Starting phenix.real_space_refine on Thu Sep 26 15:50:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vq8_21319/09_2024/6vq8_21319.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vq8_21319/09_2024/6vq8_21319.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vq8_21319/09_2024/6vq8_21319.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vq8_21319/09_2024/6vq8_21319.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vq8_21319/09_2024/6vq8_21319.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vq8_21319/09_2024/6vq8_21319.cif" } resolution = 3.9 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= 0.070 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 311 5.16 5 C 38448 2.51 5 N 10527 2.21 5 O 11426 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 272 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: 60714 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: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1726 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 3, 'TRANS': 210} 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: 1602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1602 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 5, 'TRANS': 218} 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: 709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 709 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 2, 'TRANS': 110} Unresolved non-hydrogen bonds: 213 Unresolved non-hydrogen angles: 257 Unresolved non-hydrogen dihedrals: 174 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: 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: "R" 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: "S" 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: "a" Number of atoms: 3703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 749, 3703 Classifications: {'peptide': 749} Incomplete info: {'truncation_to_alanine': 668} Link IDs: {'PTRANS': 31, 'TRANS': 717} Chain breaks: 2 Unresolved chain link angles: 31 Unresolved non-hydrogen bonds: 2555 Unresolved non-hydrogen angles: 3282 Unresolved non-hydrogen dihedrals: 2176 Unresolved non-hydrogen chiralities: 228 Planarities with less than four sites: {'GLN:plan1': 26, 'HIS:plan': 19, 'TYR:plan': 23, 'ASN:plan1': 41, 'TRP:plan': 12, 'ASP:plan': 22, 'PHE:plan': 63, 'GLU:plan': 47, 'ARG:plan': 39} Unresolved non-hydrogen planarities: 1418 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: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 384 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 6, 'TRANS': 71} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 361 Unresolved non-hydrogen dihedrals: 242 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 5, 'HIS:plan': 1, 'PHE:plan': 7, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 137 Chain: "f" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 412 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 3, 'TRANS': 80} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 259 Unresolved non-hydrogen angles: 337 Unresolved non-hydrogen dihedrals: 219 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 7, 'GLU:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 141 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: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 406 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 50} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 17 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 26.67, per 1000 atoms: 0.44 Number of scatterers: 60714 At special positions: 0 Unit cell: (173.84, 174.9, 272.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 311 16.00 P 2 15.00 O 11426 8.00 N 10527 7.00 C 38448 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: 12.24 Conformation dependent library (CDL) restraints added in 6.8 seconds 16738 Ramachandran restraints generated. 8369 Oldfield, 0 Emsley, 8369 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15618 Finding SS restraints... Secondary structure from input PDB file: 319 helices and 77 sheets defined 64.3% alpha, 63.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 23.32 Creating SS restraints... Processing helix chain 'A' and resid 105 through 114 Processing helix chain 'A' and resid 255 through 266 Processing helix chain 'A' and resid 280 through 291 removed outlier: 3.955A pdb=" N MET A 284 " --> pdb=" O ARG A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 294 No H-bonds generated for 'chain 'A' and resid 292 through 294' Processing helix chain 'A' and resid 305 through 307 No H-bonds generated for 'chain 'A' and resid 305 through 307' Processing helix chain 'A' and resid 321 through 340 removed outlier: 3.999A pdb=" N ALA A 325 " --> pdb=" O ALA A 321 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET A 340 " --> pdb=" O TYR A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 365 Processing helix chain 'A' and resid 370 through 374 Processing helix chain 'A' and resid 375 through 376 No H-bonds generated for 'chain 'A' and resid 375 through 376' Processing helix chain 'A' and resid 377 through 387 Processing helix chain 'A' and resid 412 through 416 Processing helix chain 'A' and resid 419 through 427 Processing helix chain 'A' and resid 436 through 442 removed outlier: 3.869A pdb=" N ARG A 442 " --> pdb=" O LYS A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 469 removed outlier: 4.455A pdb=" N GLU A 463 " --> pdb=" O ARG A 459 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N TYR A 464 " --> pdb=" O ALA A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 497 removed outlier: 4.140A pdb=" N ILE A 492 " --> pdb=" O ASP A 488 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEU A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) 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 593 through 616 Processing helix chain 'B' and resid 105 through 114 Processing helix chain 'B' and resid 231 through 236 removed outlier: 3.592A pdb=" N ASP B 235 " --> pdb=" O GLN B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 267 removed outlier: 3.644A pdb=" N SER B 267 " --> pdb=" O LEU B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 291 Processing helix chain 'B' and resid 306 through 309 Processing helix chain 'B' and resid 319 through 339 removed outlier: 4.616A pdb=" N ILE B 327 " --> pdb=" O ARG B 323 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N TYR B 328 " --> pdb=" O GLU B 324 " (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 377 through 387 Processing helix chain 'B' and resid 419 through 427 Processing helix chain 'B' and resid 436 through 442 Processing helix chain 'B' and resid 457 through 469 removed outlier: 4.282A pdb=" N GLU B 463 " --> pdb=" O ARG B 459 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N TYR B 464 " --> pdb=" O ALA B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 497 removed outlier: 3.867A 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 558 Processing helix chain 'B' and resid 566 through 574 Processing helix chain 'B' and resid 574 through 583 removed outlier: 3.531A pdb=" N LEU B 578 " --> pdb=" O MET B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 587 Processing helix chain 'B' and resid 593 through 616 Processing helix chain 'C' and resid 105 through 113 removed outlier: 3.652A pdb=" N SER C 111 " --> pdb=" O SER C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 255 removed outlier: 4.416A pdb=" N GLY C 255 " --> pdb=" O PHE C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 267 removed outlier: 3.531A 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 319 through 339 removed outlier: 4.594A pdb=" N ILE C 327 " --> pdb=" O ARG C 323 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N TYR C 328 " --> pdb=" O GLU C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 365 removed outlier: 3.508A pdb=" N TRP C 354 " --> pdb=" O SER C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 374 Processing helix chain 'C' and resid 377 through 388 removed outlier: 3.725A pdb=" N ARG C 388 " --> pdb=" O SER C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 416 removed outlier: 4.120A pdb=" N ASP C 416 " --> pdb=" O PRO C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 419 through 427 Processing helix chain 'C' and resid 437 through 442 Processing helix chain 'C' and resid 461 through 469 Processing helix chain 'C' and resid 471 through 489 Processing helix chain 'C' and resid 489 through 497 Processing helix chain 'C' and resid 502 through 519 Processing helix chain 'C' and resid 533 through 557 Processing helix chain 'C' and resid 566 through 574 Processing helix chain 'C' and resid 574 through 583 Processing helix chain 'C' and resid 584 through 587 Processing helix chain 'C' and resid 593 through 614 Processing helix chain 'D' and resid 124 through 128 Processing helix chain 'D' and resid 174 through 179 Processing helix chain 'D' and resid 198 through 210 removed outlier: 3.601A pdb=" N ARG D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 251 Processing helix chain 'D' and resid 253 through 255 No H-bonds generated for 'chain 'D' and resid 253 through 255' Processing helix chain 'D' and resid 269 through 272 Processing helix chain 'D' and resid 273 through 288 Processing helix chain 'D' and resid 299 through 314 removed outlier: 4.056A pdb=" N TYR D 303 " --> pdb=" O ASP D 299 " (cutoff:3.500A) 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 373 Processing helix chain 'D' and resid 380 through 385 removed outlier: 3.668A pdb=" N HIS D 384 " --> pdb=" O ASP D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 406 removed outlier: 3.511A pdb=" N ILE D 406 " --> pdb=" O MET D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 440 removed outlier: 4.343A pdb=" N VAL D 438 " --> pdb=" O ALA D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 441 through 444 Processing helix chain 'D' and resid 445 through 462 removed outlier: 4.348A pdb=" N TYR D 451 " --> pdb=" O ASP D 447 " (cutoff:3.500A) 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 removed outlier: 5.012A pdb=" N GLU D 502 " --> pdb=" O SER D 498 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 128 removed outlier: 4.085A pdb=" N LEU E 128 " --> pdb=" O GLU E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 179 Processing helix chain 'E' and resid 198 through 210 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: 3.814A pdb=" N TYR E 303 " --> pdb=" O ASP E 299 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 323 Processing helix chain 'E' and resid 326 through 336 removed outlier: 3.852A pdb=" N ILE E 334 " --> pdb=" O ASP E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 360 Processing helix chain 'E' and resid 363 through 373 Processing helix chain 'E' and resid 381 through 386 removed outlier: 3.627A pdb=" N ARG E 386 " --> pdb=" O GLN E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 401 through 406 removed outlier: 3.781A pdb=" N ILE E 406 " --> pdb=" O MET E 402 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 440 removed outlier: 4.031A pdb=" N VAL E 438 " --> pdb=" O ALA E 434 " (cutoff:3.500A) Processing helix chain 'E' and resid 441 through 444 removed outlier: 3.930A pdb=" N LEU E 444 " --> pdb=" O GLU E 441 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 441 through 444' Processing helix chain 'E' and resid 445 through 462 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 Processing helix chain 'F' and resid 159 through 161 No H-bonds generated for 'chain 'F' and resid 159 through 161' Processing helix chain 'F' and resid 174 through 178 Processing helix chain 'F' and resid 198 through 210 Processing helix chain 'F' and resid 237 through 251 removed outlier: 3.549A pdb=" N ASN F 251 " --> pdb=" O ASP F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 255 removed outlier: 4.119A pdb=" N ASP F 255 " --> pdb=" O GLY F 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 252 through 255' Processing helix chain 'F' and resid 267 through 289 removed outlier: 3.580A pdb=" N ILE F 272 " --> pdb=" O THR F 268 " (cutoff:3.500A) Proline residue: F 275 - end of helix Processing helix chain 'F' and resid 299 through 314 Processing helix chain 'F' and resid 319 through 323 Processing helix chain 'F' and resid 326 through 336 Processing helix chain 'F' and resid 357 through 360 Processing helix chain 'F' and resid 363 through 371 Processing helix chain 'F' and resid 381 through 386 Processing helix chain 'F' and resid 401 through 406 Processing helix chain 'F' and resid 414 through 440 removed outlier: 3.691A pdb=" N VAL F 438 " --> pdb=" O ALA F 434 " (cutoff:3.500A) 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 14 through 22 removed outlier: 4.245A pdb=" N THR G 18 " --> pdb=" O THR G 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 32 Processing helix chain 'G' and resid 47 through 80 Processing helix chain 'G' and resid 97 through 104 Processing helix chain 'G' and resid 117 through 157 removed outlier: 3.503A pdb=" N ASN G 157 " --> pdb=" O LEU G 153 " (cutoff:3.500A) Processing helix chain 'G' and resid 165 through 169 removed outlier: 4.263A pdb=" N GLU G 168 " --> pdb=" O SER G 165 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 175 removed outlier: 3.604A pdb=" N PHE G 175 " --> pdb=" O LYS G 172 " (cutoff:3.500A) Processing helix chain 'G' and resid 193 through 201 Processing helix chain 'G' and resid 202 through 204 No H-bonds generated for 'chain 'G' and resid 202 through 204' 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 341 removed outlier: 4.123A pdb=" N HIS G 341 " --> pdb=" O GLU G 337 " (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 217 Processing helix chain 'I' and resid 4 through 107 Processing helix chain 'I' and resid 108 through 128 removed outlier: 4.629A pdb=" N VAL I 114 " --> pdb=" O THR I 110 " (cutoff:3.500A) 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 159 Proline residue: I 153 - end of helix removed outlier: 3.606A pdb=" N ILE I 157 " --> pdb=" O PRO I 153 " (cutoff:3.500A) Processing helix chain 'I' and resid 196 through 217 removed outlier: 3.949A pdb=" N GLN I 206 " --> pdb=" O LEU I 202 " (cutoff:3.500A) Proline residue: I 209 - end of helix Processing helix chain 'J' and resid 4 through 107 removed outlier: 3.574A pdb=" N LYS J 52 " --> pdb=" O THR J 48 " (cutoff:3.500A) Processing helix chain 'J' and resid 109 through 128 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 160 Proline residue: J 153 - end of helix Processing helix chain 'J' and resid 196 through 205 Processing helix chain 'J' and resid 207 through 217 removed outlier: 3.613A pdb=" N GLY J 213 " --> pdb=" O PRO J 209 " (cutoff:3.500A) Processing helix chain 'K' and resid 4 through 107 removed outlier: 3.588A pdb=" N VAL K 8 " --> pdb=" O SER K 4 " (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: 3.522A 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 195 through 207 Processing helix chain 'K' and resid 207 through 217 removed outlier: 3.507A 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: 3.805A pdb=" N LEU L 78 " --> pdb=" O VAL L 74 " (cutoff:3.500A) removed outlier: 3.661A 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 89 removed outlier: 4.043A pdb=" N SER M 70 " --> pdb=" O GLN M 66 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ALA M 71 " --> pdb=" O GLY M 67 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU M 72 " --> pdb=" O ASN M 68 " (cutoff:3.500A) Processing helix chain 'M' and resid 91 through 105 Processing helix chain 'N' and resid 4 through 104 removed outlier: 3.793A pdb=" N GLN N 66 " --> pdb=" O ALA N 62 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU N 74 " --> pdb=" O SER N 70 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN N 91 " --> pdb=" O SER N 87 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N GLU N 93 " --> pdb=" O GLN N 89 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N ARG N 94 " --> pdb=" O ARG N 90 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 91 removed outlier: 3.845A pdb=" N GLN O 66 " --> pdb=" O ALA O 62 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ASN O 91 " --> pdb=" O SER O 87 " (cutoff:3.500A) Processing helix chain 'O' and resid 91 through 105 Processing helix chain 'Q' and resid 14 through 37 Processing helix chain 'Q' and resid 42 through 49 Processing helix chain 'Q' and resid 49 through 54 Processing helix chain 'Q' and resid 61 through 71 Processing helix chain 'Q' and resid 77 through 97 removed outlier: 3.907A pdb=" N LEU Q 88 " --> pdb=" O ARG Q 84 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU Q 91 " --> pdb=" O ILE Q 87 " (cutoff:3.500A) Processing helix chain 'Q' and resid 104 through 117 Processing helix chain 'Q' and resid 124 through 140 removed outlier: 3.524A pdb=" N LEU Q 140 " --> pdb=" O LEU Q 136 " (cutoff:3.500A) Processing helix chain 'Q' and resid 146 through 167 Processing helix chain 'Q' and resid 172 through 188 Processing helix chain 'Q' and resid 192 through 205 Processing helix chain 'Q' and resid 218 through 233 removed outlier: 3.561A pdb=" N MET Q 229 " --> pdb=" O LEU Q 225 " (cutoff:3.500A) Processing helix chain 'R' and resid 14 through 37 Processing helix chain 'R' and resid 42 through 48 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 Processing helix chain 'R' and resid 104 through 118 Processing helix chain 'R' and resid 120 through 123 Processing helix chain 'R' and resid 124 through 142 removed outlier: 3.949A pdb=" N ASN R 142 " --> pdb=" O ASP R 138 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 167 Processing helix chain 'R' and resid 172 through 187 Processing helix chain 'R' and resid 192 through 206 Processing helix chain 'R' and resid 218 through 234 Processing helix chain 'S' and resid 14 through 37 removed outlier: 3.506A pdb=" N HIS S 19 " --> pdb=" O SER S 15 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 49 removed outlier: 3.679A pdb=" N TYR S 49 " --> pdb=" O ILE S 45 " (cutoff:3.500A) Processing helix chain 'S' and resid 49 through 54 Processing helix chain 'S' and resid 62 through 72 Processing helix chain 'S' and resid 77 through 97 Processing helix chain 'S' and resid 104 through 117 Processing helix chain 'S' and resid 120 through 123 Processing helix chain 'S' and resid 124 through 140 removed outlier: 3.694A pdb=" N LEU S 140 " --> pdb=" O LEU S 136 " (cutoff:3.500A) Processing helix chain 'S' and resid 141 through 143 No H-bonds generated for 'chain 'S' and resid 141 through 143' Processing helix chain 'S' and resid 146 through 167 removed outlier: 3.541A pdb=" N GLN S 165 " --> pdb=" O MET S 161 " (cutoff:3.500A) Processing helix chain 'S' and resid 172 through 187 Processing helix chain 'S' and resid 193 through 207 Processing helix chain 'a' and resid 19 through 33 Processing helix chain 'a' and resid 45 through 50 Processing helix chain 'a' and resid 51 through 75 Processing helix chain 'a' and resid 84 through 88 Processing helix chain 'a' and resid 93 through 132 Processing helix chain 'a' and resid 179 through 191 Processing helix chain 'a' and resid 226 through 240 Processing helix chain 'a' and resid 251 through 309 removed outlier: 3.623A pdb=" N LYS a 255 " --> pdb=" O PRO a 251 " (cutoff:3.500A) Processing helix chain 'a' and resid 326 through 344 Processing helix chain 'a' and resid 370 through 380 removed outlier: 4.462A pdb=" N PHE a 374 " --> pdb=" O PHE a 370 " (cutoff:3.500A) Processing helix chain 'a' and resid 391 through 407 removed outlier: 4.686A 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 Processing helix chain 'a' and resid 481 through 488 removed outlier: 3.631A pdb=" N ILE a 487 " --> pdb=" O PRO a 483 " (cutoff:3.500A) Processing helix chain 'a' and resid 492 through 497 removed outlier: 4.320A 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: 4.577A pdb=" N ASN a 534 " --> pdb=" O LEU a 530 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER a 556 " --> pdb=" O GLY a 552 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU a 557 " --> pdb=" O VAL a 553 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE a 558 " --> pdb=" O SER a 554 " (cutoff:3.500A) Processing helix chain 'a' and resid 565 through 571 removed outlier: 3.813A pdb=" N ILE a 569 " --> pdb=" O LYS a 565 " (cutoff:3.500A) Processing helix chain 'a' and resid 572 through 598 removed outlier: 4.227A pdb=" N TYR a 586 " --> pdb=" O SER a 582 " (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 647 Processing helix chain 'a' and resid 647 through 667 removed outlier: 3.561A pdb=" N MET a 651 " --> pdb=" O CYS a 647 " (cutoff:3.500A) removed outlier: 5.798A 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 removed outlier: 3.572A pdb=" N ILE a 733 " --> pdb=" O CYS a 729 " (cutoff:3.500A) Processing helix chain 'a' and resid 739 through 759 removed outlier: 4.258A 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 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: 3.602A pdb=" N TRP b 49 " --> pdb=" O SER b 45 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER b 61 " --> pdb=" O ALA b 57 " (cutoff:3.500A) removed outlier: 3.552A 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: 4.085A pdb=" N LYS b 89 " --> pdb=" O ARG b 85 " (cutoff:3.500A) Processing helix chain 'b' and resid 91 through 113 Processing helix chain 'b' and resid 127 through 169 removed outlier: 3.929A pdb=" N GLN b 168 " --> pdb=" O LEU b 164 " (cutoff:3.500A) Processing helix chain 'b' and resid 172 through 198 removed outlier: 4.197A pdb=" N ILE b 178 " --> pdb=" O VAL b 174 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N VAL b 179 " --> pdb=" O LYS b 175 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLU b 180 " --> pdb=" O ILE b 176 " (cutoff:3.500A) Processing helix chain 'c' and resid 416 through 442 Processing helix chain 'd' and resid 8 through 25 removed outlier: 4.126A pdb=" N ASP d 12 " --> pdb=" O TYR d 8 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N TYR d 15 " --> pdb=" O VAL d 11 " (cutoff:3.500A) removed outlier: 5.308A 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: 4.898A pdb=" N PHE d 96 " --> pdb=" O PRO d 92 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE d 100 " --> pdb=" O PHE d 96 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TYR d 104 " --> pdb=" O ILE d 100 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP d 107 " --> pdb=" O SER d 103 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N THR d 114 " --> pdb=" O ILE d 110 " (cutoff:3.500A) removed outlier: 3.717A 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: 4.100A pdb=" N ALA d 162 " --> pdb=" O PRO d 159 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP d 166 " --> pdb=" O PHE d 163 " (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: 3.637A 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: 4.437A 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 338 removed outlier: 3.708A 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 removed outlier: 3.575A pdb=" N ARG e 77 " --> pdb=" O ILE e 73 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N PHE e 78 " --> pdb=" O TRP e 74 " (cutoff:3.500A) Processing helix chain 'f' and resid 8 through 36 Processing helix chain 'f' and resid 54 through 90 removed outlier: 3.967A pdb=" N ILE f 58 " --> pdb=" O GLY f 54 " (cutoff:3.500A) Processing helix chain 'g' and resid 10 through 46 removed outlier: 3.613A pdb=" N PHE g 14 " --> pdb=" O TYR g 10 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLY g 15 " --> pdb=" O SER g 11 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET g 23 " --> pdb=" O ALA g 19 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER g 26 " --> pdb=" O ALA g 22 " (cutoff:3.500A) removed outlier: 3.910A 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 Processing helix chain 'g' and resid 127 through 153 removed outlier: 3.839A pdb=" N SER g 153 " --> pdb=" O ALA g 149 " (cutoff:3.500A) Processing helix chain 'h' and resid 11 through 46 removed outlier: 4.421A pdb=" N GLY h 15 " --> pdb=" O SER h 11 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL h 46 " --> pdb=" O ALA h 42 " (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: 4.453A pdb=" N GLY h 130 " --> pdb=" O ARG h 126 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY h 145 " --> pdb=" O LEU h 141 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR h 154 " --> pdb=" O LEU h 150 " (cutoff:3.500A) Processing helix chain 'i' and resid 10 through 48 removed outlier: 4.083A pdb=" N PHE i 14 " --> pdb=" O TYR i 10 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLY i 15 " --> pdb=" O SER i 11 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N MET i 23 " --> pdb=" O ALA i 19 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER i 26 " --> pdb=" O ALA i 22 " (cutoff:3.500A) removed outlier: 3.522A 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: 3.900A pdb=" N GLN i 123 " --> pdb=" O ARG i 119 " (cutoff:3.500A) Processing helix chain 'i' and resid 126 through 154 removed outlier: 4.604A pdb=" N GLY i 130 " --> pdb=" O ARG i 126 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY i 145 " --> pdb=" O LEU i 141 " (cutoff:3.500A) Processing helix chain 'j' and resid 11 through 48 removed outlier: 4.303A pdb=" N GLY j 15 " --> pdb=" O SER j 11 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET j 23 " --> pdb=" O ALA j 19 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL j 46 " --> pdb=" O ALA j 42 " (cutoff:3.500A) removed outlier: 4.457A 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: 3.613A pdb=" N ILE j 64 " --> pdb=" O VAL j 60 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ILE j 65 " --> pdb=" O MET j 61 " (cutoff:3.500A) removed outlier: 3.875A 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: 4.483A pdb=" N GLY j 130 " --> pdb=" O ARG j 126 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY j 145 " --> pdb=" O LEU j 141 " (cutoff:3.500A) Processing helix chain 'k' and resid 10 through 48 removed outlier: 3.899A pdb=" N PHE k 14 " --> pdb=" O TYR k 10 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLY k 15 " --> pdb=" O SER k 11 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET k 23 " --> pdb=" O ALA k 19 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N VAL k 46 " --> pdb=" O ALA k 42 " (cutoff:3.500A) removed outlier: 4.165A 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: 4.418A pdb=" N GLY l 15 " --> pdb=" O SER l 11 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL l 46 " --> pdb=" O ALA l 42 " (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: 3.737A pdb=" N GLN l 123 " --> pdb=" O ARG l 119 " (cutoff:3.500A) Processing helix chain 'l' and resid 126 through 155 removed outlier: 4.391A pdb=" N GLY l 130 " --> pdb=" O ARG l 126 " (cutoff:3.500A) Processing helix chain 'm' and resid 10 through 45 removed outlier: 3.641A 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: 4.732A 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: 3.990A pdb=" N GLN m 123 " --> pdb=" O ARG m 119 " (cutoff:3.500A) Processing helix chain 'm' and resid 126 through 154 removed outlier: 4.365A pdb=" N GLY m 130 " --> pdb=" O ARG m 126 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY m 145 " --> pdb=" O LEU m 141 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR m 154 " --> pdb=" O LEU m 150 " (cutoff:3.500A) Processing helix chain 'n' and resid 11 through 46 removed outlier: 4.511A pdb=" N GLY n 15 " --> pdb=" O SER n 11 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET n 23 " --> pdb=" O ALA n 19 " (cutoff:3.500A) removed outlier: 3.790A 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 removed outlier: 3.567A pdb=" N SER n 79 " --> pdb=" O LEU n 75 " (cutoff:3.500A) Processing helix chain 'n' and resid 86 through 124 removed outlier: 3.590A pdb=" N ARG n 119 " --> pdb=" O ASP n 115 " (cutoff:3.500A) Processing helix chain 'n' and resid 126 through 154 removed outlier: 4.631A pdb=" N GLY n 130 " --> pdb=" O ARG n 126 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY n 145 " --> pdb=" O LEU n 141 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR n 154 " --> pdb=" O LEU n 150 " (cutoff:3.500A) Processing helix chain 'o' and resid 10 through 48 removed outlier: 4.311A pdb=" N PHE o 14 " --> pdb=" O TYR o 10 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLY o 15 " --> pdb=" O SER o 11 " (cutoff:3.500A) removed outlier: 3.871A 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: 3.527A pdb=" N VAL o 60 " --> pdb=" O ILE o 56 " (cutoff:3.500A) Processing helix chain 'o' and resid 86 through 124 Processing helix chain 'o' and resid 127 through 154 removed outlier: 3.662A pdb=" N THR o 154 " --> pdb=" O LEU o 150 " (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: 5.967A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL I 181 " --> pdb=" O ASN I 194 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N THR A 30 " --> pdb=" O HIS A 22 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N VAL A 24 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N VAL A 28 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N MET A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N LEU A 57 " --> pdb=" O MET A 61 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N THR A 63 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU E 70 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE E 71 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL J 181 " --> pdb=" O ASN J 194 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 164 through 167 removed outlier: 5.967A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL I 181 " --> pdb=" O ASN I 194 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 42 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N GLU A 41 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU E 70 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE E 71 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL J 181 " --> pdb=" O ASN J 194 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 164 through 167 removed outlier: 5.967A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL I 181 " --> pdb=" O ASN I 194 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL D 95 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N VAL D 89 " --> pdb=" O LYS D 93 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LYS D 93 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU C 42 " --> pdb=" O THR C 82 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU F 70 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ILE F 71 " --> pdb=" O THR F 115 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N MET K 132 " --> pdb=" O GLN K 166 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'I' and resid 164 through 167 removed outlier: 5.967A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL I 181 " --> pdb=" O ASN I 194 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL D 95 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N VAL D 89 " --> pdb=" O LYS D 93 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LYS D 93 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N THR C 63 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N LEU C 57 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N MET C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N CYS C 32 " --> pdb=" O VAL C 21 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N VAL C 21 " --> pdb=" O CYS C 32 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU F 70 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ILE F 71 " --> pdb=" O THR F 115 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N MET K 132 " --> pdb=" O GLN K 166 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 164 through 167 removed outlier: 5.967A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL I 181 " --> pdb=" O ASN I 194 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N THR A 30 " --> pdb=" O HIS A 22 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N VAL A 24 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N VAL A 28 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N MET A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N LEU A 57 " --> pdb=" O MET A 61 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N THR A 63 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N THR B 30 " --> pdb=" O HIS B 22 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL B 24 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL B 28 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N MET B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N LEU B 57 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR B 63 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA F 94 " --> pdb=" O LEU F 60 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLN F 97 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL F 86 " --> pdb=" O GLN F 97 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU F 70 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ILE F 71 " --> pdb=" O THR F 115 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N MET K 132 " --> pdb=" O GLN K 166 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 164 through 167 removed outlier: 5.967A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL I 181 " --> pdb=" O ASN I 194 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N THR A 30 " --> pdb=" O HIS A 22 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N VAL A 24 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N VAL A 28 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N MET A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N LEU A 57 " --> pdb=" O MET A 61 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N THR A 63 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA F 94 " --> pdb=" O LEU F 60 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLN F 97 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL F 86 " --> pdb=" O GLN F 97 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU F 70 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ILE F 71 " --> pdb=" O THR F 115 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N MET K 132 " --> pdb=" O GLN K 166 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 164 through 167 removed outlier: 5.967A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL I 181 " --> pdb=" O ASN I 194 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 42 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N GLU A 41 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N THR B 30 " --> pdb=" O HIS B 22 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL B 24 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL B 28 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N MET B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N LEU B 57 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR B 63 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA F 94 " --> pdb=" O LEU F 60 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLN F 97 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL F 86 " --> pdb=" O GLN F 97 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU F 70 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ILE F 71 " --> pdb=" O THR F 115 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N MET K 132 " --> pdb=" O GLN K 166 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 164 through 167 removed outlier: 5.967A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL I 181 " --> pdb=" O ASN I 194 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 42 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N GLU A 41 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA F 94 " --> pdb=" O LEU F 60 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLN F 97 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL F 86 " --> pdb=" O GLN F 97 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU F 70 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ILE F 71 " --> pdb=" O THR F 115 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N MET K 132 " --> pdb=" O GLN K 166 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 164 through 167 removed outlier: 5.967A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL I 181 " --> pdb=" O ASN I 194 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL D 95 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N VAL D 89 " --> pdb=" O LYS D 93 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LYS D 93 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU C 42 " --> pdb=" O THR C 82 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL F 86 " --> pdb=" O GLN F 97 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLN F 97 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA F 94 " --> pdb=" O LEU F 60 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU E 70 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE E 71 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL J 181 " --> pdb=" O ASN J 194 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 164 through 167 removed outlier: 5.967A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL I 181 " --> pdb=" O ASN I 194 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL D 95 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N VAL D 89 " --> pdb=" O LYS D 93 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LYS D 93 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU C 42 " --> pdb=" O THR C 82 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL F 86 " --> pdb=" O GLN F 97 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLN F 97 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA F 94 " --> pdb=" O LEU F 60 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR B 63 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N LEU B 57 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N MET B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL B 28 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL B 24 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N THR B 30 " --> pdb=" O HIS B 22 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU E 70 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE E 71 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL J 181 " --> pdb=" O ASN J 194 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 164 through 167 removed outlier: 5.967A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL I 181 " --> pdb=" O ASN I 194 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL D 95 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N VAL D 89 " --> pdb=" O LYS D 93 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LYS D 93 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N THR C 63 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N LEU C 57 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N MET C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N CYS C 32 " --> pdb=" O VAL C 21 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N VAL C 21 " --> pdb=" O CYS C 32 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL F 86 " --> pdb=" O GLN F 97 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLN F 97 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA F 94 " --> pdb=" O LEU F 60 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU E 70 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE E 71 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL J 181 " --> pdb=" O ASN J 194 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 164 through 167 removed outlier: 5.967A pdb=" N MET I 132 " --> pdb=" O GLN I 166 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL I 181 " --> pdb=" O ASN I 194 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL D 95 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N VAL D 89 " --> pdb=" O LYS D 93 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LYS D 93 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N THR C 63 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N LEU C 57 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N MET C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N CYS C 32 " --> pdb=" O VAL C 21 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N VAL C 21 " --> pdb=" O CYS C 32 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL F 86 " --> pdb=" O GLN F 97 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLN F 97 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA F 94 " --> pdb=" O LEU F 60 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR B 63 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N LEU B 57 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N MET B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL B 28 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL B 24 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N THR B 30 " --> pdb=" O HIS B 22 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU E 70 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE E 71 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL J 181 " --> pdb=" O ASN J 194 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 164 through 167 removed outlier: 3.506A pdb=" N VAL J 181 " --> pdb=" O ASN J 194 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE E 71 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU E 70 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N THR B 30 " --> pdb=" O HIS B 22 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL B 24 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL B 28 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N MET B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N LEU B 57 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR B 63 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA F 94 " --> pdb=" O LEU F 60 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLN F 97 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL F 86 " --> pdb=" O GLN F 97 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU F 70 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ILE F 71 " --> pdb=" O THR F 115 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N MET K 132 " --> pdb=" O GLN K 166 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 164 through 167 removed outlier: 3.506A pdb=" N VAL J 181 " --> pdb=" O ASN J 194 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE E 71 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU E 70 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA F 94 " --> pdb=" O LEU F 60 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLN F 97 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL F 86 " --> pdb=" O GLN F 97 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU F 70 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ILE F 71 " --> pdb=" O THR F 115 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N MET K 132 " --> pdb=" O GLN K 166 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 164 through 167 removed outlier: 3.506A pdb=" N VAL J 181 " --> pdb=" O ASN J 194 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE E 71 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU E 70 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N GLU A 41 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 42 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL I 181 " --> pdb=" O ASN I 194 " (cutoff:3.500A) removed outlier: 5.967A 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: 3.506A pdb=" N VAL J 181 " --> pdb=" O ASN J 194 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE E 71 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU E 70 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N THR A 63 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N LEU A 57 " --> pdb=" O MET A 61 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N MET A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N VAL A 28 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N VAL A 24 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N THR A 30 " --> pdb=" O HIS A 22 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL I 181 " --> pdb=" O ASN I 194 " (cutoff:3.500A) removed outlier: 5.967A 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: 3.506A pdb=" N VAL J 181 " --> pdb=" O ASN J 194 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE E 71 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU E 70 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N THR B 30 " --> pdb=" O HIS B 22 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL B 24 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL B 28 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N MET B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N LEU B 57 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR B 63 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA F 94 " --> pdb=" O LEU F 60 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLN F 97 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL F 86 " --> pdb=" O GLN F 97 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N VAL C 21 " --> pdb=" O CYS C 32 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N CYS C 32 " --> pdb=" O VAL C 21 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N MET C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N LEU C 57 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N THR C 63 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LYS D 93 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N VAL D 89 " --> pdb=" O LYS D 93 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL D 95 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL I 181 " --> pdb=" O ASN I 194 " (cutoff:3.500A) removed outlier: 5.967A 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: 3.506A pdb=" N VAL J 181 " --> pdb=" O ASN J 194 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE E 71 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU E 70 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N THR B 30 " --> pdb=" O HIS B 22 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL B 24 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL B 28 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N MET B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N LEU B 57 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR B 63 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA F 94 " --> pdb=" O LEU F 60 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLN F 97 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL F 86 " --> pdb=" O GLN F 97 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU C 42 " --> pdb=" O THR C 82 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LYS D 93 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N VAL D 89 " --> pdb=" O LYS D 93 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL D 95 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL I 181 " --> pdb=" O ASN I 194 " (cutoff:3.500A) removed outlier: 5.967A 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: 3.506A pdb=" N VAL J 181 " --> pdb=" O ASN J 194 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE E 71 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU E 70 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA F 94 " --> pdb=" O LEU F 60 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLN F 97 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL F 86 " --> pdb=" O GLN F 97 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N VAL C 21 " --> pdb=" O CYS C 32 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N CYS C 32 " --> pdb=" O VAL C 21 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N MET C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N LEU C 57 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N THR C 63 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LYS D 93 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N VAL D 89 " --> pdb=" O LYS D 93 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL D 95 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL I 181 " --> pdb=" O ASN I 194 " (cutoff:3.500A) removed outlier: 5.967A 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: 3.506A pdb=" N VAL J 181 " --> pdb=" O ASN J 194 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE E 71 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU E 70 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA F 94 " --> pdb=" O LEU F 60 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLN F 97 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL F 86 " --> pdb=" O GLN F 97 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU C 42 " --> pdb=" O THR C 82 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LYS D 93 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N VAL D 89 " --> pdb=" O LYS D 93 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL D 95 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL I 181 " --> pdb=" O ASN I 194 " (cutoff:3.500A) removed outlier: 5.967A 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: 3.506A pdb=" N VAL J 181 " --> pdb=" O ASN J 194 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE E 71 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU E 70 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N GLU A 41 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 42 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL D 95 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N VAL D 89 " --> pdb=" O LYS D 93 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LYS D 93 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU C 42 " --> pdb=" O THR C 82 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU F 70 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ILE F 71 " --> pdb=" O THR F 115 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N MET K 132 " --> pdb=" O GLN K 166 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 164 through 167 removed outlier: 3.506A pdb=" N VAL J 181 " --> pdb=" O ASN J 194 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE E 71 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU E 70 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N GLU A 41 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 42 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL D 95 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N VAL D 89 " --> pdb=" O LYS D 93 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LYS D 93 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N THR C 63 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N LEU C 57 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N MET C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N CYS C 32 " --> pdb=" O VAL C 21 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N VAL C 21 " --> pdb=" O CYS C 32 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU F 70 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ILE F 71 " --> pdb=" O THR F 115 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N MET K 132 " --> pdb=" O GLN K 166 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 164 through 167 removed outlier: 3.506A pdb=" N VAL J 181 " --> pdb=" O ASN J 194 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE E 71 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU E 70 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N THR A 63 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N LEU A 57 " --> pdb=" O MET A 61 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N MET A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N VAL A 28 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N VAL A 24 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N THR A 30 " --> pdb=" O HIS A 22 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL D 95 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N VAL D 89 " --> pdb=" O LYS D 93 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LYS D 93 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU C 42 " --> pdb=" O THR C 82 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU F 70 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ILE F 71 " --> pdb=" O THR F 115 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N MET K 132 " --> pdb=" O GLN K 166 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 164 through 167 removed outlier: 3.506A pdb=" N VAL J 181 " --> pdb=" O ASN J 194 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE E 71 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU E 70 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N THR A 63 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N LEU A 57 " --> pdb=" O MET A 61 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N MET A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N VAL A 28 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N VAL A 24 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N THR A 30 " --> pdb=" O HIS A 22 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL D 95 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N VAL D 89 " --> pdb=" O LYS D 93 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LYS D 93 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N THR C 63 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N LEU C 57 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N MET C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N CYS C 32 " --> pdb=" O VAL C 21 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N VAL C 21 " --> pdb=" O CYS C 32 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU F 70 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ILE F 71 " --> pdb=" O THR F 115 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N MET K 132 " --> pdb=" O GLN K 166 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 164 through 167 removed outlier: 6.204A pdb=" N MET K 132 " --> pdb=" O GLN K 166 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ILE F 71 " --> pdb=" O THR F 115 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU F 70 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N VAL C 21 " --> pdb=" O CYS C 32 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N CYS C 32 " --> pdb=" O VAL C 21 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N MET C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N LEU C 57 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N THR C 63 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LYS D 93 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N VAL D 89 " --> pdb=" O LYS D 93 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL D 95 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL I 181 " --> pdb=" O ASN I 194 " (cutoff:3.500A) removed outlier: 5.967A 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: 6.204A pdb=" N MET K 132 " --> pdb=" O GLN K 166 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ILE F 71 " --> pdb=" O THR F 115 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU F 70 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU C 42 " --> pdb=" O THR C 82 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LYS D 93 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N VAL D 89 " --> pdb=" O LYS D 93 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL D 95 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL I 181 " --> pdb=" O ASN I 194 " (cutoff:3.500A) removed outlier: 5.967A 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: 6.204A pdb=" N MET K 132 " --> pdb=" O GLN K 166 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ILE F 71 " --> pdb=" O THR F 115 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU F 70 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL F 86 " --> pdb=" O GLN F 97 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLN F 97 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA F 94 " --> pdb=" O LEU F 60 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU E 70 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE E 71 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL J 181 " --> pdb=" O ASN J 194 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 164 through 167 removed outlier: 6.204A pdb=" N MET K 132 " --> pdb=" O GLN K 166 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ILE F 71 " --> pdb=" O THR F 115 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU F 70 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL F 86 " --> pdb=" O GLN F 97 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLN F 97 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA F 94 " --> pdb=" O LEU F 60 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR B 63 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N LEU B 57 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N MET B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL B 28 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL B 24 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N THR B 30 " --> pdb=" O HIS B 22 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU E 70 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE E 71 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL J 181 " --> pdb=" O ASN J 194 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 164 through 167 removed outlier: 6.204A pdb=" N MET K 132 " --> pdb=" O GLN K 166 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ILE F 71 " --> pdb=" O THR F 115 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU F 70 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N VAL C 21 " --> pdb=" O CYS C 32 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N CYS C 32 " --> pdb=" O VAL C 21 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N MET C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N LEU C 57 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N THR C 63 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LYS D 93 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N VAL D 89 " --> pdb=" O LYS D 93 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL D 95 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N THR A 30 " --> pdb=" O HIS A 22 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N VAL A 24 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N VAL A 28 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N MET A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N LEU A 57 " --> pdb=" O MET A 61 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N THR A 63 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU E 70 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE E 71 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL J 181 " --> pdb=" O ASN J 194 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 164 through 167 removed outlier: 6.204A pdb=" N MET K 132 " --> pdb=" O GLN K 166 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ILE F 71 " --> pdb=" O THR F 115 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU F 70 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N VAL C 21 " --> pdb=" O CYS C 32 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N CYS C 32 " --> pdb=" O VAL C 21 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N MET C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N LEU C 57 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N THR C 63 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LYS D 93 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N VAL D 89 " --> pdb=" O LYS D 93 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL D 95 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 42 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N GLU A 41 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU E 70 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE E 71 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL J 181 " --> pdb=" O ASN J 194 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 164 through 167 removed outlier: 6.204A pdb=" N MET K 132 " --> pdb=" O GLN K 166 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ILE F 71 " --> pdb=" O THR F 115 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU F 70 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU C 42 " --> pdb=" O THR C 82 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LYS D 93 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N VAL D 89 " --> pdb=" O LYS D 93 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL D 95 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N THR A 30 " --> pdb=" O HIS A 22 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N VAL A 24 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N VAL A 28 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N MET A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N LEU A 57 " --> pdb=" O MET A 61 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N THR A 63 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU E 70 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE E 71 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL J 181 " --> pdb=" O ASN J 194 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 164 through 167 removed outlier: 6.204A pdb=" N MET K 132 " --> pdb=" O GLN K 166 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ILE F 71 " --> pdb=" O THR F 115 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU F 70 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU C 42 " --> pdb=" O THR C 82 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LYS D 93 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N VAL D 89 " --> pdb=" O LYS D 93 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL D 95 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 42 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N GLU A 41 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU E 70 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE E 71 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ILE J 190 " --> pdb=" O ASN J 185 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL J 181 " --> pdb=" O ASN J 194 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 164 through 167 removed outlier: 6.204A pdb=" N MET K 132 " --> pdb=" O GLN K 166 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ILE F 71 " --> pdb=" O THR F 115 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU F 70 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL F 86 " --> pdb=" O GLN F 97 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLN F 97 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA F 94 " --> pdb=" O LEU F 60 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N GLU A 41 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 42 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL I 181 " --> pdb=" O ASN I 194 " (cutoff:3.500A) removed outlier: 5.967A 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: 6.204A pdb=" N MET K 132 " --> pdb=" O GLN K 166 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ILE F 71 " --> pdb=" O THR F 115 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU F 70 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL F 86 " --> pdb=" O GLN F 97 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLN F 97 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA F 94 " --> pdb=" O LEU F 60 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N THR A 63 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N LEU A 57 " --> pdb=" O MET A 61 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N MET A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N VAL A 28 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N VAL A 24 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N THR A 30 " --> pdb=" O HIS A 22 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL I 181 " --> pdb=" O ASN I 194 " (cutoff:3.500A) removed outlier: 5.967A 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: 6.204A pdb=" N MET K 132 " --> pdb=" O GLN K 166 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ILE F 71 " --> pdb=" O THR F 115 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU F 70 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL F 86 " --> pdb=" O GLN F 97 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLN F 97 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA F 94 " --> pdb=" O LEU F 60 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR B 63 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N LEU B 57 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N MET B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL B 28 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL B 24 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N THR B 30 " --> pdb=" O HIS B 22 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N GLU A 41 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 42 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL I 181 " --> pdb=" O ASN I 194 " (cutoff:3.500A) removed outlier: 5.967A 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: 6.204A pdb=" N MET K 132 " --> pdb=" O GLN K 166 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ILE F 71 " --> pdb=" O THR F 115 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU F 70 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL F 86 " --> pdb=" O GLN F 97 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLN F 97 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA F 94 " --> pdb=" O LEU F 60 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR B 63 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N LEU B 57 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N MET B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL B 28 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL B 24 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N THR B 30 " --> pdb=" O HIS B 22 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N THR A 63 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N LEU A 57 " --> pdb=" O MET A 61 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N MET A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N VAL A 28 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N VAL A 24 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N THR A 30 " --> pdb=" O HIS A 22 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL I 181 " --> pdb=" O ASN I 194 " (cutoff:3.500A) removed outlier: 5.967A 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: 6.207A pdb=" N PHE A 99 " --> pdb=" O ALA A 313 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ILE A 273 " --> pdb=" O SER A 345 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ARG A 391 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 98 through 99 removed outlier: 6.207A pdb=" N PHE A 99 " --> pdb=" O ALA A 313 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ILE A 273 " --> pdb=" O SER A 345 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 164 through 167 removed outlier: 4.039A pdb=" N GLY A 154 " --> pdb=" O ILE A 166 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 146 through 147 removed outlier: 6.549A pdb=" N GLU A 193 " --> pdb=" O THR A 177 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 87 through 90 Processing sheet with id=AE7, first strand: chain 'B' and resid 164 through 167 removed outlier: 4.120A pdb=" N GLY B 154 " --> pdb=" O ILE B 166 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 146 through 147 removed outlier: 6.455A pdb=" N GLU B 193 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 219 through 221 removed outlier: 4.066A pdb=" N ARG B 391 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL B 271 " --> pdb=" O SER B 345 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N MET B 347 " --> pdb=" O VAL B 271 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE B 273 " --> pdb=" O MET B 347 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 219 through 221 removed outlier: 4.066A pdb=" N ARG B 391 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR B 246 " --> pdb=" O GLY B 408 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 295 through 297 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 removed outlier: 6.306A pdb=" N ILE C 272 " --> pdb=" O ALA C 310 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N VAL C 312 " --> pdb=" O ILE C 272 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N TYR C 274 " --> pdb=" O VAL C 312 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL C 344 " --> pdb=" O SER C 405 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 163 through 167 removed outlier: 3.982A pdb=" N GLY C 154 " --> pdb=" O ILE C 166 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N GLU C 134 " --> pdb=" O ASN C 157 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 146 through 147 removed outlier: 6.410A pdb=" N GLU C 193 " --> pdb=" O THR C 177 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 409 through 410 removed outlier: 7.446A pdb=" N VAL C 410 " --> pdb=" O THR C 246 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ILE C 248 " --> pdb=" O VAL C 410 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 295 through 297 Processing sheet with id=AF9, first strand: chain 'D' and resid 120 through 123 Processing sheet with id=AG1, first strand: chain 'D' and resid 131 through 133 removed outlier: 6.698A pdb=" N PHE D 132 " --> pdb=" O LEU D 261 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N LEU D 263 " --> pdb=" O PHE D 132 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ILE D 229 " --> pdb=" O CYS D 258 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N PHE D 260 " --> pdb=" O ILE D 229 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N PHE D 231 " --> pdb=" O PHE D 260 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N ASN D 262 " --> pdb=" O PHE D 231 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ALA D 233 " --> pdb=" O ASN D 262 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'D' and resid 163 through 164 removed outlier: 4.395A pdb=" N ARG D 340 " --> pdb=" O ILE D 164 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'D' and resid 183 through 184 removed outlier: 4.391A pdb=" N ILE D 183 " --> pdb=" O ILE D 170 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'D' and resid 192 through 193 Processing sheet with id=AG5, first strand: chain 'D' and resid 375 through 376 Processing sheet with id=AG6, first strand: chain 'E' and resid 120 through 123 Processing sheet with id=AG7, first strand: chain 'E' and resid 130 through 133 removed outlier: 6.696A pdb=" N ARG E 130 " --> pdb=" O LEU E 259 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N LEU E 261 " --> pdb=" O ARG E 130 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N PHE E 132 " --> pdb=" O LEU E 261 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N LEU E 263 " --> pdb=" O PHE E 132 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ALA E 228 " --> pdb=" O LEU E 294 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N ILE E 296 " --> pdb=" O ALA E 228 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL E 230 " --> pdb=" O ILE E 296 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'E' and resid 163 through 164 removed outlier: 4.010A pdb=" N ARG E 340 " --> pdb=" O ILE E 164 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'E' and resid 169 through 170 removed outlier: 4.595A pdb=" N ILE E 183 " --> pdb=" O ILE E 170 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'E' and resid 191 through 193 removed outlier: 6.500A pdb=" N ILE E 191 " --> pdb=" O LEU E 354 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH1 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 131 through 133 removed outlier: 8.750A pdb=" N CYS F 258 " --> pdb=" O PHE F 227 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ILE F 229 " --> pdb=" O CYS F 258 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N PHE F 260 " --> pdb=" O ILE F 229 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N PHE F 231 " --> pdb=" O PHE F 260 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ASN F 262 " --> pdb=" O PHE F 231 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ALA F 233 " --> pdb=" O ASN F 262 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ARG F 340 " --> pdb=" O ILE F 164 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'F' and resid 170 through 171 Processing sheet with id=AH5, first strand: chain 'F' and resid 191 through 194 removed outlier: 6.201A pdb=" N ILE F 191 " --> pdb=" O LEU F 354 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N MET F 356 " --> pdb=" O ILE F 191 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N SER F 193 " --> pdb=" O MET F 356 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH5 Processing sheet with id=AH6, first strand: chain 'G' and resid 34 through 37 Processing sheet with id=AH7, first strand: chain 'G' and resid 214 through 218 removed outlier: 5.987A pdb=" N VAL G 215 " --> pdb=" O ASN G 226 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ASN G 226 " --> pdb=" O VAL G 215 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'H' and resid 93 through 99 Processing sheet with id=AH9, first strand: chain 'L' and resid 36 through 38 removed outlier: 8.550A pdb=" N LEU L 37 " --> pdb=" O ILE L 8 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL L 10 " --> pdb=" O LEU L 37 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ALA L 9 " --> pdb=" O LEU L 65 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N ASN L 67 " --> pdb=" O ALA L 9 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ILE L 11 " --> pdb=" O ASN L 67 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ILE L 64 " --> pdb=" O LEU L 89 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ILE L 91 " --> pdb=" O ILE L 64 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE L 66 " --> pdb=" O ILE L 91 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH9 Processing sheet with id=AI1, first strand: chain 'a' and resid 36 through 38 removed outlier: 4.012A pdb=" N GLN a 36 " --> pdb=" O TRP a 324 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLU a 322 " --> pdb=" O ARG a 38 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'a' and resid 36 through 38 removed outlier: 4.012A pdb=" N GLN a 36 " --> pdb=" O TRP a 324 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLU a 322 " --> pdb=" O ARG a 38 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE a 351 " --> pdb=" O PHE a 16 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'a' and resid 174 through 175 removed outlier: 3.791A pdb=" N VAL a 174 " --> pdb=" O SER a 243 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'a' and resid 198 through 202 removed outlier: 4.519A pdb=" N LYS a 217 " --> pdb=" O ILE a 202 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'a' and resid 362 through 363 7418 hydrogen bonds defined for protein. 21255 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: 67.25 Time building geometry restraints manager: 14.61 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: 10391 1.30 - 1.43: 14561 1.43 - 1.56: 36122 1.56 - 1.69: 3 1.69 - 1.81: 561 Bond restraints: 61638 Sorted by residual: bond pdb=" C ASP B 290 " pdb=" N PHE B 291 " ideal model delta sigma weight residual 1.334 1.216 0.118 1.26e-02 6.30e+03 8.76e+01 bond pdb=" N PRO F 391 " pdb=" CA PRO F 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 E 504 " pdb=" N PRO E 505 " ideal model delta sigma weight residual 1.337 1.407 -0.070 1.06e-02 8.90e+03 4.38e+01 bond pdb=" N PRO E 352 " pdb=" CA PRO E 352 " ideal model delta sigma weight residual 1.466 1.537 -0.071 1.24e-02 6.50e+03 3.29e+01 bond pdb=" C ASN A 397 " pdb=" N PRO A 398 " ideal model delta sigma weight residual 1.336 1.397 -0.061 1.08e-02 8.57e+03 3.19e+01 ... (remaining 61633 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 79461 2.17 - 4.35: 3855 4.35 - 6.52: 291 6.52 - 8.70: 47 8.70 - 10.87: 19 Bond angle restraints: 83673 Sorted by residual: angle pdb=" C ILE F 189 " pdb=" N PRO F 190 " pdb=" CA PRO F 190 " ideal model delta sigma weight residual 119.85 129.35 -9.50 1.01e+00 9.80e-01 8.85e+01 angle pdb=" C ARG A 215 " pdb=" N PRO A 216 " pdb=" CA PRO A 216 " ideal model delta sigma weight residual 119.76 129.35 -9.59 1.03e+00 9.43e-01 8.66e+01 angle pdb=" C SER B 411 " pdb=" N PRO B 412 " pdb=" CA PRO B 412 " ideal model delta sigma weight residual 120.38 129.06 -8.68 1.03e+00 9.43e-01 7.10e+01 angle pdb=" C ILE L 91 " pdb=" N PRO L 92 " pdb=" CA PRO L 92 " ideal model delta sigma weight residual 119.76 127.77 -8.01 1.00e+00 1.00e+00 6.42e+01 angle pdb=" C LEU F 395 " pdb=" N PRO F 396 " pdb=" CA PRO F 396 " ideal model delta sigma weight residual 120.04 128.50 -8.46 1.08e+00 8.57e-01 6.14e+01 ... (remaining 83668 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.67: 36324 23.67 - 47.34: 640 47.34 - 71.01: 144 71.01 - 94.68: 57 94.68 - 118.35: 2 Dihedral angle restraints: 37167 sinusoidal: 12878 harmonic: 24289 Sorted by residual: dihedral pdb=" C5' ADP A 701 " pdb=" O5' ADP A 701 " pdb=" PA ADP A 701 " pdb=" O2A ADP A 701 " ideal model delta sinusoidal sigma weight residual -60.00 -178.35 118.35 1 2.00e+01 2.50e-03 3.54e+01 dihedral pdb=" CA GLY O 64 " pdb=" C GLY O 64 " pdb=" N SER O 65 " pdb=" CA SER O 65 " ideal model delta harmonic sigma weight residual 180.00 -152.25 -27.75 0 5.00e+00 4.00e-02 3.08e+01 dihedral pdb=" O2A ADP A 701 " pdb=" O3A ADP A 701 " pdb=" PA ADP A 701 " pdb=" PB ADP A 701 " ideal model delta sinusoidal sigma weight residual -60.00 38.47 -98.47 1 2.00e+01 2.50e-03 2.75e+01 ... (remaining 37164 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 7026 0.063 - 0.125: 2278 0.125 - 0.188: 413 0.188 - 0.250: 145 0.250 - 0.313: 9 Chirality restraints: 9871 Sorted by residual: chirality pdb=" CA TYR o 68 " pdb=" N TYR o 68 " pdb=" C TYR o 68 " pdb=" CB TYR o 68 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" CA TYR l 68 " pdb=" N TYR l 68 " pdb=" C TYR l 68 " pdb=" CB TYR l 68 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" CA MET a 10 " pdb=" N MET a 10 " pdb=" C MET a 10 " pdb=" CB MET a 10 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 9868 not shown) Planarity restraints: 10900 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU o 86 " -0.023 2.00e-02 2.50e+03 4.57e-02 2.09e+01 pdb=" C LEU o 86 " 0.079 2.00e-02 2.50e+03 pdb=" O LEU o 86 " -0.029 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 THR a 113 " 0.021 2.00e-02 2.50e+03 4.32e-02 1.87e+01 pdb=" C THR a 113 " -0.075 2.00e-02 2.50e+03 pdb=" O THR a 113 " 0.028 2.00e-02 2.50e+03 pdb=" N ASN a 114 " 0.025 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 4.30e-02 1.85e+01 pdb=" C ASN k 7 " 0.074 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 10897 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 9567 2.76 - 3.29: 64662 3.29 - 3.83: 101893 3.83 - 4.36: 122070 4.36 - 4.90: 202497 Nonbonded interactions: 500689 Sorted by model distance: nonbonded pdb=" N ASP a 208 " pdb=" O ASP a 213 " model vdw 2.220 3.120 nonbonded pdb=" OH TYR Q 126 " pdb=" OG1 THR Q 169 " model vdw 2.221 3.040 nonbonded pdb=" OD1 ASP D 266 " pdb=" NZ LYS S 9 " model vdw 2.305 3.120 nonbonded pdb=" CB ALA B 499 " pdb=" CA GLY H 103 " model vdw 2.331 3.860 nonbonded pdb=" NZ LYS H 55 " pdb=" OD2 ASP L 99 " model vdw 2.336 3.120 ... (remaining 500684 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 17 through 616) selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = (chain 'I' and resid 3 through 226) selection = chain 'J' selection = (chain 'K' and resid 3 through 226) } ncs_group { reference = (chain 'M' and resid 4 through 116) selection = (chain 'N' and resid 4 through 116) 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: 2.110 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: 0.430 Process input model: 170.210 Find NCS groups from input model: 1.790 Set up NCS constraints: 0.410 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: 0.020 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 180.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 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 61638 Z= 0.605 Angle : 0.975 10.874 83673 Z= 0.721 Chirality : 0.064 0.313 9871 Planarity : 0.005 0.046 10900 Dihedral : 10.710 118.352 21549 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.52 % Favored : 97.29 % Rotamer: Outliers : 0.78 % Allowed : 0.80 % Favored : 98.42 % 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: 0.61 (0.09), residues: 8369 helix: 0.90 (0.07), residues: 4959 sheet: -0.12 (0.18), residues: 703 loop : -0.18 (0.12), residues: 2707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Q 55 HIS 0.002 0.000 HIS F 199 PHE 0.013 0.000 PHE H 44 TYR 0.016 0.000 TYR D 389 ARG 0.004 0.000 ARG D 208 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16738 Ramachandran restraints generated. 8369 Oldfield, 0 Emsley, 8369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16738 Ramachandran restraints generated. 8369 Oldfield, 0 Emsley, 8369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1996 residues out of total 7117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 1952 time to evaluate : 5.445 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: A 53 GLU cc_start: 0.7603 (tt0) cc_final: 0.7339 (tt0) REVERT: A 231 GLN cc_start: 0.9241 (mm-40) cc_final: 0.8988 (mm-40) REVERT: A 254 CYS cc_start: 0.8355 (m) cc_final: 0.7616 (m) REVERT: A 318 MET cc_start: 0.9183 (mtt) cc_final: 0.8801 (mtp) REVERT: A 331 ILE cc_start: 0.9592 (tt) cc_final: 0.9340 (tt) REVERT: A 436 ASP cc_start: 0.8480 (t0) cc_final: 0.7961 (t70) REVERT: A 491 GLU cc_start: 0.8959 (tt0) cc_final: 0.8740 (tm-30) REVERT: A 516 LYS cc_start: 0.9347 (mttt) cc_final: 0.9081 (tttm) REVERT: A 523 ASN cc_start: 0.8800 (t0) cc_final: 0.8594 (t0) REVERT: A 550 MET cc_start: 0.8642 (mtm) cc_final: 0.8125 (mtm) REVERT: B 306 MET cc_start: 0.8558 (ptm) cc_final: 0.7795 (tmm) REVERT: B 309 THR cc_start: 0.9166 (m) cc_final: 0.8786 (m) REVERT: B 324 GLU cc_start: 0.9123 (tt0) cc_final: 0.8842 (tm-30) REVERT: B 356 GLU cc_start: 0.9234 (tp30) cc_final: 0.8971 (tp30) REVERT: B 433 TRP cc_start: 0.8589 (m-10) cc_final: 0.8329 (m-10) REVERT: B 458 MET cc_start: 0.8695 (mmt) cc_final: 0.8449 (mmt) REVERT: B 550 MET cc_start: 0.9266 (mtm) cc_final: 0.7778 (mtp) REVERT: B 584 MET cc_start: 0.8667 (mtm) cc_final: 0.8335 (mtp) REVERT: C 166 ILE cc_start: 0.9335 (mm) cc_final: 0.8804 (tp) REVERT: C 205 MET cc_start: 0.8593 (mtm) cc_final: 0.8156 (mtt) REVERT: C 286 GLU cc_start: 0.9013 (tt0) cc_final: 0.8572 (tp30) REVERT: C 323 ARG cc_start: 0.8476 (mtm110) cc_final: 0.8235 (mtm-85) REVERT: C 340 MET cc_start: 0.8684 (mtt) cc_final: 0.8483 (mtm) REVERT: C 347 MET cc_start: 0.8410 (ttm) cc_final: 0.8062 (tmm) REVERT: C 349 ASP cc_start: 0.7941 (t0) cc_final: 0.7355 (t70) REVERT: C 361 ILE cc_start: 0.9297 (mt) cc_final: 0.9070 (tp) REVERT: C 399 GLU cc_start: 0.7397 (mm-30) cc_final: 0.6674 (mm-30) REVERT: C 416 ASP cc_start: 0.7424 (t0) cc_final: 0.6773 (t0) REVERT: C 458 MET cc_start: 0.8799 (mtp) cc_final: 0.7629 (mtt) REVERT: C 465 TYR cc_start: 0.9035 (m-80) cc_final: 0.8739 (m-80) REVERT: C 536 LYS cc_start: 0.9235 (tttt) cc_final: 0.8699 (tttp) REVERT: D 128 LEU cc_start: 0.9299 (mt) cc_final: 0.9000 (pt) REVERT: D 257 VAL cc_start: 0.9434 (t) cc_final: 0.9021 (p) REVERT: D 382 GLN cc_start: 0.9059 (mp10) cc_final: 0.8842 (mp10) REVERT: D 484 LEU cc_start: 0.9735 (mt) cc_final: 0.9483 (mt) REVERT: D 495 ILE cc_start: 0.9606 (mt) cc_final: 0.9232 (tt) REVERT: E 72 VAL cc_start: 0.9265 (t) cc_final: 0.8990 (m) REVERT: E 202 ILE cc_start: 0.9672 (mt) cc_final: 0.9463 (mm) REVERT: E 262 ASN cc_start: 0.9129 (t0) cc_final: 0.8856 (t0) REVERT: E 270 GLU cc_start: 0.8871 (tt0) cc_final: 0.8490 (tm-30) REVERT: E 309 GLU cc_start: 0.8410 (tt0) cc_final: 0.8206 (tm-30) REVERT: E 328 TYR cc_start: 0.8843 (t80) cc_final: 0.8201 (t80) REVERT: E 341 VAL cc_start: 0.8775 (m) cc_final: 0.8434 (p) REVERT: F 88 GLU cc_start: 0.8350 (tt0) cc_final: 0.8096 (tm-30) REVERT: F 183 ILE cc_start: 0.9716 (mt) cc_final: 0.9440 (pt) REVERT: F 205 GLN cc_start: 0.9315 (tt0) cc_final: 0.8899 (tp40) REVERT: F 298 THR cc_start: 0.8760 (m) cc_final: 0.8356 (m) REVERT: F 299 ASP cc_start: 0.8437 (m-30) cc_final: 0.7758 (m-30) REVERT: F 309 GLU cc_start: 0.9150 (tm-30) cc_final: 0.8852 (tm-30) REVERT: F 317 VAL cc_start: 0.9171 (t) cc_final: 0.8941 (p) REVERT: F 351 ILE cc_start: 0.9574 (mt) cc_final: 0.9237 (mm) REVERT: F 353 ILE cc_start: 0.9609 (mt) cc_final: 0.9384 (mm) REVERT: F 435 MET cc_start: 0.9097 (tpp) cc_final: 0.8684 (tpt) REVERT: F 492 LEU cc_start: 0.9368 (mt) cc_final: 0.8992 (mp) REVERT: H 58 MET cc_start: 0.8740 (tmm) cc_final: 0.8520 (mmt) REVERT: H 67 PHE cc_start: 0.9154 (t80) cc_final: 0.8580 (t80) REVERT: H 94 ILE cc_start: 0.9400 (mm) cc_final: 0.8897 (pt) REVERT: H 99 ASP cc_start: 0.8513 (t0) cc_final: 0.7926 (p0) REVERT: H 155 PHE cc_start: 0.8481 (t80) cc_final: 0.8186 (t80) REVERT: H 190 GLU cc_start: 0.9132 (mm-30) cc_final: 0.8632 (tm-30) REVERT: I 70 ILE cc_start: 0.9434 (OUTLIER) cc_final: 0.9079 (mt) REVERT: I 97 GLU cc_start: 0.9354 (tp30) cc_final: 0.8852 (tp30) REVERT: I 177 ILE cc_start: 0.9334 (mm) cc_final: 0.8950 (mm) REVERT: I 203 ILE cc_start: 0.9505 (mt) cc_final: 0.9215 (tp) REVERT: J 81 LEU cc_start: 0.9651 (mt) cc_final: 0.9384 (mt) REVERT: J 119 LEU cc_start: 0.9550 (mt) cc_final: 0.9154 (mt) REVERT: J 194 ASN cc_start: 0.8734 (t0) cc_final: 0.7406 (t0) REVERT: J 221 ASN cc_start: 0.8986 (m-40) cc_final: 0.8594 (t0) REVERT: K 70 ILE cc_start: 0.9694 (mt) cc_final: 0.9482 (mm) REVERT: K 73 SER cc_start: 0.8678 (m) cc_final: 0.8006 (p) REVERT: K 92 THR cc_start: 0.9580 (m) cc_final: 0.9230 (p) REVERT: K 121 LEU cc_start: 0.9645 (mt) cc_final: 0.9403 (mm) REVERT: K 125 TYR cc_start: 0.9068 (m-80) cc_final: 0.8786 (m-10) REVERT: K 133 ILE cc_start: 0.9467 (mt) cc_final: 0.9107 (tp) REVERT: K 164 ASP cc_start: 0.8342 (t0) cc_final: 0.8011 (t0) REVERT: K 177 ILE cc_start: 0.9508 (mt) cc_final: 0.9302 (mp) REVERT: K 194 ASN cc_start: 0.8915 (t0) cc_final: 0.8574 (t0) REVERT: K 203 ILE cc_start: 0.9705 (mt) cc_final: 0.9476 (tp) REVERT: L 8 ILE cc_start: 0.9517 (mt) cc_final: 0.9271 (mp) REVERT: L 22 LEU cc_start: 0.9647 (mt) cc_final: 0.9264 (mt) REVERT: L 27 GLU cc_start: 0.8957 (pt0) cc_final: 0.8215 (pt0) REVERT: L 33 HIS cc_start: 0.8629 (m170) cc_final: 0.8181 (m90) REVERT: L 35 ASN cc_start: 0.8991 (p0) cc_final: 0.8422 (p0) REVERT: L 37 LEU cc_start: 0.8540 (tp) cc_final: 0.8117 (tp) REVERT: L 46 ASN cc_start: 0.9589 (m-40) cc_final: 0.9267 (p0) REVERT: L 47 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8615 (mm-30) REVERT: L 51 THR cc_start: 0.9116 (m) cc_final: 0.8818 (p) REVERT: Q 66 LEU cc_start: 0.9550 (tp) cc_final: 0.9297 (tt) REVERT: Q 132 GLN cc_start: 0.9345 (mt0) cc_final: 0.9141 (mt0) REVERT: Q 151 PHE cc_start: 0.8769 (m-10) cc_final: 0.8191 (m-10) REVERT: Q 197 TYR cc_start: 0.7817 (m-80) cc_final: 0.7292 (m-80) REVERT: Q 228 THR cc_start: 0.8982 (m) cc_final: 0.8607 (p) REVERT: Q 229 MET cc_start: 0.9118 (tpp) cc_final: 0.8721 (tpt) REVERT: R 46 ARG cc_start: 0.8862 (mtp85) cc_final: 0.8407 (ttp-110) REVERT: R 90 GLU cc_start: 0.9328 (mm-30) cc_final: 0.9121 (mm-30) REVERT: R 109 GLU cc_start: 0.9123 (mt-10) cc_final: 0.8244 (mm-30) REVERT: R 125 ASP cc_start: 0.9026 (m-30) cc_final: 0.8705 (p0) REVERT: R 130 LEU cc_start: 0.9580 (mt) cc_final: 0.9220 (tp) REVERT: R 137 THR cc_start: 0.9547 (p) cc_final: 0.9322 (t) REVERT: R 139 TYR cc_start: 0.8962 (t80) cc_final: 0.8738 (t80) REVERT: R 151 PHE cc_start: 0.9168 (m-10) cc_final: 0.8646 (m-10) REVERT: R 170 GLU cc_start: 0.8427 (mm-30) cc_final: 0.8114 (pp20) REVERT: b 4 LEU cc_start: 0.8628 (mt) cc_final: 0.8363 (mm) REVERT: b 8 TYR cc_start: 0.8723 (m-80) cc_final: 0.8397 (m-80) REVERT: b 74 SER cc_start: 0.8115 (m) cc_final: 0.7260 (p) REVERT: b 157 ILE cc_start: 0.8993 (mt) cc_final: 0.8743 (mm) REVERT: c 431 PHE cc_start: 0.9068 (m-80) cc_final: 0.8800 (m-80) REVERT: c 449 PHE cc_start: 0.5677 (m-80) cc_final: 0.5164 (m-10) REVERT: d 10 ASN cc_start: 0.9008 (m-40) cc_final: 0.8646 (t0) REVERT: d 85 MET cc_start: 0.9245 (mtm) cc_final: 0.9015 (mtt) REVERT: d 139 GLU cc_start: 0.8811 (mm-30) cc_final: 0.8560 (tp30) REVERT: d 185 LEU cc_start: 0.9662 (mt) cc_final: 0.9432 (mm) REVERT: d 190 LEU cc_start: 0.9565 (tp) cc_final: 0.9301 (pp) REVERT: d 244 CYS cc_start: 0.7855 (m) cc_final: 0.7413 (m) REVERT: d 279 GLU cc_start: 0.9135 (mm-30) cc_final: 0.8892 (pt0) REVERT: d 298 GLU cc_start: 0.9342 (tt0) cc_final: 0.9135 (pt0) REVERT: d 325 GLU cc_start: 0.9147 (tt0) cc_final: 0.8687 (tp30) REVERT: d 334 GLU cc_start: 0.9106 (mt-10) cc_final: 0.8770 (pt0) REVERT: d 340 HIS cc_start: 0.7985 (m-70) cc_final: 0.7716 (m90) REVERT: g 23 MET cc_start: 0.8951 (tpt) cc_final: 0.8673 (mmm) REVERT: g 32 TYR cc_start: 0.9111 (t80) cc_final: 0.8786 (t80) REVERT: g 76 ILE cc_start: 0.8485 (mt) cc_final: 0.8110 (tt) REVERT: g 112 ILE cc_start: 0.9364 (mt) cc_final: 0.9027 (mt) REVERT: g 119 ARG cc_start: 0.7704 (mtm-85) cc_final: 0.7425 (ptt180) REVERT: g 152 LEU cc_start: 0.9149 (mt) cc_final: 0.8857 (mt) REVERT: h 28 MET cc_start: 0.9269 (mtp) cc_final: 0.9004 (tpt) REVERT: h 32 TYR cc_start: 0.8182 (t80) cc_final: 0.7924 (t80) REVERT: h 112 ILE cc_start: 0.9001 (mm) cc_final: 0.8529 (mt) REVERT: h 139 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8001 (mm-30) REVERT: i 13 PHE cc_start: 0.8665 (t80) cc_final: 0.8334 (t80) REVERT: i 25 PHE cc_start: 0.9233 (m-80) cc_final: 0.8804 (m-80) REVERT: i 32 TYR cc_start: 0.7166 (t80) cc_final: 0.6834 (t80) REVERT: i 48 ARG cc_start: 0.8140 (ptm160) cc_final: 0.7906 (mtm110) REVERT: i 65 ILE cc_start: 0.8944 (OUTLIER) cc_final: 0.8635 (mm) REVERT: i 88 ARG cc_start: 0.8261 (mtm180) cc_final: 0.7879 (ttp-170) REVERT: k 25 PHE cc_start: 0.8965 (m-80) cc_final: 0.8290 (m-80) REVERT: l 14 PHE cc_start: 0.8986 (m-80) cc_final: 0.8768 (m-80) REVERT: l 134 ILE cc_start: 0.9102 (mt) cc_final: 0.8729 (tt) REVERT: m 39 THR cc_start: 0.7438 (m) cc_final: 0.7088 (p) REVERT: m 141 LEU cc_start: 0.7393 (OUTLIER) cc_final: 0.7059 (tp) REVERT: n 13 PHE cc_start: 0.9011 (t80) cc_final: 0.8792 (t80) REVERT: n 139 GLU cc_start: 0.6486 (OUTLIER) cc_final: 0.6099 (mm-30) REVERT: n 141 LEU cc_start: 0.6582 (mt) cc_final: 0.5446 (tp) REVERT: o 25 PHE cc_start: 0.9067 (m-80) cc_final: 0.8860 (m-80) REVERT: o 28 MET cc_start: 0.8669 (mtp) cc_final: 0.8435 (mtp) REVERT: o 119 ARG cc_start: 0.8032 (mtm-85) cc_final: 0.7716 (mtt-85) REVERT: p 312 TRP cc_start: 0.8372 (m100) cc_final: 0.7956 (m100) outliers start: 44 outliers final: 13 residues processed: 1974 average time/residue: 0.5882 time to fit residues: 1946.8338 Evaluate side-chains 1173 residues out of total 7117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 1155 time to evaluate : 5.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain g residue 143 LEU Chi-restraints excluded: chain h residue 139 GLU Chi-restraints excluded: chain i residue 65 ILE Chi-restraints excluded: chain j residue 139 GLU Chi-restraints excluded: chain j residue 140 VAL Chi-restraints excluded: chain j residue 143 LEU Chi-restraints excluded: chain k residue 143 LEU Chi-restraints excluded: chain l residue 140 VAL Chi-restraints excluded: chain l residue 143 LEU Chi-restraints excluded: chain m residue 65 ILE Chi-restraints excluded: chain m residue 141 LEU Chi-restraints excluded: chain n residue 139 GLU Chi-restraints excluded: chain n residue 143 LEU Chi-restraints excluded: chain o residue 65 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 836 random chunks: chunk 705 optimal weight: 10.0000 chunk 633 optimal weight: 0.9990 chunk 351 optimal weight: 7.9990 chunk 216 optimal weight: 5.9990 chunk 427 optimal weight: 5.9990 chunk 338 optimal weight: 40.0000 chunk 655 optimal weight: 6.9990 chunk 253 optimal weight: 0.7980 chunk 398 optimal weight: 20.0000 chunk 487 optimal weight: 4.9990 chunk 759 optimal weight: 7.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 ASN ** A 573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 GLN B 146 HIS B 314 ASN ** B 573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 468 HIS E 97 GLN ** F 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 181 ASN H 88 ASN H 137 ASN ** I 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 77 ASN ** J 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 34 GLN R 50 GLN S 117 GLN ** d 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 13 ASN d 340 HIS i 92 GLN i 123 GLN ** j 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 308 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 61638 Z= 0.318 Angle : 0.739 12.645 83673 Z= 0.389 Chirality : 0.046 0.342 9871 Planarity : 0.005 0.087 10900 Dihedral : 5.244 112.239 9057 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.95 % Favored : 98.04 % Rotamer: Outliers : 3.01 % Allowed : 11.91 % Favored : 85.08 % 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: 1.92 (0.09), residues: 8369 helix: 2.21 (0.07), residues: 4905 sheet: -0.14 (0.19), residues: 706 loop : 0.01 (0.12), residues: 2758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 567 HIS 0.010 0.001 HIS Q 184 PHE 0.042 0.002 PHE h 25 TYR 0.036 0.002 TYR b 103 ARG 0.012 0.001 ARG j 48 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16738 Ramachandran restraints generated. 8369 Oldfield, 0 Emsley, 8369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16738 Ramachandran restraints generated. 8369 Oldfield, 0 Emsley, 8369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1355 residues out of total 7117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 1185 time to evaluate : 5.377 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: A 42 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.8835 (mp) REVERT: A 95 MET cc_start: 0.8195 (mmt) cc_final: 0.7848 (tpp) REVERT: A 167 MET cc_start: 0.9292 (mtm) cc_final: 0.9043 (mtt) REVERT: A 254 CYS cc_start: 0.8795 (m) cc_final: 0.8211 (m) REVERT: A 306 MET cc_start: 0.8454 (tpp) cc_final: 0.8235 (tpp) REVERT: A 318 MET cc_start: 0.9263 (mtt) cc_final: 0.8707 (mtp) REVERT: A 347 MET cc_start: 0.8310 (ptp) cc_final: 0.8082 (ptp) REVERT: A 472 PHE cc_start: 0.8434 (t80) cc_final: 0.8181 (t80) REVERT: A 491 GLU cc_start: 0.9008 (tt0) cc_final: 0.8773 (tm-30) REVERT: A 510 GLU cc_start: 0.8739 (tm-30) cc_final: 0.8391 (tm-30) REVERT: A 516 LYS cc_start: 0.9329 (mttt) cc_final: 0.9051 (tttm) REVERT: A 574 MET cc_start: 0.8866 (mtt) cc_final: 0.8400 (mmm) REVERT: A 590 VAL cc_start: 0.9322 (m) cc_final: 0.8795 (p) REVERT: B 167 MET cc_start: 0.8426 (mtt) cc_final: 0.8164 (mtt) REVERT: B 306 MET cc_start: 0.8611 (ptm) cc_final: 0.8002 (tmm) REVERT: B 318 MET cc_start: 0.9165 (tpp) cc_final: 0.8908 (mmm) REVERT: B 324 GLU cc_start: 0.9318 (tt0) cc_final: 0.9008 (tm-30) REVERT: B 347 MET cc_start: 0.8710 (tpp) cc_final: 0.8481 (tpp) REVERT: B 356 GLU cc_start: 0.9199 (tp30) cc_final: 0.8826 (tp30) REVERT: B 458 MET cc_start: 0.8692 (mmt) cc_final: 0.8387 (mmt) REVERT: B 550 MET cc_start: 0.9406 (mtm) cc_final: 0.8891 (mtp) REVERT: B 567 TRP cc_start: 0.9027 (t-100) cc_final: 0.8054 (t-100) REVERT: B 574 MET cc_start: 0.8790 (ptp) cc_final: 0.8543 (mpp) REVERT: B 608 MET cc_start: 0.8886 (ttp) cc_final: 0.7331 (ttm) REVERT: C 61 MET cc_start: 0.9055 (mmm) cc_final: 0.8684 (tpp) REVERT: C 100 ASP cc_start: 0.8644 (t0) cc_final: 0.8411 (t0) REVERT: C 166 ILE cc_start: 0.9318 (mm) cc_final: 0.8974 (tp) REVERT: C 205 MET cc_start: 0.8716 (mtm) cc_final: 0.8399 (mtt) REVERT: C 286 GLU cc_start: 0.9165 (tt0) cc_final: 0.8727 (tp30) REVERT: C 323 ARG cc_start: 0.8989 (mtm110) cc_final: 0.8515 (mtm-85) REVERT: C 347 MET cc_start: 0.8467 (ttm) cc_final: 0.8141 (tmm) REVERT: C 349 ASP cc_start: 0.7919 (t0) cc_final: 0.7260 (t0) REVERT: C 416 ASP cc_start: 0.7701 (t0) cc_final: 0.7149 (t0) REVERT: C 458 MET cc_start: 0.8809 (mtp) cc_final: 0.8499 (mtt) REVERT: C 461 LEU cc_start: 0.9580 (mt) cc_final: 0.9320 (mm) REVERT: C 465 TYR cc_start: 0.9043 (m-80) cc_final: 0.8796 (m-80) REVERT: C 466 ASP cc_start: 0.9153 (m-30) cc_final: 0.8920 (m-30) REVERT: C 536 LYS cc_start: 0.9037 (tttt) cc_final: 0.8722 (tttp) REVERT: C 550 MET cc_start: 0.9531 (mmp) cc_final: 0.9273 (mmm) REVERT: D 254 MET cc_start: 0.8483 (tpp) cc_final: 0.7688 (mmt) REVERT: D 270 GLU cc_start: 0.8490 (mt-10) cc_final: 0.7987 (tt0) REVERT: D 382 GLN cc_start: 0.9101 (mp10) cc_final: 0.8788 (mp10) REVERT: D 402 MET cc_start: 0.8921 (ttp) cc_final: 0.8520 (ttt) REVERT: D 484 LEU cc_start: 0.9679 (mt) cc_final: 0.9422 (mt) REVERT: D 495 ILE cc_start: 0.9545 (mt) cc_final: 0.9235 (tt) REVERT: E 87 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.8476 (mt) REVERT: E 113 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7943 (pt0) REVERT: E 154 MET cc_start: 0.9322 (tpt) cc_final: 0.9107 (mmm) REVERT: E 234 MET cc_start: 0.8655 (mtm) cc_final: 0.8073 (pmm) REVERT: E 254 MET cc_start: 0.8164 (mmm) cc_final: 0.7880 (mmm) REVERT: E 270 GLU cc_start: 0.9005 (tt0) cc_final: 0.8434 (pt0) REVERT: E 283 GLU cc_start: 0.8815 (mt-10) cc_final: 0.8360 (mt-10) REVERT: E 309 GLU cc_start: 0.8528 (tt0) cc_final: 0.8288 (tm-30) REVERT: E 316 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7598 (mt-10) REVERT: E 330 ASP cc_start: 0.9273 (m-30) cc_final: 0.8607 (t0) REVERT: E 341 VAL cc_start: 0.9134 (m) cc_final: 0.8826 (p) REVERT: E 402 MET cc_start: 0.8929 (tmm) cc_final: 0.8571 (tpp) REVERT: F 169 MET cc_start: 0.8748 (tmm) cc_final: 0.8394 (tmm) REVERT: F 183 ILE cc_start: 0.9719 (mt) cc_final: 0.9194 (pt) REVERT: F 187 GLN cc_start: 0.8998 (pp30) cc_final: 0.8728 (pp30) REVERT: F 205 GLN cc_start: 0.9397 (tt0) cc_final: 0.9005 (tt0) REVERT: F 298 THR cc_start: 0.8949 (m) cc_final: 0.8266 (p) REVERT: F 299 ASP cc_start: 0.8319 (m-30) cc_final: 0.7758 (m-30) REVERT: F 309 GLU cc_start: 0.9234 (tm-30) cc_final: 0.8944 (tm-30) REVERT: F 317 VAL cc_start: 0.9311 (t) cc_final: 0.8993 (p) REVERT: F 351 ILE cc_start: 0.9586 (mt) cc_final: 0.9330 (mm) REVERT: F 353 ILE cc_start: 0.9640 (mt) cc_final: 0.9429 (mm) REVERT: F 356 MET cc_start: 0.8640 (mtm) cc_final: 0.8402 (mtm) REVERT: F 410 MET cc_start: 0.8380 (OUTLIER) cc_final: 0.8050 (mmm) REVERT: F 411 THR cc_start: 0.9233 (p) cc_final: 0.9018 (p) REVERT: F 435 MET cc_start: 0.9210 (tpp) cc_final: 0.8830 (tpp) REVERT: F 492 LEU cc_start: 0.9499 (mt) cc_final: 0.9108 (mp) REVERT: H 16 GLN cc_start: 0.9116 (tt0) cc_final: 0.8595 (tm-30) REVERT: H 31 ASN cc_start: 0.9257 (m-40) cc_final: 0.8983 (m110) REVERT: H 67 PHE cc_start: 0.9144 (t80) cc_final: 0.8552 (t80) REVERT: H 79 PHE cc_start: 0.9489 (p90) cc_final: 0.9284 (p90) REVERT: H 91 GLN cc_start: 0.9329 (pt0) cc_final: 0.8927 (pm20) REVERT: H 155 PHE cc_start: 0.8577 (t80) cc_final: 0.8216 (t80) REVERT: H 190 GLU cc_start: 0.9199 (mm-30) cc_final: 0.8890 (mm-30) REVERT: H 193 GLU cc_start: 0.9147 (tm-30) cc_final: 0.8697 (tm-30) REVERT: H 206 GLN cc_start: 0.9159 (tm-30) cc_final: 0.8849 (tm-30) REVERT: H 207 GLU cc_start: 0.9073 (tm-30) cc_final: 0.8795 (pp20) REVERT: I 129 GLU cc_start: 0.9281 (mm-30) cc_final: 0.8562 (tp30) REVERT: I 177 ILE cc_start: 0.9184 (mm) cc_final: 0.8929 (mm) REVERT: I 182 GLU cc_start: 0.7561 (pt0) cc_final: 0.7204 (pt0) REVERT: J 119 LEU cc_start: 0.9469 (mt) cc_final: 0.9211 (mt) REVERT: J 194 ASN cc_start: 0.8127 (t0) cc_final: 0.7739 (p0) REVERT: J 207 MET cc_start: 0.9195 (mmp) cc_final: 0.8904 (mmp) REVERT: J 208 MET cc_start: 0.8981 (mmm) cc_final: 0.8721 (mmt) REVERT: K 75 LEU cc_start: 0.9660 (OUTLIER) cc_final: 0.9408 (mt) REVERT: K 121 LEU cc_start: 0.9607 (mt) cc_final: 0.9214 (mm) REVERT: K 125 TYR cc_start: 0.9023 (m-80) cc_final: 0.8681 (m-10) REVERT: K 133 ILE cc_start: 0.9595 (mt) cc_final: 0.9366 (tp) REVERT: K 154 MET cc_start: 0.9428 (mtt) cc_final: 0.9063 (ptp) REVERT: K 164 ASP cc_start: 0.8547 (t0) cc_final: 0.8203 (t0) REVERT: K 184 TYR cc_start: 0.8590 (m-10) cc_final: 0.7823 (m-80) REVERT: K 194 ASN cc_start: 0.9115 (t0) cc_final: 0.8810 (t0) REVERT: K 207 MET cc_start: 0.8580 (tpp) cc_final: 0.8087 (tpp) REVERT: L 18 THR cc_start: 0.9524 (p) cc_final: 0.9271 (p) REVERT: L 22 LEU cc_start: 0.9671 (mt) cc_final: 0.9117 (mm) REVERT: L 27 GLU cc_start: 0.9029 (pt0) cc_final: 0.8605 (pt0) REVERT: L 33 HIS cc_start: 0.8524 (m170) cc_final: 0.8255 (m170) REVERT: L 37 LEU cc_start: 0.8488 (tp) cc_final: 0.8185 (tp) REVERT: L 46 ASN cc_start: 0.9602 (m-40) cc_final: 0.9365 (t0) REVERT: L 47 GLU cc_start: 0.9054 (mt-10) cc_final: 0.8828 (mm-30) REVERT: L 53 ARG cc_start: 0.9249 (ptp90) cc_final: 0.8779 (ptp90) REVERT: L 65 LEU cc_start: 0.9204 (mm) cc_final: 0.8997 (mm) REVERT: L 79 ASP cc_start: 0.9292 (m-30) cc_final: 0.9082 (m-30) REVERT: M 74 GLU cc_start: 0.9511 (OUTLIER) cc_final: 0.9278 (mp0) REVERT: O 84 MET cc_start: 0.8990 (mmm) cc_final: 0.8704 (mmt) REVERT: Q 33 MET cc_start: 0.8397 (tpt) cc_final: 0.8139 (tmm) REVERT: Q 66 LEU cc_start: 0.9630 (tp) cc_final: 0.9270 (tt) REVERT: Q 188 MET cc_start: 0.8502 (mmm) cc_final: 0.8286 (mmm) REVERT: R 46 ARG cc_start: 0.9329 (mtp85) cc_final: 0.8904 (mtp85) REVERT: R 109 GLU cc_start: 0.9083 (mt-10) cc_final: 0.8827 (pp20) REVERT: R 125 ASP cc_start: 0.9190 (m-30) cc_final: 0.8817 (p0) REVERT: R 130 LEU cc_start: 0.9549 (mt) cc_final: 0.9257 (tp) REVERT: R 139 TYR cc_start: 0.8971 (t80) cc_final: 0.8673 (t80) REVERT: S 126 TYR cc_start: 0.8956 (m-80) cc_final: 0.8750 (m-10) REVERT: S 156 THR cc_start: 0.9308 (m) cc_final: 0.9103 (p) REVERT: S 197 TYR cc_start: 0.7117 (OUTLIER) cc_final: 0.6582 (m-80) REVERT: b 4 LEU cc_start: 0.8526 (mt) cc_final: 0.8255 (mm) REVERT: b 8 TYR cc_start: 0.8803 (m-80) cc_final: 0.8393 (m-80) REVERT: b 157 ILE cc_start: 0.8954 (mt) cc_final: 0.8725 (mm) REVERT: b 193 VAL cc_start: 0.8554 (t) cc_final: 0.8212 (m) REVERT: b 203 MET cc_start: 0.6262 (OUTLIER) cc_final: 0.5726 (mmm) REVERT: c 431 PHE cc_start: 0.9064 (m-80) cc_final: 0.8680 (m-80) REVERT: c 440 ILE cc_start: 0.9654 (mt) cc_final: 0.9400 (pt) REVERT: d 10 ASN cc_start: 0.8987 (m-40) cc_final: 0.8615 (t0) REVERT: d 85 MET cc_start: 0.9060 (mtm) cc_final: 0.8779 (mtm) REVERT: d 88 HIS cc_start: 0.8539 (m90) cc_final: 0.8213 (m90) REVERT: d 105 MET cc_start: 0.8964 (mmm) cc_final: 0.8548 (mmt) REVERT: d 135 PHE cc_start: 0.7884 (OUTLIER) cc_final: 0.7520 (m-10) REVERT: d 138 MET cc_start: 0.8382 (mmp) cc_final: 0.8112 (mmm) REVERT: d 180 ILE cc_start: 0.9688 (mm) cc_final: 0.9486 (mt) REVERT: d 190 LEU cc_start: 0.9551 (tp) cc_final: 0.9270 (pp) REVERT: d 197 CYS cc_start: 0.9397 (m) cc_final: 0.8860 (p) REVERT: d 325 GLU cc_start: 0.9271 (tt0) cc_final: 0.8826 (tm-30) REVERT: d 334 GLU cc_start: 0.9016 (mt-10) cc_final: 0.8673 (pt0) REVERT: g 23 MET cc_start: 0.8892 (tpt) cc_final: 0.8608 (tpp) REVERT: g 32 TYR cc_start: 0.8962 (t80) cc_final: 0.8274 (t80) REVERT: g 37 SER cc_start: 0.8694 (m) cc_final: 0.8486 (p) REVERT: g 53 MET cc_start: 0.8575 (ptt) cc_final: 0.8044 (pmm) REVERT: g 108 PHE cc_start: 0.8972 (m-10) cc_final: 0.8434 (m-10) REVERT: g 119 ARG cc_start: 0.7907 (mtm-85) cc_final: 0.7640 (ptt180) REVERT: h 14 PHE cc_start: 0.8903 (m-80) cc_final: 0.8581 (m-80) REVERT: h 28 MET cc_start: 0.9272 (mtp) cc_final: 0.9006 (tpt) REVERT: h 53 MET cc_start: 0.8169 (pmm) cc_final: 0.7544 (pmm) REVERT: h 112 ILE cc_start: 0.9163 (mm) cc_final: 0.8868 (mt) REVERT: i 25 PHE cc_start: 0.9241 (m-80) cc_final: 0.8787 (m-80) REVERT: i 88 ARG cc_start: 0.8179 (mtm180) cc_final: 0.7653 (ttp-170) REVERT: i 123 GLN cc_start: 0.8265 (mm110) cc_final: 0.8038 (mm-40) REVERT: j 28 MET cc_start: 0.8056 (mmt) cc_final: 0.7704 (mmt) REVERT: k 41 ILE cc_start: 0.8688 (mm) cc_final: 0.8393 (pt) REVERT: m 39 THR cc_start: 0.8103 (m) cc_final: 0.7738 (p) REVERT: m 55 SER cc_start: 0.8913 (m) cc_final: 0.8499 (p) REVERT: m 141 LEU cc_start: 0.7587 (OUTLIER) cc_final: 0.6893 (tp) REVERT: n 139 GLU cc_start: 0.6920 (OUTLIER) cc_final: 0.6032 (mm-30) REVERT: n 141 LEU cc_start: 0.6623 (mt) cc_final: 0.6014 (tp) REVERT: o 17 MET cc_start: 0.8681 (mtp) cc_final: 0.8396 (mtp) REVERT: o 25 PHE cc_start: 0.9175 (m-80) cc_final: 0.8915 (m-80) REVERT: o 61 MET cc_start: 0.5348 (mmt) cc_final: 0.5074 (mtt) REVERT: o 104 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7733 (mt) REVERT: o 131 MET cc_start: 0.8545 (ppp) cc_final: 0.8318 (ppp) REVERT: p 312 TRP cc_start: 0.8454 (m100) cc_final: 0.7919 (m100) REVERT: p 330 ASN cc_start: 0.9110 (m-40) cc_final: 0.8763 (m110) REVERT: p 338 ILE cc_start: 0.7930 (pt) cc_final: 0.7664 (pt) outliers start: 170 outliers final: 86 residues processed: 1274 average time/residue: 0.6089 time to fit residues: 1337.5853 Evaluate side-chains 1100 residues out of total 7117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 1002 time to evaluate : 5.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 164 HIS Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 371 ASP Chi-restraints excluded: chain C residue 394 CYS Chi-restraints excluded: chain C residue 482 ILE Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 334 ILE Chi-restraints excluded: chain D residue 448 ASP Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 113 GLU Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 336 GLU Chi-restraints excluded: chain E residue 447 ASP Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 207 CYS Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 410 MET Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain I residue 66 GLN Chi-restraints excluded: chain I residue 96 ASN Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 152 ILE Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain M residue 74 GLU Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain N residue 106 VAL Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 52 VAL Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain R residue 87 ILE Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 158 VAL Chi-restraints excluded: chain S residue 197 TYR Chi-restraints excluded: chain b residue 26 TYR Chi-restraints excluded: chain b residue 100 VAL Chi-restraints excluded: chain b residue 103 TYR Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain b residue 176 ILE Chi-restraints excluded: chain b residue 179 VAL Chi-restraints excluded: chain b residue 203 MET Chi-restraints excluded: chain c residue 414 PHE Chi-restraints excluded: chain c residue 448 ARG Chi-restraints excluded: chain d residue 6 GLU Chi-restraints excluded: chain d residue 13 ASN Chi-restraints excluded: chain d residue 63 SER Chi-restraints excluded: chain d residue 70 ILE Chi-restraints excluded: chain d residue 135 PHE Chi-restraints excluded: chain d residue 183 ASN Chi-restraints excluded: chain g residue 34 THR Chi-restraints excluded: chain g residue 84 ILE Chi-restraints excluded: chain g residue 143 LEU Chi-restraints excluded: chain h residue 143 LEU Chi-restraints excluded: chain i residue 14 PHE Chi-restraints excluded: chain i residue 60 VAL Chi-restraints excluded: chain i residue 140 VAL Chi-restraints excluded: chain j residue 139 GLU Chi-restraints excluded: chain j residue 140 VAL Chi-restraints excluded: chain k residue 14 PHE Chi-restraints excluded: chain k residue 143 LEU Chi-restraints excluded: chain l residue 140 VAL Chi-restraints excluded: chain m residue 140 VAL Chi-restraints excluded: chain m residue 141 LEU Chi-restraints excluded: chain n residue 104 LEU Chi-restraints excluded: chain n residue 121 THR Chi-restraints excluded: chain n residue 139 GLU Chi-restraints excluded: chain o residue 21 SER Chi-restraints excluded: chain o residue 104 LEU Chi-restraints excluded: chain o residue 121 THR Chi-restraints excluded: chain o residue 123 GLN Chi-restraints excluded: chain p residue 301 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 836 random chunks: chunk 421 optimal weight: 20.0000 chunk 235 optimal weight: 4.9990 chunk 631 optimal weight: 6.9990 chunk 516 optimal weight: 10.0000 chunk 209 optimal weight: 1.9990 chunk 760 optimal weight: 30.0000 chunk 821 optimal weight: 0.3980 chunk 677 optimal weight: 5.9990 chunk 754 optimal weight: 30.0000 chunk 259 optimal weight: 8.9990 chunk 610 optimal weight: 20.0000 overall best weight: 4.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS ** A 573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 573 HIS D 187 GLN E 97 GLN E 251 ASN ** J 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 160 GLN ** S 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 197 GLN ** d 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 13 ASN d 30 GLN ** d 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 340 HIS m 124 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 61638 Z= 0.304 Angle : 0.704 12.242 83673 Z= 0.364 Chirality : 0.045 0.263 9871 Planarity : 0.005 0.064 10900 Dihedral : 4.905 117.697 9036 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.53 % Favored : 97.45 % Rotamer: Outliers : 2.97 % Allowed : 12.32 % Favored : 84.71 % 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: 1.91 (0.09), residues: 8369 helix: 2.29 (0.07), residues: 4895 sheet: -0.21 (0.19), residues: 663 loop : -0.17 (0.12), residues: 2811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 567 HIS 0.008 0.001 HIS b 128 PHE 0.049 0.002 PHE h 25 TYR 0.042 0.002 TYR b 103 ARG 0.008 0.001 ARG k 48 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16738 Ramachandran restraints generated. 8369 Oldfield, 0 Emsley, 8369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16738 Ramachandran restraints generated. 8369 Oldfield, 0 Emsley, 8369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1205 residues out of total 7117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 1037 time to evaluate : 5.391 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 95 MET cc_start: 0.8344 (mmt) cc_final: 0.7970 (tpp) REVERT: A 173 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.7885 (pmt100) REVERT: A 254 CYS cc_start: 0.8825 (m) cc_final: 0.8249 (m) REVERT: A 318 MET cc_start: 0.9248 (mtt) cc_final: 0.8653 (mtp) REVERT: A 472 PHE cc_start: 0.8417 (t80) cc_final: 0.8163 (t80) REVERT: A 491 GLU cc_start: 0.8984 (tt0) cc_final: 0.8767 (tm-30) REVERT: A 510 GLU cc_start: 0.8731 (tm-30) cc_final: 0.8330 (tm-30) REVERT: A 516 LYS cc_start: 0.9426 (mttt) cc_final: 0.9130 (tmtt) REVERT: A 518 ASP cc_start: 0.7999 (m-30) cc_final: 0.7610 (t0) REVERT: A 574 MET cc_start: 0.8962 (mtt) cc_final: 0.8388 (mmm) REVERT: B 95 MET cc_start: 0.9032 (tpp) cc_final: 0.8728 (tpp) REVERT: B 306 MET cc_start: 0.8669 (ptm) cc_final: 0.8032 (tmm) REVERT: B 318 MET cc_start: 0.9222 (tpp) cc_final: 0.8945 (mmm) REVERT: B 347 MET cc_start: 0.8586 (tpp) cc_final: 0.8358 (tpp) REVERT: B 356 GLU cc_start: 0.9172 (tp30) cc_final: 0.8792 (tp30) REVERT: B 368 MET cc_start: 0.9096 (mmm) cc_final: 0.8836 (tpp) REVERT: B 426 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8889 (mm) REVERT: B 432 PHE cc_start: 0.8832 (t80) cc_final: 0.8290 (t80) REVERT: B 458 MET cc_start: 0.8707 (mmt) cc_final: 0.8273 (mmt) REVERT: B 550 MET cc_start: 0.9380 (mtm) cc_final: 0.9114 (mtp) REVERT: B 608 MET cc_start: 0.8856 (ttp) cc_final: 0.7963 (ttp) REVERT: C 61 MET cc_start: 0.8988 (mmm) cc_final: 0.8549 (mmm) REVERT: C 68 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7962 (pm20) REVERT: C 284 MET cc_start: 0.9430 (tpp) cc_final: 0.9166 (mmm) REVERT: C 286 GLU cc_start: 0.9203 (tt0) cc_final: 0.8686 (tp30) REVERT: C 416 ASP cc_start: 0.7668 (t0) cc_final: 0.7140 (t0) REVERT: C 458 MET cc_start: 0.8803 (mtp) cc_final: 0.8354 (mtt) REVERT: C 540 MET cc_start: 0.8941 (mmm) cc_final: 0.8706 (mmm) REVERT: C 550 MET cc_start: 0.9537 (mmp) cc_final: 0.9310 (mtt) REVERT: D 169 MET cc_start: 0.8395 (tmm) cc_final: 0.8103 (tmm) REVERT: D 231 PHE cc_start: 0.8842 (t80) cc_final: 0.8624 (t80) REVERT: D 254 MET cc_start: 0.8458 (tpp) cc_final: 0.7999 (mmm) REVERT: D 270 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8095 (tt0) REVERT: D 382 GLN cc_start: 0.9208 (mp10) cc_final: 0.8877 (mp10) REVERT: D 402 MET cc_start: 0.8705 (ttp) cc_final: 0.8360 (ttt) REVERT: D 459 GLU cc_start: 0.8873 (OUTLIER) cc_final: 0.8461 (mp0) REVERT: D 484 LEU cc_start: 0.9708 (mt) cc_final: 0.9465 (mt) REVERT: D 495 ILE cc_start: 0.9523 (mt) cc_final: 0.9232 (tt) REVERT: E 87 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8833 (mt) REVERT: E 113 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7917 (pt0) REVERT: E 148 GLU cc_start: 0.8322 (tt0) cc_final: 0.8050 (tt0) REVERT: E 154 MET cc_start: 0.9369 (tpt) cc_final: 0.9144 (mmm) REVERT: E 169 MET cc_start: 0.8469 (ttt) cc_final: 0.8188 (ttt) REVERT: E 254 MET cc_start: 0.8360 (mmm) cc_final: 0.8104 (mmm) REVERT: E 262 ASN cc_start: 0.9123 (t0) cc_final: 0.8163 (t0) REVERT: E 270 GLU cc_start: 0.8974 (tt0) cc_final: 0.8515 (pt0) REVERT: E 316 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7666 (mt-10) REVERT: E 330 ASP cc_start: 0.9347 (m-30) cc_final: 0.8892 (t70) REVERT: E 341 VAL cc_start: 0.9187 (m) cc_final: 0.8977 (p) REVERT: E 356 MET cc_start: 0.8806 (mtm) cc_final: 0.8356 (mtm) REVERT: F 153 ILE cc_start: 0.9115 (pp) cc_final: 0.8776 (tt) REVERT: F 169 MET cc_start: 0.8807 (tmm) cc_final: 0.8406 (tmm) REVERT: F 183 ILE cc_start: 0.9730 (mt) cc_final: 0.9212 (pt) REVERT: F 187 GLN cc_start: 0.9152 (pp30) cc_final: 0.8751 (pp30) REVERT: F 205 GLN cc_start: 0.9339 (tt0) cc_final: 0.8988 (tt0) REVERT: F 299 ASP cc_start: 0.8293 (m-30) cc_final: 0.7596 (m-30) REVERT: F 309 GLU cc_start: 0.9215 (tm-30) cc_final: 0.8902 (tm-30) REVERT: F 351 ILE cc_start: 0.9587 (mt) cc_final: 0.9291 (mm) REVERT: F 353 ILE cc_start: 0.9663 (mt) cc_final: 0.9451 (mm) REVERT: F 410 MET cc_start: 0.8253 (OUTLIER) cc_final: 0.7951 (mmm) REVERT: F 435 MET cc_start: 0.9241 (tpp) cc_final: 0.8787 (tpp) REVERT: F 491 MET cc_start: 0.8685 (mtp) cc_final: 0.8401 (ptp) REVERT: F 492 LEU cc_start: 0.9490 (mt) cc_final: 0.9057 (mp) REVERT: H 31 ASN cc_start: 0.9340 (m-40) cc_final: 0.9069 (m110) REVERT: H 67 PHE cc_start: 0.9134 (t80) cc_final: 0.8660 (t80) REVERT: H 79 PHE cc_start: 0.9495 (p90) cc_final: 0.9188 (p90) REVERT: H 91 GLN cc_start: 0.9355 (pt0) cc_final: 0.9138 (pt0) REVERT: H 190 GLU cc_start: 0.9265 (mm-30) cc_final: 0.8799 (tm-30) REVERT: H 193 GLU cc_start: 0.9268 (tm-30) cc_final: 0.8798 (tm-30) REVERT: I 72 MET cc_start: 0.9104 (mmm) cc_final: 0.8903 (mmm) REVERT: I 129 GLU cc_start: 0.9204 (mm-30) cc_final: 0.8449 (tp30) REVERT: I 182 GLU cc_start: 0.7583 (pt0) cc_final: 0.7272 (pt0) REVERT: J 72 MET cc_start: 0.9076 (ppp) cc_final: 0.8863 (ppp) REVERT: J 76 MET cc_start: 0.8972 (mmm) cc_final: 0.8715 (mmm) REVERT: J 194 ASN cc_start: 0.8123 (t0) cc_final: 0.7580 (t0) REVERT: J 207 MET cc_start: 0.9203 (mmp) cc_final: 0.8910 (mmm) REVERT: J 208 MET cc_start: 0.9053 (mmm) cc_final: 0.8771 (mmt) REVERT: K 75 LEU cc_start: 0.9705 (OUTLIER) cc_final: 0.9475 (mt) REVERT: K 125 TYR cc_start: 0.9057 (m-80) cc_final: 0.8857 (m-10) REVERT: K 129 GLU cc_start: 0.8345 (tt0) cc_final: 0.7587 (tt0) REVERT: K 132 MET cc_start: 0.8490 (mmm) cc_final: 0.7786 (mmm) REVERT: K 133 ILE cc_start: 0.9609 (mt) cc_final: 0.9382 (tp) REVERT: K 184 TYR cc_start: 0.8637 (m-10) cc_final: 0.8115 (m-10) REVERT: K 207 MET cc_start: 0.8711 (tpp) cc_final: 0.8152 (tpp) REVERT: L 22 LEU cc_start: 0.9664 (mt) cc_final: 0.9307 (mm) REVERT: L 27 GLU cc_start: 0.9122 (pt0) cc_final: 0.8678 (pt0) REVERT: L 33 HIS cc_start: 0.8555 (m170) cc_final: 0.8258 (m170) REVERT: L 46 ASN cc_start: 0.9571 (m-40) cc_final: 0.9364 (t0) REVERT: L 47 GLU cc_start: 0.9127 (mt-10) cc_final: 0.8903 (mm-30) REVERT: L 55 PHE cc_start: 0.9402 (m-10) cc_final: 0.9082 (m-10) REVERT: L 98 TYR cc_start: 0.7849 (t80) cc_final: 0.7619 (t80) REVERT: M 99 LEU cc_start: 0.9787 (tp) cc_final: 0.9536 (tt) REVERT: N 102 MET cc_start: 0.8953 (mpp) cc_final: 0.8742 (mpp) REVERT: O 80 GLN cc_start: 0.9559 (mt0) cc_final: 0.9313 (mm110) REVERT: O 84 MET cc_start: 0.9024 (mmm) cc_final: 0.8750 (mmt) REVERT: Q 33 MET cc_start: 0.8689 (tpt) cc_final: 0.8015 (tmm) REVERT: Q 66 LEU cc_start: 0.9606 (tp) cc_final: 0.9285 (tt) REVERT: Q 151 PHE cc_start: 0.8781 (m-10) cc_final: 0.8517 (m-10) REVERT: Q 188 MET cc_start: 0.8616 (mmm) cc_final: 0.8352 (mmm) REVERT: R 109 GLU cc_start: 0.9115 (mt-10) cc_final: 0.8853 (pp20) REVERT: R 125 ASP cc_start: 0.9247 (m-30) cc_final: 0.8796 (p0) REVERT: R 130 LEU cc_start: 0.9460 (mt) cc_final: 0.9220 (tp) REVERT: R 139 TYR cc_start: 0.9021 (t80) cc_final: 0.8748 (t80) REVERT: S 197 TYR cc_start: 0.7120 (OUTLIER) cc_final: 0.6580 (m-80) REVERT: b 157 ILE cc_start: 0.8969 (mt) cc_final: 0.8729 (mm) REVERT: c 421 MET cc_start: 0.8853 (mtt) cc_final: 0.8445 (mtt) REVERT: c 435 TYR cc_start: 0.9156 (t80) cc_final: 0.8812 (t80) REVERT: d 10 ASN cc_start: 0.9086 (m-40) cc_final: 0.8652 (t0) REVERT: d 105 MET cc_start: 0.9076 (mmm) cc_final: 0.8668 (mmt) REVERT: d 135 PHE cc_start: 0.7868 (OUTLIER) cc_final: 0.7473 (m-80) REVERT: d 138 MET cc_start: 0.8413 (mmp) cc_final: 0.8208 (mmm) REVERT: d 152 ASN cc_start: 0.9318 (m-40) cc_final: 0.9045 (t0) REVERT: d 190 LEU cc_start: 0.9572 (tp) cc_final: 0.9316 (pp) REVERT: d 197 CYS cc_start: 0.9397 (m) cc_final: 0.9060 (p) REVERT: d 307 LEU cc_start: 0.9204 (mp) cc_final: 0.8902 (tp) REVERT: d 321 LEU cc_start: 0.9514 (OUTLIER) cc_final: 0.9217 (mt) REVERT: d 325 GLU cc_start: 0.9357 (tt0) cc_final: 0.8663 (tp30) REVERT: d 334 GLU cc_start: 0.9047 (mt-10) cc_final: 0.8609 (pt0) REVERT: d 340 HIS cc_start: 0.8569 (m-70) cc_final: 0.8003 (m90) REVERT: g 32 TYR cc_start: 0.8935 (t80) cc_final: 0.8631 (t80) REVERT: g 37 SER cc_start: 0.8725 (m) cc_final: 0.8472 (p) REVERT: g 53 MET cc_start: 0.8687 (ptt) cc_final: 0.8146 (pmm) REVERT: g 152 LEU cc_start: 0.8913 (mm) cc_final: 0.8633 (tp) REVERT: h 28 MET cc_start: 0.9296 (mtp) cc_final: 0.9058 (tpt) REVERT: h 44 MET cc_start: 0.6888 (tpt) cc_final: 0.6667 (mpp) REVERT: h 53 MET cc_start: 0.8254 (pmm) cc_final: 0.7607 (pmm) REVERT: i 13 PHE cc_start: 0.8464 (t80) cc_final: 0.8177 (t80) REVERT: i 25 PHE cc_start: 0.9217 (m-80) cc_final: 0.8794 (m-80) REVERT: i 47 MET cc_start: 0.8929 (ptm) cc_final: 0.8235 (ppp) REVERT: i 88 ARG cc_start: 0.8080 (mtm180) cc_final: 0.7518 (ttp-170) REVERT: j 23 MET cc_start: 0.3639 (tpt) cc_final: 0.3398 (tpt) REVERT: j 25 PHE cc_start: 0.8810 (m-80) cc_final: 0.8542 (m-80) REVERT: j 47 MET cc_start: 0.8676 (ppp) cc_final: 0.8350 (ppp) REVERT: k 21 SER cc_start: 0.9318 (m) cc_final: 0.9029 (p) REVERT: k 25 PHE cc_start: 0.8766 (m-80) cc_final: 0.8356 (m-80) REVERT: k 41 ILE cc_start: 0.8805 (mm) cc_final: 0.8499 (pt) REVERT: k 115 ASP cc_start: 0.8094 (m-30) cc_final: 0.7793 (m-30) REVERT: k 131 MET cc_start: 0.6954 (ppp) cc_final: 0.6725 (ppp) REVERT: l 131 MET cc_start: 0.4017 (ptt) cc_final: 0.3514 (ppp) REVERT: l 144 TYR cc_start: 0.7937 (m-10) cc_final: 0.7692 (m-10) REVERT: m 39 THR cc_start: 0.8006 (m) cc_final: 0.7728 (p) REVERT: m 47 MET cc_start: 0.5808 (mmt) cc_final: 0.5603 (mmp) REVERT: m 53 MET cc_start: 0.5706 (mmp) cc_final: 0.5453 (mmp) REVERT: m 55 SER cc_start: 0.8939 (m) cc_final: 0.8561 (p) REVERT: m 141 LEU cc_start: 0.7391 (OUTLIER) cc_final: 0.6777 (tp) REVERT: n 141 LEU cc_start: 0.7010 (mt) cc_final: 0.6240 (tp) REVERT: o 17 MET cc_start: 0.8723 (mtp) cc_final: 0.8433 (mtp) REVERT: o 36 LYS cc_start: 0.8999 (mtpp) cc_final: 0.8750 (mtmm) REVERT: o 131 MET cc_start: 0.8620 (ppp) cc_final: 0.8284 (ppp) REVERT: p 312 TRP cc_start: 0.8438 (m100) cc_final: 0.7925 (m100) REVERT: p 330 ASN cc_start: 0.9035 (m-40) cc_final: 0.8796 (m-40) REVERT: p 338 ILE cc_start: 0.7981 (OUTLIER) cc_final: 0.7394 (pt) REVERT: p 342 MET cc_start: 0.7280 (mmt) cc_final: 0.6642 (mmt) outliers start: 168 outliers final: 99 residues processed: 1134 average time/residue: 0.5494 time to fit residues: 1077.6231 Evaluate side-chains 1047 residues out of total 7117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 935 time to evaluate : 5.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain C residue 68 GLU Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 371 ASP Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 394 CYS Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 334 ILE Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 448 ASP Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 113 GLU Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 336 GLU Chi-restraints excluded: chain E residue 360 ASP Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 207 CYS Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 410 MET Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 38 ASP Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 74 PHE Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain I residue 66 GLN Chi-restraints excluded: chain I residue 208 MET Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain K residue 152 ILE Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain M residue 74 GLU Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain N residue 106 VAL Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 52 VAL Chi-restraints excluded: chain Q residue 95 VAL Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 133 LEU Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 197 TYR Chi-restraints excluded: chain b residue 26 TYR Chi-restraints excluded: chain b residue 54 ILE Chi-restraints excluded: chain b residue 56 LEU Chi-restraints excluded: chain b residue 103 TYR Chi-restraints excluded: chain c residue 414 PHE Chi-restraints excluded: chain c residue 448 ARG Chi-restraints excluded: chain d residue 6 GLU Chi-restraints excluded: chain d residue 63 SER Chi-restraints excluded: chain d residue 70 ILE Chi-restraints excluded: chain d residue 135 PHE Chi-restraints excluded: chain d residue 168 ILE Chi-restraints excluded: chain d residue 183 ASN Chi-restraints excluded: chain d residue 321 LEU Chi-restraints excluded: chain g residue 34 THR Chi-restraints excluded: chain g residue 84 ILE Chi-restraints excluded: chain h residue 143 LEU Chi-restraints excluded: chain i residue 60 VAL Chi-restraints excluded: chain i residue 136 ILE Chi-restraints excluded: chain i residue 140 VAL Chi-restraints excluded: chain i residue 144 TYR Chi-restraints excluded: chain k residue 143 LEU Chi-restraints excluded: chain k residue 150 LEU Chi-restraints excluded: chain l residue 54 LYS Chi-restraints excluded: chain l residue 110 ILE Chi-restraints excluded: chain l residue 119 ARG Chi-restraints excluded: chain l residue 140 VAL Chi-restraints excluded: chain m residue 44 MET Chi-restraints excluded: chain m residue 93 LEU Chi-restraints excluded: chain m residue 121 THR Chi-restraints excluded: chain m residue 140 VAL Chi-restraints excluded: chain m residue 141 LEU Chi-restraints excluded: chain o residue 6 ASN Chi-restraints excluded: chain o residue 13 PHE Chi-restraints excluded: chain o residue 123 GLN Chi-restraints excluded: chain o residue 137 PHE Chi-restraints excluded: chain p residue 338 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 836 random chunks: chunk 751 optimal weight: 40.0000 chunk 571 optimal weight: 50.0000 chunk 394 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 362 optimal weight: 4.9990 chunk 510 optimal weight: 10.0000 chunk 763 optimal weight: 2.9990 chunk 808 optimal weight: 30.0000 chunk 398 optimal weight: 10.0000 chunk 723 optimal weight: 5.9990 chunk 217 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 ASN ** A 573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 GLN H 16 GLN ** I 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 50 GLN R 19 HIS R 117 GLN ** b 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 197 GLN ** d 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 338 GLN ** j 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.4463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 61638 Z= 0.343 Angle : 0.706 14.451 83673 Z= 0.364 Chirality : 0.045 0.324 9871 Planarity : 0.004 0.057 10900 Dihedral : 4.664 122.952 9027 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.63 % Favored : 97.36 % Rotamer: Outliers : 3.49 % Allowed : 13.20 % Favored : 83.31 % 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: 1.80 (0.09), residues: 8369 helix: 2.17 (0.07), residues: 4941 sheet: -0.26 (0.19), residues: 683 loop : -0.19 (0.12), residues: 2745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 567 HIS 0.008 0.001 HIS b 128 PHE 0.059 0.002 PHE h 25 TYR 0.045 0.002 TYR b 103 ARG 0.005 0.001 ARG h 119 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16738 Ramachandran restraints generated. 8369 Oldfield, 0 Emsley, 8369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16738 Ramachandran restraints generated. 8369 Oldfield, 0 Emsley, 8369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1148 residues out of total 7117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 951 time to evaluate : 5.402 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 34 MET cc_start: 0.9310 (tpp) cc_final: 0.8964 (mmm) REVERT: A 164 HIS cc_start: 0.9010 (OUTLIER) cc_final: 0.8684 (t70) REVERT: A 167 MET cc_start: 0.9379 (mtm) cc_final: 0.8915 (mtt) REVERT: A 173 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.7959 (pmt100) REVERT: A 472 PHE cc_start: 0.8480 (t80) cc_final: 0.8222 (t80) REVERT: A 491 GLU cc_start: 0.9024 (tt0) cc_final: 0.8806 (tm-30) REVERT: A 510 GLU cc_start: 0.8797 (tm-30) cc_final: 0.8441 (tm-30) REVERT: A 516 LYS cc_start: 0.9478 (mttt) cc_final: 0.9147 (tttm) REVERT: A 518 ASP cc_start: 0.7882 (m-30) cc_final: 0.7594 (m-30) REVERT: B 95 MET cc_start: 0.8999 (tpp) cc_final: 0.8710 (tpp) REVERT: B 306 MET cc_start: 0.8695 (ptm) cc_final: 0.8330 (tmm) REVERT: B 318 MET cc_start: 0.9238 (tpp) cc_final: 0.8954 (mmm) REVERT: B 356 GLU cc_start: 0.9223 (tp30) cc_final: 0.8812 (tp30) REVERT: B 368 MET cc_start: 0.9067 (mmm) cc_final: 0.8690 (ttm) REVERT: B 428 ILE cc_start: 0.9411 (mt) cc_final: 0.9076 (mm) REVERT: B 458 MET cc_start: 0.8752 (mmt) cc_final: 0.8311 (mmt) REVERT: B 471 GLU cc_start: 0.8922 (OUTLIER) cc_final: 0.8687 (pm20) REVERT: B 492 ILE cc_start: 0.9559 (OUTLIER) cc_final: 0.9338 (mm) REVERT: B 584 MET cc_start: 0.8854 (OUTLIER) cc_final: 0.8500 (mpp) REVERT: B 608 MET cc_start: 0.8867 (ttp) cc_final: 0.7256 (ttp) REVERT: C 61 MET cc_start: 0.9065 (mmm) cc_final: 0.8760 (mmm) REVERT: C 284 MET cc_start: 0.9416 (tpp) cc_final: 0.9120 (mmm) REVERT: C 286 GLU cc_start: 0.9250 (tt0) cc_final: 0.9022 (tm-30) REVERT: C 416 ASP cc_start: 0.8066 (t0) cc_final: 0.7661 (t0) REVERT: C 458 MET cc_start: 0.8809 (mtp) cc_final: 0.8356 (mtt) REVERT: C 461 LEU cc_start: 0.9592 (OUTLIER) cc_final: 0.9381 (mm) REVERT: C 550 MET cc_start: 0.9535 (mmp) cc_final: 0.9304 (mmp) REVERT: D 169 MET cc_start: 0.8564 (tmm) cc_final: 0.8286 (tmm) REVERT: D 254 MET cc_start: 0.8483 (tpp) cc_final: 0.8013 (mmm) REVERT: D 270 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8144 (tt0) REVERT: D 382 GLN cc_start: 0.9270 (mp10) cc_final: 0.8977 (mp10) REVERT: D 459 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.8418 (mp0) REVERT: D 484 LEU cc_start: 0.9738 (mt) cc_final: 0.9493 (mt) REVERT: D 495 ILE cc_start: 0.9503 (mt) cc_final: 0.9199 (tt) REVERT: E 87 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8664 (mt) REVERT: E 113 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7964 (pt0) REVERT: E 148 GLU cc_start: 0.8463 (tt0) cc_final: 0.8139 (tt0) REVERT: E 154 MET cc_start: 0.9428 (tpt) cc_final: 0.9222 (mmm) REVERT: E 254 MET cc_start: 0.8377 (mmm) cc_final: 0.8065 (mmm) REVERT: E 262 ASN cc_start: 0.9118 (t0) cc_final: 0.8271 (t0) REVERT: E 270 GLU cc_start: 0.9013 (tt0) cc_final: 0.8535 (pt0) REVERT: E 309 GLU cc_start: 0.8687 (tm-30) cc_final: 0.8384 (tm-30) REVERT: E 316 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7605 (mt-10) REVERT: E 330 ASP cc_start: 0.9367 (OUTLIER) cc_final: 0.8897 (t70) REVERT: E 356 MET cc_start: 0.8835 (mtm) cc_final: 0.8437 (mtm) REVERT: E 382 GLN cc_start: 0.8727 (mp10) cc_final: 0.8401 (mp10) REVERT: F 44 ARG cc_start: 0.9039 (mtt180) cc_final: 0.8504 (mtp85) REVERT: F 153 ILE cc_start: 0.9173 (pp) cc_final: 0.8851 (tt) REVERT: F 169 MET cc_start: 0.8946 (tmm) cc_final: 0.8509 (tmm) REVERT: F 183 ILE cc_start: 0.9725 (mt) cc_final: 0.9259 (pt) REVERT: F 187 GLN cc_start: 0.9248 (pp30) cc_final: 0.8838 (pp30) REVERT: F 205 GLN cc_start: 0.9337 (tt0) cc_final: 0.9012 (tt0) REVERT: F 256 ASN cc_start: 0.8987 (m-40) cc_final: 0.8492 (p0) REVERT: F 299 ASP cc_start: 0.8266 (m-30) cc_final: 0.7607 (m-30) REVERT: F 309 GLU cc_start: 0.9202 (tm-30) cc_final: 0.8890 (tm-30) REVERT: F 351 ILE cc_start: 0.9581 (mt) cc_final: 0.9275 (mm) REVERT: F 353 ILE cc_start: 0.9683 (mt) cc_final: 0.9461 (mm) REVERT: F 410 MET cc_start: 0.8349 (OUTLIER) cc_final: 0.8076 (mmm) REVERT: F 435 MET cc_start: 0.9254 (tpp) cc_final: 0.8816 (tpt) REVERT: F 492 LEU cc_start: 0.9510 (mt) cc_final: 0.9078 (mp) REVERT: H 31 ASN cc_start: 0.9378 (m-40) cc_final: 0.9034 (m110) REVERT: H 79 PHE cc_start: 0.9533 (p90) cc_final: 0.9187 (p90) REVERT: H 91 GLN cc_start: 0.9363 (pt0) cc_final: 0.9087 (pt0) REVERT: H 190 GLU cc_start: 0.9309 (mm-30) cc_final: 0.8817 (tm-30) REVERT: H 193 GLU cc_start: 0.9313 (tm-30) cc_final: 0.8884 (tm-30) REVERT: I 72 MET cc_start: 0.9207 (mmm) cc_final: 0.8990 (mmm) REVERT: I 177 ILE cc_start: 0.9188 (mm) cc_final: 0.8963 (mm) REVERT: I 182 GLU cc_start: 0.7739 (pt0) cc_final: 0.7356 (pt0) REVERT: I 207 MET cc_start: 0.9519 (mmt) cc_final: 0.9158 (mmm) REVERT: J 72 MET cc_start: 0.9164 (ppp) cc_final: 0.8735 (ppp) REVERT: J 76 MET cc_start: 0.8912 (mmm) cc_final: 0.8634 (mmm) REVERT: J 207 MET cc_start: 0.9255 (mmp) cc_final: 0.8959 (mmm) REVERT: K 75 LEU cc_start: 0.9731 (OUTLIER) cc_final: 0.9523 (mt) REVERT: K 129 GLU cc_start: 0.8275 (tt0) cc_final: 0.7595 (tt0) REVERT: K 132 MET cc_start: 0.8263 (mmm) cc_final: 0.7657 (mmm) REVERT: K 133 ILE cc_start: 0.9623 (mt) cc_final: 0.9403 (tp) REVERT: K 154 MET cc_start: 0.9502 (mtt) cc_final: 0.9196 (ptp) REVERT: K 184 TYR cc_start: 0.8657 (m-10) cc_final: 0.8155 (m-10) REVERT: K 207 MET cc_start: 0.8739 (tpp) cc_final: 0.8173 (tpp) REVERT: L 22 LEU cc_start: 0.9668 (mt) cc_final: 0.9432 (tp) REVERT: L 27 GLU cc_start: 0.9159 (pt0) cc_final: 0.8738 (pt0) REVERT: L 33 HIS cc_start: 0.8613 (m170) cc_final: 0.8293 (m170) REVERT: L 46 ASN cc_start: 0.9579 (m-40) cc_final: 0.9371 (t0) REVERT: L 47 GLU cc_start: 0.9174 (mt-10) cc_final: 0.8905 (mm-30) REVERT: M 99 LEU cc_start: 0.9785 (tp) cc_final: 0.9491 (tt) REVERT: M 102 MET cc_start: 0.9530 (mpp) cc_final: 0.9026 (mpp) REVERT: N 84 MET cc_start: 0.9146 (mtm) cc_final: 0.8705 (ptp) REVERT: N 96 LEU cc_start: 0.9667 (pp) cc_final: 0.9425 (pp) REVERT: N 102 MET cc_start: 0.8981 (mpp) cc_final: 0.8744 (mpp) REVERT: O 84 MET cc_start: 0.9061 (mmm) cc_final: 0.8849 (mmm) REVERT: Q 66 LEU cc_start: 0.9594 (tp) cc_final: 0.9349 (tt) REVERT: Q 188 MET cc_start: 0.8697 (mmm) cc_final: 0.8451 (mmm) REVERT: Q 234 MET cc_start: 0.9012 (tmm) cc_final: 0.8651 (tmm) REVERT: R 77 ASP cc_start: 0.9300 (t0) cc_final: 0.9070 (t0) REVERT: R 79 ASP cc_start: 0.9463 (m-30) cc_final: 0.9243 (p0) REVERT: R 109 GLU cc_start: 0.9155 (mt-10) cc_final: 0.8884 (pp20) REVERT: R 130 LEU cc_start: 0.9411 (mt) cc_final: 0.9132 (tp) REVERT: R 197 TYR cc_start: 0.8978 (m-80) cc_final: 0.8673 (m-80) REVERT: S 197 TYR cc_start: 0.7223 (OUTLIER) cc_final: 0.6651 (m-80) REVERT: b 19 MET cc_start: 0.7764 (tmm) cc_final: 0.7497 (ppp) REVERT: b 48 MET cc_start: 0.8419 (ppp) cc_final: 0.8071 (ppp) REVERT: b 157 ILE cc_start: 0.9013 (mt) cc_final: 0.8776 (mm) REVERT: b 177 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7777 (tp) REVERT: d 10 ASN cc_start: 0.9118 (m-40) cc_final: 0.8773 (t0) REVERT: d 88 HIS cc_start: 0.8757 (m90) cc_final: 0.8468 (m90) REVERT: d 105 MET cc_start: 0.9019 (mmm) cc_final: 0.8686 (mmt) REVERT: d 138 MET cc_start: 0.8317 (mmp) cc_final: 0.8015 (mmm) REVERT: d 139 GLU cc_start: 0.7844 (tp30) cc_final: 0.7144 (tm-30) REVERT: d 152 ASN cc_start: 0.9361 (m-40) cc_final: 0.8997 (p0) REVERT: d 190 LEU cc_start: 0.9548 (tp) cc_final: 0.9299 (pp) REVERT: d 197 CYS cc_start: 0.9406 (m) cc_final: 0.9108 (p) REVERT: d 321 LEU cc_start: 0.9486 (OUTLIER) cc_final: 0.9174 (mt) REVERT: d 325 GLU cc_start: 0.9393 (tt0) cc_final: 0.8944 (tm-30) REVERT: d 329 ILE cc_start: 0.9692 (mt) cc_final: 0.9336 (mm) REVERT: d 334 GLU cc_start: 0.8975 (mt-10) cc_final: 0.8482 (pt0) REVERT: g 37 SER cc_start: 0.8642 (m) cc_final: 0.8415 (p) REVERT: g 53 MET cc_start: 0.8602 (ptt) cc_final: 0.8001 (pmm) REVERT: g 119 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.8117 (mtp180) REVERT: h 28 MET cc_start: 0.9291 (mtp) cc_final: 0.9046 (tpt) REVERT: h 53 MET cc_start: 0.8277 (pmm) cc_final: 0.8038 (pmm) REVERT: i 13 PHE cc_start: 0.8614 (t80) cc_final: 0.8282 (t80) REVERT: i 25 PHE cc_start: 0.9229 (m-80) cc_final: 0.8905 (m-80) REVERT: i 47 MET cc_start: 0.8742 (ptm) cc_final: 0.8281 (ppp) REVERT: i 88 ARG cc_start: 0.8113 (mtm180) cc_final: 0.7434 (ttp-170) REVERT: j 25 PHE cc_start: 0.8785 (m-80) cc_final: 0.8422 (m-80) REVERT: j 47 MET cc_start: 0.8525 (ppp) cc_final: 0.8292 (ppp) REVERT: j 48 ARG cc_start: 0.8928 (mtt-85) cc_final: 0.8571 (mtm180) REVERT: k 21 SER cc_start: 0.9294 (m) cc_final: 0.9021 (p) REVERT: k 25 PHE cc_start: 0.8723 (m-80) cc_final: 0.8345 (m-80) REVERT: k 32 TYR cc_start: 0.7448 (t80) cc_final: 0.7233 (t80) REVERT: k 41 ILE cc_start: 0.8672 (mm) cc_final: 0.8414 (pt) REVERT: k 47 MET cc_start: 0.6521 (OUTLIER) cc_final: 0.5453 (ttp) REVERT: k 115 ASP cc_start: 0.8119 (OUTLIER) cc_final: 0.7520 (m-30) REVERT: k 152 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7451 (tp) REVERT: l 23 MET cc_start: 0.7050 (tpt) cc_final: 0.6547 (tpt) REVERT: l 47 MET cc_start: 0.6527 (ttt) cc_final: 0.6220 (ttp) REVERT: l 131 MET cc_start: 0.4289 (ptt) cc_final: 0.3664 (ppp) REVERT: m 39 THR cc_start: 0.8062 (m) cc_final: 0.7800 (p) REVERT: m 47 MET cc_start: 0.5966 (mmp) cc_final: 0.5550 (mmp) REVERT: m 104 LEU cc_start: 0.9391 (mt) cc_final: 0.9150 (mt) REVERT: m 141 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.6930 (tp) REVERT: o 17 MET cc_start: 0.8755 (mtp) cc_final: 0.8528 (mtp) REVERT: o 23 MET cc_start: 0.8501 (tpt) cc_final: 0.8287 (tpt) REVERT: o 131 MET cc_start: 0.8457 (ppp) cc_final: 0.8113 (ppp) REVERT: o 143 LEU cc_start: 0.8769 (mm) cc_final: 0.8438 (pp) REVERT: p 312 TRP cc_start: 0.8356 (m100) cc_final: 0.7665 (m100) REVERT: p 330 ASN cc_start: 0.8989 (m-40) cc_final: 0.8708 (m110) outliers start: 197 outliers final: 122 residues processed: 1070 average time/residue: 0.5381 time to fit residues: 1002.5405 Evaluate side-chains 1023 residues out of total 7117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 880 time to evaluate : 5.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 HIS Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 450 TRP Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 584 MET Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 371 ASP Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 394 CYS Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 584 MET Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 448 ASP Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 113 GLU Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 330 ASP Chi-restraints excluded: chain E residue 336 GLU Chi-restraints excluded: chain E residue 360 ASP Chi-restraints excluded: chain E residue 448 ASP Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 207 CYS Chi-restraints excluded: chain F residue 257 VAL Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 365 ILE Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 410 MET Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain H residue 38 ASP Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 74 PHE Chi-restraints excluded: chain H residue 109 PHE Chi-restraints excluded: chain I residue 66 GLN Chi-restraints excluded: chain I residue 208 MET Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain M residue 74 GLU Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain N residue 106 VAL Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 52 VAL Chi-restraints excluded: chain Q residue 88 LEU Chi-restraints excluded: chain Q residue 95 VAL Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 133 LEU Chi-restraints excluded: chain Q residue 134 ASN Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 197 TYR Chi-restraints excluded: chain S residue 198 HIS Chi-restraints excluded: chain b residue 26 TYR Chi-restraints excluded: chain b residue 103 TYR Chi-restraints excluded: chain b residue 122 ASP Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain b residue 177 LEU Chi-restraints excluded: chain c residue 430 LEU Chi-restraints excluded: chain c residue 438 HIS Chi-restraints excluded: chain c residue 448 ARG Chi-restraints excluded: chain d residue 6 GLU Chi-restraints excluded: chain d residue 63 SER Chi-restraints excluded: chain d residue 70 ILE Chi-restraints excluded: chain d residue 168 ILE Chi-restraints excluded: chain d residue 173 LEU Chi-restraints excluded: chain d residue 183 ASN Chi-restraints excluded: chain d residue 233 SER Chi-restraints excluded: chain d residue 244 CYS Chi-restraints excluded: chain d residue 321 LEU Chi-restraints excluded: chain g residue 34 THR Chi-restraints excluded: chain g residue 61 MET Chi-restraints excluded: chain g residue 84 ILE Chi-restraints excluded: chain g residue 119 ARG Chi-restraints excluded: chain g residue 141 LEU Chi-restraints excluded: chain h residue 108 PHE Chi-restraints excluded: chain i residue 60 VAL Chi-restraints excluded: chain i residue 140 VAL Chi-restraints excluded: chain k residue 47 MET Chi-restraints excluded: chain k residue 85 THR Chi-restraints excluded: chain k residue 108 PHE Chi-restraints excluded: chain k residue 115 ASP Chi-restraints excluded: chain k residue 150 LEU Chi-restraints excluded: chain k residue 152 LEU Chi-restraints excluded: chain l residue 54 LYS Chi-restraints excluded: chain l residue 119 ARG Chi-restraints excluded: chain l residue 140 VAL Chi-restraints excluded: chain m residue 93 LEU Chi-restraints excluded: chain m residue 121 THR Chi-restraints excluded: chain m residue 133 LEU Chi-restraints excluded: chain m residue 140 VAL Chi-restraints excluded: chain m residue 141 LEU Chi-restraints excluded: chain n residue 104 LEU Chi-restraints excluded: chain n residue 134 ILE Chi-restraints excluded: chain o residue 6 ASN Chi-restraints excluded: chain o residue 13 PHE Chi-restraints excluded: chain o residue 21 SER Chi-restraints excluded: chain o residue 123 GLN Chi-restraints excluded: chain o residue 137 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 836 random chunks: chunk 673 optimal weight: 7.9990 chunk 458 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 chunk 601 optimal weight: 10.0000 chunk 333 optimal weight: 50.0000 chunk 689 optimal weight: 40.0000 chunk 558 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 412 optimal weight: 4.9990 chunk 725 optimal weight: 10.0000 chunk 203 optimal weight: 6.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 521 GLN D 62 HIS ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 113 HIS ** I 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 198 HIS Q 207 GLN R 21 GLN S 19 HIS S 50 GLN S 160 GLN ** b 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 118 HIS ** d 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.5030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.104 61638 Z= 0.490 Angle : 0.797 14.851 83673 Z= 0.411 Chirality : 0.047 0.265 9871 Planarity : 0.005 0.118 10900 Dihedral : 4.879 127.494 9025 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 18.14 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.43 % Favored : 96.55 % Rotamer: Outliers : 3.82 % Allowed : 14.37 % Favored : 81.81 % 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: 1.39 (0.09), residues: 8369 helix: 1.88 (0.07), residues: 4955 sheet: -0.50 (0.19), residues: 700 loop : -0.43 (0.12), residues: 2714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 122 HIS 0.010 0.002 HIS Q 19 PHE 0.055 0.003 PHE l 25 TYR 0.046 0.002 TYR b 103 ARG 0.012 0.001 ARG n 48 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16738 Ramachandran restraints generated. 8369 Oldfield, 0 Emsley, 8369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16738 Ramachandran restraints generated. 8369 Oldfield, 0 Emsley, 8369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1089 residues out of total 7117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 873 time to evaluate : 5.334 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: A 164 HIS cc_start: 0.9035 (OUTLIER) cc_final: 0.8752 (t70) REVERT: A 167 MET cc_start: 0.9428 (mtm) cc_final: 0.8711 (mtt) REVERT: A 173 ARG cc_start: 0.8967 (OUTLIER) cc_final: 0.8042 (pmt100) REVERT: A 318 MET cc_start: 0.9228 (mtt) cc_final: 0.8736 (mtp) REVERT: A 416 ASP cc_start: 0.8573 (t0) cc_final: 0.8330 (t0) REVERT: A 491 GLU cc_start: 0.9070 (tt0) cc_final: 0.8869 (tm-30) REVERT: A 510 GLU cc_start: 0.8831 (tm-30) cc_final: 0.8496 (tm-30) REVERT: A 516 LYS cc_start: 0.9523 (mttt) cc_final: 0.9137 (tttm) REVERT: A 518 ASP cc_start: 0.7672 (m-30) cc_final: 0.7343 (m-30) REVERT: B 306 MET cc_start: 0.8767 (ptm) cc_final: 0.8382 (tmm) REVERT: B 318 MET cc_start: 0.9343 (tpp) cc_final: 0.8191 (mpp) REVERT: B 347 MET cc_start: 0.8896 (tpp) cc_final: 0.8671 (tpt) REVERT: B 458 MET cc_start: 0.8867 (mmt) cc_final: 0.8427 (mmt) REVERT: B 584 MET cc_start: 0.8872 (OUTLIER) cc_final: 0.8474 (mpp) REVERT: B 606 GLU cc_start: 0.9222 (mt-10) cc_final: 0.8927 (mt-10) REVERT: B 608 MET cc_start: 0.8929 (ttp) cc_final: 0.8236 (ttt) REVERT: C 39 MET cc_start: 0.8888 (tmm) cc_final: 0.8128 (tmm) REVERT: C 234 LEU cc_start: 0.9121 (mp) cc_final: 0.8896 (tt) REVERT: C 399 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7545 (mm-30) REVERT: C 416 ASP cc_start: 0.8430 (t0) cc_final: 0.8180 (t0) REVERT: C 458 MET cc_start: 0.8834 (mtp) cc_final: 0.8149 (mtt) REVERT: C 540 MET cc_start: 0.8964 (mmm) cc_final: 0.8724 (mmm) REVERT: C 544 MET cc_start: 0.9288 (OUTLIER) cc_final: 0.9050 (tpp) REVERT: C 550 MET cc_start: 0.9544 (mmp) cc_final: 0.9295 (mmp) REVERT: D 254 MET cc_start: 0.8593 (tpp) cc_final: 0.8125 (mmm) REVERT: D 270 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8144 (tt0) REVERT: D 484 LEU cc_start: 0.9774 (mt) cc_final: 0.9549 (mt) REVERT: D 495 ILE cc_start: 0.9472 (mt) cc_final: 0.9180 (tt) REVERT: E 148 GLU cc_start: 0.8600 (tt0) cc_final: 0.8290 (tt0) REVERT: E 270 GLU cc_start: 0.9043 (tt0) cc_final: 0.8669 (tt0) REVERT: E 309 GLU cc_start: 0.8757 (tm-30) cc_final: 0.8400 (tm-30) REVERT: E 316 GLU cc_start: 0.8299 (mt-10) cc_final: 0.7720 (mt-10) REVERT: E 330 ASP cc_start: 0.9482 (OUTLIER) cc_final: 0.8991 (t70) REVERT: E 356 MET cc_start: 0.8881 (mtm) cc_final: 0.8547 (mtm) REVERT: E 382 GLN cc_start: 0.8748 (mp10) cc_final: 0.8494 (mp10) REVERT: F 153 ILE cc_start: 0.9196 (pp) cc_final: 0.8906 (tt) REVERT: F 169 MET cc_start: 0.8969 (tmm) cc_final: 0.8549 (tmm) REVERT: F 180 MET cc_start: 0.8931 (mmm) cc_final: 0.8601 (mmm) REVERT: F 183 ILE cc_start: 0.9681 (mt) cc_final: 0.9277 (pt) REVERT: F 187 GLN cc_start: 0.9364 (pp30) cc_final: 0.8929 (pp30) REVERT: F 254 MET cc_start: 0.8711 (mmm) cc_final: 0.8048 (tpp) REVERT: F 299 ASP cc_start: 0.8362 (m-30) cc_final: 0.7701 (m-30) REVERT: F 309 GLU cc_start: 0.9219 (tm-30) cc_final: 0.8960 (tm-30) REVERT: F 351 ILE cc_start: 0.9589 (mt) cc_final: 0.9290 (mm) REVERT: F 353 ILE cc_start: 0.9698 (mt) cc_final: 0.9487 (mm) REVERT: F 435 MET cc_start: 0.9280 (tpp) cc_final: 0.8851 (tpt) REVERT: F 491 MET cc_start: 0.8659 (mtp) cc_final: 0.8303 (ptp) REVERT: H 31 ASN cc_start: 0.9399 (m-40) cc_final: 0.9085 (m110) REVERT: H 79 PHE cc_start: 0.9582 (p90) cc_final: 0.9260 (p90) REVERT: H 91 GLN cc_start: 0.9317 (pt0) cc_final: 0.9012 (pm20) REVERT: H 190 GLU cc_start: 0.9324 (mm-30) cc_final: 0.8962 (mm-30) REVERT: H 193 GLU cc_start: 0.9412 (tm-30) cc_final: 0.9000 (tm-30) REVERT: I 72 MET cc_start: 0.9289 (mmm) cc_final: 0.9072 (mmm) REVERT: I 182 GLU cc_start: 0.7792 (pt0) cc_final: 0.7408 (pt0) REVERT: I 207 MET cc_start: 0.9534 (mmt) cc_final: 0.9208 (mmm) REVERT: J 72 MET cc_start: 0.9250 (ppp) cc_final: 0.8672 (ppp) REVERT: J 76 MET cc_start: 0.8983 (mmm) cc_final: 0.8661 (mmm) REVERT: J 119 LEU cc_start: 0.9534 (mt) cc_final: 0.9219 (mt) REVERT: J 207 MET cc_start: 0.9367 (mmp) cc_final: 0.9009 (mmm) REVERT: J 208 MET cc_start: 0.9292 (mmm) cc_final: 0.8937 (mmt) REVERT: K 129 GLU cc_start: 0.8237 (tt0) cc_final: 0.7540 (tt0) REVERT: K 132 MET cc_start: 0.7926 (mmm) cc_final: 0.7146 (mmm) REVERT: K 133 ILE cc_start: 0.9667 (mt) cc_final: 0.9422 (tp) REVERT: K 184 TYR cc_start: 0.8761 (m-10) cc_final: 0.8029 (m-10) REVERT: K 207 MET cc_start: 0.8811 (tpp) cc_final: 0.8330 (tpp) REVERT: K 208 MET cc_start: 0.9509 (tpp) cc_final: 0.9302 (tpp) REVERT: L 22 LEU cc_start: 0.9682 (mt) cc_final: 0.9468 (tp) REVERT: L 27 GLU cc_start: 0.9243 (pt0) cc_final: 0.8924 (pt0) REVERT: L 33 HIS cc_start: 0.8602 (m170) cc_final: 0.8269 (m-70) REVERT: L 46 ASN cc_start: 0.9584 (m-40) cc_final: 0.9382 (t0) REVERT: L 47 GLU cc_start: 0.9230 (mt-10) cc_final: 0.8971 (mm-30) REVERT: M 99 LEU cc_start: 0.9794 (tp) cc_final: 0.9453 (tt) REVERT: M 102 MET cc_start: 0.9482 (mpp) cc_final: 0.9092 (mpp) REVERT: N 84 MET cc_start: 0.9190 (mtm) cc_final: 0.8628 (ptm) REVERT: N 102 MET cc_start: 0.8976 (mpp) cc_final: 0.8759 (mpp) REVERT: O 84 MET cc_start: 0.9126 (mmm) cc_final: 0.8920 (mmm) REVERT: Q 33 MET cc_start: 0.8979 (tmm) cc_final: 0.8523 (tmm) REVERT: Q 66 LEU cc_start: 0.9586 (tp) cc_final: 0.9360 (tt) REVERT: Q 188 MET cc_start: 0.8807 (mmm) cc_final: 0.8549 (mmm) REVERT: Q 234 MET cc_start: 0.9037 (tmm) cc_final: 0.8763 (tmm) REVERT: R 33 MET cc_start: 0.9073 (tmm) cc_final: 0.8860 (tmm) REVERT: R 109 GLU cc_start: 0.9164 (mt-10) cc_final: 0.8875 (pp20) REVERT: R 130 LEU cc_start: 0.9461 (mt) cc_final: 0.9142 (tp) REVERT: R 139 TYR cc_start: 0.9071 (t80) cc_final: 0.8673 (t80) REVERT: R 225 LEU cc_start: 0.9617 (pp) cc_final: 0.9220 (pp) REVERT: S 197 TYR cc_start: 0.7527 (OUTLIER) cc_final: 0.6876 (m-80) REVERT: b 157 ILE cc_start: 0.9045 (mt) cc_final: 0.8806 (mm) REVERT: b 177 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.7878 (tp) REVERT: c 441 LEU cc_start: 0.9323 (mm) cc_final: 0.9117 (mt) REVERT: d 10 ASN cc_start: 0.9142 (m-40) cc_final: 0.8912 (t0) REVERT: d 88 HIS cc_start: 0.8678 (m90) cc_final: 0.8383 (m90) REVERT: d 138 MET cc_start: 0.8283 (mmp) cc_final: 0.8028 (mmm) REVERT: d 152 ASN cc_start: 0.9434 (m-40) cc_final: 0.9107 (t0) REVERT: d 164 PHE cc_start: 0.9271 (m-80) cc_final: 0.9040 (m-80) REVERT: d 176 MET cc_start: 0.8247 (tpp) cc_final: 0.8035 (tmm) REVERT: d 307 LEU cc_start: 0.9262 (mp) cc_final: 0.8935 (tp) REVERT: d 325 GLU cc_start: 0.9438 (tt0) cc_final: 0.8968 (tm-30) REVERT: d 329 ILE cc_start: 0.9718 (mt) cc_final: 0.9362 (mm) REVERT: d 334 GLU cc_start: 0.8995 (mt-10) cc_final: 0.8582 (pt0) REVERT: g 37 SER cc_start: 0.8662 (m) cc_final: 0.8435 (p) REVERT: g 53 MET cc_start: 0.8556 (ptt) cc_final: 0.7890 (pmm) REVERT: g 108 PHE cc_start: 0.9157 (m-10) cc_final: 0.8800 (m-10) REVERT: h 53 MET cc_start: 0.8294 (pmm) cc_final: 0.7895 (pmm) REVERT: i 13 PHE cc_start: 0.8611 (t80) cc_final: 0.8337 (t80) REVERT: i 47 MET cc_start: 0.8672 (ptm) cc_final: 0.8100 (ppp) REVERT: i 61 MET cc_start: 0.5903 (ptp) cc_final: 0.5448 (ptp) REVERT: i 68 TYR cc_start: 0.7652 (m-80) cc_final: 0.7032 (m-80) REVERT: i 88 ARG cc_start: 0.8014 (mtm180) cc_final: 0.7193 (ttp-170) REVERT: j 25 PHE cc_start: 0.8835 (m-10) cc_final: 0.8525 (m-10) REVERT: j 47 MET cc_start: 0.8576 (ppp) cc_final: 0.8331 (ppp) REVERT: j 55 SER cc_start: 0.8612 (OUTLIER) cc_final: 0.8174 (p) REVERT: j 123 GLN cc_start: 0.8338 (mt0) cc_final: 0.7917 (mt0) REVERT: k 25 PHE cc_start: 0.8737 (m-80) cc_final: 0.8385 (m-80) REVERT: k 32 TYR cc_start: 0.7552 (t80) cc_final: 0.7338 (t80) REVERT: k 41 ILE cc_start: 0.8842 (mm) cc_final: 0.8617 (pt) REVERT: k 44 MET cc_start: 0.4856 (mmm) cc_final: 0.4166 (mmt) REVERT: k 47 MET cc_start: 0.6213 (OUTLIER) cc_final: 0.4764 (ttp) REVERT: k 78 ASN cc_start: 0.8270 (m-40) cc_final: 0.7590 (t0) REVERT: k 131 MET cc_start: 0.6707 (ppp) cc_final: 0.6493 (ppp) REVERT: l 13 PHE cc_start: 0.8536 (OUTLIER) cc_final: 0.7994 (m-80) REVERT: l 23 MET cc_start: 0.7214 (tpt) cc_final: 0.6780 (tpt) REVERT: l 44 MET cc_start: 0.6839 (mmm) cc_final: 0.6366 (mmm) REVERT: l 131 MET cc_start: 0.4977 (ptt) cc_final: 0.4403 (ppp) REVERT: m 47 MET cc_start: 0.5941 (OUTLIER) cc_final: 0.5647 (mmp) REVERT: m 104 LEU cc_start: 0.9410 (mt) cc_final: 0.9113 (mt) REVERT: m 141 LEU cc_start: 0.7591 (OUTLIER) cc_final: 0.6916 (tp) REVERT: n 44 MET cc_start: 0.5810 (tpt) cc_final: 0.5404 (tpt) REVERT: n 134 ILE cc_start: 0.9018 (OUTLIER) cc_final: 0.8515 (tp) REVERT: o 17 MET cc_start: 0.8778 (mtp) cc_final: 0.8493 (mtp) REVERT: p 312 TRP cc_start: 0.8347 (m100) cc_final: 0.7547 (m100) REVERT: p 330 ASN cc_start: 0.8983 (m-40) cc_final: 0.8638 (m110) REVERT: p 338 ILE cc_start: 0.8021 (pt) cc_final: 0.7378 (pp) REVERT: p 342 MET cc_start: 0.7227 (mmt) cc_final: 0.6966 (mmm) outliers start: 216 outliers final: 147 residues processed: 1014 average time/residue: 0.5516 time to fit residues: 979.3239 Evaluate side-chains 967 residues out of total 7117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 806 time to evaluate : 5.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 HIS Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 584 MET Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 607 ASP Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 450 TRP Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 505 ASP Chi-restraints excluded: chain B residue 584 MET Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 371 ASP Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 394 CYS Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 482 ILE Chi-restraints excluded: chain C residue 544 MET Chi-restraints excluded: chain C residue 545 ILE Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 207 CYS Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 334 ILE Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 448 ASP Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 330 ASP Chi-restraints excluded: chain E residue 336 GLU Chi-restraints excluded: chain E residue 360 ASP Chi-restraints excluded: chain E residue 431 ASP Chi-restraints excluded: chain E residue 448 ASP Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 207 CYS Chi-restraints excluded: chain F residue 257 VAL Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 365 ILE Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain H residue 38 ASP Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 74 PHE Chi-restraints excluded: chain H residue 109 PHE Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain I residue 208 MET Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain K residue 152 ILE Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 42 ASP Chi-restraints excluded: chain M residue 74 GLU Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain N residue 82 GLN Chi-restraints excluded: chain N residue 106 VAL Chi-restraints excluded: chain O residue 96 LEU Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 52 VAL Chi-restraints excluded: chain Q residue 88 LEU Chi-restraints excluded: chain Q residue 95 VAL Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 133 LEU Chi-restraints excluded: chain Q residue 134 ASN Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain S residue 65 ILE Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 197 TYR Chi-restraints excluded: chain S residue 198 HIS Chi-restraints excluded: chain b residue 100 VAL Chi-restraints excluded: chain b residue 103 TYR Chi-restraints excluded: chain b residue 122 ASP Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain b residue 177 LEU Chi-restraints excluded: chain c residue 414 PHE Chi-restraints excluded: chain c residue 430 LEU Chi-restraints excluded: chain c residue 438 HIS Chi-restraints excluded: chain c residue 448 ARG Chi-restraints excluded: chain d residue 6 GLU Chi-restraints excluded: chain d residue 13 ASN Chi-restraints excluded: chain d residue 63 SER Chi-restraints excluded: chain d residue 70 ILE Chi-restraints excluded: chain d residue 168 ILE Chi-restraints excluded: chain d residue 173 LEU Chi-restraints excluded: chain d residue 183 ASN Chi-restraints excluded: chain d residue 233 SER Chi-restraints excluded: chain d residue 244 CYS Chi-restraints excluded: chain g residue 34 THR Chi-restraints excluded: chain g residue 61 MET Chi-restraints excluded: chain g residue 84 ILE Chi-restraints excluded: chain g residue 141 LEU Chi-restraints excluded: chain h residue 108 PHE Chi-restraints excluded: chain h residue 143 LEU Chi-restraints excluded: chain i residue 60 VAL Chi-restraints excluded: chain i residue 108 PHE Chi-restraints excluded: chain i residue 140 VAL Chi-restraints excluded: chain j residue 55 SER Chi-restraints excluded: chain j residue 71 VAL Chi-restraints excluded: chain k residue 47 MET Chi-restraints excluded: chain k residue 85 THR Chi-restraints excluded: chain l residue 13 PHE Chi-restraints excluded: chain l residue 54 LYS Chi-restraints excluded: chain l residue 61 MET Chi-restraints excluded: chain l residue 140 VAL Chi-restraints excluded: chain m residue 47 MET Chi-restraints excluded: chain m residue 93 LEU Chi-restraints excluded: chain m residue 121 THR Chi-restraints excluded: chain m residue 133 LEU Chi-restraints excluded: chain m residue 140 VAL Chi-restraints excluded: chain m residue 141 LEU Chi-restraints excluded: chain n residue 104 LEU Chi-restraints excluded: chain n residue 121 THR Chi-restraints excluded: chain n residue 134 ILE Chi-restraints excluded: chain n residue 140 VAL Chi-restraints excluded: chain o residue 13 PHE Chi-restraints excluded: chain o residue 21 SER Chi-restraints excluded: chain o residue 123 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 836 random chunks: chunk 271 optimal weight: 4.9990 chunk 727 optimal weight: 30.0000 chunk 159 optimal weight: 0.3980 chunk 474 optimal weight: 30.0000 chunk 199 optimal weight: 0.8980 chunk 808 optimal weight: 40.0000 chunk 671 optimal weight: 0.8980 chunk 374 optimal weight: 50.0000 chunk 67 optimal weight: 0.8980 chunk 267 optimal weight: 6.9990 chunk 424 optimal weight: 4.9990 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 543 ASN ** F 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 GLN H 137 ASN ** I 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 113 ASN O 75 GLN R 21 GLN R 134 ASN ** b 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.5119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 61638 Z= 0.211 Angle : 0.697 15.002 83673 Z= 0.348 Chirality : 0.045 0.317 9871 Planarity : 0.004 0.062 10900 Dihedral : 4.653 126.627 9025 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.87 % Favored : 97.11 % Rotamer: Outliers : 2.64 % Allowed : 16.32 % Favored : 81.04 % 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: 1.67 (0.09), residues: 8369 helix: 2.12 (0.07), residues: 4962 sheet: -0.36 (0.20), residues: 670 loop : -0.37 (0.12), residues: 2737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 567 HIS 0.006 0.001 HIS b 128 PHE 0.067 0.002 PHE m 25 TYR 0.043 0.002 TYR b 103 ARG 0.014 0.001 ARG L 53 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16738 Ramachandran restraints generated. 8369 Oldfield, 0 Emsley, 8369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16738 Ramachandran restraints generated. 8369 Oldfield, 0 Emsley, 8369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1101 residues out of total 7117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 952 time to evaluate : 5.411 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: A 61 MET cc_start: 0.8899 (tpp) cc_final: 0.8696 (mmm) REVERT: A 164 HIS cc_start: 0.9049 (OUTLIER) cc_final: 0.8762 (t70) REVERT: A 173 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.7347 (pmt100) REVERT: A 318 MET cc_start: 0.9260 (mtt) cc_final: 0.8772 (mtp) REVERT: A 491 GLU cc_start: 0.9004 (tt0) cc_final: 0.8770 (tm-30) REVERT: A 510 GLU cc_start: 0.8633 (tm-30) cc_final: 0.8306 (tm-30) REVERT: A 516 LYS cc_start: 0.9451 (mttt) cc_final: 0.9097 (tttm) REVERT: A 540 MET cc_start: 0.8790 (ppp) cc_final: 0.8109 (ppp) REVERT: A 544 MET cc_start: 0.8905 (mtp) cc_final: 0.8143 (mtp) REVERT: B 95 MET cc_start: 0.9034 (tpp) cc_final: 0.8731 (tpp) REVERT: B 306 MET cc_start: 0.8599 (ptm) cc_final: 0.8144 (tmm) REVERT: B 318 MET cc_start: 0.9249 (tpp) cc_final: 0.9012 (mmm) REVERT: B 356 GLU cc_start: 0.9175 (tp30) cc_final: 0.8751 (tp30) REVERT: B 368 MET cc_start: 0.9062 (mmm) cc_final: 0.8709 (ttm) REVERT: B 381 ARG cc_start: 0.9137 (mmt-90) cc_final: 0.8843 (mmm-85) REVERT: B 426 LEU cc_start: 0.9397 (OUTLIER) cc_final: 0.9180 (mm) REVERT: B 432 PHE cc_start: 0.8763 (t80) cc_final: 0.8322 (t80) REVERT: B 458 MET cc_start: 0.8750 (mmt) cc_final: 0.8276 (mmt) REVERT: B 584 MET cc_start: 0.8864 (OUTLIER) cc_final: 0.8468 (mpp) REVERT: C 227 LEU cc_start: 0.9110 (tp) cc_final: 0.8873 (tp) REVERT: C 399 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7536 (mm-30) REVERT: C 540 MET cc_start: 0.8865 (mmm) cc_final: 0.8566 (mmm) REVERT: C 544 MET cc_start: 0.9235 (OUTLIER) cc_final: 0.9033 (tpp) REVERT: D 169 MET cc_start: 0.8688 (tmm) cc_final: 0.8252 (tmm) REVERT: D 254 MET cc_start: 0.8597 (tpp) cc_final: 0.8120 (mmm) REVERT: D 270 GLU cc_start: 0.8741 (mt-10) cc_final: 0.8207 (tt0) REVERT: D 484 LEU cc_start: 0.9744 (mt) cc_final: 0.9503 (mt) REVERT: D 495 ILE cc_start: 0.9435 (mt) cc_final: 0.9185 (tt) REVERT: E 154 MET cc_start: 0.9458 (tpt) cc_final: 0.9248 (mmm) REVERT: E 254 MET cc_start: 0.8488 (mmm) cc_final: 0.8148 (mmm) REVERT: E 270 GLU cc_start: 0.9034 (tt0) cc_final: 0.8594 (tm-30) REVERT: E 309 GLU cc_start: 0.8784 (tm-30) cc_final: 0.8388 (tm-30) REVERT: E 316 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7718 (mt-10) REVERT: E 330 ASP cc_start: 0.9356 (OUTLIER) cc_final: 0.8867 (t70) REVERT: E 356 MET cc_start: 0.8756 (mtm) cc_final: 0.8405 (mtm) REVERT: E 491 MET cc_start: 0.8937 (mpp) cc_final: 0.8692 (pmm) REVERT: F 153 ILE cc_start: 0.9113 (pp) cc_final: 0.8866 (tt) REVERT: F 169 MET cc_start: 0.8868 (tmm) cc_final: 0.8527 (tmm) REVERT: F 180 MET cc_start: 0.8696 (mmm) cc_final: 0.8334 (mmm) REVERT: F 183 ILE cc_start: 0.9683 (mt) cc_final: 0.9243 (pt) REVERT: F 187 GLN cc_start: 0.9134 (pp30) cc_final: 0.8772 (pp30) REVERT: F 238 MET cc_start: 0.9182 (tpp) cc_final: 0.8946 (mmm) REVERT: F 309 GLU cc_start: 0.9127 (tm-30) cc_final: 0.8787 (tm-30) REVERT: F 351 ILE cc_start: 0.9526 (mt) cc_final: 0.9289 (mm) REVERT: F 356 MET cc_start: 0.8935 (mtm) cc_final: 0.8586 (mtm) REVERT: F 402 MET cc_start: 0.9201 (mmm) cc_final: 0.8904 (mmm) REVERT: F 410 MET cc_start: 0.8298 (mtp) cc_final: 0.7907 (mtp) REVERT: F 435 MET cc_start: 0.9252 (tpp) cc_final: 0.8791 (tpt) REVERT: F 491 MET cc_start: 0.8747 (mtp) cc_final: 0.8461 (ptp) REVERT: F 492 LEU cc_start: 0.9500 (mt) cc_final: 0.9121 (mp) REVERT: H 31 ASN cc_start: 0.9369 (m-40) cc_final: 0.9043 (m110) REVERT: H 79 PHE cc_start: 0.9497 (p90) cc_final: 0.9133 (p90) REVERT: H 91 GLN cc_start: 0.9341 (pt0) cc_final: 0.9010 (pm20) REVERT: H 190 GLU cc_start: 0.9279 (mm-30) cc_final: 0.9028 (mm-30) REVERT: H 193 GLU cc_start: 0.9346 (tm-30) cc_final: 0.8901 (tm-30) REVERT: I 72 MET cc_start: 0.9310 (mmm) cc_final: 0.9022 (mmm) REVERT: I 182 GLU cc_start: 0.7794 (pt0) cc_final: 0.7471 (pt0) REVERT: I 207 MET cc_start: 0.9491 (mmt) cc_final: 0.9149 (mmm) REVERT: J 72 MET cc_start: 0.9213 (ppp) cc_final: 0.8903 (ppp) REVERT: J 76 MET cc_start: 0.8883 (mmm) cc_final: 0.8670 (mmm) REVERT: J 196 LEU cc_start: 0.9619 (OUTLIER) cc_final: 0.9309 (pp) REVERT: J 207 MET cc_start: 0.9285 (mmp) cc_final: 0.8867 (mmp) REVERT: K 129 GLU cc_start: 0.8203 (tt0) cc_final: 0.7458 (tt0) REVERT: K 132 MET cc_start: 0.8074 (mmm) cc_final: 0.7334 (mmm) REVERT: K 154 MET cc_start: 0.9524 (mtt) cc_final: 0.9254 (ptp) REVERT: K 184 TYR cc_start: 0.8606 (m-80) cc_final: 0.8154 (m-10) REVERT: K 207 MET cc_start: 0.8708 (tpp) cc_final: 0.8217 (tpp) REVERT: K 208 MET cc_start: 0.9519 (tpp) cc_final: 0.9113 (tpp) REVERT: L 22 LEU cc_start: 0.9647 (mt) cc_final: 0.9445 (tp) REVERT: L 27 GLU cc_start: 0.9170 (pt0) cc_final: 0.8758 (pt0) REVERT: L 33 HIS cc_start: 0.8683 (m170) cc_final: 0.8311 (m-70) REVERT: L 46 ASN cc_start: 0.9557 (m-40) cc_final: 0.9345 (t0) REVERT: L 47 GLU cc_start: 0.9210 (mt-10) cc_final: 0.8949 (mm-30) REVERT: L 53 ARG cc_start: 0.9137 (ptp90) cc_final: 0.8881 (ptp-170) REVERT: M 99 LEU cc_start: 0.9786 (tp) cc_final: 0.9437 (tt) REVERT: M 102 MET cc_start: 0.9481 (mpp) cc_final: 0.9109 (mpp) REVERT: N 84 MET cc_start: 0.9046 (mtm) cc_final: 0.8668 (ptp) REVERT: O 84 MET cc_start: 0.9065 (mmm) cc_final: 0.8844 (mmm) REVERT: Q 33 MET cc_start: 0.8903 (tmm) cc_final: 0.8456 (tmm) REVERT: Q 66 LEU cc_start: 0.9591 (tp) cc_final: 0.9321 (tt) REVERT: Q 188 MET cc_start: 0.8699 (mmm) cc_final: 0.8442 (mmm) REVERT: Q 234 MET cc_start: 0.8972 (tmm) cc_final: 0.8713 (tmm) REVERT: R 33 MET cc_start: 0.9067 (tmm) cc_final: 0.8822 (tmm) REVERT: R 109 GLU cc_start: 0.9097 (mt-10) cc_final: 0.8828 (pp20) REVERT: R 130 LEU cc_start: 0.9378 (mt) cc_final: 0.9107 (tp) REVERT: S 152 LEU cc_start: 0.8962 (mt) cc_final: 0.8694 (mt) REVERT: S 197 TYR cc_start: 0.7449 (OUTLIER) cc_final: 0.6795 (m-80) REVERT: b 19 MET cc_start: 0.7688 (tmm) cc_final: 0.7404 (ppp) REVERT: b 157 ILE cc_start: 0.9122 (mt) cc_final: 0.8870 (mm) REVERT: b 177 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.7913 (tp) REVERT: c 441 LEU cc_start: 0.9260 (mm) cc_final: 0.9036 (mt) REVERT: d 10 ASN cc_start: 0.9089 (m-40) cc_final: 0.8779 (t0) REVERT: d 152 ASN cc_start: 0.9433 (m-40) cc_final: 0.9090 (t0) REVERT: d 197 CYS cc_start: 0.9395 (m) cc_final: 0.9190 (p) REVERT: d 334 GLU cc_start: 0.9001 (mt-10) cc_final: 0.8563 (pt0) REVERT: d 350 ILE cc_start: 0.7643 (pt) cc_final: 0.7315 (mm) REVERT: g 37 SER cc_start: 0.8566 (m) cc_final: 0.8325 (p) REVERT: g 53 MET cc_start: 0.8538 (ptt) cc_final: 0.7903 (pmm) REVERT: g 108 PHE cc_start: 0.9175 (m-10) cc_final: 0.8904 (m-10) REVERT: h 53 MET cc_start: 0.8411 (pmm) cc_final: 0.8012 (pmm) REVERT: i 13 PHE cc_start: 0.8670 (t80) cc_final: 0.8341 (t80) REVERT: i 47 MET cc_start: 0.8554 (ptm) cc_final: 0.8130 (ppp) REVERT: i 61 MET cc_start: 0.5866 (ptp) cc_final: 0.5504 (ptp) REVERT: i 68 TYR cc_start: 0.7554 (m-80) cc_final: 0.7127 (m-80) REVERT: i 88 ARG cc_start: 0.8170 (mtm180) cc_final: 0.7394 (ttp-170) REVERT: j 44 MET cc_start: 0.6791 (mmm) cc_final: 0.6427 (mmm) REVERT: j 48 ARG cc_start: 0.8893 (mtt-85) cc_final: 0.8629 (mtm180) REVERT: j 55 SER cc_start: 0.8520 (OUTLIER) cc_final: 0.8076 (p) REVERT: k 25 PHE cc_start: 0.8698 (m-80) cc_final: 0.8334 (m-80) REVERT: k 32 TYR cc_start: 0.7555 (t80) cc_final: 0.7349 (t80) REVERT: k 78 ASN cc_start: 0.8199 (m-40) cc_final: 0.7513 (t0) REVERT: l 13 PHE cc_start: 0.8450 (OUTLIER) cc_final: 0.8002 (m-80) REVERT: l 23 MET cc_start: 0.7118 (tpt) cc_final: 0.6742 (tpt) REVERT: l 47 MET cc_start: 0.6078 (ttt) cc_final: 0.5377 (ptm) REVERT: l 131 MET cc_start: 0.4718 (ptt) cc_final: 0.4316 (ppp) REVERT: m 104 LEU cc_start: 0.9429 (mt) cc_final: 0.9160 (mt) REVERT: m 141 LEU cc_start: 0.7625 (OUTLIER) cc_final: 0.6923 (tp) REVERT: n 68 TYR cc_start: 0.7390 (m-10) cc_final: 0.6857 (m-10) REVERT: o 17 MET cc_start: 0.8793 (mtp) cc_final: 0.8583 (mtp) REVERT: o 47 MET cc_start: 0.8612 (ppp) cc_final: 0.8273 (ppp) REVERT: o 131 MET cc_start: 0.8207 (ppp) cc_final: 0.7950 (ppp) REVERT: o 143 LEU cc_start: 0.8804 (mm) cc_final: 0.8542 (pp) REVERT: p 312 TRP cc_start: 0.8300 (m100) cc_final: 0.7428 (m100) REVERT: p 330 ASN cc_start: 0.8948 (m-40) cc_final: 0.8591 (m110) REVERT: p 338 ILE cc_start: 0.7942 (pt) cc_final: 0.7435 (pp) REVERT: p 342 MET cc_start: 0.7142 (mmt) cc_final: 0.6218 (mmm) outliers start: 149 outliers final: 91 residues processed: 1041 average time/residue: 0.5295 time to fit residues: 964.0346 Evaluate side-chains 972 residues out of total 7117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 869 time to evaluate : 5.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 HIS Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 584 MET Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 450 TRP Chi-restraints excluded: chain B residue 584 MET Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 371 ASP Chi-restraints excluded: chain C residue 394 CYS Chi-restraints excluded: chain C residue 450 TRP Chi-restraints excluded: chain C residue 544 MET Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 334 ILE Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 330 ASP Chi-restraints excluded: chain E residue 336 GLU Chi-restraints excluded: chain E residue 360 ASP Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 365 ILE Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain H residue 38 ASP Chi-restraints excluded: chain H residue 74 PHE Chi-restraints excluded: chain H residue 109 PHE Chi-restraints excluded: chain I residue 128 LEU Chi-restraints excluded: chain I residue 208 MET Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 182 GLU Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain L residue 42 ASP Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain M residue 74 GLU Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain N residue 74 GLU Chi-restraints excluded: chain N residue 82 GLN Chi-restraints excluded: chain N residue 106 VAL Chi-restraints excluded: chain Q residue 52 VAL Chi-restraints excluded: chain Q residue 91 LEU Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 133 LEU Chi-restraints excluded: chain Q residue 134 ASN Chi-restraints excluded: chain R residue 134 ASN Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 197 TYR Chi-restraints excluded: chain S residue 198 HIS Chi-restraints excluded: chain b residue 177 LEU Chi-restraints excluded: chain c residue 430 LEU Chi-restraints excluded: chain c residue 438 HIS Chi-restraints excluded: chain c residue 448 ARG Chi-restraints excluded: chain d residue 6 GLU Chi-restraints excluded: chain d residue 63 SER Chi-restraints excluded: chain d residue 93 LEU Chi-restraints excluded: chain d residue 168 ILE Chi-restraints excluded: chain g residue 61 MET Chi-restraints excluded: chain g residue 84 ILE Chi-restraints excluded: chain g residue 141 LEU Chi-restraints excluded: chain g residue 143 LEU Chi-restraints excluded: chain h residue 108 PHE Chi-restraints excluded: chain i residue 60 VAL Chi-restraints excluded: chain i residue 70 LEU Chi-restraints excluded: chain j residue 55 SER Chi-restraints excluded: chain k residue 108 PHE Chi-restraints excluded: chain l residue 13 PHE Chi-restraints excluded: chain l residue 53 MET Chi-restraints excluded: chain l residue 54 LYS Chi-restraints excluded: chain l residue 140 VAL Chi-restraints excluded: chain m residue 93 LEU Chi-restraints excluded: chain m residue 121 THR Chi-restraints excluded: chain m residue 133 LEU Chi-restraints excluded: chain m residue 140 VAL Chi-restraints excluded: chain m residue 141 LEU Chi-restraints excluded: chain n residue 104 LEU Chi-restraints excluded: chain o residue 123 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 836 random chunks: chunk 779 optimal weight: 40.0000 chunk 91 optimal weight: 0.7980 chunk 460 optimal weight: 0.0970 chunk 590 optimal weight: 50.0000 chunk 457 optimal weight: 9.9990 chunk 680 optimal weight: 20.0000 chunk 451 optimal weight: 30.0000 chunk 805 optimal weight: 8.9990 chunk 504 optimal weight: 20.0000 chunk 491 optimal weight: 6.9990 chunk 372 optimal weight: 50.0000 overall best weight: 5.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 ASN ** I 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 71 GLN ** J 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 123 GLN ** m 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.5430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 61638 Z= 0.367 Angle : 0.760 16.550 83673 Z= 0.383 Chirality : 0.046 0.345 9871 Planarity : 0.005 0.057 10900 Dihedral : 4.726 128.317 9025 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 17.45 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.36 % Favored : 96.62 % Rotamer: Outliers : 2.73 % Allowed : 17.66 % Favored : 79.61 % 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: 1.51 (0.09), residues: 8369 helix: 2.01 (0.07), residues: 4986 sheet: -0.39 (0.20), residues: 661 loop : -0.50 (0.12), residues: 2722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 567 HIS 0.008 0.001 HIS Q 19 PHE 0.062 0.002 PHE h 25 TYR 0.055 0.002 TYR k 68 ARG 0.009 0.001 ARG L 32 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16738 Ramachandran restraints generated. 8369 Oldfield, 0 Emsley, 8369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16738 Ramachandran restraints generated. 8369 Oldfield, 0 Emsley, 8369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1014 residues out of total 7117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 860 time to evaluate : 5.371 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: A 39 MET cc_start: 0.8711 (tpp) cc_final: 0.8426 (tpp) REVERT: A 61 MET cc_start: 0.8977 (tpp) cc_final: 0.8768 (mmp) REVERT: A 164 HIS cc_start: 0.9091 (OUTLIER) cc_final: 0.8465 (t70) REVERT: A 167 MET cc_start: 0.9360 (mtm) cc_final: 0.8671 (mtt) REVERT: A 173 ARG cc_start: 0.8994 (OUTLIER) cc_final: 0.7531 (pmt100) REVERT: A 254 CYS cc_start: 0.8693 (m) cc_final: 0.7964 (m) REVERT: A 318 MET cc_start: 0.9276 (mtt) cc_final: 0.8777 (mtt) REVERT: A 346 MET cc_start: 0.9081 (ttt) cc_final: 0.8730 (ttm) REVERT: A 347 MET cc_start: 0.8134 (mtm) cc_final: 0.7628 (ttp) REVERT: A 491 GLU cc_start: 0.9051 (tt0) cc_final: 0.8751 (tm-30) REVERT: A 510 GLU cc_start: 0.8769 (tm-30) cc_final: 0.8425 (tm-30) REVERT: A 516 LYS cc_start: 0.9474 (mttt) cc_final: 0.9142 (tmtt) REVERT: A 518 ASP cc_start: 0.7480 (m-30) cc_final: 0.7220 (m-30) REVERT: B 95 MET cc_start: 0.9106 (tpp) cc_final: 0.8815 (tpp) REVERT: B 306 MET cc_start: 0.8705 (ptm) cc_final: 0.8282 (tmm) REVERT: B 318 MET cc_start: 0.9312 (tpp) cc_final: 0.8260 (mpp) REVERT: B 368 MET cc_start: 0.9068 (mmm) cc_final: 0.8657 (ttm) REVERT: B 432 PHE cc_start: 0.8921 (t80) cc_final: 0.8444 (t80) REVERT: B 458 MET cc_start: 0.8835 (mmt) cc_final: 0.8419 (mmt) REVERT: B 550 MET cc_start: 0.9186 (ptm) cc_final: 0.8909 (ptm) REVERT: B 584 MET cc_start: 0.8720 (OUTLIER) cc_final: 0.8425 (mpp) REVERT: C 458 MET cc_start: 0.8778 (mtp) cc_final: 0.8344 (mtt) REVERT: C 540 MET cc_start: 0.8919 (mmm) cc_final: 0.8706 (mmm) REVERT: C 544 MET cc_start: 0.9238 (OUTLIER) cc_final: 0.8980 (tpp) REVERT: C 550 MET cc_start: 0.9279 (mtt) cc_final: 0.9043 (mtp) REVERT: D 254 MET cc_start: 0.8595 (tpp) cc_final: 0.8082 (mmm) REVERT: D 270 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.8281 (tt0) REVERT: D 433 GLN cc_start: 0.9555 (tt0) cc_final: 0.9071 (tm-30) REVERT: D 484 LEU cc_start: 0.9760 (mt) cc_final: 0.9530 (mt) REVERT: D 495 ILE cc_start: 0.9428 (mt) cc_final: 0.9176 (tt) REVERT: E 148 GLU cc_start: 0.8560 (tt0) cc_final: 0.8152 (tm-30) REVERT: E 234 MET cc_start: 0.8869 (OUTLIER) cc_final: 0.8084 (pmm) REVERT: E 270 GLU cc_start: 0.9027 (tt0) cc_final: 0.8589 (pt0) REVERT: E 309 GLU cc_start: 0.8766 (tm-30) cc_final: 0.8390 (tm-30) REVERT: E 316 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7662 (mt-10) REVERT: E 330 ASP cc_start: 0.9422 (OUTLIER) cc_final: 0.8877 (t70) REVERT: E 356 MET cc_start: 0.8852 (mtm) cc_final: 0.8508 (mtm) REVERT: F 97 GLN cc_start: 0.8552 (tm-30) cc_final: 0.8332 (tm-30) REVERT: F 153 ILE cc_start: 0.9157 (pp) cc_final: 0.8902 (tt) REVERT: F 169 MET cc_start: 0.8942 (tmm) cc_final: 0.8567 (tmm) REVERT: F 180 MET cc_start: 0.8816 (mmm) cc_final: 0.8534 (mmm) REVERT: F 183 ILE cc_start: 0.9670 (mt) cc_final: 0.9233 (pt) REVERT: F 187 GLN cc_start: 0.9286 (pp30) cc_final: 0.8871 (pp30) REVERT: F 254 MET cc_start: 0.8778 (mmm) cc_final: 0.8069 (tpp) REVERT: F 299 ASP cc_start: 0.8230 (m-30) cc_final: 0.7622 (m-30) REVERT: F 309 GLU cc_start: 0.9197 (tm-30) cc_final: 0.8890 (tm-30) REVERT: F 356 MET cc_start: 0.9016 (mtm) cc_final: 0.8662 (mtm) REVERT: F 410 MET cc_start: 0.8439 (mtp) cc_final: 0.8047 (mtp) REVERT: F 435 MET cc_start: 0.9267 (tpp) cc_final: 0.8840 (tpt) REVERT: H 31 ASN cc_start: 0.9377 (m-40) cc_final: 0.9040 (m110) REVERT: H 79 PHE cc_start: 0.9550 (p90) cc_final: 0.9186 (p90) REVERT: H 91 GLN cc_start: 0.9348 (pt0) cc_final: 0.9048 (pm20) REVERT: H 190 GLU cc_start: 0.9310 (mm-30) cc_final: 0.8724 (tm-30) REVERT: H 193 GLU cc_start: 0.9390 (tm-30) cc_final: 0.8967 (tm-30) REVERT: I 72 MET cc_start: 0.9374 (mmm) cc_final: 0.9126 (mmm) REVERT: I 76 MET cc_start: 0.9356 (mpp) cc_final: 0.9116 (mpp) REVERT: I 182 GLU cc_start: 0.7707 (pt0) cc_final: 0.7320 (pt0) REVERT: I 207 MET cc_start: 0.9545 (mmt) cc_final: 0.9153 (mmm) REVERT: J 72 MET cc_start: 0.9300 (ppp) cc_final: 0.8782 (ppp) REVERT: J 76 MET cc_start: 0.8993 (mmm) cc_final: 0.8721 (mmm) REVERT: J 207 MET cc_start: 0.9375 (mmp) cc_final: 0.8984 (mmm) REVERT: J 208 MET cc_start: 0.9262 (mmm) cc_final: 0.8938 (mmt) REVERT: K 129 GLU cc_start: 0.8228 (tt0) cc_final: 0.7474 (tt0) REVERT: K 132 MET cc_start: 0.7794 (mmm) cc_final: 0.7326 (mmm) REVERT: K 154 MET cc_start: 0.9563 (mtt) cc_final: 0.9255 (ptp) REVERT: K 184 TYR cc_start: 0.8662 (m-80) cc_final: 0.8081 (m-10) REVERT: K 207 MET cc_start: 0.8780 (tpp) cc_final: 0.8276 (tpp) REVERT: L 27 GLU cc_start: 0.9246 (pt0) cc_final: 0.8833 (pt0) REVERT: L 33 HIS cc_start: 0.8716 (m170) cc_final: 0.8338 (m-70) REVERT: L 47 GLU cc_start: 0.9247 (mt-10) cc_final: 0.9006 (mm-30) REVERT: L 53 ARG cc_start: 0.9159 (ptp90) cc_final: 0.8864 (ptp-170) REVERT: M 99 LEU cc_start: 0.9752 (tp) cc_final: 0.9496 (tt) REVERT: M 102 MET cc_start: 0.9384 (mpp) cc_final: 0.9033 (mpp) REVERT: N 84 MET cc_start: 0.9113 (mtm) cc_final: 0.8667 (ptp) REVERT: Q 33 MET cc_start: 0.8942 (tmm) cc_final: 0.8471 (tmm) REVERT: Q 66 LEU cc_start: 0.9601 (tp) cc_final: 0.9350 (tt) REVERT: Q 188 MET cc_start: 0.8770 (mmm) cc_final: 0.8473 (mmm) REVERT: Q 234 MET cc_start: 0.8960 (tmm) cc_final: 0.8748 (tmm) REVERT: R 33 MET cc_start: 0.9071 (tmm) cc_final: 0.8832 (tmm) REVERT: R 109 GLU cc_start: 0.9159 (mt-10) cc_final: 0.8892 (pp20) REVERT: R 188 MET cc_start: 0.8487 (tpp) cc_final: 0.8213 (tpp) REVERT: S 33 MET cc_start: 0.8105 (tpt) cc_final: 0.7818 (tpt) REVERT: S 152 LEU cc_start: 0.9124 (mt) cc_final: 0.8870 (mt) REVERT: S 197 TYR cc_start: 0.7411 (OUTLIER) cc_final: 0.6753 (m-80) REVERT: b 19 MET cc_start: 0.7721 (tmm) cc_final: 0.7470 (ppp) REVERT: b 157 ILE cc_start: 0.9109 (mt) cc_final: 0.8878 (mm) REVERT: b 177 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.7942 (tp) REVERT: c 421 MET cc_start: 0.9006 (mtt) cc_final: 0.8380 (mmm) REVERT: c 441 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.9070 (mt) REVERT: c 449 PHE cc_start: 0.6738 (m-10) cc_final: 0.6473 (m-10) REVERT: d 10 ASN cc_start: 0.9134 (m-40) cc_final: 0.8877 (t0) REVERT: d 88 HIS cc_start: 0.8902 (m90) cc_final: 0.8624 (m90) REVERT: d 105 MET cc_start: 0.8973 (mmm) cc_final: 0.8475 (mmp) REVERT: d 152 ASN cc_start: 0.9447 (m-40) cc_final: 0.9108 (t0) REVERT: d 164 PHE cc_start: 0.9457 (m-80) cc_final: 0.9138 (m-80) REVERT: d 197 CYS cc_start: 0.9424 (m) cc_final: 0.9155 (p) REVERT: d 325 GLU cc_start: 0.9461 (tt0) cc_final: 0.9017 (tm-30) REVERT: d 334 GLU cc_start: 0.9038 (mt-10) cc_final: 0.8603 (pt0) REVERT: d 350 ILE cc_start: 0.7967 (pt) cc_final: 0.7577 (mm) REVERT: g 53 MET cc_start: 0.8460 (ptt) cc_final: 0.7753 (pmm) REVERT: g 108 PHE cc_start: 0.9210 (m-10) cc_final: 0.8962 (m-10) REVERT: g 131 MET cc_start: 0.8748 (ppp) cc_final: 0.8525 (ppp) REVERT: i 13 PHE cc_start: 0.8689 (t80) cc_final: 0.8481 (t80) REVERT: i 47 MET cc_start: 0.8503 (ptm) cc_final: 0.8040 (ppp) REVERT: i 61 MET cc_start: 0.6010 (ptp) cc_final: 0.5634 (ptp) REVERT: i 68 TYR cc_start: 0.7529 (m-10) cc_final: 0.7115 (m-80) REVERT: i 88 ARG cc_start: 0.8137 (mtm180) cc_final: 0.7226 (ttp-170) REVERT: j 28 MET cc_start: 0.7757 (mmp) cc_final: 0.7500 (mmt) REVERT: j 55 SER cc_start: 0.8605 (OUTLIER) cc_final: 0.8198 (p) REVERT: k 25 PHE cc_start: 0.8706 (m-80) cc_final: 0.8361 (m-80) REVERT: k 44 MET cc_start: 0.3851 (mmm) cc_final: 0.2893 (mmt) REVERT: k 47 MET cc_start: 0.6592 (ppp) cc_final: 0.6337 (ppp) REVERT: k 61 MET cc_start: 0.6254 (ptp) cc_final: 0.5973 (ptp) REVERT: k 78 ASN cc_start: 0.8217 (m-40) cc_final: 0.7550 (t0) REVERT: k 131 MET cc_start: 0.6710 (ppp) cc_final: 0.6456 (ppp) REVERT: l 13 PHE cc_start: 0.8496 (OUTLIER) cc_final: 0.8104 (m-80) REVERT: l 23 MET cc_start: 0.7107 (tpt) cc_final: 0.6667 (tpt) REVERT: l 44 MET cc_start: 0.6709 (mmm) cc_final: 0.6254 (mtt) REVERT: l 131 MET cc_start: 0.5023 (ptt) cc_final: 0.4510 (ppp) REVERT: l 139 GLU cc_start: 0.7061 (mm-30) cc_final: 0.6686 (mm-30) REVERT: m 32 TYR cc_start: 0.6357 (t80) cc_final: 0.6087 (t80) REVERT: m 104 LEU cc_start: 0.9433 (mt) cc_final: 0.9150 (mt) REVERT: m 141 LEU cc_start: 0.7634 (OUTLIER) cc_final: 0.6931 (tp) REVERT: n 45 SER cc_start: 0.8807 (m) cc_final: 0.8385 (t) REVERT: n 47 MET cc_start: 0.8201 (ttp) cc_final: 0.7722 (ptp) REVERT: n 134 ILE cc_start: 0.8993 (OUTLIER) cc_final: 0.8501 (tp) REVERT: o 17 MET cc_start: 0.8808 (mtp) cc_final: 0.8553 (mtp) REVERT: o 47 MET cc_start: 0.8572 (ppp) cc_final: 0.8235 (ppp) REVERT: o 131 MET cc_start: 0.8265 (ppp) cc_final: 0.7949 (ppp) REVERT: p 330 ASN cc_start: 0.8932 (m-40) cc_final: 0.8586 (m110) outliers start: 154 outliers final: 116 residues processed: 953 average time/residue: 0.5354 time to fit residues: 899.8934 Evaluate side-chains 961 residues out of total 7117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 831 time to evaluate : 5.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 164 HIS Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 584 MET Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 607 ASP Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 450 TRP Chi-restraints excluded: chain B residue 584 MET Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 371 ASP Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 394 CYS Chi-restraints excluded: chain C residue 450 TRP Chi-restraints excluded: chain C residue 544 MET Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 234 MET 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 279 LEU Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 330 ASP Chi-restraints excluded: chain E residue 336 GLU Chi-restraints excluded: chain E residue 360 ASP Chi-restraints excluded: chain E residue 410 MET Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 229 ILE Chi-restraints excluded: chain F residue 257 VAL Chi-restraints excluded: chain F residue 365 ILE Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain H residue 38 ASP Chi-restraints excluded: chain H residue 74 PHE Chi-restraints excluded: chain H residue 109 PHE Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain I residue 128 LEU Chi-restraints excluded: chain I residue 208 MET Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 182 GLU Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain K residue 152 ILE Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain M residue 74 GLU Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain N residue 82 GLN Chi-restraints excluded: chain N residue 106 VAL Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 52 VAL Chi-restraints excluded: chain Q residue 91 LEU Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 133 LEU Chi-restraints excluded: chain Q residue 134 ASN Chi-restraints excluded: chain R residue 79 ASP Chi-restraints excluded: chain R residue 125 ASP Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 197 TYR Chi-restraints excluded: chain S residue 198 HIS Chi-restraints excluded: chain b residue 103 TYR Chi-restraints excluded: chain b residue 177 LEU Chi-restraints excluded: chain c residue 430 LEU Chi-restraints excluded: chain c residue 438 HIS Chi-restraints excluded: chain c residue 441 LEU Chi-restraints excluded: chain c residue 448 ARG Chi-restraints excluded: chain d residue 6 GLU Chi-restraints excluded: chain d residue 63 SER Chi-restraints excluded: chain d residue 93 LEU Chi-restraints excluded: chain d residue 168 ILE Chi-restraints excluded: chain d residue 173 LEU Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain d residue 233 SER Chi-restraints excluded: chain d residue 315 PHE Chi-restraints excluded: chain g residue 34 THR Chi-restraints excluded: chain g residue 61 MET Chi-restraints excluded: chain g residue 84 ILE Chi-restraints excluded: chain g residue 141 LEU Chi-restraints excluded: chain g residue 143 LEU Chi-restraints excluded: chain h residue 108 PHE Chi-restraints excluded: chain i residue 60 VAL Chi-restraints excluded: chain i residue 70 LEU Chi-restraints excluded: chain j residue 55 SER Chi-restraints excluded: chain k residue 108 PHE Chi-restraints excluded: chain l residue 13 PHE Chi-restraints excluded: chain l residue 54 LYS Chi-restraints excluded: chain l residue 61 MET Chi-restraints excluded: chain l residue 140 VAL Chi-restraints excluded: chain m residue 93 LEU Chi-restraints excluded: chain m residue 133 LEU Chi-restraints excluded: chain m residue 140 VAL Chi-restraints excluded: chain m residue 141 LEU Chi-restraints excluded: chain n residue 104 LEU Chi-restraints excluded: chain n residue 134 ILE Chi-restraints excluded: chain o residue 13 PHE Chi-restraints excluded: chain o residue 21 SER Chi-restraints excluded: chain o residue 123 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 836 random chunks: chunk 498 optimal weight: 3.9990 chunk 321 optimal weight: 30.0000 chunk 481 optimal weight: 6.9990 chunk 242 optimal weight: 0.6980 chunk 158 optimal weight: 10.0000 chunk 156 optimal weight: 1.9990 chunk 512 optimal weight: 10.0000 chunk 548 optimal weight: 50.0000 chunk 398 optimal weight: 8.9990 chunk 75 optimal weight: 10.0000 chunk 633 optimal weight: 0.8980 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.5554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 61638 Z= 0.258 Angle : 0.738 17.482 83673 Z= 0.368 Chirality : 0.046 0.402 9871 Planarity : 0.004 0.055 10900 Dihedral : 4.669 128.533 9025 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.07 % Favored : 96.89 % Rotamer: Outliers : 2.71 % Allowed : 18.39 % Favored : 78.90 % 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: 1.53 (0.09), residues: 8369 helix: 2.01 (0.07), residues: 4998 sheet: -0.37 (0.20), residues: 668 loop : -0.48 (0.12), residues: 2703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 567 HIS 0.005 0.001 HIS b 128 PHE 0.063 0.002 PHE h 25 TYR 0.051 0.002 TYR b 103 ARG 0.009 0.001 ARG M 79 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16738 Ramachandran restraints generated. 8369 Oldfield, 0 Emsley, 8369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16738 Ramachandran restraints generated. 8369 Oldfield, 0 Emsley, 8369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1057 residues out of total 7117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 904 time to evaluate : 5.357 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: A 39 MET cc_start: 0.8702 (tpp) cc_final: 0.8472 (tpp) REVERT: A 164 HIS cc_start: 0.9011 (OUTLIER) cc_final: 0.8666 (t70) REVERT: A 167 MET cc_start: 0.9225 (mtm) cc_final: 0.8674 (mtt) REVERT: A 173 ARG cc_start: 0.8922 (OUTLIER) cc_final: 0.7342 (pmt100) REVERT: A 318 MET cc_start: 0.9291 (mtt) cc_final: 0.8800 (mtt) REVERT: A 368 MET cc_start: 0.9415 (tpt) cc_final: 0.8946 (tpp) REVERT: A 387 GLU cc_start: 0.8822 (tm-30) cc_final: 0.8611 (tm-30) REVERT: A 491 GLU cc_start: 0.9031 (tt0) cc_final: 0.8809 (tm-30) REVERT: A 510 GLU cc_start: 0.8660 (tm-30) cc_final: 0.8339 (tm-30) REVERT: A 516 LYS cc_start: 0.9346 (mttt) cc_final: 0.9115 (tmtt) REVERT: A 517 ASP cc_start: 0.8854 (p0) cc_final: 0.8555 (p0) REVERT: B 95 MET cc_start: 0.9138 (tpp) cc_final: 0.8846 (tpp) REVERT: B 306 MET cc_start: 0.8672 (ptm) cc_final: 0.8254 (tmm) REVERT: B 318 MET cc_start: 0.9260 (tpp) cc_final: 0.8198 (mpp) REVERT: B 368 MET cc_start: 0.9033 (mmm) cc_final: 0.8654 (ttm) REVERT: B 381 ARG cc_start: 0.9196 (mmt-90) cc_final: 0.8861 (mmm-85) REVERT: B 432 PHE cc_start: 0.8836 (t80) cc_final: 0.8326 (t80) REVERT: B 458 MET cc_start: 0.8779 (mmt) cc_final: 0.8323 (mmt) REVERT: B 544 MET cc_start: 0.9024 (mtp) cc_final: 0.8727 (mmm) REVERT: B 550 MET cc_start: 0.9116 (ptm) cc_final: 0.8898 (ptm) REVERT: B 584 MET cc_start: 0.8659 (OUTLIER) cc_final: 0.8320 (mpp) REVERT: B 606 GLU cc_start: 0.9211 (mt-10) cc_final: 0.8896 (mt-10) REVERT: C 69 GLU cc_start: 0.8500 (tp30) cc_final: 0.8223 (tp30) REVERT: C 318 MET cc_start: 0.9363 (mmm) cc_final: 0.9132 (mmm) REVERT: C 458 MET cc_start: 0.8783 (mtp) cc_final: 0.8384 (mtt) REVERT: C 540 MET cc_start: 0.8888 (mmm) cc_final: 0.8663 (mmm) REVERT: C 544 MET cc_start: 0.9215 (OUTLIER) cc_final: 0.8980 (tpp) REVERT: C 550 MET cc_start: 0.9295 (mtt) cc_final: 0.9034 (mtp) REVERT: D 254 MET cc_start: 0.8569 (tpp) cc_final: 0.8090 (mmm) REVERT: D 270 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8253 (tt0) REVERT: D 433 GLN cc_start: 0.9539 (tt0) cc_final: 0.9081 (tm-30) REVERT: D 495 ILE cc_start: 0.9386 (mt) cc_final: 0.9174 (tt) REVERT: E 148 GLU cc_start: 0.8579 (tt0) cc_final: 0.8121 (tm-30) REVERT: E 234 MET cc_start: 0.8732 (OUTLIER) cc_final: 0.7913 (pmm) REVERT: E 270 GLU cc_start: 0.9040 (tt0) cc_final: 0.8598 (pt0) REVERT: E 309 GLU cc_start: 0.8809 (tm-30) cc_final: 0.8424 (tm-30) REVERT: E 316 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7837 (mt-10) REVERT: E 330 ASP cc_start: 0.9376 (OUTLIER) cc_final: 0.8874 (t70) REVERT: E 356 MET cc_start: 0.8792 (mtm) cc_final: 0.8475 (mtm) REVERT: E 449 LEU cc_start: 0.9267 (mt) cc_final: 0.8920 (mt) REVERT: E 491 MET cc_start: 0.8891 (mpp) cc_final: 0.8682 (pmm) REVERT: F 97 GLN cc_start: 0.8506 (tm-30) cc_final: 0.8277 (tm-30) REVERT: F 153 ILE cc_start: 0.9123 (pp) cc_final: 0.8874 (tt) REVERT: F 169 MET cc_start: 0.8919 (tmm) cc_final: 0.8548 (tmm) REVERT: F 180 MET cc_start: 0.8772 (mmm) cc_final: 0.8430 (mmm) REVERT: F 183 ILE cc_start: 0.9675 (mt) cc_final: 0.9299 (pt) REVERT: F 187 GLN cc_start: 0.9117 (pp30) cc_final: 0.8782 (pp30) REVERT: F 254 MET cc_start: 0.8730 (mmm) cc_final: 0.8068 (tpp) REVERT: F 309 GLU cc_start: 0.9148 (tm-30) cc_final: 0.8823 (tm-30) REVERT: F 356 MET cc_start: 0.9007 (mtm) cc_final: 0.8655 (mtm) REVERT: F 402 MET cc_start: 0.9253 (mmm) cc_final: 0.8924 (mmm) REVERT: F 410 MET cc_start: 0.8372 (mtp) cc_final: 0.8049 (mtp) REVERT: F 435 MET cc_start: 0.9257 (tpp) cc_final: 0.8873 (tpp) REVERT: F 491 MET cc_start: 0.8792 (mtp) cc_final: 0.8483 (ptp) REVERT: F 492 LEU cc_start: 0.9512 (mt) cc_final: 0.9032 (mp) REVERT: H 31 ASN cc_start: 0.9367 (m-40) cc_final: 0.9014 (m110) REVERT: H 79 PHE cc_start: 0.9525 (p90) cc_final: 0.9143 (p90) REVERT: H 193 GLU cc_start: 0.9353 (tm-30) cc_final: 0.8933 (tm-30) REVERT: I 72 MET cc_start: 0.9392 (mmm) cc_final: 0.9126 (mmm) REVERT: I 76 MET cc_start: 0.9362 (mpp) cc_final: 0.9073 (mpp) REVERT: I 182 GLU cc_start: 0.7782 (pt0) cc_final: 0.7391 (pt0) REVERT: I 207 MET cc_start: 0.9527 (mmt) cc_final: 0.9117 (mmm) REVERT: J 72 MET cc_start: 0.9259 (ppp) cc_final: 0.8738 (ppp) REVERT: J 76 MET cc_start: 0.8981 (mmm) cc_final: 0.8696 (mmm) REVERT: J 207 MET cc_start: 0.9349 (mmp) cc_final: 0.8974 (mmm) REVERT: J 208 MET cc_start: 0.9231 (mmm) cc_final: 0.8901 (mmt) REVERT: K 129 GLU cc_start: 0.8295 (tt0) cc_final: 0.7466 (tt0) REVERT: K 132 MET cc_start: 0.7979 (mmm) cc_final: 0.7514 (mmm) REVERT: K 154 MET cc_start: 0.9568 (mtt) cc_final: 0.9243 (ptp) REVERT: K 184 TYR cc_start: 0.8630 (m-80) cc_final: 0.8102 (m-10) REVERT: K 207 MET cc_start: 0.8845 (tpp) cc_final: 0.8341 (tpp) REVERT: L 27 GLU cc_start: 0.9199 (pt0) cc_final: 0.8788 (pt0) REVERT: L 33 HIS cc_start: 0.8712 (m170) cc_final: 0.8325 (m-70) REVERT: L 47 GLU cc_start: 0.9310 (mt-10) cc_final: 0.9008 (mm-30) REVERT: L 53 ARG cc_start: 0.9134 (ptp90) cc_final: 0.8719 (ptp-170) REVERT: M 99 LEU cc_start: 0.9747 (tp) cc_final: 0.9459 (tt) REVERT: M 102 MET cc_start: 0.9366 (OUTLIER) cc_final: 0.9022 (mpp) REVERT: N 84 MET cc_start: 0.9054 (mtm) cc_final: 0.8652 (ptp) REVERT: Q 33 MET cc_start: 0.8877 (tmm) cc_final: 0.8384 (tmm) REVERT: Q 66 LEU cc_start: 0.9611 (tp) cc_final: 0.9340 (tt) REVERT: Q 109 GLU cc_start: 0.9367 (mt-10) cc_final: 0.9063 (mm-30) REVERT: Q 188 MET cc_start: 0.8720 (mmm) cc_final: 0.8426 (mmm) REVERT: Q 234 MET cc_start: 0.8913 (tmm) cc_final: 0.8713 (tmm) REVERT: R 33 MET cc_start: 0.9084 (tmm) cc_final: 0.8870 (tmm) REVERT: R 48 ASP cc_start: 0.9382 (t0) cc_final: 0.8938 (t0) REVERT: R 109 GLU cc_start: 0.9156 (mt-10) cc_final: 0.8875 (pp20) REVERT: S 33 MET cc_start: 0.8006 (tpt) cc_final: 0.7703 (tpt) REVERT: S 197 TYR cc_start: 0.7485 (OUTLIER) cc_final: 0.6813 (m-80) REVERT: b 19 MET cc_start: 0.7724 (tmm) cc_final: 0.7485 (ppp) REVERT: b 157 ILE cc_start: 0.9180 (mt) cc_final: 0.8938 (mm) REVERT: b 177 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8030 (tp) REVERT: c 421 MET cc_start: 0.8993 (mtt) cc_final: 0.8347 (mmm) REVERT: c 441 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.9070 (mt) REVERT: c 449 PHE cc_start: 0.6789 (m-10) cc_final: 0.4473 (m-10) REVERT: d 10 ASN cc_start: 0.9126 (m-40) cc_final: 0.8861 (t0) REVERT: d 16 LEU cc_start: 0.8822 (mt) cc_final: 0.8267 (mt) REVERT: d 88 HIS cc_start: 0.8872 (m90) cc_final: 0.8529 (m90) REVERT: d 105 MET cc_start: 0.8937 (mmm) cc_final: 0.8596 (mmm) REVERT: d 152 ASN cc_start: 0.9424 (m-40) cc_final: 0.9085 (t0) REVERT: d 164 PHE cc_start: 0.9454 (m-80) cc_final: 0.8734 (m-80) REVERT: d 307 LEU cc_start: 0.9049 (mp) cc_final: 0.8638 (tt) REVERT: d 325 GLU cc_start: 0.9456 (tt0) cc_final: 0.8986 (tm-30) REVERT: d 334 GLU cc_start: 0.9022 (mt-10) cc_final: 0.8601 (pt0) REVERT: d 350 ILE cc_start: 0.7977 (pt) cc_final: 0.7658 (mm) REVERT: g 53 MET cc_start: 0.8386 (ptt) cc_final: 0.7721 (pmm) REVERT: g 131 MET cc_start: 0.8670 (ppp) cc_final: 0.8465 (ppp) REVERT: i 61 MET cc_start: 0.6353 (ptp) cc_final: 0.6018 (ptp) REVERT: i 68 TYR cc_start: 0.7382 (m-10) cc_final: 0.7003 (m-80) REVERT: i 131 MET cc_start: 0.7195 (ppp) cc_final: 0.6625 (ppp) REVERT: j 55 SER cc_start: 0.8577 (OUTLIER) cc_final: 0.8231 (p) REVERT: k 13 PHE cc_start: 0.8499 (OUTLIER) cc_final: 0.8203 (m-10) REVERT: k 25 PHE cc_start: 0.8709 (m-80) cc_final: 0.8373 (m-80) REVERT: k 61 MET cc_start: 0.6188 (ptp) cc_final: 0.5759 (ptm) REVERT: k 78 ASN cc_start: 0.8190 (m-40) cc_final: 0.7508 (t0) REVERT: k 131 MET cc_start: 0.6884 (ppp) cc_final: 0.6604 (ppp) REVERT: l 13 PHE cc_start: 0.8507 (OUTLIER) cc_final: 0.8110 (m-80) REVERT: l 23 MET cc_start: 0.7070 (tpt) cc_final: 0.6614 (tpt) REVERT: l 44 MET cc_start: 0.6703 (mmm) cc_final: 0.6254 (mtt) REVERT: l 131 MET cc_start: 0.5087 (ptt) cc_final: 0.4655 (ppp) REVERT: m 17 MET cc_start: 0.9051 (mtm) cc_final: 0.8844 (ptt) REVERT: m 32 TYR cc_start: 0.6395 (t80) cc_final: 0.6155 (t80) REVERT: m 44 MET cc_start: 0.7804 (mmm) cc_final: 0.7390 (mmm) REVERT: m 104 LEU cc_start: 0.9468 (mt) cc_final: 0.9206 (mt) REVERT: m 141 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7105 (tp) REVERT: n 68 TYR cc_start: 0.7349 (m-10) cc_final: 0.6942 (m-10) REVERT: n 131 MET cc_start: 0.6342 (ppp) cc_final: 0.6084 (ppp) REVERT: o 17 MET cc_start: 0.8796 (mtp) cc_final: 0.8579 (mtp) REVERT: o 47 MET cc_start: 0.8483 (ppp) cc_final: 0.8261 (ppp) REVERT: p 330 ASN cc_start: 0.8945 (m-40) cc_final: 0.8571 (m110) REVERT: p 342 MET cc_start: 0.7314 (mmm) cc_final: 0.7033 (mmm) outliers start: 153 outliers final: 107 residues processed: 999 average time/residue: 0.5263 time to fit residues: 918.8979 Evaluate side-chains 970 residues out of total 7117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 848 time to evaluate : 5.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 164 HIS Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 584 MET Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 607 ASP Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 139 LYS Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 450 TRP Chi-restraints excluded: chain B residue 584 MET Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 371 ASP Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 450 TRP Chi-restraints excluded: chain C residue 544 MET Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 207 CYS Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain E residue 262 ASN Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 330 ASP Chi-restraints excluded: chain E residue 336 GLU Chi-restraints excluded: chain E residue 360 ASP Chi-restraints excluded: chain E residue 410 MET Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 229 ILE Chi-restraints excluded: chain F residue 257 VAL Chi-restraints excluded: chain F residue 365 ILE Chi-restraints excluded: chain H residue 38 ASP Chi-restraints excluded: chain H residue 74 PHE Chi-restraints excluded: chain H residue 109 PHE Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain I residue 128 LEU Chi-restraints excluded: chain I residue 208 MET Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 182 GLU Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain K residue 152 ILE Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain M residue 74 GLU Chi-restraints excluded: chain M residue 102 MET Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain N residue 82 GLN Chi-restraints excluded: chain N residue 106 VAL Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 52 VAL Chi-restraints excluded: chain Q residue 91 LEU Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 133 LEU Chi-restraints excluded: chain Q residue 134 ASN Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 186 LEU Chi-restraints excluded: chain S residue 197 TYR Chi-restraints excluded: chain S residue 198 HIS Chi-restraints excluded: chain b residue 177 LEU Chi-restraints excluded: chain c residue 430 LEU Chi-restraints excluded: chain c residue 438 HIS Chi-restraints excluded: chain c residue 441 LEU Chi-restraints excluded: chain c residue 448 ARG Chi-restraints excluded: chain d residue 6 GLU Chi-restraints excluded: chain d residue 63 SER Chi-restraints excluded: chain d residue 93 LEU Chi-restraints excluded: chain d residue 173 LEU Chi-restraints excluded: chain d residue 183 ASN Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain g residue 34 THR Chi-restraints excluded: chain g residue 61 MET Chi-restraints excluded: chain g residue 84 ILE Chi-restraints excluded: chain g residue 141 LEU Chi-restraints excluded: chain g residue 143 LEU Chi-restraints excluded: chain h residue 108 PHE Chi-restraints excluded: chain i residue 60 VAL Chi-restraints excluded: chain i residue 70 LEU Chi-restraints excluded: chain i residue 140 VAL Chi-restraints excluded: chain j residue 55 SER Chi-restraints excluded: chain k residue 13 PHE Chi-restraints excluded: chain k residue 108 PHE Chi-restraints excluded: chain l residue 13 PHE Chi-restraints excluded: chain l residue 54 LYS Chi-restraints excluded: chain l residue 140 VAL Chi-restraints excluded: chain m residue 93 LEU Chi-restraints excluded: chain m residue 121 THR Chi-restraints excluded: chain m residue 133 LEU Chi-restraints excluded: chain m residue 140 VAL Chi-restraints excluded: chain m residue 141 LEU Chi-restraints excluded: chain n residue 104 LEU Chi-restraints excluded: chain n residue 134 ILE Chi-restraints excluded: chain o residue 123 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 836 random chunks: chunk 732 optimal weight: 9.9990 chunk 771 optimal weight: 30.0000 chunk 704 optimal weight: 10.0000 chunk 750 optimal weight: 30.0000 chunk 451 optimal weight: 10.0000 chunk 327 optimal weight: 7.9990 chunk 589 optimal weight: 20.0000 chunk 230 optimal weight: 0.9980 chunk 678 optimal weight: 8.9990 chunk 710 optimal weight: 40.0000 chunk 748 optimal weight: 10.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 78 GLN ** I 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 142 ASN S 134 ASN S 177 GLN ** b 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 243 HIS d 308 ASN ** d 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.5857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.098 61638 Z= 0.477 Angle : 0.849 21.394 83673 Z= 0.430 Chirality : 0.048 0.551 9871 Planarity : 0.005 0.055 10900 Dihedral : 4.911 131.074 9025 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 20.02 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.87 % Favored : 96.09 % Rotamer: Outliers : 2.58 % Allowed : 19.15 % Favored : 78.27 % 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: 1.14 (0.09), residues: 8369 helix: 1.71 (0.07), residues: 5036 sheet: -0.50 (0.20), residues: 661 loop : -0.71 (0.12), residues: 2672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.002 TRP B 567 HIS 0.013 0.002 HIS d 88 PHE 0.065 0.003 PHE h 25 TYR 0.056 0.002 TYR b 103 ARG 0.010 0.001 ARG D 82 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16738 Ramachandran restraints generated. 8369 Oldfield, 0 Emsley, 8369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16738 Ramachandran restraints generated. 8369 Oldfield, 0 Emsley, 8369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 968 residues out of total 7117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 822 time to evaluate : 5.329 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: A 39 MET cc_start: 0.8705 (tpp) cc_final: 0.8472 (tpp) REVERT: A 61 MET cc_start: 0.9147 (mmp) cc_final: 0.8914 (mmm) REVERT: A 164 HIS cc_start: 0.9289 (OUTLIER) cc_final: 0.8544 (t70) REVERT: A 167 MET cc_start: 0.9352 (mtm) cc_final: 0.8676 (mtt) REVERT: A 173 ARG cc_start: 0.9067 (OUTLIER) cc_final: 0.7743 (pmt100) REVERT: A 318 MET cc_start: 0.9276 (mtt) cc_final: 0.8784 (mtt) REVERT: A 346 MET cc_start: 0.9061 (ttt) cc_final: 0.8685 (ttt) REVERT: A 491 GLU cc_start: 0.8995 (tt0) cc_final: 0.8719 (tm-30) REVERT: A 510 GLU cc_start: 0.8799 (tm-30) cc_final: 0.8464 (tm-30) REVERT: A 516 LYS cc_start: 0.9477 (mttt) cc_final: 0.9171 (tmtt) REVERT: A 574 MET cc_start: 0.8909 (mtt) cc_final: 0.8668 (mmt) REVERT: B 306 MET cc_start: 0.8748 (ptm) cc_final: 0.8344 (tmm) REVERT: B 318 MET cc_start: 0.9367 (tpp) cc_final: 0.8390 (mpp) REVERT: B 347 MET cc_start: 0.8651 (tpt) cc_final: 0.8283 (tpp) REVERT: B 368 MET cc_start: 0.9089 (mmm) cc_final: 0.8655 (ttm) REVERT: B 458 MET cc_start: 0.8888 (mmt) cc_final: 0.8431 (mmt) REVERT: B 544 MET cc_start: 0.9067 (mtp) cc_final: 0.8732 (mmm) REVERT: B 584 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.8376 (mpp) REVERT: C 39 MET cc_start: 0.8838 (tmm) cc_final: 0.8185 (tmm) REVERT: C 234 LEU cc_start: 0.9063 (mp) cc_final: 0.8791 (tt) REVERT: C 458 MET cc_start: 0.8850 (mtp) cc_final: 0.8427 (mtt) REVERT: C 544 MET cc_start: 0.9240 (OUTLIER) cc_final: 0.8987 (tpp) REVERT: C 550 MET cc_start: 0.9285 (mtt) cc_final: 0.9068 (mtp) REVERT: D 254 MET cc_start: 0.8661 (tpp) cc_final: 0.8166 (mmm) REVERT: D 270 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8163 (tt0) REVERT: D 433 GLN cc_start: 0.9560 (tt0) cc_final: 0.9121 (tm-30) REVERT: D 495 ILE cc_start: 0.9420 (mt) cc_final: 0.9171 (tt) REVERT: E 148 GLU cc_start: 0.8737 (tt0) cc_final: 0.8262 (tm-30) REVERT: E 234 MET cc_start: 0.8958 (OUTLIER) cc_final: 0.8183 (pmm) REVERT: E 270 GLU cc_start: 0.9044 (tt0) cc_final: 0.8605 (pt0) REVERT: E 309 GLU cc_start: 0.8836 (tm-30) cc_final: 0.8482 (tm-30) REVERT: E 316 GLU cc_start: 0.8320 (mt-10) cc_final: 0.7745 (mt-10) REVERT: E 330 ASP cc_start: 0.9482 (OUTLIER) cc_final: 0.8976 (t70) REVERT: E 356 MET cc_start: 0.8881 (mtm) cc_final: 0.8563 (mtm) REVERT: F 153 ILE cc_start: 0.9122 (pp) cc_final: 0.8885 (tt) REVERT: F 169 MET cc_start: 0.8974 (tmm) cc_final: 0.8594 (tmm) REVERT: F 180 MET cc_start: 0.8934 (mmm) cc_final: 0.8667 (mmm) REVERT: F 183 ILE cc_start: 0.9648 (mt) cc_final: 0.9278 (pt) REVERT: F 187 GLN cc_start: 0.9321 (pp30) cc_final: 0.8944 (pp30) REVERT: F 254 MET cc_start: 0.8849 (mmm) cc_final: 0.8245 (tpp) REVERT: F 299 ASP cc_start: 0.8285 (m-30) cc_final: 0.7646 (m-30) REVERT: F 309 GLU cc_start: 0.9246 (tm-30) cc_final: 0.8993 (tm-30) REVERT: F 356 MET cc_start: 0.9095 (mtm) cc_final: 0.8764 (mtm) REVERT: F 410 MET cc_start: 0.8513 (mtp) cc_final: 0.8156 (mtp) REVERT: F 435 MET cc_start: 0.9291 (tpp) cc_final: 0.8938 (tpp) REVERT: F 491 MET cc_start: 0.8758 (mtp) cc_final: 0.8408 (ptp) REVERT: H 31 ASN cc_start: 0.9393 (m-40) cc_final: 0.9041 (m110) REVERT: H 79 PHE cc_start: 0.9567 (p90) cc_final: 0.9202 (p90) REVERT: H 193 GLU cc_start: 0.9446 (tm-30) cc_final: 0.9078 (tm-30) REVERT: I 72 MET cc_start: 0.9464 (mmm) cc_final: 0.9220 (mmm) REVERT: I 76 MET cc_start: 0.9410 (mpp) cc_final: 0.9092 (mpp) REVERT: I 182 GLU cc_start: 0.7764 (pt0) cc_final: 0.7375 (pt0) REVERT: I 207 MET cc_start: 0.9535 (mmt) cc_final: 0.9147 (mmm) REVERT: J 72 MET cc_start: 0.9340 (ppp) cc_final: 0.8720 (ppp) REVERT: J 76 MET cc_start: 0.9045 (mmm) cc_final: 0.8725 (mmm) REVERT: J 182 GLU cc_start: 0.8512 (tt0) cc_final: 0.8158 (tt0) REVERT: J 207 MET cc_start: 0.9423 (mmp) cc_final: 0.9039 (mmm) REVERT: J 208 MET cc_start: 0.9291 (mmm) cc_final: 0.8970 (mmt) REVERT: K 129 GLU cc_start: 0.8296 (tt0) cc_final: 0.7637 (tt0) REVERT: K 184 TYR cc_start: 0.8733 (m-80) cc_final: 0.8142 (m-10) REVERT: K 207 MET cc_start: 0.8906 (tpp) cc_final: 0.8378 (tpp) REVERT: K 208 MET cc_start: 0.9530 (tpp) cc_final: 0.9018 (tpp) REVERT: L 27 GLU cc_start: 0.9251 (pt0) cc_final: 0.8896 (pt0) REVERT: L 47 GLU cc_start: 0.9353 (mt-10) cc_final: 0.9057 (mm-30) REVERT: L 53 ARG cc_start: 0.9081 (ptp90) cc_final: 0.8697 (ptp-170) REVERT: M 99 LEU cc_start: 0.9754 (tp) cc_final: 0.9416 (tt) REVERT: M 102 MET cc_start: 0.9331 (OUTLIER) cc_final: 0.9009 (mpp) REVERT: N 84 MET cc_start: 0.9157 (mtm) cc_final: 0.8743 (ptp) REVERT: Q 33 MET cc_start: 0.8900 (tmm) cc_final: 0.8501 (tmm) REVERT: Q 66 LEU cc_start: 0.9592 (tp) cc_final: 0.9357 (tt) REVERT: Q 188 MET cc_start: 0.8870 (mmm) cc_final: 0.8563 (mmm) REVERT: R 33 MET cc_start: 0.9117 (tmm) cc_final: 0.8881 (tmm) REVERT: R 109 GLU cc_start: 0.9158 (mt-10) cc_final: 0.8884 (pp20) REVERT: S 197 TYR cc_start: 0.7369 (OUTLIER) cc_final: 0.6723 (m-80) REVERT: b 19 MET cc_start: 0.7722 (tmm) cc_final: 0.7481 (ppp) REVERT: b 122 ASP cc_start: 0.7956 (t70) cc_final: 0.7734 (t70) REVERT: b 157 ILE cc_start: 0.9089 (mt) cc_final: 0.8864 (mm) REVERT: b 177 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8272 (tp) REVERT: c 421 MET cc_start: 0.9003 (mtt) cc_final: 0.8334 (mmm) REVERT: c 449 PHE cc_start: 0.6213 (m-10) cc_final: 0.5959 (m-10) REVERT: d 107 ASP cc_start: 0.9654 (m-30) cc_final: 0.9394 (p0) REVERT: d 138 MET cc_start: 0.8385 (mmm) cc_final: 0.8018 (mmm) REVERT: d 152 ASN cc_start: 0.9417 (m-40) cc_final: 0.9074 (t0) REVERT: d 164 PHE cc_start: 0.9444 (m-80) cc_final: 0.9062 (m-80) REVERT: d 307 LEU cc_start: 0.9071 (mp) cc_final: 0.8619 (tt) REVERT: d 325 GLU cc_start: 0.9471 (tt0) cc_final: 0.9047 (tm-30) REVERT: d 334 GLU cc_start: 0.9066 (mt-10) cc_final: 0.8678 (pt0) REVERT: d 350 ILE cc_start: 0.7993 (pt) cc_final: 0.7621 (mm) REVERT: g 53 MET cc_start: 0.8453 (ptt) cc_final: 0.7813 (pmm) REVERT: i 61 MET cc_start: 0.6157 (ptp) cc_final: 0.5799 (ptp) REVERT: i 68 TYR cc_start: 0.7424 (m-10) cc_final: 0.7056 (m-80) REVERT: i 88 ARG cc_start: 0.8052 (mtm180) cc_final: 0.7176 (ttp-170) REVERT: j 55 SER cc_start: 0.8632 (OUTLIER) cc_final: 0.8292 (p) REVERT: k 13 PHE cc_start: 0.8505 (OUTLIER) cc_final: 0.8216 (m-10) REVERT: k 25 PHE cc_start: 0.8773 (m-80) cc_final: 0.8432 (m-80) REVERT: k 44 MET cc_start: 0.4143 (mmm) cc_final: 0.3908 (mmm) REVERT: k 61 MET cc_start: 0.6544 (ptp) cc_final: 0.6236 (ptp) REVERT: k 78 ASN cc_start: 0.8239 (m-40) cc_final: 0.7576 (t0) REVERT: k 152 LEU cc_start: 0.8327 (mm) cc_final: 0.7660 (tp) REVERT: l 13 PHE cc_start: 0.8582 (OUTLIER) cc_final: 0.8238 (m-80) REVERT: l 23 MET cc_start: 0.7243 (tpt) cc_final: 0.6783 (tpt) REVERT: l 44 MET cc_start: 0.6480 (mmm) cc_final: 0.6121 (mmm) REVERT: l 131 MET cc_start: 0.5318 (ptt) cc_final: 0.4832 (ppp) REVERT: m 23 MET cc_start: 0.6287 (tpt) cc_final: 0.5468 (mmm) REVERT: m 32 TYR cc_start: 0.6461 (t80) cc_final: 0.6242 (t80) REVERT: m 47 MET cc_start: 0.6523 (ptt) cc_final: 0.5448 (mmm) REVERT: m 104 LEU cc_start: 0.9445 (mt) cc_final: 0.9171 (mt) REVERT: m 141 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7525 (tp) REVERT: n 131 MET cc_start: 0.6267 (ppp) cc_final: 0.6024 (ppp) REVERT: o 17 MET cc_start: 0.8821 (mtp) cc_final: 0.8611 (mtp) REVERT: o 47 MET cc_start: 0.8553 (ppp) cc_final: 0.8306 (ppp) REVERT: o 61 MET cc_start: 0.4732 (ptp) cc_final: 0.4228 (ptm) REVERT: p 312 TRP cc_start: 0.8314 (m100) cc_final: 0.7571 (m100) REVERT: p 330 ASN cc_start: 0.8967 (m-40) cc_final: 0.8615 (m110) outliers start: 146 outliers final: 117 residues processed: 914 average time/residue: 0.5269 time to fit residues: 848.5225 Evaluate side-chains 927 residues out of total 7117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 796 time to evaluate : 5.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 164 HIS Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 505 ASP Chi-restraints excluded: chain A residue 523 ASN Chi-restraints excluded: chain A residue 584 MET Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 607 ASP Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 450 TRP Chi-restraints excluded: chain B residue 584 MET Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 371 ASP Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 450 TRP Chi-restraints excluded: chain C residue 544 MET Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 207 CYS Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 334 ILE Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain E residue 262 ASN Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 330 ASP Chi-restraints excluded: chain E residue 336 GLU Chi-restraints excluded: chain E residue 360 ASP Chi-restraints excluded: chain E residue 410 MET Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 229 ILE Chi-restraints excluded: chain F residue 257 VAL Chi-restraints excluded: chain F residue 365 ILE Chi-restraints excluded: chain F residue 380 ASP Chi-restraints excluded: chain H residue 38 ASP Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 74 PHE Chi-restraints excluded: chain H residue 109 PHE Chi-restraints excluded: chain H residue 112 TYR Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain I residue 128 LEU Chi-restraints excluded: chain I residue 208 MET Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain K residue 152 ILE Chi-restraints excluded: chain L residue 30 LYS Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain M residue 74 GLU Chi-restraints excluded: chain M residue 102 MET Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain N residue 82 GLN Chi-restraints excluded: chain N residue 106 VAL Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 52 VAL Chi-restraints excluded: chain Q residue 91 LEU Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 133 LEU Chi-restraints excluded: chain Q residue 134 ASN Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 186 LEU Chi-restraints excluded: chain S residue 197 TYR Chi-restraints excluded: chain S residue 198 HIS Chi-restraints excluded: chain b residue 177 LEU Chi-restraints excluded: chain c residue 430 LEU Chi-restraints excluded: chain c residue 432 ILE Chi-restraints excluded: chain c residue 438 HIS Chi-restraints excluded: chain c residue 448 ARG Chi-restraints excluded: chain d residue 6 GLU Chi-restraints excluded: chain d residue 63 SER Chi-restraints excluded: chain d residue 93 LEU Chi-restraints excluded: chain d residue 173 LEU Chi-restraints excluded: chain d residue 183 ASN Chi-restraints excluded: chain d residue 315 PHE Chi-restraints excluded: chain g residue 34 THR Chi-restraints excluded: chain g residue 61 MET Chi-restraints excluded: chain g residue 84 ILE Chi-restraints excluded: chain g residue 115 ASP Chi-restraints excluded: chain g residue 141 LEU Chi-restraints excluded: chain g residue 143 LEU Chi-restraints excluded: chain h residue 108 PHE Chi-restraints excluded: chain i residue 57 ILE Chi-restraints excluded: chain i residue 60 VAL Chi-restraints excluded: chain i residue 70 LEU Chi-restraints excluded: chain i residue 140 VAL Chi-restraints excluded: chain j residue 55 SER Chi-restraints excluded: chain k residue 13 PHE Chi-restraints excluded: chain l residue 13 PHE Chi-restraints excluded: chain l residue 54 LYS Chi-restraints excluded: chain l residue 140 VAL Chi-restraints excluded: chain m residue 93 LEU Chi-restraints excluded: chain m residue 118 VAL Chi-restraints excluded: chain m residue 121 THR Chi-restraints excluded: chain m residue 133 LEU Chi-restraints excluded: chain m residue 140 VAL Chi-restraints excluded: chain m residue 141 LEU Chi-restraints excluded: chain n residue 104 LEU Chi-restraints excluded: chain n residue 134 ILE Chi-restraints excluded: chain o residue 123 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 836 random chunks: chunk 493 optimal weight: 3.9990 chunk 794 optimal weight: 5.9990 chunk 484 optimal weight: 0.9990 chunk 376 optimal weight: 7.9990 chunk 551 optimal weight: 50.0000 chunk 832 optimal weight: 3.9990 chunk 766 optimal weight: 5.9990 chunk 663 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 512 optimal weight: 2.9990 chunk 406 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 GLN I 122 GLN ** J 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.5914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 61638 Z= 0.266 Angle : 0.787 19.788 83673 Z= 0.390 Chirality : 0.047 0.476 9871 Planarity : 0.004 0.056 10900 Dihedral : 4.792 129.970 9025 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.33 % Favored : 96.63 % Rotamer: Outliers : 2.19 % Allowed : 19.88 % Favored : 77.93 % 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: 1.34 (0.09), residues: 8369 helix: 1.85 (0.07), residues: 5021 sheet: -0.30 (0.20), residues: 682 loop : -0.60 (0.12), residues: 2666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP B 567 HIS 0.008 0.001 HIS d 88 PHE 0.068 0.002 PHE h 25 TYR 0.054 0.002 TYR b 103 ARG 0.007 0.001 ARG N 79 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16738 Ramachandran restraints generated. 8369 Oldfield, 0 Emsley, 8369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16738 Ramachandran restraints generated. 8369 Oldfield, 0 Emsley, 8369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 991 residues out of total 7117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 867 time to evaluate : 5.894 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: A 39 MET cc_start: 0.8687 (tpp) cc_final: 0.8345 (tpp) REVERT: A 61 MET cc_start: 0.9127 (mmp) cc_final: 0.8863 (mmm) REVERT: A 164 HIS cc_start: 0.9086 (OUTLIER) cc_final: 0.8117 (t70) REVERT: A 167 MET cc_start: 0.9216 (mtm) cc_final: 0.8563 (mtt) REVERT: A 173 ARG cc_start: 0.9028 (OUTLIER) cc_final: 0.7771 (pmt100) REVERT: A 318 MET cc_start: 0.9279 (mtt) cc_final: 0.8845 (mtp) REVERT: A 340 MET cc_start: 0.8673 (mmm) cc_final: 0.8463 (mmm) REVERT: A 368 MET cc_start: 0.9437 (tpt) cc_final: 0.9021 (tpp) REVERT: A 387 GLU cc_start: 0.8849 (tm-30) cc_final: 0.8613 (tm-30) REVERT: A 491 GLU cc_start: 0.8960 (tt0) cc_final: 0.8571 (tm-30) REVERT: A 510 GLU cc_start: 0.8657 (tm-30) cc_final: 0.8294 (tm-30) REVERT: A 516 LYS cc_start: 0.9462 (mttt) cc_final: 0.9206 (tmtt) REVERT: A 574 MET cc_start: 0.8892 (mtt) cc_final: 0.8665 (mmt) REVERT: B 95 MET cc_start: 0.9089 (tpp) cc_final: 0.8756 (tpp) REVERT: B 284 MET cc_start: 0.9352 (mmm) cc_final: 0.9088 (mmm) REVERT: B 306 MET cc_start: 0.8680 (ptm) cc_final: 0.8267 (tmm) REVERT: B 318 MET cc_start: 0.9310 (tpp) cc_final: 0.8335 (mpp) REVERT: B 347 MET cc_start: 0.8496 (tpt) cc_final: 0.8116 (tpp) REVERT: B 368 MET cc_start: 0.9013 (mmm) cc_final: 0.8662 (ttm) REVERT: B 381 ARG cc_start: 0.9229 (mmt-90) cc_final: 0.8895 (mmm-85) REVERT: B 432 PHE cc_start: 0.8857 (t80) cc_final: 0.8357 (t80) REVERT: B 458 MET cc_start: 0.8824 (mmt) cc_final: 0.8390 (mmt) REVERT: B 540 MET cc_start: 0.8860 (ptp) cc_final: 0.8011 (pmm) REVERT: B 584 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.8381 (mpp) REVERT: C 39 MET cc_start: 0.8767 (tmm) cc_final: 0.8246 (tmm) REVERT: C 340 MET cc_start: 0.9191 (tpp) cc_final: 0.8781 (tpp) REVERT: C 458 MET cc_start: 0.8755 (mtp) cc_final: 0.8488 (mtt) REVERT: C 544 MET cc_start: 0.9221 (OUTLIER) cc_final: 0.8990 (tpp) REVERT: C 550 MET cc_start: 0.9336 (mtt) cc_final: 0.9097 (mtp) REVERT: D 127 MET cc_start: 0.8833 (mtp) cc_final: 0.8457 (ptp) REVERT: D 254 MET cc_start: 0.8650 (tpp) cc_final: 0.8135 (mmm) REVERT: D 270 GLU cc_start: 0.8739 (mt-10) cc_final: 0.8283 (tt0) REVERT: D 402 MET cc_start: 0.9139 (mmm) cc_final: 0.8750 (mpp) REVERT: D 433 GLN cc_start: 0.9535 (tt0) cc_final: 0.9138 (tm-30) REVERT: D 491 MET cc_start: 0.9039 (mpp) cc_final: 0.8730 (pmm) REVERT: E 87 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.7981 (mm) REVERT: E 148 GLU cc_start: 0.8713 (tt0) cc_final: 0.8184 (tm-30) REVERT: E 234 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.8026 (pmm) REVERT: E 270 GLU cc_start: 0.9048 (tt0) cc_final: 0.8608 (pt0) REVERT: E 309 GLU cc_start: 0.8814 (tm-30) cc_final: 0.8445 (tm-30) REVERT: E 316 GLU cc_start: 0.8228 (mt-10) cc_final: 0.7718 (mt-10) REVERT: E 330 ASP cc_start: 0.9375 (OUTLIER) cc_final: 0.8871 (t70) REVERT: E 356 MET cc_start: 0.8796 (mtm) cc_final: 0.8480 (mtm) REVERT: E 432 VAL cc_start: 0.9647 (t) cc_final: 0.9435 (p) REVERT: F 153 ILE cc_start: 0.9058 (pp) cc_final: 0.8832 (tt) REVERT: F 169 MET cc_start: 0.8933 (tmm) cc_final: 0.8530 (tmm) REVERT: F 180 MET cc_start: 0.8843 (mmm) cc_final: 0.8478 (mmm) REVERT: F 183 ILE cc_start: 0.9679 (mt) cc_final: 0.9312 (pt) REVERT: F 187 GLN cc_start: 0.9115 (pp30) cc_final: 0.8831 (pp30) REVERT: F 309 GLU cc_start: 0.9168 (tm-30) cc_final: 0.8827 (tm-30) REVERT: F 356 MET cc_start: 0.9066 (mtm) cc_final: 0.8709 (mtm) REVERT: F 402 MET cc_start: 0.9272 (mmm) cc_final: 0.8665 (tpp) REVERT: F 410 MET cc_start: 0.8388 (mtp) cc_final: 0.8042 (mtp) REVERT: F 435 MET cc_start: 0.9256 (tpp) cc_final: 0.8884 (tpp) REVERT: F 491 MET cc_start: 0.8809 (mtp) cc_final: 0.8449 (ptp) REVERT: H 31 ASN cc_start: 0.9402 (m-40) cc_final: 0.9056 (m110) REVERT: H 79 PHE cc_start: 0.9524 (p90) cc_final: 0.9145 (p90) REVERT: H 193 GLU cc_start: 0.9368 (tm-30) cc_final: 0.8962 (tm-30) REVERT: I 72 MET cc_start: 0.9433 (mmm) cc_final: 0.9178 (mmm) REVERT: I 76 MET cc_start: 0.9391 (mpp) cc_final: 0.9029 (mpp) REVERT: I 182 GLU cc_start: 0.7787 (pt0) cc_final: 0.7436 (pt0) REVERT: I 207 MET cc_start: 0.9542 (mmt) cc_final: 0.9145 (mmm) REVERT: I 208 MET cc_start: 0.9118 (OUTLIER) cc_final: 0.8748 (mtt) REVERT: J 72 MET cc_start: 0.9267 (ppp) cc_final: 0.8687 (ppp) REVERT: J 76 MET cc_start: 0.8977 (mmm) cc_final: 0.8650 (mmm) REVERT: J 207 MET cc_start: 0.9375 (mmp) cc_final: 0.8896 (mmp) REVERT: J 208 MET cc_start: 0.9253 (mmm) cc_final: 0.8921 (mmt) REVERT: K 129 GLU cc_start: 0.8334 (tt0) cc_final: 0.7513 (tt0) REVERT: K 132 MET cc_start: 0.8006 (mmm) cc_final: 0.7628 (mmm) REVERT: K 154 MET cc_start: 0.9534 (mtt) cc_final: 0.9279 (ptp) REVERT: K 184 TYR cc_start: 0.8669 (m-80) cc_final: 0.8138 (m-10) REVERT: K 207 MET cc_start: 0.8863 (tpp) cc_final: 0.8362 (tpp) REVERT: L 27 GLU cc_start: 0.9214 (pt0) cc_final: 0.8765 (pt0) REVERT: L 33 HIS cc_start: 0.8736 (m170) cc_final: 0.8328 (m-70) REVERT: L 47 GLU cc_start: 0.9360 (mt-10) cc_final: 0.9056 (mm-30) REVERT: L 53 ARG cc_start: 0.9070 (ptp90) cc_final: 0.8738 (ptp-170) REVERT: M 78 ARG cc_start: 0.9417 (ptp-170) cc_final: 0.9207 (ptt-90) REVERT: M 99 LEU cc_start: 0.9736 (tp) cc_final: 0.9457 (tt) REVERT: M 102 MET cc_start: 0.9322 (OUTLIER) cc_final: 0.8990 (mpp) REVERT: N 84 MET cc_start: 0.9063 (mtm) cc_final: 0.8615 (ptm) REVERT: N 105 ASP cc_start: 0.9216 (t0) cc_final: 0.8998 (t0) REVERT: Q 66 LEU cc_start: 0.9622 (tp) cc_final: 0.9356 (tt) REVERT: Q 188 MET cc_start: 0.8766 (mmm) cc_final: 0.8469 (mmm) REVERT: R 33 MET cc_start: 0.9087 (tmm) cc_final: 0.8853 (tmm) REVERT: R 48 ASP cc_start: 0.9404 (t0) cc_final: 0.8996 (t0) REVERT: R 78 LEU cc_start: 0.9628 (tp) cc_final: 0.9394 (pt) REVERT: R 109 GLU cc_start: 0.9142 (mt-10) cc_final: 0.8842 (pp20) REVERT: S 197 TYR cc_start: 0.7231 (OUTLIER) cc_final: 0.6587 (m-80) REVERT: b 19 MET cc_start: 0.7702 (tmm) cc_final: 0.7464 (ppp) REVERT: b 157 ILE cc_start: 0.9170 (mt) cc_final: 0.8926 (mm) REVERT: b 177 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8179 (tp) REVERT: b 181 ILE cc_start: 0.9102 (mm) cc_final: 0.8896 (mt) REVERT: c 421 MET cc_start: 0.8993 (mtt) cc_final: 0.8327 (mmm) REVERT: c 449 PHE cc_start: 0.6271 (m-10) cc_final: 0.5846 (m-10) REVERT: d 105 MET cc_start: 0.8769 (mmm) cc_final: 0.8461 (mmp) REVERT: d 152 ASN cc_start: 0.9394 (m-40) cc_final: 0.9044 (t0) REVERT: d 164 PHE cc_start: 0.9430 (m-80) cc_final: 0.8685 (m-80) REVERT: d 307 LEU cc_start: 0.9056 (mp) cc_final: 0.8584 (tt) REVERT: d 325 GLU cc_start: 0.9418 (tt0) cc_final: 0.8903 (tm-30) REVERT: d 334 GLU cc_start: 0.9044 (mt-10) cc_final: 0.8625 (pt0) REVERT: d 350 ILE cc_start: 0.8028 (pt) cc_final: 0.7731 (mm) REVERT: g 41 ILE cc_start: 0.8861 (mm) cc_final: 0.8542 (tp) REVERT: g 53 MET cc_start: 0.8414 (ptt) cc_final: 0.7821 (pmm) REVERT: g 76 ILE cc_start: 0.8629 (mt) cc_final: 0.8173 (tt) REVERT: i 61 MET cc_start: 0.6466 (ptp) cc_final: 0.6213 (ptp) REVERT: i 68 TYR cc_start: 0.7426 (m-10) cc_final: 0.7068 (m-80) REVERT: i 88 ARG cc_start: 0.8111 (mtm180) cc_final: 0.7212 (ttp-170) REVERT: j 55 SER cc_start: 0.8521 (OUTLIER) cc_final: 0.8237 (p) REVERT: k 13 PHE cc_start: 0.8411 (OUTLIER) cc_final: 0.8115 (m-10) REVERT: k 23 MET cc_start: 0.6791 (tpt) cc_final: 0.6382 (mmm) REVERT: k 25 PHE cc_start: 0.8710 (m-80) cc_final: 0.8380 (m-80) REVERT: k 44 MET cc_start: 0.3898 (mmm) cc_final: 0.3444 (mmm) REVERT: k 61 MET cc_start: 0.6115 (ptp) cc_final: 0.5798 (ptm) REVERT: k 78 ASN cc_start: 0.8191 (m-40) cc_final: 0.7502 (t0) REVERT: k 131 MET cc_start: 0.7269 (ppp) cc_final: 0.5887 (tpp) REVERT: k 152 LEU cc_start: 0.8296 (mm) cc_final: 0.7607 (tp) REVERT: l 13 PHE cc_start: 0.8559 (OUTLIER) cc_final: 0.8250 (m-80) REVERT: l 23 MET cc_start: 0.7192 (tpt) cc_final: 0.6857 (tpt) REVERT: l 47 MET cc_start: 0.6232 (ppp) cc_final: 0.5491 (ppp) REVERT: l 131 MET cc_start: 0.5352 (ptt) cc_final: 0.4858 (ppp) REVERT: m 23 MET cc_start: 0.6285 (tpt) cc_final: 0.5541 (mmm) REVERT: m 39 THR cc_start: 0.7860 (m) cc_final: 0.7518 (p) REVERT: m 104 LEU cc_start: 0.9451 (mt) cc_final: 0.9163 (mt) REVERT: m 141 LEU cc_start: 0.7810 (mp) cc_final: 0.7294 (tp) REVERT: n 131 MET cc_start: 0.6202 (ppp) cc_final: 0.5949 (ppp) REVERT: o 17 MET cc_start: 0.8778 (mtp) cc_final: 0.8568 (mtp) REVERT: o 32 TYR cc_start: 0.9155 (t80) cc_final: 0.8626 (t80) REVERT: o 47 MET cc_start: 0.8647 (ppp) cc_final: 0.8419 (ppp) REVERT: o 61 MET cc_start: 0.4685 (ptp) cc_final: 0.3992 (ptp) REVERT: p 330 ASN cc_start: 0.8933 (m-40) cc_final: 0.8543 (m110) outliers start: 124 outliers final: 95 residues processed: 942 average time/residue: 0.5261 time to fit residues: 868.7351 Evaluate side-chains 931 residues out of total 7117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 822 time to evaluate : 5.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 164 HIS Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 584 MET Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 607 ASP Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 139 LYS Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 450 TRP Chi-restraints excluded: chain B residue 584 MET Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 371 ASP Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 450 TRP Chi-restraints excluded: chain C residue 544 MET Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 207 CYS Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain E residue 262 ASN Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 330 ASP Chi-restraints excluded: chain E residue 336 GLU Chi-restraints excluded: chain E residue 360 ASP Chi-restraints excluded: chain E residue 410 MET Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 229 ILE Chi-restraints excluded: chain F residue 257 VAL Chi-restraints excluded: chain F residue 365 ILE Chi-restraints excluded: chain H residue 38 ASP Chi-restraints excluded: chain H residue 74 PHE Chi-restraints excluded: chain H residue 109 PHE Chi-restraints excluded: chain H residue 112 TYR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain I residue 128 LEU Chi-restraints excluded: chain I residue 208 MET Chi-restraints excluded: chain J residue 182 GLU Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain M residue 74 GLU Chi-restraints excluded: chain M residue 102 MET Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain N residue 82 GLN Chi-restraints excluded: chain N residue 106 VAL Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 52 VAL Chi-restraints excluded: chain Q residue 91 LEU Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 133 LEU Chi-restraints excluded: chain Q residue 134 ASN Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 197 TYR Chi-restraints excluded: chain S residue 198 HIS Chi-restraints excluded: chain b residue 177 LEU Chi-restraints excluded: chain c residue 432 ILE Chi-restraints excluded: chain c residue 448 ARG Chi-restraints excluded: chain d residue 6 GLU Chi-restraints excluded: chain d residue 63 SER Chi-restraints excluded: chain d residue 93 LEU Chi-restraints excluded: chain d residue 173 LEU Chi-restraints excluded: chain d residue 183 ASN Chi-restraints excluded: chain d residue 315 PHE Chi-restraints excluded: chain g residue 34 THR Chi-restraints excluded: chain g residue 61 MET Chi-restraints excluded: chain g residue 84 ILE Chi-restraints excluded: chain g residue 115 ASP Chi-restraints excluded: chain g residue 146 LEU Chi-restraints excluded: chain h residue 108 PHE Chi-restraints excluded: chain i residue 57 ILE Chi-restraints excluded: chain i residue 140 VAL Chi-restraints excluded: chain j residue 47 MET Chi-restraints excluded: chain j residue 55 SER Chi-restraints excluded: chain k residue 13 PHE Chi-restraints excluded: chain l residue 13 PHE Chi-restraints excluded: chain l residue 54 LYS Chi-restraints excluded: chain l residue 140 VAL Chi-restraints excluded: chain m residue 93 LEU Chi-restraints excluded: chain m residue 118 VAL Chi-restraints excluded: chain m residue 121 THR Chi-restraints excluded: chain m residue 133 LEU Chi-restraints excluded: chain n residue 134 ILE Chi-restraints excluded: chain o residue 123 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 836 random chunks: chunk 526 optimal weight: 20.0000 chunk 706 optimal weight: 9.9990 chunk 203 optimal weight: 9.9990 chunk 611 optimal weight: 50.0000 chunk 97 optimal weight: 5.9990 chunk 184 optimal weight: 1.9990 chunk 664 optimal weight: 20.0000 chunk 278 optimal weight: 6.9990 chunk 682 optimal weight: 10.0000 chunk 84 optimal weight: 5.9990 chunk 122 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 543 ASN ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 134 ASN ** b 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.083335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.056084 restraints weight = 277936.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.057512 restraints weight = 139038.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.058363 restraints weight = 84456.109| |-----------------------------------------------------------------------------| r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.6098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 61638 Z= 0.395 Angle : 0.828 19.939 83673 Z= 0.415 Chirality : 0.048 0.396 9871 Planarity : 0.005 0.065 10900 Dihedral : 4.849 131.113 9023 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 19.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.85 % Favored : 96.12 % Rotamer: Outliers : 2.34 % Allowed : 20.00 % Favored : 77.66 % 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: 1.15 (0.09), residues: 8369 helix: 1.71 (0.07), residues: 5028 sheet: -0.46 (0.20), residues: 669 loop : -0.70 (0.12), residues: 2672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP B 567 HIS 0.008 0.001 HIS Q 19 PHE 0.066 0.002 PHE h 25 TYR 0.056 0.002 TYR b 103 ARG 0.019 0.001 ARG C 364 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16249.87 seconds wall clock time: 280 minutes 58.70 seconds (16858.70 seconds total)