Starting phenix.real_space_refine on Thu Sep 26 23:58:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vq7_21318/09_2024/6vq7_21318.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vq7_21318/09_2024/6vq7_21318.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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vq7_21318/09_2024/6vq7_21318.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vq7_21318/09_2024/6vq7_21318.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vq7_21318/09_2024/6vq7_21318.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vq7_21318/09_2024/6vq7_21318.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.006 sd= 0.067 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 2 5.49 5 Mg 1 5.21 5 S 335 5.16 5 C 39740 2.51 5 N 10666 2.21 5 O 11581 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 298 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 62325 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 4651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4651 Classifications: {'peptide': 600} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 569} Chain: "B" Number of atoms: 4651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4651 Classifications: {'peptide': 600} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 569} Chain: "C" Number of atoms: 4651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4651 Classifications: {'peptide': 600} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 569} Chain: "D" Number of atoms: 3595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3595 Classifications: {'peptide': 459} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 431} Chain breaks: 1 Chain: "E" Number of atoms: 3595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3595 Classifications: {'peptide': 459} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 431} Chain breaks: 1 Chain: "F" Number of atoms: 3595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3595 Classifications: {'peptide': 459} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 431} Chain breaks: 1 Chain: "G" Number of atoms: 1790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 1790 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 325} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 350} Chain breaks: 1 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 1192 Unresolved non-hydrogen angles: 1522 Unresolved non-hydrogen dihedrals: 998 Unresolved non-hydrogen chiralities: 105 Planarities with less than four sites: {'GLN:plan1': 16, 'ARG:plan': 14, 'TYR:plan': 15, 'ASN:plan1': 22, 'TRP:plan': 6, 'HIS:plan': 6, 'PHE:plan': 14, 'GLU:plan': 25, 'ASP:plan': 24} Unresolved non-hydrogen planarities: 645 Chain: "H" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1716 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 210} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "I" Number of atoms: 1607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1607 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 5, 'TRANS': 219} Unresolved non-hydrogen bonds: 218 Unresolved non-hydrogen angles: 268 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 13, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 132 Chain: "J" Number of atoms: 1607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1607 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 5, 'TRANS': 219} Unresolved non-hydrogen bonds: 218 Unresolved non-hydrogen angles: 268 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 13, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 132 Chain: "K" Number of atoms: 1607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1607 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 5, 'TRANS': 219} Unresolved non-hydrogen bonds: 218 Unresolved non-hydrogen angles: 268 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 13, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 132 Chain: "L" Number of atoms: 866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 866 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 105} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "M" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 714 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 2, 'TRANS': 111} Unresolved non-hydrogen bonds: 214 Unresolved non-hydrogen angles: 258 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 13, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 147 Chain: "N" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 714 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 2, 'TRANS': 111} Unresolved non-hydrogen bonds: 214 Unresolved non-hydrogen angles: 258 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 13, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 147 Chain: "O" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 714 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 2, 'TRANS': 111} Unresolved non-hydrogen bonds: 214 Unresolved non-hydrogen angles: 258 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 13, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 147 Chain: "Q" Number of atoms: 1722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1722 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 8, 'TRANS': 203} Chain: "R" Number of atoms: 1878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1878 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 222} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 1824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1824 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 9, 'TRANS': 214} Chain: "a" Number of atoms: 5009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5009 Classifications: {'peptide': 750} Incomplete info: {'truncation_to_alanine': 315} Link IDs: {'PTRANS': 31, 'TRANS': 718} Chain breaks: 2 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 1147 Unresolved non-hydrogen angles: 1454 Unresolved non-hydrogen dihedrals: 941 Unresolved non-hydrogen chiralities: 97 Planarities with less than four sites: {'GLN:plan1': 17, 'HIS:plan': 4, 'TYR:plan': 4, 'ASN:plan1': 23, 'TRP:plan': 4, 'ASP:plan': 15, 'PHE:plan': 20, 'GLU:plan': 34, 'ARG:plan': 28} Unresolved non-hydrogen planarities: 662 Chain: "b" Number of atoms: 1503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1503 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 5, 'TRANS': 197} Chain: "c" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 337 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "d" Number of atoms: 2833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2833 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 13, 'TRANS': 336} Chain: "e" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 71} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "f" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 452 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 3, 'TRANS': 80} Chain breaks: 1 Unresolved non-hydrogen bonds: 210 Unresolved non-hydrogen angles: 271 Unresolved non-hydrogen dihedrals: 168 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 6, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 107 Chain: "g" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "h" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "i" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "j" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "k" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "l" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "m" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "n" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "o" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "p" Number of atoms: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 432 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 1, 'TRANS': 50} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 26.82, per 1000 atoms: 0.43 Number of scatterers: 62325 At special positions: 0 Unit cell: (169.6, 174.9, 272.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 335 16.00 P 2 15.00 Mg 1 11.99 O 11581 8.00 N 10666 7.00 C 39740 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: 12.81 Conformation dependent library (CDL) restraints added in 6.6 seconds 16744 Ramachandran restraints generated. 8372 Oldfield, 0 Emsley, 8372 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15624 Finding SS restraints... Secondary structure from input PDB file: 314 helices and 77 sheets defined 64.0% alpha, 61.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 23.55 Creating SS restraints... Processing helix chain 'A' and resid 105 through 113 removed outlier: 3.657A pdb=" N SER A 111 " --> pdb=" O SER A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 255 removed outlier: 4.388A pdb=" N GLY A 255 " --> pdb=" O PHE A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 267 removed outlier: 3.558A pdb=" N SER A 267 " --> pdb=" O LEU A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 291 Processing helix chain 'A' and resid 319 through 339 removed outlier: 4.514A pdb=" N ILE A 327 " --> pdb=" O ARG A 323 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N TYR A 328 " --> pdb=" O GLU A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 365 removed outlier: 3.530A pdb=" N TRP A 354 " --> pdb=" O SER A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 374 Processing helix chain 'A' and resid 377 through 388 removed outlier: 3.707A pdb=" N ARG A 388 " --> pdb=" O SER A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 416 removed outlier: 4.145A pdb=" N ASP A 416 " --> pdb=" O PRO A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 427 Processing helix chain 'A' and resid 437 through 442 Processing helix chain 'A' and resid 461 through 469 Processing helix chain 'A' and resid 471 through 489 Processing helix chain 'A' and resid 489 through 497 Processing helix chain 'A' and resid 502 through 519 Processing helix chain 'A' and resid 533 through 557 Processing helix chain 'A' and resid 566 through 574 Processing helix chain 'A' and resid 574 through 584 Processing helix chain 'A' and resid 585 through 587 No H-bonds generated for 'chain 'A' and resid 585 through 587' Processing helix chain 'A' and resid 593 through 614 Processing helix chain 'B' and resid 105 through 114 removed outlier: 3.599A pdb=" N GLN B 114 " --> pdb=" O SER B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 266 Processing helix chain 'B' and resid 280 through 291 removed outlier: 3.828A pdb=" N MET B 284 " --> pdb=" O ARG B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 294 No H-bonds generated for 'chain 'B' and resid 292 through 294' Processing helix chain 'B' and resid 305 through 307 No H-bonds generated for 'chain 'B' and resid 305 through 307' Processing helix chain 'B' and resid 321 through 340 removed outlier: 4.015A pdb=" N ALA B 325 " --> pdb=" O ALA B 321 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET B 340 " --> pdb=" O TYR B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 365 Processing helix chain 'B' and resid 370 through 374 Processing helix chain 'B' and resid 375 through 376 No H-bonds generated for 'chain 'B' and resid 375 through 376' Processing helix chain 'B' and resid 377 through 387 Processing helix chain 'B' and resid 412 through 416 Processing helix chain 'B' and resid 419 through 427 Processing helix chain 'B' and resid 436 through 442 removed outlier: 3.886A pdb=" N ARG B 442 " --> pdb=" O LYS B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 469 removed outlier: 4.407A pdb=" N GLU B 463 " --> pdb=" O ARG B 459 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N TYR B 464 " --> pdb=" O ALA B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 497 removed outlier: 4.088A pdb=" N ILE B 492 " --> pdb=" O ASP B 488 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LEU B 495 " --> pdb=" O GLU B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 519 Processing helix chain 'B' and resid 533 through 557 Processing helix chain 'B' and resid 566 through 574 Processing helix chain 'B' and resid 574 through 584 Processing helix chain 'B' and resid 593 through 616 Processing helix chain 'C' and resid 105 through 114 Processing helix chain 'C' and resid 231 through 236 removed outlier: 3.532A pdb=" N ASP C 235 " --> pdb=" O GLN C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 267 removed outlier: 3.640A pdb=" N SER C 267 " --> pdb=" O LEU C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 291 Processing helix chain 'C' and resid 306 through 309 Processing helix chain 'C' and resid 319 through 339 removed outlier: 4.646A pdb=" N ILE C 327 " --> pdb=" O ARG C 323 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N TYR C 328 " --> pdb=" O GLU C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 365 Processing helix chain 'C' and resid 370 through 374 Processing helix chain 'C' and resid 377 through 387 Processing helix chain 'C' and resid 419 through 427 Processing helix chain 'C' and resid 436 through 442 Processing helix chain 'C' and resid 457 through 469 removed outlier: 4.302A pdb=" N GLU C 463 " --> pdb=" O ARG C 459 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N TYR C 464 " --> pdb=" O ALA C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 497 removed outlier: 3.594A pdb=" N ILE C 492 " --> pdb=" O ASP C 488 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU C 495 " --> pdb=" O GLU C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 519 Processing helix chain 'C' and resid 533 through 558 Processing helix chain 'C' and resid 566 through 574 Processing helix chain 'C' and resid 574 through 583 removed outlier: 3.874A pdb=" N LEU C 578 " --> pdb=" O MET C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 584 through 588 removed outlier: 4.473A pdb=" N ASP C 588 " --> pdb=" O LYS C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 593 through 616 Processing helix chain 'D' and resid 159 through 161 No H-bonds generated for 'chain 'D' and resid 159 through 161' Processing helix chain 'D' and resid 174 through 178 Processing helix chain 'D' and resid 198 through 210 Processing helix chain 'D' and resid 237 through 251 removed outlier: 3.554A pdb=" N ASN D 251 " --> pdb=" O ASP D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 255 removed outlier: 4.100A pdb=" N ASP D 255 " --> pdb=" O GLY D 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 252 through 255' Processing helix chain 'D' and resid 269 through 289 Proline residue: D 275 - end of helix Processing helix chain 'D' and resid 299 through 314 Processing helix chain 'D' and resid 319 through 323 Processing helix chain 'D' and resid 326 through 336 Processing helix chain 'D' and resid 357 through 360 Processing helix chain 'D' and resid 363 through 371 Processing helix chain 'D' and resid 381 through 386 Processing helix chain 'D' and resid 401 through 406 Processing helix chain 'D' and resid 414 through 440 removed outlier: 3.665A pdb=" N VAL D 438 " --> pdb=" O ALA D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 462 Processing helix chain 'D' and resid 472 through 485 Processing helix chain 'D' and resid 486 through 487 No H-bonds generated for 'chain 'D' and resid 486 through 487' Processing helix chain 'D' and resid 488 through 492 Processing helix chain 'D' and resid 496 through 504 Processing helix chain 'E' and resid 124 through 128 Processing helix chain 'E' and resid 174 through 179 Processing helix chain 'E' and resid 198 through 210 removed outlier: 3.645A pdb=" N ARG E 208 " --> pdb=" O ALA E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 251 Processing helix chain 'E' and resid 253 through 255 No H-bonds generated for 'chain 'E' and resid 253 through 255' Processing helix chain 'E' and resid 269 through 272 Processing helix chain 'E' and resid 273 through 288 Processing helix chain 'E' and resid 299 through 314 removed outlier: 4.070A pdb=" N TYR E 303 " --> pdb=" O ASP E 299 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 336 Processing helix chain 'E' and resid 357 through 360 Processing helix chain 'E' and resid 363 through 373 Processing helix chain 'E' and resid 380 through 385 removed outlier: 3.643A pdb=" N HIS E 384 " --> pdb=" O ASP E 380 " (cutoff:3.500A) Processing helix chain 'E' and resid 401 through 406 Processing helix chain 'E' and resid 414 through 440 removed outlier: 4.358A pdb=" N VAL E 438 " --> pdb=" O ALA E 434 " (cutoff:3.500A) Processing helix chain 'E' and resid 441 through 444 Processing helix chain 'E' and resid 445 through 462 removed outlier: 4.374A pdb=" N TYR E 451 " --> pdb=" O ASP E 447 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS E 460 " --> pdb=" O GLN E 456 " (cutoff:3.500A) Processing helix chain 'E' and resid 472 through 485 Processing helix chain 'E' and resid 486 through 487 No H-bonds generated for 'chain 'E' and resid 486 through 487' Processing helix chain 'E' and resid 488 through 492 Processing helix chain 'E' and resid 496 through 504 removed outlier: 4.955A pdb=" N GLU E 502 " --> pdb=" O SER E 498 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 128 removed outlier: 4.091A pdb=" N LEU F 128 " --> pdb=" O GLU F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 179 Processing helix chain 'F' and resid 198 through 210 Processing helix chain 'F' and resid 237 through 251 Processing helix chain 'F' and resid 253 through 255 No H-bonds generated for 'chain 'F' and resid 253 through 255' Processing helix chain 'F' and resid 269 through 272 Processing helix chain 'F' and resid 273 through 288 Processing helix chain 'F' and resid 299 through 314 removed outlier: 3.823A pdb=" N TYR F 303 " --> pdb=" O ASP F 299 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 323 Processing helix chain 'F' and resid 326 through 336 removed outlier: 3.749A pdb=" N ILE F 334 " --> pdb=" O ASP F 330 " (cutoff:3.500A) Processing helix chain 'F' and resid 357 through 360 Processing helix chain 'F' and resid 363 through 373 Processing helix chain 'F' and resid 381 through 386 removed outlier: 3.635A pdb=" N ARG F 386 " --> pdb=" O GLN F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 406 removed outlier: 3.838A pdb=" N ILE F 406 " --> pdb=" O MET F 402 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 440 removed outlier: 4.093A pdb=" N VAL F 438 " --> pdb=" O ALA F 434 " (cutoff:3.500A) Processing helix chain 'F' and resid 441 through 444 removed outlier: 3.911A pdb=" N LEU F 444 " --> pdb=" O GLU F 441 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 441 through 444' Processing helix chain 'F' and resid 445 through 462 Processing helix chain 'F' and resid 472 through 485 Processing helix chain 'F' and resid 486 through 487 No H-bonds generated for 'chain 'F' and resid 486 through 487' Processing helix chain 'F' and resid 488 through 492 Processing helix chain 'F' and resid 496 through 504 Processing helix chain 'G' and resid 13 through 23 Processing helix chain 'G' and resid 27 through 32 Processing helix chain 'G' and resid 47 through 80 removed outlier: 3.582A pdb=" N LEU G 80 " --> pdb=" O MET G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 104 Processing helix chain 'G' and resid 117 through 157 Processing helix chain 'G' and resid 193 through 203 removed outlier: 3.605A pdb=" N ILE G 198 " --> pdb=" O HIS G 194 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU G 202 " --> pdb=" O ILE G 198 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N THR G 203 " --> pdb=" O LYS G 199 " (cutoff:3.500A) Processing helix chain 'G' and resid 233 through 244 Processing helix chain 'G' and resid 254 through 311 Proline residue: G 278 - end of helix Processing helix chain 'G' and resid 327 through 344 removed outlier: 5.117A pdb=" N HIS G 341 " --> pdb=" O GLU G 337 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N LEU G 342 " --> pdb=" O LEU G 338 " (cutoff:3.500A) Processing helix chain 'H' and resid 12 through 77 Processing helix chain 'H' and resid 79 through 86 Processing helix chain 'H' and resid 127 through 175 Processing helix chain 'H' and resid 175 through 216 Processing helix chain 'I' and resid 4 through 107 Processing helix chain 'I' and resid 109 through 128 Processing helix chain 'I' and resid 137 through 139 No H-bonds generated for 'chain 'I' and resid 137 through 139' Processing helix chain 'I' and resid 140 through 160 removed outlier: 3.533A pdb=" N ALA I 146 " --> pdb=" O PRO I 142 " (cutoff:3.500A) Proline residue: I 153 - end of helix Processing helix chain 'I' and resid 195 through 207 Processing helix chain 'I' and resid 207 through 217 Processing helix chain 'J' and resid 4 through 107 Processing helix chain 'J' and resid 108 through 128 removed outlier: 4.570A pdb=" N VAL J 114 " --> pdb=" O THR J 110 " (cutoff:3.500A) Processing helix chain 'J' and resid 137 through 139 No H-bonds generated for 'chain 'J' and resid 137 through 139' Processing helix chain 'J' and resid 140 through 159 Proline residue: J 153 - end of helix removed outlier: 3.536A pdb=" N ILE J 157 " --> pdb=" O PRO J 153 " (cutoff:3.500A) Processing helix chain 'J' and resid 195 through 217 removed outlier: 3.919A pdb=" N GLN J 206 " --> pdb=" O LEU J 202 " (cutoff:3.500A) Proline residue: J 209 - end of helix Processing helix chain 'K' and resid 4 through 107 removed outlier: 3.789A pdb=" N VAL K 8 " --> pdb=" O SER K 4 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA K 27 " --> pdb=" O ALA K 23 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 128 Processing helix chain 'K' and resid 137 through 139 No H-bonds generated for 'chain 'K' and resid 137 through 139' Processing helix chain 'K' and resid 140 through 160 removed outlier: 3.503A pdb=" N ALA K 146 " --> pdb=" O PRO K 142 " (cutoff:3.500A) Proline residue: K 153 - end of helix Processing helix chain 'K' and resid 196 through 205 Processing helix chain 'K' and resid 207 through 217 removed outlier: 3.631A pdb=" N GLY K 213 " --> pdb=" O PRO K 209 " (cutoff:3.500A) Processing helix chain 'L' and resid 13 through 23 Processing helix chain 'L' and resid 44 through 57 Processing helix chain 'L' and resid 68 through 74 Processing helix chain 'L' and resid 74 through 81 removed outlier: 3.742A pdb=" N LEU L 78 " --> pdb=" O VAL L 74 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N HIS L 81 " --> pdb=" O ALA L 77 " (cutoff:3.500A) Processing helix chain 'L' and resid 103 through 109 Processing helix chain 'M' and resid 4 through 91 removed outlier: 4.280A pdb=" N ASN M 91 " --> pdb=" O SER M 87 " (cutoff:3.500A) Processing helix chain 'M' and resid 91 through 105 Processing helix chain 'N' and resid 4 through 89 Processing helix chain 'N' and resid 91 through 105 Processing helix chain 'O' and resid 4 through 104 removed outlier: 3.608A pdb=" N ASN O 91 " --> pdb=" O SER O 87 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N GLU O 93 " --> pdb=" O GLN O 89 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N ARG O 94 " --> pdb=" O ARG O 90 " (cutoff:3.500A) Processing helix chain 'Q' and resid 14 through 37 Processing helix chain 'Q' and resid 42 through 49 removed outlier: 3.628A pdb=" N TYR Q 49 " --> pdb=" O ILE Q 45 " (cutoff:3.500A) Processing helix chain 'Q' and resid 49 through 54 Processing helix chain 'Q' and resid 62 through 72 Processing helix chain 'Q' and resid 77 through 97 Processing helix chain 'Q' and resid 104 through 117 Processing helix chain 'Q' and resid 120 through 123 Processing helix chain 'Q' and resid 124 through 140 removed outlier: 3.796A pdb=" N LEU Q 140 " --> pdb=" O LEU Q 136 " (cutoff:3.500A) Processing helix chain 'Q' and resid 141 through 143 No H-bonds generated for 'chain 'Q' and resid 141 through 143' Processing helix chain 'Q' and resid 146 through 167 removed outlier: 3.551A pdb=" N GLN Q 165 " --> pdb=" O MET Q 161 " (cutoff:3.500A) Processing helix chain 'Q' and resid 172 through 187 Processing helix chain 'Q' and resid 193 through 207 Processing helix chain 'R' and resid 14 through 37 Processing helix chain 'R' and resid 42 through 49 Processing helix chain 'R' and resid 49 through 54 Processing helix chain 'R' and resid 61 through 71 Processing helix chain 'R' and resid 77 through 97 removed outlier: 3.895A pdb=" N LEU R 88 " --> pdb=" O ARG R 84 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU R 91 " --> pdb=" O ILE R 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 104 through 117 Processing helix chain 'R' and resid 124 through 140 Processing helix chain 'R' and resid 146 through 167 Processing helix chain 'R' and resid 172 through 188 Processing helix chain 'R' and resid 192 through 205 Processing helix chain 'R' and resid 218 through 233 removed outlier: 3.587A pdb=" N MET R 229 " --> pdb=" O LEU R 225 " (cutoff:3.500A) Processing helix chain 'S' and resid 14 through 37 Processing helix chain 'S' and resid 42 through 48 Processing helix chain 'S' and resid 49 through 54 Processing helix chain 'S' and resid 61 through 71 Processing helix chain 'S' and resid 77 through 97 Processing helix chain 'S' and resid 104 through 118 Processing helix chain 'S' and resid 120 through 123 Processing helix chain 'S' and resid 124 through 142 removed outlier: 3.909A pdb=" N ASN S 142 " --> pdb=" O ASP S 138 " (cutoff:3.500A) Processing helix chain 'S' and resid 146 through 167 Processing helix chain 'S' and resid 172 through 187 Processing helix chain 'S' and resid 192 through 206 Processing helix chain 'S' and resid 218 through 234 Processing helix chain 'a' and resid 19 through 33 removed outlier: 3.589A pdb=" N CYS a 24 " --> pdb=" O GLU a 20 " (cutoff:3.500A) Processing helix chain 'a' and resid 45 through 50 Processing helix chain 'a' and resid 51 through 75 Processing helix chain 'a' and resid 93 through 132 removed outlier: 3.584A pdb=" N ALA a 99 " --> pdb=" O ILE a 95 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLU a 127 " --> pdb=" O LEU a 123 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU a 128 " --> pdb=" O GLU a 124 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS a 129 " --> pdb=" O LEU a 125 " (cutoff:3.500A) Processing helix chain 'a' and resid 179 through 189 Processing helix chain 'a' and resid 226 through 240 Processing helix chain 'a' and resid 251 through 309 removed outlier: 4.044A pdb=" N LYS a 255 " --> pdb=" O PRO a 251 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N VAL a 292 " --> pdb=" O LYS a 288 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ILE a 295 " --> pdb=" O ARG a 291 " (cutoff:3.500A) Processing helix chain 'a' and resid 329 through 344 removed outlier: 3.501A pdb=" N SER a 344 " --> pdb=" O GLY a 340 " (cutoff:3.500A) Processing helix chain 'a' and resid 371 through 380 Processing helix chain 'a' and resid 391 through 407 removed outlier: 4.914A pdb=" N ILE a 397 " --> pdb=" O PRO a 393 " (cutoff:3.500A) Proline residue: a 400 - end of helix Processing helix chain 'a' and resid 409 through 426 Processing helix chain 'a' and resid 426 through 432 Processing helix chain 'a' and resid 437 through 446 Processing helix chain 'a' and resid 446 through 465 removed outlier: 3.519A pdb=" N LEU a 452 " --> pdb=" O TYR a 448 " (cutoff:3.500A) Processing helix chain 'a' and resid 481 through 488 Processing helix chain 'a' and resid 492 through 497 removed outlier: 4.391A pdb=" N LEU a 496 " --> pdb=" O GLU a 492 " (cutoff:3.500A) Processing helix chain 'a' and resid 498 through 500 No H-bonds generated for 'chain 'a' and resid 498 through 500' Processing helix chain 'a' and resid 520 through 526 Processing helix chain 'a' and resid 528 through 563 removed outlier: 4.567A pdb=" N ASN a 534 " --> pdb=" O LEU a 530 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER a 556 " --> pdb=" O GLY a 552 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU a 557 " --> pdb=" O VAL a 553 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N PHE a 558 " --> pdb=" O SER a 554 " (cutoff:3.500A) Processing helix chain 'a' and resid 565 through 571 removed outlier: 3.728A pdb=" N ILE a 569 " --> pdb=" O LYS a 565 " (cutoff:3.500A) Processing helix chain 'a' and resid 572 through 598 removed outlier: 4.304A pdb=" N TYR a 586 " --> pdb=" O SER a 582 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU a 587 " --> pdb=" O LEU a 583 " (cutoff:3.500A) Processing helix chain 'a' and resid 599 through 603 Processing helix chain 'a' and resid 608 through 619 Processing helix chain 'a' and resid 632 through 667 removed outlier: 3.706A pdb=" N VAL a 648 " --> pdb=" O ALA a 644 " (cutoff:3.500A) Proline residue: a 649 - end of helix removed outlier: 5.751A pdb=" N LYS a 655 " --> pdb=" O MET a 651 " (cutoff:3.500A) Proline residue: a 656 - end of helix Processing helix chain 'a' and resid 713 through 739 Processing helix chain 'a' and resid 739 through 759 removed outlier: 4.214A pdb=" N TRP a 743 " --> pdb=" O TYR a 739 " (cutoff:3.500A) Processing helix chain 'a' and resid 761 through 765 Processing helix chain 'a' and resid 768 through 791 removed outlier: 3.518A pdb=" N PHE a 778 " --> pdb=" O LEU a 774 " (cutoff:3.500A) Processing helix chain 'a' and resid 793 through 810 Processing helix chain 'a' and resid 811 through 815 Processing helix chain 'b' and resid 3 through 29 Processing helix chain 'b' and resid 36 through 44 Processing helix chain 'b' and resid 45 through 80 removed outlier: 3.618A pdb=" N SER b 61 " --> pdb=" O ALA b 57 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER b 75 " --> pdb=" O ILE b 71 " (cutoff:3.500A) Processing helix chain 'b' and resid 81 through 82 No H-bonds generated for 'chain 'b' and resid 81 through 82' Processing helix chain 'b' and resid 83 through 84 No H-bonds generated for 'chain 'b' and resid 83 through 84' Processing helix chain 'b' and resid 85 through 90 removed outlier: 4.220A pdb=" N LYS b 89 " --> pdb=" O ARG b 85 " (cutoff:3.500A) Processing helix chain 'b' and resid 91 through 113 removed outlier: 3.760A pdb=" N GLY b 104 " --> pdb=" O VAL b 100 " (cutoff:3.500A) Processing helix chain 'b' and resid 127 through 169 removed outlier: 3.860A pdb=" N GLN b 168 " --> pdb=" O LEU b 164 " (cutoff:3.500A) Processing helix chain 'b' and resid 172 through 198 removed outlier: 4.093A pdb=" N ILE b 178 " --> pdb=" O VAL b 174 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N VAL b 179 " --> pdb=" O LYS b 175 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLU b 180 " --> pdb=" O ILE b 176 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY b 187 " --> pdb=" O GLY b 183 " (cutoff:3.500A) Processing helix chain 'c' and resid 416 through 442 Processing helix chain 'd' and resid 8 through 25 removed outlier: 4.241A pdb=" N ASP d 12 " --> pdb=" O TYR d 8 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N TYR d 15 " --> pdb=" O VAL d 11 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N LEU d 16 " --> pdb=" O ASP d 12 " (cutoff:3.500A) Processing helix chain 'd' and resid 29 through 38 Processing helix chain 'd' and resid 41 through 50 Processing helix chain 'd' and resid 66 through 88 Processing helix chain 'd' and resid 90 through 116 removed outlier: 4.715A pdb=" N PHE d 96 " --> pdb=" O PRO d 92 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE d 100 " --> pdb=" O PHE d 96 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N TYR d 104 " --> pdb=" O ILE d 100 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASP d 107 " --> pdb=" O SER d 103 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR d 114 " --> pdb=" O ILE d 110 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY d 115 " --> pdb=" O LEU d 111 " (cutoff:3.500A) Processing helix chain 'd' and resid 121 through 126 Processing helix chain 'd' and resid 127 through 129 No H-bonds generated for 'chain 'd' and resid 127 through 129' Processing helix chain 'd' and resid 146 through 157 Processing helix chain 'd' and resid 158 through 167 removed outlier: 4.209A pdb=" N ALA d 162 " --> pdb=" O PRO d 159 " (cutoff:3.500A) Processing helix chain 'd' and resid 170 through 176 Processing helix chain 'd' and resid 177 through 200 Processing helix chain 'd' and resid 202 through 227 Proline residue: d 210 - end of helix Processing helix chain 'd' and resid 228 through 230 No H-bonds generated for 'chain 'd' and resid 228 through 230' Processing helix chain 'd' and resid 233 through 240 removed outlier: 3.608A pdb=" N LEU d 240 " --> pdb=" O ASP d 236 " (cutoff:3.500A) Processing helix chain 'd' and resid 251 through 258 Processing helix chain 'd' and resid 260 through 269 Processing helix chain 'd' and resid 271 through 281 removed outlier: 4.448A pdb=" N LEU d 277 " --> pdb=" O GLU d 273 " (cutoff:3.500A) Processing helix chain 'd' and resid 289 through 305 Processing helix chain 'd' and resid 306 through 308 No H-bonds generated for 'chain 'd' and resid 306 through 308' Processing helix chain 'd' and resid 312 through 339 removed outlier: 3.611A pdb=" N TYR d 316 " --> pdb=" O PHE d 312 " (cutoff:3.500A) Processing helix chain 'd' and resid 340 through 344 Processing helix chain 'e' and resid 6 through 23 Processing helix chain 'e' and resid 24 through 27 Processing helix chain 'e' and resid 33 through 58 Processing helix chain 'e' and resid 69 through 78 Processing helix chain 'f' and resid 8 through 36 Processing helix chain 'f' and resid 54 through 90 removed outlier: 4.191A pdb=" N ILE f 58 " --> pdb=" O GLY f 54 " (cutoff:3.500A) Processing helix chain 'g' and resid 10 through 46 removed outlier: 3.645A pdb=" N PHE g 14 " --> pdb=" O TYR g 10 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY g 15 " --> pdb=" O SER g 11 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER g 26 " --> pdb=" O ALA g 22 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL g 46 " --> pdb=" O ALA g 42 " (cutoff:3.500A) Processing helix chain 'g' and resid 48 through 52 Processing helix chain 'g' and resid 53 through 55 No H-bonds generated for 'chain 'g' and resid 53 through 55' Processing helix chain 'g' and resid 56 through 78 Processing helix chain 'g' and resid 86 through 124 removed outlier: 3.544A pdb=" N ARG g 119 " --> pdb=" O ASP g 115 " (cutoff:3.500A) Processing helix chain 'g' and resid 127 through 153 removed outlier: 3.781A pdb=" N SER g 153 " --> pdb=" O ALA g 149 " (cutoff:3.500A) Processing helix chain 'h' and resid 11 through 45 removed outlier: 4.636A pdb=" N GLY h 15 " --> pdb=" O SER h 11 " (cutoff:3.500A) Processing helix chain 'h' and resid 48 through 52 Processing helix chain 'h' and resid 56 through 78 Processing helix chain 'h' and resid 86 through 124 Processing helix chain 'h' and resid 126 through 154 removed outlier: 4.586A pdb=" N GLY h 130 " --> pdb=" O ARG h 126 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY h 145 " --> pdb=" O LEU h 141 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR h 154 " --> pdb=" O LEU h 150 " (cutoff:3.500A) Processing helix chain 'i' and resid 11 through 48 removed outlier: 4.316A pdb=" N GLY i 15 " --> pdb=" O SER i 11 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N MET i 23 " --> pdb=" O ALA i 19 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER i 26 " --> pdb=" O ALA i 22 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL i 46 " --> pdb=" O ALA i 42 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N MET i 47 " --> pdb=" O ALA i 43 " (cutoff:3.500A) Processing helix chain 'i' and resid 49 through 52 Processing helix chain 'i' and resid 56 through 78 Processing helix chain 'i' and resid 86 through 124 removed outlier: 3.829A pdb=" N GLN i 123 " --> pdb=" O ARG i 119 " (cutoff:3.500A) Processing helix chain 'i' and resid 126 through 154 removed outlier: 4.572A pdb=" N GLY i 130 " --> pdb=" O ARG i 126 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY i 145 " --> pdb=" O LEU i 141 " (cutoff:3.500A) Processing helix chain 'j' and resid 12 through 48 removed outlier: 3.554A pdb=" N MET j 23 " --> pdb=" O ALA j 19 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL j 46 " --> pdb=" O ALA j 42 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N MET j 47 " --> pdb=" O ALA j 43 " (cutoff:3.500A) Processing helix chain 'j' and resid 49 through 52 Processing helix chain 'j' and resid 53 through 55 No H-bonds generated for 'chain 'j' and resid 53 through 55' Processing helix chain 'j' and resid 56 through 78 removed outlier: 3.751A pdb=" N ILE j 64 " --> pdb=" O VAL j 60 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE j 65 " --> pdb=" O MET j 61 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA j 66 " --> pdb=" O ALA j 62 " (cutoff:3.500A) Processing helix chain 'j' and resid 86 through 124 Processing helix chain 'j' and resid 126 through 154 removed outlier: 4.469A pdb=" N GLY j 130 " --> pdb=" O ARG j 126 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLY j 145 " --> pdb=" O LEU j 141 " (cutoff:3.500A) Processing helix chain 'k' and resid 10 through 48 removed outlier: 3.953A pdb=" N PHE k 14 " --> pdb=" O TYR k 10 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLY k 15 " --> pdb=" O SER k 11 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET k 23 " --> pdb=" O ALA k 19 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA k 43 " --> pdb=" O THR k 39 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N VAL k 46 " --> pdb=" O ALA k 42 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N MET k 47 " --> pdb=" O ALA k 43 " (cutoff:3.500A) Processing helix chain 'k' and resid 49 through 52 Processing helix chain 'k' and resid 53 through 55 No H-bonds generated for 'chain 'k' and resid 53 through 55' Processing helix chain 'k' and resid 56 through 80 Processing helix chain 'k' and resid 86 through 124 Processing helix chain 'k' and resid 127 through 154 Processing helix chain 'l' and resid 11 through 48 removed outlier: 4.421A pdb=" N GLY l 15 " --> pdb=" O SER l 11 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL l 46 " --> pdb=" O ALA l 42 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N MET l 47 " --> pdb=" O ALA l 43 " (cutoff:3.500A) Processing helix chain 'l' and resid 49 through 52 Processing helix chain 'l' and resid 53 through 55 No H-bonds generated for 'chain 'l' and resid 53 through 55' Processing helix chain 'l' and resid 56 through 80 Processing helix chain 'l' and resid 86 through 124 removed outlier: 3.869A pdb=" N GLN l 123 " --> pdb=" O ARG l 119 " (cutoff:3.500A) Processing helix chain 'l' and resid 126 through 155 removed outlier: 4.340A pdb=" N GLY l 130 " --> pdb=" O ARG l 126 " (cutoff:3.500A) Processing helix chain 'm' and resid 10 through 45 removed outlier: 3.608A pdb=" N SER m 26 " --> pdb=" O ALA m 22 " (cutoff:3.500A) Processing helix chain 'm' and resid 46 through 47 No H-bonds generated for 'chain 'm' and resid 46 through 47' Processing helix chain 'm' and resid 48 through 55 removed outlier: 4.677A pdb=" N MET m 53 " --> pdb=" O GLU m 50 " (cutoff:3.500A) Processing helix chain 'm' and resid 56 through 80 Processing helix chain 'm' and resid 86 through 124 removed outlier: 3.944A pdb=" N GLN m 123 " --> pdb=" O ARG m 119 " (cutoff:3.500A) Processing helix chain 'm' and resid 126 through 154 removed outlier: 4.522A pdb=" N GLY m 130 " --> pdb=" O ARG m 126 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE m 137 " --> pdb=" O LEU m 133 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR m 154 " --> pdb=" O LEU m 150 " (cutoff:3.500A) Processing helix chain 'n' and resid 10 through 46 removed outlier: 4.389A pdb=" N PHE n 14 " --> pdb=" O TYR n 10 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLY n 15 " --> pdb=" O SER n 11 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET n 23 " --> pdb=" O ALA n 19 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL n 46 " --> pdb=" O ALA n 42 " (cutoff:3.500A) Processing helix chain 'n' and resid 48 through 52 Processing helix chain 'n' and resid 56 through 79 Processing helix chain 'n' and resid 86 through 123 removed outlier: 3.621A pdb=" N ARG n 119 " --> pdb=" O ASP n 115 " (cutoff:3.500A) Processing helix chain 'n' and resid 126 through 154 removed outlier: 4.651A pdb=" N GLY n 130 " --> pdb=" O ARG n 126 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY n 145 " --> pdb=" O LEU n 141 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR n 154 " --> pdb=" O LEU n 150 " (cutoff:3.500A) Processing helix chain 'o' and resid 11 through 48 removed outlier: 4.409A pdb=" N GLY o 15 " --> pdb=" O SER o 11 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET o 23 " --> pdb=" O ALA o 19 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N MET o 47 " --> pdb=" O ALA o 43 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 52 Processing helix chain 'o' and resid 53 through 55 No H-bonds generated for 'chain 'o' and resid 53 through 55' Processing helix chain 'o' and resid 56 through 80 removed outlier: 3.511A pdb=" N VAL o 72 " --> pdb=" O TYR o 68 " (cutoff:3.500A) Processing helix chain 'o' and resid 86 through 124 Processing helix chain 'o' and resid 126 through 154 removed outlier: 4.695A pdb=" N GLY o 130 " --> pdb=" O ARG o 126 " (cutoff:3.500A) Processing helix chain 'p' and resid 302 through 330 Processing helix chain 'p' and resid 338 through 343 Processing sheet with id=AA1, first strand: chain 'I' and resid 164 through 167 removed outlier: 6.197A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE I 183 " --> pdb=" O VAL I 192 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N VAL A 21 " --> pdb=" O CYS A 32 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N CYS A 32 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG A 56 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLN A 65 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ILE A 54 " --> pdb=" O GLN A 65 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE E 59 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N VAL E 53 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU E 57 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 164 through 167 removed outlier: 6.197A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE I 183 " --> pdb=" O VAL I 192 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE E 59 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N VAL E 53 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU E 57 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 164 through 167 removed outlier: 6.197A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE I 183 " --> pdb=" O VAL I 192 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N VAL D 86 " --> pdb=" O GLN D 97 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLN D 97 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA D 94 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'I' and resid 164 through 167 removed outlier: 6.197A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE I 183 " --> pdb=" O VAL I 192 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N VAL D 86 " --> pdb=" O GLN D 97 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLN D 97 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA D 94 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N THR C 63 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N LEU C 57 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N MET C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL C 28 " --> pdb=" O VAL C 24 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N VAL C 24 " --> pdb=" O VAL C 28 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N THR C 30 " --> pdb=" O HIS C 22 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 164 through 167 removed outlier: 6.197A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE I 183 " --> pdb=" O VAL I 192 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N VAL A 21 " --> pdb=" O CYS A 32 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N CYS A 32 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG A 56 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLN A 65 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ILE A 54 " --> pdb=" O GLN A 65 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE E 59 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N VAL E 53 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU E 57 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N THR B 30 " --> pdb=" O HIS B 22 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N VAL B 24 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N VAL B 28 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N MET B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU B 57 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N THR B 63 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LYS F 93 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N VAL F 89 " --> pdb=" O LYS F 93 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL F 95 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 164 through 167 removed outlier: 6.197A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE I 183 " --> pdb=" O VAL I 192 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N VAL A 21 " --> pdb=" O CYS A 32 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N CYS A 32 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG A 56 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLN A 65 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ILE A 54 " --> pdb=" O GLN A 65 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE E 59 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N VAL E 53 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU E 57 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU B 42 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N GLU B 41 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LYS F 93 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N VAL F 89 " --> pdb=" O LYS F 93 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL F 95 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 164 through 167 removed outlier: 6.197A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE I 183 " --> pdb=" O VAL I 192 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE E 59 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N VAL E 53 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU E 57 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N THR B 30 " --> pdb=" O HIS B 22 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N VAL B 24 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N VAL B 28 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N MET B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU B 57 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N THR B 63 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LYS F 93 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N VAL F 89 " --> pdb=" O LYS F 93 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL F 95 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 164 through 167 removed outlier: 6.197A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE I 183 " --> pdb=" O VAL I 192 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE E 59 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N VAL E 53 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU E 57 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU B 42 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N GLU B 41 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LYS F 93 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N VAL F 89 " --> pdb=" O LYS F 93 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL F 95 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 164 through 167 removed outlier: 6.197A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE I 183 " --> pdb=" O VAL I 192 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N VAL D 86 " --> pdb=" O GLN D 97 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLN D 97 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA D 94 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL F 95 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N VAL F 89 " --> pdb=" O LYS F 93 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LYS F 93 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N GLU B 41 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU B 42 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 164 through 167 removed outlier: 6.197A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE I 183 " --> pdb=" O VAL I 192 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N VAL D 86 " --> pdb=" O GLN D 97 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLN D 97 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA D 94 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL F 95 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N VAL F 89 " --> pdb=" O LYS F 93 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LYS F 93 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N THR B 63 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU B 57 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N MET B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N VAL B 28 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N VAL B 24 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N THR B 30 " --> pdb=" O HIS B 22 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 164 through 167 removed outlier: 6.197A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE I 183 " --> pdb=" O VAL I 192 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N VAL D 86 " --> pdb=" O GLN D 97 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLN D 97 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA D 94 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N THR C 63 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N LEU C 57 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N MET C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL C 28 " --> pdb=" O VAL C 24 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N VAL C 24 " --> pdb=" O VAL C 28 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N THR C 30 " --> pdb=" O HIS C 22 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL F 95 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N VAL F 89 " --> pdb=" O LYS F 93 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LYS F 93 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N GLU B 41 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU B 42 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 164 through 167 removed outlier: 6.197A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE I 183 " --> pdb=" O VAL I 192 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N VAL D 86 " --> pdb=" O GLN D 97 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLN D 97 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA D 94 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N THR C 63 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N LEU C 57 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N MET C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL C 28 " --> pdb=" O VAL C 24 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N VAL C 24 " --> pdb=" O VAL C 28 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N THR C 30 " --> pdb=" O HIS C 22 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL F 95 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N VAL F 89 " --> pdb=" O LYS F 93 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LYS F 93 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N THR B 63 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU B 57 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N MET B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N VAL B 28 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N VAL B 24 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N THR B 30 " --> pdb=" O HIS B 22 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 164 through 167 removed outlier: 5.817A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N THR B 30 " --> pdb=" O HIS B 22 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N VAL B 24 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N VAL B 28 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N MET B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU B 57 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N THR B 63 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LYS F 93 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N VAL F 89 " --> pdb=" O LYS F 93 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL F 95 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 164 through 167 removed outlier: 5.817A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU B 42 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N GLU B 41 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LYS F 93 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N VAL F 89 " --> pdb=" O LYS F 93 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL F 95 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 164 through 167 removed outlier: 5.817A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU E 57 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N VAL E 53 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE E 59 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE I 183 " --> pdb=" O VAL I 192 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 164 through 167 removed outlier: 5.817A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU E 57 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N VAL E 53 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE E 59 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ILE A 54 " --> pdb=" O GLN A 65 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLN A 65 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG A 56 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N CYS A 32 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N VAL A 21 " --> pdb=" O CYS A 32 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE I 183 " --> pdb=" O VAL I 192 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 164 through 167 removed outlier: 5.817A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N THR B 30 " --> pdb=" O HIS B 22 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N VAL B 24 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N VAL B 28 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N MET B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU B 57 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N THR B 63 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LYS F 93 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N VAL F 89 " --> pdb=" O LYS F 93 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL F 95 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N THR C 30 " --> pdb=" O HIS C 22 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N VAL C 24 " --> pdb=" O VAL C 28 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL C 28 " --> pdb=" O VAL C 24 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N MET C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N LEU C 57 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N THR C 63 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA D 94 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLN D 97 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N VAL D 86 " --> pdb=" O GLN D 97 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE I 183 " --> pdb=" O VAL I 192 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 164 through 167 removed outlier: 5.817A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N THR B 30 " --> pdb=" O HIS B 22 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N VAL B 24 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N VAL B 28 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N MET B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU B 57 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N THR B 63 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LYS F 93 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N VAL F 89 " --> pdb=" O LYS F 93 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL F 95 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA D 94 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLN D 97 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N VAL D 86 " --> pdb=" O GLN D 97 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE I 183 " --> pdb=" O VAL I 192 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 164 through 167 removed outlier: 5.817A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU B 42 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N GLU B 41 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LYS F 93 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N VAL F 89 " --> pdb=" O LYS F 93 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL F 95 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N THR C 30 " --> pdb=" O HIS C 22 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N VAL C 24 " --> pdb=" O VAL C 28 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL C 28 " --> pdb=" O VAL C 24 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N MET C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N LEU C 57 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N THR C 63 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA D 94 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLN D 97 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N VAL D 86 " --> pdb=" O GLN D 97 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE I 183 " --> pdb=" O VAL I 192 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 164 through 167 removed outlier: 5.817A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU B 42 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N GLU B 41 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LYS F 93 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N VAL F 89 " --> pdb=" O LYS F 93 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL F 95 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA D 94 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLN D 97 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N VAL D 86 " --> pdb=" O GLN D 97 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE I 183 " --> pdb=" O VAL I 192 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 164 through 167 removed outlier: 5.817A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU E 57 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N VAL E 53 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE E 59 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N VAL D 86 " --> pdb=" O GLN D 97 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLN D 97 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA D 94 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 164 through 167 removed outlier: 5.817A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU E 57 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N VAL E 53 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE E 59 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N VAL D 86 " --> pdb=" O GLN D 97 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLN D 97 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA D 94 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N THR C 63 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N LEU C 57 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N MET C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL C 28 " --> pdb=" O VAL C 24 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N VAL C 24 " --> pdb=" O VAL C 28 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N THR C 30 " --> pdb=" O HIS C 22 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 164 through 167 removed outlier: 5.817A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU E 57 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N VAL E 53 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE E 59 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ILE A 54 " --> pdb=" O GLN A 65 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLN A 65 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG A 56 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N CYS A 32 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N VAL A 21 " --> pdb=" O CYS A 32 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N VAL D 86 " --> pdb=" O GLN D 97 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLN D 97 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA D 94 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 164 through 167 removed outlier: 5.817A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU E 57 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N VAL E 53 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE E 59 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ILE A 54 " --> pdb=" O GLN A 65 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLN A 65 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG A 56 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N CYS A 32 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N VAL A 21 " --> pdb=" O CYS A 32 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N VAL D 86 " --> pdb=" O GLN D 97 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLN D 97 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA D 94 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N THR C 63 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N LEU C 57 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N MET C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL C 28 " --> pdb=" O VAL C 24 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N VAL C 24 " --> pdb=" O VAL C 28 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N THR C 30 " --> pdb=" O HIS C 22 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 164 through 167 removed outlier: 5.901A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N THR C 30 " --> pdb=" O HIS C 22 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N VAL C 24 " --> pdb=" O VAL C 28 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL C 28 " --> pdb=" O VAL C 24 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N MET C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N LEU C 57 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N THR C 63 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA D 94 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLN D 97 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N VAL D 86 " --> pdb=" O GLN D 97 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE I 183 " --> pdb=" O VAL I 192 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 164 through 167 removed outlier: 5.901A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA D 94 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLN D 97 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N VAL D 86 " --> pdb=" O GLN D 97 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE I 183 " --> pdb=" O VAL I 192 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 164 through 167 removed outlier: 5.901A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL F 95 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N VAL F 89 " --> pdb=" O LYS F 93 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LYS F 93 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N GLU B 41 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU B 42 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 164 through 167 removed outlier: 5.901A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL F 95 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N VAL F 89 " --> pdb=" O LYS F 93 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LYS F 93 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N THR B 63 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU B 57 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N MET B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N VAL B 28 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N VAL B 24 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N THR B 30 " --> pdb=" O HIS B 22 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 164 through 167 removed outlier: 5.901A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N THR C 30 " --> pdb=" O HIS C 22 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N VAL C 24 " --> pdb=" O VAL C 28 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL C 28 " --> pdb=" O VAL C 24 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N MET C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N LEU C 57 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N THR C 63 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA D 94 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLN D 97 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N VAL D 86 " --> pdb=" O GLN D 97 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N VAL A 21 " --> pdb=" O CYS A 32 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N CYS A 32 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG A 56 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLN A 65 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ILE A 54 " --> pdb=" O GLN A 65 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE E 59 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N VAL E 53 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU E 57 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 164 through 167 removed outlier: 5.901A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N THR C 30 " --> pdb=" O HIS C 22 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N VAL C 24 " --> pdb=" O VAL C 28 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL C 28 " --> pdb=" O VAL C 24 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N MET C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N LEU C 57 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N THR C 63 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA D 94 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLN D 97 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N VAL D 86 " --> pdb=" O GLN D 97 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE E 59 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N VAL E 53 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU E 57 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 164 through 167 removed outlier: 5.901A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA D 94 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLN D 97 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N VAL D 86 " --> pdb=" O GLN D 97 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N VAL A 21 " --> pdb=" O CYS A 32 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N CYS A 32 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG A 56 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLN A 65 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ILE A 54 " --> pdb=" O GLN A 65 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE E 59 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N VAL E 53 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU E 57 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 164 through 167 removed outlier: 5.901A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA D 94 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLN D 97 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N VAL D 86 " --> pdb=" O GLN D 97 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE E 59 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N VAL E 53 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU E 57 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 164 through 167 removed outlier: 5.901A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL F 95 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N VAL F 89 " --> pdb=" O LYS F 93 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LYS F 93 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N GLU B 41 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU B 42 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU E 57 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N VAL E 53 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE E 59 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE I 183 " --> pdb=" O VAL I 192 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 164 through 167 removed outlier: 5.901A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL F 95 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N VAL F 89 " --> pdb=" O LYS F 93 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LYS F 93 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N GLU B 41 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU B 42 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU E 57 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N VAL E 53 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE E 59 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ILE A 54 " --> pdb=" O GLN A 65 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLN A 65 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG A 56 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N CYS A 32 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N VAL A 21 " --> pdb=" O CYS A 32 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE I 183 " --> pdb=" O VAL I 192 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 164 through 167 removed outlier: 5.901A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL F 95 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N VAL F 89 " --> pdb=" O LYS F 93 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LYS F 93 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N THR B 63 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU B 57 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N MET B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N VAL B 28 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N VAL B 24 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N THR B 30 " --> pdb=" O HIS B 22 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU E 57 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N VAL E 53 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE E 59 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE I 183 " --> pdb=" O VAL I 192 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 164 through 167 removed outlier: 5.901A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL F 95 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N VAL F 89 " --> pdb=" O LYS F 93 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LYS F 93 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N THR B 63 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU B 57 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N MET B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N VAL B 28 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N VAL B 24 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N THR B 30 " --> pdb=" O HIS B 22 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU E 57 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N VAL E 53 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE E 59 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ILE A 54 " --> pdb=" O GLN A 65 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLN A 65 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG A 56 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N CYS A 32 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N VAL A 21 " --> pdb=" O CYS A 32 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE I 183 " --> pdb=" O VAL I 192 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 87 through 90 Processing sheet with id=AE2, first strand: chain 'A' and resid 98 through 99 removed outlier: 6.344A pdb=" N ILE A 272 " --> pdb=" O ALA A 310 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N VAL A 312 " --> pdb=" O ILE A 272 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N TYR A 274 " --> pdb=" O VAL A 312 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 163 through 167 removed outlier: 4.007A pdb=" N GLY A 154 " --> pdb=" O ILE A 166 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLU A 134 " --> pdb=" O ASN A 157 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 146 through 147 removed outlier: 6.349A pdb=" N GLU A 193 " --> pdb=" O THR A 177 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 409 through 410 removed outlier: 7.492A pdb=" N VAL A 410 " --> pdb=" O THR A 246 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ILE A 248 " --> pdb=" O VAL A 410 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 295 through 297 Processing sheet with id=AE7, first strand: chain 'B' and resid 87 through 90 Processing sheet with id=AE8, first strand: chain 'B' and resid 98 through 99 removed outlier: 6.368A pdb=" N PHE B 99 " --> pdb=" O ALA B 313 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ILE B 273 " --> pdb=" O SER B 345 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA B 348 " --> pdb=" O VAL B 407 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ARG B 391 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 98 through 99 removed outlier: 6.368A pdb=" N PHE B 99 " --> pdb=" O ALA B 313 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ILE B 273 " --> pdb=" O SER B 345 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA B 348 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 164 through 167 removed outlier: 4.056A pdb=" N GLY B 154 " --> pdb=" O ILE B 166 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 146 through 147 removed outlier: 6.588A pdb=" N GLU B 193 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 87 through 90 Processing sheet with id=AF4, first strand: chain 'C' and resid 98 through 99 Processing sheet with id=AF5, first strand: chain 'C' and resid 164 through 167 removed outlier: 4.077A pdb=" N GLY C 154 " --> pdb=" O ILE C 166 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 146 through 147 removed outlier: 6.530A pdb=" N GLU C 193 " --> pdb=" O THR C 177 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 219 through 221 removed outlier: 4.097A pdb=" N ARG C 391 " --> pdb=" O LEU C 221 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL C 271 " --> pdb=" O SER C 345 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N MET C 347 " --> pdb=" O VAL C 271 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ILE C 273 " --> pdb=" O MET C 347 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 219 through 221 removed outlier: 4.097A pdb=" N ARG C 391 " --> pdb=" O LEU C 221 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N THR C 246 " --> pdb=" O GLY C 408 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N THR C 245 " --> pdb=" O VAL C 431 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 295 through 297 Processing sheet with id=AG1, first strand: chain 'D' and resid 120 through 123 Processing sheet with id=AG2, first strand: chain 'D' and resid 131 through 133 removed outlier: 6.647A pdb=" N ALA D 228 " --> pdb=" O LEU D 294 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N ILE D 296 " --> pdb=" O ALA D 228 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL D 230 " --> pdb=" O ILE D 296 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N THR D 298 " --> pdb=" O VAL D 230 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ALA D 232 " --> pdb=" O THR D 298 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ARG D 340 " --> pdb=" O ILE D 164 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'D' and resid 170 through 171 Processing sheet with id=AG4, first strand: chain 'D' and resid 191 through 194 removed outlier: 6.244A pdb=" N ILE D 191 " --> pdb=" O LEU D 354 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N MET D 356 " --> pdb=" O ILE D 191 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N SER D 193 " --> pdb=" O MET D 356 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain 'E' and resid 120 through 123 Processing sheet with id=AG6, first strand: chain 'E' and resid 131 through 133 removed outlier: 6.666A pdb=" N PHE E 132 " --> pdb=" O LEU E 261 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N LEU E 263 " --> pdb=" O PHE E 132 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ILE E 229 " --> pdb=" O CYS E 258 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N PHE E 260 " --> pdb=" O ILE E 229 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N PHE E 231 " --> pdb=" O PHE E 260 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N ASN E 262 " --> pdb=" O PHE E 231 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ALA E 233 " --> pdb=" O ASN E 262 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'E' and resid 163 through 164 removed outlier: 4.411A pdb=" N ARG E 340 " --> pdb=" O ILE E 164 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'E' and resid 183 through 184 removed outlier: 4.350A pdb=" N ILE E 183 " --> pdb=" O ILE E 170 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'E' and resid 192 through 193 Processing sheet with id=AH1, first strand: chain 'E' and resid 375 through 376 removed outlier: 3.508A pdb=" N LEU E 398 " --> pdb=" O GLN E 376 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'F' and resid 120 through 123 Processing sheet with id=AH3, first strand: chain 'F' and resid 130 through 133 removed outlier: 6.722A pdb=" N ARG F 130 " --> pdb=" O LEU F 259 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N LEU F 261 " --> pdb=" O ARG F 130 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N PHE F 132 " --> pdb=" O LEU F 261 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N LEU F 263 " --> pdb=" O PHE F 132 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ALA F 228 " --> pdb=" O LEU F 294 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N ILE F 296 " --> pdb=" O ALA F 228 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N VAL F 230 " --> pdb=" O ILE F 296 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'F' and resid 163 through 164 removed outlier: 3.976A pdb=" N ARG F 340 " --> pdb=" O ILE F 164 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'F' and resid 169 through 170 removed outlier: 4.687A pdb=" N ILE F 183 " --> pdb=" O ILE F 170 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'F' and resid 191 through 193 Processing sheet with id=AH7, first strand: chain 'G' and resid 34 through 38 removed outlier: 3.985A pdb=" N ALA G 318 " --> pdb=" O PHE G 38 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N GLN G 317 " --> pdb=" O ALA G 9 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL G 370 " --> pdb=" O SER G 8 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'G' and resid 214 through 218 removed outlier: 7.139A pdb=" N LEU G 224 " --> pdb=" O LEU G 216 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N GLU G 218 " --> pdb=" O SER G 222 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N SER G 222 " --> pdb=" O GLU G 218 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'H' and resid 93 through 99 Processing sheet with id=AI1, first strand: chain 'L' and resid 36 through 38 removed outlier: 8.521A pdb=" N LEU L 37 " --> pdb=" O ILE L 8 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL L 10 " --> pdb=" O LEU L 37 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ALA L 9 " --> pdb=" O LEU L 65 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N ASN L 67 " --> pdb=" O ALA L 9 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N ILE L 11 " --> pdb=" O ASN L 67 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'a' and resid 36 through 37 removed outlier: 3.722A pdb=" N ASN a 311 " --> pdb=" O ILE a 320 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'a' and resid 36 through 37 Processing sheet with id=AI4, first strand: chain 'a' and resid 197 through 202 Processing sheet with id=AI5, first strand: chain 'a' and resid 362 through 363 7362 hydrogen bonds defined for protein. 21048 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: 66.98 Time building geometry restraints manager: 15.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 10471 1.30 - 1.43: 15343 1.43 - 1.56: 36976 1.56 - 1.68: 3 1.68 - 1.81: 602 Bond restraints: 63395 Sorted by residual: bond pdb=" C ASP C 290 " pdb=" N PHE C 291 " ideal model delta sigma weight residual 1.334 1.216 0.118 1.26e-02 6.30e+03 8.81e+01 bond pdb=" N PRO D 391 " pdb=" CA PRO D 391 " ideal model delta sigma weight residual 1.469 1.531 -0.063 7.40e-03 1.83e+04 7.16e+01 bond pdb=" C TYR F 504 " pdb=" N PRO F 505 " ideal model delta sigma weight residual 1.337 1.406 -0.069 1.06e-02 8.90e+03 4.29e+01 bond pdb=" C ARG C 104 " pdb=" N PRO C 105 " ideal model delta sigma weight residual 1.333 1.393 -0.060 1.01e-02 9.80e+03 3.48e+01 bond pdb=" N PRO F 352 " pdb=" CA PRO F 352 " ideal model delta sigma weight residual 1.466 1.538 -0.071 1.24e-02 6.50e+03 3.32e+01 ... (remaining 63390 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 81771 2.19 - 4.38: 3851 4.38 - 6.57: 304 6.57 - 8.76: 53 8.76 - 10.95: 18 Bond angle restraints: 85997 Sorted by residual: angle pdb=" C ILE D 189 " pdb=" N PRO D 190 " pdb=" CA PRO D 190 " ideal model delta sigma weight residual 119.85 129.28 -9.43 1.01e+00 9.80e-01 8.72e+01 angle pdb=" C ARG B 215 " pdb=" N PRO B 216 " pdb=" CA PRO B 216 " ideal model delta sigma weight residual 119.76 129.26 -9.50 1.03e+00 9.43e-01 8.50e+01 angle pdb=" C SER C 411 " pdb=" N PRO C 412 " pdb=" CA PRO C 412 " ideal model delta sigma weight residual 120.38 129.04 -8.66 1.03e+00 9.43e-01 7.07e+01 angle pdb=" N GLN d 171 " pdb=" CA GLN d 171 " pdb=" C GLN d 171 " ideal model delta sigma weight residual 111.28 102.51 8.77 1.09e+00 8.42e-01 6.47e+01 angle pdb=" C LEU D 395 " pdb=" N PRO D 396 " pdb=" CA PRO D 396 " ideal model delta sigma weight residual 120.04 128.55 -8.51 1.08e+00 8.57e-01 6.21e+01 ... (remaining 85992 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.67: 37198 23.67 - 47.33: 703 47.33 - 71.00: 158 71.00 - 94.66: 62 94.66 - 118.33: 2 Dihedral angle restraints: 38123 sinusoidal: 13801 harmonic: 24322 Sorted by residual: dihedral pdb=" C5' ADP B 701 " pdb=" O5' ADP B 701 " pdb=" PA ADP B 701 " pdb=" O2A ADP B 701 " ideal model delta sinusoidal sigma weight residual -60.00 -178.33 118.33 1 2.00e+01 2.50e-03 3.54e+01 dihedral pdb=" CA LYS I 59 " pdb=" C LYS I 59 " pdb=" N LYS I 60 " pdb=" CA LYS I 60 " ideal model delta harmonic sigma weight residual 180.00 -153.56 -26.44 0 5.00e+00 4.00e-02 2.80e+01 dihedral pdb=" O2A ADP B 701 " pdb=" O3A ADP B 701 " pdb=" PA ADP B 701 " pdb=" PB ADP B 701 " ideal model delta sinusoidal sigma weight residual -60.00 38.43 -98.42 1 2.00e+01 2.50e-03 2.75e+01 ... (remaining 38120 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 7321 0.071 - 0.142: 2348 0.142 - 0.213: 272 0.213 - 0.284: 85 0.284 - 0.355: 10 Chirality restraints: 10036 Sorted by residual: chirality pdb=" CA PHE H 155 " pdb=" N PHE H 155 " pdb=" C PHE H 155 " pdb=" CB PHE H 155 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.35 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" CA TYR h 68 " pdb=" N TYR h 68 " pdb=" C TYR h 68 " pdb=" CB TYR h 68 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" CA LEU H 48 " pdb=" N LEU H 48 " pdb=" C LEU H 48 " pdb=" CB LEU H 48 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.53e+00 ... (remaining 10033 not shown) Planarity restraints: 11103 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU o 86 " 0.023 2.00e-02 2.50e+03 4.60e-02 2.12e+01 pdb=" C LEU o 86 " -0.080 2.00e-02 2.50e+03 pdb=" O LEU o 86 " 0.030 2.00e-02 2.50e+03 pdb=" N TYR o 87 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP G 236 " -0.022 2.00e-02 2.50e+03 4.47e-02 2.00e+01 pdb=" C ASP G 236 " 0.077 2.00e-02 2.50e+03 pdb=" O ASP G 236 " -0.029 2.00e-02 2.50e+03 pdb=" N PHE G 237 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN k 7 " -0.022 2.00e-02 2.50e+03 4.34e-02 1.88e+01 pdb=" C ASN k 7 " 0.075 2.00e-02 2.50e+03 pdb=" O ASN k 7 " -0.028 2.00e-02 2.50e+03 pdb=" N PRO k 8 " -0.025 2.00e-02 2.50e+03 ... (remaining 11100 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 9529 2.76 - 3.29: 66420 3.29 - 3.83: 104798 3.83 - 4.36: 126681 4.36 - 4.90: 209248 Nonbonded interactions: 516676 Sorted by model distance: nonbonded pdb=" OG SER a 738 " pdb=" NH1 ARG a 741 " model vdw 2.219 3.120 nonbonded pdb=" O TYR G 181 " pdb=" N LYS G 231 " model vdw 2.271 3.120 nonbonded pdb=" OG SER B 269 " pdb=" OG SER B 345 " model vdw 2.303 3.040 nonbonded pdb=" NZ LYS H 55 " pdb=" OD2 ASP L 103 " model vdw 2.331 3.120 nonbonded pdb=" NZ LYS H 55 " pdb=" OD2 ASP L 99 " model vdw 2.352 3.120 ... (remaining 516671 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' selection = (chain 'B' and resid 17 through 616) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' } ncs_group { reference = (chain 'Q' and resid 12 through 218) selection = (chain 'R' and resid 12 through 218) selection = (chain 'S' and resid 12 through 218) } ncs_group { reference = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 1.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 1.850 Check model and map are aligned: 0.350 Set scattering table: 0.450 Process input model: 171.690 Find NCS groups from input model: 1.790 Set up NCS constraints: 0.420 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:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 181.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 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 : 0.009 0.118 63395 Z= 0.601 Angle : 0.981 10.952 85997 Z= 0.724 Chirality : 0.065 0.355 10036 Planarity : 0.005 0.046 11103 Dihedral : 10.857 118.330 22499 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.46 % Favored : 97.34 % Rotamer: Outliers : 0.61 % Allowed : 0.81 % Favored : 98.59 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.09), residues: 8372 helix: 0.94 (0.07), residues: 4967 sheet: -0.08 (0.18), residues: 707 loop : -0.19 (0.12), residues: 2698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 55 HIS 0.003 0.000 HIS D 199 PHE 0.011 0.000 PHE n 137 TYR 0.016 0.000 TYR E 389 ARG 0.004 0.000 ARG E 208 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16744 Ramachandran restraints generated. 8372 Oldfield, 0 Emsley, 8372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16744 Ramachandran restraints generated. 8372 Oldfield, 0 Emsley, 8372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1941 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 1904 time to evaluate : 5.303 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: 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: 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: A 65 GLN cc_start: 0.9198 (tp40) cc_final: 0.8314 (tm-30) REVERT: A 106 LEU cc_start: 0.9713 (mt) cc_final: 0.9390 (mm) REVERT: A 203 LEU cc_start: 0.9264 (mt) cc_final: 0.9051 (mp) REVERT: A 263 LEU cc_start: 0.9603 (tp) cc_final: 0.9253 (pp) REVERT: A 264 SER cc_start: 0.9493 (p) cc_final: 0.9240 (p) REVERT: A 328 TYR cc_start: 0.9315 (m-80) cc_final: 0.9092 (m-10) REVERT: A 329 THR cc_start: 0.9509 (m) cc_final: 0.9131 (p) REVERT: A 331 ILE cc_start: 0.9812 (tt) cc_final: 0.9530 (tt) REVERT: A 356 GLU cc_start: 0.9362 (tp30) cc_final: 0.8925 (tp30) REVERT: A 399 GLU cc_start: 0.6798 (mm-30) cc_final: 0.6567 (mm-30) REVERT: A 422 THR cc_start: 0.9651 (m) cc_final: 0.9338 (m) REVERT: A 520 LEU cc_start: 0.9507 (mt) cc_final: 0.9120 (tt) REVERT: A 540 MET cc_start: 0.9290 (mtp) cc_final: 0.9041 (mtp) REVERT: A 550 MET cc_start: 0.9020 (mmm) cc_final: 0.8661 (mmm) REVERT: A 567 TRP cc_start: 0.9337 (t-100) cc_final: 0.9010 (t-100) REVERT: A 590 VAL cc_start: 0.8845 (t) cc_final: 0.8297 (p) REVERT: B 54 ILE cc_start: 0.9654 (mt) cc_final: 0.9448 (mm) REVERT: B 61 MET cc_start: 0.9293 (mtp) cc_final: 0.8919 (mtt) REVERT: B 66 VAL cc_start: 0.9677 (t) cc_final: 0.9451 (m) REVERT: B 117 TYR cc_start: 0.8575 (m-80) cc_final: 0.8256 (m-80) REVERT: B 147 ILE cc_start: 0.9558 (pt) cc_final: 0.9159 (mm) REVERT: B 273 ILE cc_start: 0.9745 (mm) cc_final: 0.9408 (mt) REVERT: B 293 GLU cc_start: 0.9045 (mm-30) cc_final: 0.8833 (mm-30) REVERT: B 306 MET cc_start: 0.8694 (tpp) cc_final: 0.8334 (tpp) REVERT: B 331 ILE cc_start: 0.9711 (tp) cc_final: 0.9426 (tt) REVERT: B 433 TRP cc_start: 0.9413 (m-10) cc_final: 0.8962 (m-10) REVERT: B 447 SER cc_start: 0.8708 (p) cc_final: 0.8141 (p) REVERT: B 458 MET cc_start: 0.8797 (mtp) cc_final: 0.8397 (mmm) REVERT: B 523 ASN cc_start: 0.9351 (t0) cc_final: 0.9144 (t0) REVERT: B 540 MET cc_start: 0.8831 (ptm) cc_final: 0.8163 (ttm) REVERT: B 590 VAL cc_start: 0.9312 (t) cc_final: 0.8893 (p) REVERT: C 50 LEU cc_start: 0.9668 (mt) cc_final: 0.9461 (mt) REVERT: C 65 GLN cc_start: 0.8924 (tp40) cc_final: 0.7888 (tp-100) REVERT: C 99 PHE cc_start: 0.8911 (m-80) cc_final: 0.8595 (m-80) REVERT: C 106 LEU cc_start: 0.9475 (mt) cc_final: 0.9260 (mp) REVERT: C 108 ASP cc_start: 0.9451 (m-30) cc_final: 0.9180 (t0) REVERT: C 147 ILE cc_start: 0.9642 (pt) cc_final: 0.9283 (mm) REVERT: C 237 LEU cc_start: 0.9724 (mt) cc_final: 0.9360 (mt) REVERT: C 282 ASN cc_start: 0.8524 (m-40) cc_final: 0.8175 (m-40) REVERT: C 318 MET cc_start: 0.9528 (mmm) cc_final: 0.9063 (mmm) REVERT: C 324 GLU cc_start: 0.9138 (tt0) cc_final: 0.8909 (tm-30) REVERT: C 327 ILE cc_start: 0.9560 (mm) cc_final: 0.9246 (mt) REVERT: C 328 TYR cc_start: 0.9361 (m-80) cc_final: 0.9039 (m-10) REVERT: C 345 SER cc_start: 0.9373 (t) cc_final: 0.9048 (t) REVERT: C 356 GLU cc_start: 0.9412 (tp30) cc_final: 0.9193 (mm-30) REVERT: C 385 PHE cc_start: 0.9562 (t80) cc_final: 0.9352 (t80) REVERT: C 436 ASP cc_start: 0.8433 (t70) cc_final: 0.8120 (t0) REVERT: C 520 LEU cc_start: 0.9730 (mt) cc_final: 0.9472 (mt) REVERT: C 550 MET cc_start: 0.9435 (mtm) cc_final: 0.8985 (mtp) REVERT: D 97 GLN cc_start: 0.9399 (tt0) cc_final: 0.9187 (tm-30) REVERT: D 153 ILE cc_start: 0.9456 (pt) cc_final: 0.9216 (pt) REVERT: D 234 MET cc_start: 0.8259 (mpp) cc_final: 0.7557 (mtm) REVERT: D 254 MET cc_start: 0.8043 (tpp) cc_final: 0.7817 (mmm) REVERT: D 299 ASP cc_start: 0.8956 (m-30) cc_final: 0.8611 (m-30) REVERT: D 300 MET cc_start: 0.9177 (mmm) cc_final: 0.8939 (mmm) REVERT: D 302 SER cc_start: 0.9582 (m) cc_final: 0.9335 (t) REVERT: D 435 MET cc_start: 0.9405 (tpp) cc_final: 0.9173 (tpp) REVERT: E 57 LEU cc_start: 0.9536 (mt) cc_final: 0.9235 (mt) REVERT: E 74 LEU cc_start: 0.9709 (pt) cc_final: 0.9314 (pp) REVERT: E 87 LEU cc_start: 0.9126 (mt) cc_final: 0.8819 (mm) REVERT: E 127 MET cc_start: 0.9178 (mtp) cc_final: 0.8731 (mtt) REVERT: E 154 MET cc_start: 0.9350 (mmm) cc_final: 0.9115 (mmm) REVERT: E 170 ILE cc_start: 0.9517 (mt) cc_final: 0.9188 (mm) REVERT: E 183 ILE cc_start: 0.9252 (mm) cc_final: 0.8793 (tt) REVERT: E 288 GLN cc_start: 0.9062 (mt0) cc_final: 0.8296 (mp10) REVERT: E 305 GLU cc_start: 0.9296 (mt-10) cc_final: 0.9083 (tm-30) REVERT: E 352 PRO cc_start: 0.8853 (Cg_exo) cc_final: 0.8500 (Cg_endo) REVERT: E 360 ASP cc_start: 0.8431 (t0) cc_final: 0.7983 (t0) REVERT: E 410 MET cc_start: 0.7931 (mmm) cc_final: 0.7635 (mmm) REVERT: E 417 ASP cc_start: 0.8942 (m-30) cc_final: 0.8640 (m-30) REVERT: F 112 CYS cc_start: 0.8969 (m) cc_final: 0.8629 (p) REVERT: F 127 MET cc_start: 0.8972 (mtp) cc_final: 0.8604 (mtp) REVERT: F 183 ILE cc_start: 0.9609 (mt) cc_final: 0.9268 (mt) REVERT: F 205 GLN cc_start: 0.9396 (tt0) cc_final: 0.9030 (tt0) REVERT: F 249 GLU cc_start: 0.9305 (mt-10) cc_final: 0.9092 (mt-10) REVERT: F 262 ASN cc_start: 0.9080 (t0) cc_final: 0.8046 (t0) REVERT: F 268 THR cc_start: 0.9205 (p) cc_final: 0.8829 (t) REVERT: F 305 GLU cc_start: 0.9345 (mt-10) cc_final: 0.9138 (mt-10) REVERT: F 309 GLU cc_start: 0.9153 (tt0) cc_final: 0.8929 (tt0) REVERT: F 316 GLU cc_start: 0.9183 (tp30) cc_final: 0.8852 (tp30) REVERT: F 342 GLU cc_start: 0.8503 (tt0) cc_final: 0.8213 (pp20) REVERT: F 359 ASP cc_start: 0.8603 (m-30) cc_final: 0.8388 (t0) REVERT: F 425 CYS cc_start: 0.9500 (m) cc_final: 0.9241 (m) REVERT: F 453 GLU cc_start: 0.9297 (tt0) cc_final: 0.9030 (tp30) REVERT: F 481 TRP cc_start: 0.8823 (m100) cc_final: 0.8451 (m100) REVERT: H 14 MET cc_start: 0.8746 (tpt) cc_final: 0.8308 (tpt) REVERT: H 20 LYS cc_start: 0.9187 (mttt) cc_final: 0.8959 (ptpp) REVERT: H 23 LEU cc_start: 0.9565 (tp) cc_final: 0.9318 (tt) REVERT: H 24 LYS cc_start: 0.9681 (tttt) cc_final: 0.9422 (ptpp) REVERT: H 58 MET cc_start: 0.7741 (tmm) cc_final: 0.7253 (tmm) REVERT: H 81 THR cc_start: 0.9258 (m) cc_final: 0.8893 (p) REVERT: H 91 GLN cc_start: 0.9097 (tt0) cc_final: 0.8601 (tt0) REVERT: H 99 ASP cc_start: 0.9069 (t0) cc_final: 0.8665 (p0) REVERT: H 138 TYR cc_start: 0.8840 (m-80) cc_final: 0.8328 (m-80) REVERT: H 190 GLU cc_start: 0.9374 (mm-30) cc_final: 0.8891 (tm-30) REVERT: H 197 GLU cc_start: 0.8719 (pt0) cc_final: 0.8337 (pt0) REVERT: I 76 MET cc_start: 0.9292 (mtm) cc_final: 0.8538 (ptm) REVERT: I 127 LEU cc_start: 0.9441 (tp) cc_final: 0.9106 (tp) REVERT: I 132 MET cc_start: 0.8803 (mtt) cc_final: 0.8527 (mtt) REVERT: I 177 ILE cc_start: 0.9718 (mt) cc_final: 0.9144 (mp) REVERT: I 198 SER cc_start: 0.9649 (m) cc_final: 0.9379 (p) REVERT: I 203 ILE cc_start: 0.9691 (mp) cc_final: 0.9354 (tt) REVERT: J 76 MET cc_start: 0.9135 (mmm) cc_final: 0.8928 (mmp) REVERT: J 97 GLU cc_start: 0.9543 (tp30) cc_final: 0.9190 (tp30) REVERT: J 127 LEU cc_start: 0.9647 (mt) cc_final: 0.9420 (mt) REVERT: J 203 ILE cc_start: 0.9799 (mt) cc_final: 0.9498 (tp) REVERT: K 76 MET cc_start: 0.9579 (mtm) cc_final: 0.9326 (ptp) REVERT: K 96 ASN cc_start: 0.9703 (m-40) cc_final: 0.9498 (m-40) REVERT: K 115 LEU cc_start: 0.9840 (tp) cc_final: 0.9616 (pp) REVERT: K 127 LEU cc_start: 0.9633 (mt) cc_final: 0.9137 (mt) REVERT: K 132 MET cc_start: 0.8187 (mtt) cc_final: 0.7616 (mtt) REVERT: K 197 GLU cc_start: 0.8804 (mp0) cc_final: 0.8463 (mp0) REVERT: L 18 THR cc_start: 0.9491 (m) cc_final: 0.9278 (p) REVERT: L 20 PHE cc_start: 0.9511 (m-80) cc_final: 0.9200 (m-80) REVERT: L 37 LEU cc_start: 0.9143 (tp) cc_final: 0.8906 (tp) REVERT: L 59 ASP cc_start: 0.8822 (p0) cc_final: 0.8612 (t0) REVERT: L 73 MET cc_start: 0.8222 (mtm) cc_final: 0.7789 (mtm) REVERT: M 102 MET cc_start: 0.9183 (mtm) cc_final: 0.8265 (ttm) REVERT: M 105 ASP cc_start: 0.8480 (t0) cc_final: 0.7760 (p0) REVERT: N 79 ARG cc_start: 0.8966 (mtm-85) cc_final: 0.8512 (ptp-170) REVERT: O 110 VAL cc_start: 0.9306 (t) cc_final: 0.9007 (p) REVERT: Q 13 LEU cc_start: 0.9365 (mt) cc_final: 0.9158 (mm) REVERT: Q 35 THR cc_start: 0.9311 (m) cc_final: 0.9043 (p) REVERT: Q 62 PHE cc_start: 0.8577 (t80) cc_final: 0.8315 (t80) REVERT: Q 98 ILE cc_start: 0.9468 (pt) cc_final: 0.9196 (mm) REVERT: R 17 GLN cc_start: 0.9201 (tp40) cc_final: 0.8693 (tp40) REVERT: R 101 PHE cc_start: 0.8688 (m-80) cc_final: 0.8312 (m-80) REVERT: R 109 GLU cc_start: 0.9258 (mt-10) cc_final: 0.9013 (mm-30) REVERT: R 127 HIS cc_start: 0.8917 (t70) cc_final: 0.8712 (t70) REVERT: R 161 MET cc_start: 0.9517 (tmm) cc_final: 0.9232 (tmm) REVERT: R 200 PHE cc_start: 0.9212 (t80) cc_final: 0.8957 (t80) REVERT: R 228 THR cc_start: 0.9347 (m) cc_final: 0.9055 (p) REVERT: R 229 MET cc_start: 0.9306 (tpp) cc_final: 0.9073 (tpt) REVERT: S 78 LEU cc_start: 0.9791 (tp) cc_final: 0.9319 (mt) REVERT: S 79 ASP cc_start: 0.9100 (m-30) cc_final: 0.8521 (t0) REVERT: S 115 MET cc_start: 0.9533 (mtt) cc_final: 0.9208 (ptm) REVERT: S 229 MET cc_start: 0.9433 (mtp) cc_final: 0.9012 (mmm) REVERT: a 397 ILE cc_start: 0.8998 (mm) cc_final: 0.8759 (mm) REVERT: a 540 MET cc_start: 0.8830 (ttm) cc_final: 0.8527 (ptm) REVERT: a 587 LEU cc_start: 0.8596 (tp) cc_final: 0.8362 (tt) REVERT: a 591 ILE cc_start: 0.8528 (mt) cc_final: 0.7637 (mt) REVERT: a 616 MET cc_start: 0.8862 (ttp) cc_final: 0.7960 (tpp) REVERT: a 713 ASP cc_start: 0.7012 (t0) cc_final: 0.6524 (p0) REVERT: a 743 TRP cc_start: 0.8568 (t60) cc_final: 0.8139 (t60) REVERT: a 749 HIS cc_start: 0.7886 (t70) cc_final: 0.7608 (t70) REVERT: b 8 TYR cc_start: 0.7867 (m-80) cc_final: 0.7634 (m-80) REVERT: b 19 MET cc_start: 0.8959 (mtp) cc_final: 0.8428 (mmm) REVERT: b 27 THR cc_start: 0.8562 (m) cc_final: 0.8177 (p) REVERT: b 30 ASP cc_start: 0.8725 (t0) cc_final: 0.8416 (p0) REVERT: b 122 ASP cc_start: 0.7686 (t0) cc_final: 0.7463 (t0) REVERT: b 179 VAL cc_start: 0.9122 (t) cc_final: 0.8908 (t) REVERT: c 420 TRP cc_start: 0.9036 (t-100) cc_final: 0.8750 (t-100) REVERT: c 428 PHE cc_start: 0.8540 (m-80) cc_final: 0.8218 (m-80) REVERT: c 439 MET cc_start: 0.8921 (mmm) cc_final: 0.8633 (mmm) REVERT: d 118 HIS cc_start: 0.9282 (m-70) cc_final: 0.8908 (m170) REVERT: d 190 LEU cc_start: 0.9527 (mt) cc_final: 0.8822 (mt) REVERT: d 320 LYS cc_start: 0.9640 (mmtt) cc_final: 0.9416 (mmmt) REVERT: d 323 GLU cc_start: 0.9119 (tt0) cc_final: 0.8660 (pt0) REVERT: d 348 ILE cc_start: 0.8242 (mm) cc_final: 0.7719 (mt) REVERT: g 14 PHE cc_start: 0.8102 (m-80) cc_final: 0.7860 (m-80) REVERT: g 139 GLU cc_start: 0.6202 (OUTLIER) cc_final: 0.5704 (mm-30) REVERT: h 78 ASN cc_start: 0.8304 (m-40) cc_final: 0.8026 (p0) REVERT: i 139 GLU cc_start: 0.6250 (OUTLIER) cc_final: 0.5876 (mm-30) REVERT: j 78 ASN cc_start: 0.8761 (m-40) cc_final: 0.8555 (p0) REVERT: k 115 ASP cc_start: 0.8091 (t70) cc_final: 0.7304 (p0) REVERT: k 137 PHE cc_start: 0.6502 (m-80) cc_final: 0.6023 (m-80) REVERT: l 25 PHE cc_start: 0.8870 (m-80) cc_final: 0.8662 (m-10) REVERT: l 36 LYS cc_start: 0.8770 (mmtt) cc_final: 0.8270 (mttp) REVERT: l 139 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6581 (mt-10) REVERT: m 14 PHE cc_start: 0.9139 (m-80) cc_final: 0.8785 (m-80) REVERT: m 32 TYR cc_start: 0.8626 (t80) cc_final: 0.8213 (t80) REVERT: m 37 SER cc_start: 0.8752 (m) cc_final: 0.8524 (p) REVERT: m 67 ILE cc_start: 0.9260 (mt) cc_final: 0.8997 (mt) REVERT: m 71 VAL cc_start: 0.9639 (t) cc_final: 0.9376 (t) REVERT: m 110 ILE cc_start: 0.8589 (mt) cc_final: 0.8122 (tp) REVERT: n 23 MET cc_start: 0.8516 (tpt) cc_final: 0.7630 (tpt) REVERT: n 36 LYS cc_start: 0.8038 (mmtt) cc_final: 0.7477 (ttmm) REVERT: n 53 MET cc_start: 0.7032 (mmp) cc_final: 0.5746 (ttm) REVERT: n 143 LEU cc_start: 0.9403 (tp) cc_final: 0.9045 (tp) REVERT: o 9 GLU cc_start: 0.8484 (mp0) cc_final: 0.8112 (tm-30) REVERT: o 21 SER cc_start: 0.9742 (m) cc_final: 0.9212 (p) REVERT: o 23 MET cc_start: 0.7058 (tpt) cc_final: 0.6720 (mmm) REVERT: o 25 PHE cc_start: 0.8945 (m-80) cc_final: 0.8546 (m-80) REVERT: o 41 ILE cc_start: 0.9431 (mt) cc_final: 0.9219 (mm) REVERT: o 64 ILE cc_start: 0.7792 (mt) cc_final: 0.7396 (mt) REVERT: p 303 TYR cc_start: 0.7507 (t80) cc_final: 0.7250 (t80) REVERT: p 338 ILE cc_start: 0.9172 (pt) cc_final: 0.8371 (pt) outliers start: 37 outliers final: 9 residues processed: 1927 average time/residue: 0.6120 time to fit residues: 1976.7772 Evaluate side-chains 1103 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 1091 time to evaluate : 5.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 94 ILE Chi-restraints excluded: chain b residue 102 ILE Chi-restraints excluded: chain g residue 139 GLU Chi-restraints excluded: chain h residue 143 LEU Chi-restraints excluded: chain i residue 139 GLU Chi-restraints excluded: chain i residue 140 VAL Chi-restraints excluded: chain j residue 143 LEU Chi-restraints excluded: chain l residue 139 GLU Chi-restraints excluded: chain l residue 140 VAL Chi-restraints excluded: chain n residue 65 ILE Chi-restraints excluded: chain n residue 140 VAL Chi-restraints excluded: chain o residue 140 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 837 random chunks: chunk 706 optimal weight: 50.0000 chunk 634 optimal weight: 30.0000 chunk 352 optimal weight: 3.9990 chunk 216 optimal weight: 1.9990 chunk 427 optimal weight: 2.9990 chunk 338 optimal weight: 40.0000 chunk 656 optimal weight: 0.9980 chunk 253 optimal weight: 0.9990 chunk 398 optimal weight: 40.0000 chunk 488 optimal weight: 3.9990 chunk 760 optimal weight: 30.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN A 573 HIS ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 573 HIS C 146 HIS D 181 ASN D 358 ASN D 497 GLN E 456 GLN F 156 GLN F 161 GLN F 497 GLN H 16 GLN H 137 ASN ** H 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 66 GLN J 66 GLN L 67 ASN N 80 GLN ** N 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 91 ASN ** Q 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 34 GLN R 184 HIS S 76 ASN a 721 GLN ** a 802 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 438 HIS d 145 GLN ** d 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 123 GLN l 123 GLN m 78 ASN o 7 ASN o 78 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 63395 Z= 0.265 Angle : 0.745 13.313 85997 Z= 0.383 Chirality : 0.046 0.310 10036 Planarity : 0.005 0.073 11103 Dihedral : 4.933 116.964 9081 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.01 % Allowed : 10.61 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.09), residues: 8372 helix: 2.07 (0.07), residues: 4922 sheet: 0.25 (0.20), residues: 651 loop : -0.12 (0.12), residues: 2799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP a 808 HIS 0.009 0.001 HIS R 184 PHE 0.045 0.002 PHE o 90 TYR 0.043 0.002 TYR g 144 ARG 0.021 0.001 ARG i 126 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16744 Ramachandran restraints generated. 8372 Oldfield, 0 Emsley, 8372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16744 Ramachandran restraints generated. 8372 Oldfield, 0 Emsley, 8372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1327 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 1205 time to evaluate : 5.319 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: 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: 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: A 53 GLU cc_start: 0.8708 (pt0) cc_final: 0.8466 (pt0) REVERT: A 67 TYR cc_start: 0.8712 (m-10) cc_final: 0.8416 (m-10) REVERT: A 108 ASP cc_start: 0.9352 (m-30) cc_final: 0.9150 (m-30) REVERT: A 116 ILE cc_start: 0.9446 (pt) cc_final: 0.9049 (mm) REVERT: A 203 LEU cc_start: 0.9337 (mt) cc_final: 0.9131 (mp) REVERT: A 263 LEU cc_start: 0.9705 (tp) cc_final: 0.9279 (pp) REVERT: A 296 MET cc_start: 0.8543 (pmm) cc_final: 0.8150 (pmm) REVERT: A 340 MET cc_start: 0.9045 (ttm) cc_final: 0.8805 (ttm) REVERT: A 346 MET cc_start: 0.8299 (tmm) cc_final: 0.7989 (tmm) REVERT: A 356 GLU cc_start: 0.9382 (tp30) cc_final: 0.8971 (tp30) REVERT: A 360 GLU cc_start: 0.8413 (tm-30) cc_final: 0.8190 (tm-30) REVERT: A 371 ASP cc_start: 0.9361 (t0) cc_final: 0.8957 (t0) REVERT: A 540 MET cc_start: 0.9358 (mtp) cc_final: 0.9095 (mtp) REVERT: A 574 MET cc_start: 0.9075 (ptp) cc_final: 0.8864 (mtm) REVERT: B 34 MET cc_start: 0.9421 (mmm) cc_final: 0.9009 (mmm) REVERT: B 39 MET cc_start: 0.8516 (ttm) cc_final: 0.8286 (ttm) REVERT: B 61 MET cc_start: 0.9297 (mtp) cc_final: 0.9088 (mtt) REVERT: B 283 GLU cc_start: 0.9573 (mm-30) cc_final: 0.9323 (mp0) REVERT: B 293 GLU cc_start: 0.9053 (mm-30) cc_final: 0.8826 (mm-30) REVERT: B 306 MET cc_start: 0.8838 (tpp) cc_final: 0.8437 (tpp) REVERT: B 318 MET cc_start: 0.9677 (mtp) cc_final: 0.8981 (mtp) REVERT: B 331 ILE cc_start: 0.9620 (tp) cc_final: 0.9327 (tt) REVERT: B 433 TRP cc_start: 0.9197 (m-10) cc_final: 0.8802 (m-10) REVERT: B 458 MET cc_start: 0.8795 (mtp) cc_final: 0.8372 (mmm) REVERT: B 507 ILE cc_start: 0.9487 (mt) cc_final: 0.9277 (mm) REVERT: B 518 ASP cc_start: 0.7198 (t0) cc_final: 0.6540 (t0) REVERT: B 540 MET cc_start: 0.8977 (ptm) cc_final: 0.8609 (ttp) REVERT: B 584 MET cc_start: 0.8240 (mtp) cc_final: 0.7848 (mpp) REVERT: C 50 LEU cc_start: 0.9607 (mt) cc_final: 0.9403 (mt) REVERT: C 65 GLN cc_start: 0.8497 (tp40) cc_final: 0.8090 (tp-100) REVERT: C 99 PHE cc_start: 0.9135 (m-80) cc_final: 0.8804 (m-80) REVERT: C 147 ILE cc_start: 0.9713 (pt) cc_final: 0.9487 (mm) REVERT: C 318 MET cc_start: 0.9575 (mmm) cc_final: 0.8965 (mmm) REVERT: C 324 GLU cc_start: 0.9383 (tt0) cc_final: 0.8813 (tp30) REVERT: C 345 SER cc_start: 0.9304 (t) cc_final: 0.9087 (t) REVERT: C 354 TRP cc_start: 0.8592 (t60) cc_final: 0.6789 (t60) REVERT: C 436 ASP cc_start: 0.8533 (t70) cc_final: 0.8162 (t0) REVERT: C 540 MET cc_start: 0.8922 (mtp) cc_final: 0.8398 (mtp) REVERT: C 544 MET cc_start: 0.8969 (mtt) cc_final: 0.8442 (mtm) REVERT: C 550 MET cc_start: 0.9498 (mtm) cc_final: 0.9066 (mtp) REVERT: C 584 MET cc_start: 0.8722 (mtp) cc_final: 0.8513 (mtp) REVERT: D 88 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7910 (tm-30) REVERT: D 97 GLN cc_start: 0.9454 (tt0) cc_final: 0.9020 (tm-30) REVERT: D 169 MET cc_start: 0.8848 (tmm) cc_final: 0.8137 (tmm) REVERT: D 234 MET cc_start: 0.8182 (mpp) cc_final: 0.7867 (mtm) REVERT: D 298 THR cc_start: 0.9404 (m) cc_final: 0.8843 (p) REVERT: D 299 ASP cc_start: 0.9004 (m-30) cc_final: 0.8644 (m-30) REVERT: D 300 MET cc_start: 0.8957 (mmm) cc_final: 0.7994 (mmm) REVERT: D 302 SER cc_start: 0.9652 (m) cc_final: 0.9387 (t) REVERT: D 354 LEU cc_start: 0.9357 (mm) cc_final: 0.8748 (tt) REVERT: D 358 ASN cc_start: 0.7809 (OUTLIER) cc_final: 0.7577 (m110) REVERT: D 435 MET cc_start: 0.9377 (tpp) cc_final: 0.9020 (tpp) REVERT: E 127 MET cc_start: 0.9331 (mtp) cc_final: 0.8909 (mtt) REVERT: E 180 MET cc_start: 0.8985 (mmm) cc_final: 0.8379 (mmm) REVERT: E 254 MET cc_start: 0.7958 (mmm) cc_final: 0.7729 (mmm) REVERT: E 261 LEU cc_start: 0.9715 (OUTLIER) cc_final: 0.9507 (mm) REVERT: E 283 GLU cc_start: 0.8794 (tm-30) cc_final: 0.8214 (tm-30) REVERT: E 288 GLN cc_start: 0.8898 (mt0) cc_final: 0.8639 (mp10) REVERT: E 300 MET cc_start: 0.9370 (mmm) cc_final: 0.9037 (mmm) REVERT: E 305 GLU cc_start: 0.9327 (mt-10) cc_final: 0.8936 (tm-30) REVERT: E 327 MET cc_start: 0.9348 (ttt) cc_final: 0.9135 (ttm) REVERT: E 356 MET cc_start: 0.8642 (ttp) cc_final: 0.7867 (ttm) REVERT: E 360 ASP cc_start: 0.8588 (t0) cc_final: 0.8048 (t0) REVERT: E 495 ILE cc_start: 0.8908 (mt) cc_final: 0.8160 (tt) REVERT: F 127 MET cc_start: 0.9132 (mtp) cc_final: 0.8698 (mtp) REVERT: F 254 MET cc_start: 0.8719 (tmm) cc_final: 0.8366 (tpp) REVERT: F 268 THR cc_start: 0.9399 (p) cc_final: 0.9107 (t) REVERT: F 283 GLU cc_start: 0.9003 (mt-10) cc_final: 0.8761 (mt-10) REVERT: F 300 MET cc_start: 0.9553 (mmm) cc_final: 0.9183 (mmm) REVERT: F 305 GLU cc_start: 0.9321 (mt-10) cc_final: 0.9061 (mt-10) REVERT: F 309 GLU cc_start: 0.9263 (tt0) cc_final: 0.9054 (tt0) REVERT: F 316 GLU cc_start: 0.9232 (tp30) cc_final: 0.8913 (tp30) REVERT: F 453 GLU cc_start: 0.9302 (tt0) cc_final: 0.9017 (tp30) REVERT: H 11 PRO cc_start: 0.8779 (Cg_exo) cc_final: 0.8051 (Cg_endo) REVERT: H 24 LYS cc_start: 0.9595 (tttt) cc_final: 0.9150 (mttt) REVERT: H 31 ASN cc_start: 0.9528 (m-40) cc_final: 0.9250 (m110) REVERT: H 58 MET cc_start: 0.8217 (tmm) cc_final: 0.7858 (tmm) REVERT: H 81 THR cc_start: 0.9069 (m) cc_final: 0.8851 (p) REVERT: H 99 ASP cc_start: 0.9133 (t0) cc_final: 0.8743 (p0) REVERT: H 109 PHE cc_start: 0.8574 (m-80) cc_final: 0.7662 (m-80) REVERT: H 138 TYR cc_start: 0.8981 (m-80) cc_final: 0.8586 (m-80) REVERT: H 159 ASP cc_start: 0.9321 (t0) cc_final: 0.8769 (t0) REVERT: H 190 GLU cc_start: 0.9360 (mm-30) cc_final: 0.8900 (tm-30) REVERT: I 198 SER cc_start: 0.9701 (m) cc_final: 0.9467 (p) REVERT: I 203 ILE cc_start: 0.9732 (mp) cc_final: 0.9440 (tt) REVERT: I 210 GLU cc_start: 0.9585 (mm-30) cc_final: 0.9383 (pp20) REVERT: J 97 GLU cc_start: 0.9516 (tp30) cc_final: 0.9057 (tp30) REVERT: J 127 LEU cc_start: 0.9452 (mt) cc_final: 0.9152 (mt) REVERT: J 132 MET cc_start: 0.8468 (mmm) cc_final: 0.8174 (mmm) REVERT: J 203 ILE cc_start: 0.9744 (mt) cc_final: 0.9511 (tp) REVERT: J 210 GLU cc_start: 0.8986 (mp0) cc_final: 0.8183 (mp0) REVERT: K 76 MET cc_start: 0.9671 (mtm) cc_final: 0.9283 (ptp) REVERT: K 96 ASN cc_start: 0.9737 (m-40) cc_final: 0.9534 (m110) REVERT: K 97 GLU cc_start: 0.9302 (tp30) cc_final: 0.9038 (tm-30) REVERT: K 129 GLU cc_start: 0.8527 (tt0) cc_final: 0.7795 (tm-30) REVERT: K 197 GLU cc_start: 0.9037 (mp0) cc_final: 0.8675 (pm20) REVERT: K 207 MET cc_start: 0.9190 (tpp) cc_final: 0.8774 (tpp) REVERT: K 208 MET cc_start: 0.9250 (mmt) cc_final: 0.9030 (mmm) REVERT: L 20 PHE cc_start: 0.9439 (m-80) cc_final: 0.9013 (m-80) REVERT: L 73 MET cc_start: 0.8399 (mtm) cc_final: 0.7855 (mtm) REVERT: L 94 LYS cc_start: 0.8800 (ttpt) cc_final: 0.8408 (ttmt) REVERT: M 105 ASP cc_start: 0.8475 (t0) cc_final: 0.8052 (t0) REVERT: N 84 MET cc_start: 0.8824 (mtp) cc_final: 0.8569 (mmm) REVERT: N 102 MET cc_start: 0.9422 (mtt) cc_final: 0.9168 (mmm) REVERT: O 88 GLN cc_start: 0.9403 (tt0) cc_final: 0.9183 (tm-30) REVERT: O 110 VAL cc_start: 0.9393 (t) cc_final: 0.9135 (p) REVERT: O 114 TYR cc_start: 0.8073 (t80) cc_final: 0.7841 (t80) REVERT: Q 35 THR cc_start: 0.9333 (m) cc_final: 0.9074 (p) REVERT: Q 98 ILE cc_start: 0.9436 (pt) cc_final: 0.9177 (mm) REVERT: Q 161 MET cc_start: 0.9324 (tmm) cc_final: 0.8968 (ppp) REVERT: R 101 PHE cc_start: 0.8779 (m-80) cc_final: 0.8399 (m-80) REVERT: R 155 MET cc_start: 0.9389 (OUTLIER) cc_final: 0.8573 (mpp) REVERT: R 161 MET cc_start: 0.9517 (tmm) cc_final: 0.9289 (tmm) REVERT: R 200 PHE cc_start: 0.9256 (t80) cc_final: 0.8984 (t80) REVERT: S 76 ASN cc_start: 0.8629 (OUTLIER) cc_final: 0.7745 (m-40) REVERT: S 78 LEU cc_start: 0.9787 (tp) cc_final: 0.9348 (mt) REVERT: S 85 SER cc_start: 0.9789 (t) cc_final: 0.9479 (p) REVERT: S 115 MET cc_start: 0.9530 (mtt) cc_final: 0.9221 (ptm) REVERT: S 229 MET cc_start: 0.9450 (mtp) cc_final: 0.9076 (mmm) REVERT: a 394 TYR cc_start: 0.7710 (m-80) cc_final: 0.6822 (t80) REVERT: a 616 MET cc_start: 0.8813 (ttp) cc_final: 0.8294 (ttt) REVERT: a 713 ASP cc_start: 0.6930 (t0) cc_final: 0.6442 (p0) REVERT: a 730 LEU cc_start: 0.9319 (mt) cc_final: 0.9027 (pp) REVERT: a 756 LEU cc_start: 0.9318 (mt) cc_final: 0.9027 (pp) REVERT: a 805 ARG cc_start: 0.9537 (mtm110) cc_final: 0.9303 (mtm110) REVERT: b 19 MET cc_start: 0.8964 (mtp) cc_final: 0.8448 (mmm) REVERT: b 30 ASP cc_start: 0.8717 (t0) cc_final: 0.8278 (p0) REVERT: b 137 MET cc_start: 0.8992 (ttm) cc_final: 0.8382 (mmt) REVERT: c 428 PHE cc_start: 0.8484 (m-80) cc_final: 0.8194 (m-80) REVERT: c 439 MET cc_start: 0.8993 (mmm) cc_final: 0.8706 (mmm) REVERT: c 443 LEU cc_start: 0.8408 (tp) cc_final: 0.8096 (mt) REVERT: d 118 HIS cc_start: 0.9447 (m-70) cc_final: 0.8944 (m170) REVERT: d 119 GLN cc_start: 0.9220 (tt0) cc_final: 0.8711 (tm-30) REVERT: d 316 TYR cc_start: 0.9147 (t80) cc_final: 0.8248 (t80) REVERT: d 320 LYS cc_start: 0.9668 (mmtt) cc_final: 0.9286 (mmmt) REVERT: d 323 GLU cc_start: 0.9086 (tt0) cc_final: 0.8616 (pt0) REVERT: d 348 ILE cc_start: 0.8056 (mm) cc_final: 0.7647 (mt) REVERT: g 32 TYR cc_start: 0.8814 (t80) cc_final: 0.8210 (t80) REVERT: g 61 MET cc_start: 0.4217 (mtp) cc_final: 0.4005 (mtp) REVERT: g 104 LEU cc_start: 0.8920 (mt) cc_final: 0.8294 (mt) REVERT: h 76 ILE cc_start: 0.7752 (mt) cc_final: 0.7417 (tt) REVERT: h 78 ASN cc_start: 0.8352 (m-40) cc_final: 0.8128 (p0) REVERT: j 34 THR cc_start: 0.8430 (p) cc_final: 0.8229 (p) REVERT: j 47 MET cc_start: 0.9108 (ptm) cc_final: 0.8727 (ppp) REVERT: k 17 MET cc_start: 0.8794 (mmp) cc_final: 0.8449 (mmm) REVERT: k 57 ILE cc_start: 0.9392 (OUTLIER) cc_final: 0.9135 (mm) REVERT: k 97 LEU cc_start: 0.9536 (mm) cc_final: 0.9331 (mt) REVERT: l 23 MET cc_start: 0.8579 (tpp) cc_final: 0.8102 (ppp) REVERT: l 36 LYS cc_start: 0.8458 (mmtt) cc_final: 0.8209 (mttp) REVERT: l 47 MET cc_start: 0.9284 (ttm) cc_final: 0.9079 (ptm) REVERT: l 53 MET cc_start: 0.8506 (mmp) cc_final: 0.8120 (ttt) REVERT: l 61 MET cc_start: 0.6114 (mtt) cc_final: 0.5510 (mtt) REVERT: l 115 ASP cc_start: 0.8275 (t0) cc_final: 0.7633 (m-30) REVERT: m 23 MET cc_start: 0.8134 (tpt) cc_final: 0.7791 (tpt) REVERT: m 32 TYR cc_start: 0.8413 (t80) cc_final: 0.8100 (t80) REVERT: m 67 ILE cc_start: 0.9197 (mt) cc_final: 0.8913 (mt) REVERT: m 71 VAL cc_start: 0.9374 (t) cc_final: 0.9077 (t) REVERT: m 75 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8479 (pp) REVERT: m 112 ILE cc_start: 0.9480 (mt) cc_final: 0.9265 (mt) REVERT: n 13 PHE cc_start: 0.9022 (t80) cc_final: 0.8573 (t80) REVERT: n 23 MET cc_start: 0.8346 (tpt) cc_final: 0.7393 (tpt) REVERT: n 53 MET cc_start: 0.6840 (mmp) cc_final: 0.5527 (ttm) REVERT: o 9 GLU cc_start: 0.8424 (mp0) cc_final: 0.8018 (tm-30) REVERT: o 21 SER cc_start: 0.9695 (m) cc_final: 0.9076 (p) REVERT: o 44 MET cc_start: 0.9131 (ttp) cc_final: 0.8531 (tpp) REVERT: o 47 MET cc_start: 0.8769 (ptm) cc_final: 0.8497 (ppp) outliers start: 122 outliers final: 58 residues processed: 1282 average time/residue: 0.5800 time to fit residues: 1271.4133 Evaluate side-chains 1011 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 947 time to evaluate : 5.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 584 MET Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 394 CYS Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 301 SER Chi-restraints excluded: chain D residue 311 SER Chi-restraints excluded: chain D residue 334 ILE Chi-restraints excluded: chain D residue 358 ASN Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 448 ASP Chi-restraints excluded: chain F residue 334 ILE Chi-restraints excluded: chain F residue 372 ILE Chi-restraints excluded: chain H residue 172 ILE Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain K residue 128 LEU Chi-restraints excluded: chain L residue 7 LEU Chi-restraints excluded: chain Q residue 52 VAL Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 179 PHE Chi-restraints excluded: chain Q residue 198 HIS Chi-restraints excluded: chain R residue 155 MET Chi-restraints excluded: chain R residue 213 PHE Chi-restraints excluded: chain S residue 76 ASN Chi-restraints excluded: chain S residue 213 PHE Chi-restraints excluded: chain a residue 466 ASP Chi-restraints excluded: chain a residue 797 LEU Chi-restraints excluded: chain b residue 94 ILE Chi-restraints excluded: chain b residue 142 LEU Chi-restraints excluded: chain b residue 176 ILE Chi-restraints excluded: chain c residue 432 ILE Chi-restraints excluded: chain d residue 6 GLU Chi-restraints excluded: chain g residue 13 PHE Chi-restraints excluded: chain g residue 60 VAL Chi-restraints excluded: chain h residue 143 LEU Chi-restraints excluded: chain i residue 39 THR Chi-restraints excluded: chain i residue 72 VAL Chi-restraints excluded: chain i residue 123 GLN Chi-restraints excluded: chain i residue 134 ILE Chi-restraints excluded: chain i residue 140 VAL Chi-restraints excluded: chain k residue 7 ASN Chi-restraints excluded: chain k residue 9 GLU Chi-restraints excluded: chain k residue 57 ILE Chi-restraints excluded: chain k residue 140 VAL Chi-restraints excluded: chain l residue 13 PHE Chi-restraints excluded: chain l residue 152 LEU Chi-restraints excluded: chain m residue 75 LEU Chi-restraints excluded: chain m residue 80 LEU Chi-restraints excluded: chain m residue 93 LEU Chi-restraints excluded: chain n residue 150 LEU Chi-restraints excluded: chain o residue 140 VAL Chi-restraints excluded: chain p residue 307 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 837 random chunks: chunk 422 optimal weight: 8.9990 chunk 235 optimal weight: 10.0000 chunk 632 optimal weight: 7.9990 chunk 517 optimal weight: 9.9990 chunk 209 optimal weight: 8.9990 chunk 761 optimal weight: 7.9990 chunk 822 optimal weight: 20.0000 chunk 678 optimal weight: 9.9990 chunk 755 optimal weight: 20.0000 chunk 259 optimal weight: 10.0000 chunk 610 optimal weight: 8.9990 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 468 HIS B 146 HIS ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 468 HIS ** B 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 573 HIS ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 GLN C 468 HIS E 62 HIS F 97 GLN ** H 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 91 GLN H 137 ASN ** I 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 76 HIS N 75 GLN ** N 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 17 GLN R 21 GLN R 50 GLN S 50 GLN S 160 GLN ** S 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 802 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 84 HIS ** d 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 123 GLN j 78 ASN l 123 GLN p 308 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.4418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.142 63395 Z= 0.483 Angle : 0.848 15.643 85997 Z= 0.442 Chirality : 0.048 0.269 10036 Planarity : 0.006 0.080 11103 Dihedral : 4.976 138.458 9064 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 18.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.17 % Allowed : 12.30 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.09), residues: 8372 helix: 1.73 (0.07), residues: 4951 sheet: -0.26 (0.19), residues: 752 loop : -0.30 (0.12), residues: 2669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 354 HIS 0.012 0.002 HIS S 184 PHE 0.039 0.003 PHE o 90 TYR 0.046 0.003 TYR m 68 ARG 0.015 0.001 ARG k 119 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16744 Ramachandran restraints generated. 8372 Oldfield, 0 Emsley, 8372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16744 Ramachandran restraints generated. 8372 Oldfield, 0 Emsley, 8372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1113 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 920 time to evaluate : 5.356 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: 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: A 61 MET cc_start: 0.9168 (tpp) cc_final: 0.8833 (tpp) REVERT: A 100 ASP cc_start: 0.8707 (t0) cc_final: 0.8339 (t0) REVERT: A 116 ILE cc_start: 0.9547 (OUTLIER) cc_final: 0.9136 (mm) REVERT: A 296 MET cc_start: 0.8508 (pmm) cc_final: 0.8148 (pmm) REVERT: A 340 MET cc_start: 0.8868 (ttm) cc_final: 0.8658 (ttm) REVERT: A 346 MET cc_start: 0.8577 (tmm) cc_final: 0.8304 (tmm) REVERT: A 360 GLU cc_start: 0.8822 (tm-30) cc_final: 0.8481 (tm-30) REVERT: A 371 ASP cc_start: 0.9414 (t0) cc_final: 0.9097 (t0) REVERT: A 540 MET cc_start: 0.9435 (mtp) cc_final: 0.9016 (mtp) REVERT: A 574 MET cc_start: 0.9226 (ptp) cc_final: 0.8832 (mpp) REVERT: B 306 MET cc_start: 0.9113 (tpp) cc_final: 0.8853 (tpp) REVERT: B 318 MET cc_start: 0.9595 (mtp) cc_final: 0.8899 (mtp) REVERT: B 346 MET cc_start: 0.8821 (tmm) cc_final: 0.8619 (tmm) REVERT: B 458 MET cc_start: 0.8935 (mtp) cc_final: 0.8364 (mmm) REVERT: B 487 GLU cc_start: 0.9309 (tm-30) cc_final: 0.8448 (tm-30) REVERT: B 507 ILE cc_start: 0.9568 (mt) cc_final: 0.9350 (mm) REVERT: B 518 ASP cc_start: 0.7585 (t0) cc_final: 0.7258 (t0) REVERT: B 540 MET cc_start: 0.8987 (ptm) cc_final: 0.8755 (ttp) REVERT: C 65 GLN cc_start: 0.8518 (tp40) cc_final: 0.8086 (tp-100) REVERT: C 99 PHE cc_start: 0.9391 (m-80) cc_final: 0.9088 (m-80) REVERT: C 201 GLU cc_start: 0.9159 (OUTLIER) cc_final: 0.8888 (mp0) REVERT: C 205 MET cc_start: 0.8743 (mtm) cc_final: 0.7913 (ttp) REVERT: C 318 MET cc_start: 0.9592 (mmm) cc_final: 0.9031 (mmm) REVERT: C 416 ASP cc_start: 0.6300 (OUTLIER) cc_final: 0.6091 (p0) REVERT: C 436 ASP cc_start: 0.8515 (t70) cc_final: 0.8187 (t0) REVERT: C 481 GLU cc_start: 0.9129 (OUTLIER) cc_final: 0.8668 (pt0) REVERT: C 540 MET cc_start: 0.9050 (mtp) cc_final: 0.8713 (mtp) REVERT: C 544 MET cc_start: 0.9091 (mtt) cc_final: 0.8867 (mtp) REVERT: C 550 MET cc_start: 0.9369 (mtm) cc_final: 0.8779 (mtp) REVERT: C 584 MET cc_start: 0.8964 (mtp) cc_final: 0.8718 (mtp) REVERT: D 97 GLN cc_start: 0.9357 (tt0) cc_final: 0.8927 (tm-30) REVERT: D 231 PHE cc_start: 0.9254 (t80) cc_final: 0.9006 (t80) REVERT: D 234 MET cc_start: 0.8746 (mpp) cc_final: 0.8069 (mtm) REVERT: D 298 THR cc_start: 0.9550 (m) cc_final: 0.9238 (p) REVERT: D 299 ASP cc_start: 0.9153 (m-30) cc_final: 0.8893 (m-30) REVERT: D 300 MET cc_start: 0.9425 (mmm) cc_final: 0.8886 (mmm) REVERT: D 309 GLU cc_start: 0.9351 (tp30) cc_final: 0.8860 (tm-30) REVERT: D 348 ILE cc_start: 0.9592 (mt) cc_final: 0.9375 (mt) REVERT: D 356 MET cc_start: 0.9002 (ttm) cc_final: 0.8768 (tpp) REVERT: D 360 ASP cc_start: 0.9241 (t0) cc_final: 0.8977 (t0) REVERT: D 435 MET cc_start: 0.9428 (tpp) cc_final: 0.9178 (tpp) REVERT: E 87 LEU cc_start: 0.9237 (mt) cc_final: 0.9021 (mm) REVERT: E 127 MET cc_start: 0.9255 (mtp) cc_final: 0.8672 (mtt) REVERT: E 180 MET cc_start: 0.9031 (mmm) cc_final: 0.8542 (mmm) REVERT: E 254 MET cc_start: 0.8631 (mmm) cc_final: 0.8291 (mmm) REVERT: E 305 GLU cc_start: 0.9366 (mt-10) cc_final: 0.9134 (tm-30) REVERT: E 356 MET cc_start: 0.8688 (ttp) cc_final: 0.8299 (ttp) REVERT: E 360 ASP cc_start: 0.8736 (t0) cc_final: 0.8037 (t0) REVERT: F 97 GLN cc_start: 0.9238 (pt0) cc_final: 0.8644 (pp30) REVERT: F 112 CYS cc_start: 0.9186 (m) cc_final: 0.8693 (p) REVERT: F 127 MET cc_start: 0.9248 (mtp) cc_final: 0.8863 (mtp) REVERT: F 254 MET cc_start: 0.8829 (mmm) cc_final: 0.8368 (tmm) REVERT: F 268 THR cc_start: 0.9534 (p) cc_final: 0.9087 (t) REVERT: F 283 GLU cc_start: 0.9137 (mt-10) cc_final: 0.8827 (mp0) REVERT: F 300 MET cc_start: 0.9607 (mmm) cc_final: 0.9344 (mmm) REVERT: F 356 MET cc_start: 0.8713 (ttm) cc_final: 0.8449 (ttm) REVERT: F 402 MET cc_start: 0.9007 (ttm) cc_final: 0.8678 (ttm) REVERT: F 453 GLU cc_start: 0.9369 (tt0) cc_final: 0.9069 (tp30) REVERT: H 16 GLN cc_start: 0.9610 (tt0) cc_final: 0.9187 (tm-30) REVERT: H 20 LYS cc_start: 0.9373 (mtmt) cc_final: 0.8841 (mtmm) REVERT: H 78 ASP cc_start: 0.9417 (t0) cc_final: 0.9199 (t0) REVERT: H 91 GLN cc_start: 0.9355 (OUTLIER) cc_final: 0.9148 (tp40) REVERT: H 109 PHE cc_start: 0.8705 (m-80) cc_final: 0.7916 (m-80) REVERT: H 190 GLU cc_start: 0.9304 (mm-30) cc_final: 0.8810 (tm-30) REVERT: I 203 ILE cc_start: 0.9814 (mp) cc_final: 0.9538 (tt) REVERT: I 210 GLU cc_start: 0.9561 (mm-30) cc_final: 0.9320 (mp0) REVERT: J 97 GLU cc_start: 0.9526 (tp30) cc_final: 0.9076 (tp30) REVERT: J 203 ILE cc_start: 0.9761 (mt) cc_final: 0.9520 (tp) REVERT: J 207 MET cc_start: 0.9228 (tpp) cc_final: 0.8777 (tpp) REVERT: J 210 GLU cc_start: 0.8831 (mp0) cc_final: 0.8554 (mp0) REVERT: K 76 MET cc_start: 0.9665 (mtm) cc_final: 0.9457 (ptp) REVERT: K 133 ILE cc_start: 0.9290 (mt) cc_final: 0.8897 (tp) REVERT: K 182 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8070 (tt0) REVERT: K 197 GLU cc_start: 0.9078 (mp0) cc_final: 0.8698 (pm20) REVERT: K 207 MET cc_start: 0.9392 (tpp) cc_final: 0.8952 (tpp) REVERT: K 208 MET cc_start: 0.9358 (mmt) cc_final: 0.9086 (mmm) REVERT: K 221 ASN cc_start: 0.9393 (m-40) cc_final: 0.9012 (m110) REVERT: L 22 LEU cc_start: 0.9478 (mt) cc_final: 0.9240 (mt) REVERT: L 73 MET cc_start: 0.8585 (mtm) cc_final: 0.8128 (mtp) REVERT: L 94 LYS cc_start: 0.8978 (ttpt) cc_final: 0.8671 (ttmt) REVERT: M 102 MET cc_start: 0.9339 (mtp) cc_final: 0.8861 (ttm) REVERT: M 105 ASP cc_start: 0.8574 (t0) cc_final: 0.8203 (t0) REVERT: N 102 MET cc_start: 0.9534 (mtt) cc_final: 0.9200 (mmm) REVERT: O 75 GLN cc_start: 0.9429 (mt0) cc_final: 0.9226 (mt0) REVERT: O 88 GLN cc_start: 0.9535 (tt0) cc_final: 0.9314 (tm-30) REVERT: Q 35 THR cc_start: 0.9363 (m) cc_final: 0.9141 (p) REVERT: Q 98 ILE cc_start: 0.9540 (pt) cc_final: 0.9327 (mm) REVERT: R 136 LEU cc_start: 0.9847 (OUTLIER) cc_final: 0.9609 (pp) REVERT: R 155 MET cc_start: 0.9381 (OUTLIER) cc_final: 0.8789 (mpp) REVERT: R 181 LEU cc_start: 0.9402 (mt) cc_final: 0.9129 (pp) REVERT: S 103 MET cc_start: 0.7992 (tpp) cc_final: 0.7789 (tpp) REVERT: S 115 MET cc_start: 0.9548 (mtt) cc_final: 0.9320 (mtp) REVERT: S 179 PHE cc_start: 0.9179 (m-80) cc_final: 0.8952 (t80) REVERT: S 229 MET cc_start: 0.9514 (mtp) cc_final: 0.9168 (mmm) REVERT: a 397 ILE cc_start: 0.9101 (mm) cc_final: 0.8786 (mp) REVERT: a 616 MET cc_start: 0.9022 (ttp) cc_final: 0.8487 (ttt) REVERT: a 713 ASP cc_start: 0.6692 (t0) cc_final: 0.6164 (p0) REVERT: b 19 MET cc_start: 0.8940 (mtp) cc_final: 0.8369 (mmm) REVERT: b 60 LEU cc_start: 0.9083 (tp) cc_final: 0.8703 (tt) REVERT: b 137 MET cc_start: 0.8994 (ttm) cc_final: 0.8699 (tpp) REVERT: c 421 MET cc_start: 0.9095 (mtt) cc_final: 0.8647 (mmt) REVERT: d 6 GLU cc_start: 0.9196 (OUTLIER) cc_final: 0.7896 (pp20) REVERT: d 118 HIS cc_start: 0.9458 (m-70) cc_final: 0.8959 (m-70) REVERT: d 119 GLN cc_start: 0.9305 (tt0) cc_final: 0.8882 (tm-30) REVERT: d 293 ARG cc_start: 0.9252 (mmt180) cc_final: 0.9013 (mmm160) REVERT: d 299 VAL cc_start: 0.9364 (p) cc_final: 0.9160 (m) REVERT: d 316 TYR cc_start: 0.9279 (t80) cc_final: 0.8940 (t80) REVERT: d 323 GLU cc_start: 0.9140 (tt0) cc_final: 0.8876 (pt0) REVERT: d 348 ILE cc_start: 0.8514 (mm) cc_final: 0.8053 (mt) REVERT: g 23 MET cc_start: 0.6516 (tpt) cc_final: 0.5951 (tpt) REVERT: g 32 TYR cc_start: 0.8850 (t80) cc_final: 0.8313 (t80) REVERT: g 82 ASP cc_start: 0.7696 (t0) cc_final: 0.7227 (m-30) REVERT: g 101 LEU cc_start: 0.9135 (tp) cc_final: 0.8561 (mt) REVERT: g 104 LEU cc_start: 0.9051 (mt) cc_final: 0.8279 (mt) REVERT: h 76 ILE cc_start: 0.7742 (mt) cc_final: 0.7369 (tt) REVERT: i 23 MET cc_start: 0.7538 (mmm) cc_final: 0.7126 (mmt) REVERT: i 47 MET cc_start: 0.7393 (ptm) cc_final: 0.7044 (tmm) REVERT: i 53 MET cc_start: 0.7942 (mmt) cc_final: 0.7053 (mtp) REVERT: i 97 LEU cc_start: 0.9367 (mm) cc_final: 0.9025 (pp) REVERT: i 108 PHE cc_start: 0.7891 (OUTLIER) cc_final: 0.7655 (m-10) REVERT: i 123 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.7552 (pm20) REVERT: j 108 PHE cc_start: 0.8416 (m-10) cc_final: 0.8126 (m-80) REVERT: j 131 MET cc_start: 0.5760 (ppp) cc_final: 0.5408 (ppp) REVERT: k 97 LEU cc_start: 0.9493 (mm) cc_final: 0.9287 (mt) REVERT: k 131 MET cc_start: 0.7258 (tmm) cc_final: 0.6368 (ppp) REVERT: k 147 ILE cc_start: 0.7642 (OUTLIER) cc_final: 0.7352 (tt) REVERT: k 152 LEU cc_start: 0.7559 (tp) cc_final: 0.7348 (tp) REVERT: l 23 MET cc_start: 0.8782 (tpp) cc_final: 0.8558 (tpp) REVERT: l 28 MET cc_start: 0.8861 (mmp) cc_final: 0.8593 (mmp) REVERT: l 53 MET cc_start: 0.8678 (OUTLIER) cc_final: 0.8240 (ttt) REVERT: l 68 TYR cc_start: 0.9179 (m-10) cc_final: 0.8957 (m-10) REVERT: l 115 ASP cc_start: 0.7896 (t0) cc_final: 0.7572 (m-30) REVERT: m 17 MET cc_start: 0.9109 (ptt) cc_final: 0.8797 (tmm) REVERT: m 32 TYR cc_start: 0.8439 (t80) cc_final: 0.8103 (t80) REVERT: m 112 ILE cc_start: 0.9495 (mt) cc_final: 0.9177 (mt) REVERT: n 13 PHE cc_start: 0.9087 (t80) cc_final: 0.8683 (t80) REVERT: n 17 MET cc_start: 0.9471 (ptt) cc_final: 0.9220 (ptt) REVERT: n 36 LYS cc_start: 0.7866 (mmtt) cc_final: 0.7269 (mtpp) REVERT: n 53 MET cc_start: 0.7489 (mmp) cc_final: 0.5868 (ttp) REVERT: o 23 MET cc_start: 0.7214 (tpt) cc_final: 0.6916 (tpt) REVERT: o 25 PHE cc_start: 0.8785 (m-80) cc_final: 0.8414 (m-80) REVERT: o 47 MET cc_start: 0.8789 (ptm) cc_final: 0.8469 (ppp) REVERT: o 119 ARG cc_start: 0.8330 (mtp85) cc_final: 0.7960 (mmm-85) REVERT: p 328 ILE cc_start: 0.9562 (mm) cc_final: 0.9314 (pt) outliers start: 193 outliers final: 109 residues processed: 1042 average time/residue: 0.5750 time to fit residues: 1036.9106 Evaluate side-chains 931 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 809 time to evaluate : 5.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 450 TRP Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 505 ASP Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 179 ILE Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 416 ASP Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 450 TRP Chi-restraints excluded: chain C residue 481 GLU Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 207 CYS Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 301 SER Chi-restraints excluded: chain D residue 311 SER Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 334 ILE Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 378 TYR Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 250 GLU Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 262 ASN Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain E residue 423 TYR Chi-restraints excluded: chain E residue 425 CYS Chi-restraints excluded: chain E residue 448 ASP Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 262 ASN Chi-restraints excluded: chain F residue 334 ILE Chi-restraints excluded: chain F residue 383 LEU Chi-restraints excluded: chain F residue 398 LEU Chi-restraints excluded: chain F residue 410 MET Chi-restraints excluded: chain F residue 425 CYS Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 67 PHE Chi-restraints excluded: chain H residue 79 PHE Chi-restraints excluded: chain H residue 91 GLN Chi-restraints excluded: chain H residue 134 LEU Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain I residue 167 ILE Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain K residue 128 LEU Chi-restraints excluded: chain K residue 182 GLU Chi-restraints excluded: chain L residue 7 LEU Chi-restraints excluded: chain L residue 29 ASN Chi-restraints excluded: chain N residue 94 ARG Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 121 LEU Chi-restraints excluded: chain Q residue 159 LEU Chi-restraints excluded: chain Q residue 179 PHE Chi-restraints excluded: chain Q residue 198 HIS Chi-restraints excluded: chain R residue 13 LEU Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 155 MET Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain S residue 95 VAL Chi-restraints excluded: chain S residue 198 HIS Chi-restraints excluded: chain S residue 203 TYR Chi-restraints excluded: chain S residue 213 PHE Chi-restraints excluded: chain a residue 610 LEU Chi-restraints excluded: chain a residue 733 ILE Chi-restraints excluded: chain a residue 749 HIS Chi-restraints excluded: chain a residue 752 LEU Chi-restraints excluded: chain a residue 792 LEU Chi-restraints excluded: chain a residue 797 LEU Chi-restraints excluded: chain b residue 94 ILE Chi-restraints excluded: chain b residue 138 PHE Chi-restraints excluded: chain b residue 176 ILE Chi-restraints excluded: chain c residue 431 PHE Chi-restraints excluded: chain c residue 437 LEU Chi-restraints excluded: chain d residue 6 GLU Chi-restraints excluded: chain g residue 13 PHE Chi-restraints excluded: chain g residue 60 VAL Chi-restraints excluded: chain h residue 32 TYR Chi-restraints excluded: chain h residue 101 LEU Chi-restraints excluded: chain h residue 144 TYR Chi-restraints excluded: chain i residue 39 THR Chi-restraints excluded: chain i residue 108 PHE Chi-restraints excluded: chain i residue 123 GLN Chi-restraints excluded: chain i residue 134 ILE Chi-restraints excluded: chain j residue 123 GLN Chi-restraints excluded: chain k residue 7 ASN Chi-restraints excluded: chain k residue 9 GLU Chi-restraints excluded: chain k residue 57 ILE Chi-restraints excluded: chain k residue 140 VAL Chi-restraints excluded: chain k residue 147 ILE Chi-restraints excluded: chain l residue 13 PHE Chi-restraints excluded: chain l residue 53 MET Chi-restraints excluded: chain l residue 67 ILE Chi-restraints excluded: chain m residue 41 ILE Chi-restraints excluded: chain m residue 93 LEU Chi-restraints excluded: chain m residue 108 PHE Chi-restraints excluded: chain m residue 121 THR Chi-restraints excluded: chain n residue 44 MET Chi-restraints excluded: chain n residue 143 LEU Chi-restraints excluded: chain n residue 147 ILE Chi-restraints excluded: chain n residue 150 LEU Chi-restraints excluded: chain o residue 39 THR Chi-restraints excluded: chain p residue 307 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 837 random chunks: chunk 752 optimal weight: 30.0000 chunk 572 optimal weight: 30.0000 chunk 395 optimal weight: 20.0000 chunk 84 optimal weight: 0.9990 chunk 363 optimal weight: 20.0000 chunk 511 optimal weight: 4.9990 chunk 764 optimal weight: 5.9990 chunk 809 optimal weight: 0.7980 chunk 399 optimal weight: 20.0000 chunk 724 optimal weight: 8.9990 chunk 218 optimal weight: 5.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN B 573 HIS C 103 GLN D 358 ASN ** F 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 19 HIS Q 117 GLN Q 135 GLN ** Q 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 17 GLN R 21 GLN S 117 GLN ** S 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 802 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 438 HIS d 145 GLN ** d 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 123 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.4714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 63395 Z= 0.267 Angle : 0.707 12.637 85997 Z= 0.360 Chirality : 0.045 0.299 10036 Planarity : 0.005 0.064 11103 Dihedral : 4.668 138.013 9060 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.40 % Allowed : 13.45 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.09), residues: 8372 helix: 2.03 (0.07), residues: 4948 sheet: -0.25 (0.19), residues: 707 loop : -0.40 (0.12), residues: 2717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 567 HIS 0.009 0.001 HIS c 438 PHE 0.034 0.002 PHE o 90 TYR 0.058 0.002 TYR m 68 ARG 0.012 0.001 ARG M 78 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16744 Ramachandran restraints generated. 8372 Oldfield, 0 Emsley, 8372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16744 Ramachandran restraints generated. 8372 Oldfield, 0 Emsley, 8372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1057 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 911 time to evaluate : 5.313 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.9156 (tpp) cc_final: 0.8695 (tpp) REVERT: A 116 ILE cc_start: 0.9508 (pt) cc_final: 0.9167 (mm) REVERT: A 205 MET cc_start: 0.8854 (pmm) cc_final: 0.8626 (pmm) REVERT: A 254 CYS cc_start: 0.6994 (p) cc_final: 0.6679 (p) REVERT: A 296 MET cc_start: 0.8480 (pmm) cc_final: 0.8249 (pmm) REVERT: A 306 MET cc_start: 0.9301 (mmt) cc_final: 0.8913 (mmt) REVERT: A 309 THR cc_start: 0.9150 (m) cc_final: 0.8715 (p) REVERT: A 346 MET cc_start: 0.8432 (tmm) cc_final: 0.8147 (tmm) REVERT: A 360 GLU cc_start: 0.8761 (tm-30) cc_final: 0.8348 (tm-30) REVERT: A 371 ASP cc_start: 0.9407 (t0) cc_final: 0.9116 (t0) REVERT: A 540 MET cc_start: 0.9416 (mtp) cc_final: 0.9102 (mtp) REVERT: A 567 TRP cc_start: 0.9389 (t-100) cc_final: 0.9056 (t-100) REVERT: A 574 MET cc_start: 0.9188 (ptp) cc_final: 0.8794 (mpp) REVERT: A 608 MET cc_start: 0.8752 (ppp) cc_final: 0.8500 (ppp) REVERT: B 34 MET cc_start: 0.9598 (mmm) cc_final: 0.8564 (mmm) REVERT: B 61 MET cc_start: 0.9409 (mtt) cc_final: 0.8789 (tpp) REVERT: B 306 MET cc_start: 0.9131 (tpp) cc_final: 0.8902 (tpp) REVERT: B 318 MET cc_start: 0.9614 (mtp) cc_final: 0.8951 (mtp) REVERT: B 458 MET cc_start: 0.8882 (mtp) cc_final: 0.8328 (mmm) REVERT: B 480 LYS cc_start: 0.9365 (pttt) cc_final: 0.9052 (pttm) REVERT: B 518 ASP cc_start: 0.7735 (t0) cc_final: 0.7463 (t0) REVERT: B 608 MET cc_start: 0.9041 (mpp) cc_final: 0.8822 (ptp) REVERT: C 65 GLN cc_start: 0.8516 (tp40) cc_final: 0.8100 (tp40) REVERT: C 99 PHE cc_start: 0.9316 (m-80) cc_final: 0.9006 (m-80) REVERT: C 147 ILE cc_start: 0.9676 (pt) cc_final: 0.9476 (mm) REVERT: C 205 MET cc_start: 0.8685 (mtm) cc_final: 0.8087 (ttp) REVERT: C 306 MET cc_start: 0.8753 (OUTLIER) cc_final: 0.8144 (mpp) REVERT: C 318 MET cc_start: 0.9604 (mmm) cc_final: 0.9035 (mmm) REVERT: C 324 GLU cc_start: 0.9505 (tt0) cc_final: 0.9024 (tm-30) REVERT: C 436 ASP cc_start: 0.8507 (t70) cc_final: 0.8162 (t0) REVERT: C 540 MET cc_start: 0.8963 (mtp) cc_final: 0.8556 (mtp) REVERT: C 544 MET cc_start: 0.9073 (mtt) cc_final: 0.8656 (mtm) REVERT: C 550 MET cc_start: 0.9301 (mtm) cc_final: 0.8752 (mtp) REVERT: C 584 MET cc_start: 0.8913 (OUTLIER) cc_final: 0.8631 (mtp) REVERT: D 97 GLN cc_start: 0.9302 (tt0) cc_final: 0.8993 (tm-30) REVERT: D 169 MET cc_start: 0.8878 (tmm) cc_final: 0.8355 (tmm) REVERT: D 231 PHE cc_start: 0.9180 (t80) cc_final: 0.8938 (t80) REVERT: D 234 MET cc_start: 0.8562 (mpp) cc_final: 0.7823 (mtm) REVERT: D 270 GLU cc_start: 0.9340 (OUTLIER) cc_final: 0.8155 (mm-30) REVERT: D 298 THR cc_start: 0.9536 (m) cc_final: 0.9147 (p) REVERT: D 299 ASP cc_start: 0.8970 (m-30) cc_final: 0.8693 (m-30) REVERT: D 300 MET cc_start: 0.9226 (mmm) cc_final: 0.8722 (mmm) REVERT: D 309 GLU cc_start: 0.9303 (tp30) cc_final: 0.8843 (tm-30) REVERT: D 316 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7901 (tm-30) REVERT: D 327 MET cc_start: 0.9389 (ttp) cc_final: 0.9105 (mtp) REVERT: D 356 MET cc_start: 0.8896 (ttm) cc_final: 0.8521 (tpp) REVERT: D 410 MET cc_start: 0.9137 (mtm) cc_final: 0.8130 (ptp) REVERT: D 435 MET cc_start: 0.9421 (tpp) cc_final: 0.9163 (tpp) REVERT: E 87 LEU cc_start: 0.9166 (mt) cc_final: 0.8963 (mt) REVERT: E 127 MET cc_start: 0.9288 (mtp) cc_final: 0.8728 (mtt) REVERT: E 180 MET cc_start: 0.9033 (mmm) cc_final: 0.8293 (mmm) REVERT: E 254 MET cc_start: 0.8693 (mmm) cc_final: 0.8307 (mmm) REVERT: E 305 GLU cc_start: 0.9337 (mt-10) cc_final: 0.9064 (tm-30) REVERT: E 356 MET cc_start: 0.8668 (ttp) cc_final: 0.8141 (ttm) REVERT: E 360 ASP cc_start: 0.8765 (t0) cc_final: 0.8135 (t0) REVERT: E 402 MET cc_start: 0.8607 (mtp) cc_final: 0.8331 (mmm) REVERT: F 97 GLN cc_start: 0.9238 (pt0) cc_final: 0.8418 (pp30) REVERT: F 112 CYS cc_start: 0.9161 (m) cc_final: 0.8647 (p) REVERT: F 127 MET cc_start: 0.9218 (mtp) cc_final: 0.8759 (mtp) REVERT: F 254 MET cc_start: 0.8852 (mmm) cc_final: 0.8305 (tmm) REVERT: F 268 THR cc_start: 0.9561 (p) cc_final: 0.9181 (t) REVERT: F 283 GLU cc_start: 0.9099 (mt-10) cc_final: 0.8869 (mt-10) REVERT: F 305 GLU cc_start: 0.9014 (mt-10) cc_final: 0.8480 (mp0) REVERT: F 356 MET cc_start: 0.8665 (OUTLIER) cc_final: 0.8424 (ttm) REVERT: F 402 MET cc_start: 0.8904 (ttm) cc_final: 0.8256 (ttm) REVERT: F 453 GLU cc_start: 0.9329 (tt0) cc_final: 0.9040 (tp30) REVERT: H 20 LYS cc_start: 0.9397 (mtmt) cc_final: 0.9183 (pttm) REVERT: H 58 MET cc_start: 0.8318 (tmm) cc_final: 0.7882 (tmm) REVERT: H 109 PHE cc_start: 0.8644 (m-80) cc_final: 0.7833 (m-80) REVERT: H 190 GLU cc_start: 0.9284 (mm-30) cc_final: 0.8902 (tm-30) REVERT: H 206 GLN cc_start: 0.9488 (mm-40) cc_final: 0.8577 (tp40) REVERT: I 76 MET cc_start: 0.9208 (mmm) cc_final: 0.9006 (mmm) REVERT: I 129 GLU cc_start: 0.8865 (tm-30) cc_final: 0.8149 (tm-30) REVERT: I 132 MET cc_start: 0.8881 (OUTLIER) cc_final: 0.8644 (mmt) REVERT: I 203 ILE cc_start: 0.9794 (mp) cc_final: 0.9419 (tt) REVERT: J 97 GLU cc_start: 0.9519 (tp30) cc_final: 0.9046 (tp30) REVERT: J 127 LEU cc_start: 0.9479 (mt) cc_final: 0.9244 (mt) REVERT: J 207 MET cc_start: 0.9182 (tpp) cc_final: 0.8700 (tpp) REVERT: K 72 MET cc_start: 0.9391 (ppp) cc_final: 0.9107 (ppp) REVERT: K 76 MET cc_start: 0.9629 (mtm) cc_final: 0.9327 (ptp) REVERT: K 115 LEU cc_start: 0.9828 (OUTLIER) cc_final: 0.9600 (pp) REVERT: K 133 ILE cc_start: 0.9291 (mt) cc_final: 0.8865 (tp) REVERT: K 182 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8043 (tt0) REVERT: K 197 GLU cc_start: 0.9046 (mp0) cc_final: 0.8707 (mp0) REVERT: K 207 MET cc_start: 0.9343 (tpp) cc_final: 0.8796 (tpp) REVERT: K 221 ASN cc_start: 0.9417 (m-40) cc_final: 0.9081 (m110) REVERT: L 20 PHE cc_start: 0.9576 (m-80) cc_final: 0.9250 (m-80) REVERT: L 22 LEU cc_start: 0.9488 (mt) cc_final: 0.9239 (mt) REVERT: L 46 ASN cc_start: 0.9257 (t0) cc_final: 0.8855 (p0) REVERT: L 47 GLU cc_start: 0.9489 (mp0) cc_final: 0.9235 (mp0) REVERT: L 73 MET cc_start: 0.8583 (mtm) cc_final: 0.8210 (mtm) REVERT: L 94 LYS cc_start: 0.8924 (ttpt) cc_final: 0.8602 (ttmt) REVERT: M 102 MET cc_start: 0.9376 (mtp) cc_final: 0.8869 (ttm) REVERT: M 105 ASP cc_start: 0.8553 (t0) cc_final: 0.8175 (t0) REVERT: N 84 MET cc_start: 0.9101 (mtp) cc_final: 0.8757 (ttm) REVERT: N 102 MET cc_start: 0.9512 (mtt) cc_final: 0.9147 (mmm) REVERT: Q 35 THR cc_start: 0.9319 (m) cc_final: 0.9099 (p) REVERT: Q 98 ILE cc_start: 0.9473 (pt) cc_final: 0.9268 (mm) REVERT: Q 179 PHE cc_start: 0.9335 (OUTLIER) cc_final: 0.8965 (t80) REVERT: R 155 MET cc_start: 0.9467 (OUTLIER) cc_final: 0.8989 (mpp) REVERT: R 181 LEU cc_start: 0.9395 (mt) cc_final: 0.9124 (pp) REVERT: S 103 MET cc_start: 0.7941 (tpp) cc_final: 0.7641 (tpp) REVERT: S 115 MET cc_start: 0.9552 (mtt) cc_final: 0.9272 (ptm) REVERT: S 133 LEU cc_start: 0.9654 (pp) cc_final: 0.9416 (pp) REVERT: S 161 MET cc_start: 0.9256 (ppp) cc_final: 0.8999 (ppp) REVERT: S 179 PHE cc_start: 0.9256 (m-80) cc_final: 0.9033 (t80) REVERT: S 229 MET cc_start: 0.9482 (mtp) cc_final: 0.9168 (mmm) REVERT: a 616 MET cc_start: 0.9077 (ttp) cc_final: 0.8491 (ttt) REVERT: a 645 MET cc_start: 0.7740 (ttt) cc_final: 0.7265 (ptt) REVERT: a 713 ASP cc_start: 0.6752 (t0) cc_final: 0.6155 (p0) REVERT: a 743 TRP cc_start: 0.8546 (t60) cc_final: 0.8344 (t60) REVERT: a 805 ARG cc_start: 0.9541 (mtm110) cc_final: 0.9151 (ptt180) REVERT: b 19 MET cc_start: 0.8942 (mtp) cc_final: 0.8332 (mmm) REVERT: b 30 ASP cc_start: 0.8784 (t0) cc_final: 0.8367 (p0) REVERT: b 48 MET cc_start: 0.9453 (OUTLIER) cc_final: 0.9064 (mtp) REVERT: c 420 TRP cc_start: 0.9085 (t-100) cc_final: 0.8535 (t-100) REVERT: c 429 MET cc_start: 0.9274 (ttt) cc_final: 0.8396 (tmm) REVERT: d 118 HIS cc_start: 0.9391 (m-70) cc_final: 0.8856 (m170) REVERT: d 119 GLN cc_start: 0.9333 (tt0) cc_final: 0.8889 (tm-30) REVERT: d 138 MET cc_start: 0.7978 (tpp) cc_final: 0.7348 (tpp) REVERT: d 183 ASN cc_start: 0.9516 (t0) cc_final: 0.9280 (t0) REVERT: d 316 TYR cc_start: 0.9208 (t80) cc_final: 0.8939 (t80) REVERT: d 323 GLU cc_start: 0.9090 (tt0) cc_final: 0.8572 (pt0) REVERT: d 348 ILE cc_start: 0.8540 (mm) cc_final: 0.8055 (mt) REVERT: g 23 MET cc_start: 0.6237 (tpt) cc_final: 0.5800 (tpt) REVERT: g 32 TYR cc_start: 0.8775 (t80) cc_final: 0.8425 (t80) REVERT: g 104 LEU cc_start: 0.9114 (mt) cc_final: 0.8826 (tp) REVERT: h 32 TYR cc_start: 0.6341 (OUTLIER) cc_final: 0.5604 (t80) REVERT: h 76 ILE cc_start: 0.7693 (mt) cc_final: 0.7158 (tt) REVERT: h 104 LEU cc_start: 0.9072 (tp) cc_final: 0.8573 (mt) REVERT: i 23 MET cc_start: 0.7305 (OUTLIER) cc_final: 0.6941 (mmt) REVERT: i 53 MET cc_start: 0.8177 (mmt) cc_final: 0.7208 (mtp) REVERT: i 97 LEU cc_start: 0.9391 (mm) cc_final: 0.9043 (pp) REVERT: i 108 PHE cc_start: 0.7869 (OUTLIER) cc_final: 0.7480 (m-10) REVERT: i 115 ASP cc_start: 0.6287 (t0) cc_final: 0.5796 (p0) REVERT: j 47 MET cc_start: 0.9206 (ppp) cc_final: 0.8949 (ppp) REVERT: j 131 MET cc_start: 0.5644 (ppp) cc_final: 0.5394 (ppp) REVERT: k 17 MET cc_start: 0.8914 (mmp) cc_final: 0.8456 (mmm) REVERT: k 131 MET cc_start: 0.7149 (tmm) cc_final: 0.6336 (ppp) REVERT: k 147 ILE cc_start: 0.7774 (OUTLIER) cc_final: 0.7540 (tt) REVERT: k 152 LEU cc_start: 0.7410 (tp) cc_final: 0.7207 (tp) REVERT: l 23 MET cc_start: 0.8704 (tpp) cc_final: 0.8475 (tpp) REVERT: l 25 PHE cc_start: 0.8966 (m-80) cc_final: 0.8623 (m-80) REVERT: l 47 MET cc_start: 0.8984 (ptm) cc_final: 0.8670 (ppp) REVERT: l 53 MET cc_start: 0.8624 (OUTLIER) cc_final: 0.8275 (ttt) REVERT: l 78 ASN cc_start: 0.6850 (OUTLIER) cc_final: 0.6457 (p0) REVERT: l 104 LEU cc_start: 0.9472 (tp) cc_final: 0.9152 (mt) REVERT: l 115 ASP cc_start: 0.7984 (OUTLIER) cc_final: 0.7563 (m-30) REVERT: m 23 MET cc_start: 0.8358 (tpp) cc_final: 0.7577 (tpt) REVERT: m 32 TYR cc_start: 0.8411 (t80) cc_final: 0.8209 (t80) REVERT: m 37 SER cc_start: 0.9101 (m) cc_final: 0.8805 (p) REVERT: m 143 LEU cc_start: 0.9350 (mm) cc_final: 0.9121 (mp) REVERT: n 13 PHE cc_start: 0.9039 (t80) cc_final: 0.8578 (t80) REVERT: n 17 MET cc_start: 0.9421 (ptt) cc_final: 0.9106 (ptt) REVERT: n 23 MET cc_start: 0.8487 (tpt) cc_final: 0.7418 (tpt) REVERT: n 36 LYS cc_start: 0.7778 (mmtt) cc_final: 0.7178 (mtpp) REVERT: n 53 MET cc_start: 0.7421 (mmp) cc_final: 0.5788 (ttp) REVERT: o 23 MET cc_start: 0.7197 (tpt) cc_final: 0.6292 (tpt) REVERT: o 25 PHE cc_start: 0.8775 (m-80) cc_final: 0.8458 (m-80) REVERT: o 47 MET cc_start: 0.8757 (ptm) cc_final: 0.8457 (ppp) REVERT: o 137 PHE cc_start: 0.8479 (m-80) cc_final: 0.8265 (m-80) outliers start: 146 outliers final: 85 residues processed: 1000 average time/residue: 0.5611 time to fit residues: 972.8609 Evaluate side-chains 923 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 821 time to evaluate : 5.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 450 TRP Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 179 ILE Chi-restraints excluded: chain C residue 306 MET Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 450 TRP Chi-restraints excluded: chain C residue 584 MET Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 207 CYS Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 334 ILE Chi-restraints excluded: chain D residue 378 TYR Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 262 ASN Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 448 ASP Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 262 ASN Chi-restraints excluded: chain F residue 334 ILE Chi-restraints excluded: chain F residue 356 MET Chi-restraints excluded: chain F residue 398 LEU Chi-restraints excluded: chain H residue 79 PHE Chi-restraints excluded: chain H residue 134 LEU Chi-restraints excluded: chain H residue 176 ILE Chi-restraints excluded: chain I residue 132 MET Chi-restraints excluded: chain I residue 167 ILE Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain K residue 128 LEU Chi-restraints excluded: chain K residue 182 GLU Chi-restraints excluded: chain L residue 29 ASN Chi-restraints excluded: chain N residue 94 ARG Chi-restraints excluded: chain Q residue 52 VAL Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 117 GLN Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 121 LEU Chi-restraints excluded: chain Q residue 159 LEU Chi-restraints excluded: chain Q residue 169 THR Chi-restraints excluded: chain Q residue 179 PHE Chi-restraints excluded: chain Q residue 181 LEU Chi-restraints excluded: chain Q residue 198 HIS Chi-restraints excluded: chain R residue 155 MET Chi-restraints excluded: chain S residue 198 HIS Chi-restraints excluded: chain S residue 203 TYR Chi-restraints excluded: chain S residue 213 PHE Chi-restraints excluded: chain a residue 536 PHE Chi-restraints excluded: chain a residue 610 LEU Chi-restraints excluded: chain a residue 733 ILE Chi-restraints excluded: chain a residue 749 HIS Chi-restraints excluded: chain a residue 752 LEU Chi-restraints excluded: chain b residue 48 MET Chi-restraints excluded: chain b residue 94 ILE Chi-restraints excluded: chain b residue 138 PHE Chi-restraints excluded: chain c residue 437 LEU Chi-restraints excluded: chain d residue 6 GLU Chi-restraints excluded: chain e residue 60 LEU Chi-restraints excluded: chain g residue 13 PHE Chi-restraints excluded: chain g residue 60 VAL Chi-restraints excluded: chain g residue 126 ARG Chi-restraints excluded: chain g residue 150 LEU Chi-restraints excluded: chain h residue 32 TYR Chi-restraints excluded: chain h residue 101 LEU Chi-restraints excluded: chain i residue 23 MET Chi-restraints excluded: chain i residue 39 THR Chi-restraints excluded: chain i residue 108 PHE Chi-restraints excluded: chain i residue 134 ILE Chi-restraints excluded: chain j residue 64 ILE Chi-restraints excluded: chain k residue 7 ASN Chi-restraints excluded: chain k residue 13 PHE Chi-restraints excluded: chain k residue 57 ILE Chi-restraints excluded: chain k residue 140 VAL Chi-restraints excluded: chain k residue 147 ILE Chi-restraints excluded: chain l residue 7 ASN Chi-restraints excluded: chain l residue 13 PHE Chi-restraints excluded: chain l residue 53 MET Chi-restraints excluded: chain l residue 78 ASN Chi-restraints excluded: chain l residue 115 ASP Chi-restraints excluded: chain m residue 93 LEU Chi-restraints excluded: chain m residue 108 PHE Chi-restraints excluded: chain m residue 139 GLU Chi-restraints excluded: chain m residue 140 VAL Chi-restraints excluded: chain n residue 143 LEU Chi-restraints excluded: chain n residue 147 ILE Chi-restraints excluded: chain n residue 150 LEU Chi-restraints excluded: chain o residue 39 THR Chi-restraints excluded: chain o residue 118 VAL Chi-restraints excluded: chain p residue 307 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 837 random chunks: chunk 673 optimal weight: 5.9990 chunk 459 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 602 optimal weight: 5.9990 chunk 333 optimal weight: 10.0000 chunk 690 optimal weight: 8.9990 chunk 559 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 413 optimal weight: 5.9990 chunk 726 optimal weight: 40.0000 chunk 204 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 HIS ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 ASN ** C 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 251 ASN ** F 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 74 ASN ** N 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 117 GLN ** Q 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 17 GLN R 117 GLN R 198 HIS ** S 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 802 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.5110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.109 63395 Z= 0.365 Angle : 0.753 12.387 85997 Z= 0.384 Chirality : 0.045 0.295 10036 Planarity : 0.005 0.072 11103 Dihedral : 4.719 140.638 9060 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.14 % Favored : 96.85 % Rotamer: Outliers : 3.08 % Allowed : 14.13 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.09), residues: 8372 helix: 1.90 (0.07), residues: 4974 sheet: -0.37 (0.20), residues: 691 loop : -0.49 (0.12), residues: 2707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 567 HIS 0.008 0.001 HIS B 22 PHE 0.038 0.002 PHE j 25 TYR 0.052 0.002 TYR k 68 ARG 0.011 0.001 ARG k 119 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16744 Ramachandran restraints generated. 8372 Oldfield, 0 Emsley, 8372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16744 Ramachandran restraints generated. 8372 Oldfield, 0 Emsley, 8372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1025 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 838 time to evaluate : 5.910 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: 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: A 61 MET cc_start: 0.9152 (tpp) cc_final: 0.8807 (tpp) REVERT: A 116 ILE cc_start: 0.9531 (pt) cc_final: 0.9194 (mm) REVERT: A 139 LYS cc_start: 0.9202 (OUTLIER) cc_final: 0.8917 (pttm) REVERT: A 205 MET cc_start: 0.8898 (pmm) cc_final: 0.8650 (pmm) REVERT: A 296 MET cc_start: 0.8509 (pmm) cc_final: 0.8230 (pmm) REVERT: A 306 MET cc_start: 0.9230 (mmt) cc_final: 0.8983 (mmt) REVERT: A 340 MET cc_start: 0.9052 (OUTLIER) cc_final: 0.8784 (ttp) REVERT: A 346 MET cc_start: 0.8569 (tmm) cc_final: 0.8228 (tmm) REVERT: A 360 GLU cc_start: 0.8851 (tm-30) cc_final: 0.8582 (tm-30) REVERT: A 371 ASP cc_start: 0.9422 (t0) cc_final: 0.9188 (t0) REVERT: A 540 MET cc_start: 0.9342 (mtp) cc_final: 0.8752 (mtp) REVERT: A 567 TRP cc_start: 0.9384 (t-100) cc_final: 0.8964 (t-100) REVERT: A 574 MET cc_start: 0.9244 (ptp) cc_final: 0.8863 (mpp) REVERT: A 584 MET cc_start: 0.8802 (ptm) cc_final: 0.8186 (ptp) REVERT: B 34 MET cc_start: 0.9608 (mmm) cc_final: 0.8729 (mmm) REVERT: B 306 MET cc_start: 0.9189 (tpp) cc_final: 0.8837 (tpp) REVERT: B 318 MET cc_start: 0.9588 (mtp) cc_final: 0.9017 (mtp) REVERT: B 367 GLU cc_start: 0.8633 (mm-30) cc_final: 0.8414 (mm-30) REVERT: B 458 MET cc_start: 0.8952 (mtp) cc_final: 0.8687 (mmm) REVERT: B 487 GLU cc_start: 0.9055 (tm-30) cc_final: 0.8750 (tm-30) REVERT: B 491 GLU cc_start: 0.8429 (mm-30) cc_final: 0.8029 (mm-30) REVERT: B 518 ASP cc_start: 0.7615 (t0) cc_final: 0.7048 (t0) REVERT: C 65 GLN cc_start: 0.8537 (tp40) cc_final: 0.8115 (tp40) REVERT: C 99 PHE cc_start: 0.9355 (m-80) cc_final: 0.9099 (m-80) REVERT: C 205 MET cc_start: 0.8767 (mtm) cc_final: 0.8143 (ttp) REVERT: C 306 MET cc_start: 0.8752 (OUTLIER) cc_final: 0.8172 (mpp) REVERT: C 318 MET cc_start: 0.9580 (mmm) cc_final: 0.9062 (mmm) REVERT: C 324 GLU cc_start: 0.9515 (tt0) cc_final: 0.8950 (tm-30) REVERT: C 436 ASP cc_start: 0.8514 (t70) cc_final: 0.8200 (t0) REVERT: C 550 MET cc_start: 0.9351 (mtm) cc_final: 0.8783 (mtp) REVERT: D 97 GLN cc_start: 0.9344 (tt0) cc_final: 0.9010 (tm-30) REVERT: D 231 PHE cc_start: 0.9323 (t80) cc_final: 0.9071 (t80) REVERT: D 234 MET cc_start: 0.8770 (mpp) cc_final: 0.8207 (mtm) REVERT: D 270 GLU cc_start: 0.9389 (OUTLIER) cc_final: 0.8212 (mm-30) REVERT: D 299 ASP cc_start: 0.8996 (m-30) cc_final: 0.8678 (m-30) REVERT: D 300 MET cc_start: 0.9363 (mmm) cc_final: 0.9151 (mmm) REVERT: D 309 GLU cc_start: 0.9304 (tp30) cc_final: 0.8902 (tm-30) REVERT: D 314 ARG cc_start: 0.8682 (ttm110) cc_final: 0.8448 (ttm110) REVERT: D 327 MET cc_start: 0.9434 (ttp) cc_final: 0.9093 (mtp) REVERT: D 356 MET cc_start: 0.8708 (ttm) cc_final: 0.8299 (ttm) REVERT: D 435 MET cc_start: 0.9461 (tpp) cc_final: 0.9199 (tpp) REVERT: E 87 LEU cc_start: 0.9227 (mt) cc_final: 0.9000 (mt) REVERT: E 180 MET cc_start: 0.9127 (mmm) cc_final: 0.8340 (mmm) REVERT: E 234 MET cc_start: 0.9126 (ptt) cc_final: 0.8718 (ptt) REVERT: E 254 MET cc_start: 0.8801 (mmm) cc_final: 0.8399 (mmm) REVERT: E 305 GLU cc_start: 0.9352 (mt-10) cc_final: 0.9108 (tm-30) REVERT: E 356 MET cc_start: 0.8711 (ttp) cc_final: 0.8306 (ttp) REVERT: E 360 ASP cc_start: 0.8849 (t0) cc_final: 0.8287 (t0) REVERT: E 402 MET cc_start: 0.8595 (mtp) cc_final: 0.8341 (mmm) REVERT: F 97 GLN cc_start: 0.9264 (pt0) cc_final: 0.8587 (pp30) REVERT: F 112 CYS cc_start: 0.9172 (m) cc_final: 0.8654 (p) REVERT: F 254 MET cc_start: 0.8931 (mmm) cc_final: 0.8407 (tmm) REVERT: F 268 THR cc_start: 0.9532 (p) cc_final: 0.9121 (t) REVERT: F 283 GLU cc_start: 0.9133 (mt-10) cc_final: 0.8896 (mt-10) REVERT: F 300 MET cc_start: 0.9622 (mmm) cc_final: 0.8862 (mmm) REVERT: F 305 GLU cc_start: 0.9026 (mt-10) cc_final: 0.8465 (mp0) REVERT: F 356 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.8481 (ttm) REVERT: F 402 MET cc_start: 0.9051 (ttm) cc_final: 0.8536 (ttm) REVERT: F 410 MET cc_start: 0.9168 (mtm) cc_final: 0.8848 (ptp) REVERT: H 109 PHE cc_start: 0.8647 (m-80) cc_final: 0.7898 (m-80) REVERT: H 190 GLU cc_start: 0.9322 (mm-30) cc_final: 0.8819 (tm-30) REVERT: I 129 GLU cc_start: 0.8927 (tm-30) cc_final: 0.8185 (tm-30) REVERT: I 132 MET cc_start: 0.8917 (OUTLIER) cc_final: 0.8656 (mmt) REVERT: I 203 ILE cc_start: 0.9802 (mp) cc_final: 0.9514 (tt) REVERT: J 97 GLU cc_start: 0.9527 (tp30) cc_final: 0.9068 (tp30) REVERT: J 132 MET cc_start: 0.8459 (mmm) cc_final: 0.8177 (mmm) REVERT: J 207 MET cc_start: 0.9176 (tpp) cc_final: 0.8585 (tpp) REVERT: J 210 GLU cc_start: 0.8717 (mp0) cc_final: 0.8389 (mp0) REVERT: K 72 MET cc_start: 0.9443 (ppp) cc_final: 0.9215 (ppp) REVERT: K 76 MET cc_start: 0.9637 (mtm) cc_final: 0.9380 (ptp) REVERT: K 97 GLU cc_start: 0.9377 (tp30) cc_final: 0.8905 (tm-30) REVERT: K 133 ILE cc_start: 0.9324 (mt) cc_final: 0.8923 (tp) REVERT: K 182 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8076 (tt0) REVERT: K 197 GLU cc_start: 0.9071 (mp0) cc_final: 0.8741 (mp0) REVERT: K 207 MET cc_start: 0.9371 (tpp) cc_final: 0.9153 (tpp) REVERT: K 208 MET cc_start: 0.9333 (mmt) cc_final: 0.9046 (mmm) REVERT: L 22 LEU cc_start: 0.9521 (mt) cc_final: 0.9294 (mt) REVERT: L 47 GLU cc_start: 0.9505 (mp0) cc_final: 0.9296 (pm20) REVERT: L 73 MET cc_start: 0.8563 (mtm) cc_final: 0.8107 (mtp) REVERT: L 94 LYS cc_start: 0.8919 (ttpt) cc_final: 0.8584 (ttmt) REVERT: M 102 MET cc_start: 0.9404 (OUTLIER) cc_final: 0.8999 (ttm) REVERT: M 105 ASP cc_start: 0.8636 (t0) cc_final: 0.8296 (t0) REVERT: N 84 MET cc_start: 0.9091 (mtp) cc_final: 0.8807 (ttm) REVERT: N 102 MET cc_start: 0.9492 (mtt) cc_final: 0.9150 (mmm) REVERT: Q 35 THR cc_start: 0.9302 (m) cc_final: 0.9093 (p) REVERT: Q 161 MET cc_start: 0.9356 (tmm) cc_final: 0.9072 (ppp) REVERT: Q 179 PHE cc_start: 0.9350 (OUTLIER) cc_final: 0.8944 (t80) REVERT: R 155 MET cc_start: 0.9469 (OUTLIER) cc_final: 0.9040 (mpp) REVERT: R 161 MET cc_start: 0.9343 (tmm) cc_final: 0.9091 (ppp) REVERT: R 181 LEU cc_start: 0.9428 (mt) cc_final: 0.9198 (pp) REVERT: S 103 MET cc_start: 0.7969 (tpp) cc_final: 0.7701 (tpp) REVERT: S 115 MET cc_start: 0.9547 (mtt) cc_final: 0.9281 (ptm) REVERT: S 133 LEU cc_start: 0.9683 (pp) cc_final: 0.9457 (pp) REVERT: S 161 MET cc_start: 0.9372 (ppp) cc_final: 0.9111 (ppp) REVERT: S 179 PHE cc_start: 0.9317 (m-80) cc_final: 0.9022 (t80) REVERT: S 188 MET cc_start: 0.9242 (mmp) cc_final: 0.9009 (mmm) REVERT: S 229 MET cc_start: 0.9531 (mtp) cc_final: 0.9195 (mmm) REVERT: a 423 MET cc_start: 0.8474 (ttp) cc_final: 0.8211 (ptm) REVERT: a 447 ARG cc_start: 0.7185 (OUTLIER) cc_final: 0.6131 (ptp90) REVERT: a 538 MET cc_start: 0.6002 (ppp) cc_final: 0.5713 (ppp) REVERT: a 616 MET cc_start: 0.9090 (ttp) cc_final: 0.8423 (ttt) REVERT: a 645 MET cc_start: 0.7717 (ttt) cc_final: 0.7217 (ptt) REVERT: a 651 MET cc_start: 0.6709 (mtm) cc_final: 0.6242 (pmm) REVERT: a 791 LEU cc_start: 0.9540 (OUTLIER) cc_final: 0.9032 (tp) REVERT: b 48 MET cc_start: 0.9493 (OUTLIER) cc_final: 0.9207 (mtp) REVERT: b 137 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.8338 (tpp) REVERT: c 421 MET cc_start: 0.8954 (mtt) cc_final: 0.8459 (mmt) REVERT: c 429 MET cc_start: 0.9311 (ttt) cc_final: 0.8439 (tmm) REVERT: c 451 ASP cc_start: 0.3887 (t0) cc_final: 0.3224 (p0) REVERT: d 118 HIS cc_start: 0.9393 (m-70) cc_final: 0.9181 (m-70) REVERT: d 119 GLN cc_start: 0.9332 (tt0) cc_final: 0.8810 (tm-30) REVERT: d 138 MET cc_start: 0.8081 (tpp) cc_final: 0.7661 (tpp) REVERT: d 316 TYR cc_start: 0.9259 (t80) cc_final: 0.9038 (t80) REVERT: d 323 GLU cc_start: 0.9130 (tt0) cc_final: 0.8680 (pt0) REVERT: d 348 ILE cc_start: 0.8559 (mm) cc_final: 0.8175 (mt) REVERT: g 23 MET cc_start: 0.6256 (tpt) cc_final: 0.5797 (tpt) REVERT: g 32 TYR cc_start: 0.8856 (t80) cc_final: 0.8457 (t80) REVERT: g 101 LEU cc_start: 0.9123 (tp) cc_final: 0.8473 (mt) REVERT: g 104 LEU cc_start: 0.9077 (mt) cc_final: 0.8844 (tp) REVERT: h 32 TYR cc_start: 0.6278 (OUTLIER) cc_final: 0.5503 (t80) REVERT: h 76 ILE cc_start: 0.7797 (mt) cc_final: 0.7249 (tt) REVERT: h 104 LEU cc_start: 0.9116 (tp) cc_final: 0.8641 (mt) REVERT: i 23 MET cc_start: 0.7416 (OUTLIER) cc_final: 0.7064 (mmt) REVERT: i 53 MET cc_start: 0.7915 (mmt) cc_final: 0.7126 (mtp) REVERT: i 65 ILE cc_start: 0.8016 (mm) cc_final: 0.7760 (mt) REVERT: i 97 LEU cc_start: 0.9428 (mm) cc_final: 0.9096 (pp) REVERT: i 108 PHE cc_start: 0.7902 (OUTLIER) cc_final: 0.7535 (m-10) REVERT: j 34 THR cc_start: 0.8533 (p) cc_final: 0.8322 (p) REVERT: j 47 MET cc_start: 0.9147 (ppp) cc_final: 0.8733 (ppp) REVERT: j 131 MET cc_start: 0.5555 (ppp) cc_final: 0.5340 (ppp) REVERT: j 144 TYR cc_start: 0.7492 (m-10) cc_final: 0.7289 (m-10) REVERT: k 23 MET cc_start: 0.6726 (tpt) cc_final: 0.6360 (tpt) REVERT: k 131 MET cc_start: 0.7145 (tmm) cc_final: 0.6357 (ppp) REVERT: k 147 ILE cc_start: 0.7462 (OUTLIER) cc_final: 0.7158 (tt) REVERT: l 23 MET cc_start: 0.8700 (tpp) cc_final: 0.8456 (tpp) REVERT: l 25 PHE cc_start: 0.8959 (m-80) cc_final: 0.8614 (m-80) REVERT: l 28 MET cc_start: 0.8790 (mmp) cc_final: 0.8581 (mmp) REVERT: l 47 MET cc_start: 0.8929 (OUTLIER) cc_final: 0.8670 (ppp) REVERT: l 48 ARG cc_start: 0.9279 (OUTLIER) cc_final: 0.8720 (ttm170) REVERT: l 53 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.8307 (ttt) REVERT: l 78 ASN cc_start: 0.6785 (OUTLIER) cc_final: 0.6394 (p0) REVERT: l 104 LEU cc_start: 0.9433 (tp) cc_final: 0.9103 (mt) REVERT: l 115 ASP cc_start: 0.7980 (t0) cc_final: 0.7608 (m-30) REVERT: m 23 MET cc_start: 0.8517 (tpp) cc_final: 0.7856 (tpt) REVERT: m 32 TYR cc_start: 0.8503 (t80) cc_final: 0.8113 (t80) REVERT: m 37 SER cc_start: 0.9125 (m) cc_final: 0.8863 (p) REVERT: m 144 TYR cc_start: 0.9388 (m-10) cc_final: 0.8872 (m-10) REVERT: n 13 PHE cc_start: 0.9027 (t80) cc_final: 0.8386 (t80) REVERT: n 17 MET cc_start: 0.9420 (ptt) cc_final: 0.8997 (ptt) REVERT: n 36 LYS cc_start: 0.7767 (mmtt) cc_final: 0.7316 (mtpp) REVERT: o 23 MET cc_start: 0.7341 (tpt) cc_final: 0.6397 (tpt) REVERT: o 25 PHE cc_start: 0.8759 (m-80) cc_final: 0.8401 (m-80) REVERT: p 314 MET cc_start: 0.9206 (mtm) cc_final: 0.8892 (mtm) REVERT: p 328 ILE cc_start: 0.9588 (mm) cc_final: 0.9336 (pt) outliers start: 187 outliers final: 106 residues processed: 956 average time/residue: 0.6085 time to fit residues: 1012.1573 Evaluate side-chains 910 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 782 time to evaluate : 5.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 450 TRP Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 117 TYR Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 179 ILE Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 306 MET Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 450 TRP Chi-restraints excluded: chain C residue 584 MET Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 334 ILE Chi-restraints excluded: chain D residue 378 TYR Chi-restraints excluded: chain D residue 491 MET Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 262 ASN Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 432 VAL Chi-restraints excluded: chain E residue 448 ASP Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 262 ASN Chi-restraints excluded: chain F residue 281 THR Chi-restraints excluded: chain F residue 330 ASP Chi-restraints excluded: chain F residue 334 ILE Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain F residue 356 MET Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain H residue 49 LYS Chi-restraints excluded: chain H residue 67 PHE Chi-restraints excluded: chain H residue 79 PHE Chi-restraints excluded: chain H residue 134 LEU Chi-restraints excluded: chain I residue 132 MET Chi-restraints excluded: chain I residue 167 ILE Chi-restraints excluded: chain K residue 128 LEU Chi-restraints excluded: chain K residue 182 GLU Chi-restraints excluded: chain L residue 29 ASN Chi-restraints excluded: chain M residue 102 MET Chi-restraints excluded: chain N residue 94 ARG Chi-restraints excluded: chain O residue 74 GLU Chi-restraints excluded: chain Q residue 52 VAL Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 121 LEU Chi-restraints excluded: chain Q residue 159 LEU Chi-restraints excluded: chain Q residue 169 THR Chi-restraints excluded: chain Q residue 179 PHE Chi-restraints excluded: chain Q residue 181 LEU Chi-restraints excluded: chain Q residue 198 HIS Chi-restraints excluded: chain R residue 155 MET Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain S residue 198 HIS Chi-restraints excluded: chain S residue 203 TYR Chi-restraints excluded: chain a residue 447 ARG Chi-restraints excluded: chain a residue 536 PHE Chi-restraints excluded: chain a residue 610 LEU Chi-restraints excluded: chain a residue 749 HIS Chi-restraints excluded: chain a residue 752 LEU Chi-restraints excluded: chain a residue 791 LEU Chi-restraints excluded: chain b residue 48 MET Chi-restraints excluded: chain b residue 94 ILE Chi-restraints excluded: chain b residue 137 MET Chi-restraints excluded: chain b residue 138 PHE Chi-restraints excluded: chain b residue 195 ILE Chi-restraints excluded: chain d residue 6 GLU Chi-restraints excluded: chain e residue 60 LEU Chi-restraints excluded: chain g residue 13 PHE Chi-restraints excluded: chain g residue 60 VAL Chi-restraints excluded: chain g residue 126 ARG Chi-restraints excluded: chain g residue 150 LEU Chi-restraints excluded: chain h residue 32 TYR Chi-restraints excluded: chain h residue 115 ASP Chi-restraints excluded: chain h residue 144 TYR Chi-restraints excluded: chain i residue 23 MET Chi-restraints excluded: chain i residue 39 THR Chi-restraints excluded: chain i residue 108 PHE Chi-restraints excluded: chain i residue 134 ILE Chi-restraints excluded: chain j residue 64 ILE Chi-restraints excluded: chain j residue 123 GLN Chi-restraints excluded: chain j residue 140 VAL Chi-restraints excluded: chain k residue 7 ASN Chi-restraints excluded: chain k residue 13 PHE Chi-restraints excluded: chain k residue 57 ILE Chi-restraints excluded: chain k residue 108 PHE Chi-restraints excluded: chain k residue 119 ARG Chi-restraints excluded: chain k residue 140 VAL Chi-restraints excluded: chain k residue 147 ILE Chi-restraints excluded: chain l residue 7 ASN Chi-restraints excluded: chain l residue 13 PHE Chi-restraints excluded: chain l residue 47 MET Chi-restraints excluded: chain l residue 48 ARG Chi-restraints excluded: chain l residue 53 MET Chi-restraints excluded: chain l residue 67 ILE Chi-restraints excluded: chain l residue 78 ASN Chi-restraints excluded: chain l residue 140 VAL Chi-restraints excluded: chain l residue 152 LEU Chi-restraints excluded: chain m residue 93 LEU Chi-restraints excluded: chain m residue 108 PHE Chi-restraints excluded: chain m residue 139 GLU Chi-restraints excluded: chain m residue 140 VAL Chi-restraints excluded: chain n residue 133 LEU Chi-restraints excluded: chain n residue 150 LEU Chi-restraints excluded: chain o residue 118 VAL Chi-restraints excluded: chain p residue 307 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 837 random chunks: chunk 272 optimal weight: 2.9990 chunk 728 optimal weight: 40.0000 chunk 159 optimal weight: 7.9990 chunk 475 optimal weight: 10.0000 chunk 199 optimal weight: 0.9990 chunk 809 optimal weight: 0.0070 chunk 672 optimal weight: 8.9990 chunk 374 optimal weight: 20.0000 chunk 67 optimal weight: 1.9990 chunk 267 optimal weight: 5.9990 chunk 425 optimal weight: 5.9990 overall best weight: 2.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 543 ASN ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 ASN ** C 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 376 GLN ** H 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 117 GLN Q 142 ASN ** Q 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 17 GLN ** a 802 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 438 HIS d 171 GLN ** d 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.5250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 63395 Z= 0.227 Angle : 0.717 14.069 85997 Z= 0.355 Chirality : 0.044 0.271 10036 Planarity : 0.004 0.073 11103 Dihedral : 4.592 138.195 9060 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.87 % Favored : 97.12 % Rotamer: Outliers : 2.52 % Allowed : 15.36 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.09), residues: 8372 helix: 2.06 (0.07), residues: 4944 sheet: -0.22 (0.20), residues: 662 loop : -0.46 (0.12), residues: 2766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 567 HIS 0.008 0.001 HIS a 802 PHE 0.048 0.002 PHE j 25 TYR 0.062 0.002 TYR m 68 ARG 0.011 0.000 ARG k 119 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16744 Ramachandran restraints generated. 8372 Oldfield, 0 Emsley, 8372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16744 Ramachandran restraints generated. 8372 Oldfield, 0 Emsley, 8372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1022 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 869 time to evaluate : 5.374 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: 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: A 34 MET cc_start: 0.8860 (mmm) cc_final: 0.8650 (mmm) REVERT: A 61 MET cc_start: 0.9151 (tpp) cc_final: 0.8700 (tpp) REVERT: A 116 ILE cc_start: 0.9503 (pt) cc_final: 0.9196 (mm) REVERT: A 139 LYS cc_start: 0.9190 (OUTLIER) cc_final: 0.8935 (pttm) REVERT: A 205 MET cc_start: 0.8913 (pmm) cc_final: 0.8447 (pmm) REVERT: A 246 THR cc_start: 0.9019 (t) cc_final: 0.8680 (m) REVERT: A 254 CYS cc_start: 0.6856 (p) cc_final: 0.6592 (p) REVERT: A 296 MET cc_start: 0.8445 (pmm) cc_final: 0.8225 (pmm) REVERT: A 340 MET cc_start: 0.8982 (OUTLIER) cc_final: 0.8635 (ttp) REVERT: A 346 MET cc_start: 0.8561 (tmm) cc_final: 0.8269 (tmm) REVERT: A 360 GLU cc_start: 0.8857 (tm-30) cc_final: 0.8514 (tm-30) REVERT: A 371 ASP cc_start: 0.9414 (t0) cc_final: 0.9106 (t0) REVERT: A 540 MET cc_start: 0.9325 (mtp) cc_final: 0.8877 (mtp) REVERT: A 567 TRP cc_start: 0.9372 (t-100) cc_final: 0.8935 (t-100) REVERT: A 574 MET cc_start: 0.9190 (ptp) cc_final: 0.8892 (mpp) REVERT: A 584 MET cc_start: 0.8770 (ptm) cc_final: 0.8189 (ptp) REVERT: B 34 MET cc_start: 0.9612 (mmm) cc_final: 0.8721 (mmm) REVERT: B 42 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8848 (mm) REVERT: B 61 MET cc_start: 0.9353 (mtt) cc_final: 0.9011 (tpp) REVERT: B 80 LEU cc_start: 0.9544 (tp) cc_final: 0.9183 (pp) REVERT: B 95 MET cc_start: 0.8847 (tpp) cc_final: 0.8590 (tpp) REVERT: B 306 MET cc_start: 0.9232 (tpp) cc_final: 0.8842 (tpp) REVERT: B 318 MET cc_start: 0.9588 (mtp) cc_final: 0.8803 (mtp) REVERT: B 340 MET cc_start: 0.9116 (ttm) cc_final: 0.8847 (tpp) REVERT: B 367 GLU cc_start: 0.8596 (mm-30) cc_final: 0.8367 (mm-30) REVERT: B 458 MET cc_start: 0.8914 (mtp) cc_final: 0.8634 (mmm) REVERT: B 487 GLU cc_start: 0.9043 (tm-30) cc_final: 0.8647 (tm-30) REVERT: B 491 GLU cc_start: 0.8499 (mm-30) cc_final: 0.8047 (mm-30) REVERT: B 571 ARG cc_start: 0.9380 (ttt180) cc_final: 0.9172 (ptm160) REVERT: C 61 MET cc_start: 0.9013 (mmm) cc_final: 0.8450 (mmm) REVERT: C 65 GLN cc_start: 0.8465 (tp40) cc_final: 0.8070 (tp40) REVERT: C 99 PHE cc_start: 0.9301 (m-80) cc_final: 0.9041 (m-80) REVERT: C 205 MET cc_start: 0.8743 (mtm) cc_final: 0.8199 (ttp) REVERT: C 306 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.8129 (mpp) REVERT: C 318 MET cc_start: 0.9594 (mmm) cc_final: 0.9104 (mmm) REVERT: C 324 GLU cc_start: 0.9511 (tt0) cc_final: 0.9012 (tm-30) REVERT: C 436 ASP cc_start: 0.8506 (t70) cc_final: 0.8181 (t0) REVERT: C 550 MET cc_start: 0.9356 (mtm) cc_final: 0.8887 (mtp) REVERT: D 97 GLN cc_start: 0.9279 (tt0) cc_final: 0.8944 (tm-30) REVERT: D 234 MET cc_start: 0.8613 (mpp) cc_final: 0.8148 (mtm) REVERT: D 270 GLU cc_start: 0.9354 (OUTLIER) cc_final: 0.8113 (mm-30) REVERT: D 299 ASP cc_start: 0.8878 (m-30) cc_final: 0.8526 (m-30) REVERT: D 300 MET cc_start: 0.9283 (mmm) cc_final: 0.8773 (mmm) REVERT: D 309 GLU cc_start: 0.9317 (tp30) cc_final: 0.8842 (tm-30) REVERT: D 327 MET cc_start: 0.9412 (ttp) cc_final: 0.9023 (mtp) REVERT: D 356 MET cc_start: 0.8719 (ttm) cc_final: 0.8393 (ttm) REVERT: D 410 MET cc_start: 0.9118 (mtm) cc_final: 0.8119 (ptp) REVERT: D 435 MET cc_start: 0.9440 (tpp) cc_final: 0.9165 (tpp) REVERT: E 87 LEU cc_start: 0.9135 (mt) cc_final: 0.8913 (mt) REVERT: E 180 MET cc_start: 0.9071 (mmm) cc_final: 0.8221 (mmm) REVERT: E 201 GLU cc_start: 0.9010 (mp0) cc_final: 0.8788 (mp0) REVERT: E 234 MET cc_start: 0.8987 (ptt) cc_final: 0.8608 (ptt) REVERT: E 254 MET cc_start: 0.8811 (mmm) cc_final: 0.8299 (mmm) REVERT: E 305 GLU cc_start: 0.9276 (mt-10) cc_final: 0.9035 (tm-30) REVERT: E 356 MET cc_start: 0.8673 (ttp) cc_final: 0.8209 (ttp) REVERT: E 360 ASP cc_start: 0.8875 (t0) cc_final: 0.8337 (t0) REVERT: E 402 MET cc_start: 0.8572 (mtp) cc_final: 0.8317 (mmm) REVERT: F 97 GLN cc_start: 0.9241 (pt0) cc_final: 0.8507 (pp30) REVERT: F 254 MET cc_start: 0.8849 (mmm) cc_final: 0.8263 (tmm) REVERT: F 268 THR cc_start: 0.9547 (p) cc_final: 0.9123 (t) REVERT: F 270 GLU cc_start: 0.9265 (pt0) cc_final: 0.8855 (pt0) REVERT: F 305 GLU cc_start: 0.9025 (mt-10) cc_final: 0.8458 (mp0) REVERT: F 309 GLU cc_start: 0.9442 (tt0) cc_final: 0.9015 (tp30) REVERT: F 356 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.8433 (ttm) REVERT: F 376 GLN cc_start: 0.9435 (OUTLIER) cc_final: 0.8940 (pm20) REVERT: F 402 MET cc_start: 0.8938 (ttm) cc_final: 0.8447 (ttm) REVERT: F 410 MET cc_start: 0.9079 (mtm) cc_final: 0.8850 (ptp) REVERT: H 58 MET cc_start: 0.8520 (tmm) cc_final: 0.8301 (tmm) REVERT: H 109 PHE cc_start: 0.8572 (m-80) cc_final: 0.7798 (m-80) REVERT: H 190 GLU cc_start: 0.9320 (mm-30) cc_final: 0.8873 (tm-30) REVERT: I 129 GLU cc_start: 0.8842 (tm-30) cc_final: 0.8146 (tm-30) REVERT: I 132 MET cc_start: 0.8846 (OUTLIER) cc_final: 0.8637 (mmt) REVERT: I 203 ILE cc_start: 0.9785 (mp) cc_final: 0.9488 (tt) REVERT: I 208 MET cc_start: 0.9503 (mmm) cc_final: 0.9294 (mmm) REVERT: J 97 GLU cc_start: 0.9523 (tp30) cc_final: 0.9034 (tp30) REVERT: J 127 LEU cc_start: 0.9514 (mt) cc_final: 0.9259 (mt) REVERT: J 207 MET cc_start: 0.9136 (tpp) cc_final: 0.8628 (tpp) REVERT: J 210 GLU cc_start: 0.8592 (mp0) cc_final: 0.8352 (mp0) REVERT: K 72 MET cc_start: 0.9415 (ppp) cc_final: 0.9194 (ppp) REVERT: K 76 MET cc_start: 0.9628 (mtm) cc_final: 0.9415 (ptp) REVERT: K 97 GLU cc_start: 0.9359 (tp30) cc_final: 0.8993 (tm-30) REVERT: K 133 ILE cc_start: 0.9295 (mt) cc_final: 0.8897 (tp) REVERT: K 182 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8089 (tt0) REVERT: K 197 GLU cc_start: 0.9040 (mp0) cc_final: 0.8694 (mp0) REVERT: K 207 MET cc_start: 0.9340 (tpp) cc_final: 0.9113 (tpp) REVERT: K 208 MET cc_start: 0.9314 (mmt) cc_final: 0.9008 (mmm) REVERT: L 20 PHE cc_start: 0.9601 (m-80) cc_final: 0.9289 (m-80) REVERT: L 22 LEU cc_start: 0.9535 (mt) cc_final: 0.9319 (mt) REVERT: L 47 GLU cc_start: 0.9510 (mp0) cc_final: 0.9307 (pm20) REVERT: L 73 MET cc_start: 0.8468 (mtm) cc_final: 0.8001 (mtp) REVERT: L 94 LYS cc_start: 0.8936 (ttpt) cc_final: 0.8574 (ttmt) REVERT: M 102 MET cc_start: 0.9370 (mtp) cc_final: 0.8981 (ttm) REVERT: M 105 ASP cc_start: 0.8601 (t0) cc_final: 0.8240 (t0) REVERT: N 79 ARG cc_start: 0.9459 (ttm110) cc_final: 0.9196 (ttm110) REVERT: N 84 MET cc_start: 0.9055 (mtp) cc_final: 0.8769 (ttm) REVERT: N 102 MET cc_start: 0.9482 (mtt) cc_final: 0.9176 (mmm) REVERT: O 102 MET cc_start: 0.9347 (mtp) cc_final: 0.9101 (ptm) REVERT: Q 35 THR cc_start: 0.9256 (m) cc_final: 0.9030 (p) REVERT: Q 179 PHE cc_start: 0.9331 (OUTLIER) cc_final: 0.8951 (t80) REVERT: R 155 MET cc_start: 0.9499 (OUTLIER) cc_final: 0.9065 (mpp) REVERT: R 181 LEU cc_start: 0.9422 (mt) cc_final: 0.9166 (pp) REVERT: S 115 MET cc_start: 0.9550 (mtt) cc_final: 0.9250 (ptm) REVERT: S 133 LEU cc_start: 0.9668 (OUTLIER) cc_final: 0.9444 (pp) REVERT: S 179 PHE cc_start: 0.9297 (m-80) cc_final: 0.9036 (t80) REVERT: S 188 MET cc_start: 0.9223 (mmp) cc_final: 0.8942 (mmp) REVERT: S 203 TYR cc_start: 0.8822 (OUTLIER) cc_final: 0.8157 (t80) REVERT: S 229 MET cc_start: 0.9468 (mtp) cc_final: 0.9158 (mmm) REVERT: a 447 ARG cc_start: 0.7155 (OUTLIER) cc_final: 0.6221 (ptp90) REVERT: a 538 MET cc_start: 0.5883 (ppp) cc_final: 0.5650 (ppp) REVERT: a 616 MET cc_start: 0.9088 (ttp) cc_final: 0.8394 (ttt) REVERT: a 645 MET cc_start: 0.7717 (ttt) cc_final: 0.7174 (ptt) REVERT: a 651 MET cc_start: 0.6415 (mtm) cc_final: 0.5928 (mtt) REVERT: a 791 LEU cc_start: 0.9481 (OUTLIER) cc_final: 0.8876 (tp) REVERT: b 48 MET cc_start: 0.9474 (OUTLIER) cc_final: 0.8998 (mtp) REVERT: b 137 MET cc_start: 0.8572 (OUTLIER) cc_final: 0.8256 (tpp) REVERT: c 429 MET cc_start: 0.9286 (ttt) cc_final: 0.8418 (tmm) REVERT: c 451 ASP cc_start: 0.4036 (t0) cc_final: 0.3318 (p0) REVERT: d 118 HIS cc_start: 0.9366 (m-70) cc_final: 0.9137 (m-70) REVERT: d 119 GLN cc_start: 0.9320 (tt0) cc_final: 0.8807 (tm-30) REVERT: d 138 MET cc_start: 0.8088 (tpp) cc_final: 0.7661 (tpp) REVERT: d 323 GLU cc_start: 0.9106 (tt0) cc_final: 0.8625 (pt0) REVERT: d 348 ILE cc_start: 0.8530 (mm) cc_final: 0.8291 (mm) REVERT: g 23 MET cc_start: 0.6086 (tpt) cc_final: 0.5624 (tpt) REVERT: g 32 TYR cc_start: 0.8859 (t80) cc_final: 0.8384 (t80) REVERT: g 101 LEU cc_start: 0.9070 (tp) cc_final: 0.8416 (mt) REVERT: g 104 LEU cc_start: 0.9054 (mt) cc_final: 0.8846 (tp) REVERT: h 32 TYR cc_start: 0.6288 (OUTLIER) cc_final: 0.5488 (t80) REVERT: h 76 ILE cc_start: 0.7817 (mt) cc_final: 0.7523 (tt) REVERT: h 104 LEU cc_start: 0.9123 (tp) cc_final: 0.8769 (mt) REVERT: i 23 MET cc_start: 0.7461 (OUTLIER) cc_final: 0.7060 (mmt) REVERT: i 53 MET cc_start: 0.8005 (mmt) cc_final: 0.7063 (mtp) REVERT: i 65 ILE cc_start: 0.8039 (mm) cc_final: 0.7778 (mt) REVERT: i 97 LEU cc_start: 0.9360 (mm) cc_final: 0.9026 (pp) REVERT: i 108 PHE cc_start: 0.7846 (OUTLIER) cc_final: 0.7475 (m-10) REVERT: j 47 MET cc_start: 0.9094 (ppp) cc_final: 0.8775 (ppp) REVERT: j 61 MET cc_start: 0.6624 (ttm) cc_final: 0.6162 (ptm) REVERT: j 131 MET cc_start: 0.5538 (ppp) cc_final: 0.5331 (ppp) REVERT: j 144 TYR cc_start: 0.7476 (m-10) cc_final: 0.7214 (m-10) REVERT: k 17 MET cc_start: 0.8938 (mmp) cc_final: 0.8390 (mmm) REVERT: k 23 MET cc_start: 0.7402 (tpt) cc_final: 0.6880 (tpt) REVERT: k 68 TYR cc_start: 0.6259 (m-80) cc_final: 0.5599 (m-80) REVERT: k 131 MET cc_start: 0.7008 (tmm) cc_final: 0.6287 (ppp) REVERT: k 147 ILE cc_start: 0.7460 (OUTLIER) cc_final: 0.7095 (tt) REVERT: l 53 MET cc_start: 0.8648 (OUTLIER) cc_final: 0.8339 (ttt) REVERT: l 78 ASN cc_start: 0.6609 (OUTLIER) cc_final: 0.6298 (p0) REVERT: l 104 LEU cc_start: 0.9435 (tp) cc_final: 0.9218 (mt) REVERT: m 23 MET cc_start: 0.8524 (tpp) cc_final: 0.7819 (tpt) REVERT: m 28 MET cc_start: 0.8950 (mmp) cc_final: 0.8746 (mmm) REVERT: m 32 TYR cc_start: 0.8465 (t80) cc_final: 0.8044 (t80) REVERT: m 93 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8939 (tp) REVERT: n 13 PHE cc_start: 0.9028 (t80) cc_final: 0.8636 (t80) REVERT: n 17 MET cc_start: 0.9409 (ptt) cc_final: 0.9155 (ptt) REVERT: n 23 MET cc_start: 0.8505 (tpt) cc_final: 0.7510 (tpt) REVERT: n 36 LYS cc_start: 0.7576 (mmtt) cc_final: 0.7114 (mtpp) REVERT: n 44 MET cc_start: 0.9087 (tpt) cc_final: 0.8788 (tpt) REVERT: n 123 GLN cc_start: 0.8566 (mp10) cc_final: 0.7711 (mt0) REVERT: o 21 SER cc_start: 0.9662 (m) cc_final: 0.9040 (p) REVERT: o 23 MET cc_start: 0.7336 (tpt) cc_final: 0.6397 (tpt) REVERT: o 25 PHE cc_start: 0.8743 (m-80) cc_final: 0.8439 (m-80) REVERT: o 32 TYR cc_start: 0.8766 (t80) cc_final: 0.8402 (t80) outliers start: 153 outliers final: 95 residues processed: 967 average time/residue: 0.5725 time to fit residues: 961.1461 Evaluate side-chains 919 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 800 time to evaluate : 5.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 450 TRP Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 179 ILE Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 306 MET Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 450 TRP Chi-restraints excluded: chain C residue 584 MET Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 207 CYS Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 334 ILE Chi-restraints excluded: chain D residue 378 TYR Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 262 ASN Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 448 ASP Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 262 ASN Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 334 ILE Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain F residue 356 MET Chi-restraints excluded: chain F residue 376 GLN Chi-restraints excluded: chain H residue 79 PHE Chi-restraints excluded: chain H residue 134 LEU Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 132 MET Chi-restraints excluded: chain I residue 167 ILE Chi-restraints excluded: chain K residue 128 LEU Chi-restraints excluded: chain K residue 182 GLU Chi-restraints excluded: chain L residue 29 ASN Chi-restraints excluded: chain L residue 81 HIS Chi-restraints excluded: chain N residue 70 SER Chi-restraints excluded: chain N residue 74 GLU Chi-restraints excluded: chain O residue 74 GLU Chi-restraints excluded: chain Q residue 52 VAL Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 117 GLN Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 121 LEU Chi-restraints excluded: chain Q residue 159 LEU Chi-restraints excluded: chain Q residue 169 THR Chi-restraints excluded: chain Q residue 179 PHE Chi-restraints excluded: chain Q residue 181 LEU Chi-restraints excluded: chain Q residue 198 HIS Chi-restraints excluded: chain R residue 155 MET Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain S residue 133 LEU Chi-restraints excluded: chain S residue 198 HIS Chi-restraints excluded: chain S residue 203 TYR Chi-restraints excluded: chain a residue 447 ARG Chi-restraints excluded: chain a residue 536 PHE Chi-restraints excluded: chain a residue 610 LEU Chi-restraints excluded: chain a residue 733 ILE Chi-restraints excluded: chain a residue 749 HIS Chi-restraints excluded: chain a residue 752 LEU Chi-restraints excluded: chain a residue 791 LEU Chi-restraints excluded: chain b residue 48 MET Chi-restraints excluded: chain b residue 94 ILE Chi-restraints excluded: chain b residue 137 MET Chi-restraints excluded: chain b residue 138 PHE Chi-restraints excluded: chain b residue 195 ILE Chi-restraints excluded: chain c residue 415 PHE Chi-restraints excluded: chain d residue 6 GLU Chi-restraints excluded: chain d residue 171 GLN Chi-restraints excluded: chain e residue 60 LEU Chi-restraints excluded: chain g residue 13 PHE Chi-restraints excluded: chain g residue 60 VAL Chi-restraints excluded: chain g residue 126 ARG Chi-restraints excluded: chain g residue 150 LEU Chi-restraints excluded: chain h residue 32 TYR Chi-restraints excluded: chain h residue 115 ASP Chi-restraints excluded: chain i residue 23 MET Chi-restraints excluded: chain i residue 39 THR Chi-restraints excluded: chain i residue 108 PHE Chi-restraints excluded: chain i residue 134 ILE Chi-restraints excluded: chain j residue 140 VAL Chi-restraints excluded: chain k residue 7 ASN Chi-restraints excluded: chain k residue 13 PHE Chi-restraints excluded: chain k residue 108 PHE Chi-restraints excluded: chain k residue 119 ARG Chi-restraints excluded: chain k residue 140 VAL Chi-restraints excluded: chain k residue 147 ILE Chi-restraints excluded: chain l residue 13 PHE Chi-restraints excluded: chain l residue 48 ARG Chi-restraints excluded: chain l residue 53 MET Chi-restraints excluded: chain l residue 67 ILE Chi-restraints excluded: chain l residue 78 ASN Chi-restraints excluded: chain l residue 152 LEU Chi-restraints excluded: chain m residue 93 LEU Chi-restraints excluded: chain m residue 139 GLU Chi-restraints excluded: chain m residue 140 VAL Chi-restraints excluded: chain n residue 127 LEU Chi-restraints excluded: chain n residue 150 LEU Chi-restraints excluded: chain o residue 118 VAL Chi-restraints excluded: chain p residue 307 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 837 random chunks: chunk 780 optimal weight: 20.0000 chunk 91 optimal weight: 4.9990 chunk 461 optimal weight: 30.0000 chunk 591 optimal weight: 40.0000 chunk 458 optimal weight: 9.9990 chunk 681 optimal weight: 7.9990 chunk 452 optimal weight: 40.0000 chunk 806 optimal weight: 8.9990 chunk 504 optimal weight: 10.0000 chunk 491 optimal weight: 6.9990 chunk 372 optimal weight: 8.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 345 ASN H 16 GLN ** H 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 GLN ** H 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 50 GLN Q 117 GLN ** Q 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 30 GLN ** d 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.5610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.126 63395 Z= 0.426 Angle : 0.809 13.493 85997 Z= 0.413 Chirality : 0.046 0.291 10036 Planarity : 0.005 0.082 11103 Dihedral : 4.782 139.911 9060 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 19.37 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.50 % Favored : 96.48 % Rotamer: Outliers : 2.91 % Allowed : 15.89 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.09), residues: 8372 helix: 1.77 (0.07), residues: 5018 sheet: -0.48 (0.20), residues: 663 loop : -0.62 (0.12), residues: 2691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP p 312 HIS 0.008 0.002 HIS a 802 PHE 0.045 0.002 PHE m 13 TYR 0.057 0.002 TYR m 68 ARG 0.019 0.001 ARG m 119 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16744 Ramachandran restraints generated. 8372 Oldfield, 0 Emsley, 8372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16744 Ramachandran restraints generated. 8372 Oldfield, 0 Emsley, 8372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 968 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 791 time to evaluate : 5.456 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: 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: A 61 MET cc_start: 0.9185 (tpp) cc_final: 0.8837 (tpp) REVERT: A 116 ILE cc_start: 0.9524 (OUTLIER) cc_final: 0.9214 (mm) REVERT: A 139 LYS cc_start: 0.9261 (OUTLIER) cc_final: 0.8999 (pttp) REVERT: A 205 MET cc_start: 0.8872 (pmm) cc_final: 0.8365 (pmm) REVERT: A 296 MET cc_start: 0.8520 (pmm) cc_final: 0.8292 (pmm) REVERT: A 340 MET cc_start: 0.9060 (OUTLIER) cc_final: 0.8787 (ttp) REVERT: A 346 MET cc_start: 0.8663 (tmm) cc_final: 0.8282 (tmm) REVERT: A 360 GLU cc_start: 0.8938 (tm-30) cc_final: 0.8613 (tm-30) REVERT: A 540 MET cc_start: 0.9313 (mtp) cc_final: 0.8725 (mtp) REVERT: A 567 TRP cc_start: 0.9414 (t-100) cc_final: 0.8949 (t-100) REVERT: A 584 MET cc_start: 0.8907 (ptm) cc_final: 0.8153 (ptp) REVERT: A 608 MET cc_start: 0.8937 (ppp) cc_final: 0.8606 (ppp) REVERT: B 34 MET cc_start: 0.9622 (mmm) cc_final: 0.8835 (mmm) REVERT: B 39 MET cc_start: 0.9235 (tpp) cc_final: 0.8504 (tpp) REVERT: B 61 MET cc_start: 0.9357 (mtt) cc_final: 0.9073 (tpp) REVERT: B 80 LEU cc_start: 0.9536 (tp) cc_final: 0.9174 (pp) REVERT: B 306 MET cc_start: 0.9266 (tpp) cc_final: 0.8884 (tpp) REVERT: B 318 MET cc_start: 0.9565 (mtp) cc_final: 0.8859 (mtp) REVERT: B 346 MET cc_start: 0.9250 (OUTLIER) cc_final: 0.8835 (tmm) REVERT: B 367 GLU cc_start: 0.8679 (mm-30) cc_final: 0.8448 (mm-30) REVERT: B 458 MET cc_start: 0.8961 (mtp) cc_final: 0.8699 (mmm) REVERT: B 480 LYS cc_start: 0.9435 (pttt) cc_final: 0.9113 (ptpp) REVERT: B 487 GLU cc_start: 0.9072 (tm-30) cc_final: 0.8621 (tm-30) REVERT: B 491 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8107 (mm-30) REVERT: B 584 MET cc_start: 0.9365 (OUTLIER) cc_final: 0.9141 (mpp) REVERT: C 61 MET cc_start: 0.9034 (mmm) cc_final: 0.8797 (mmm) REVERT: C 65 GLN cc_start: 0.8570 (tp40) cc_final: 0.8169 (tp40) REVERT: C 99 PHE cc_start: 0.9389 (m-80) cc_final: 0.9189 (m-80) REVERT: C 306 MET cc_start: 0.8802 (OUTLIER) cc_final: 0.8286 (mpp) REVERT: C 318 MET cc_start: 0.9605 (mmm) cc_final: 0.9138 (mmm) REVERT: C 324 GLU cc_start: 0.9526 (tt0) cc_final: 0.8975 (tm-30) REVERT: C 436 ASP cc_start: 0.8590 (t70) cc_final: 0.8275 (t0) REVERT: C 540 MET cc_start: 0.9198 (ptt) cc_final: 0.8882 (ptm) REVERT: C 550 MET cc_start: 0.9360 (mtm) cc_final: 0.8808 (mtp) REVERT: D 97 GLN cc_start: 0.9333 (tt0) cc_final: 0.8937 (tm-30) REVERT: D 234 MET cc_start: 0.8806 (mpp) cc_final: 0.8186 (mtm) REVERT: D 254 MET cc_start: 0.8659 (mmm) cc_final: 0.8030 (tpp) REVERT: D 270 GLU cc_start: 0.9405 (OUTLIER) cc_final: 0.8287 (mm-30) REVERT: D 273 ILE cc_start: 0.9687 (OUTLIER) cc_final: 0.9483 (pp) REVERT: D 299 ASP cc_start: 0.8984 (m-30) cc_final: 0.8665 (m-30) REVERT: D 300 MET cc_start: 0.9461 (mmm) cc_final: 0.9063 (mmm) REVERT: D 309 GLU cc_start: 0.9314 (tp30) cc_final: 0.8867 (tm-30) REVERT: D 348 ILE cc_start: 0.9535 (mt) cc_final: 0.9278 (mt) REVERT: D 356 MET cc_start: 0.8643 (ttm) cc_final: 0.8321 (ttm) REVERT: D 410 MET cc_start: 0.9160 (mtm) cc_final: 0.8196 (ptp) REVERT: D 435 MET cc_start: 0.9462 (tpp) cc_final: 0.9205 (tpp) REVERT: E 87 LEU cc_start: 0.9224 (mt) cc_final: 0.8984 (mm) REVERT: E 127 MET cc_start: 0.9229 (mtp) cc_final: 0.8557 (mtt) REVERT: E 180 MET cc_start: 0.9157 (mmm) cc_final: 0.8371 (mmm) REVERT: E 234 MET cc_start: 0.9015 (ptt) cc_final: 0.8593 (ptt) REVERT: E 254 MET cc_start: 0.8932 (mmm) cc_final: 0.8529 (mmm) REVERT: E 300 MET cc_start: 0.9267 (mmm) cc_final: 0.8997 (mmm) REVERT: E 356 MET cc_start: 0.8738 (ttp) cc_final: 0.8279 (ttp) REVERT: E 360 ASP cc_start: 0.8933 (t0) cc_final: 0.8213 (t0) REVERT: F 97 GLN cc_start: 0.9309 (pt0) cc_final: 0.8600 (pp30) REVERT: F 112 CYS cc_start: 0.9183 (m) cc_final: 0.8609 (p) REVERT: F 254 MET cc_start: 0.8880 (mmm) cc_final: 0.8369 (tmm) REVERT: F 268 THR cc_start: 0.9555 (p) cc_final: 0.9092 (t) REVERT: F 305 GLU cc_start: 0.9078 (mt-10) cc_final: 0.8621 (mt-10) REVERT: F 309 GLU cc_start: 0.9414 (tt0) cc_final: 0.9037 (tp30) REVERT: F 336 GLU cc_start: 0.9043 (tp30) cc_final: 0.8784 (tp30) REVERT: F 356 MET cc_start: 0.8821 (OUTLIER) cc_final: 0.8524 (ttm) REVERT: F 402 MET cc_start: 0.9012 (ttm) cc_final: 0.8707 (ttp) REVERT: F 410 MET cc_start: 0.9145 (mtm) cc_final: 0.8931 (ptp) REVERT: H 109 PHE cc_start: 0.8651 (m-80) cc_final: 0.7981 (m-80) REVERT: H 190 GLU cc_start: 0.9328 (mm-30) cc_final: 0.8839 (tm-30) REVERT: I 129 GLU cc_start: 0.8853 (tm-30) cc_final: 0.8168 (tm-30) REVERT: I 132 MET cc_start: 0.8888 (OUTLIER) cc_final: 0.8649 (mmt) REVERT: I 203 ILE cc_start: 0.9817 (mp) cc_final: 0.9551 (tt) REVERT: I 208 MET cc_start: 0.9553 (mmm) cc_final: 0.9304 (mmm) REVERT: J 97 GLU cc_start: 0.9534 (tp30) cc_final: 0.9076 (tp30) REVERT: J 207 MET cc_start: 0.9117 (tpp) cc_final: 0.8661 (tpp) REVERT: J 210 GLU cc_start: 0.8604 (mp0) cc_final: 0.8057 (mp0) REVERT: K 72 MET cc_start: 0.9464 (ppp) cc_final: 0.9225 (ppp) REVERT: K 76 MET cc_start: 0.9635 (mtm) cc_final: 0.9369 (ptp) REVERT: K 97 GLU cc_start: 0.9368 (tp30) cc_final: 0.9055 (tm-30) REVERT: K 115 LEU cc_start: 0.9850 (OUTLIER) cc_final: 0.9588 (pp) REVERT: K 133 ILE cc_start: 0.9372 (mt) cc_final: 0.9010 (tp) REVERT: K 182 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.8182 (tt0) REVERT: K 197 GLU cc_start: 0.9090 (mp0) cc_final: 0.8772 (mp0) REVERT: K 207 MET cc_start: 0.9409 (tpp) cc_final: 0.9188 (tpp) REVERT: K 208 MET cc_start: 0.9334 (mmt) cc_final: 0.9042 (mmm) REVERT: L 37 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8863 (mm) REVERT: L 73 MET cc_start: 0.8608 (mtm) cc_final: 0.8123 (mtp) REVERT: L 94 LYS cc_start: 0.9008 (ttpt) cc_final: 0.8715 (ttmt) REVERT: M 102 MET cc_start: 0.9382 (mtp) cc_final: 0.9041 (ttm) REVERT: M 105 ASP cc_start: 0.8560 (t0) cc_final: 0.8171 (t0) REVERT: N 79 ARG cc_start: 0.9484 (ttm110) cc_final: 0.9176 (ttm110) REVERT: N 84 MET cc_start: 0.9131 (mtp) cc_final: 0.8841 (ttm) REVERT: N 102 MET cc_start: 0.9542 (mtt) cc_final: 0.9165 (mmm) REVERT: Q 35 THR cc_start: 0.9345 (m) cc_final: 0.9117 (p) REVERT: Q 179 PHE cc_start: 0.9359 (OUTLIER) cc_final: 0.8927 (t80) REVERT: Q 186 LEU cc_start: 0.9560 (tp) cc_final: 0.9343 (mt) REVERT: R 48 ASP cc_start: 0.9360 (OUTLIER) cc_final: 0.8960 (t0) REVERT: R 155 MET cc_start: 0.9478 (OUTLIER) cc_final: 0.9019 (mpp) REVERT: R 161 MET cc_start: 0.9142 (ppp) cc_final: 0.8722 (ppp) REVERT: R 181 LEU cc_start: 0.9451 (mt) cc_final: 0.9219 (pp) REVERT: S 103 MET cc_start: 0.7970 (tpp) cc_final: 0.7574 (tpp) REVERT: S 115 MET cc_start: 0.9562 (mtt) cc_final: 0.9297 (ptm) REVERT: S 133 LEU cc_start: 0.9697 (OUTLIER) cc_final: 0.9477 (pp) REVERT: S 179 PHE cc_start: 0.9347 (m-80) cc_final: 0.8981 (t80) REVERT: S 188 MET cc_start: 0.9285 (mmp) cc_final: 0.8986 (mmp) REVERT: S 229 MET cc_start: 0.9491 (mtp) cc_final: 0.9204 (mmm) REVERT: a 423 MET cc_start: 0.8228 (ptm) cc_final: 0.7972 (ppp) REVERT: a 616 MET cc_start: 0.9111 (ttp) cc_final: 0.8463 (ttt) REVERT: a 645 MET cc_start: 0.7720 (ttt) cc_final: 0.7165 (ptt) REVERT: a 651 MET cc_start: 0.6705 (mtm) cc_final: 0.6227 (mtt) REVERT: a 759 MET cc_start: 0.8304 (mmm) cc_final: 0.7825 (tpp) REVERT: a 791 LEU cc_start: 0.9418 (OUTLIER) cc_final: 0.8966 (tp) REVERT: b 48 MET cc_start: 0.9517 (mtm) cc_final: 0.9258 (mtp) REVERT: b 107 MET cc_start: 0.7063 (mtp) cc_final: 0.6789 (mtp) REVERT: b 137 MET cc_start: 0.8553 (OUTLIER) cc_final: 0.8159 (tpp) REVERT: c 421 MET cc_start: 0.8937 (mtt) cc_final: 0.8424 (mmt) REVERT: c 429 MET cc_start: 0.9317 (ttt) cc_final: 0.8431 (tmm) REVERT: d 85 MET cc_start: 0.8975 (mpp) cc_final: 0.8765 (pmm) REVERT: d 118 HIS cc_start: 0.9382 (m-70) cc_final: 0.8982 (m-70) REVERT: d 119 GLN cc_start: 0.9360 (tt0) cc_final: 0.8862 (tm-30) REVERT: d 138 MET cc_start: 0.8216 (tpp) cc_final: 0.7758 (tpp) REVERT: d 322 LYS cc_start: 0.9525 (pttt) cc_final: 0.9134 (ptmt) REVERT: d 323 GLU cc_start: 0.9154 (tt0) cc_final: 0.8615 (pt0) REVERT: d 348 ILE cc_start: 0.8691 (mm) cc_final: 0.8471 (mm) REVERT: g 23 MET cc_start: 0.5988 (tpt) cc_final: 0.5548 (tpt) REVERT: g 101 LEU cc_start: 0.9054 (tp) cc_final: 0.8370 (mt) REVERT: h 32 TYR cc_start: 0.6343 (OUTLIER) cc_final: 0.5457 (t80) REVERT: i 23 MET cc_start: 0.7570 (OUTLIER) cc_final: 0.7222 (mmt) REVERT: i 53 MET cc_start: 0.8005 (mmt) cc_final: 0.7119 (mtp) REVERT: i 65 ILE cc_start: 0.8132 (mm) cc_final: 0.7898 (mt) REVERT: i 97 LEU cc_start: 0.9318 (mm) cc_final: 0.9005 (pp) REVERT: i 108 PHE cc_start: 0.7958 (OUTLIER) cc_final: 0.7614 (m-10) REVERT: i 115 ASP cc_start: 0.6765 (OUTLIER) cc_final: 0.6433 (m-30) REVERT: j 47 MET cc_start: 0.9202 (ppp) cc_final: 0.8782 (ppp) REVERT: j 61 MET cc_start: 0.6638 (ttm) cc_final: 0.6001 (ptm) REVERT: j 144 TYR cc_start: 0.7571 (m-10) cc_final: 0.7352 (m-10) REVERT: k 23 MET cc_start: 0.7695 (tpt) cc_final: 0.7226 (tpt) REVERT: k 44 MET cc_start: 0.8693 (mmm) cc_final: 0.7940 (mtm) REVERT: k 47 MET cc_start: 0.6043 (ptm) cc_final: 0.5619 (ptm) REVERT: k 131 MET cc_start: 0.7142 (tmm) cc_final: 0.6402 (ppp) REVERT: l 23 MET cc_start: 0.8878 (tpp) cc_final: 0.8375 (ppp) REVERT: l 53 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.8371 (ttt) REVERT: l 78 ASN cc_start: 0.6610 (OUTLIER) cc_final: 0.6225 (p0) REVERT: l 104 LEU cc_start: 0.9455 (tp) cc_final: 0.9231 (mt) REVERT: m 32 TYR cc_start: 0.8490 (t80) cc_final: 0.8042 (t80) REVERT: m 108 PHE cc_start: 0.9178 (t80) cc_final: 0.8969 (t80) REVERT: m 115 ASP cc_start: 0.8966 (t0) cc_final: 0.8604 (m-30) REVERT: m 131 MET cc_start: 0.8767 (ppp) cc_final: 0.8228 (ppp) REVERT: n 13 PHE cc_start: 0.8992 (t80) cc_final: 0.8407 (t80) REVERT: n 17 MET cc_start: 0.9430 (ptt) cc_final: 0.9058 (ptt) REVERT: n 23 MET cc_start: 0.8547 (tpt) cc_final: 0.7640 (tpt) REVERT: n 44 MET cc_start: 0.9104 (tpt) cc_final: 0.8730 (tpt) REVERT: n 90 PHE cc_start: 0.8930 (m-80) cc_final: 0.8700 (m-80) REVERT: n 123 GLN cc_start: 0.8612 (mp10) cc_final: 0.7954 (mt0) REVERT: o 21 SER cc_start: 0.9695 (m) cc_final: 0.9069 (p) REVERT: o 23 MET cc_start: 0.7551 (tpt) cc_final: 0.6588 (tpt) REVERT: o 25 PHE cc_start: 0.8752 (m-80) cc_final: 0.8461 (m-80) REVERT: o 44 MET cc_start: 0.9234 (mmm) cc_final: 0.8582 (mmm) outliers start: 177 outliers final: 116 residues processed: 910 average time/residue: 0.6279 time to fit residues: 1003.2959 Evaluate side-chains 899 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 758 time to evaluate : 5.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 450 TRP Chi-restraints excluded: chain A residue 505 ASP Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 584 MET Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 179 ILE Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 306 MET Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 450 TRP Chi-restraints excluded: chain C residue 584 MET Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 289 CYS Chi-restraints excluded: chain D residue 334 ILE Chi-restraints excluded: chain D residue 378 TYR Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 262 ASN Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 432 VAL Chi-restraints excluded: chain E residue 448 ASP Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 262 ASN Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 334 ILE Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain F residue 356 MET Chi-restraints excluded: chain H residue 49 LYS Chi-restraints excluded: chain H residue 67 PHE Chi-restraints excluded: chain H residue 79 PHE Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 132 MET Chi-restraints excluded: chain I residue 167 ILE Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain K residue 128 LEU Chi-restraints excluded: chain K residue 182 GLU Chi-restraints excluded: chain L residue 29 ASN Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 46 ASN Chi-restraints excluded: chain L residue 81 HIS Chi-restraints excluded: chain N residue 70 SER Chi-restraints excluded: chain N residue 74 GLU Chi-restraints excluded: chain O residue 74 GLU Chi-restraints excluded: chain Q residue 52 VAL Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 117 GLN Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 121 LEU Chi-restraints excluded: chain Q residue 159 LEU Chi-restraints excluded: chain Q residue 169 THR Chi-restraints excluded: chain Q residue 179 PHE Chi-restraints excluded: chain Q residue 181 LEU Chi-restraints excluded: chain Q residue 198 HIS Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 48 ASP Chi-restraints excluded: chain R residue 155 MET Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 133 LEU Chi-restraints excluded: chain S residue 198 HIS Chi-restraints excluded: chain S residue 203 TYR Chi-restraints excluded: chain a residue 447 ARG Chi-restraints excluded: chain a residue 536 PHE Chi-restraints excluded: chain a residue 591 ILE Chi-restraints excluded: chain a residue 610 LEU Chi-restraints excluded: chain a residue 749 HIS Chi-restraints excluded: chain a residue 752 LEU Chi-restraints excluded: chain a residue 791 LEU Chi-restraints excluded: chain a residue 830 HIS Chi-restraints excluded: chain b residue 94 ILE Chi-restraints excluded: chain b residue 137 MET Chi-restraints excluded: chain b residue 138 PHE Chi-restraints excluded: chain c residue 415 PHE Chi-restraints excluded: chain d residue 6 GLU Chi-restraints excluded: chain e residue 36 VAL Chi-restraints excluded: chain e residue 60 LEU Chi-restraints excluded: chain g residue 13 PHE Chi-restraints excluded: chain g residue 60 VAL Chi-restraints excluded: chain g residue 126 ARG Chi-restraints excluded: chain g residue 150 LEU Chi-restraints excluded: chain h residue 32 TYR Chi-restraints excluded: chain i residue 23 MET Chi-restraints excluded: chain i residue 108 PHE Chi-restraints excluded: chain i residue 115 ASP Chi-restraints excluded: chain i residue 134 ILE Chi-restraints excluded: chain j residue 123 GLN Chi-restraints excluded: chain j residue 140 VAL Chi-restraints excluded: chain k residue 7 ASN Chi-restraints excluded: chain k residue 13 PHE Chi-restraints excluded: chain k residue 108 PHE Chi-restraints excluded: chain k residue 140 VAL Chi-restraints excluded: chain l residue 13 PHE Chi-restraints excluded: chain l residue 53 MET Chi-restraints excluded: chain l residue 67 ILE Chi-restraints excluded: chain l residue 78 ASN Chi-restraints excluded: chain l residue 119 ARG Chi-restraints excluded: chain l residue 152 LEU Chi-restraints excluded: chain m residue 57 ILE Chi-restraints excluded: chain m residue 104 LEU Chi-restraints excluded: chain m residue 139 GLU Chi-restraints excluded: chain m residue 140 VAL Chi-restraints excluded: chain n residue 127 LEU Chi-restraints excluded: chain n residue 147 ILE Chi-restraints excluded: chain n residue 150 LEU Chi-restraints excluded: chain o residue 118 VAL Chi-restraints excluded: chain o residue 143 LEU Chi-restraints excluded: chain p residue 307 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 837 random chunks: chunk 499 optimal weight: 10.0000 chunk 322 optimal weight: 50.0000 chunk 481 optimal weight: 8.9990 chunk 243 optimal weight: 4.9990 chunk 158 optimal weight: 1.9990 chunk 156 optimal weight: 0.9990 chunk 512 optimal weight: 2.9990 chunk 549 optimal weight: 50.0000 chunk 398 optimal weight: 10.0000 chunk 75 optimal weight: 6.9990 chunk 634 optimal weight: 0.0970 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN A 164 HIS ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 ASN ** C 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 GLN ** H 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 17 GLN ** a 749 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 438 HIS ** d 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 309 GLN ** i 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.5674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 63395 Z= 0.234 Angle : 0.747 15.207 85997 Z= 0.369 Chirality : 0.045 0.425 10036 Planarity : 0.004 0.082 11103 Dihedral : 4.635 137.877 9060 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.03 % Favored : 96.94 % Rotamer: Outliers : 2.35 % Allowed : 16.84 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.09), residues: 8372 helix: 1.99 (0.07), residues: 4949 sheet: -0.14 (0.20), residues: 630 loop : -0.55 (0.12), residues: 2793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP p 312 HIS 0.013 0.001 HIS a 802 PHE 0.047 0.002 PHE j 25 TYR 0.048 0.002 TYR m 68 ARG 0.014 0.001 ARG k 119 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16744 Ramachandran restraints generated. 8372 Oldfield, 0 Emsley, 8372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16744 Ramachandran restraints generated. 8372 Oldfield, 0 Emsley, 8372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 996 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 853 time to evaluate : 5.319 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: 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: A 34 MET cc_start: 0.8936 (mmm) cc_final: 0.8729 (mmm) REVERT: A 61 MET cc_start: 0.9166 (tpp) cc_final: 0.8736 (tpp) REVERT: A 116 ILE cc_start: 0.9484 (pt) cc_final: 0.9204 (mm) REVERT: A 139 LYS cc_start: 0.9215 (OUTLIER) cc_final: 0.8969 (pttm) REVERT: A 205 MET cc_start: 0.8879 (pmm) cc_final: 0.8412 (pmm) REVERT: A 296 MET cc_start: 0.8434 (pmm) cc_final: 0.8221 (pmm) REVERT: A 340 MET cc_start: 0.8952 (OUTLIER) cc_final: 0.8626 (ttp) REVERT: A 360 GLU cc_start: 0.8854 (tm-30) cc_final: 0.8444 (tm-30) REVERT: A 540 MET cc_start: 0.9242 (mtp) cc_final: 0.8838 (mtp) REVERT: A 567 TRP cc_start: 0.9425 (t-100) cc_final: 0.9052 (t-100) REVERT: A 574 MET cc_start: 0.8806 (mtm) cc_final: 0.8600 (mtt) REVERT: A 584 MET cc_start: 0.8825 (ptm) cc_final: 0.8201 (ptp) REVERT: A 608 MET cc_start: 0.8867 (ppp) cc_final: 0.8614 (ppp) REVERT: B 34 MET cc_start: 0.9631 (mmm) cc_final: 0.8812 (mmm) REVERT: B 39 MET cc_start: 0.9220 (tpp) cc_final: 0.8546 (tpp) REVERT: B 42 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8826 (mm) REVERT: B 61 MET cc_start: 0.9364 (mtt) cc_final: 0.9036 (tpp) REVERT: B 80 LEU cc_start: 0.9520 (tp) cc_final: 0.9152 (pp) REVERT: B 306 MET cc_start: 0.9260 (tpp) cc_final: 0.9024 (tpp) REVERT: B 318 MET cc_start: 0.9560 (mtp) cc_final: 0.8919 (mtp) REVERT: B 367 GLU cc_start: 0.8582 (mm-30) cc_final: 0.8307 (mm-30) REVERT: B 458 MET cc_start: 0.8927 (mtp) cc_final: 0.8608 (mmm) REVERT: B 480 LYS cc_start: 0.9424 (pttt) cc_final: 0.9078 (ptpp) REVERT: B 487 GLU cc_start: 0.9057 (tm-30) cc_final: 0.8548 (tm-30) REVERT: B 491 GLU cc_start: 0.8526 (mm-30) cc_final: 0.8066 (mm-30) REVERT: B 518 ASP cc_start: 0.7958 (t0) cc_final: 0.7680 (m-30) REVERT: B 540 MET cc_start: 0.8654 (tpp) cc_final: 0.8204 (tpp) REVERT: B 571 ARG cc_start: 0.9398 (ttt180) cc_final: 0.9178 (ptm160) REVERT: C 61 MET cc_start: 0.9035 (mmm) cc_final: 0.8811 (mmm) REVERT: C 65 GLN cc_start: 0.8478 (tp40) cc_final: 0.8096 (tp40) REVERT: C 99 PHE cc_start: 0.9324 (m-80) cc_final: 0.9089 (m-80) REVERT: C 205 MET cc_start: 0.8817 (mtm) cc_final: 0.8314 (ttp) REVERT: C 306 MET cc_start: 0.8827 (OUTLIER) cc_final: 0.8231 (mpp) REVERT: C 318 MET cc_start: 0.9627 (mmm) cc_final: 0.9190 (mmm) REVERT: C 324 GLU cc_start: 0.9508 (tt0) cc_final: 0.8979 (tm-30) REVERT: C 436 ASP cc_start: 0.8576 (t70) cc_final: 0.8278 (t0) REVERT: C 550 MET cc_start: 0.9372 (mtm) cc_final: 0.8827 (mtp) REVERT: D 97 GLN cc_start: 0.9293 (tt0) cc_final: 0.8841 (tm-30) REVERT: D 169 MET cc_start: 0.8901 (tmm) cc_final: 0.8648 (tmm) REVERT: D 234 MET cc_start: 0.8651 (mpp) cc_final: 0.8144 (mtm) REVERT: D 270 GLU cc_start: 0.9370 (OUTLIER) cc_final: 0.8123 (mm-30) REVERT: D 273 ILE cc_start: 0.9693 (OUTLIER) cc_final: 0.9461 (pp) REVERT: D 299 ASP cc_start: 0.8783 (m-30) cc_final: 0.8481 (m-30) REVERT: D 300 MET cc_start: 0.9369 (mmm) cc_final: 0.9168 (mmm) REVERT: D 309 GLU cc_start: 0.9283 (tp30) cc_final: 0.8868 (tm-30) REVERT: D 348 ILE cc_start: 0.9547 (mt) cc_final: 0.9346 (mt) REVERT: D 356 MET cc_start: 0.8639 (ttm) cc_final: 0.8308 (ttm) REVERT: D 410 MET cc_start: 0.9136 (mtm) cc_final: 0.8116 (ptp) REVERT: D 435 MET cc_start: 0.9441 (tpp) cc_final: 0.9179 (tpp) REVERT: E 87 LEU cc_start: 0.9171 (mt) cc_final: 0.8942 (mt) REVERT: E 127 MET cc_start: 0.9245 (mtp) cc_final: 0.8586 (mtt) REVERT: E 180 MET cc_start: 0.9069 (mmm) cc_final: 0.8172 (mmm) REVERT: E 234 MET cc_start: 0.8865 (ptt) cc_final: 0.8460 (ptt) REVERT: E 254 MET cc_start: 0.8916 (mmm) cc_final: 0.8367 (mmm) REVERT: E 305 GLU cc_start: 0.9276 (mt-10) cc_final: 0.9035 (tm-30) REVERT: E 356 MET cc_start: 0.8671 (ttp) cc_final: 0.8211 (ttm) REVERT: E 360 ASP cc_start: 0.8927 (t0) cc_final: 0.8413 (t0) REVERT: F 97 GLN cc_start: 0.9266 (pt0) cc_final: 0.8681 (pp30) REVERT: F 112 CYS cc_start: 0.9146 (m) cc_final: 0.8592 (p) REVERT: F 254 MET cc_start: 0.8854 (mmm) cc_final: 0.8285 (tmm) REVERT: F 268 THR cc_start: 0.9541 (p) cc_final: 0.9144 (t) REVERT: F 283 GLU cc_start: 0.9108 (mt-10) cc_final: 0.8780 (mp0) REVERT: F 305 GLU cc_start: 0.9063 (mt-10) cc_final: 0.8589 (mt-10) REVERT: F 309 GLU cc_start: 0.9395 (tt0) cc_final: 0.9024 (tp30) REVERT: F 336 GLU cc_start: 0.8953 (tp30) cc_final: 0.8579 (tp30) REVERT: F 356 MET cc_start: 0.8711 (OUTLIER) cc_final: 0.8454 (ttm) REVERT: F 402 MET cc_start: 0.8926 (ttm) cc_final: 0.8722 (ttm) REVERT: F 410 MET cc_start: 0.9063 (mtm) cc_final: 0.8836 (ptp) REVERT: H 109 PHE cc_start: 0.8561 (m-80) cc_final: 0.7852 (m-80) REVERT: H 190 GLU cc_start: 0.9334 (mm-30) cc_final: 0.8836 (tm-30) REVERT: I 203 ILE cc_start: 0.9782 (mp) cc_final: 0.9491 (tt) REVERT: I 208 MET cc_start: 0.9574 (mmm) cc_final: 0.9309 (mmm) REVERT: J 97 GLU cc_start: 0.9528 (tp30) cc_final: 0.9038 (tp30) REVERT: J 127 LEU cc_start: 0.9531 (mt) cc_final: 0.9271 (mt) REVERT: J 207 MET cc_start: 0.9114 (tpp) cc_final: 0.8864 (tpp) REVERT: K 72 MET cc_start: 0.9397 (ppp) cc_final: 0.8751 (tmm) REVERT: K 76 MET cc_start: 0.9608 (mtm) cc_final: 0.8835 (ptm) REVERT: K 97 GLU cc_start: 0.9363 (tp30) cc_final: 0.9038 (tm-30) REVERT: K 115 LEU cc_start: 0.9811 (OUTLIER) cc_final: 0.9566 (pp) REVERT: K 133 ILE cc_start: 0.9304 (mt) cc_final: 0.8946 (tp) REVERT: K 182 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8151 (tt0) REVERT: K 197 GLU cc_start: 0.9012 (mp0) cc_final: 0.8683 (mp0) REVERT: K 207 MET cc_start: 0.9344 (tpp) cc_final: 0.9113 (tpp) REVERT: K 208 MET cc_start: 0.9281 (mmt) cc_final: 0.8998 (mmm) REVERT: L 32 ARG cc_start: 0.8801 (ttm-80) cc_final: 0.8508 (ttm-80) REVERT: L 37 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8819 (mm) REVERT: L 73 MET cc_start: 0.8559 (mtm) cc_final: 0.8132 (mtm) REVERT: L 94 LYS cc_start: 0.9008 (ttpt) cc_final: 0.8723 (ttmt) REVERT: M 102 MET cc_start: 0.9390 (mtp) cc_final: 0.9018 (ttm) REVERT: M 105 ASP cc_start: 0.8510 (t0) cc_final: 0.8084 (t0) REVERT: N 84 MET cc_start: 0.9125 (mtp) cc_final: 0.8819 (ttm) REVERT: N 102 MET cc_start: 0.9527 (mtt) cc_final: 0.9177 (mmm) REVERT: O 102 MET cc_start: 0.9301 (mtp) cc_final: 0.9065 (ptm) REVERT: Q 35 THR cc_start: 0.9298 (m) cc_final: 0.9080 (p) REVERT: Q 179 PHE cc_start: 0.9334 (OUTLIER) cc_final: 0.8947 (t80) REVERT: Q 186 LEU cc_start: 0.9574 (tp) cc_final: 0.9365 (mt) REVERT: R 48 ASP cc_start: 0.9359 (OUTLIER) cc_final: 0.9013 (t0) REVERT: R 155 MET cc_start: 0.9474 (OUTLIER) cc_final: 0.9044 (mpp) REVERT: R 161 MET cc_start: 0.9115 (ppp) cc_final: 0.8707 (ppp) REVERT: R 181 LEU cc_start: 0.9426 (mt) cc_final: 0.9184 (pp) REVERT: R 188 MET cc_start: 0.8960 (mmm) cc_final: 0.8732 (mpp) REVERT: S 103 MET cc_start: 0.7933 (tpp) cc_final: 0.7545 (tpp) REVERT: S 115 MET cc_start: 0.9549 (mtt) cc_final: 0.9235 (ptm) REVERT: S 133 LEU cc_start: 0.9670 (OUTLIER) cc_final: 0.9434 (pp) REVERT: S 179 PHE cc_start: 0.9322 (m-80) cc_final: 0.9036 (t80) REVERT: S 188 MET cc_start: 0.9216 (mmp) cc_final: 0.8942 (mmp) REVERT: S 203 TYR cc_start: 0.8851 (OUTLIER) cc_final: 0.8239 (t80) REVERT: S 229 MET cc_start: 0.9455 (mtp) cc_final: 0.9176 (mmm) REVERT: a 423 MET cc_start: 0.8540 (ptm) cc_final: 0.8338 (ppp) REVERT: a 616 MET cc_start: 0.9094 (ttp) cc_final: 0.8408 (ttt) REVERT: a 645 MET cc_start: 0.7473 (ttt) cc_final: 0.6886 (ptt) REVERT: a 651 MET cc_start: 0.6476 (mtm) cc_final: 0.6174 (mtt) REVERT: a 759 MET cc_start: 0.8236 (mmm) cc_final: 0.7770 (tpp) REVERT: a 791 LEU cc_start: 0.9440 (OUTLIER) cc_final: 0.8950 (tp) REVERT: b 48 MET cc_start: 0.9477 (OUTLIER) cc_final: 0.8940 (mtp) REVERT: b 107 MET cc_start: 0.6936 (mtp) cc_final: 0.6728 (mtp) REVERT: b 137 MET cc_start: 0.8606 (OUTLIER) cc_final: 0.8215 (tpp) REVERT: c 421 MET cc_start: 0.8889 (mtt) cc_final: 0.8660 (mtt) REVERT: c 429 MET cc_start: 0.9283 (ttt) cc_final: 0.8392 (tmm) REVERT: d 118 HIS cc_start: 0.9356 (m-70) cc_final: 0.9102 (m-70) REVERT: d 119 GLN cc_start: 0.9344 (tt0) cc_final: 0.8876 (tm-30) REVERT: d 243 HIS cc_start: 0.9268 (m90) cc_final: 0.9055 (m-70) REVERT: d 247 LEU cc_start: 0.9264 (mm) cc_final: 0.8779 (tp) REVERT: d 323 GLU cc_start: 0.9092 (tt0) cc_final: 0.8583 (pt0) REVERT: d 348 ILE cc_start: 0.8644 (mm) cc_final: 0.8415 (mm) REVERT: e 37 ILE cc_start: 0.6619 (mt) cc_final: 0.6318 (tt) REVERT: g 44 MET cc_start: 0.7519 (OUTLIER) cc_final: 0.6737 (tmm) REVERT: h 32 TYR cc_start: 0.6318 (OUTLIER) cc_final: 0.5478 (t80) REVERT: h 76 ILE cc_start: 0.7862 (mt) cc_final: 0.7287 (tt) REVERT: h 104 LEU cc_start: 0.9028 (tp) cc_final: 0.8533 (mt) REVERT: h 131 MET cc_start: 0.7610 (ppp) cc_final: 0.6578 (ppp) REVERT: i 23 MET cc_start: 0.7519 (OUTLIER) cc_final: 0.7156 (mmm) REVERT: i 53 MET cc_start: 0.7949 (mmt) cc_final: 0.7029 (mtp) REVERT: i 65 ILE cc_start: 0.8043 (mm) cc_final: 0.7798 (mt) REVERT: i 97 LEU cc_start: 0.9254 (mm) cc_final: 0.8948 (pp) REVERT: i 108 PHE cc_start: 0.7963 (OUTLIER) cc_final: 0.7581 (m-10) REVERT: j 47 MET cc_start: 0.9228 (ppp) cc_final: 0.8903 (ppp) REVERT: j 61 MET cc_start: 0.6813 (ttm) cc_final: 0.6280 (ptm) REVERT: j 131 MET cc_start: 0.5567 (ppp) cc_final: 0.5277 (ppp) REVERT: j 144 TYR cc_start: 0.7507 (m-10) cc_final: 0.7277 (m-10) REVERT: k 17 MET cc_start: 0.8948 (mmp) cc_final: 0.8372 (mmm) REVERT: k 23 MET cc_start: 0.7693 (tpt) cc_final: 0.7079 (tpt) REVERT: k 44 MET cc_start: 0.8805 (mmm) cc_final: 0.8156 (mtm) REVERT: k 47 MET cc_start: 0.5993 (ptm) cc_final: 0.5522 (ptm) REVERT: k 131 MET cc_start: 0.7048 (tmm) cc_final: 0.6351 (ppp) REVERT: l 53 MET cc_start: 0.8688 (mmp) cc_final: 0.8354 (ttt) REVERT: l 78 ASN cc_start: 0.6494 (OUTLIER) cc_final: 0.6048 (p0) REVERT: l 104 LEU cc_start: 0.9424 (tp) cc_final: 0.9203 (mt) REVERT: l 112 ILE cc_start: 0.9282 (tt) cc_final: 0.9072 (tp) REVERT: m 32 TYR cc_start: 0.8349 (t80) cc_final: 0.7988 (t80) REVERT: m 108 PHE cc_start: 0.9092 (t80) cc_final: 0.8820 (t80) REVERT: m 115 ASP cc_start: 0.8878 (t0) cc_final: 0.8551 (m-30) REVERT: m 131 MET cc_start: 0.8999 (ppp) cc_final: 0.8501 (ppp) REVERT: n 13 PHE cc_start: 0.9035 (t80) cc_final: 0.8469 (t80) REVERT: n 17 MET cc_start: 0.9399 (ptt) cc_final: 0.9011 (ptt) REVERT: n 36 LYS cc_start: 0.6683 (mmtt) cc_final: 0.6164 (mtpp) REVERT: n 47 MET cc_start: 0.9037 (ptp) cc_final: 0.8779 (mmm) REVERT: n 53 MET cc_start: 0.7924 (mmt) cc_final: 0.7664 (mmp) REVERT: n 90 PHE cc_start: 0.8889 (m-80) cc_final: 0.8649 (m-80) REVERT: n 123 GLN cc_start: 0.8472 (mp10) cc_final: 0.7550 (mt0) REVERT: o 21 SER cc_start: 0.9685 (m) cc_final: 0.9018 (p) REVERT: o 23 MET cc_start: 0.7483 (tpt) cc_final: 0.6563 (tpt) REVERT: o 25 PHE cc_start: 0.8793 (m-80) cc_final: 0.8495 (m-80) REVERT: o 44 MET cc_start: 0.9279 (mmm) cc_final: 0.8617 (mmm) REVERT: p 331 MET cc_start: 0.7878 (tpp) cc_final: 0.7634 (tmm) outliers start: 143 outliers final: 96 residues processed: 946 average time/residue: 0.5386 time to fit residues: 892.6048 Evaluate side-chains 915 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 796 time to evaluate : 5.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 450 TRP Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 306 MET Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 450 TRP Chi-restraints excluded: chain C residue 584 MET Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 250 GLU Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 334 ILE Chi-restraints excluded: chain D residue 378 TYR Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 432 VAL Chi-restraints excluded: chain E residue 448 ASP Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 249 GLU Chi-restraints excluded: chain F residue 262 ASN Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 334 ILE Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain F residue 356 MET Chi-restraints excluded: chain H residue 79 PHE Chi-restraints excluded: chain I residue 132 MET Chi-restraints excluded: chain I residue 167 ILE Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain K residue 128 LEU Chi-restraints excluded: chain K residue 182 GLU Chi-restraints excluded: chain L residue 29 ASN Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 81 HIS Chi-restraints excluded: chain N residue 70 SER Chi-restraints excluded: chain N residue 74 GLU Chi-restraints excluded: chain O residue 74 GLU Chi-restraints excluded: chain Q residue 52 VAL Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 117 GLN Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 121 LEU Chi-restraints excluded: chain Q residue 146 THR Chi-restraints excluded: chain Q residue 159 LEU Chi-restraints excluded: chain Q residue 169 THR Chi-restraints excluded: chain Q residue 179 PHE Chi-restraints excluded: chain Q residue 181 LEU Chi-restraints excluded: chain Q residue 198 HIS Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 48 ASP Chi-restraints excluded: chain R residue 155 MET Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain S residue 133 LEU Chi-restraints excluded: chain S residue 134 ASN Chi-restraints excluded: chain S residue 198 HIS Chi-restraints excluded: chain S residue 203 TYR Chi-restraints excluded: chain a residue 536 PHE Chi-restraints excluded: chain a residue 591 ILE Chi-restraints excluded: chain a residue 610 LEU Chi-restraints excluded: chain a residue 749 HIS Chi-restraints excluded: chain a residue 752 LEU Chi-restraints excluded: chain a residue 791 LEU Chi-restraints excluded: chain a residue 830 HIS Chi-restraints excluded: chain b residue 48 MET Chi-restraints excluded: chain b residue 60 LEU Chi-restraints excluded: chain b residue 94 ILE Chi-restraints excluded: chain b residue 137 MET Chi-restraints excluded: chain b residue 138 PHE Chi-restraints excluded: chain c residue 415 PHE Chi-restraints excluded: chain d residue 6 GLU Chi-restraints excluded: chain e residue 36 VAL Chi-restraints excluded: chain e residue 60 LEU Chi-restraints excluded: chain g residue 44 MET Chi-restraints excluded: chain g residue 60 VAL Chi-restraints excluded: chain g residue 150 LEU Chi-restraints excluded: chain h residue 32 TYR Chi-restraints excluded: chain i residue 23 MET Chi-restraints excluded: chain i residue 108 PHE Chi-restraints excluded: chain i residue 115 ASP Chi-restraints excluded: chain i residue 134 ILE Chi-restraints excluded: chain k residue 7 ASN Chi-restraints excluded: chain k residue 108 PHE Chi-restraints excluded: chain k residue 147 ILE Chi-restraints excluded: chain l residue 13 PHE Chi-restraints excluded: chain l residue 67 ILE Chi-restraints excluded: chain l residue 78 ASN Chi-restraints excluded: chain l residue 152 LEU Chi-restraints excluded: chain m residue 104 LEU Chi-restraints excluded: chain m residue 139 GLU Chi-restraints excluded: chain m residue 140 VAL Chi-restraints excluded: chain n residue 127 LEU Chi-restraints excluded: chain n residue 150 LEU Chi-restraints excluded: chain o residue 143 LEU Chi-restraints excluded: chain p residue 307 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 837 random chunks: chunk 733 optimal weight: 7.9990 chunk 772 optimal weight: 6.9990 chunk 705 optimal weight: 40.0000 chunk 751 optimal weight: 5.9990 chunk 452 optimal weight: 50.0000 chunk 327 optimal weight: 6.9990 chunk 590 optimal weight: 20.0000 chunk 230 optimal weight: 0.2980 chunk 679 optimal weight: 10.0000 chunk 711 optimal weight: 7.9990 chunk 749 optimal weight: 7.9990 overall best weight: 5.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 543 ASN H 16 GLN ** H 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 751 GLN ** a 812 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 118 HIS d 142 ASN ** d 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.5919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 63395 Z= 0.341 Angle : 0.791 14.878 85997 Z= 0.397 Chirality : 0.046 0.353 10036 Planarity : 0.005 0.081 11103 Dihedral : 4.718 139.070 9060 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 19.03 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.73 % Favored : 96.24 % Rotamer: Outliers : 2.47 % Allowed : 17.20 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.09), residues: 8372 helix: 1.88 (0.07), residues: 4949 sheet: -0.45 (0.20), residues: 649 loop : -0.65 (0.12), residues: 2774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP p 312 HIS 0.005 0.001 HIS a 802 PHE 0.053 0.002 PHE j 25 TYR 0.050 0.002 TYR m 68 ARG 0.013 0.001 ARG k 119 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16744 Ramachandran restraints generated. 8372 Oldfield, 0 Emsley, 8372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16744 Ramachandran restraints generated. 8372 Oldfield, 0 Emsley, 8372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 943 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 793 time to evaluate : 5.476 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: 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: A 34 MET cc_start: 0.9001 (mmm) cc_final: 0.8782 (mmm) REVERT: A 61 MET cc_start: 0.9150 (tpp) cc_final: 0.8733 (tpp) REVERT: A 116 ILE cc_start: 0.9504 (OUTLIER) cc_final: 0.9227 (mm) REVERT: A 139 LYS cc_start: 0.9233 (OUTLIER) cc_final: 0.9004 (pttm) REVERT: A 205 MET cc_start: 0.8846 (pmm) cc_final: 0.8344 (pmm) REVERT: A 263 LEU cc_start: 0.9727 (tp) cc_final: 0.9326 (pp) REVERT: A 347 MET cc_start: 0.8461 (tpt) cc_final: 0.8139 (mtt) REVERT: A 360 GLU cc_start: 0.8957 (tm-30) cc_final: 0.8566 (tm-30) REVERT: A 371 ASP cc_start: 0.9092 (t0) cc_final: 0.8889 (t0) REVERT: A 540 MET cc_start: 0.9266 (mtp) cc_final: 0.8819 (mtp) REVERT: A 567 TRP cc_start: 0.9414 (t-100) cc_final: 0.9068 (t-100) REVERT: A 574 MET cc_start: 0.8921 (mtm) cc_final: 0.8706 (mtt) REVERT: A 584 MET cc_start: 0.8873 (ptm) cc_final: 0.8212 (ptp) REVERT: A 608 MET cc_start: 0.8961 (ppp) cc_final: 0.8684 (ppp) REVERT: B 34 MET cc_start: 0.9649 (mmm) cc_final: 0.8892 (mmm) REVERT: B 39 MET cc_start: 0.9238 (tpp) cc_final: 0.8602 (tpp) REVERT: B 42 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8843 (mm) REVERT: B 61 MET cc_start: 0.9344 (mtt) cc_final: 0.9038 (tpp) REVERT: B 80 LEU cc_start: 0.9540 (tp) cc_final: 0.9176 (pp) REVERT: B 95 MET cc_start: 0.8807 (tpp) cc_final: 0.8425 (tpp) REVERT: B 306 MET cc_start: 0.9226 (tpp) cc_final: 0.8819 (tpp) REVERT: B 318 MET cc_start: 0.9562 (mtp) cc_final: 0.8853 (mtp) REVERT: B 367 GLU cc_start: 0.8668 (mm-30) cc_final: 0.8422 (mm-30) REVERT: B 458 MET cc_start: 0.8965 (mtp) cc_final: 0.8671 (mmm) REVERT: B 480 LYS cc_start: 0.9429 (pttt) cc_final: 0.9143 (pttm) REVERT: B 518 ASP cc_start: 0.8038 (t0) cc_final: 0.7660 (m-30) REVERT: B 540 MET cc_start: 0.8877 (tpp) cc_final: 0.8620 (tpt) REVERT: C 50 LEU cc_start: 0.9517 (OUTLIER) cc_final: 0.9295 (tp) REVERT: C 61 MET cc_start: 0.9011 (mmm) cc_final: 0.8804 (mmm) REVERT: C 65 GLN cc_start: 0.8520 (tp40) cc_final: 0.8132 (tp40) REVERT: C 99 PHE cc_start: 0.9384 (m-80) cc_final: 0.9177 (m-80) REVERT: C 205 MET cc_start: 0.8831 (mtm) cc_final: 0.8223 (ttp) REVERT: C 306 MET cc_start: 0.8852 (OUTLIER) cc_final: 0.8254 (mpp) REVERT: C 318 MET cc_start: 0.9628 (mmm) cc_final: 0.9205 (mmm) REVERT: C 324 GLU cc_start: 0.9529 (tt0) cc_final: 0.8973 (tm-30) REVERT: C 436 ASP cc_start: 0.8615 (t70) cc_final: 0.8316 (t0) REVERT: C 550 MET cc_start: 0.9344 (mtm) cc_final: 0.8802 (mtp) REVERT: C 584 MET cc_start: 0.9005 (OUTLIER) cc_final: 0.8470 (mpp) REVERT: D 97 GLN cc_start: 0.9329 (tt0) cc_final: 0.8779 (tm-30) REVERT: D 231 PHE cc_start: 0.8865 (t80) cc_final: 0.8600 (t80) REVERT: D 249 GLU cc_start: 0.9539 (mt-10) cc_final: 0.9112 (mt-10) REVERT: D 270 GLU cc_start: 0.9418 (OUTLIER) cc_final: 0.8269 (mm-30) REVERT: D 283 GLU cc_start: 0.9145 (mt-10) cc_final: 0.8746 (mt-10) REVERT: D 299 ASP cc_start: 0.8898 (m-30) cc_final: 0.8644 (m-30) REVERT: D 300 MET cc_start: 0.9472 (mmm) cc_final: 0.9249 (mmm) REVERT: D 309 GLU cc_start: 0.9273 (tp30) cc_final: 0.8888 (tm-30) REVERT: D 327 MET cc_start: 0.9308 (mtp) cc_final: 0.9038 (mtp) REVERT: D 348 ILE cc_start: 0.9530 (mt) cc_final: 0.9280 (mt) REVERT: D 356 MET cc_start: 0.8588 (ttm) cc_final: 0.8291 (ttm) REVERT: D 410 MET cc_start: 0.9136 (mtm) cc_final: 0.8130 (ptp) REVERT: D 435 MET cc_start: 0.9435 (tpp) cc_final: 0.9184 (tpp) REVERT: E 87 LEU cc_start: 0.9229 (mt) cc_final: 0.8985 (mm) REVERT: E 127 MET cc_start: 0.9231 (mtp) cc_final: 0.8528 (mtt) REVERT: E 234 MET cc_start: 0.8946 (ptt) cc_final: 0.8485 (ptt) REVERT: E 254 MET cc_start: 0.9005 (mmm) cc_final: 0.8590 (mmm) REVERT: E 305 GLU cc_start: 0.9307 (mt-10) cc_final: 0.8928 (tm-30) REVERT: E 356 MET cc_start: 0.8715 (ttp) cc_final: 0.8156 (ttm) REVERT: E 360 ASP cc_start: 0.8988 (t0) cc_final: 0.8305 (t0) REVERT: E 435 MET cc_start: 0.9053 (mtp) cc_final: 0.8742 (ptp) REVERT: F 97 GLN cc_start: 0.9296 (pt0) cc_final: 0.8726 (pp30) REVERT: F 112 CYS cc_start: 0.9194 (m) cc_final: 0.8617 (p) REVERT: F 268 THR cc_start: 0.9554 (p) cc_final: 0.9215 (t) REVERT: F 269 ILE cc_start: 0.9527 (OUTLIER) cc_final: 0.9122 (mm) REVERT: F 305 GLU cc_start: 0.9097 (mt-10) cc_final: 0.8649 (mt-10) REVERT: F 336 GLU cc_start: 0.8984 (tp30) cc_final: 0.8654 (tp30) REVERT: F 356 MET cc_start: 0.8775 (OUTLIER) cc_final: 0.8505 (ttm) REVERT: F 410 MET cc_start: 0.9085 (mtm) cc_final: 0.8823 (ptp) REVERT: H 109 PHE cc_start: 0.8625 (m-80) cc_final: 0.8009 (m-80) REVERT: H 190 GLU cc_start: 0.9321 (mm-30) cc_final: 0.8794 (tm-30) REVERT: I 208 MET cc_start: 0.9581 (mmm) cc_final: 0.9289 (mmm) REVERT: J 97 GLU cc_start: 0.9534 (tp30) cc_final: 0.9065 (tp30) REVERT: J 207 MET cc_start: 0.9157 (tpp) cc_final: 0.8882 (tpp) REVERT: J 210 GLU cc_start: 0.8611 (tm-30) cc_final: 0.8391 (tm-30) REVERT: K 76 MET cc_start: 0.9613 (mtm) cc_final: 0.9332 (mtp) REVERT: K 97 GLU cc_start: 0.9373 (tp30) cc_final: 0.9067 (tm-30) REVERT: K 133 ILE cc_start: 0.9368 (mt) cc_final: 0.9040 (tp) REVERT: K 182 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8116 (tt0) REVERT: K 197 GLU cc_start: 0.9078 (mp0) cc_final: 0.8733 (mp0) REVERT: K 207 MET cc_start: 0.9395 (tpp) cc_final: 0.9171 (tpp) REVERT: K 208 MET cc_start: 0.9311 (mmt) cc_final: 0.9026 (mmm) REVERT: L 32 ARG cc_start: 0.8800 (ttm-80) cc_final: 0.8523 (ttm-80) REVERT: L 37 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8791 (mm) REVERT: L 73 MET cc_start: 0.8611 (mtm) cc_final: 0.8244 (mtm) REVERT: L 94 LYS cc_start: 0.9030 (ttpt) cc_final: 0.8731 (ttmt) REVERT: M 102 MET cc_start: 0.9378 (mtp) cc_final: 0.9155 (ttm) REVERT: M 105 ASP cc_start: 0.8509 (t0) cc_final: 0.8061 (t0) REVERT: N 84 MET cc_start: 0.9158 (mtp) cc_final: 0.8841 (ttm) REVERT: N 102 MET cc_start: 0.9540 (mtt) cc_final: 0.9184 (mmm) REVERT: O 102 MET cc_start: 0.9304 (mtp) cc_final: 0.9065 (ptm) REVERT: Q 35 THR cc_start: 0.9360 (m) cc_final: 0.9143 (p) REVERT: Q 179 PHE cc_start: 0.9373 (OUTLIER) cc_final: 0.8941 (t80) REVERT: Q 186 LEU cc_start: 0.9618 (tp) cc_final: 0.9374 (mt) REVERT: R 48 ASP cc_start: 0.9360 (OUTLIER) cc_final: 0.8969 (t0) REVERT: R 155 MET cc_start: 0.9435 (OUTLIER) cc_final: 0.8989 (mpp) REVERT: R 161 MET cc_start: 0.9170 (ppp) cc_final: 0.8802 (ppp) REVERT: R 188 MET cc_start: 0.9086 (mmm) cc_final: 0.8655 (mpp) REVERT: S 103 MET cc_start: 0.8013 (tpp) cc_final: 0.7565 (tpp) REVERT: S 115 MET cc_start: 0.9575 (mtt) cc_final: 0.9287 (ptm) REVERT: S 133 LEU cc_start: 0.9693 (OUTLIER) cc_final: 0.9471 (pp) REVERT: S 179 PHE cc_start: 0.9362 (m-80) cc_final: 0.8994 (t80) REVERT: S 188 MET cc_start: 0.9260 (mmp) cc_final: 0.8949 (mmp) REVERT: S 229 MET cc_start: 0.9441 (mtp) cc_final: 0.9208 (mmm) REVERT: a 538 MET cc_start: 0.5724 (ppp) cc_final: 0.5515 (ppp) REVERT: a 616 MET cc_start: 0.9143 (ttp) cc_final: 0.8494 (ttt) REVERT: a 645 MET cc_start: 0.7471 (ttt) cc_final: 0.6891 (ptt) REVERT: a 651 MET cc_start: 0.6588 (mtm) cc_final: 0.6314 (mtt) REVERT: a 759 MET cc_start: 0.8253 (mmm) cc_final: 0.7820 (tpp) REVERT: a 791 LEU cc_start: 0.9467 (OUTLIER) cc_final: 0.8861 (tp) REVERT: b 48 MET cc_start: 0.9515 (OUTLIER) cc_final: 0.9076 (mtp) REVERT: b 107 MET cc_start: 0.7234 (mtp) cc_final: 0.6975 (mtp) REVERT: b 111 ILE cc_start: 0.8287 (OUTLIER) cc_final: 0.7966 (mt) REVERT: b 137 MET cc_start: 0.8595 (OUTLIER) cc_final: 0.8373 (tpp) REVERT: c 429 MET cc_start: 0.9298 (ttt) cc_final: 0.8413 (tmm) REVERT: d 118 HIS cc_start: 0.9192 (m90) cc_final: 0.8878 (m-70) REVERT: d 119 GLN cc_start: 0.9356 (tt0) cc_final: 0.8771 (tm-30) REVERT: d 243 HIS cc_start: 0.9283 (m90) cc_final: 0.9051 (m-70) REVERT: d 322 LYS cc_start: 0.9483 (pttt) cc_final: 0.9165 (ptmt) REVERT: d 323 GLU cc_start: 0.9117 (tt0) cc_final: 0.8564 (pt0) REVERT: d 348 ILE cc_start: 0.8659 (mm) cc_final: 0.8450 (mm) REVERT: e 37 ILE cc_start: 0.6587 (mt) cc_final: 0.6306 (tt) REVERT: g 44 MET cc_start: 0.7614 (OUTLIER) cc_final: 0.6878 (tmm) REVERT: h 32 TYR cc_start: 0.6394 (OUTLIER) cc_final: 0.5467 (t80) REVERT: h 44 MET cc_start: 0.6257 (ttt) cc_final: 0.6017 (tpp) REVERT: h 104 LEU cc_start: 0.9088 (tp) cc_final: 0.8588 (mt) REVERT: h 131 MET cc_start: 0.7760 (ppp) cc_final: 0.6668 (ppp) REVERT: i 23 MET cc_start: 0.7480 (OUTLIER) cc_final: 0.7108 (mmm) REVERT: i 53 MET cc_start: 0.7885 (mmt) cc_final: 0.6967 (mtp) REVERT: i 61 MET cc_start: 0.0939 (mtm) cc_final: 0.0705 (ptm) REVERT: i 65 ILE cc_start: 0.8195 (mm) cc_final: 0.7988 (mt) REVERT: i 97 LEU cc_start: 0.9270 (mm) cc_final: 0.8951 (pp) REVERT: i 108 PHE cc_start: 0.8247 (OUTLIER) cc_final: 0.7862 (m-10) REVERT: i 115 ASP cc_start: 0.7050 (OUTLIER) cc_final: 0.6719 (m-30) REVERT: j 47 MET cc_start: 0.9285 (ppp) cc_final: 0.8900 (ppp) REVERT: j 108 PHE cc_start: 0.8151 (m-80) cc_final: 0.7658 (t80) REVERT: j 131 MET cc_start: 0.5713 (ppp) cc_final: 0.5394 (ppp) REVERT: j 144 TYR cc_start: 0.7596 (m-10) cc_final: 0.7358 (m-10) REVERT: k 23 MET cc_start: 0.7514 (tpt) cc_final: 0.6972 (tpt) REVERT: k 44 MET cc_start: 0.8901 (mmm) cc_final: 0.8340 (mtm) REVERT: k 47 MET cc_start: 0.6234 (ptm) cc_final: 0.5729 (tmm) REVERT: k 131 MET cc_start: 0.7129 (tmm) cc_final: 0.6430 (ppp) REVERT: l 53 MET cc_start: 0.8689 (mmp) cc_final: 0.8313 (ttt) REVERT: l 104 LEU cc_start: 0.9417 (tp) cc_final: 0.9192 (mt) REVERT: l 137 PHE cc_start: 0.8015 (m-10) cc_final: 0.7646 (m-80) REVERT: m 23 MET cc_start: 0.8384 (tpp) cc_final: 0.7823 (tpt) REVERT: m 32 TYR cc_start: 0.8328 (t80) cc_final: 0.7874 (t80) REVERT: m 131 MET cc_start: 0.9019 (ppp) cc_final: 0.8554 (ppp) REVERT: n 13 PHE cc_start: 0.9045 (t80) cc_final: 0.8477 (t80) REVERT: n 17 MET cc_start: 0.9421 (ptt) cc_final: 0.9037 (ptt) REVERT: n 36 LYS cc_start: 0.6684 (mmtt) cc_final: 0.6153 (mtpp) REVERT: n 47 MET cc_start: 0.9004 (ptp) cc_final: 0.8786 (mmm) REVERT: n 53 MET cc_start: 0.7984 (mmt) cc_final: 0.6440 (ttp) REVERT: n 90 PHE cc_start: 0.8844 (m-10) cc_final: 0.8641 (m-80) REVERT: n 104 LEU cc_start: 0.9535 (pp) cc_final: 0.9229 (mt) REVERT: n 123 GLN cc_start: 0.8531 (mp10) cc_final: 0.7680 (mt0) REVERT: o 21 SER cc_start: 0.9692 (m) cc_final: 0.9039 (p) REVERT: o 23 MET cc_start: 0.7549 (tpt) cc_final: 0.6671 (tpt) REVERT: o 25 PHE cc_start: 0.8788 (m-80) cc_final: 0.8481 (m-80) REVERT: o 44 MET cc_start: 0.9318 (mmm) cc_final: 0.8658 (mmm) outliers start: 150 outliers final: 103 residues processed: 894 average time/residue: 0.5597 time to fit residues: 872.3933 Evaluate side-chains 893 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 766 time to evaluate : 5.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 450 TRP Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 306 MET Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 450 TRP Chi-restraints excluded: chain C residue 584 MET Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 250 GLU Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 334 ILE Chi-restraints excluded: chain D residue 378 TYR Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 188 LYS Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 327 MET Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 432 VAL Chi-restraints excluded: chain E residue 448 ASP Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 249 GLU Chi-restraints excluded: chain F residue 262 ASN Chi-restraints excluded: chain F residue 269 ILE Chi-restraints excluded: chain F residue 270 GLU Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 334 ILE Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain F residue 356 MET Chi-restraints excluded: chain H residue 79 PHE Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 167 ILE Chi-restraints excluded: chain K residue 128 LEU Chi-restraints excluded: chain K residue 182 GLU Chi-restraints excluded: chain L residue 29 ASN Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain N residue 70 SER Chi-restraints excluded: chain N residue 74 GLU Chi-restraints excluded: chain O residue 74 GLU Chi-restraints excluded: chain Q residue 52 VAL Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 121 LEU Chi-restraints excluded: chain Q residue 146 THR Chi-restraints excluded: chain Q residue 159 LEU Chi-restraints excluded: chain Q residue 179 PHE Chi-restraints excluded: chain Q residue 181 LEU Chi-restraints excluded: chain Q residue 198 HIS Chi-restraints excluded: chain R residue 48 ASP Chi-restraints excluded: chain R residue 155 MET Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain S residue 133 LEU Chi-restraints excluded: chain S residue 134 ASN Chi-restraints excluded: chain S residue 198 HIS Chi-restraints excluded: chain S residue 203 TYR Chi-restraints excluded: chain a residue 536 PHE Chi-restraints excluded: chain a residue 591 ILE Chi-restraints excluded: chain a residue 610 LEU Chi-restraints excluded: chain a residue 749 HIS Chi-restraints excluded: chain a residue 751 GLN Chi-restraints excluded: chain a residue 752 LEU Chi-restraints excluded: chain a residue 791 LEU Chi-restraints excluded: chain a residue 830 HIS Chi-restraints excluded: chain b residue 48 MET Chi-restraints excluded: chain b residue 60 LEU Chi-restraints excluded: chain b residue 111 ILE Chi-restraints excluded: chain b residue 137 MET Chi-restraints excluded: chain b residue 138 PHE Chi-restraints excluded: chain c residue 415 PHE Chi-restraints excluded: chain d residue 6 GLU Chi-restraints excluded: chain e residue 36 VAL Chi-restraints excluded: chain e residue 60 LEU Chi-restraints excluded: chain g residue 44 MET Chi-restraints excluded: chain g residue 60 VAL Chi-restraints excluded: chain g residue 126 ARG Chi-restraints excluded: chain g residue 150 LEU Chi-restraints excluded: chain h residue 32 TYR Chi-restraints excluded: chain i residue 23 MET Chi-restraints excluded: chain i residue 108 PHE Chi-restraints excluded: chain i residue 115 ASP Chi-restraints excluded: chain i residue 134 ILE Chi-restraints excluded: chain k residue 7 ASN Chi-restraints excluded: chain k residue 108 PHE Chi-restraints excluded: chain k residue 119 ARG Chi-restraints excluded: chain k residue 140 VAL Chi-restraints excluded: chain l residue 13 PHE Chi-restraints excluded: chain l residue 152 LEU Chi-restraints excluded: chain m residue 17 MET Chi-restraints excluded: chain m residue 57 ILE Chi-restraints excluded: chain m residue 104 LEU Chi-restraints excluded: chain m residue 140 VAL Chi-restraints excluded: chain n residue 127 LEU Chi-restraints excluded: chain n residue 133 LEU Chi-restraints excluded: chain n residue 150 LEU Chi-restraints excluded: chain o residue 118 VAL Chi-restraints excluded: chain o residue 143 LEU Chi-restraints excluded: chain p residue 307 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 837 random chunks: chunk 493 optimal weight: 6.9990 chunk 794 optimal weight: 10.0000 chunk 485 optimal weight: 0.0010 chunk 377 optimal weight: 50.0000 chunk 552 optimal weight: 50.0000 chunk 833 optimal weight: 6.9990 chunk 767 optimal weight: 30.0000 chunk 664 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 512 optimal weight: 3.9990 chunk 407 optimal weight: 4.9990 overall best weight: 2.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 GLN ** H 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 749 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 812 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 78 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.5980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 63395 Z= 0.226 Angle : 0.789 17.236 85997 Z= 0.386 Chirality : 0.047 0.423 10036 Planarity : 0.004 0.083 11103 Dihedral : 4.629 138.041 9058 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 16.64 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.17 % Favored : 96.80 % Rotamer: Outliers : 2.04 % Allowed : 17.60 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.09), residues: 8372 helix: 1.93 (0.07), residues: 4957 sheet: -0.07 (0.21), residues: 608 loop : -0.59 (0.12), residues: 2807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP b 16 HIS 0.007 0.001 HIS c 438 PHE 0.057 0.002 PHE j 25 TYR 0.061 0.002 TYR m 68 ARG 0.013 0.000 ARG k 119 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16744 Ramachandran restraints generated. 8372 Oldfield, 0 Emsley, 8372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16744 Ramachandran restraints generated. 8372 Oldfield, 0 Emsley, 8372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 970 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 846 time to evaluate : 5.444 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: 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: A 34 MET cc_start: 0.8992 (mmm) cc_final: 0.8744 (mmm) REVERT: A 61 MET cc_start: 0.9142 (tpp) cc_final: 0.8724 (tpp) REVERT: A 99 PHE cc_start: 0.8971 (m-80) cc_final: 0.8712 (m-10) REVERT: A 116 ILE cc_start: 0.9476 (pt) cc_final: 0.9226 (mm) REVERT: A 139 LYS cc_start: 0.9186 (OUTLIER) cc_final: 0.8957 (pttm) REVERT: A 205 MET cc_start: 0.8830 (pmm) cc_final: 0.8349 (pmm) REVERT: A 263 LEU cc_start: 0.9713 (tp) cc_final: 0.9394 (pp) REVERT: A 347 MET cc_start: 0.8287 (tpt) cc_final: 0.8042 (mtt) REVERT: A 360 GLU cc_start: 0.8892 (tm-30) cc_final: 0.8457 (tm-30) REVERT: A 371 ASP cc_start: 0.9084 (t0) cc_final: 0.8874 (t0) REVERT: A 540 MET cc_start: 0.9221 (mtp) cc_final: 0.8845 (mtp) REVERT: A 567 TRP cc_start: 0.9431 (t-100) cc_final: 0.9042 (t-100) REVERT: A 584 MET cc_start: 0.8788 (ptm) cc_final: 0.8137 (ptp) REVERT: A 608 MET cc_start: 0.8897 (ppp) cc_final: 0.8647 (ppp) REVERT: B 34 MET cc_start: 0.9644 (mmm) cc_final: 0.8827 (mmm) REVERT: B 39 MET cc_start: 0.9190 (tpp) cc_final: 0.8539 (tpp) REVERT: B 42 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8778 (mm) REVERT: B 61 MET cc_start: 0.9387 (mtt) cc_final: 0.9091 (tpp) REVERT: B 80 LEU cc_start: 0.9521 (tp) cc_final: 0.9174 (pp) REVERT: B 95 MET cc_start: 0.8854 (tpp) cc_final: 0.8523 (tpp) REVERT: B 306 MET cc_start: 0.9250 (tpp) cc_final: 0.8888 (tpp) REVERT: B 318 MET cc_start: 0.9559 (mtp) cc_final: 0.8777 (mtp) REVERT: B 458 MET cc_start: 0.8940 (mtp) cc_final: 0.8624 (mmm) REVERT: B 480 LYS cc_start: 0.9416 (pttt) cc_final: 0.9162 (pttm) REVERT: B 491 GLU cc_start: 0.8576 (mm-30) cc_final: 0.8265 (mm-30) REVERT: B 540 MET cc_start: 0.8845 (tpp) cc_final: 0.8544 (tpt) REVERT: B 571 ARG cc_start: 0.9424 (ttt180) cc_final: 0.9155 (ptm160) REVERT: C 50 LEU cc_start: 0.9488 (OUTLIER) cc_final: 0.9258 (tp) REVERT: C 65 GLN cc_start: 0.8440 (tp40) cc_final: 0.8088 (tp40) REVERT: C 99 PHE cc_start: 0.9320 (m-80) cc_final: 0.9112 (m-80) REVERT: C 205 MET cc_start: 0.8809 (mtm) cc_final: 0.8298 (ttp) REVERT: C 306 MET cc_start: 0.8789 (OUTLIER) cc_final: 0.8115 (mpp) REVERT: C 318 MET cc_start: 0.9619 (mmm) cc_final: 0.9259 (mmm) REVERT: C 324 GLU cc_start: 0.9501 (tt0) cc_final: 0.8994 (tm-30) REVERT: C 436 ASP cc_start: 0.8560 (t70) cc_final: 0.8276 (t0) REVERT: C 550 MET cc_start: 0.9363 (mtm) cc_final: 0.8981 (mtp) REVERT: C 584 MET cc_start: 0.8988 (OUTLIER) cc_final: 0.8604 (mpp) REVERT: D 97 GLN cc_start: 0.9288 (tt0) cc_final: 0.8820 (tm-30) REVERT: D 169 MET cc_start: 0.8848 (tmm) cc_final: 0.8594 (tmm) REVERT: D 231 PHE cc_start: 0.8665 (t80) cc_final: 0.8452 (t80) REVERT: D 270 GLU cc_start: 0.9376 (OUTLIER) cc_final: 0.8155 (mm-30) REVERT: D 299 ASP cc_start: 0.8746 (m-30) cc_final: 0.8509 (m-30) REVERT: D 300 MET cc_start: 0.9408 (mmm) cc_final: 0.9179 (mmm) REVERT: D 309 GLU cc_start: 0.9278 (tp30) cc_final: 0.8870 (tm-30) REVERT: D 327 MET cc_start: 0.9271 (mtp) cc_final: 0.8995 (mtp) REVERT: D 356 MET cc_start: 0.8579 (ttm) cc_final: 0.8251 (ttm) REVERT: D 410 MET cc_start: 0.9099 (mtm) cc_final: 0.8065 (ptp) REVERT: D 435 MET cc_start: 0.9423 (tpp) cc_final: 0.9167 (tpp) REVERT: E 127 MET cc_start: 0.9282 (mtp) cc_final: 0.8590 (mtt) REVERT: E 234 MET cc_start: 0.8801 (ptt) cc_final: 0.8480 (ptt) REVERT: E 254 MET cc_start: 0.8951 (mmm) cc_final: 0.8384 (mmm) REVERT: E 305 GLU cc_start: 0.9298 (mt-10) cc_final: 0.9066 (tm-30) REVERT: E 356 MET cc_start: 0.8682 (ttp) cc_final: 0.8266 (ttm) REVERT: E 360 ASP cc_start: 0.8993 (t0) cc_final: 0.8422 (t0) REVERT: E 435 MET cc_start: 0.9015 (mtp) cc_final: 0.8668 (ptp) REVERT: F 97 GLN cc_start: 0.9270 (pt0) cc_final: 0.8688 (pp30) REVERT: F 112 CYS cc_start: 0.9188 (m) cc_final: 0.8584 (p) REVERT: F 268 THR cc_start: 0.9542 (p) cc_final: 0.9167 (t) REVERT: F 283 GLU cc_start: 0.9116 (mt-10) cc_final: 0.8776 (mp0) REVERT: F 305 GLU cc_start: 0.9051 (mt-10) cc_final: 0.8513 (mt-10) REVERT: F 309 GLU cc_start: 0.9395 (tt0) cc_final: 0.9127 (tp30) REVERT: F 330 ASP cc_start: 0.9240 (OUTLIER) cc_final: 0.8980 (t70) REVERT: F 336 GLU cc_start: 0.8919 (tp30) cc_final: 0.8532 (tp30) REVERT: F 356 MET cc_start: 0.8764 (OUTLIER) cc_final: 0.8538 (ttm) REVERT: H 99 ASP cc_start: 0.9157 (t0) cc_final: 0.8796 (p0) REVERT: H 109 PHE cc_start: 0.8584 (m-80) cc_final: 0.7923 (m-80) REVERT: H 190 GLU cc_start: 0.9336 (mm-30) cc_final: 0.8809 (tm-30) REVERT: I 208 MET cc_start: 0.9609 (mmm) cc_final: 0.9401 (mmm) REVERT: J 97 GLU cc_start: 0.9533 (tp30) cc_final: 0.9025 (tp30) REVERT: J 127 LEU cc_start: 0.9543 (mt) cc_final: 0.9295 (mt) REVERT: J 207 MET cc_start: 0.9095 (tpp) cc_final: 0.8800 (tpp) REVERT: J 210 GLU cc_start: 0.8542 (tm-30) cc_final: 0.8270 (tm-30) REVERT: K 76 MET cc_start: 0.9537 (mtm) cc_final: 0.9253 (ptp) REVERT: K 97 GLU cc_start: 0.9366 (tp30) cc_final: 0.8985 (tm-30) REVERT: K 115 LEU cc_start: 0.9820 (tt) cc_final: 0.9529 (pp) REVERT: K 133 ILE cc_start: 0.9330 (mt) cc_final: 0.8993 (tp) REVERT: K 182 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.7992 (tt0) REVERT: K 197 GLU cc_start: 0.9038 (mp0) cc_final: 0.8658 (mp0) REVERT: K 207 MET cc_start: 0.9358 (tpp) cc_final: 0.9068 (tpp) REVERT: L 6 LYS cc_start: 0.9294 (mmmm) cc_final: 0.9076 (mmmt) REVERT: L 32 ARG cc_start: 0.8732 (ttm-80) cc_final: 0.8431 (ttm-80) REVERT: L 37 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8717 (mm) REVERT: L 73 MET cc_start: 0.8624 (mtm) cc_final: 0.8115 (mtp) REVERT: L 94 LYS cc_start: 0.9047 (ttpt) cc_final: 0.8756 (ttmt) REVERT: M 102 MET cc_start: 0.9477 (mtp) cc_final: 0.9228 (ttm) REVERT: N 84 MET cc_start: 0.9111 (mtp) cc_final: 0.8805 (ttm) REVERT: N 102 MET cc_start: 0.9533 (mtt) cc_final: 0.9168 (mmm) REVERT: O 102 MET cc_start: 0.9280 (mtp) cc_final: 0.9028 (ptm) REVERT: Q 35 THR cc_start: 0.9304 (m) cc_final: 0.9079 (p) REVERT: Q 179 PHE cc_start: 0.9306 (OUTLIER) cc_final: 0.8901 (t80) REVERT: Q 186 LEU cc_start: 0.9584 (tp) cc_final: 0.9383 (mt) REVERT: R 48 ASP cc_start: 0.9359 (OUTLIER) cc_final: 0.9039 (t0) REVERT: R 155 MET cc_start: 0.9501 (OUTLIER) cc_final: 0.9018 (mpp) REVERT: R 161 MET cc_start: 0.9131 (ppp) cc_final: 0.8787 (ppp) REVERT: R 188 MET cc_start: 0.9152 (mmm) cc_final: 0.8754 (mpp) REVERT: S 103 MET cc_start: 0.7915 (tpp) cc_final: 0.7499 (tpp) REVERT: S 115 MET cc_start: 0.9537 (mtt) cc_final: 0.9264 (ptm) REVERT: S 133 LEU cc_start: 0.9682 (OUTLIER) cc_final: 0.9458 (pp) REVERT: S 179 PHE cc_start: 0.9376 (m-80) cc_final: 0.9052 (t80) REVERT: S 188 MET cc_start: 0.9232 (mmp) cc_final: 0.8959 (mmp) REVERT: S 203 TYR cc_start: 0.8858 (OUTLIER) cc_final: 0.8312 (t80) REVERT: S 229 MET cc_start: 0.9419 (mtp) cc_final: 0.9180 (mmm) REVERT: a 423 MET cc_start: 0.8088 (ppp) cc_final: 0.7851 (ppp) REVERT: a 645 MET cc_start: 0.7433 (ttt) cc_final: 0.6872 (ptt) REVERT: a 651 MET cc_start: 0.6363 (mtm) cc_final: 0.6070 (mtt) REVERT: a 759 MET cc_start: 0.8246 (mmm) cc_final: 0.7841 (tpp) REVERT: a 791 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.8990 (tp) REVERT: b 16 TRP cc_start: 0.9117 (m100) cc_final: 0.8147 (m100) REVERT: b 48 MET cc_start: 0.9483 (OUTLIER) cc_final: 0.9223 (mtp) REVERT: b 137 MET cc_start: 0.8505 (OUTLIER) cc_final: 0.8186 (tpp) REVERT: b 197 GLN cc_start: 0.7483 (tp-100) cc_final: 0.6955 (tm-30) REVERT: c 421 MET cc_start: 0.8910 (mtt) cc_final: 0.8497 (mmt) REVERT: c 429 MET cc_start: 0.9274 (ttt) cc_final: 0.8412 (tmm) REVERT: d 118 HIS cc_start: 0.9209 (m90) cc_final: 0.8689 (m-70) REVERT: d 119 GLN cc_start: 0.9345 (tt0) cc_final: 0.8786 (tm-30) REVERT: d 243 HIS cc_start: 0.9265 (m90) cc_final: 0.8984 (m-70) REVERT: d 247 LEU cc_start: 0.9272 (mm) cc_final: 0.8799 (tp) REVERT: d 322 LYS cc_start: 0.9482 (pttt) cc_final: 0.9199 (ptmt) REVERT: d 323 GLU cc_start: 0.9102 (tt0) cc_final: 0.8528 (pt0) REVERT: d 348 ILE cc_start: 0.8619 (mm) cc_final: 0.8407 (mm) REVERT: e 37 ILE cc_start: 0.6866 (mt) cc_final: 0.6549 (tt) REVERT: g 44 MET cc_start: 0.7624 (OUTLIER) cc_final: 0.6524 (tmm) REVERT: h 32 TYR cc_start: 0.6308 (OUTLIER) cc_final: 0.5377 (t80) REVERT: h 104 LEU cc_start: 0.9069 (tp) cc_final: 0.8563 (mt) REVERT: h 131 MET cc_start: 0.7857 (ppp) cc_final: 0.6645 (ppp) REVERT: i 23 MET cc_start: 0.7336 (OUTLIER) cc_final: 0.6923 (mmm) REVERT: i 53 MET cc_start: 0.7748 (mmt) cc_final: 0.6839 (mtp) REVERT: i 97 LEU cc_start: 0.9254 (mm) cc_final: 0.8956 (pp) REVERT: i 108 PHE cc_start: 0.8190 (OUTLIER) cc_final: 0.7814 (m-10) REVERT: j 47 MET cc_start: 0.9282 (ppp) cc_final: 0.8863 (ppp) REVERT: j 61 MET cc_start: 0.6638 (ttm) cc_final: 0.6403 (ptm) REVERT: j 108 PHE cc_start: 0.8104 (m-80) cc_final: 0.7628 (t80) REVERT: j 131 MET cc_start: 0.5619 (ppp) cc_final: 0.5327 (ppp) REVERT: j 144 TYR cc_start: 0.7501 (m-10) cc_final: 0.7267 (m-10) REVERT: k 17 MET cc_start: 0.9002 (mmp) cc_final: 0.8486 (mmm) REVERT: k 23 MET cc_start: 0.7392 (tpt) cc_final: 0.6732 (tpt) REVERT: k 44 MET cc_start: 0.8879 (mmm) cc_final: 0.8434 (mtm) REVERT: k 131 MET cc_start: 0.7075 (tmm) cc_final: 0.6400 (ppp) REVERT: l 53 MET cc_start: 0.8685 (mmp) cc_final: 0.8293 (ttt) REVERT: l 104 LEU cc_start: 0.9406 (tp) cc_final: 0.9192 (mt) REVERT: l 137 PHE cc_start: 0.8099 (m-10) cc_final: 0.7859 (m-80) REVERT: m 23 MET cc_start: 0.8427 (tpp) cc_final: 0.7973 (tpt) REVERT: m 28 MET cc_start: 0.9093 (tpt) cc_final: 0.8778 (mmp) REVERT: m 32 TYR cc_start: 0.8332 (t80) cc_final: 0.7946 (t80) REVERT: m 131 MET cc_start: 0.9131 (ppp) cc_final: 0.8657 (ppp) REVERT: n 13 PHE cc_start: 0.9030 (t80) cc_final: 0.8496 (t80) REVERT: n 14 PHE cc_start: 0.8586 (m-80) cc_final: 0.8223 (m-80) REVERT: n 17 MET cc_start: 0.9389 (ptt) cc_final: 0.8928 (ptt) REVERT: n 23 MET cc_start: 0.8464 (tpt) cc_final: 0.7409 (tpt) REVERT: n 36 LYS cc_start: 0.6630 (mmtt) cc_final: 0.6137 (mtpp) REVERT: n 53 MET cc_start: 0.7841 (mmt) cc_final: 0.6336 (ttp) REVERT: n 70 LEU cc_start: 0.9020 (tp) cc_final: 0.8799 (tp) REVERT: n 90 PHE cc_start: 0.8806 (m-10) cc_final: 0.8499 (m-80) REVERT: n 104 LEU cc_start: 0.9501 (pp) cc_final: 0.9144 (mt) REVERT: n 123 GLN cc_start: 0.8393 (mp10) cc_final: 0.7668 (mt0) REVERT: o 21 SER cc_start: 0.9691 (m) cc_final: 0.9014 (p) REVERT: o 23 MET cc_start: 0.7484 (tpt) cc_final: 0.6633 (tpt) REVERT: o 25 PHE cc_start: 0.8746 (m-80) cc_final: 0.8432 (m-80) REVERT: o 44 MET cc_start: 0.9315 (mmm) cc_final: 0.8648 (mmm) REVERT: o 110 ILE cc_start: 0.8858 (mm) cc_final: 0.8638 (tp) outliers start: 124 outliers final: 92 residues processed: 928 average time/residue: 0.5541 time to fit residues: 893.0895 Evaluate side-chains 928 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 814 time to evaluate : 5.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 450 TRP Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 306 MET Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 450 TRP Chi-restraints excluded: chain C residue 584 MET Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 250 GLU Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 334 ILE Chi-restraints excluded: chain D residue 378 TYR Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 432 VAL Chi-restraints excluded: chain E residue 448 ASP Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 249 GLU Chi-restraints excluded: chain F residue 262 ASN Chi-restraints excluded: chain F residue 270 GLU Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 330 ASP Chi-restraints excluded: chain F residue 334 ILE Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain F residue 356 MET Chi-restraints excluded: chain H residue 79 PHE Chi-restraints excluded: chain I residue 167 ILE Chi-restraints excluded: chain K residue 128 LEU Chi-restraints excluded: chain K residue 182 GLU Chi-restraints excluded: chain L residue 29 ASN Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain N residue 74 GLU Chi-restraints excluded: chain O residue 74 GLU Chi-restraints excluded: chain Q residue 52 VAL Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 117 GLN Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 121 LEU Chi-restraints excluded: chain Q residue 146 THR Chi-restraints excluded: chain Q residue 159 LEU Chi-restraints excluded: chain Q residue 169 THR Chi-restraints excluded: chain Q residue 179 PHE Chi-restraints excluded: chain Q residue 181 LEU Chi-restraints excluded: chain Q residue 198 HIS Chi-restraints excluded: chain R residue 48 ASP Chi-restraints excluded: chain R residue 155 MET Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain S residue 133 LEU Chi-restraints excluded: chain S residue 134 ASN Chi-restraints excluded: chain S residue 198 HIS Chi-restraints excluded: chain S residue 203 TYR Chi-restraints excluded: chain a residue 536 PHE Chi-restraints excluded: chain a residue 591 ILE Chi-restraints excluded: chain a residue 610 LEU Chi-restraints excluded: chain a residue 749 HIS Chi-restraints excluded: chain a residue 752 LEU Chi-restraints excluded: chain a residue 791 LEU Chi-restraints excluded: chain a residue 830 HIS Chi-restraints excluded: chain b residue 48 MET Chi-restraints excluded: chain b residue 60 LEU Chi-restraints excluded: chain b residue 137 MET Chi-restraints excluded: chain b residue 138 PHE Chi-restraints excluded: chain c residue 415 PHE Chi-restraints excluded: chain d residue 6 GLU Chi-restraints excluded: chain e residue 36 VAL Chi-restraints excluded: chain e residue 60 LEU Chi-restraints excluded: chain g residue 44 MET Chi-restraints excluded: chain g residue 60 VAL Chi-restraints excluded: chain g residue 126 ARG Chi-restraints excluded: chain g residue 150 LEU Chi-restraints excluded: chain h residue 32 TYR Chi-restraints excluded: chain h residue 115 ASP Chi-restraints excluded: chain i residue 23 MET Chi-restraints excluded: chain i residue 108 PHE Chi-restraints excluded: chain i residue 115 ASP Chi-restraints excluded: chain j residue 123 GLN Chi-restraints excluded: chain k residue 7 ASN Chi-restraints excluded: chain k residue 108 PHE Chi-restraints excluded: chain k residue 119 ARG Chi-restraints excluded: chain l residue 13 PHE Chi-restraints excluded: chain l residue 78 ASN Chi-restraints excluded: chain l residue 152 LEU Chi-restraints excluded: chain m residue 17 MET Chi-restraints excluded: chain m residue 57 ILE Chi-restraints excluded: chain m residue 140 VAL Chi-restraints excluded: chain n residue 133 LEU Chi-restraints excluded: chain n residue 150 LEU Chi-restraints excluded: chain o residue 118 VAL Chi-restraints excluded: chain o residue 143 LEU Chi-restraints excluded: chain p residue 307 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 837 random chunks: chunk 527 optimal weight: 9.9990 chunk 707 optimal weight: 9.9990 chunk 203 optimal weight: 10.0000 chunk 612 optimal weight: 30.0000 chunk 98 optimal weight: 0.8980 chunk 184 optimal weight: 5.9990 chunk 665 optimal weight: 10.0000 chunk 278 optimal weight: 0.9990 chunk 682 optimal weight: 20.0000 chunk 84 optimal weight: 0.9990 chunk 122 optimal weight: 0.8980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 80 GLN ** O 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 751 GLN ** a 812 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 84 HIS ** d 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 78 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.093914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.077815 restraints weight = 419739.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.079161 restraints weight = 183135.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.080039 restraints weight = 101188.083| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.6076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 63395 Z= 0.224 Angle : 0.797 17.285 85997 Z= 0.389 Chirality : 0.047 0.397 10036 Planarity : 0.004 0.082 11103 Dihedral : 4.603 136.567 9058 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.40 % Favored : 96.56 % Rotamer: Outliers : 1.92 % Allowed : 18.26 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.09), residues: 8372 helix: 1.94 (0.07), residues: 4971 sheet: -0.11 (0.21), residues: 615 loop : -0.59 (0.12), residues: 2786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP b 16 HIS 0.007 0.001 HIS c 438 PHE 0.055 0.002 PHE j 25 TYR 0.070 0.002 TYR m 68 ARG 0.017 0.001 ARG O 79 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16437.53 seconds wall clock time: 284 minutes 55.87 seconds (17095.87 seconds total)