 7 or (resid 8 through 9 and (name N or name CA o \ r name C or name O or name CB )) or resid 10 through 59 or (resid 60 and (name N \ or name CA or name C or name O or name CB )) or resid 61 or (resid 62 and (name \ N or name CA or name C or name O or name CB )) or resid 63 through 68 or (resid \ 69 through 70 and (name N or name CA or name C or name O or name CB )) or resid \ 71 through 74)) selection = (chain 'L' and (resid 1 through 7 or (resid 8 through 9 and (name N or name CA o \ r name C or name O or name CB )) or resid 10 through 68 or (resid 69 through 70 \ and (name N or name CA or name C or name O or name CB )) or resid 71 through 74) \ ) selection = (chain 'M' and (resid 1 through 7 or (resid 8 through 9 and (name N or name CA o \ r name C or name O or name CB )) or resid 10 through 59 or (resid 60 and (name N \ or name CA or name C or name O or name CB )) or resid 61 or (resid 62 and (name \ N or name CA or name C or name O or name CB )) or resid 63 through 68 or (resid \ 69 through 70 and (name N or name CA or name C or name O or name CB )) or resid \ 71 through 74)) selection = (chain 'N' and (resid 1 through 7 or (resid 8 through 9 and (name N or name CA o \ r name C or name O or name CB )) or resid 10 through 59 or (resid 60 and (name N \ or name CA or name C or name O or name CB )) or resid 61 or (resid 62 and (name \ N or name CA or name C or name O or name CB )) or resid 63 through 68 or (resid \ 69 through 70 and (name N or name CA or name C or name O or name CB )) or resid \ 71 through 74)) selection = (chain 'O' and (resid 1 through 7 or (resid 8 through 9 and (name N or name CA o \ r name C or name O or name CB )) or resid 10 through 59 or (resid 60 and (name N \ or name CA or name C or name O or name CB )) or resid 61 or (resid 62 and (name \ N or name CA or name C or name O or name CB )) or resid 63 through 68 or (resid \ 69 through 70 and (name N or name CA or name C or name O or name CB )) or resid \ 71 through 74)) selection = (chain 'P' and (resid 1 through 59 or (resid 60 and (name N or name CA or name C \ or name O or name CB )) or resid 61 or (resid 62 and (name N or name CA or name \ C or name O or name CB )) or resid 63 through 68 or (resid 69 through 70 and (n \ ame N or name CA or name C or name O or name CB )) or resid 71 through 74)) selection = (chain 'Q' and (resid 1 through 7 or (resid 8 through 9 and (name N or name CA o \ r name C or name O or name CB )) or resid 10 through 59 or (resid 60 and (name N \ or name CA or name C or name O or name CB )) or resid 61 or (resid 62 and (name \ N or name CA or name C or name O or name CB )) or resid 63 through 74)) selection = (chain 'R' and (resid 1 through 7 or (resid 8 through 9 and (name N or name CA o \ r name C or name O or name CB )) or resid 10 through 59 or (resid 60 and (name N \ or name CA or name C or name O or name CB )) or resid 61 or (resid 62 and (name \ N or name CA or name C or name O or name CB )) or resid 63 through 68 or (resid \ 69 through 70 and (name N or name CA or name C or name O or name CB )) or resid \ 71 through 74)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 8.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.020 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 38.280 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 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 0.041 39730 Z= 0.250 Angle : 0.869 15.328 53722 Z= 0.491 Chirality : 0.050 0.387 6270 Planarity : 0.006 0.174 6893 Dihedral : 15.338 89.929 14645 Min Nonbonded Distance : 1.093 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.12 % Allowed : 20.80 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.12), residues: 5073 helix: 1.01 (0.10), residues: 2642 sheet: 0.60 (0.22), residues: 520 loop : -0.09 (0.15), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG b 143 TYR 0.112 0.003 TYR d 85 PHE 0.060 0.003 PHE R 54 TRP 0.015 0.001 TRP 8 9 HIS 0.011 0.001 HIS F 367 Details of bonding type rmsd covalent geometry : bond 0.00428 (39730) covalent geometry : angle 0.86910 (53722) hydrogen bonds : bond 0.12411 ( 2221) hydrogen bonds : angle 6.21534 ( 6426) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10146 Ramachandran restraints generated. 5073 Oldfield, 0 Emsley, 5073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10146 Ramachandran restraints generated. 5073 Oldfield, 0 Emsley, 5073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 4173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 520 time to evaluate : 1.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 12 MET cc_start: 0.8144 (mmm) cc_final: 0.7374 (mtt) REVERT: C 52 MET cc_start: 0.9262 (ttp) cc_final: 0.8280 (tmm) REVERT: C 393 GLU cc_start: 0.9037 (tm-30) cc_final: 0.8793 (tm-30) REVERT: A 146 MET cc_start: 0.9216 (tmm) cc_final: 0.8588 (tmm) REVERT: B 146 MET cc_start: 0.9277 (tmm) cc_final: 0.8720 (tmm) REVERT: B 312 MET cc_start: 0.8192 (tpp) cc_final: 0.7799 (tpp) REVERT: B 352 LEU cc_start: 0.9533 (mt) cc_final: 0.9305 (mm) REVERT: B 390 MET cc_start: 0.9680 (tpp) cc_final: 0.9401 (tpp) REVERT: B 394 LEU cc_start: 0.9580 (mt) cc_final: 0.9055 (mt) REVERT: F 352 ASP cc_start: 0.9251 (m-30) cc_final: 0.8809 (p0) REVERT: F 358 MET cc_start: 0.8722 (tmm) cc_final: 0.8102 (tmm) REVERT: D 200 MET cc_start: 0.9415 (mmm) cc_final: 0.9201 (mmm) REVERT: D 393 MET cc_start: 0.8782 (ppp) cc_final: 0.8552 (ppp) REVERT: D 459 MET cc_start: 0.9406 (tpp) cc_final: 0.8878 (mmm) REVERT: E 22 ASP cc_start: 0.8848 (t0) cc_final: 0.8519 (t0) REVERT: E 95 MET cc_start: 0.8909 (pmm) cc_final: 0.8707 (pmm) REVERT: E 126 MET cc_start: 0.8742 (ttm) cc_final: 0.8460 (ttm) REVERT: E 222 MET cc_start: 0.9100 (mpp) cc_final: 0.8796 (mpp) REVERT: E 358 MET cc_start: 0.9504 (mmm) cc_final: 0.8755 (mmm) REVERT: E 459 MET cc_start: 0.8834 (mmm) cc_final: 0.7990 (mmm) REVERT: G 163 ASN cc_start: 0.9540 (m-40) cc_final: 0.9047 (p0) REVERT: G 193 TYR cc_start: 0.9453 (m-80) cc_final: 0.9246 (m-80) REVERT: G 264 GLU cc_start: 0.9442 (pp20) cc_final: 0.9060 (pp20) REVERT: H 56 GLN cc_start: 0.8652 (mm-40) cc_final: 0.8429 (mm-40) REVERT: H 73 SER cc_start: 0.9573 (m) cc_final: 0.9201 (t) REVERT: H 139 GLU cc_start: 0.9604 (pt0) cc_final: 0.9247 (tp30) REVERT: H 143 LYS cc_start: 0.9542 (ptpp) cc_final: 0.8785 (pttm) REVERT: I 18 CYS cc_start: 0.9644 (m) cc_final: 0.9440 (p) REVERT: I 43 LYS cc_start: 0.9677 (mmmt) cc_final: 0.9444 (mmmt) REVERT: I 46 LYS cc_start: 0.8286 (mmtm) cc_final: 0.8024 (mmmt) REVERT: K 56 LEU cc_start: 0.9092 (tp) cc_final: 0.8890 (tp) REVERT: M 56 LEU cc_start: 0.9515 (tt) cc_final: 0.9280 (mt) REVERT: N 60 MET cc_start: 0.7893 (mmt) cc_final: 0.6984 (ptm) REVERT: O 60 MET cc_start: 0.8007 (mmt) cc_final: 0.7437 (mmt) REVERT: P 66 MET cc_start: 0.9031 (mtt) cc_final: 0.8804 (mmt) REVERT: Q 21 SER cc_start: 0.8383 (p) cc_final: 0.7672 (m) REVERT: Q 66 MET cc_start: 0.8897 (mtp) cc_final: 0.8592 (mtp) REVERT: Q 75 MET cc_start: 0.8674 (mmm) cc_final: 0.8420 (mmp) REVERT: R 25 ILE cc_start: 0.8579 (mt) cc_final: 0.8374 (mt) REVERT: R 60 MET cc_start: 0.7829 (ptt) cc_final: 0.7175 (ppp) REVERT: R 66 MET cc_start: 0.9051 (tpt) cc_final: 0.8733 (ppp) REVERT: S 94 ARG cc_start: 0.9335 (mmm-85) cc_final: 0.9121 (mmm-85) REVERT: a 58 MET cc_start: 0.9253 (mpp) cc_final: 0.8366 (mpp) REVERT: a 128 PHE cc_start: 0.8979 (m-80) cc_final: 0.8198 (m-80) REVERT: a 193 PHE cc_start: 0.8905 (t80) cc_final: 0.8632 (t80) REVERT: b 58 PHE cc_start: 0.7779 (m-80) cc_final: 0.7514 (m-80) REVERT: g 52 LEU cc_start: 0.4914 (OUTLIER) cc_final: 0.4585 (mm) REVERT: h 14 LYS cc_start: 0.9834 (mmmt) cc_final: 0.9544 (mmmm) REVERT: j 13 MET cc_start: 0.8641 (ttt) cc_final: 0.8330 (ptm) outliers start: 5 outliers final: 1 residues processed: 524 average time/residue: 0.2154 time to fit residues: 190.7654 Evaluate side-chains 407 residues out of total 4173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 405 time to evaluate : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain g residue 36 GLU Chi-restraints excluded: chain g residue 52 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 432 optimal weight: 2.9990 chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 3.9990 chunk 455 optimal weight: 8.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 7.9990 chunk 494 optimal weight: 30.0000 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 36 ASN ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 GLN F 223 ASN ** a 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 83 ASN ** b 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.052080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.034707 restraints weight = 285050.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.035803 restraints weight = 154926.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.036564 restraints weight = 100946.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.037080 restraints weight = 73259.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.037421 restraints weight = 57619.220| |-----------------------------------------------------------------------------| r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 39730 Z= 0.161 Angle : 0.632 10.467 53722 Z= 0.319 Chirality : 0.042 0.214 6270 Planarity : 0.004 0.050 6893 Dihedral : 4.821 67.396 5574 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.95 % Allowed : 19.77 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.12), residues: 5073 helix: 1.31 (0.10), residues: 2658 sheet: 0.49 (0.22), residues: 524 loop : -0.08 (0.15), residues: 1891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 408 TYR 0.027 0.001 TYR d 56 PHE 0.050 0.002 PHE P 63 TRP 0.008 0.001 TRP d 152 HIS 0.007 0.001 HIS b 145 Details of bonding type rmsd covalent geometry : bond 0.00338 (39730) covalent geometry : angle 0.63224 (53722) hydrogen bonds : bond 0.04210 ( 2221) hydrogen bonds : angle 5.14427 ( 6426) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10146 Ramachandran restraints generated. 5073 Oldfield, 0 Emsley, 5073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10146 Ramachandran restraints generated. 5073 Oldfield, 0 Emsley, 5073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 4173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 428 time to evaluate : 1.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 12 MET cc_start: 0.8462 (mmm) cc_final: 0.7735 (mtt) REVERT: C 52 MET cc_start: 0.9245 (ttp) cc_final: 0.8238 (tmm) REVERT: C 181 ASP cc_start: 0.9172 (m-30) cc_final: 0.8930 (m-30) REVERT: C 390 MET cc_start: 0.9507 (tpp) cc_final: 0.9270 (tpt) REVERT: C 436 MET cc_start: 0.8973 (ptm) cc_final: 0.8758 (ptm) REVERT: C 453 LEU cc_start: 0.9421 (mp) cc_final: 0.9216 (mt) REVERT: A 146 MET cc_start: 0.9175 (tmm) cc_final: 0.8582 (tmm) REVERT: A 460 LYS cc_start: 0.9781 (OUTLIER) cc_final: 0.9442 (ptpt) REVERT: B 52 MET cc_start: 0.8976 (tpt) cc_final: 0.8774 (tpt) REVERT: B 146 MET cc_start: 0.9116 (tmm) cc_final: 0.8541 (tmm) REVERT: B 312 MET cc_start: 0.8127 (tpp) cc_final: 0.7797 (tpp) REVERT: B 390 MET cc_start: 0.9637 (tpp) cc_final: 0.9330 (tpp) REVERT: B 394 LEU cc_start: 0.9536 (mt) cc_final: 0.8922 (mt) REVERT: B 428 LEU cc_start: 0.9569 (OUTLIER) cc_final: 0.9299 (mm) REVERT: F 358 MET cc_start: 0.9024 (tmm) cc_final: 0.8815 (tmm) REVERT: D 76 LEU cc_start: 0.9718 (OUTLIER) cc_final: 0.9328 (mm) REVERT: D 200 MET cc_start: 0.9351 (mmm) cc_final: 0.9088 (mmm) REVERT: D 294 GLU cc_start: 0.8714 (mt-10) cc_final: 0.8444 (mt-10) REVERT: D 345 TYR cc_start: 0.7282 (OUTLIER) cc_final: 0.6892 (t80) REVERT: D 358 MET cc_start: 0.9006 (mmp) cc_final: 0.8792 (mmp) REVERT: E 22 ASP cc_start: 0.8747 (t0) cc_final: 0.8490 (t0) REVERT: E 95 MET cc_start: 0.8426 (pmm) cc_final: 0.8010 (pmm) REVERT: E 126 MET cc_start: 0.8611 (ttm) cc_final: 0.8351 (ttm) REVERT: G 25 MET cc_start: 0.9336 (mmp) cc_final: 0.9070 (mmp) REVERT: G 163 ASN cc_start: 0.9557 (m-40) cc_final: 0.9142 (p0) REVERT: H 73 SER cc_start: 0.9552 (m) cc_final: 0.9266 (t) REVERT: H 136 GLU cc_start: 0.9435 (pp20) cc_final: 0.8981 (pp20) REVERT: H 139 GLU cc_start: 0.9569 (pt0) cc_final: 0.9306 (tp30) REVERT: I 18 CYS cc_start: 0.9670 (m) cc_final: 0.9409 (p) REVERT: I 43 LYS cc_start: 0.9628 (mmmt) cc_final: 0.9382 (mmmt) REVERT: I 46 LYS cc_start: 0.8271 (mmtm) cc_final: 0.8002 (mmmt) REVERT: K 29 PHE cc_start: 0.9454 (m-80) cc_final: 0.8781 (m-80) REVERT: L 56 LEU cc_start: 0.9491 (tt) cc_final: 0.9282 (pp) REVERT: M 75 MET cc_start: 0.7919 (mmm) cc_final: 0.7413 (mpp) REVERT: N 60 MET cc_start: 0.8069 (mmt) cc_final: 0.6988 (ttp) REVERT: P 60 MET cc_start: 0.6764 (tpt) cc_final: 0.6509 (tpt) REVERT: P 62 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.8907 (tp) REVERT: Q 21 SER cc_start: 0.8948 (p) cc_final: 0.8568 (m) REVERT: Q 60 MET cc_start: 0.7561 (tpp) cc_final: 0.7167 (tpp) REVERT: S 17 ARG cc_start: 0.9563 (OUTLIER) cc_final: 0.8718 (ttp-170) REVERT: S 94 ARG cc_start: 0.9373 (mmm-85) cc_final: 0.9160 (mmm-85) REVERT: a 58 MET cc_start: 0.9338 (mpp) cc_final: 0.8907 (mpp) REVERT: a 73 MET cc_start: 0.8498 (mtp) cc_final: 0.8006 (mtp) REVERT: a 193 PHE cc_start: 0.9052 (t80) cc_final: 0.8796 (t80) REVERT: b 58 PHE cc_start: 0.7837 (m-80) cc_final: 0.7618 (m-80) REVERT: g 36 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7879 (tt0) REVERT: h 14 LYS cc_start: 0.9838 (mmmt) cc_final: 0.9565 (mmmm) outliers start: 120 outliers final: 53 residues processed: 517 average time/residue: 0.2118 time to fit residues: 186.0778 Evaluate side-chains 454 residues out of total 4173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 394 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 312 MET Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 227 LYS Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain F residue 289 MET Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain F residue 435 LYS Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 345 TYR Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain G residue 4 LYS Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain H residue 124 ASP Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain L residue 4 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 54 PHE Chi-restraints excluded: chain M residue 63 PHE Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain O residue 32 LEU Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 72 LEU Chi-restraints excluded: chain P residue 28 VAL Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain P residue 62 LEU Chi-restraints excluded: chain Q residue 48 SER Chi-restraints excluded: chain Q residue 54 PHE Chi-restraints excluded: chain R residue 33 ILE Chi-restraints excluded: chain S residue 17 ARG Chi-restraints excluded: chain S residue 174 SER Chi-restraints excluded: chain a residue 78 PHE Chi-restraints excluded: chain b residue 140 TYR Chi-restraints excluded: chain d residue 105 THR Chi-restraints excluded: chain e residue 50 ARG Chi-restraints excluded: chain f residue 72 CYS Chi-restraints excluded: chain g residue 36 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 261 optimal weight: 8.9990 chunk 29 optimal weight: 0.0770 chunk 418 optimal weight: 2.9990 chunk 405 optimal weight: 0.0870 chunk 175 optimal weight: 3.9990 chunk 409 optimal weight: 8.9990 chunk 222 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 chunk 338 optimal weight: 20.0000 chunk 301 optimal weight: 2.9990 chunk 69 optimal weight: 0.1980 overall best weight: 1.2720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 36 ASN ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 GLN H 35 GLN S 180 GLN ** a 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.052706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.035194 restraints weight = 290066.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.036316 restraints weight = 157247.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.037074 restraints weight = 102139.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.037606 restraints weight = 74010.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.037980 restraints weight = 57961.494| |-----------------------------------------------------------------------------| r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 39730 Z= 0.121 Angle : 0.616 12.741 53722 Z= 0.305 Chirality : 0.042 0.256 6270 Planarity : 0.003 0.053 6893 Dihedral : 4.651 61.219 5572 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.65 % Allowed : 19.97 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.12), residues: 5073 helix: 1.39 (0.10), residues: 2654 sheet: 0.52 (0.22), residues: 523 loop : -0.03 (0.15), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 38 TYR 0.022 0.001 TYR j 17 PHE 0.047 0.001 PHE P 63 TRP 0.009 0.001 TRP a 68 HIS 0.004 0.001 HIS F 367 Details of bonding type rmsd covalent geometry : bond 0.00253 (39730) covalent geometry : angle 0.61557 (53722) hydrogen bonds : bond 0.03965 ( 2221) hydrogen bonds : angle 4.87639 ( 6426) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10146 Ramachandran restraints generated. 5073 Oldfield, 0 Emsley, 5073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10146 Ramachandran restraints generated. 5073 Oldfield, 0 Emsley, 5073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 4173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 429 time to evaluate : 1.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 12 MET cc_start: 0.8551 (mmm) cc_final: 0.8132 (mtt) REVERT: 8 20 LEU cc_start: 0.5604 (mp) cc_final: 0.5231 (mp) REVERT: C 52 MET cc_start: 0.9234 (ttp) cc_final: 0.8227 (tmm) REVERT: C 181 ASP cc_start: 0.9149 (m-30) cc_final: 0.8856 (m-30) REVERT: C 436 MET cc_start: 0.8913 (ptm) cc_final: 0.8634 (ptm) REVERT: C 453 LEU cc_start: 0.9382 (mp) cc_final: 0.9178 (mt) REVERT: A 146 MET cc_start: 0.9164 (tmm) cc_final: 0.8548 (tmm) REVERT: A 436 MET cc_start: 0.9071 (ppp) cc_final: 0.8427 (ppp) REVERT: A 460 LYS cc_start: 0.9776 (OUTLIER) cc_final: 0.9441 (ptpt) REVERT: B 52 MET cc_start: 0.8961 (tpt) cc_final: 0.8569 (tpp) REVERT: B 146 MET cc_start: 0.9126 (tmm) cc_final: 0.8494 (tmm) REVERT: B 201 CYS cc_start: 0.9143 (t) cc_final: 0.8504 (t) REVERT: B 312 MET cc_start: 0.8050 (tpp) cc_final: 0.7605 (tpp) REVERT: B 390 MET cc_start: 0.9642 (tpp) cc_final: 0.9321 (tpp) REVERT: B 394 LEU cc_start: 0.9577 (mt) cc_final: 0.9008 (mt) REVERT: F 358 MET cc_start: 0.9068 (tmm) cc_final: 0.8834 (tmm) REVERT: D 76 LEU cc_start: 0.9718 (OUTLIER) cc_final: 0.9318 (mm) REVERT: D 126 MET cc_start: 0.9232 (mmp) cc_final: 0.8802 (mmp) REVERT: D 200 MET cc_start: 0.9339 (mmm) cc_final: 0.9070 (mmm) REVERT: D 345 TYR cc_start: 0.7280 (OUTLIER) cc_final: 0.6747 (t80) REVERT: E 95 MET cc_start: 0.8340 (pmm) cc_final: 0.7833 (pmm) REVERT: E 126 MET cc_start: 0.8549 (ttm) cc_final: 0.8325 (ttm) REVERT: E 292 MET cc_start: 0.9578 (tmm) cc_final: 0.9313 (tmm) REVERT: E 358 MET cc_start: 0.9488 (mmm) cc_final: 0.8731 (tpp) REVERT: G 25 MET cc_start: 0.9358 (mmp) cc_final: 0.9098 (mmp) REVERT: G 163 ASN cc_start: 0.9570 (m-40) cc_final: 0.9117 (p0) REVERT: G 242 MET cc_start: 0.9004 (mpp) cc_final: 0.8789 (mpp) REVERT: H 73 SER cc_start: 0.9548 (m) cc_final: 0.9269 (t) REVERT: H 135 ILE cc_start: 0.9746 (pt) cc_final: 0.9462 (tp) REVERT: I 14 TYR cc_start: 0.9505 (t80) cc_final: 0.9177 (t80) REVERT: I 43 LYS cc_start: 0.9658 (mmmt) cc_final: 0.9428 (mmmt) REVERT: I 46 LYS cc_start: 0.8245 (mmtm) cc_final: 0.7971 (mmmt) REVERT: M 75 MET cc_start: 0.7988 (mmm) cc_final: 0.7438 (mpp) REVERT: O 60 MET cc_start: 0.8063 (mmt) cc_final: 0.7704 (tpp) REVERT: P 62 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.8952 (tp) REVERT: P 66 MET cc_start: 0.8809 (mmm) cc_final: 0.8191 (mmm) REVERT: Q 21 SER cc_start: 0.8925 (p) cc_final: 0.8414 (m) REVERT: Q 60 MET cc_start: 0.7864 (tpp) cc_final: 0.7296 (tpp) REVERT: R 60 MET cc_start: 0.8038 (ptt) cc_final: 0.7463 (tmm) REVERT: a 11 THR cc_start: 0.4818 (OUTLIER) cc_final: 0.4552 (m) REVERT: a 57 MET cc_start: 0.9454 (mtt) cc_final: 0.9234 (mmm) REVERT: a 58 MET cc_start: 0.9356 (mpp) cc_final: 0.8668 (mpp) REVERT: a 71 MET cc_start: 0.8663 (ppp) cc_final: 0.8427 (ppp) REVERT: a 73 MET cc_start: 0.8440 (mtp) cc_final: 0.8117 (mtp) REVERT: a 131 GLN cc_start: 0.8733 (mm-40) cc_final: 0.8262 (tp-100) REVERT: a 193 PHE cc_start: 0.9029 (t80) cc_final: 0.8800 (t80) REVERT: b 58 PHE cc_start: 0.7829 (m-80) cc_final: 0.7589 (m-80) REVERT: d 21 ARG cc_start: 0.1306 (OUTLIER) cc_final: -0.0227 (mtm-85) REVERT: g 36 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7717 (tt0) REVERT: h 14 LYS cc_start: 0.9830 (mmmt) cc_final: 0.9561 (mmmm) outliers start: 108 outliers final: 60 residues processed: 510 average time/residue: 0.2117 time to fit residues: 184.1706 Evaluate side-chains 468 residues out of total 4173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 401 time to evaluate : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 227 LYS Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 209 LYS Chi-restraints excluded: chain F residue 289 MET Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain F residue 435 LYS Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 345 TYR Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 427 HIS Chi-restraints excluded: chain G residue 4 LYS Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain H residue 124 ASP Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain L residue 4 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 54 PHE Chi-restraints excluded: chain M residue 32 LEU Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain O residue 32 LEU Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 72 LEU Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 28 VAL Chi-restraints excluded: chain P residue 32 LEU Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain P residue 62 LEU Chi-restraints excluded: chain Q residue 54 PHE Chi-restraints excluded: chain R residue 63 PHE Chi-restraints excluded: chain S residue 180 GLN Chi-restraints excluded: chain a residue 11 THR Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 150 PHE Chi-restraints excluded: chain b residue 140 TYR Chi-restraints excluded: chain d residue 21 ARG Chi-restraints excluded: chain e residue 50 ARG Chi-restraints excluded: chain f residue 72 CYS Chi-restraints excluded: chain g residue 36 GLU Chi-restraints excluded: chain j residue 9 VAL Chi-restraints excluded: chain j residue 21 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 302 optimal weight: 0.4980 chunk 22 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 112 optimal weight: 9.9990 chunk 273 optimal weight: 0.0010 chunk 165 optimal weight: 6.9990 chunk 221 optimal weight: 6.9990 chunk 314 optimal weight: 0.7980 chunk 398 optimal weight: 0.1980 chunk 85 optimal weight: 5.9990 chunk 366 optimal weight: 7.9990 overall best weight: 0.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 36 ASN C 70 ASN ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 190 ASN B 349 GLN Q 39 ASN S 180 GLN ** a 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.053126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.035714 restraints weight = 289112.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.036806 restraints weight = 156594.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.037558 restraints weight = 101348.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.038087 restraints weight = 73355.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.038459 restraints weight = 57441.752| |-----------------------------------------------------------------------------| r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 39730 Z= 0.110 Angle : 0.615 13.170 53722 Z= 0.301 Chirality : 0.042 0.280 6270 Planarity : 0.003 0.054 6893 Dihedral : 4.547 55.496 5572 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.85 % Allowed : 20.63 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.12), residues: 5073 helix: 1.40 (0.10), residues: 2667 sheet: 0.59 (0.22), residues: 521 loop : -0.03 (0.15), residues: 1885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG b 141 TYR 0.024 0.001 TYR d 56 PHE 0.049 0.001 PHE P 63 TRP 0.009 0.001 TRP a 68 HIS 0.006 0.001 HIS b 145 Details of bonding type rmsd covalent geometry : bond 0.00230 (39730) covalent geometry : angle 0.61550 (53722) hydrogen bonds : bond 0.03792 ( 2221) hydrogen bonds : angle 4.74245 ( 6426) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10146 Ramachandran restraints generated. 5073 Oldfield, 0 Emsley, 5073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10146 Ramachandran restraints generated. 5073 Oldfield, 0 Emsley, 5073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 4173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 437 time to evaluate : 1.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 12 MET cc_start: 0.8504 (mmm) cc_final: 0.7832 (mtp) REVERT: C 52 MET cc_start: 0.9197 (ttp) cc_final: 0.8140 (tmm) REVERT: C 181 ASP cc_start: 0.9182 (m-30) cc_final: 0.8844 (m-30) REVERT: C 436 MET cc_start: 0.8836 (ptm) cc_final: 0.8468 (ptm) REVERT: C 453 LEU cc_start: 0.9324 (mp) cc_final: 0.9122 (mt) REVERT: A 46 ASN cc_start: 0.9367 (OUTLIER) cc_final: 0.8814 (t0) REVERT: A 146 MET cc_start: 0.9201 (tmm) cc_final: 0.8561 (tmm) REVERT: A 172 GLN cc_start: 0.5210 (OUTLIER) cc_final: 0.4637 (mm-40) REVERT: A 312 MET cc_start: 0.9039 (mmm) cc_final: 0.8783 (mmp) REVERT: A 428 LEU cc_start: 0.9793 (OUTLIER) cc_final: 0.9576 (mm) REVERT: A 436 MET cc_start: 0.9078 (ppp) cc_final: 0.8742 (ppp) REVERT: B 52 MET cc_start: 0.8940 (tpt) cc_final: 0.8365 (tpp) REVERT: B 64 LEU cc_start: 0.9521 (OUTLIER) cc_final: 0.9118 (mm) REVERT: B 146 MET cc_start: 0.9108 (tmm) cc_final: 0.8427 (tmm) REVERT: B 201 CYS cc_start: 0.8911 (t) cc_final: 0.8286 (t) REVERT: B 312 MET cc_start: 0.8090 (tpp) cc_final: 0.7585 (tpp) REVERT: B 390 MET cc_start: 0.9663 (tpp) cc_final: 0.9336 (tpp) REVERT: B 394 LEU cc_start: 0.9578 (mt) cc_final: 0.9010 (mt) REVERT: F 127 SER cc_start: 0.9249 (OUTLIER) cc_final: 0.8999 (m) REVERT: F 352 ASP cc_start: 0.9391 (m-30) cc_final: 0.8923 (p0) REVERT: F 358 MET cc_start: 0.9094 (tmm) cc_final: 0.8840 (tmm) REVERT: F 399 GLU cc_start: 0.9707 (OUTLIER) cc_final: 0.9476 (pm20) REVERT: D 76 LEU cc_start: 0.9714 (OUTLIER) cc_final: 0.9323 (mm) REVERT: D 126 MET cc_start: 0.9203 (mmp) cc_final: 0.8719 (mmp) REVERT: D 200 MET cc_start: 0.9371 (mmm) cc_final: 0.9150 (mmm) REVERT: D 345 TYR cc_start: 0.7243 (OUTLIER) cc_final: 0.6675 (t80) REVERT: D 358 MET cc_start: 0.8906 (mmp) cc_final: 0.8456 (mmp) REVERT: D 393 MET cc_start: 0.9155 (ppp) cc_final: 0.8808 (ppp) REVERT: E 63 MET cc_start: 0.8200 (mmm) cc_final: 0.7620 (mmm) REVERT: E 95 MET cc_start: 0.8273 (pmm) cc_final: 0.7700 (pmm) REVERT: E 126 MET cc_start: 0.8599 (ttm) cc_final: 0.8370 (ttm) REVERT: E 292 MET cc_start: 0.9528 (tmm) cc_final: 0.9289 (tmm) REVERT: G 25 MET cc_start: 0.9383 (mmp) cc_final: 0.9153 (mmp) REVERT: G 163 ASN cc_start: 0.9583 (m-40) cc_final: 0.9107 (p0) REVERT: H 73 SER cc_start: 0.9541 (m) cc_final: 0.9267 (t) REVERT: H 135 ILE cc_start: 0.9747 (pt) cc_final: 0.9482 (tp) REVERT: I 14 TYR cc_start: 0.9628 (t80) cc_final: 0.9120 (t80) REVERT: L 29 PHE cc_start: 0.9408 (m-10) cc_final: 0.8954 (m-10) REVERT: M 75 MET cc_start: 0.8083 (mmm) cc_final: 0.7512 (mpp) REVERT: O 60 MET cc_start: 0.8111 (mmt) cc_final: 0.7756 (tpp) REVERT: O 75 MET cc_start: 0.8300 (mmt) cc_final: 0.7815 (mmp) REVERT: P 62 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.8853 (tp) REVERT: P 66 MET cc_start: 0.8992 (mmm) cc_final: 0.8509 (mmm) REVERT: Q 21 SER cc_start: 0.8905 (p) cc_final: 0.8513 (m) REVERT: Q 60 MET cc_start: 0.7929 (tpp) cc_final: 0.7355 (tpp) REVERT: R 69 PHE cc_start: 0.9130 (p90) cc_final: 0.8913 (p90) REVERT: S 118 CYS cc_start: 0.8697 (m) cc_final: 0.8485 (t) REVERT: a 11 THR cc_start: 0.4864 (OUTLIER) cc_final: 0.4471 (m) REVERT: a 14 ILE cc_start: 0.7748 (OUTLIER) cc_final: 0.7473 (mp) REVERT: a 57 MET cc_start: 0.9436 (mtt) cc_final: 0.9194 (mmm) REVERT: a 58 MET cc_start: 0.9386 (mpp) cc_final: 0.8729 (mpp) REVERT: a 71 MET cc_start: 0.8695 (ppp) cc_final: 0.8469 (ppp) REVERT: a 73 MET cc_start: 0.8401 (mtp) cc_final: 0.8036 (mtp) REVERT: a 131 GLN cc_start: 0.8741 (mm-40) cc_final: 0.8274 (tp-100) REVERT: a 150 PHE cc_start: 0.9720 (OUTLIER) cc_final: 0.9370 (p90) REVERT: b 58 PHE cc_start: 0.7811 (m-80) cc_final: 0.7602 (m-80) REVERT: d 21 ARG cc_start: 0.1612 (OUTLIER) cc_final: -0.0117 (mtm-85) REVERT: f 69 LEU cc_start: 0.9536 (OUTLIER) cc_final: 0.9207 (pp) REVERT: g 36 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7743 (tt0) REVERT: h 43 LEU cc_start: 0.9272 (mt) cc_final: 0.9008 (mt) REVERT: h 49 MET cc_start: 0.9021 (ppp) cc_final: 0.8312 (ppp) outliers start: 116 outliers final: 61 residues processed: 526 average time/residue: 0.2117 time to fit residues: 190.5530 Evaluate side-chains 481 residues out of total 4173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 405 time to evaluate : 1.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 302 HIS Chi-restraints excluded: chain C residue 312 MET Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 172 GLN Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 209 LYS Chi-restraints excluded: chain F residue 289 MET Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 386 ASP Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain F residue 399 GLU Chi-restraints excluded: chain F residue 435 LYS Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 345 TYR Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 427 HIS Chi-restraints excluded: chain G residue 4 LYS Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain H residue 124 ASP Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain L residue 4 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 54 PHE Chi-restraints excluded: chain M residue 32 LEU Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain O residue 31 SER Chi-restraints excluded: chain O residue 32 LEU Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 72 LEU Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 28 VAL Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain P residue 62 LEU Chi-restraints excluded: chain Q residue 54 PHE Chi-restraints excluded: chain R residue 63 PHE Chi-restraints excluded: chain S residue 174 SER Chi-restraints excluded: chain S residue 180 GLN Chi-restraints excluded: chain a residue 11 THR Chi-restraints excluded: chain a residue 14 ILE Chi-restraints excluded: chain a residue 33 THR Chi-restraints excluded: chain a residue 38 VAL Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 150 PHE Chi-restraints excluded: chain b residue 140 TYR Chi-restraints excluded: chain d residue 21 ARG Chi-restraints excluded: chain e residue 50 ARG Chi-restraints excluded: chain f residue 69 LEU Chi-restraints excluded: chain g residue 31 TYR Chi-restraints excluded: chain g residue 36 GLU Chi-restraints excluded: chain j residue 9 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 89 optimal weight: 0.9990 chunk 136 optimal weight: 0.0370 chunk 171 optimal weight: 7.9990 chunk 201 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 chunk 238 optimal weight: 0.0980 chunk 156 optimal weight: 0.6980 chunk 276 optimal weight: 8.9990 chunk 56 optimal weight: 0.8980 chunk 275 optimal weight: 2.9990 chunk 324 optimal weight: 6.9990 overall best weight: 0.5460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 341 ASN S 180 GLN ** a 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 145 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.053597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.036057 restraints weight = 286269.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.037205 restraints weight = 154569.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.037976 restraints weight = 100157.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.038511 restraints weight = 72360.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.038870 restraints weight = 56647.829| |-----------------------------------------------------------------------------| r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 39730 Z= 0.108 Angle : 0.642 16.036 53722 Z= 0.310 Chirality : 0.042 0.282 6270 Planarity : 0.003 0.053 6893 Dihedral : 4.456 55.143 5572 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.55 % Allowed : 21.37 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.12), residues: 5073 helix: 1.41 (0.10), residues: 2674 sheet: 0.71 (0.23), residues: 501 loop : -0.01 (0.15), residues: 1898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 37 TYR 0.038 0.001 TYR h 50 PHE 0.028 0.001 PHE N 69 TRP 0.008 0.001 TRP a 68 HIS 0.003 0.000 HIS b 145 Details of bonding type rmsd covalent geometry : bond 0.00224 (39730) covalent geometry : angle 0.64248 (53722) hydrogen bonds : bond 0.03728 ( 2221) hydrogen bonds : angle 4.66339 ( 6426) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10146 Ramachandran restraints generated. 5073 Oldfield, 0 Emsley, 5073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10146 Ramachandran restraints generated. 5073 Oldfield, 0 Emsley, 5073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 4173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 429 time to evaluate : 1.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 12 MET cc_start: 0.8454 (mmm) cc_final: 0.7734 (mtp) REVERT: C 52 MET cc_start: 0.9215 (ttp) cc_final: 0.8440 (tmm) REVERT: C 181 ASP cc_start: 0.9163 (m-30) cc_final: 0.8824 (m-30) REVERT: C 436 MET cc_start: 0.8851 (ptm) cc_final: 0.8631 (ptm) REVERT: C 453 LEU cc_start: 0.9305 (mp) cc_final: 0.9092 (mt) REVERT: A 146 MET cc_start: 0.9184 (tmm) cc_final: 0.8547 (tmm) REVERT: A 172 GLN cc_start: 0.5567 (OUTLIER) cc_final: 0.5231 (mm-40) REVERT: A 312 MET cc_start: 0.9024 (mmm) cc_final: 0.8762 (mmp) REVERT: A 428 LEU cc_start: 0.9781 (OUTLIER) cc_final: 0.9572 (mm) REVERT: A 436 MET cc_start: 0.9108 (ppp) cc_final: 0.8827 (ppp) REVERT: B 52 MET cc_start: 0.8930 (tpt) cc_final: 0.8531 (tpp) REVERT: B 64 LEU cc_start: 0.9520 (OUTLIER) cc_final: 0.9112 (mm) REVERT: B 146 MET cc_start: 0.9083 (tmm) cc_final: 0.8499 (tmm) REVERT: B 201 CYS cc_start: 0.8901 (t) cc_final: 0.8276 (t) REVERT: B 312 MET cc_start: 0.8094 (tpp) cc_final: 0.7559 (tpp) REVERT: B 390 MET cc_start: 0.9634 (tpp) cc_final: 0.9315 (tpp) REVERT: B 394 LEU cc_start: 0.9591 (mt) cc_final: 0.9029 (mt) REVERT: B 426 GLU cc_start: 0.9059 (mt-10) cc_final: 0.8399 (pt0) REVERT: F 127 SER cc_start: 0.9226 (OUTLIER) cc_final: 0.8983 (m) REVERT: F 167 MET cc_start: 0.9638 (mmm) cc_final: 0.9269 (mmm) REVERT: F 352 ASP cc_start: 0.9342 (m-30) cc_final: 0.8925 (p0) REVERT: F 358 MET cc_start: 0.9103 (tmm) cc_final: 0.8834 (tmm) REVERT: F 399 GLU cc_start: 0.9710 (OUTLIER) cc_final: 0.9468 (pm20) REVERT: D 76 LEU cc_start: 0.9712 (OUTLIER) cc_final: 0.9319 (mm) REVERT: D 126 MET cc_start: 0.9190 (mmp) cc_final: 0.8635 (mmp) REVERT: D 200 MET cc_start: 0.9302 (mmm) cc_final: 0.9085 (mmm) REVERT: D 254 PHE cc_start: 0.9341 (m-10) cc_final: 0.9044 (m-10) REVERT: D 345 TYR cc_start: 0.7266 (OUTLIER) cc_final: 0.6723 (t80) REVERT: D 358 MET cc_start: 0.8988 (mmp) cc_final: 0.8502 (mmp) REVERT: D 412 ARG cc_start: 0.9445 (mpt180) cc_final: 0.9099 (mmt-90) REVERT: D 459 MET cc_start: 0.9393 (tpp) cc_final: 0.9127 (mmm) REVERT: E 95 MET cc_start: 0.8180 (pmm) cc_final: 0.7575 (pmm) REVERT: E 126 MET cc_start: 0.8525 (ttm) cc_final: 0.8303 (ttm) REVERT: G 163 ASN cc_start: 0.9571 (m-40) cc_final: 0.9126 (p0) REVERT: G 264 GLU cc_start: 0.9303 (pp20) cc_final: 0.8974 (pp20) REVERT: H 73 SER cc_start: 0.9549 (m) cc_final: 0.9267 (t) REVERT: H 135 ILE cc_start: 0.9747 (pt) cc_final: 0.9473 (tp) REVERT: I 14 TYR cc_start: 0.9614 (t80) cc_final: 0.9121 (t80) REVERT: J 39 LYS cc_start: 0.9661 (ttpp) cc_final: 0.9448 (ptmt) REVERT: K 29 PHE cc_start: 0.8864 (t80) cc_final: 0.8308 (t80) REVERT: L 29 PHE cc_start: 0.9425 (m-10) cc_final: 0.8962 (m-10) REVERT: L 54 PHE cc_start: 0.9281 (OUTLIER) cc_final: 0.8935 (t80) REVERT: M 75 MET cc_start: 0.8125 (mmm) cc_final: 0.7597 (mpp) REVERT: O 75 MET cc_start: 0.8256 (mmt) cc_final: 0.7710 (mmm) REVERT: P 29 PHE cc_start: 0.9472 (m-80) cc_final: 0.9250 (m-80) REVERT: P 62 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.8841 (tt) REVERT: P 66 MET cc_start: 0.8959 (mmm) cc_final: 0.8499 (mmm) REVERT: Q 21 SER cc_start: 0.8895 (p) cc_final: 0.8412 (m) REVERT: R 60 MET cc_start: 0.7917 (ptt) cc_final: 0.7209 (tmm) REVERT: a 11 THR cc_start: 0.4859 (OUTLIER) cc_final: 0.4465 (m) REVERT: a 14 ILE cc_start: 0.7870 (OUTLIER) cc_final: 0.7619 (mp) REVERT: a 57 MET cc_start: 0.9418 (mtt) cc_final: 0.9159 (mmm) REVERT: a 58 MET cc_start: 0.9428 (mpp) cc_final: 0.8783 (mpp) REVERT: a 71 MET cc_start: 0.8741 (ppp) cc_final: 0.8486 (ppp) REVERT: a 73 MET cc_start: 0.8417 (mtp) cc_final: 0.8037 (mtp) REVERT: a 85 LEU cc_start: 0.9093 (mp) cc_final: 0.8853 (tt) REVERT: a 131 GLN cc_start: 0.8760 (mm-40) cc_final: 0.8247 (tp-100) REVERT: a 150 PHE cc_start: 0.9718 (m-80) cc_final: 0.9402 (p90) REVERT: d 21 ARG cc_start: 0.2061 (OUTLIER) cc_final: 0.0320 (mtm-85) REVERT: g 36 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7659 (tt0) REVERT: h 43 LEU cc_start: 0.9256 (mt) cc_final: 0.8991 (mt) outliers start: 104 outliers final: 60 residues processed: 503 average time/residue: 0.2075 time to fit residues: 179.9092 Evaluate side-chains 479 residues out of total 4173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 406 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 302 HIS Chi-restraints excluded: chain C residue 312 MET Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 172 GLN Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 209 LYS Chi-restraints excluded: chain F residue 289 MET Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain F residue 399 GLU Chi-restraints excluded: chain F residue 435 LYS Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 345 TYR Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain H residue 124 ASP Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain L residue 4 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 54 PHE Chi-restraints excluded: chain M residue 32 LEU Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain O residue 31 SER Chi-restraints excluded: chain O residue 32 LEU Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 72 LEU Chi-restraints excluded: chain P residue 28 VAL Chi-restraints excluded: chain P residue 32 LEU Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain P residue 62 LEU Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain S residue 174 SER Chi-restraints excluded: chain a residue 11 THR Chi-restraints excluded: chain a residue 14 ILE Chi-restraints excluded: chain a residue 25 LEU Chi-restraints excluded: chain a residue 33 THR Chi-restraints excluded: chain a residue 38 VAL Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain b residue 140 TYR Chi-restraints excluded: chain d residue 21 ARG Chi-restraints excluded: chain d residue 33 TRP Chi-restraints excluded: chain e residue 50 ARG Chi-restraints excluded: chain g residue 36 GLU Chi-restraints excluded: chain j residue 9 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 53 optimal weight: 6.9990 chunk 413 optimal weight: 5.9990 chunk 52 optimal weight: 9.9990 chunk 463 optimal weight: 20.0000 chunk 117 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 chunk 340 optimal weight: 5.9990 chunk 146 optimal weight: 4.9990 chunk 446 optimal weight: 5.9990 chunk 300 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 GLN B 341 ASN ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.050028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.033078 restraints weight = 298373.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.034104 restraints weight = 164056.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.034815 restraints weight = 107790.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.035297 restraints weight = 78923.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.035654 restraints weight = 62542.713| |-----------------------------------------------------------------------------| r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 39730 Z= 0.338 Angle : 0.793 13.811 53722 Z= 0.407 Chirality : 0.045 0.412 6270 Planarity : 0.005 0.063 6893 Dihedral : 5.005 54.665 5572 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 4.20 % Allowed : 20.92 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.12), residues: 5073 helix: 0.96 (0.10), residues: 2677 sheet: 0.19 (0.22), residues: 530 loop : -0.21 (0.15), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 171 TYR 0.045 0.002 TYR h 50 PHE 0.055 0.002 PHE P 63 TRP 0.010 0.002 TRP d 152 HIS 0.009 0.002 HIS A 302 Details of bonding type rmsd covalent geometry : bond 0.00687 (39730) covalent geometry : angle 0.79318 (53722) hydrogen bonds : bond 0.04393 ( 2221) hydrogen bonds : angle 5.25496 ( 6426) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10146 Ramachandran restraints generated. 5073 Oldfield, 0 Emsley, 5073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10146 Ramachandran restraints generated. 5073 Oldfield, 0 Emsley, 5073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 4173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 384 time to evaluate : 1.542 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: 8 12 MET cc_start: 0.8762 (mmm) cc_final: 0.7539 (mtp) REVERT: C 52 MET cc_start: 0.9255 (ttp) cc_final: 0.8443 (tmm) REVERT: C 181 ASP cc_start: 0.9226 (m-30) cc_final: 0.8957 (m-30) REVERT: C 390 MET cc_start: 0.9578 (tpt) cc_final: 0.9296 (mtt) REVERT: C 436 MET cc_start: 0.8620 (ptm) cc_final: 0.8406 (ptm) REVERT: A 46 ASN cc_start: 0.9099 (OUTLIER) cc_final: 0.8722 (t0) REVERT: A 146 MET cc_start: 0.9175 (tmm) cc_final: 0.8583 (tmm) REVERT: A 172 GLN cc_start: 0.5929 (OUTLIER) cc_final: 0.5272 (mm-40) REVERT: B 52 MET cc_start: 0.9152 (tpt) cc_final: 0.8689 (tpp) REVERT: B 64 LEU cc_start: 0.9626 (OUTLIER) cc_final: 0.9377 (mm) REVERT: B 146 MET cc_start: 0.9117 (tmm) cc_final: 0.8598 (tmm) REVERT: B 312 MET cc_start: 0.8325 (tpp) cc_final: 0.7777 (tpp) REVERT: B 373 ARG cc_start: 0.6403 (mmt180) cc_final: 0.6110 (mmt180) REVERT: B 390 MET cc_start: 0.9618 (tpp) cc_final: 0.9311 (tpp) REVERT: B 394 LEU cc_start: 0.9525 (mt) cc_final: 0.8965 (mt) REVERT: F 393 MET cc_start: 0.9550 (mmm) cc_final: 0.9347 (mmm) REVERT: D 76 LEU cc_start: 0.9716 (OUTLIER) cc_final: 0.9257 (mm) REVERT: D 126 MET cc_start: 0.9232 (mmp) cc_final: 0.8888 (mmm) REVERT: D 200 MET cc_start: 0.9409 (mmm) cc_final: 0.9160 (mmm) REVERT: D 294 GLU cc_start: 0.8678 (mt-10) cc_final: 0.8123 (mt-10) REVERT: D 345 TYR cc_start: 0.6991 (OUTLIER) cc_final: 0.5877 (t80) REVERT: D 358 MET cc_start: 0.9104 (mmp) cc_final: 0.8683 (mmp) REVERT: E 56 SER cc_start: 0.9753 (OUTLIER) cc_final: 0.9518 (p) REVERT: E 95 MET cc_start: 0.9344 (pmm) cc_final: 0.8627 (pmm) REVERT: G 72 SER cc_start: 0.8507 (OUTLIER) cc_final: 0.8251 (p) REVERT: G 163 ASN cc_start: 0.9559 (m-40) cc_final: 0.9220 (p0) REVERT: H 135 ILE cc_start: 0.9759 (pt) cc_final: 0.9479 (tp) REVERT: I 14 TYR cc_start: 0.9702 (t80) cc_final: 0.9136 (t80) REVERT: J 39 LYS cc_start: 0.9651 (ttpp) cc_final: 0.9426 (ptmt) REVERT: M 75 MET cc_start: 0.8285 (mmm) cc_final: 0.7880 (mpp) REVERT: P 62 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.8880 (tt) REVERT: P 66 MET cc_start: 0.9046 (mmm) cc_final: 0.8337 (mmm) REVERT: Q 21 SER cc_start: 0.9058 (p) cc_final: 0.8595 (m) REVERT: S 72 MET cc_start: 0.9252 (tmm) cc_final: 0.8971 (tmm) REVERT: S 109 MET cc_start: 0.9715 (tpp) cc_final: 0.9452 (tpp) REVERT: a 14 ILE cc_start: 0.7756 (OUTLIER) cc_final: 0.7528 (mp) REVERT: a 57 MET cc_start: 0.9517 (mtt) cc_final: 0.9221 (mmm) REVERT: a 58 MET cc_start: 0.9513 (mpp) cc_final: 0.9064 (mpp) REVERT: a 71 MET cc_start: 0.8622 (ppp) cc_final: 0.8363 (ppp) REVERT: a 73 MET cc_start: 0.8354 (mtp) cc_final: 0.8007 (mtp) REVERT: a 104 MET cc_start: 0.8314 (mtp) cc_final: 0.7718 (mmt) REVERT: d 21 ARG cc_start: 0.2342 (OUTLIER) cc_final: 0.0530 (mtm-85) REVERT: d 145 ASP cc_start: 0.8534 (OUTLIER) cc_final: 0.8276 (t70) REVERT: h 10 LEU cc_start: 0.9662 (OUTLIER) cc_final: 0.9081 (mm) REVERT: h 14 LYS cc_start: 0.9832 (mmmt) cc_final: 0.9561 (mmtt) REVERT: h 52 LYS cc_start: 0.6509 (OUTLIER) cc_final: 0.6093 (mmmt) outliers start: 171 outliers final: 112 residues processed: 510 average time/residue: 0.2133 time to fit residues: 185.5813 Evaluate side-chains 505 residues out of total 4173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 380 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 20 LEU Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 312 MET Chi-restraints excluded: chain C residue 429 LYS Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 172 GLN Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 227 LYS Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 209 LYS Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 257 ASN Chi-restraints excluded: chain F residue 289 MET Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 386 ASP Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain F residue 435 LYS Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 296 ILE Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 345 TYR Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 400 ASP Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 304 ILE Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 427 HIS Chi-restraints excluded: chain G residue 4 LYS Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 72 SER Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain H residue 124 ASP Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain J residue 31 GLU Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 54 PHE Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 54 PHE Chi-restraints excluded: chain M residue 32 LEU Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 63 PHE Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain O residue 31 SER Chi-restraints excluded: chain O residue 32 LEU Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 69 PHE Chi-restraints excluded: chain P residue 28 VAL Chi-restraints excluded: chain P residue 32 LEU Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain P residue 62 LEU Chi-restraints excluded: chain Q residue 54 PHE Chi-restraints excluded: chain S residue 174 SER Chi-restraints excluded: chain a residue 14 ILE Chi-restraints excluded: chain a residue 25 LEU Chi-restraints excluded: chain a residue 33 THR Chi-restraints excluded: chain a residue 38 VAL Chi-restraints excluded: chain a residue 48 TRP Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 78 PHE Chi-restraints excluded: chain a residue 150 PHE Chi-restraints excluded: chain a residue 196 LEU Chi-restraints excluded: chain a residue 217 LEU Chi-restraints excluded: chain b residue 44 TYR Chi-restraints excluded: chain b residue 140 TYR Chi-restraints excluded: chain d residue 21 ARG Chi-restraints excluded: chain d residue 33 TRP Chi-restraints excluded: chain d residue 73 PHE Chi-restraints excluded: chain d residue 145 ASP Chi-restraints excluded: chain e residue 50 ARG Chi-restraints excluded: chain f residue 28 PHE Chi-restraints excluded: chain g residue 31 TYR Chi-restraints excluded: chain g residue 36 GLU Chi-restraints excluded: chain h residue 10 LEU Chi-restraints excluded: chain h residue 50 TYR Chi-restraints excluded: chain h residue 52 LYS Chi-restraints excluded: chain j residue 6 ILE Chi-restraints excluded: chain j residue 9 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 172 optimal weight: 0.8980 chunk 166 optimal weight: 1.9990 chunk 486 optimal weight: 5.9990 chunk 239 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 130 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 52 optimal weight: 6.9990 chunk 397 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.052228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.034891 restraints weight = 291601.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.036022 restraints weight = 155871.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.036774 restraints weight = 100495.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.037300 restraints weight = 72605.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.037669 restraints weight = 56787.743| |-----------------------------------------------------------------------------| r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 39730 Z= 0.125 Angle : 0.679 14.212 53722 Z= 0.330 Chirality : 0.043 0.286 6270 Planarity : 0.003 0.059 6893 Dihedral : 4.673 51.605 5572 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.65 % Allowed : 22.74 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.12), residues: 5073 helix: 1.28 (0.10), residues: 2678 sheet: 0.34 (0.22), residues: 541 loop : -0.08 (0.15), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG e 55 TYR 0.041 0.001 TYR h 50 PHE 0.053 0.002 PHE P 63 TRP 0.008 0.001 TRP d 152 HIS 0.003 0.001 HIS A 263 Details of bonding type rmsd covalent geometry : bond 0.00267 (39730) covalent geometry : angle 0.67902 (53722) hydrogen bonds : bond 0.03954 ( 2221) hydrogen bonds : angle 4.82721 ( 6426) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10146 Ramachandran restraints generated. 5073 Oldfield, 0 Emsley, 5073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10146 Ramachandran restraints generated. 5073 Oldfield, 0 Emsley, 5073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 4173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 417 time to evaluate : 1.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 12 MET cc_start: 0.8389 (mmm) cc_final: 0.7687 (mtp) REVERT: 8 16 MET cc_start: 0.6627 (ppp) cc_final: 0.6427 (tmm) REVERT: C 52 MET cc_start: 0.9220 (ttp) cc_final: 0.8341 (tmm) REVERT: C 181 ASP cc_start: 0.9204 (m-30) cc_final: 0.8803 (m-30) REVERT: C 383 MET cc_start: 0.9513 (mmm) cc_final: 0.9209 (mmm) REVERT: C 436 MET cc_start: 0.8654 (ptm) cc_final: 0.8365 (ptm) REVERT: A 46 ASN cc_start: 0.9372 (OUTLIER) cc_final: 0.8855 (t0) REVERT: A 146 MET cc_start: 0.9135 (tmm) cc_final: 0.8534 (tmm) REVERT: A 172 GLN cc_start: 0.5875 (OUTLIER) cc_final: 0.5293 (mm-40) REVERT: A 220 LEU cc_start: 0.9657 (tp) cc_final: 0.9208 (pp) REVERT: A 436 MET cc_start: 0.8972 (ppp) cc_final: 0.8400 (ppp) REVERT: B 52 MET cc_start: 0.9125 (tpt) cc_final: 0.8634 (tpp) REVERT: B 64 LEU cc_start: 0.9571 (OUTLIER) cc_final: 0.9146 (mm) REVERT: B 146 MET cc_start: 0.9133 (tmm) cc_final: 0.8528 (tmm) REVERT: B 312 MET cc_start: 0.8218 (tpp) cc_final: 0.7651 (tpp) REVERT: B 390 MET cc_start: 0.9631 (tpp) cc_final: 0.9298 (tpp) REVERT: B 394 LEU cc_start: 0.9581 (mt) cc_final: 0.9024 (mt) REVERT: F 167 MET cc_start: 0.9610 (mmm) cc_final: 0.9392 (mmm) REVERT: F 393 MET cc_start: 0.9487 (mmm) cc_final: 0.9262 (mmm) REVERT: F 459 MET cc_start: 0.9500 (tpp) cc_final: 0.9208 (mmm) REVERT: D 76 LEU cc_start: 0.9716 (OUTLIER) cc_final: 0.9275 (mm) REVERT: D 126 MET cc_start: 0.9196 (mmp) cc_final: 0.8620 (mmp) REVERT: D 200 MET cc_start: 0.9395 (mmm) cc_final: 0.9129 (mmm) REVERT: D 257 ASN cc_start: 0.9070 (t0) cc_final: 0.8482 (p0) REVERT: D 345 TYR cc_start: 0.6880 (OUTLIER) cc_final: 0.6043 (t80) REVERT: D 358 MET cc_start: 0.9108 (mmp) cc_final: 0.8610 (mmp) REVERT: D 393 MET cc_start: 0.9135 (ppp) cc_final: 0.8878 (ppp) REVERT: D 459 MET cc_start: 0.9395 (tpp) cc_final: 0.9001 (mmm) REVERT: E 63 MET cc_start: 0.8130 (mmm) cc_final: 0.7330 (mmm) REVERT: E 95 MET cc_start: 0.9268 (pmm) cc_final: 0.8648 (pmm) REVERT: G 25 MET cc_start: 0.9341 (mmp) cc_final: 0.9096 (mmp) REVERT: G 72 SER cc_start: 0.8434 (OUTLIER) cc_final: 0.8214 (p) REVERT: G 163 ASN cc_start: 0.9508 (m-40) cc_final: 0.9185 (p0) REVERT: H 135 ILE cc_start: 0.9750 (pt) cc_final: 0.9472 (tp) REVERT: I 14 TYR cc_start: 0.9671 (t80) cc_final: 0.9089 (t80) REVERT: J 17 ASP cc_start: 0.9319 (m-30) cc_final: 0.8950 (p0) REVERT: J 39 LYS cc_start: 0.9646 (ttpp) cc_final: 0.9415 (ptmt) REVERT: K 29 PHE cc_start: 0.8872 (t80) cc_final: 0.8246 (t80) REVERT: L 54 PHE cc_start: 0.9292 (OUTLIER) cc_final: 0.8934 (t80) REVERT: O 75 MET cc_start: 0.8349 (mmt) cc_final: 0.7873 (mmm) REVERT: P 62 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.8899 (tp) REVERT: P 66 MET cc_start: 0.8915 (mmm) cc_final: 0.8490 (mmm) REVERT: S 72 MET cc_start: 0.9232 (tmm) cc_final: 0.8943 (tmm) REVERT: S 118 CYS cc_start: 0.8719 (m) cc_final: 0.8446 (t) REVERT: a 11 THR cc_start: 0.4541 (OUTLIER) cc_final: 0.4140 (m) REVERT: a 57 MET cc_start: 0.9433 (mtt) cc_final: 0.9165 (mmm) REVERT: a 58 MET cc_start: 0.9423 (mpp) cc_final: 0.8915 (mpp) REVERT: a 71 MET cc_start: 0.8594 (ppp) cc_final: 0.8349 (ppp) REVERT: a 73 MET cc_start: 0.8421 (mtp) cc_final: 0.8062 (mtp) REVERT: a 104 MET cc_start: 0.8234 (mtp) cc_final: 0.7713 (mmt) REVERT: a 150 PHE cc_start: 0.9778 (OUTLIER) cc_final: 0.9440 (p90) REVERT: d 21 ARG cc_start: 0.2310 (OUTLIER) cc_final: 0.1167 (mtm-85) REVERT: g 36 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7943 (tt0) REVERT: h 43 LEU cc_start: 0.9279 (mt) cc_final: 0.8978 (mt) REVERT: h 52 LYS cc_start: 0.6712 (OUTLIER) cc_final: 0.6315 (mmmt) outliers start: 108 outliers final: 76 residues processed: 486 average time/residue: 0.2048 time to fit residues: 171.5007 Evaluate side-chains 484 residues out of total 4173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 395 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 20 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 312 MET Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 172 GLN Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 209 LYS Chi-restraints excluded: chain F residue 261 PHE Chi-restraints excluded: chain F residue 289 MET Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 435 LYS Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 345 TYR Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 427 HIS Chi-restraints excluded: chain G residue 4 LYS Chi-restraints excluded: chain G residue 72 SER Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 246 LEU Chi-restraints excluded: chain G residue 264 GLU Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain H residue 124 ASP Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain L residue 4 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 33 ILE Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 54 PHE Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain M residue 32 LEU Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain O residue 31 SER Chi-restraints excluded: chain O residue 32 LEU Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 72 LEU Chi-restraints excluded: chain P residue 28 VAL Chi-restraints excluded: chain P residue 32 LEU Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain P residue 62 LEU Chi-restraints excluded: chain Q residue 54 PHE Chi-restraints excluded: chain S residue 174 SER Chi-restraints excluded: chain a residue 11 THR Chi-restraints excluded: chain a residue 25 LEU Chi-restraints excluded: chain a residue 38 VAL Chi-restraints excluded: chain a residue 78 PHE Chi-restraints excluded: chain a residue 150 PHE Chi-restraints excluded: chain b residue 140 TYR Chi-restraints excluded: chain d residue 21 ARG Chi-restraints excluded: chain d residue 33 TRP Chi-restraints excluded: chain e residue 50 ARG Chi-restraints excluded: chain f residue 28 PHE Chi-restraints excluded: chain g residue 31 TYR Chi-restraints excluded: chain g residue 36 GLU Chi-restraints excluded: chain h residue 50 TYR Chi-restraints excluded: chain h residue 52 LYS Chi-restraints excluded: chain j residue 9 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 391 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 chunk 450 optimal weight: 3.9990 chunk 372 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 111 optimal weight: 0.0770 chunk 88 optimal weight: 2.9990 chunk 232 optimal weight: 1.9990 chunk 365 optimal weight: 10.0000 chunk 482 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 overall best weight: 1.5544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.052288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.034895 restraints weight = 292620.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.036032 restraints weight = 157655.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.036786 restraints weight = 101966.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.037282 restraints weight = 73749.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.037672 restraints weight = 58092.299| |-----------------------------------------------------------------------------| r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 39730 Z= 0.133 Angle : 0.681 13.924 53722 Z= 0.330 Chirality : 0.043 0.297 6270 Planarity : 0.003 0.057 6893 Dihedral : 4.584 51.199 5572 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.38 % Allowed : 23.21 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.12), residues: 5073 helix: 1.28 (0.10), residues: 2679 sheet: 0.35 (0.22), residues: 548 loop : -0.04 (0.15), residues: 1846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 37 TYR 0.038 0.001 TYR h 50 PHE 0.057 0.002 PHE P 63 TRP 0.008 0.001 TRP d 152 HIS 0.003 0.001 HIS f 87 Details of bonding type rmsd covalent geometry : bond 0.00284 (39730) covalent geometry : angle 0.68061 (53722) hydrogen bonds : bond 0.03864 ( 2221) hydrogen bonds : angle 4.79599 ( 6426) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10146 Ramachandran restraints generated. 5073 Oldfield, 0 Emsley, 5073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10146 Ramachandran restraints generated. 5073 Oldfield, 0 Emsley, 5073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 4173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 400 time to evaluate : 1.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 12 MET cc_start: 0.8402 (mmm) cc_final: 0.7730 (mtt) REVERT: C 52 MET cc_start: 0.9174 (ttp) cc_final: 0.8200 (tmm) REVERT: C 383 MET cc_start: 0.9556 (mmm) cc_final: 0.9322 (mmm) REVERT: C 436 MET cc_start: 0.8660 (ptm) cc_final: 0.8388 (ptm) REVERT: A 46 ASN cc_start: 0.9354 (OUTLIER) cc_final: 0.8851 (t0) REVERT: A 146 MET cc_start: 0.9154 (tmm) cc_final: 0.8563 (tmm) REVERT: A 172 GLN cc_start: 0.6042 (OUTLIER) cc_final: 0.5381 (mm-40) REVERT: A 436 MET cc_start: 0.8917 (ppp) cc_final: 0.8686 (ppp) REVERT: B 52 MET cc_start: 0.9123 (tpt) cc_final: 0.8614 (tpp) REVERT: B 64 LEU cc_start: 0.9555 (OUTLIER) cc_final: 0.9134 (mm) REVERT: B 146 MET cc_start: 0.9012 (tmm) cc_final: 0.8468 (tmm) REVERT: B 312 MET cc_start: 0.8316 (tpp) cc_final: 0.7812 (tpp) REVERT: B 390 MET cc_start: 0.9636 (tpp) cc_final: 0.9294 (tpp) REVERT: B 394 LEU cc_start: 0.9578 (mt) cc_final: 0.9024 (mt) REVERT: F 459 MET cc_start: 0.9520 (tpp) cc_final: 0.9276 (mmm) REVERT: D 76 LEU cc_start: 0.9694 (OUTLIER) cc_final: 0.9227 (mm) REVERT: D 126 MET cc_start: 0.9181 (mmp) cc_final: 0.8585 (mmp) REVERT: D 200 MET cc_start: 0.9389 (mmm) cc_final: 0.9114 (mmm) REVERT: D 294 GLU cc_start: 0.9052 (tt0) cc_final: 0.8313 (mt-10) REVERT: D 345 TYR cc_start: 0.6830 (OUTLIER) cc_final: 0.5925 (t80) REVERT: D 358 MET cc_start: 0.9131 (mmp) cc_final: 0.8618 (mmp) REVERT: D 393 MET cc_start: 0.9141 (ppp) cc_final: 0.8878 (ppp) REVERT: D 459 MET cc_start: 0.9404 (tpp) cc_final: 0.8863 (mmm) REVERT: E 95 MET cc_start: 0.9247 (pmm) cc_final: 0.8604 (pmm) REVERT: E 222 MET cc_start: 0.9035 (mpp) cc_final: 0.8789 (mpp) REVERT: G 25 MET cc_start: 0.9324 (mmp) cc_final: 0.9087 (mmp) REVERT: G 72 SER cc_start: 0.8450 (OUTLIER) cc_final: 0.8224 (p) REVERT: G 163 ASN cc_start: 0.9509 (m-40) cc_final: 0.9186 (p0) REVERT: G 229 MET cc_start: 0.8806 (ttm) cc_final: 0.8491 (tpp) REVERT: H 135 ILE cc_start: 0.9735 (pt) cc_final: 0.9439 (tp) REVERT: I 14 TYR cc_start: 0.9679 (t80) cc_final: 0.9108 (t80) REVERT: J 39 LYS cc_start: 0.9649 (ttpp) cc_final: 0.9431 (ptmt) REVERT: K 29 PHE cc_start: 0.8971 (t80) cc_final: 0.8366 (t80) REVERT: L 54 PHE cc_start: 0.9377 (OUTLIER) cc_final: 0.9034 (t80) REVERT: O 75 MET cc_start: 0.8340 (mmt) cc_final: 0.7867 (mmm) REVERT: P 62 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.8877 (tp) REVERT: P 66 MET cc_start: 0.8926 (mmm) cc_final: 0.8481 (mmm) REVERT: R 60 MET cc_start: 0.7184 (ptm) cc_final: 0.6694 (ppp) REVERT: S 72 MET cc_start: 0.9246 (tmm) cc_final: 0.8950 (tmm) REVERT: S 118 CYS cc_start: 0.8728 (m) cc_final: 0.8445 (t) REVERT: a 11 THR cc_start: 0.4558 (OUTLIER) cc_final: 0.4119 (m) REVERT: a 57 MET cc_start: 0.9439 (mtt) cc_final: 0.9200 (mmm) REVERT: a 58 MET cc_start: 0.9441 (mpp) cc_final: 0.8787 (mpp) REVERT: a 71 MET cc_start: 0.8599 (ppp) cc_final: 0.8362 (ppp) REVERT: a 73 MET cc_start: 0.8447 (mtp) cc_final: 0.8100 (mtp) REVERT: a 104 MET cc_start: 0.8342 (mtp) cc_final: 0.7841 (mmt) REVERT: a 150 PHE cc_start: 0.9785 (OUTLIER) cc_final: 0.9456 (p90) REVERT: d 21 ARG cc_start: 0.2271 (OUTLIER) cc_final: 0.1125 (mtm-85) REVERT: g 21 TYR cc_start: 0.3714 (OUTLIER) cc_final: 0.3458 (p90) REVERT: h 43 LEU cc_start: 0.9236 (mt) cc_final: 0.8930 (mt) REVERT: h 52 LYS cc_start: 0.6715 (OUTLIER) cc_final: 0.6190 (mmmt) outliers start: 97 outliers final: 77 residues processed: 465 average time/residue: 0.2094 time to fit residues: 168.6876 Evaluate side-chains 483 residues out of total 4173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 393 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 20 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 312 MET Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 172 GLN Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 209 LYS Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 289 MET Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 386 ASP Chi-restraints excluded: chain F residue 435 LYS Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 345 TYR Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 427 HIS Chi-restraints excluded: chain G residue 4 LYS Chi-restraints excluded: chain G residue 72 SER Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain H residue 124 ASP Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 33 ILE Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 54 PHE Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain M residue 32 LEU Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain O residue 31 SER Chi-restraints excluded: chain O residue 32 LEU Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 72 LEU Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain P residue 62 LEU Chi-restraints excluded: chain Q residue 54 PHE Chi-restraints excluded: chain S residue 174 SER Chi-restraints excluded: chain a residue 11 THR Chi-restraints excluded: chain a residue 25 LEU Chi-restraints excluded: chain a residue 38 VAL Chi-restraints excluded: chain a residue 150 PHE Chi-restraints excluded: chain b residue 140 TYR Chi-restraints excluded: chain d residue 21 ARG Chi-restraints excluded: chain d residue 33 TRP Chi-restraints excluded: chain e residue 50 ARG Chi-restraints excluded: chain f residue 28 PHE Chi-restraints excluded: chain g residue 21 TYR Chi-restraints excluded: chain g residue 31 TYR Chi-restraints excluded: chain g residue 36 GLU Chi-restraints excluded: chain g residue 98 ILE Chi-restraints excluded: chain h residue 52 LYS Chi-restraints excluded: chain j residue 9 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 322 optimal weight: 5.9990 chunk 94 optimal weight: 0.9990 chunk 350 optimal weight: 0.7980 chunk 490 optimal weight: 9.9990 chunk 84 optimal weight: 0.9990 chunk 433 optimal weight: 20.0000 chunk 5 optimal weight: 8.9990 chunk 335 optimal weight: 0.8980 chunk 324 optimal weight: 9.9990 chunk 134 optimal weight: 0.4980 chunk 347 optimal weight: 10.0000 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 GLN B 341 ASN ** a 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.053013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.035487 restraints weight = 288346.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.036619 restraints weight = 155960.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.037386 restraints weight = 101010.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.037922 restraints weight = 73014.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.038259 restraints weight = 57153.319| |-----------------------------------------------------------------------------| r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 39730 Z= 0.113 Angle : 0.694 14.503 53722 Z= 0.331 Chirality : 0.043 0.308 6270 Planarity : 0.003 0.056 6893 Dihedral : 4.453 50.260 5572 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.26 % Allowed : 23.45 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.12), residues: 5073 helix: 1.33 (0.10), residues: 2683 sheet: 0.60 (0.23), residues: 519 loop : -0.04 (0.15), residues: 1871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 37 TYR 0.035 0.001 TYR h 50 PHE 0.056 0.001 PHE P 63 TRP 0.011 0.001 TRP j 10 HIS 0.003 0.000 HIS A 263 Details of bonding type rmsd covalent geometry : bond 0.00239 (39730) covalent geometry : angle 0.69360 (53722) hydrogen bonds : bond 0.03723 ( 2221) hydrogen bonds : angle 4.69227 ( 6426) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10146 Ramachandran restraints generated. 5073 Oldfield, 0 Emsley, 5073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10146 Ramachandran restraints generated. 5073 Oldfield, 0 Emsley, 5073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 4173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 416 time to evaluate : 1.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 12 MET cc_start: 0.8497 (mmm) cc_final: 0.8113 (mtt) REVERT: C 52 MET cc_start: 0.9072 (ttp) cc_final: 0.7989 (tmm) REVERT: C 383 MET cc_start: 0.9522 (mmm) cc_final: 0.9265 (mmm) REVERT: C 436 MET cc_start: 0.8786 (ptm) cc_final: 0.8490 (ptm) REVERT: A 146 MET cc_start: 0.9161 (tmm) cc_final: 0.8583 (tmm) REVERT: A 220 LEU cc_start: 0.9620 (tp) cc_final: 0.9134 (pp) REVERT: B 52 MET cc_start: 0.9148 (tpt) cc_final: 0.8617 (tpp) REVERT: B 64 LEU cc_start: 0.9573 (OUTLIER) cc_final: 0.9150 (mm) REVERT: B 146 MET cc_start: 0.8881 (tmm) cc_final: 0.8395 (tmm) REVERT: B 312 MET cc_start: 0.8265 (tpp) cc_final: 0.7727 (tpp) REVERT: B 390 MET cc_start: 0.9639 (tpp) cc_final: 0.9296 (tpp) REVERT: B 394 LEU cc_start: 0.9587 (mt) cc_final: 0.9050 (mt) REVERT: F 352 ASP cc_start: 0.9388 (m-30) cc_final: 0.8941 (p0) REVERT: F 459 MET cc_start: 0.9491 (tpp) cc_final: 0.9288 (mmm) REVERT: D 76 LEU cc_start: 0.9704 (OUTLIER) cc_final: 0.9296 (mm) REVERT: D 126 MET cc_start: 0.9129 (mmp) cc_final: 0.8559 (mmp) REVERT: D 182 VAL cc_start: 0.9798 (t) cc_final: 0.9583 (m) REVERT: D 200 MET cc_start: 0.9366 (mmm) cc_final: 0.9132 (mmm) REVERT: D 257 ASN cc_start: 0.9115 (t0) cc_final: 0.8388 (p0) REVERT: D 294 GLU cc_start: 0.9013 (tt0) cc_final: 0.8197 (mt-10) REVERT: D 345 TYR cc_start: 0.6887 (OUTLIER) cc_final: 0.5999 (t80) REVERT: D 358 MET cc_start: 0.9129 (mmp) cc_final: 0.8617 (mmp) REVERT: D 412 ARG cc_start: 0.9476 (mpt180) cc_final: 0.9064 (mmt-90) REVERT: D 459 MET cc_start: 0.9392 (tpp) cc_final: 0.8893 (mmm) REVERT: E 63 MET cc_start: 0.7945 (mmm) cc_final: 0.7031 (mmm) REVERT: E 222 MET cc_start: 0.8942 (mpp) cc_final: 0.8640 (mpp) REVERT: G 25 MET cc_start: 0.9306 (mmp) cc_final: 0.9060 (mmp) REVERT: G 72 SER cc_start: 0.8424 (OUTLIER) cc_final: 0.8217 (p) REVERT: G 163 ASN cc_start: 0.9512 (m-40) cc_final: 0.9164 (p0) REVERT: G 264 GLU cc_start: 0.9465 (OUTLIER) cc_final: 0.9027 (pp20) REVERT: H 134 ARG cc_start: 0.9597 (ttm110) cc_final: 0.9269 (ptp-110) REVERT: H 135 ILE cc_start: 0.9722 (pt) cc_final: 0.9442 (tp) REVERT: I 14 TYR cc_start: 0.9659 (t80) cc_final: 0.9148 (t80) REVERT: J 17 ASP cc_start: 0.9279 (m-30) cc_final: 0.8934 (p0) REVERT: J 39 LYS cc_start: 0.9636 (ttpp) cc_final: 0.9400 (ptmt) REVERT: K 29 PHE cc_start: 0.8999 (t80) cc_final: 0.8382 (t80) REVERT: L 54 PHE cc_start: 0.9381 (OUTLIER) cc_final: 0.9068 (t80) REVERT: M 75 MET cc_start: 0.8202 (mmm) cc_final: 0.7932 (mmm) REVERT: O 75 MET cc_start: 0.8411 (mmt) cc_final: 0.7970 (mmm) REVERT: P 62 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.8828 (tp) REVERT: P 66 MET cc_start: 0.8899 (mmm) cc_final: 0.8472 (mmm) REVERT: R 60 MET cc_start: 0.7612 (ptm) cc_final: 0.7240 (ppp) REVERT: S 72 MET cc_start: 0.9251 (tmm) cc_final: 0.8946 (tmm) REVERT: S 118 CYS cc_start: 0.8653 (m) cc_final: 0.8424 (t) REVERT: a 11 THR cc_start: 0.4478 (OUTLIER) cc_final: 0.4032 (m) REVERT: a 57 MET cc_start: 0.9410 (mtt) cc_final: 0.9170 (mmm) REVERT: a 58 MET cc_start: 0.9431 (mpp) cc_final: 0.8752 (mpp) REVERT: a 71 MET cc_start: 0.8624 (ppp) cc_final: 0.8369 (ppp) REVERT: a 73 MET cc_start: 0.8495 (mtp) cc_final: 0.8113 (mtp) REVERT: a 104 MET cc_start: 0.8372 (mtp) cc_final: 0.8137 (mtp) REVERT: a 150 PHE cc_start: 0.9790 (OUTLIER) cc_final: 0.9562 (p90) REVERT: d 21 ARG cc_start: 0.2227 (OUTLIER) cc_final: 0.0296 (mtm-85) REVERT: g 21 TYR cc_start: 0.3721 (OUTLIER) cc_final: 0.3442 (p90) REVERT: h 43 LEU cc_start: 0.9235 (mt) cc_final: 0.8915 (mt) REVERT: h 52 LYS cc_start: 0.6786 (OUTLIER) cc_final: 0.6260 (mmmt) outliers start: 92 outliers final: 72 residues processed: 478 average time/residue: 0.2130 time to fit residues: 174.4475 Evaluate side-chains 487 residues out of total 4173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 403 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 312 MET Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 209 LYS Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 289 MET Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 435 LYS Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 345 TYR Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 427 HIS Chi-restraints excluded: chain G residue 4 LYS Chi-restraints excluded: chain G residue 72 SER Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 246 LEU Chi-restraints excluded: chain G residue 264 GLU Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 124 ASP Chi-restraints excluded: chain H residue 145 LEU Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain L residue 4 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 54 PHE Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain M residue 32 LEU Chi-restraints excluded: chain M residue 33 ILE Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain O residue 31 SER Chi-restraints excluded: chain O residue 32 LEU Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 72 LEU Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain P residue 62 LEU Chi-restraints excluded: chain S residue 174 SER Chi-restraints excluded: chain a residue 11 THR Chi-restraints excluded: chain a residue 25 LEU Chi-restraints excluded: chain a residue 38 VAL Chi-restraints excluded: chain a residue 150 PHE Chi-restraints excluded: chain b residue 140 TYR Chi-restraints excluded: chain d residue 21 ARG Chi-restraints excluded: chain d residue 33 TRP Chi-restraints excluded: chain e residue 50 ARG Chi-restraints excluded: chain f residue 28 PHE Chi-restraints excluded: chain g residue 21 TYR Chi-restraints excluded: chain g residue 31 TYR Chi-restraints excluded: chain g residue 36 GLU Chi-restraints excluded: chain h residue 52 LYS Chi-restraints excluded: chain j residue 9 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 9 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 chunk 363 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 34 optimal weight: 0.1980 chunk 163 optimal weight: 8.9990 chunk 51 optimal weight: 3.9990 chunk 184 optimal weight: 0.5980 chunk 42 optimal weight: 0.0770 chunk 334 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.053529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.035961 restraints weight = 286590.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.037121 restraints weight = 155035.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.037891 restraints weight = 100217.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.038406 restraints weight = 72375.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.038799 restraints weight = 56834.170| |-----------------------------------------------------------------------------| r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 39730 Z= 0.114 Angle : 0.723 15.539 53722 Z= 0.341 Chirality : 0.043 0.294 6270 Planarity : 0.003 0.055 6893 Dihedral : 4.375 49.675 5572 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.04 % Allowed : 23.82 % Favored : 74.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.12), residues: 5073 helix: 1.30 (0.10), residues: 2683 sheet: 0.69 (0.23), residues: 521 loop : -0.03 (0.15), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 37 TYR 0.033 0.001 TYR h 50 PHE 0.057 0.002 PHE P 63 TRP 0.010 0.001 TRP a 48 HIS 0.003 0.000 HIS A 263 Details of bonding type rmsd covalent geometry : bond 0.00240 (39730) covalent geometry : angle 0.72304 (53722) hydrogen bonds : bond 0.03680 ( 2221) hydrogen bonds : angle 4.64871 ( 6426) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10146 Ramachandran restraints generated. 5073 Oldfield, 0 Emsley, 5073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10146 Ramachandran restraints generated. 5073 Oldfield, 0 Emsley, 5073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 4173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 426 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: 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 12 MET cc_start: 0.8416 (mmm) cc_final: 0.7635 (mtt) REVERT: C 52 MET cc_start: 0.9072 (ttp) cc_final: 0.8005 (tmm) REVERT: C 383 MET cc_start: 0.9494 (mmm) cc_final: 0.9225 (mmm) REVERT: C 436 MET cc_start: 0.8780 (ptm) cc_final: 0.8449 (ptm) REVERT: A 146 MET cc_start: 0.9172 (tmm) cc_final: 0.8600 (tmm) REVERT: A 220 LEU cc_start: 0.9631 (tp) cc_final: 0.9214 (pp) REVERT: B 52 MET cc_start: 0.9130 (tpt) cc_final: 0.8608 (tpp) REVERT: B 64 LEU cc_start: 0.9570 (OUTLIER) cc_final: 0.9149 (mm) REVERT: B 146 MET cc_start: 0.8789 (tmm) cc_final: 0.8349 (tmm) REVERT: B 312 MET cc_start: 0.8223 (tpp) cc_final: 0.7734 (tpp) REVERT: B 390 MET cc_start: 0.9622 (tpp) cc_final: 0.9295 (tpp) REVERT: B 394 LEU cc_start: 0.9580 (mt) cc_final: 0.9042 (mt) REVERT: F 352 ASP cc_start: 0.9316 (m-30) cc_final: 0.8929 (p0) REVERT: D 76 LEU cc_start: 0.9695 (OUTLIER) cc_final: 0.9295 (mm) REVERT: D 126 MET cc_start: 0.9095 (mmp) cc_final: 0.8489 (mmp) REVERT: D 182 VAL cc_start: 0.9791 (t) cc_final: 0.9567 (m) REVERT: D 257 ASN cc_start: 0.9076 (t0) cc_final: 0.8492 (p0) REVERT: D 294 GLU cc_start: 0.8986 (tt0) cc_final: 0.8174 (mt-10) REVERT: D 345 TYR cc_start: 0.6907 (OUTLIER) cc_final: 0.6062 (t80) REVERT: D 358 MET cc_start: 0.9127 (mmp) cc_final: 0.8591 (mmp) REVERT: D 412 ARG cc_start: 0.9469 (mpt180) cc_final: 0.9051 (mmt-90) REVERT: D 459 MET cc_start: 0.9375 (tpp) cc_final: 0.8904 (mmm) REVERT: E 63 MET cc_start: 0.8044 (mmm) cc_final: 0.7101 (mmm) REVERT: E 222 MET cc_start: 0.8909 (mpp) cc_final: 0.8614 (mpp) REVERT: G 25 MET cc_start: 0.9271 (mmp) cc_final: 0.9001 (mmp) REVERT: G 163 ASN cc_start: 0.9556 (m-40) cc_final: 0.9145 (p0) REVERT: G 264 GLU cc_start: 0.9392 (OUTLIER) cc_final: 0.8972 (pp20) REVERT: H 134 ARG cc_start: 0.9610 (ttm110) cc_final: 0.9285 (ptp-110) REVERT: H 135 ILE cc_start: 0.9708 (pt) cc_final: 0.9421 (tp) REVERT: I 14 TYR cc_start: 0.9650 (t80) cc_final: 0.9150 (t80) REVERT: J 17 ASP cc_start: 0.9267 (m-30) cc_final: 0.8921 (p0) REVERT: J 39 LYS cc_start: 0.9639 (ttpp) cc_final: 0.9432 (ptmt) REVERT: K 29 PHE cc_start: 0.8972 (t80) cc_final: 0.8360 (t80) REVERT: L 54 PHE cc_start: 0.9376 (OUTLIER) cc_final: 0.9054 (t80) REVERT: M 75 MET cc_start: 0.8020 (mmm) cc_final: 0.7753 (mmm) REVERT: O 47 PHE cc_start: 0.8868 (m-80) cc_final: 0.8621 (m-80) REVERT: O 75 MET cc_start: 0.8052 (mmt) cc_final: 0.7575 (mmm) REVERT: P 62 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.8759 (tp) REVERT: P 66 MET cc_start: 0.8897 (mmm) cc_final: 0.8558 (mmt) REVERT: R 60 MET cc_start: 0.7659 (ptm) cc_final: 0.7316 (ppp) REVERT: S 72 MET cc_start: 0.9251 (tmm) cc_final: 0.8939 (tmm) REVERT: S 118 CYS cc_start: 0.8892 (m) cc_final: 0.8585 (t) REVERT: a 11 THR cc_start: 0.4429 (OUTLIER) cc_final: 0.3977 (m) REVERT: a 71 MET cc_start: 0.8586 (ppp) cc_final: 0.8360 (ppp) REVERT: a 73 MET cc_start: 0.8551 (mtp) cc_final: 0.8185 (mtp) REVERT: a 104 MET cc_start: 0.8289 (mtp) cc_final: 0.7673 (mmt) REVERT: a 150 PHE cc_start: 0.9783 (m-80) cc_final: 0.9471 (p90) REVERT: a 196 LEU cc_start: 0.8790 (tt) cc_final: 0.8546 (pp) REVERT: a 208 MET cc_start: 0.9389 (tpt) cc_final: 0.9170 (mmm) REVERT: d 21 ARG cc_start: 0.2166 (OUTLIER) cc_final: 0.0239 (mtm-85) REVERT: g 21 TYR cc_start: 0.3639 (OUTLIER) cc_final: 0.3301 (p90) REVERT: h 43 LEU cc_start: 0.9275 (mt) cc_final: 0.8975 (mt) REVERT: h 52 LYS cc_start: 0.6825 (OUTLIER) cc_final: 0.6358 (mmmt) outliers start: 83 outliers final: 61 residues processed: 485 average time/residue: 0.2145 time to fit residues: 177.4656 Evaluate side-chains 475 residues out of total 4173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 404 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 312 MET Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 209 LYS Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 289 MET Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 435 LYS Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 345 TYR Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 427 HIS Chi-restraints excluded: chain G residue 264 GLU Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain H residue 124 ASP Chi-restraints excluded: chain H residue 145 LEU Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain L residue 4 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 54 PHE Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain M residue 32 LEU Chi-restraints excluded: chain M residue 33 ILE Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain O residue 31 SER Chi-restraints excluded: chain O residue 32 LEU Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 72 LEU Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain P residue 62 LEU Chi-restraints excluded: chain S residue 174 SER Chi-restraints excluded: chain a residue 11 THR Chi-restraints excluded: chain a residue 25 LEU Chi-restraints excluded: chain a residue 38 VAL Chi-restraints excluded: chain b residue 140 TYR Chi-restraints excluded: chain d residue 21 ARG Chi-restraints excluded: chain d residue 33 TRP Chi-restraints excluded: chain g residue 21 TYR Chi-restraints excluded: chain g residue 36 GLU Chi-restraints excluded: chain h residue 52 LYS Chi-restraints excluded: chain j residue 9 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 195 optimal weight: 0.0770 chunk 431 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 chunk 355 optimal weight: 4.9990 chunk 498 optimal weight: 20.0000 chunk 301 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 278 optimal weight: 0.0770 chunk 414 optimal weight: 20.0000 chunk 32 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.9698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.053324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.035795 restraints weight = 289384.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.036943 restraints weight = 156747.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.037698 restraints weight = 101455.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.038250 restraints weight = 73292.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.038628 restraints weight = 57262.641| |-----------------------------------------------------------------------------| r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 39730 Z= 0.117 Angle : 0.730 15.894 53722 Z= 0.344 Chirality : 0.043 0.285 6270 Planarity : 0.003 0.057 6893 Dihedral : 4.335 48.891 5572 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.09 % Allowed : 23.87 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.12), residues: 5073 helix: 1.29 (0.10), residues: 2693 sheet: 0.68 (0.22), residues: 534 loop : -0.01 (0.15), residues: 1846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 37 TYR 0.031 0.001 TYR h 50 PHE 0.058 0.002 PHE P 63 TRP 0.008 0.001 TRP a 48 HIS 0.003 0.001 HIS A 263 Details of bonding type rmsd covalent geometry : bond 0.00252 (39730) covalent geometry : angle 0.73044 (53722) hydrogen bonds : bond 0.03672 ( 2221) hydrogen bonds : angle 4.64442 ( 6426) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7712.36 seconds wall clock time: 133 minutes 43.35 seconds (8023.35 seconds total)