Starting phenix.real_space_refine on Thu Sep 26 23:35:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xbw_22121/09_2024/6xbw_22121.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xbw_22121/09_2024/6xbw_22121.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xbw_22121/09_2024/6xbw_22121.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xbw_22121/09_2024/6xbw_22121.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xbw_22121/09_2024/6xbw_22121.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xbw_22121/09_2024/6xbw_22121.cif" } resolution = 3.37 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= 0.015 sd= 1.129 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 11 5.49 5 Mg 1 5.21 5 S 357 5.16 5 C 40442 2.51 5 N 10634 2.21 5 O 11645 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 166 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: 63090 Number of models: 1 Model: "" Number of chains: 38 Chain: "A" Number of atoms: 4568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 4568 Classifications: {'peptide': 589} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 29, 'TRANS': 557} Chain breaks: 1 Chain: "B" Number of atoms: 4582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4582 Classifications: {'peptide': 590} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 559} Chain breaks: 1 Chain: "C" Number of atoms: 4628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4628 Classifications: {'peptide': 597} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 29, 'TRANS': 565} Chain: "D" Number of atoms: 3609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3609 Classifications: {'peptide': 461} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 26, 'TRANS': 432} Chain breaks: 1 Chain: "E" Number of atoms: 3585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3585 Classifications: {'peptide': 458} Link IDs: {'CIS': 1, 'PTRANS': 27, 'TRANS': 429} Chain breaks: 1 Chain: "F" Number of atoms: 3594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3594 Classifications: {'peptide': 459} Link IDs: {'CIS': 1, 'PTRANS': 27, 'TRANS': 430} Chain breaks: 1 Chain: "G" Number of atoms: 2823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2823 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 9, 'TRANS': 336} Chain breaks: 3 Chain: "H" Number of atoms: 1700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1700 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 3, 'TRANS': 207} Chain: "I" Number of atoms: 1614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1614 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 5, 'TRANS': 212} Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 193 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 9, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 95 Chain: "J" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1624 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 5, 'TRANS': 212} Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 181 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 9, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 95 Chain: "K" Number of atoms: 1595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1595 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 5, 'TRANS': 214} Unresolved non-hydrogen bonds: 192 Unresolved non-hydrogen angles: 237 Unresolved non-hydrogen dihedrals: 159 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 11, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 120 Chain: "L" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 98} Chain: "M" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 665 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 2, 'TRANS': 105} Unresolved non-hydrogen bonds: 208 Unresolved non-hydrogen angles: 251 Unresolved non-hydrogen dihedrals: 170 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 12, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 142 Chain: "N" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 665 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 2, 'TRANS': 105} Unresolved non-hydrogen bonds: 208 Unresolved non-hydrogen angles: 251 Unresolved non-hydrogen dihedrals: 170 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 12, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 142 Chain: "O" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 665 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 2, 'TRANS': 105} Unresolved non-hydrogen bonds: 208 Unresolved non-hydrogen angles: 251 Unresolved non-hydrogen dihedrals: 170 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 12, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 142 Chain: "P" Number of atoms: 2819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2819 Classifications: {'peptide': 368} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 6, 'TRANS': 361} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 211 Unresolved non-hydrogen angles: 272 Unresolved non-hydrogen dihedrals: 177 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 125 Chain: "a" Number of atoms: 6093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 6093 Classifications: {'peptide': 750} Link IDs: {'CIS': 1, 'PTRANS': 30, 'TRANS': 718} Chain breaks: 2 Chain: "b" Number of atoms: 1503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1503 Classifications: {'peptide': 204} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 198} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "d" Number of atoms: 2819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2819 Classifications: {'peptide': 348} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 334} Chain: "e" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 590 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 6, 'TRANS': 66} Chain: "s" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1668 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 5, 'TRANS': 199} Chain: "r" Number of atoms: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 385 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "c" Number of atoms: 1064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1064 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "g" Number of atoms: 1064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1064 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "k" Number of atoms: 1064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1064 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "l" Number of atoms: 1064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1064 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "m" Number of atoms: 1064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1064 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "n" Number of atoms: 1064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1064 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "o" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1073 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 146} Chain: "p" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1073 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 146} Chain: "q" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1073 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 146} Chain: "f" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 351 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain breaks: 1 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "b" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 213 Unusual residues: {'POV': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "s" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 6 Chain: "r" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 114 Unusual residues: {'OLA': 1, 'POV': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "g" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "p" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Time building chain proxies: 26.87, per 1000 atoms: 0.43 Number of scatterers: 63090 At special positions: 0 Unit cell: (224.91, 204.918, 248.234, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 357 16.00 P 11 15.00 Mg 1 11.99 O 11645 8.00 N 10634 7.00 C 40442 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS s 369 " - pdb=" SG CYS s 416 " distance=2.03 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=2, symmetry=0 Links applied NAG-ASN " NAG s 501 " - " ASN s 271 " " NAG s 502 " - " ASN s 294 " " NAG s 503 " - " ASN s 301 " " NAG s 504 " - " ASN s 348 " " NAG s 505 " - " ASN s 355 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.58 Conformation dependent library (CDL) restraints added in 6.3 seconds 16196 Ramachandran restraints generated. 8098 Oldfield, 0 Emsley, 8098 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15120 Finding SS restraints... Secondary structure from input PDB file: 297 helices and 54 sheets defined 58.1% alpha, 15.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.36 Creating SS restraints... Processing helix chain 'A' and resid 105 through 114 removed outlier: 3.645A pdb=" N SER A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER A 111 " --> pdb=" O SER A 107 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR A 113 " --> pdb=" O ILE A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 237 Processing helix chain 'A' and resid 255 through 266 Processing helix chain 'A' and resid 282 through 291 removed outlier: 3.502A pdb=" N VAL A 287 " --> pdb=" O GLU A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 339 removed outlier: 3.584A pdb=" N ALA A 325 " --> pdb=" O ALA A 321 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ILE A 327 " --> pdb=" O ARG A 323 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N TYR A 328 " --> pdb=" O GLU A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 365 removed outlier: 3.648A pdb=" N TRP A 354 " --> pdb=" O SER A 350 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 387 Processing helix chain 'A' and resid 412 through 416 removed outlier: 3.649A pdb=" N GLY A 415 " --> pdb=" O PRO A 412 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP A 416 " --> pdb=" O PRO A 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 412 through 416' Processing helix chain 'A' and resid 421 through 427 Processing helix chain 'A' and resid 436 through 442 removed outlier: 3.516A pdb=" N ALA A 440 " --> pdb=" O ASP A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 469 removed outlier: 3.768A pdb=" N LEU A 461 " --> pdb=" O TYR A 457 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N TYR A 464 " --> pdb=" O ALA A 460 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP A 466 " --> pdb=" O ASP A 462 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS A 467 " --> pdb=" O GLU A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 496 removed outlier: 3.521A pdb=" N GLU A 487 " --> pdb=" O LEU A 483 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU A 491 " --> pdb=" O GLU A 487 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ILE A 492 " --> pdb=" O ASP A 488 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL A 493 " --> pdb=" O LEU A 489 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLN A 494 " --> pdb=" O ALA A 490 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 519 removed outlier: 3.952A pdb=" N ILE A 507 " --> pdb=" O GLU A 503 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N THR A 508 " --> pdb=" O THR A 504 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU A 510 " --> pdb=" O LYS A 506 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL A 511 " --> pdb=" O ILE A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 530 Processing helix chain 'A' and resid 533 through 556 removed outlier: 3.686A pdb=" N THR A 537 " --> pdb=" O PRO A 533 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU A 541 " --> pdb=" O THR A 537 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA A 546 " --> pdb=" O SER A 542 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG A 552 " --> pdb=" O TYR A 548 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ARG A 553 " --> pdb=" O ASP A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 574 removed outlier: 3.584A pdb=" N GLU A 572 " --> pdb=" O SER A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 582 Processing helix chain 'A' and resid 593 through 609 removed outlier: 3.776A pdb=" N GLN A 603 " --> pdb=" O ALA A 599 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU A 604 " --> pdb=" O ASP A 600 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU A 605 " --> pdb=" O TYR A 601 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU A 606 " --> pdb=" O ALA A 602 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN A 609 " --> pdb=" O LEU A 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 114 removed outlier: 3.782A pdb=" N SER B 111 " --> pdb=" O SER B 107 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR B 113 " --> pdb=" O ILE B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 237 Processing helix chain 'B' and resid 260 through 266 removed outlier: 3.571A pdb=" N SER B 264 " --> pdb=" O SER B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 285 Processing helix chain 'B' and resid 286 through 291 removed outlier: 3.897A pdb=" N ASP B 290 " --> pdb=" O GLU B 286 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE B 291 " --> pdb=" O VAL B 287 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 286 through 291' Processing helix chain 'B' and resid 320 through 339 removed outlier: 4.004A pdb=" N GLU B 324 " --> pdb=" O VAL B 320 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE B 327 " --> pdb=" O ARG B 323 " (cutoff:3.500A) removed outlier: 3.689A 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 426 removed outlier: 3.597A pdb=" N ALA B 424 " --> pdb=" O PRO B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 442 removed outlier: 3.560A pdb=" N ALA B 440 " --> pdb=" O ASP B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 466 Processing helix chain 'B' and resid 471 through 494 removed outlier: 3.998A pdb=" N LEU B 475 " --> pdb=" O GLU B 471 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS B 478 " --> pdb=" O PRO B 474 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU B 481 " --> pdb=" O THR B 477 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU B 487 " --> pdb=" O LEU B 483 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU B 491 " --> pdb=" O GLU B 487 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE B 492 " --> pdb=" O ASP B 488 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN B 494 " --> pdb=" O ALA B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 519 removed outlier: 3.530A pdb=" N ILE B 507 " --> pdb=" O GLU B 503 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N THR B 508 " --> pdb=" O THR B 504 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL B 511 " --> pdb=" O ILE B 507 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS B 513 " --> pdb=" O LEU B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 558 removed outlier: 3.596A pdb=" N ASN B 543 " --> pdb=" O GLY B 539 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL B 555 " --> pdb=" O ALA B 551 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR B 557 " --> pdb=" O ARG B 553 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR B 558 " --> pdb=" O ALA B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 574 Processing helix chain 'B' and resid 576 through 583 Processing helix chain 'B' and resid 584 through 587 removed outlier: 3.870A pdb=" N LYS B 587 " --> pdb=" O MET B 584 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 584 through 587' Processing helix chain 'B' and resid 593 through 610 removed outlier: 3.682A pdb=" N ALA B 599 " --> pdb=" O ALA B 595 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET B 608 " --> pdb=" O LEU B 604 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN B 609 " --> pdb=" O LEU B 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 110 Processing helix chain 'C' and resid 231 through 237 Processing helix chain 'C' and resid 257 through 267 Processing helix chain 'C' and resid 280 through 291 removed outlier: 3.788A pdb=" N MET C 284 " --> pdb=" O ARG C 280 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER C 285 " --> pdb=" O GLY C 281 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL C 287 " --> pdb=" O GLU C 283 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG C 289 " --> pdb=" O SER C 285 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASP C 290 " --> pdb=" O GLU C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 339 removed outlier: 3.615A pdb=" N ALA C 325 " --> pdb=" O ALA C 321 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE C 327 " --> pdb=" O ARG C 323 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP C 339 " --> pdb=" O GLU C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 365 removed outlier: 3.705A pdb=" N TRP C 354 " --> pdb=" O SER C 350 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG C 364 " --> pdb=" O GLU C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 374 removed outlier: 3.937A pdb=" N TYR C 374 " --> pdb=" O ASP C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 387 Processing helix chain 'C' and resid 412 through 416 removed outlier: 3.738A pdb=" N ASP C 416 " --> pdb=" O PRO C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 427 removed outlier: 3.757A pdb=" N GLY C 427 " --> pdb=" O SER C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 442 Processing helix chain 'C' and resid 461 through 466 Processing helix chain 'C' and resid 472 through 494 removed outlier: 3.659A pdb=" N LYS C 478 " --> pdb=" O PRO C 474 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU C 481 " --> pdb=" O THR C 477 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU C 491 " --> pdb=" O GLU C 487 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ILE C 492 " --> pdb=" O ASP C 488 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN C 494 " --> pdb=" O ALA C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 501 removed outlier: 3.959A pdb=" N SER C 500 " --> pdb=" O GLY C 497 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU C 501 " --> pdb=" O LYS C 498 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 497 through 501' Processing helix chain 'C' and resid 502 through 519 removed outlier: 3.541A pdb=" N LYS C 506 " --> pdb=" O ALA C 502 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N THR C 508 " --> pdb=" O THR C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 557 removed outlier: 3.585A pdb=" N ASN C 543 " --> pdb=" O GLY C 539 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N MET C 544 " --> pdb=" O MET C 540 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL C 555 " --> pdb=" O ALA C 551 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 574 removed outlier: 3.881A pdb=" N GLU C 572 " --> pdb=" O SER C 568 " (cutoff:3.500A) Processing helix chain 'C' and resid 574 through 582 Processing helix chain 'C' and resid 583 through 587 removed outlier: 3.530A pdb=" N PHE C 586 " --> pdb=" O SER C 583 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS C 587 " --> pdb=" O MET C 584 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 583 through 587' Processing helix chain 'C' and resid 592 through 610 removed outlier: 3.941A pdb=" N LYS C 596 " --> pdb=" O ASP C 592 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU C 605 " --> pdb=" O TYR C 601 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ASN C 610 " --> pdb=" O GLU C 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 179 Processing helix chain 'D' and resid 204 through 209 Processing helix chain 'D' and resid 237 through 249 Processing helix chain 'D' and resid 250 through 252 No H-bonds generated for 'chain 'D' and resid 250 through 252' Processing helix chain 'D' and resid 272 through 285 removed outlier: 4.093A pdb=" N ARG D 276 " --> pdb=" O ILE D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 314 removed outlier: 3.916A pdb=" N GLU D 305 " --> pdb=" O SER D 301 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA D 306 " --> pdb=" O SER D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 323 Processing helix chain 'D' and resid 324 through 325 No H-bonds generated for 'chain 'D' and resid 324 through 325' Processing helix chain 'D' and resid 326 through 336 removed outlier: 4.149A pdb=" N ILE D 334 " --> pdb=" O ASP D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 360 Processing helix chain 'D' and resid 363 through 369 removed outlier: 3.778A pdb=" N THR D 369 " --> pdb=" O ILE D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 386 removed outlier: 3.522A pdb=" N ARG D 386 " --> pdb=" O GLN D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 406 removed outlier: 3.586A pdb=" N ALA D 405 " --> pdb=" O LEU D 401 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE D 406 " --> pdb=" O MET D 402 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 401 through 406' Processing helix chain 'D' and resid 414 through 439 removed outlier: 3.512A pdb=" N SER D 419 " --> pdb=" O HIS D 415 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASN D 420 " --> pdb=" O ALA D 416 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA D 434 " --> pdb=" O LYS D 430 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N MET D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ALA D 437 " --> pdb=" O GLN D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 462 removed outlier: 3.567A pdb=" N LYS D 457 " --> pdb=" O GLU D 453 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG D 460 " --> pdb=" O GLN D 456 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 483 Processing helix chain 'D' and resid 496 through 504 removed outlier: 3.504A pdb=" N SER D 501 " --> pdb=" O GLN D 497 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N GLU D 502 " --> pdb=" O SER D 498 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE D 503 " --> pdb=" O THR D 499 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 179 Processing helix chain 'E' and resid 198 through 209 Processing helix chain 'E' and resid 237 through 251 Processing helix chain 'E' and resid 252 through 255 removed outlier: 3.911A pdb=" N ASP E 255 " --> pdb=" O GLY E 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 252 through 255' Processing helix chain 'E' and resid 269 through 287 removed outlier: 4.199A pdb=" N ILE E 273 " --> pdb=" O ILE E 269 " (cutoff:3.500A) Proline residue: E 275 - end of helix removed outlier: 3.742A pdb=" N THR E 281 " --> pdb=" O LEU E 277 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N PHE E 284 " --> pdb=" O THR E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 314 removed outlier: 3.511A pdb=" N ALA E 304 " --> pdb=" O MET E 300 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 323 removed outlier: 3.825A pdb=" N GLY E 322 " --> pdb=" O GLY E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 325 No H-bonds generated for 'chain 'E' and resid 324 through 325' Processing helix chain 'E' and resid 326 through 333 Processing helix chain 'E' and resid 357 through 360 Processing helix chain 'E' and resid 363 through 373 removed outlier: 3.584A pdb=" N GLY E 370 " --> pdb=" O PRO E 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 380 through 386 removed outlier: 3.505A pdb=" N ARG E 386 " --> pdb=" O GLN E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 439 removed outlier: 3.902A pdb=" N ASN E 420 " --> pdb=" O ALA E 416 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA E 424 " --> pdb=" O ASN E 420 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA E 437 " --> pdb=" O GLN E 433 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL E 438 " --> pdb=" O ALA E 434 " (cutoff:3.500A) Processing helix chain 'E' and resid 447 through 462 removed outlier: 3.886A pdb=" N GLN E 456 " --> pdb=" O LEU E 452 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG E 460 " --> pdb=" O GLN E 456 " (cutoff:3.500A) Processing helix chain 'E' and resid 472 through 485 Processing helix chain 'E' and resid 496 through 504 removed outlier: 5.395A pdb=" N GLU E 502 " --> pdb=" O SER E 498 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N PHE E 503 " --> pdb=" O THR E 499 " (cutoff:3.500A) 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 179 Processing helix chain 'F' and resid 198 through 209 removed outlier: 3.610A pdb=" N ILE F 202 " --> pdb=" O PRO F 198 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N CYS F 207 " --> pdb=" O ALA F 203 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 249 Processing helix chain 'F' and resid 268 through 272 Processing helix chain 'F' and resid 273 through 288 removed outlier: 3.571A pdb=" N THR F 281 " --> pdb=" O LEU F 277 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA F 282 " --> pdb=" O ALA F 278 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 314 removed outlier: 3.579A pdb=" N VAL F 310 " --> pdb=" O ALA F 306 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 323 removed outlier: 4.145A pdb=" N GLY F 322 " --> pdb=" O GLY F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 325 No H-bonds generated for 'chain 'F' and resid 324 through 325' Processing helix chain 'F' and resid 326 through 336 removed outlier: 4.004A pdb=" N ILE F 334 " --> pdb=" O ASP F 330 " (cutoff:3.500A) Processing helix chain 'F' and resid 357 through 360 Processing helix chain 'F' and resid 363 through 373 removed outlier: 3.575A pdb=" N LEU F 368 " --> pdb=" O PRO F 364 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE F 372 " --> pdb=" O LEU F 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 403 removed outlier: 4.399A pdb=" N LYS F 403 " --> pdb=" O ARG F 400 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 437 removed outlier: 3.588A pdb=" N SER F 419 " --> pdb=" O HIS F 415 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ASN F 420 " --> pdb=" O ALA F 416 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA F 437 " --> pdb=" O GLN F 433 " (cutoff:3.500A) Processing helix chain 'F' and resid 447 through 462 removed outlier: 3.552A pdb=" N TYR F 451 " --> pdb=" O ASP F 447 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG F 460 " --> pdb=" O GLN F 456 " (cutoff:3.500A) Processing helix chain 'F' and resid 472 through 485 Processing helix chain 'F' and resid 496 through 504 removed outlier: 3.669A pdb=" N LEU F 500 " --> pdb=" O PRO F 496 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER F 501 " --> pdb=" O GLN F 497 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLU F 502 " --> pdb=" O SER F 498 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE F 503 " --> pdb=" O THR F 499 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 72 removed outlier: 3.613A pdb=" N SER G 55 " --> pdb=" O LEU G 51 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASP G 56 " --> pdb=" O VAL G 52 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU G 57 " --> pdb=" O GLY G 53 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA G 63 " --> pdb=" O ALA G 59 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLY G 67 " --> pdb=" O ALA G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 78 removed outlier: 3.818A pdb=" N ALA G 77 " --> pdb=" O GLN G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 102 removed outlier: 3.601A pdb=" N ILE G 102 " --> pdb=" O LEU G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 157 removed outlier: 3.787A pdb=" N ILE G 124 " --> pdb=" O ASN G 120 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER G 141 " --> pdb=" O LYS G 137 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA G 142 " --> pdb=" O SER G 138 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU G 146 " --> pdb=" O ALA G 142 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU G 154 " --> pdb=" O LEU G 150 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG G 155 " --> pdb=" O GLN G 151 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN G 157 " --> pdb=" O LEU G 153 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 175 removed outlier: 3.529A pdb=" N PHE G 175 " --> pdb=" O LYS G 172 " (cutoff:3.500A) Processing helix chain 'G' and resid 193 through 199 removed outlier: 3.520A pdb=" N LYS G 199 " --> pdb=" O ASN G 195 " (cutoff:3.500A) Processing helix chain 'G' and resid 233 through 244 Processing helix chain 'G' and resid 254 through 304 removed outlier: 4.053A pdb=" N SER G 269 " --> pdb=" O MET G 265 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLY G 277 " --> pdb=" O LYS G 273 " (cutoff:3.500A) Proline residue: G 278 - end of helix removed outlier: 3.518A pdb=" N VAL G 285 " --> pdb=" O ARG G 281 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER G 288 " --> pdb=" O LYS G 284 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS G 298 " --> pdb=" O TRP G 294 " (cutoff:3.500A) Processing helix chain 'G' and resid 327 through 341 removed outlier: 3.879A pdb=" N LEU G 338 " --> pdb=" O VAL G 334 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N HIS G 341 " --> pdb=" O GLU G 337 " (cutoff:3.500A) Processing helix chain 'H' and resid 14 through 76 removed outlier: 3.843A pdb=" N ASN H 31 " --> pdb=" O GLN H 27 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU H 32 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU H 33 " --> pdb=" O GLY H 29 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LYS H 36 " --> pdb=" O LEU H 32 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG H 43 " --> pdb=" O ALA H 39 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY H 59 " --> pdb=" O LYS H 55 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU H 60 " --> pdb=" O MET H 56 " (cutoff:3.500A) Processing helix chain 'H' and resid 81 through 86 removed outlier: 3.527A pdb=" N ASN H 86 " --> pdb=" O THR H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 133 through 175 removed outlier: 3.600A pdb=" N ALA H 141 " --> pdb=" O ASN H 137 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU H 147 " --> pdb=" O GLU H 143 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER H 154 " --> pdb=" O SER H 150 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR H 157 " --> pdb=" O THR H 153 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASP H 159 " --> pdb=" O PHE H 155 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLU H 160 " --> pdb=" O VAL H 156 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ILE H 164 " --> pdb=" O GLU H 160 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N THR H 165 " --> pdb=" O ALA H 161 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 216 removed outlier: 3.516A pdb=" N GLU H 197 " --> pdb=" O GLU H 193 " (cutoff:3.500A) Processing helix chain 'I' and resid 7 through 26 removed outlier: 3.680A pdb=" N GLN I 11 " --> pdb=" O ASP I 7 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N MET I 16 " --> pdb=" O ILE I 12 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 108 removed outlier: 4.067A pdb=" N GLU I 35 " --> pdb=" O ASP I 31 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN I 49 " --> pdb=" O LEU I 45 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU I 51 " --> pdb=" O GLN I 47 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS I 52 " --> pdb=" O THR I 48 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N MET I 54 " --> pdb=" O ARG I 50 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR I 56 " --> pdb=" O LYS I 52 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS I 62 " --> pdb=" O GLU I 58 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE I 64 " --> pdb=" O LYS I 60 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP I 89 " --> pdb=" O ARG I 85 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU I 90 " --> pdb=" O ALA I 86 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU I 94 " --> pdb=" O LEU I 90 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER I 103 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL I 105 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP I 108 " --> pdb=" O LYS I 104 " (cutoff:3.500A) Processing helix chain 'I' and resid 109 through 128 removed outlier: 4.023A pdb=" N GLY I 118 " --> pdb=" O VAL I 114 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY I 123 " --> pdb=" O LEU I 119 " (cutoff:3.500A) Processing helix chain 'I' and resid 140 through 159 Proline residue: I 153 - end of helix removed outlier: 4.274A pdb=" N VAL I 157 " --> pdb=" O PRO I 153 " (cutoff:3.500A) Processing helix chain 'I' and resid 196 through 207 removed outlier: 3.546A pdb=" N ASP I 201 " --> pdb=" O GLU I 197 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU I 202 " --> pdb=" O SER I 198 " (cutoff:3.500A) Processing helix chain 'I' and resid 209 through 214 Processing helix chain 'J' and resid 7 through 93 removed outlier: 3.652A pdb=" N MET J 15 " --> pdb=" O GLN J 11 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N PHE J 38 " --> pdb=" O ALA J 34 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE J 40 " --> pdb=" O GLU J 36 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY J 43 " --> pdb=" O ASN J 39 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN J 47 " --> pdb=" O GLY J 43 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LYS J 60 " --> pdb=" O TYR J 56 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLN J 63 " --> pdb=" O LYS J 59 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE J 64 " --> pdb=" O LYS J 60 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU J 84 " --> pdb=" O ARG J 80 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE J 91 " --> pdb=" O ARG J 87 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 108 removed outlier: 3.529A pdb=" N LYS J 104 " --> pdb=" O GLN J 100 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL J 105 " --> pdb=" O ARG J 101 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP J 108 " --> pdb=" O LYS J 104 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 128 removed outlier: 3.639A pdb=" N TYR J 112 " --> pdb=" O ASP J 108 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N VAL J 114 " --> pdb=" O THR J 110 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY J 118 " --> pdb=" O VAL J 114 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU J 121 " --> pdb=" O ASP J 117 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY J 123 " --> pdb=" O LEU J 119 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN J 126 " --> pdb=" O GLN J 122 " (cutoff:3.500A) Processing helix chain 'J' and resid 140 through 159 Proline residue: J 153 - end of helix removed outlier: 3.790A pdb=" N LYS J 156 " --> pdb=" O ILE J 152 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL J 157 " --> pdb=" O PRO J 153 " (cutoff:3.500A) Processing helix chain 'J' and resid 195 through 207 removed outlier: 3.598A pdb=" N ILE J 203 " --> pdb=" O ARG J 199 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN J 206 " --> pdb=" O LEU J 202 " (cutoff:3.500A) Processing helix chain 'J' and resid 209 through 214 removed outlier: 3.705A pdb=" N GLY J 213 " --> pdb=" O PRO J 209 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 15 removed outlier: 3.613A pdb=" N ILE K 12 " --> pdb=" O VAL K 8 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS K 14 " --> pdb=" O LYS K 10 " (cutoff:3.500A) Processing helix chain 'K' and resid 16 through 32 removed outlier: 3.603A pdb=" N GLU K 20 " --> pdb=" O MET K 16 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU K 25 " --> pdb=" O GLN K 21 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS K 26 " --> pdb=" O GLU K 22 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU K 29 " --> pdb=" O GLU K 25 " (cutoff:3.500A) Processing helix chain 'K' and resid 38 through 47 removed outlier: 3.650A pdb=" N ARG K 44 " --> pdb=" O ILE K 40 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU K 45 " --> pdb=" O GLU K 41 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN K 47 " --> pdb=" O GLY K 43 " (cutoff:3.500A) Processing helix chain 'K' and resid 48 through 108 removed outlier: 4.015A pdb=" N LYS K 52 " --> pdb=" O THR K 48 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TYR K 56 " --> pdb=" O LYS K 52 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS K 59 " --> pdb=" O GLU K 55 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLN K 67 " --> pdb=" O GLN K 63 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS K 68 " --> pdb=" O ILE K 64 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LYS K 69 " --> pdb=" O GLU K 65 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE K 70 " --> pdb=" O GLN K 66 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN K 71 " --> pdb=" O GLN K 67 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN K 74 " --> pdb=" O ILE K 70 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU K 75 " --> pdb=" O GLN K 71 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU K 90 " --> pdb=" O ALA K 86 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU K 94 " --> pdb=" O LEU K 90 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP K 108 " --> pdb=" O LYS K 104 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 128 removed outlier: 3.654A pdb=" N TYR K 112 " --> pdb=" O ASP K 108 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL K 114 " --> pdb=" O THR K 110 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLY K 118 " --> pdb=" O VAL K 114 " (cutoff:3.500A) Processing helix chain 'K' and resid 140 through 159 removed outlier: 3.574A pdb=" N ALA K 146 " --> pdb=" O PRO K 142 " (cutoff:3.500A) Proline residue: K 153 - end of helix removed outlier: 3.847A pdb=" N LYS K 156 " --> pdb=" O ILE K 152 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL K 157 " --> pdb=" O PRO K 153 " (cutoff:3.500A) Processing helix chain 'K' and resid 196 through 207 removed outlier: 3.601A pdb=" N GLN K 205 " --> pdb=" O ASP K 201 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN K 206 " --> pdb=" O LEU K 202 " (cutoff:3.500A) Processing helix chain 'K' and resid 209 through 214 removed outlier: 3.545A pdb=" N GLY K 213 " --> pdb=" O PRO K 209 " (cutoff:3.500A) Processing helix chain 'L' and resid 13 through 24 removed outlier: 3.891A pdb=" N THR L 18 " --> pdb=" O GLU L 14 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY L 19 " --> pdb=" O ASP L 15 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU L 22 " --> pdb=" O THR L 18 " (cutoff:3.500A) Processing helix chain 'L' and resid 44 through 58 removed outlier: 3.652A pdb=" N ILE L 48 " --> pdb=" O THR L 44 " (cutoff:3.500A) Processing helix chain 'L' and resid 68 through 72 Processing helix chain 'L' and resid 74 through 79 Processing helix chain 'M' and resid 7 through 20 removed outlier: 3.510A pdb=" N GLN M 13 " --> pdb=" O GLN M 9 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG M 17 " --> pdb=" O GLN M 13 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA M 18 " --> pdb=" O ALA M 14 " (cutoff:3.500A) Processing helix chain 'M' and resid 20 through 28 Processing helix chain 'M' and resid 30 through 40 removed outlier: 3.682A pdb=" N ALA M 36 " --> pdb=" O ARG M 32 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS M 37 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU M 38 " --> pdb=" O LYS M 34 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU M 39 " --> pdb=" O GLN M 35 " (cutoff:3.500A) Processing helix chain 'M' and resid 43 through 74 removed outlier: 3.703A pdb=" N TYR M 47 " --> pdb=" O GLU M 43 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU M 52 " --> pdb=" O ARG M 48 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER M 57 " --> pdb=" O GLN M 53 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN M 66 " --> pdb=" O ALA M 62 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER M 70 " --> pdb=" O GLN M 66 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA M 71 " --> pdb=" O GLY M 67 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLU M 72 " --> pdb=" O ASN M 68 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLU M 74 " --> pdb=" O SER M 70 " (cutoff:3.500A) Processing helix chain 'M' and resid 75 through 91 removed outlier: 3.635A pdb=" N SER M 87 " --> pdb=" O GLY M 83 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN M 91 " --> pdb=" O SER M 87 " (cutoff:3.500A) Processing helix chain 'M' and resid 91 through 104 removed outlier: 3.513A pdb=" N GLY M 101 " --> pdb=" O ALA M 97 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL M 103 " --> pdb=" O LEU M 99 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N CYS M 104 " --> pdb=" O LEU M 100 " (cutoff:3.500A) Processing helix chain 'N' and resid 7 through 40 removed outlier: 3.811A pdb=" N GLN N 13 " --> pdb=" O GLN N 9 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA N 14 " --> pdb=" O GLN N 10 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU N 15 " --> pdb=" O LEU N 11 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU N 20 " --> pdb=" O LYS N 16 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ARG N 31 " --> pdb=" O LYS N 27 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU N 38 " --> pdb=" O LYS N 34 " (cutoff:3.500A) Processing helix chain 'N' and resid 41 through 55 removed outlier: 3.549A pdb=" N ARG N 48 " --> pdb=" O VAL N 44 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG N 49 " --> pdb=" O ASP N 45 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU N 54 " --> pdb=" O GLU N 50 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 91 removed outlier: 3.713A pdb=" N MET N 63 " --> pdb=" O GLN N 59 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY N 67 " --> pdb=" O MET N 63 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASN N 68 " --> pdb=" O GLY N 64 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU N 69 " --> pdb=" O SER N 65 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN N 80 " --> pdb=" O ALA N 76 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN N 82 " --> pdb=" O ARG N 78 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ASN N 91 " --> pdb=" O SER N 87 " (cutoff:3.500A) Processing helix chain 'N' and resid 93 through 102 removed outlier: 3.647A pdb=" N MET N 102 " --> pdb=" O GLN N 98 " (cutoff:3.500A) Processing helix chain 'O' and resid 7 through 29 removed outlier: 4.274A pdb=" N GLN O 13 " --> pdb=" O GLN O 9 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA O 14 " --> pdb=" O GLN O 10 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA O 25 " --> pdb=" O LYS O 21 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS O 29 " --> pdb=" O ALA O 25 " (cutoff:3.500A) Processing helix chain 'O' and resid 31 through 40 removed outlier: 3.557A pdb=" N LYS O 37 " --> pdb=" O LEU O 33 " (cutoff:3.500A) Processing helix chain 'O' and resid 42 through 104 removed outlier: 4.458A pdb=" N ARG O 48 " --> pdb=" O VAL O 44 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ARG O 49 " --> pdb=" O ASP O 45 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLN O 53 " --> pdb=" O ARG O 49 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N GLU O 54 " --> pdb=" O GLU O 50 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA O 62 " --> pdb=" O LYS O 58 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N MET O 63 " --> pdb=" O GLN O 59 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY O 64 " --> pdb=" O GLN O 60 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN O 68 " --> pdb=" O GLY O 64 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER O 70 " --> pdb=" O GLN O 66 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA O 71 " --> pdb=" O GLY O 67 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU O 72 " --> pdb=" O ASN O 68 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU O 74 " --> pdb=" O SER O 70 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN O 75 " --> pdb=" O ALA O 71 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA O 76 " --> pdb=" O GLU O 72 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ARG O 90 " --> pdb=" O SER O 86 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ASN O 91 " --> pdb=" O SER O 87 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N GLU O 93 " --> pdb=" O GLN O 89 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ARG O 94 " --> pdb=" O ARG O 90 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA O 97 " --> pdb=" O GLU O 93 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN O 98 " --> pdb=" O ARG O 94 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N CYS O 104 " --> pdb=" O LEU O 100 " (cutoff:3.500A) Processing helix chain 'P' and resid 73 through 84 removed outlier: 3.612A pdb=" N THR P 82 " --> pdb=" O ILE P 78 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ILE P 84 " --> pdb=" O LEU P 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 86 through 101 Processing helix chain 'P' and resid 121 through 130 Proline residue: P 128 - end of helix Processing helix chain 'P' and resid 134 through 150 removed outlier: 3.596A pdb=" N VAL P 138 " --> pdb=" O ASP P 134 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N HIS P 139 " --> pdb=" O LEU P 135 " (cutoff:3.500A) Processing helix chain 'P' and resid 157 through 173 removed outlier: 3.749A pdb=" N TYR P 163 " --> pdb=" O SER P 159 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ASN P 166 " --> pdb=" O ASN P 162 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N TRP P 167 " --> pdb=" O TYR P 163 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE P 168 " --> pdb=" O TYR P 164 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N THR P 170 " --> pdb=" O ASN P 166 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N GLN P 171 " --> pdb=" O TRP P 167 " (cutoff:3.500A) Processing helix chain 'P' and resid 179 through 191 removed outlier: 3.676A pdb=" N ALA P 184 " --> pdb=" O VAL P 180 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU P 189 " --> pdb=" O GLY P 185 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N MET P 190 " --> pdb=" O CYS P 186 " (cutoff:3.500A) Processing helix chain 'P' and resid 193 through 205 removed outlier: 3.646A pdb=" N ARG P 197 " --> pdb=" O VAL P 193 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE P 198 " --> pdb=" O ASN P 194 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA P 199 " --> pdb=" O GLU P 195 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU P 202 " --> pdb=" O PHE P 198 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA P 203 " --> pdb=" O ALA P 199 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLY P 205 " --> pdb=" O VAL P 201 " (cutoff:3.500A) Processing helix chain 'P' and resid 206 through 214 removed outlier: 3.514A pdb=" N VAL P 212 " --> pdb=" O CYS P 208 " (cutoff:3.500A) Processing helix chain 'P' and resid 220 through 232 Processing helix chain 'P' and resid 235 through 243 removed outlier: 3.697A pdb=" N CYS P 239 " --> pdb=" O SER P 235 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU P 240 " --> pdb=" O PRO P 236 " (cutoff:3.500A) Processing helix chain 'P' and resid 246 through 256 Processing helix chain 'P' and resid 262 through 277 removed outlier: 3.537A pdb=" N ILE P 266 " --> pdb=" O LYS P 262 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA P 269 " --> pdb=" O ARG P 265 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS P 277 " --> pdb=" O ASN P 273 " (cutoff:3.500A) Processing helix chain 'P' and resid 284 through 289 Processing helix chain 'P' and resid 296 through 306 removed outlier: 3.679A pdb=" N GLU P 301 " --> pdb=" O LEU P 297 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ASN P 302 " --> pdb=" O LYS P 298 " (cutoff:3.500A) Processing helix chain 'P' and resid 310 through 330 removed outlier: 3.663A pdb=" N SER P 314 " --> pdb=" O ASP P 310 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS P 318 " --> pdb=" O SER P 314 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU P 326 " --> pdb=" O GLU P 322 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER P 327 " --> pdb=" O LYS P 323 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL P 328 " --> pdb=" O LEU P 324 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N GLN P 329 " --> pdb=" O GLY P 325 " (cutoff:3.500A) Processing helix chain 'P' and resid 334 through 344 removed outlier: 3.522A pdb=" N SER P 343 " --> pdb=" O SER P 339 " (cutoff:3.500A) Processing helix chain 'P' and resid 349 through 354 removed outlier: 4.089A pdb=" N LYS P 353 " --> pdb=" O SER P 349 " (cutoff:3.500A) Processing helix chain 'P' and resid 354 through 361 removed outlier: 3.864A pdb=" N TRP P 358 " --> pdb=" O SER P 354 " (cutoff:3.500A) Processing helix chain 'P' and resid 363 through 368 Processing helix chain 'P' and resid 373 through 383 removed outlier: 3.831A pdb=" N SER P 383 " --> pdb=" O LEU P 379 " (cutoff:3.500A) Processing helix chain 'P' and resid 387 through 403 removed outlier: 4.003A pdb=" N VAL P 391 " --> pdb=" O GLN P 387 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR P 399 " --> pdb=" O ASP P 395 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N HIS P 402 " --> pdb=" O GLU P 398 " (cutoff:3.500A) Processing helix chain 'P' and resid 405 through 414 Processing helix chain 'P' and resid 414 through 423 removed outlier: 3.669A pdb=" N LEU P 418 " --> pdb=" O GLY P 414 " (cutoff:3.500A) Processing helix chain 'P' and resid 427 through 442 removed outlier: 3.964A pdb=" N MET P 442 " --> pdb=" O VAL P 438 " (cutoff:3.500A) Processing helix chain 'a' and resid 23 through 33 Processing helix chain 'a' and resid 53 through 75 removed outlier: 3.643A pdb=" N ARG a 57 " --> pdb=" O ASN a 53 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG a 73 " --> pdb=" O GLU a 69 " (cutoff:3.500A) Processing helix chain 'a' and resid 93 through 115 removed outlier: 3.635A pdb=" N GLU a 98 " --> pdb=" O MET a 94 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA a 99 " --> pdb=" O ILE a 95 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR a 113 " --> pdb=" O LYS a 109 " (cutoff:3.500A) Processing helix chain 'a' and resid 115 through 140 removed outlier: 3.639A pdb=" N LEU a 125 " --> pdb=" O ASN a 121 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU a 127 " --> pdb=" O LEU a 123 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU a 128 " --> pdb=" O GLU a 124 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE a 131 " --> pdb=" O GLU a 127 " (cutoff:3.500A) Processing helix chain 'a' and resid 179 through 192 removed outlier: 3.552A pdb=" N ARG a 185 " --> pdb=" O PRO a 181 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG a 192 " --> pdb=" O TRP a 188 " (cutoff:3.500A) Processing helix chain 'a' and resid 230 through 240 removed outlier: 3.838A pdb=" N LYS a 235 " --> pdb=" O ASN a 231 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ILE a 236 " --> pdb=" O ARG a 232 " (cutoff:3.500A) Processing helix chain 'a' and resid 253 through 288 removed outlier: 3.815A pdb=" N LYS a 288 " --> pdb=" O GLN a 284 " (cutoff:3.500A) Processing helix chain 'a' and resid 289 through 309 removed outlier: 3.749A pdb=" N ILE a 295 " --> pdb=" O ARG a 291 " (cutoff:3.500A) Processing helix chain 'a' and resid 329 through 341 removed outlier: 3.752A pdb=" N ILE a 333 " --> pdb=" O ASP a 329 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN a 334 " --> pdb=" O LEU a 330 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG a 339 " --> pdb=" O PHE a 335 " (cutoff:3.500A) Processing helix chain 'a' and resid 371 through 382 removed outlier: 3.687A pdb=" N VAL a 378 " --> pdb=" O PHE a 374 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N TYR a 381 " --> pdb=" O ILE a 377 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY a 382 " --> pdb=" O VAL a 378 " (cutoff:3.500A) Processing helix chain 'a' and resid 391 through 407 removed outlier: 4.620A pdb=" N ILE a 397 " --> pdb=" O PRO a 393 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE a 399 " --> pdb=" O THR a 395 " (cutoff:3.500A) Proline residue: a 400 - end of helix removed outlier: 3.891A pdb=" N MET a 406 " --> pdb=" O LEU a 402 " (cutoff:3.500A) Processing helix chain 'a' and resid 409 through 426 removed outlier: 3.573A pdb=" N ARG a 426 " --> pdb=" O TRP a 422 " (cutoff:3.500A) Processing helix chain 'a' and resid 426 through 433 removed outlier: 3.790A pdb=" N GLN a 433 " --> pdb=" O ARG a 429 " (cutoff:3.500A) Processing helix chain 'a' and resid 437 through 446 removed outlier: 3.637A pdb=" N THR a 442 " --> pdb=" O GLU a 438 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ILE a 443 " --> pdb=" O MET a 439 " (cutoff:3.500A) Processing helix chain 'a' and resid 448 through 464 Processing helix chain 'a' and resid 481 through 489 Processing helix chain 'a' and resid 491 through 496 removed outlier: 4.376A pdb=" N ARG a 496 " --> pdb=" O GLU a 492 " (cutoff:3.500A) Processing helix chain 'a' and resid 521 through 526 removed outlier: 3.587A pdb=" N ILE a 525 " --> pdb=" O PRO a 521 " (cutoff:3.500A) Processing helix chain 'a' and resid 528 through 559 removed outlier: 3.715A pdb=" N PHE a 532 " --> pdb=" O ASN a 528 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER a 535 " --> pdb=" O THR a 531 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET a 538 " --> pdb=" O ASN a 534 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS a 539 " --> pdb=" O SER a 535 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL a 542 " --> pdb=" O MET a 538 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE a 547 " --> pdb=" O ILE a 543 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU a 555 " --> pdb=" O PHE a 551 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER a 556 " --> pdb=" O GLY a 552 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LEU a 557 " --> pdb=" O VAL a 553 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N PHE a 558 " --> pdb=" O SER a 554 " (cutoff:3.500A) Processing helix chain 'a' and resid 565 through 573 removed outlier: 3.826A pdb=" N ILE a 569 " --> pdb=" O LYS a 565 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR a 570 " --> pdb=" O PRO a 566 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE a 571 " --> pdb=" O LEU a 567 " (cutoff:3.500A) Processing helix chain 'a' and resid 573 through 584 Processing helix chain 'a' and resid 584 through 598 removed outlier: 3.685A pdb=" N ILE a 589 " --> pdb=" O GLY a 585 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TYR a 598 " --> pdb=" O LYS a 594 " (cutoff:3.500A) Processing helix chain 'a' and resid 608 through 618 removed outlier: 3.570A pdb=" N HIS a 612 " --> pdb=" O SER a 608 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N MET a 616 " --> pdb=" O HIS a 612 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N PHE a 617 " --> pdb=" O PHE a 613 " (cutoff:3.500A) Processing helix chain 'a' and resid 632 through 646 removed outlier: 3.635A pdb=" N CYS a 638 " --> pdb=" O LYS a 634 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N PHE a 639 " --> pdb=" O GLY a 635 " (cutoff:3.500A) Processing helix chain 'a' and resid 646 through 655 removed outlier: 4.059A pdb=" N PHE a 654 " --> pdb=" O TRP a 650 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LYS a 655 " --> pdb=" O MET a 651 " (cutoff:3.500A) Processing helix chain 'a' and resid 715 through 730 removed outlier: 3.871A pdb=" N VAL a 719 " --> pdb=" O GLY a 715 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN a 721 " --> pdb=" O THR a 717 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE a 723 " --> pdb=" O VAL a 719 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N HIS a 724 " --> pdb=" O HIS a 720 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR a 728 " --> pdb=" O HIS a 724 " (cutoff:3.500A) Processing helix chain 'a' and resid 730 through 738 Processing helix chain 'a' and resid 740 through 759 removed outlier: 4.105A pdb=" N SER a 746 " --> pdb=" O LEU a 742 " (cutoff:3.500A) Processing helix chain 'a' and resid 761 through 766 Processing helix chain 'a' and resid 773 through 790 removed outlier: 4.005A pdb=" N PHE a 778 " --> pdb=" O LEU a 774 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR a 785 " --> pdb=" O ALA a 781 " (cutoff:3.500A) Processing helix chain 'a' and resid 792 through 809 removed outlier: 3.775A pdb=" N LEU a 806 " --> pdb=" O HIS a 802 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N HIS a 807 " --> pdb=" O ALA a 803 " (cutoff:3.500A) Processing helix chain 'b' and resid 4 through 27 removed outlier: 3.673A pdb=" N TYR b 8 " --> pdb=" O LEU b 4 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL b 13 " --> pdb=" O SER b 9 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL b 21 " --> pdb=" O ALA b 17 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR b 27 " --> pdb=" O GLY b 23 " (cutoff:3.500A) Processing helix chain 'b' and resid 30 through 35 removed outlier: 3.978A pdb=" N PHE b 33 " --> pdb=" O ASP b 30 " (cutoff:3.500A) Processing helix chain 'b' and resid 36 through 44 removed outlier: 4.178A pdb=" N THR b 44 " --> pdb=" O PHE b 40 " (cutoff:3.500A) Processing helix chain 'b' and resid 45 through 80 removed outlier: 4.310A pdb=" N TRP b 49 " --> pdb=" O SER b 45 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER b 50 " --> pdb=" O PRO b 46 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE b 58 " --> pdb=" O ILE b 54 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER b 61 " --> pdb=" O ALA b 57 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY b 64 " --> pdb=" O LEU b 60 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR b 70 " --> pdb=" O ALA b 66 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE b 71 " --> pdb=" O TRP b 67 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR b 72 " --> pdb=" O GLY b 68 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER b 75 " --> pdb=" O ILE b 71 " (cutoff:3.500A) Processing helix chain 'b' and resid 85 through 90 removed outlier: 4.442A pdb=" N LYS b 89 " --> pdb=" O ARG b 85 " (cutoff:3.500A) Processing helix chain 'b' and resid 91 through 97 Processing helix chain 'b' and resid 98 through 114 removed outlier: 3.567A pdb=" N ASN b 113 " --> pdb=" O ILE b 109 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N MET b 114 " --> pdb=" O VAL b 110 " (cutoff:3.500A) Processing helix chain 'b' and resid 127 through 169 removed outlier: 3.657A pdb=" N ALA b 133 " --> pdb=" O ARG b 129 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET b 137 " --> pdb=" O ALA b 133 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N SER b 147 " --> pdb=" O THR b 143 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN b 148 " --> pdb=" O VAL b 144 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA b 167 " --> pdb=" O ALA b 163 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN b 168 " --> pdb=" O LEU b 164 " (cutoff:3.500A) Processing helix chain 'b' and resid 172 through 198 removed outlier: 4.096A pdb=" N ILE b 178 " --> pdb=" O VAL b 174 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N VAL b 179 " --> pdb=" O LYS b 175 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU b 180 " --> pdb=" O ILE b 176 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE b 181 " --> pdb=" O LEU b 177 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE b 182 " --> pdb=" O ILE b 178 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE b 186 " --> pdb=" O PHE b 182 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N GLY b 187 " --> pdb=" O GLY b 183 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU b 188 " --> pdb=" O SER b 184 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL b 193 " --> pdb=" O PHE b 189 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR b 198 " --> pdb=" O ALA b 194 " (cutoff:3.500A) Processing helix chain 'd' and resid 13 through 23 removed outlier: 3.678A pdb=" N GLY d 18 " --> pdb=" O GLY d 14 " (cutoff:3.500A) Processing helix chain 'd' and resid 24 through 27 Processing helix chain 'd' and resid 29 through 38 removed outlier: 3.571A pdb=" N ASN d 35 " --> pdb=" O ALA d 31 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU d 36 " --> pdb=" O ASP d 32 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN d 38 " --> pdb=" O LEU d 34 " (cutoff:3.500A) Processing helix chain 'd' and resid 41 through 49 removed outlier: 3.501A pdb=" N LEU d 47 " --> pdb=" O GLU d 43 " (cutoff:3.500A) Processing helix chain 'd' and resid 50 through 52 No H-bonds generated for 'chain 'd' and resid 50 through 52' Processing helix chain 'd' and resid 66 through 87 removed outlier: 3.671A pdb=" N ILE d 70 " --> pdb=" O THR d 66 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASP d 72 " --> pdb=" O SER d 68 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG d 73 " --> pdb=" O VAL d 69 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N MET d 78 " --> pdb=" O LEU d 74 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N MET d 85 " --> pdb=" O GLU d 81 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN d 87 " --> pdb=" O ARG d 83 " (cutoff:3.500A) Processing helix chain 'd' and resid 93 through 101 removed outlier: 3.526A pdb=" N ILE d 100 " --> pdb=" O PHE d 96 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR d 101 " --> pdb=" O LEU d 97 " (cutoff:3.500A) Processing helix chain 'd' and resid 101 through 118 removed outlier: 3.815A pdb=" N ASP d 107 " --> pdb=" O SER d 103 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLY d 115 " --> pdb=" O LEU d 111 " (cutoff:3.500A) Processing helix chain 'd' and resid 121 through 125 Processing helix chain 'd' and resid 151 through 156 Processing helix chain 'd' and resid 163 through 167 removed outlier: 4.062A pdb=" N ASP d 166 " --> pdb=" O PHE d 163 " (cutoff:3.500A) Processing helix chain 'd' and resid 179 through 200 removed outlier: 3.739A pdb=" N LEU d 185 " --> pdb=" O ILE d 181 " (cutoff:3.500A) Processing helix chain 'd' and resid 202 through 207 removed outlier: 3.870A pdb=" N ASP d 206 " --> pdb=" O GLY d 202 " (cutoff:3.500A) Processing helix chain 'd' and resid 208 through 227 removed outlier: 3.636A pdb=" N PHE d 214 " --> pdb=" O PRO d 210 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE d 223 " --> pdb=" O ARG d 219 " (cutoff:3.500A) Processing helix chain 'd' and resid 233 through 240 Processing helix chain 'd' and resid 250 through 256 removed outlier: 3.569A pdb=" N GLN d 254 " --> pdb=" O GLU d 250 " (cutoff:3.500A) Processing helix chain 'd' and resid 260 through 267 removed outlier: 3.514A pdb=" N VAL d 264 " --> pdb=" O ASP d 260 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL d 267 " --> pdb=" O GLN d 263 " (cutoff:3.500A) Processing helix chain 'd' and resid 289 through 304 removed outlier: 4.131A pdb=" N GLU d 296 " --> pdb=" O ASP d 292 " (cutoff:3.500A) Processing helix chain 'd' and resid 305 through 307 No H-bonds generated for 'chain 'd' and resid 305 through 307' Processing helix chain 'd' and resid 312 through 338 removed outlier: 4.046A pdb=" N TYR d 316 " --> pdb=" O PHE d 312 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN d 324 " --> pdb=" O LYS d 320 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL d 330 " --> pdb=" O CYS d 326 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN d 338 " --> pdb=" O GLU d 334 " (cutoff:3.500A) Processing helix chain 'e' and resid 9 through 17 removed outlier: 3.971A pdb=" N THR e 15 " --> pdb=" O VAL e 11 " (cutoff:3.500A) Processing helix chain 'e' and resid 33 through 57 removed outlier: 3.752A pdb=" N LEU e 50 " --> pdb=" O VAL e 46 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA e 55 " --> pdb=" O PHE e 51 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE e 56 " --> pdb=" O TRP e 52 " (cutoff:3.500A) Processing helix chain 'e' and resid 69 through 78 removed outlier: 3.928A pdb=" N TRP e 74 " --> pdb=" O ASN e 70 " (cutoff:3.500A) Processing helix chain 's' and resid 421 through 446 removed outlier: 3.808A pdb=" N LEU s 429 " --> pdb=" O TRP s 425 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE s 433 " --> pdb=" O LEU s 429 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE s 436 " --> pdb=" O LEU s 432 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE s 437 " --> pdb=" O PHE s 433 " (cutoff:3.500A) Processing helix chain 'r' and resid 303 through 331 removed outlier: 3.649A pdb=" N ASN r 309 " --> pdb=" O PRO r 305 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ILE r 314 " --> pdb=" O LEU r 310 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR r 321 " --> pdb=" O GLY r 317 " (cutoff:3.500A) Processing helix chain 'c' and resid 8 through 10 No H-bonds generated for 'chain 'c' and resid 8 through 10' Processing helix chain 'c' and resid 11 through 45 removed outlier: 4.393A pdb=" N ALA c 15 " --> pdb=" O ALA c 11 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N MET c 23 " --> pdb=" O ALA c 19 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE c 25 " --> pdb=" O ALA c 21 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N SER c 26 " --> pdb=" O ALA c 22 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N SER c 37 " --> pdb=" O GLY c 33 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY c 40 " --> pdb=" O LYS c 36 " (cutoff:3.500A) Processing helix chain 'c' and resid 56 through 80 removed outlier: 3.627A pdb=" N ALA c 62 " --> pdb=" O PRO c 58 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE c 65 " --> pdb=" O MET c 61 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA c 66 " --> pdb=" O ALA c 62 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL c 72 " --> pdb=" O TYR c 68 " (cutoff:3.500A) Processing helix chain 'c' and resid 85 through 124 removed outlier: 3.587A pdb=" N LEU c 101 " --> pdb=" O LEU c 97 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER c 102 " --> pdb=" O SER c 98 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA c 105 " --> pdb=" O LEU c 101 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG c 119 " --> pdb=" O ASP c 115 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA c 122 " --> pdb=" O VAL c 118 " (cutoff:3.500A) Processing helix chain 'c' and resid 127 through 154 removed outlier: 3.560A pdb=" N ILE c 132 " --> pdb=" O PHE c 128 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEU c 133 " --> pdb=" O VAL c 129 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU c 141 " --> pdb=" O PHE c 137 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLY c 142 " --> pdb=" O ALA c 138 " (cutoff:3.500A) Processing helix chain 'g' and resid 10 through 45 removed outlier: 4.359A pdb=" N PHE g 14 " --> pdb=" O TYR g 10 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA g 15 " --> pdb=" O ALA g 11 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N MET g 23 " --> pdb=" O ALA g 19 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER g 26 " --> pdb=" O ALA g 22 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER g 37 " --> pdb=" O GLY g 33 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY g 40 " --> pdb=" O LYS g 36 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA g 42 " --> pdb=" O GLY g 38 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N MET g 44 " --> pdb=" O GLY g 40 " (cutoff:3.500A) Processing helix chain 'g' and resid 56 through 62 Processing helix chain 'g' and resid 62 through 79 removed outlier: 3.794A pdb=" N ALA g 66 " --> pdb=" O ALA g 62 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL g 72 " --> pdb=" O TYR g 68 " (cutoff:3.500A) Processing helix chain 'g' and resid 85 through 124 removed outlier: 3.556A pdb=" N LEU g 91 " --> pdb=" O TYR g 87 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN g 92 " --> pdb=" O ARG g 88 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA g 122 " --> pdb=" O VAL g 118 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN g 123 " --> pdb=" O ARG g 119 " (cutoff:3.500A) Processing helix chain 'g' and resid 126 through 154 removed outlier: 4.414A pdb=" N GLY g 130 " --> pdb=" O ARG g 126 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE g 132 " --> pdb=" O PHE g 128 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU g 133 " --> pdb=" O VAL g 129 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LEU g 141 " --> pdb=" O PHE g 137 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N GLY g 142 " --> pdb=" O ALA g 138 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL g 148 " --> pdb=" O TYR g 144 " (cutoff:3.500A) Processing helix chain 'k' and resid 10 through 45 removed outlier: 4.335A pdb=" N PHE k 14 " --> pdb=" O TYR k 10 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA k 15 " --> pdb=" O ALA k 11 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N MET k 23 " --> pdb=" O ALA k 19 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE k 25 " --> pdb=" O ALA k 21 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N SER k 26 " --> pdb=" O ALA k 22 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER k 37 " --> pdb=" O GLY k 33 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY k 40 " --> pdb=" O LYS k 36 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA k 42 " --> pdb=" O GLY k 38 " (cutoff:3.500A) Processing helix chain 'k' and resid 49 through 55 removed outlier: 3.763A pdb=" N ILE k 52 " --> pdb=" O PRO k 49 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N MET k 53 " --> pdb=" O GLU k 50 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LYS k 54 " --> pdb=" O MET k 51 " (cutoff:3.500A) Processing helix chain 'k' and resid 56 through 62 Processing helix chain 'k' and resid 62 through 79 removed outlier: 3.619A pdb=" N ALA k 66 " --> pdb=" O ALA k 62 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL k 72 " --> pdb=" O TYR k 68 " (cutoff:3.500A) Processing helix chain 'k' and resid 85 through 122 removed outlier: 3.602A pdb=" N VAL k 99 " --> pdb=" O ALA k 95 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER k 102 " --> pdb=" O SER k 98 " (cutoff:3.500A) Processing helix chain 'k' and resid 126 through 155 removed outlier: 4.295A pdb=" N GLY k 130 " --> pdb=" O ARG k 126 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU k 133 " --> pdb=" O VAL k 129 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE k 137 " --> pdb=" O LEU k 133 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU k 141 " --> pdb=" O PHE k 137 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N GLY k 142 " --> pdb=" O ALA k 138 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL k 148 " --> pdb=" O TYR k 144 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS k 155 " --> pdb=" O ILE k 151 " (cutoff:3.500A) Processing helix chain 'l' and resid 11 through 45 removed outlier: 4.166A pdb=" N ALA l 15 " --> pdb=" O ALA l 11 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N MET l 23 " --> pdb=" O ALA l 19 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N SER l 26 " --> pdb=" O ALA l 22 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER l 37 " --> pdb=" O GLY l 33 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY l 40 " --> pdb=" O LYS l 36 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA l 42 " --> pdb=" O GLY l 38 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA l 43 " --> pdb=" O THR l 39 " (cutoff:3.500A) Processing helix chain 'l' and resid 52 through 55 Processing helix chain 'l' and resid 56 through 79 removed outlier: 3.651A pdb=" N ILE l 65 " --> pdb=" O MET l 61 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA l 66 " --> pdb=" O ALA l 62 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL l 72 " --> pdb=" O TYR l 68 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER l 79 " --> pdb=" O LEU l 75 " (cutoff:3.500A) Processing helix chain 'l' and resid 85 through 121 removed outlier: 3.633A pdb=" N VAL l 99 " --> pdb=" O ALA l 95 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N SER l 102 " --> pdb=" O SER l 98 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL l 113 " --> pdb=" O ALA l 109 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL l 118 " --> pdb=" O GLY l 114 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG l 119 " --> pdb=" O ASP l 115 " (cutoff:3.500A) Processing helix chain 'l' and resid 124 through 126 No H-bonds generated for 'chain 'l' and resid 124 through 126' Processing helix chain 'l' and resid 127 through 154 removed outlier: 3.505A pdb=" N ILE l 132 " --> pdb=" O PHE l 128 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU l 133 " --> pdb=" O VAL l 129 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE l 137 " --> pdb=" O LEU l 133 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU l 141 " --> pdb=" O PHE l 137 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLY l 142 " --> pdb=" O ALA l 138 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE l 147 " --> pdb=" O LEU l 143 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL l 148 " --> pdb=" O TYR l 144 " (cutoff:3.500A) Processing helix chain 'm' and resid 8 through 10 No H-bonds generated for 'chain 'm' and resid 8 through 10' Processing helix chain 'm' and resid 11 through 46 removed outlier: 4.130A pdb=" N ALA m 15 " --> pdb=" O ALA m 11 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N MET m 23 " --> pdb=" O ALA m 19 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N SER m 26 " --> pdb=" O ALA m 22 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER m 37 " --> pdb=" O GLY m 33 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLY m 40 " --> pdb=" O LYS m 36 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA m 42 " --> pdb=" O GLY m 38 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL m 46 " --> pdb=" O ALA m 42 " (cutoff:3.500A) Processing helix chain 'm' and resid 56 through 79 removed outlier: 3.537A pdb=" N MET m 61 " --> pdb=" O ILE m 57 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA m 66 " --> pdb=" O ALA m 62 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY m 69 " --> pdb=" O ILE m 65 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL m 72 " --> pdb=" O TYR m 68 " (cutoff:3.500A) Processing helix chain 'm' and resid 85 through 121 removed outlier: 3.532A pdb=" N LEU m 91 " --> pdb=" O TYR m 87 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN m 92 " --> pdb=" O ARG m 88 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N SER m 102 " --> pdb=" O SER m 98 " (cutoff:3.500A) Processing helix chain 'm' and resid 126 through 155 removed outlier: 4.012A pdb=" N GLY m 130 " --> pdb=" O ARG m 126 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU m 133 " --> pdb=" O VAL m 129 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LEU m 141 " --> pdb=" O PHE m 137 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLY m 142 " --> pdb=" O ALA m 138 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL m 148 " --> pdb=" O TYR m 144 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LYS m 155 " --> pdb=" O ILE m 151 " (cutoff:3.500A) Processing helix chain 'n' and resid 8 through 10 No H-bonds generated for 'chain 'n' and resid 8 through 10' Processing helix chain 'n' and resid 11 through 45 removed outlier: 4.047A pdb=" N ALA n 15 " --> pdb=" O ALA n 11 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N MET n 23 " --> pdb=" O ALA n 19 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE n 25 " --> pdb=" O ALA n 21 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N SER n 26 " --> pdb=" O ALA n 22 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER n 37 " --> pdb=" O GLY n 33 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY n 40 " --> pdb=" O LYS n 36 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA n 42 " --> pdb=" O GLY n 38 " (cutoff:3.500A) Processing helix chain 'n' and resid 56 through 79 removed outlier: 3.590A pdb=" N ILE n 64 " --> pdb=" O VAL n 60 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ILE n 65 " --> pdb=" O MET n 61 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ALA n 66 " --> pdb=" O ALA n 62 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL n 72 " --> pdb=" O TYR n 68 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER n 79 " --> pdb=" O LEU n 75 " (cutoff:3.500A) Processing helix chain 'n' and resid 85 through 124 removed outlier: 3.595A pdb=" N GLN n 92 " --> pdb=" O ARG n 88 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N SER n 102 " --> pdb=" O SER n 98 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL n 118 " --> pdb=" O GLY n 114 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG n 119 " --> pdb=" O ASP n 115 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA n 122 " --> pdb=" O VAL n 118 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLN n 123 " --> pdb=" O ARG n 119 " (cutoff:3.500A) Processing helix chain 'n' and resid 126 through 154 removed outlier: 4.335A pdb=" N GLY n 130 " --> pdb=" O ARG n 126 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE n 132 " --> pdb=" O PHE n 128 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU n 133 " --> pdb=" O VAL n 129 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE n 137 " --> pdb=" O LEU n 133 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LEU n 141 " --> pdb=" O PHE n 137 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N GLY n 142 " --> pdb=" O ALA n 138 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL n 148 " --> pdb=" O TYR n 144 " (cutoff:3.500A) Processing helix chain 'o' and resid 11 through 45 removed outlier: 4.238A pdb=" N ALA o 15 " --> pdb=" O ALA o 11 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N MET o 23 " --> pdb=" O ALA o 19 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N SER o 26 " --> pdb=" O ALA o 22 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER o 37 " --> pdb=" O GLY o 33 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY o 40 " --> pdb=" O LYS o 36 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 53 removed outlier: 3.893A pdb=" N ILE o 52 " --> pdb=" O PRO o 49 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N MET o 53 " --> pdb=" O GLU o 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 49 through 53' Processing helix chain 'o' and resid 56 through 79 removed outlier: 3.619A pdb=" N ALA o 62 " --> pdb=" O PRO o 58 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE o 65 " --> pdb=" O MET o 61 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA o 66 " --> pdb=" O ALA o 62 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL o 72 " --> pdb=" O TYR o 68 " (cutoff:3.500A) Processing helix chain 'o' and resid 85 through 122 removed outlier: 4.280A pdb=" N SER o 102 " --> pdb=" O SER o 98 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA o 122 " --> pdb=" O VAL o 118 " (cutoff:3.500A) Processing helix chain 'o' and resid 124 through 126 No H-bonds generated for 'chain 'o' and resid 124 through 126' Processing helix chain 'o' and resid 127 through 155 removed outlier: 3.602A pdb=" N ILE o 132 " --> pdb=" O PHE o 128 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU o 133 " --> pdb=" O VAL o 129 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE o 137 " --> pdb=" O LEU o 133 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LEU o 141 " --> pdb=" O PHE o 137 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLY o 142 " --> pdb=" O ALA o 138 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU o 143 " --> pdb=" O GLU o 139 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL o 148 " --> pdb=" O TYR o 144 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE o 151 " --> pdb=" O ILE o 147 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LYS o 155 " --> pdb=" O ILE o 151 " (cutoff:3.500A) Processing helix chain 'p' and resid 11 through 46 removed outlier: 4.358A pdb=" N ALA p 15 " --> pdb=" O ALA p 11 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL p 16 " --> pdb=" O SER p 12 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET p 23 " --> pdb=" O ALA p 19 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N SER p 26 " --> pdb=" O ALA p 22 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER p 37 " --> pdb=" O GLY p 33 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY p 40 " --> pdb=" O LYS p 36 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N VAL p 46 " --> pdb=" O ALA p 42 " (cutoff:3.500A) Processing helix chain 'p' and resid 56 through 78 removed outlier: 3.565A pdb=" N ALA p 62 " --> pdb=" O PRO p 58 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY p 63 " --> pdb=" O VAL p 59 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE p 65 " --> pdb=" O MET p 61 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL p 72 " --> pdb=" O TYR p 68 " (cutoff:3.500A) Processing helix chain 'p' and resid 85 through 122 removed outlier: 4.072A pdb=" N SER p 102 " --> pdb=" O SER p 98 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL p 118 " --> pdb=" O GLY p 114 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG p 119 " --> pdb=" O ASP p 115 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA p 122 " --> pdb=" O VAL p 118 " (cutoff:3.500A) Processing helix chain 'p' and resid 126 through 155 removed outlier: 4.045A pdb=" N GLY p 130 " --> pdb=" O ARG p 126 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU p 133 " --> pdb=" O VAL p 129 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LEU p 141 " --> pdb=" O PHE p 137 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N GLY p 142 " --> pdb=" O ALA p 138 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU p 143 " --> pdb=" O GLU p 139 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL p 148 " --> pdb=" O TYR p 144 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LYS p 155 " --> pdb=" O ILE p 151 " (cutoff:3.500A) Processing helix chain 'q' and resid 12 through 45 removed outlier: 3.568A pdb=" N VAL q 16 " --> pdb=" O SER q 12 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N MET q 23 " --> pdb=" O ALA q 19 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER q 26 " --> pdb=" O ALA q 22 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER q 37 " --> pdb=" O GLY q 33 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA q 42 " --> pdb=" O GLY q 38 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA q 43 " --> pdb=" O THR q 39 " (cutoff:3.500A) Processing helix chain 'q' and resid 53 through 55 No H-bonds generated for 'chain 'q' and resid 53 through 55' Processing helix chain 'q' and resid 56 through 79 removed outlier: 3.594A pdb=" N ILE q 65 " --> pdb=" O MET q 61 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA q 66 " --> pdb=" O ALA q 62 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL q 72 " --> pdb=" O TYR q 68 " (cutoff:3.500A) Processing helix chain 'q' and resid 85 through 122 removed outlier: 3.567A pdb=" N GLN q 92 " --> pdb=" O ARG q 88 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N SER q 102 " --> pdb=" O SER q 98 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG q 119 " --> pdb=" O ASP q 115 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA q 122 " --> pdb=" O VAL q 118 " (cutoff:3.500A) Processing helix chain 'q' and resid 124 through 126 No H-bonds generated for 'chain 'q' and resid 124 through 126' Processing helix chain 'q' and resid 127 through 155 removed outlier: 3.636A pdb=" N ILE q 132 " --> pdb=" O PHE q 128 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LEU q 133 " --> pdb=" O VAL q 129 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU q 141 " --> pdb=" O PHE q 137 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLY q 142 " --> pdb=" O ALA q 138 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL q 148 " --> pdb=" O TYR q 144 " (cutoff:3.500A) Processing helix chain 'f' and resid 17 through 36 removed outlier: 3.661A pdb=" N TRP f 21 " --> pdb=" O VAL f 17 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ILE f 24 " --> pdb=" O ALA f 20 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N MET f 25 " --> pdb=" O TRP f 21 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS f 36 " --> pdb=" O PHE f 32 " (cutoff:3.500A) Processing helix chain 'f' and resid 65 through 76 Processing helix chain 'f' and resid 80 through 84 removed outlier: 3.986A pdb=" N PHE f 84 " --> pdb=" O GLY f 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 19 removed outlier: 7.762A pdb=" N THR A 82 " --> pdb=" O ARG A 44 " (cutoff:3.500A) removed outlier: 9.049A pdb=" N ARG A 44 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N LYS A 84 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLU A 41 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N THR A 63 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N LEU A 57 " --> pdb=" O MET A 61 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N MET A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 166 through 167 removed outlier: 3.661A pdb=" N VAL I 181 " --> pdb=" O ASN I 194 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ILE F 71 " --> pdb=" O THR F 115 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLU F 70 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N VAL F 86 " --> pdb=" O GLN F 97 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLN F 97 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLU A 41 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N LYS A 84 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 9.049A pdb=" N ARG A 44 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N THR A 82 " --> pdb=" O ARG A 44 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 28 through 31 removed outlier: 6.548A pdb=" N MET A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N LEU A 57 " --> pdb=" O MET A 61 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N THR A 63 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLN F 97 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N VAL F 86 " --> pdb=" O GLN F 97 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N THR C 30 " --> pdb=" O HIS C 22 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N VAL C 24 " --> pdb=" O VAL C 28 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N VAL C 28 " --> pdb=" O VAL C 24 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N GLN C 65 " --> pdb=" O ILE C 54 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N ILE C 54 " --> pdb=" O GLN C 65 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLU C 41 " --> pdb=" O ILE C 54 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N LYS C 84 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 9.135A pdb=" N ARG C 44 " --> pdb=" O THR C 82 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N THR C 82 " --> pdb=" O ARG C 44 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'I' and resid 166 through 167 removed outlier: 3.661A pdb=" N VAL I 181 " --> pdb=" O ASN I 194 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ILE I 190 " --> pdb=" O ASN I 185 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ILE F 71 " --> pdb=" O THR F 115 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLU F 70 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N THR C 82 " --> pdb=" O ARG C 44 " (cutoff:3.500A) removed outlier: 9.135A pdb=" N ARG C 44 " --> pdb=" O THR C 82 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N LYS C 84 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLU C 41 " --> pdb=" O ILE C 54 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N ILE C 54 " --> pdb=" O GLN C 65 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N GLN C 65 " --> pdb=" O ILE C 54 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 87 through 90 Processing sheet with id=AA6, first strand: chain 'A' and resid 98 through 99 removed outlier: 5.632A pdb=" N PHE A 99 " --> pdb=" O ALA A 313 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ILE A 272 " --> pdb=" O ALA A 310 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N VAL A 312 " --> pdb=" O ILE A 272 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N TYR A 274 " --> pdb=" O VAL A 312 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ASN A 314 " --> pdb=" O TYR A 274 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N GLY A 276 " --> pdb=" O ASN A 314 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL A 271 " --> pdb=" O SER A 345 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N MET A 347 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE A 273 " --> pdb=" O MET A 347 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N ASP A 349 " --> pdb=" O ILE A 273 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N VAL A 275 " --> pdb=" O ASP A 349 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU A 219 " --> pdb=" O LYS A 393 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 98 through 99 removed outlier: 5.632A pdb=" N PHE A 99 " --> pdb=" O ALA A 313 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ILE A 272 " --> pdb=" O ALA A 310 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N VAL A 312 " --> pdb=" O ILE A 272 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N TYR A 274 " --> pdb=" O VAL A 312 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ASN A 314 " --> pdb=" O TYR A 274 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N GLY A 276 " --> pdb=" O ASN A 314 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL A 271 " --> pdb=" O SER A 345 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N MET A 347 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE A 273 " --> pdb=" O MET A 347 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N ASP A 349 " --> pdb=" O ILE A 273 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N VAL A 275 " --> pdb=" O ASP A 349 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N THR A 245 " --> pdb=" O VAL A 431 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 163 through 167 removed outlier: 3.825A pdb=" N ASN A 157 " --> pdb=" O ASP A 134 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N ASP A 134 " --> pdb=" O ASN A 157 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 146 through 147 removed outlier: 6.756A pdb=" N GLU A 193 " --> pdb=" O THR A 177 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU A 192 " --> pdb=" O PHE A 203 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 226 through 227 removed outlier: 4.832A pdb=" N CYS A 240 " --> pdb=" O LEU A 227 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 295 through 296 Processing sheet with id=AB3, first strand: chain 'E' and resid 50 through 54 removed outlier: 6.237A pdb=" N ILE E 59 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N VAL E 53 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LEU E 57 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLU E 70 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ILE E 71 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL K 181 " --> pdb=" O ASN K 194 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 166 through 167 removed outlier: 4.137A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N VAL D 86 " --> pdb=" O GLN D 97 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N GLN D 97 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N ILE B 54 " --> pdb=" O GLN B 65 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N GLN B 65 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N VAL B 28 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N VAL B 24 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N THR B 30 " --> pdb=" O HIS B 22 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LEU E 57 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N VAL E 53 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ILE E 59 " --> pdb=" O SER E 51 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 50 through 54 removed outlier: 6.237A pdb=" N ILE E 59 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N VAL E 53 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LEU E 57 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N THR B 82 " --> pdb=" O ARG B 44 " (cutoff:3.500A) removed outlier: 9.113A pdb=" N ARG B 44 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N LYS B 84 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLU B 41 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N GLN D 97 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N VAL D 86 " --> pdb=" O GLN D 97 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 166 through 167 removed outlier: 3.735A pdb=" N VAL K 181 " --> pdb=" O ASN K 194 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ILE E 71 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLU E 70 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N THR B 82 " --> pdb=" O ARG B 44 " (cutoff:3.500A) removed outlier: 9.113A pdb=" N ARG B 44 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N LYS B 84 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLU B 41 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N GLN D 97 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N VAL D 86 " --> pdb=" O GLN D 97 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 166 through 167 removed outlier: 4.137A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N VAL D 86 " --> pdb=" O GLN D 97 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N GLN D 97 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N ILE B 54 " --> pdb=" O GLN B 65 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N GLN B 65 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N VAL B 28 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N VAL B 24 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N THR B 30 " --> pdb=" O HIS B 22 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLU E 70 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ILE E 71 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ILE K 190 " --> pdb=" O ASN K 185 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL K 181 " --> pdb=" O ASN K 194 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 87 through 90 Processing sheet with id=AB9, first strand: chain 'B' and resid 98 through 99 removed outlier: 5.850A pdb=" N PHE B 99 " --> pdb=" O ALA B 313 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N THR B 315 " --> pdb=" O PHE B 99 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ILE B 272 " --> pdb=" O ALA B 310 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N VAL B 312 " --> pdb=" O ILE B 272 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N TYR B 274 " --> pdb=" O VAL B 312 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ASN B 314 " --> pdb=" O TYR B 274 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N GLY B 276 " --> pdb=" O ASN B 314 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL B 271 " --> pdb=" O SER B 345 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N MET B 347 " --> pdb=" O VAL B 271 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE B 273 " --> pdb=" O MET B 347 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ASP B 349 " --> pdb=" O ILE B 273 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N VAL B 275 " --> pdb=" O ASP B 349 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU B 219 " --> pdb=" O LYS B 393 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 98 through 99 removed outlier: 5.850A pdb=" N PHE B 99 " --> pdb=" O ALA B 313 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N THR B 315 " --> pdb=" O PHE B 99 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ILE B 272 " --> pdb=" O ALA B 310 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N VAL B 312 " --> pdb=" O ILE B 272 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N TYR B 274 " --> pdb=" O VAL B 312 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ASN B 314 " --> pdb=" O TYR B 274 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N GLY B 276 " --> pdb=" O ASN B 314 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL B 271 " --> pdb=" O SER B 345 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N MET B 347 " --> pdb=" O VAL B 271 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE B 273 " --> pdb=" O MET B 347 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ASP B 349 " --> pdb=" O ILE B 273 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N VAL B 275 " --> pdb=" O ASP B 349 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N THR B 245 " --> pdb=" O VAL B 431 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 163 through 167 removed outlier: 6.470A pdb=" N HIS B 164 " --> pdb=" O ILE B 155 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ILE B 155 " --> pdb=" O HIS B 164 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE B 166 " --> pdb=" O TYR B 153 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ASN B 157 " --> pdb=" O ASP B 134 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N ASP B 134 " --> pdb=" O ASN B 157 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 146 through 147 removed outlier: 6.715A pdb=" N GLU B 193 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 226 through 227 removed outlier: 4.629A pdb=" N CYS B 240 " --> pdb=" O LEU B 227 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 295 through 297 Processing sheet with id=AC6, first strand: chain 'C' and resid 87 through 90 Processing sheet with id=AC7, first strand: chain 'C' and resid 98 through 99 removed outlier: 6.045A pdb=" N PHE C 99 " --> pdb=" O ALA C 313 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N THR C 315 " --> pdb=" O PHE C 99 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL C 271 " --> pdb=" O HIS C 343 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU C 219 " --> pdb=" O LYS C 393 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 98 through 99 removed outlier: 6.045A pdb=" N PHE C 99 " --> pdb=" O ALA C 313 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N THR C 315 " --> pdb=" O PHE C 99 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL C 271 " --> pdb=" O HIS C 343 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR C 246 " --> pdb=" O GLY C 408 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N THR C 245 " --> pdb=" O VAL C 431 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 163 through 167 removed outlier: 3.522A pdb=" N GLY C 154 " --> pdb=" O ILE C 166 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ASN C 157 " --> pdb=" O ASP C 134 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N ASP C 134 " --> pdb=" O ASN C 157 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 146 through 147 removed outlier: 6.603A pdb=" N GLU C 193 " --> pdb=" O THR C 177 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 226 through 227 removed outlier: 4.520A pdb=" N CYS C 240 " --> pdb=" O LEU C 227 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 295 through 297 Processing sheet with id=AD4, first strand: chain 'D' and resid 120 through 123 removed outlier: 3.673A pdb=" N ASP D 149 " --> pdb=" O VAL D 123 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 163 through 164 removed outlier: 4.185A pdb=" N ARG D 340 " --> pdb=" O ILE D 164 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 163 through 164 removed outlier: 4.185A pdb=" N ARG D 340 " --> pdb=" O ILE D 164 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE D 191 " --> pdb=" O PRO D 352 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N TYR D 378 " --> pdb=" O PRO D 396 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 169 through 170 removed outlier: 4.854A pdb=" N ILE D 183 " --> pdb=" O ILE D 170 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 120 through 123 removed outlier: 4.032A pdb=" N ASP E 149 " --> pdb=" O VAL E 123 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 163 through 164 removed outlier: 4.104A pdb=" N ARG E 340 " --> pdb=" O ILE E 164 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 169 through 170 removed outlier: 4.093A pdb=" N ILE E 183 " --> pdb=" O ILE E 170 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 257 through 263 removed outlier: 6.615A pdb=" N ILE E 229 " --> pdb=" O CYS E 258 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N PHE E 260 " --> pdb=" O ILE E 229 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N PHE E 231 " --> pdb=" O PHE E 260 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N ASN E 262 " --> pdb=" O PHE E 231 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N ALA E 233 " --> pdb=" O ASN E 262 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 120 through 123 Processing sheet with id=AE4, first strand: chain 'F' and resid 163 through 164 removed outlier: 4.186A pdb=" N ARG F 340 " --> pdb=" O ILE F 164 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 170 through 171 Processing sheet with id=AE6, first strand: chain 'F' and resid 260 through 263 removed outlier: 7.554A pdb=" N PHE F 260 " --> pdb=" O ILE F 229 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N PHE F 231 " --> pdb=" O PHE F 260 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N ASN F 262 " --> pdb=" O PHE F 231 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ALA F 233 " --> pdb=" O ASN F 262 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL F 293 " --> pdb=" O THR F 349 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N ILE F 351 " --> pdb=" O VAL F 293 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL F 295 " --> pdb=" O ILE F 351 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ILE F 353 " --> pdb=" O VAL F 295 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LEU F 297 " --> pdb=" O ILE F 353 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N THR F 355 " --> pdb=" O LEU F 297 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 7 through 8 removed outlier: 3.631A pdb=" N SER G 8 " --> pdb=" O VAL G 370 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N VAL G 370 " --> pdb=" O SER G 8 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'G' and resid 214 through 218 removed outlier: 6.502A pdb=" N VAL G 215 " --> pdb=" O ASN G 226 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ASN G 226 " --> pdb=" O VAL G 215 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU G 186 " --> pdb=" O ARG G 249 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 92 through 101 Processing sheet with id=AF1, first strand: chain 'L' and resid 7 through 10 removed outlier: 6.858A pdb=" N LEU L 7 " --> pdb=" O ILE L 63 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N LEU L 65 " --> pdb=" O LEU L 7 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ALA L 9 " --> pdb=" O LEU L 65 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N ASN L 67 " --> pdb=" O ALA L 9 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N GLY L 62 " --> pdb=" O ALA L 87 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N LEU L 89 " --> pdb=" O GLY L 62 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE L 64 " --> pdb=" O LEU L 89 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ILE L 91 " --> pdb=" O ILE L 64 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ILE L 66 " --> pdb=" O ILE L 91 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'L' and resid 28 through 29 removed outlier: 4.051A pdb=" N ASN L 29 " --> pdb=" O HIS L 33 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N HIS L 33 " --> pdb=" O ASN L 29 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'a' and resid 36 through 37 removed outlier: 3.863A pdb=" N ILE a 351 " --> pdb=" O PHE a 16 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'a' and resid 200 through 201 removed outlier: 3.519A pdb=" N GLY a 173 " --> pdb=" O PHE a 220 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ALA a 172 " --> pdb=" O TYR a 245 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 's' and resid 256 through 257 removed outlier: 4.068A pdb=" N SER s 256 " --> pdb=" O ARG s 264 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 's' and resid 266 through 268 removed outlier: 6.009A pdb=" N SER s 366 " --> pdb=" O SER s 414 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 's' and resid 279 through 282 removed outlier: 3.688A pdb=" N HIS s 279 " --> pdb=" O TYR s 276 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 's' and resid 304 through 310 removed outlier: 3.737A pdb=" N ALA s 305 " --> pdb=" O LEU s 325 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N THR s 320 " --> pdb=" O ILE s 345 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ILE s 345 " --> pdb=" O THR s 320 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N LYS s 322 " --> pdb=" O LEU s 343 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LEU s 343 " --> pdb=" O LYS s 322 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ILE s 324 " --> pdb=" O GLU s 341 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER s 328 " --> pdb=" O TRP s 337 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG s 335 " --> pdb=" O TYR s 330 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 's' and resid 354 through 356 3612 hydrogen bonds defined for protein. 10506 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: 26.77 Time building geometry restraints manager: 13.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.93 - 1.11: 9 1.11 - 1.29: 10466 1.29 - 1.47: 24911 1.47 - 1.65: 28220 1.65 - 1.83: 628 Bond restraints: 64234 Sorted by residual: bond pdb=" C TYR A 535 " pdb=" O TYR A 535 " ideal model delta sigma weight residual 1.236 0.930 0.306 1.26e-02 6.30e+03 5.90e+02 bond pdb=" CA TYR A 535 " pdb=" C TYR A 535 " ideal model delta sigma weight residual 1.523 1.223 0.300 1.35e-02 5.49e+03 4.94e+02 bond pdb=" C ASP B 592 " pdb=" O ASP B 592 " ideal model delta sigma weight residual 1.235 0.981 0.255 1.26e-02 6.30e+03 4.08e+02 bond pdb=" C ALA s 305 " pdb=" N ARG s 306 " ideal model delta sigma weight residual 1.331 1.566 -0.235 1.22e-02 6.72e+03 3.72e+02 bond pdb=" N TYR A 535 " pdb=" CA TYR A 535 " ideal model delta sigma weight residual 1.459 1.216 0.242 1.28e-02 6.10e+03 3.58e+02 ... (remaining 64229 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.31: 86487 7.31 - 14.62: 376 14.62 - 21.93: 50 21.93 - 29.24: 11 29.24 - 36.55: 4 Bond angle restraints: 86928 Sorted by residual: angle pdb=" N LEU D 212 " pdb=" CA LEU D 212 " pdb=" C LEU D 212 " ideal model delta sigma weight residual 109.95 73.59 36.36 1.44e+00 4.82e-01 6.38e+02 angle pdb=" N PHE A 534 " pdb=" CA PHE A 534 " pdb=" C PHE A 534 " ideal model delta sigma weight residual 111.36 132.49 -21.13 1.09e+00 8.42e-01 3.76e+02 angle pdb=" C ILE B 259 " pdb=" CA ILE B 259 " pdb=" CB ILE B 259 " ideal model delta sigma weight residual 111.29 141.56 -30.27 1.64e+00 3.72e-01 3.41e+02 angle pdb=" C ARG I 161 " pdb=" CA ARG I 161 " pdb=" CB ARG I 161 " ideal model delta sigma weight residual 110.42 146.97 -36.55 1.99e+00 2.53e-01 3.37e+02 angle pdb=" C ASP B 588 " pdb=" N PRO B 589 " pdb=" CA PRO B 589 " ideal model delta sigma weight residual 119.84 141.75 -21.91 1.25e+00 6.40e-01 3.07e+02 ... (remaining 86923 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.12: 36936 28.12 - 56.25: 1633 56.25 - 84.37: 172 84.37 - 112.50: 25 112.50 - 140.62: 2 Dihedral angle restraints: 38768 sinusoidal: 15210 harmonic: 23558 Sorted by residual: dihedral pdb=" N ASP L 99 " pdb=" C ASP L 99 " pdb=" CA ASP L 99 " pdb=" CB ASP L 99 " ideal model delta harmonic sigma weight residual 122.80 161.56 -38.76 0 2.50e+00 1.60e-01 2.40e+02 dihedral pdb=" C ASP L 99 " pdb=" N ASP L 99 " pdb=" CA ASP L 99 " pdb=" CB ASP L 99 " ideal model delta harmonic sigma weight residual -122.60 -161.04 38.44 0 2.50e+00 1.60e-01 2.36e+02 dihedral pdb=" CA ASN P 369 " pdb=" C ASN P 369 " pdb=" N TYR P 370 " pdb=" CA TYR P 370 " ideal model delta harmonic sigma weight residual -180.00 -104.09 -75.91 0 5.00e+00 4.00e-02 2.30e+02 ... (remaining 38765 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.351: 9879 0.351 - 0.703: 67 0.703 - 1.054: 13 1.054 - 1.405: 4 1.405 - 1.757: 3 Chirality restraints: 9966 Sorted by residual: chirality pdb=" CA ASP L 99 " pdb=" N ASP L 99 " pdb=" C ASP L 99 " pdb=" CB ASP L 99 " both_signs ideal model delta sigma weight residual False 2.51 0.75 1.76 2.00e-01 2.50e+01 7.72e+01 chirality pdb=" CA SER B 260 " pdb=" N SER B 260 " pdb=" C SER B 260 " pdb=" CB SER B 260 " both_signs ideal model delta sigma weight residual False 2.51 0.86 1.65 2.00e-01 2.50e+01 6.83e+01 chirality pdb=" CA PHE A 534 " pdb=" N PHE A 534 " pdb=" C PHE A 534 " pdb=" CB PHE A 534 " both_signs ideal model delta sigma weight residual False 2.51 0.97 1.54 2.00e-01 2.50e+01 5.96e+01 ... (remaining 9963 not shown) Planarity restraints: 11114 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 OLA r 403 " 0.289 2.00e-02 2.50e+03 2.21e-01 4.91e+02 pdb=" C11 OLA r 403 " -0.114 2.00e-02 2.50e+03 pdb=" C8 OLA r 403 " 0.118 2.00e-02 2.50e+03 pdb=" C9 OLA r 403 " -0.293 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 535 " -0.183 2.00e-02 2.50e+03 1.12e-01 2.51e+02 pdb=" CG TYR A 535 " 0.119 2.00e-02 2.50e+03 pdb=" CD1 TYR A 535 " 0.190 2.00e-02 2.50e+03 pdb=" CD2 TYR A 535 " 0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR A 535 " -0.097 2.00e-02 2.50e+03 pdb=" CE2 TYR A 535 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR A 535 " 0.016 2.00e-02 2.50e+03 pdb=" OH TYR A 535 " -0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL N 110 " -0.040 2.00e-02 2.50e+03 9.07e-02 8.22e+01 pdb=" C VAL N 110 " 0.156 2.00e-02 2.50e+03 pdb=" O VAL N 110 " -0.064 2.00e-02 2.50e+03 pdb=" N HIS N 111 " -0.053 2.00e-02 2.50e+03 ... (remaining 11111 not shown) Histogram of nonbonded interaction distances: 1.05 - 1.82: 11 1.82 - 2.59: 658 2.59 - 3.36: 79164 3.36 - 4.13: 150276 4.13 - 4.90: 282174 Nonbonded interactions: 512283 Sorted by model distance: nonbonded pdb=" NZ LYS L 94 " pdb=" OE1 GLN d 338 " model vdw 1.049 3.120 nonbonded pdb=" O SER M 70 " pdb=" OE2 GLU M 74 " model vdw 1.277 3.040 nonbonded pdb=" O SER M 70 " pdb=" CD GLU M 74 " model vdw 1.538 3.270 nonbonded pdb=" ND2 ASN a 465 " pdb=" CB SER a 471 " model vdw 1.633 3.520 nonbonded pdb=" O SER M 70 " pdb=" OE1 GLU M 74 " model vdw 1.669 3.040 ... (remaining 512278 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 16 through 250 or resid 258 through 612)) selection = (chain 'B' and (resid 16 through 558 or resid 567 through 612)) selection = (chain 'C' and (resid 16 through 250 or resid 258 through 558 or resid 567 throu \ gh 612)) } ncs_group { reference = (chain 'D' and (resid 38 through 213 or resid 225 through 506)) selection = chain 'E' selection = (chain 'F' and (resid 38 through 213 or resid 225 through 506)) } ncs_group { reference = (chain 'I' and ((resid 6 through 59 and (name N or name CA or name C or name O o \ r name CB )) or resid 60 through 223)) selection = (chain 'J' and ((resid 6 through 59 and (name N or name CA or name C or name O o \ r name CB )) or resid 60 through 223)) selection = (chain 'K' and resid 6 through 223) } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' } ncs_group { reference = chain 'c' selection = (chain 'g' and resid 6 through 155) selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = (chain 'o' and resid 6 through 155) selection = (chain 'p' and resid 6 through 155) selection = (chain 'q' and resid 6 through 155) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.020 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: 0.050 Extract box with map and model: 2.190 Check model and map are aligned: 0.370 Set scattering table: 0.470 Process input model: 113.140 Find NCS groups from input model: 1.830 Set up NCS constraints: 0.320 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 127.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 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 : 0.010 0.434 64234 Z= 0.625 Angle : 1.298 36.550 86928 Z= 0.767 Chirality : 0.086 1.757 9966 Planarity : 0.008 0.221 11109 Dihedral : 15.498 140.621 23645 Min Nonbonded Distance : 1.049 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.27 % Favored : 96.46 % Rotamer: Outliers : 0.61 % Allowed : 7.75 % Favored : 91.64 % Cbeta Deviations : 1.06 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.08 % 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: -5.55 (0.06), residues: 8098 helix: -4.23 (0.03), residues: 4433 sheet: -2.03 (0.17), residues: 707 loop : -2.82 (0.09), residues: 2958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP e 74 HIS 0.027 0.001 HIS N 111 PHE 0.087 0.002 PHE A 534 TYR 0.190 0.002 TYR A 535 ARG 0.012 0.001 ARG P 364 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16196 Ramachandran restraints generated. 8098 Oldfield, 0 Emsley, 8098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16196 Ramachandran restraints generated. 8098 Oldfield, 0 Emsley, 8098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1547 residues out of total 6850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 1507 time to evaluate : 5.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ASP cc_start: 0.7898 (p0) cc_final: 0.7600 (p0) REVERT: A 194 LEU cc_start: 0.8532 (mt) cc_final: 0.8030 (mp) REVERT: A 232 ARG cc_start: 0.8229 (ttm110) cc_final: 0.7812 (mtm-85) REVERT: A 277 CYS cc_start: 0.7183 (t) cc_final: 0.6972 (t) REVERT: A 445 PHE cc_start: 0.7599 (m-80) cc_final: 0.7348 (m-10) REVERT: A 458 MET cc_start: 0.7846 (mtt) cc_final: 0.7494 (mtm) REVERT: A 579 TYR cc_start: 0.7748 (t80) cc_final: 0.7500 (t80) REVERT: B 134 ASP cc_start: 0.7913 (p0) cc_final: 0.7599 (p0) REVERT: B 587 LYS cc_start: 0.7767 (OUTLIER) cc_final: 0.7406 (mmtp) REVERT: B 605 LEU cc_start: 0.8454 (mp) cc_final: 0.8018 (mt) REVERT: C 109 ILE cc_start: 0.9117 (tt) cc_final: 0.8912 (tt) REVERT: C 605 LEU cc_start: 0.8250 (mp) cc_final: 0.8030 (mp) REVERT: C 610 ASN cc_start: 0.6206 (m110) cc_final: 0.5757 (m-40) REVERT: D 251 ASN cc_start: 0.8495 (OUTLIER) cc_final: 0.7998 (t0) REVERT: D 362 THR cc_start: 0.8710 (m) cc_final: 0.8448 (p) REVERT: D 433 GLN cc_start: 0.8448 (tm-30) cc_final: 0.8181 (tm-30) REVERT: E 408 GLU cc_start: 0.7050 (tp30) cc_final: 0.6824 (tp30) REVERT: F 44 ARG cc_start: 0.8509 (mtt180) cc_final: 0.8157 (mtt-85) REVERT: F 164 ILE cc_start: 0.8995 (tt) cc_final: 0.8642 (pt) REVERT: F 423 TYR cc_start: 0.7509 (t80) cc_final: 0.7288 (t80) REVERT: G 239 HIS cc_start: 0.8414 (m-70) cc_final: 0.8052 (m-70) REVERT: G 262 LYS cc_start: 0.7449 (mmmt) cc_final: 0.7231 (tptp) REVERT: H 160 GLU cc_start: 0.7528 (mt-10) cc_final: 0.7310 (mt-10) REVERT: H 200 TYR cc_start: 0.9169 (t80) cc_final: 0.8944 (t80) REVERT: I 201 ASP cc_start: 0.8049 (t0) cc_final: 0.7804 (t0) REVERT: J 61 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8279 (mm-30) REVERT: J 74 ASN cc_start: 0.8262 (t0) cc_final: 0.8061 (m110) REVERT: K 70 ILE cc_start: 0.8632 (tt) cc_final: 0.8343 (tt) REVERT: K 96 ASN cc_start: 0.8713 (m110) cc_final: 0.8497 (m110) REVERT: K 164 ASP cc_start: 0.7811 (t70) cc_final: 0.7605 (t0) REVERT: L 41 LYS cc_start: 0.8461 (tppt) cc_final: 0.8227 (mmtp) REVERT: L 106 LEU cc_start: 0.8114 (tp) cc_final: 0.7869 (tt) REVERT: N 74 GLU cc_start: 0.8142 (tm-30) cc_final: 0.7452 (tp30) REVERT: N 84 MET cc_start: 0.7949 (ptp) cc_final: 0.7629 (ptt) REVERT: O 75 GLN cc_start: 0.8401 (tp-100) cc_final: 0.7823 (mm-40) REVERT: O 85 GLN cc_start: 0.8571 (mm-40) cc_final: 0.8305 (mm-40) REVERT: O 102 MET cc_start: 0.8623 (mtm) cc_final: 0.8364 (mtp) REVERT: P 223 TYR cc_start: 0.8528 (t80) cc_final: 0.8016 (t80) REVERT: P 366 ASN cc_start: 0.6530 (OUTLIER) cc_final: 0.6319 (m-40) REVERT: a 88 VAL cc_start: 0.8081 (OUTLIER) cc_final: 0.7266 (p) REVERT: a 415 LEU cc_start: 0.9076 (mp) cc_final: 0.8852 (mp) REVERT: a 439 MET cc_start: 0.6134 (tpp) cc_final: 0.5482 (ppp) REVERT: a 610 LEU cc_start: 0.8787 (mm) cc_final: 0.8400 (mt) REVERT: b 19 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8906 (tm) REVERT: b 107 MET cc_start: 0.7891 (tpt) cc_final: 0.7614 (tpp) REVERT: d 171 GLN cc_start: 0.8061 (tt0) cc_final: 0.7535 (tp40) REVERT: e 34 ARG cc_start: 0.7084 (ttt90) cc_final: 0.6072 (tmm160) REVERT: e 48 CYS cc_start: 0.7227 (m) cc_final: 0.6957 (m) REVERT: s 436 PHE cc_start: 0.8101 (t80) cc_final: 0.7878 (t80) REVERT: r 336 TYR cc_start: 0.5518 (p90) cc_final: 0.4645 (p90) REVERT: l 115 ASP cc_start: 0.8035 (t70) cc_final: 0.7794 (t0) REVERT: m 17 MET cc_start: 0.8599 (mmp) cc_final: 0.8203 (mmp) REVERT: m 147 ILE cc_start: 0.8871 (pt) cc_final: 0.8648 (pt) REVERT: n 51 MET cc_start: 0.7985 (mpp) cc_final: 0.7566 (ptp) REVERT: p 68 TYR cc_start: 0.8486 (m-10) cc_final: 0.8227 (m-10) REVERT: p 139 GLU cc_start: 0.8021 (tm-30) cc_final: 0.7647 (tm-30) REVERT: q 50 GLU cc_start: 0.8140 (mp0) cc_final: 0.7753 (mp0) REVERT: f 25 MET cc_start: 0.7904 (ttm) cc_final: 0.7659 (ttm) outliers start: 40 outliers final: 18 residues processed: 1546 average time/residue: 0.6484 time to fit residues: 1631.7202 Evaluate side-chains 1011 residues out of total 6850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 988 time to evaluate : 5.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 534 PHE Chi-restraints excluded: chain B residue 560 GLN Chi-restraints excluded: chain B residue 587 LYS Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain D residue 250 GLU Chi-restraints excluded: chain D residue 251 ASN Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain O residue 113 ASN Chi-restraints excluded: chain P residue 296 VAL Chi-restraints excluded: chain P residue 366 ASN Chi-restraints excluded: chain a residue 88 VAL Chi-restraints excluded: chain a residue 482 ARG Chi-restraints excluded: chain b residue 19 LEU Chi-restraints excluded: chain e residue 74 TRP Chi-restraints excluded: chain s residue 270 GLN Chi-restraints excluded: chain g residue 59 VAL Chi-restraints excluded: chain k residue 59 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 806 random chunks: chunk 680 optimal weight: 0.7980 chunk 610 optimal weight: 5.9990 chunk 338 optimal weight: 9.9990 chunk 208 optimal weight: 0.8980 chunk 412 optimal weight: 30.0000 chunk 326 optimal weight: 9.9990 chunk 631 optimal weight: 1.9990 chunk 244 optimal weight: 0.0070 chunk 384 optimal weight: 9.9990 chunk 470 optimal weight: 0.0370 chunk 731 optimal weight: 5.9990 overall best weight: 0.7478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN A 225 HIS B 242 GLN B 314 ASN B 397 ASN C 213 GLN C 261 GLN C 522 GLN C 573 HIS C 603 GLN C 609 GLN E 251 ASN E 385 ASN E 482 GLN F 226 ASN F 262 ASN F 288 GLN F 385 ASN ** F 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 482 GLN G 39 ASN G 194 HIS G 239 HIS G 275 GLN H 91 GLN ** H 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 78 GLN J 78 GLN J 149 GLN J 206 GLN K 67 GLN K 100 GLN K 169 GLN L 35 ASN L 57 ASN L 67 ASN M 82 GLN ** M 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 85 GLN N 88 GLN N 113 ASN O 80 GLN ** O 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 222 GLN P 241 HIS P 273 ASN P 439 GLN P 444 HIS a 53 ASN a 76 ASN ** a 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 390 ASN a 412 HIS a 465 ASN a 534 ASN a 568 ASN a 626 ASN a 633 GLN a 735 ASN a 751 GLN a 812 GLN b 90 ASN b 132 HIS d 297 HIS d 309 GLN ** e 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 270 GLN s 336 HIS s 358 GLN c 78 ASN g 124 GLN k 81 ASN k 124 GLN l 78 ASN l 92 GLN m 78 ASN ** m 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 92 GLN n 123 GLN o 78 ASN q 78 ASN q 124 GLN Total number of N/Q/H flips: 75 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 64234 Z= 0.205 Angle : 0.687 11.991 86928 Z= 0.361 Chirality : 0.043 0.236 9966 Planarity : 0.006 0.152 11109 Dihedral : 9.026 126.534 9343 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.16 % Favored : 95.68 % Rotamer: Outliers : 2.34 % Allowed : 13.09 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.08 % Twisted Proline : 0.64 % Twisted General : 0.04 % 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: -3.07 (0.08), residues: 8098 helix: -1.72 (0.06), residues: 4480 sheet: -1.81 (0.18), residues: 710 loop : -2.35 (0.10), residues: 2908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP e 74 HIS 0.008 0.001 HIS P 139 PHE 0.035 0.001 PHE p 128 TYR 0.031 0.002 TYR L 98 ARG 0.008 0.001 ARG I 131 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16196 Ramachandran restraints generated. 8098 Oldfield, 0 Emsley, 8098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16196 Ramachandran restraints generated. 8098 Oldfield, 0 Emsley, 8098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1265 residues out of total 6850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 1113 time to evaluate : 5.573 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: A 100 ASP cc_start: 0.8159 (p0) cc_final: 0.7874 (p0) REVERT: A 232 ARG cc_start: 0.8221 (ttm110) cc_final: 0.7743 (mtm-85) REVERT: A 445 PHE cc_start: 0.7637 (m-80) cc_final: 0.7410 (m-10) REVERT: B 70 THR cc_start: 0.9265 (p) cc_final: 0.9045 (p) REVERT: B 157 ASN cc_start: 0.8045 (p0) cc_final: 0.7754 (p0) REVERT: B 605 LEU cc_start: 0.8318 (mp) cc_final: 0.7967 (tt) REVERT: D 251 ASN cc_start: 0.8648 (OUTLIER) cc_final: 0.7761 (t0) REVERT: D 298 THR cc_start: 0.9099 (OUTLIER) cc_final: 0.8857 (t) REVERT: D 326 TYR cc_start: 0.8870 (p90) cc_final: 0.8621 (p90) REVERT: E 287 TYR cc_start: 0.8112 (m-10) cc_final: 0.7827 (m-10) REVERT: E 491 MET cc_start: 0.8459 (mtp) cc_final: 0.8132 (mtm) REVERT: F 44 ARG cc_start: 0.8487 (mtt180) cc_final: 0.8228 (mtt-85) REVERT: F 212 LEU cc_start: 0.8266 (mt) cc_final: 0.7614 (mp) REVERT: F 435 MET cc_start: 0.7177 (tpt) cc_final: 0.6941 (tpt) REVERT: G 239 HIS cc_start: 0.8345 (m90) cc_final: 0.8096 (m-70) REVERT: H 206 GLN cc_start: 0.8359 (mm110) cc_final: 0.8143 (mt0) REVERT: I 88 ASP cc_start: 0.7871 (OUTLIER) cc_final: 0.7391 (t0) REVERT: J 52 LYS cc_start: 0.8348 (tptp) cc_final: 0.8069 (tppt) REVERT: J 74 ASN cc_start: 0.8235 (t0) cc_final: 0.8010 (m110) REVERT: J 157 VAL cc_start: 0.8587 (t) cc_final: 0.8376 (p) REVERT: K 162 ASP cc_start: 0.7711 (p0) cc_final: 0.7270 (t0) REVERT: K 163 VAL cc_start: 0.9138 (m) cc_final: 0.8841 (m) REVERT: L 41 LYS cc_start: 0.8473 (tppt) cc_final: 0.8221 (mmtp) REVERT: L 47 GLU cc_start: 0.8527 (mt-10) cc_final: 0.8282 (mt-10) REVERT: M 75 GLN cc_start: 0.7758 (tm-30) cc_final: 0.7500 (tm-30) REVERT: M 88 GLN cc_start: 0.8189 (tm-30) cc_final: 0.7932 (tm-30) REVERT: M 107 ARG cc_start: 0.8097 (mtm-85) cc_final: 0.7785 (mtm-85) REVERT: N 72 GLU cc_start: 0.8015 (tm-30) cc_final: 0.7796 (tp30) REVERT: N 74 GLU cc_start: 0.7756 (tm-30) cc_final: 0.7520 (tm-30) REVERT: O 79 ARG cc_start: 0.8515 (mtp180) cc_final: 0.8254 (tmt-80) REVERT: O 80 GLN cc_start: 0.7920 (mm-40) cc_final: 0.7668 (mm110) REVERT: O 106 VAL cc_start: 0.8691 (m) cc_final: 0.8486 (t) REVERT: P 287 TYR cc_start: 0.5873 (m-10) cc_final: 0.5631 (m-10) REVERT: P 366 ASN cc_start: 0.6709 (OUTLIER) cc_final: 0.6370 (m-40) REVERT: a 439 MET cc_start: 0.5766 (tpp) cc_final: 0.5376 (ppp) REVERT: d 171 GLN cc_start: 0.8010 (tt0) cc_final: 0.7498 (tp40) REVERT: e 28 VAL cc_start: 0.7649 (OUTLIER) cc_final: 0.7095 (t) REVERT: e 34 ARG cc_start: 0.6831 (ttt90) cc_final: 0.5956 (tmm160) REVERT: e 48 CYS cc_start: 0.7347 (m) cc_final: 0.6932 (m) REVERT: e 67 GLN cc_start: 0.7479 (tt0) cc_final: 0.7208 (tt0) REVERT: s 291 GLN cc_start: 0.7847 (tm-30) cc_final: 0.7286 (tm-30) REVERT: r 336 TYR cc_start: 0.5425 (p90) cc_final: 0.4695 (p90) REVERT: g 64 ILE cc_start: 0.8881 (mm) cc_final: 0.8556 (mt) REVERT: k 17 MET cc_start: 0.8315 (mmp) cc_final: 0.8028 (mmp) REVERT: m 17 MET cc_start: 0.8594 (mmp) cc_final: 0.8286 (mmp) REVERT: n 48 ARG cc_start: 0.7930 (tpp80) cc_final: 0.7531 (tpp80) REVERT: p 139 GLU cc_start: 0.8175 (tm-30) cc_final: 0.7825 (tm-30) REVERT: q 50 GLU cc_start: 0.8137 (mp0) cc_final: 0.7726 (mp0) REVERT: f 32 PHE cc_start: 0.8040 (m-80) cc_final: 0.7761 (m-80) outliers start: 152 outliers final: 81 residues processed: 1207 average time/residue: 0.6524 time to fit residues: 1334.5235 Evaluate side-chains 1024 residues out of total 6850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 938 time to evaluate : 5.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 534 PHE Chi-restraints excluded: chain A residue 573 HIS Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 488 ASP Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain C residue 18 PHE Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 138 CYS Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 481 GLU Chi-restraints excluded: chain C residue 609 GLN Chi-restraints excluded: chain D residue 251 ASN Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain E residue 330 ASP Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain G residue 75 TYR Chi-restraints excluded: chain G residue 112 TYR Chi-restraints excluded: chain G residue 175 PHE Chi-restraints excluded: chain I residue 73 SER Chi-restraints excluded: chain I residue 88 ASP Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain J residue 162 ASP Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain O residue 113 ASN Chi-restraints excluded: chain P residue 66 LEU Chi-restraints excluded: chain P residue 187 LEU Chi-restraints excluded: chain P residue 242 LEU Chi-restraints excluded: chain P residue 296 VAL Chi-restraints excluded: chain P residue 366 ASN Chi-restraints excluded: chain a residue 330 LEU Chi-restraints excluded: chain a residue 390 ASN Chi-restraints excluded: chain a residue 472 LEU Chi-restraints excluded: chain a residue 756 LEU Chi-restraints excluded: chain a residue 830 HIS Chi-restraints excluded: chain b residue 128 HIS Chi-restraints excluded: chain d residue 41 THR Chi-restraints excluded: chain d residue 124 GLU Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain e residue 10 VAL Chi-restraints excluded: chain e residue 27 PHE Chi-restraints excluded: chain e residue 28 VAL Chi-restraints excluded: chain e residue 57 LEU Chi-restraints excluded: chain e residue 73 ILE Chi-restraints excluded: chain s residue 265 ILE Chi-restraints excluded: chain s residue 319 VAL Chi-restraints excluded: chain s residue 342 ASN Chi-restraints excluded: chain s residue 343 LEU Chi-restraints excluded: chain s residue 425 TRP Chi-restraints excluded: chain s residue 429 LEU Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain g residue 50 GLU Chi-restraints excluded: chain g residue 59 VAL Chi-restraints excluded: chain g residue 67 ILE Chi-restraints excluded: chain k residue 56 ILE Chi-restraints excluded: chain k residue 59 VAL Chi-restraints excluded: chain k residue 147 ILE Chi-restraints excluded: chain l residue 64 ILE Chi-restraints excluded: chain l residue 146 LEU Chi-restraints excluded: chain l residue 147 ILE Chi-restraints excluded: chain m residue 59 VAL Chi-restraints excluded: chain m residue 81 ASN Chi-restraints excluded: chain n residue 9 GLU Chi-restraints excluded: chain n residue 143 LEU Chi-restraints excluded: chain p residue 59 VAL Chi-restraints excluded: chain q residue 45 SER Chi-restraints excluded: chain q residue 59 VAL Chi-restraints excluded: chain q residue 91 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 806 random chunks: chunk 406 optimal weight: 7.9990 chunk 227 optimal weight: 0.7980 chunk 609 optimal weight: 7.9990 chunk 498 optimal weight: 6.9990 chunk 201 optimal weight: 1.9990 chunk 733 optimal weight: 1.9990 chunk 792 optimal weight: 4.9990 chunk 653 optimal weight: 3.9990 chunk 727 optimal weight: 7.9990 chunk 249 optimal weight: 2.9990 chunk 588 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 GLN C 430 GLN C 573 HIS ** C 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 456 GLN ** F 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 288 GLN ** F 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 88 GLN ** H 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 152 GLN K 96 ASN K 169 GLN K 221 ASN L 35 ASN M 111 HIS M 113 ASN N 85 GLN N 113 ASN O 113 ASN ** P 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 369 ASN P 439 GLN P 444 HIS ** a 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 278 HIS a 720 HIS ** b 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 64234 Z= 0.306 Angle : 0.668 12.272 86928 Z= 0.345 Chirality : 0.044 0.215 9966 Planarity : 0.005 0.151 11109 Dihedral : 8.543 129.237 9319 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.54 % Favored : 95.34 % Rotamer: Outliers : 3.14 % Allowed : 15.55 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.08 % Twisted Proline : 0.64 % Twisted General : 0.05 % 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: -1.83 (0.09), residues: 8098 helix: -0.49 (0.07), residues: 4530 sheet: -1.57 (0.18), residues: 709 loop : -2.17 (0.10), residues: 2859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP e 74 HIS 0.018 0.001 HIS P 139 PHE 0.021 0.001 PHE E 260 TYR 0.030 0.002 TYR o 144 ARG 0.008 0.001 ARG P 143 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16196 Ramachandran restraints generated. 8098 Oldfield, 0 Emsley, 8098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16196 Ramachandran restraints generated. 8098 Oldfield, 0 Emsley, 8098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1173 residues out of total 6850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 969 time to evaluate : 5.563 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: A 232 ARG cc_start: 0.8326 (ttm110) cc_final: 0.7946 (mtm-85) REVERT: A 445 PHE cc_start: 0.7622 (m-80) cc_final: 0.7366 (m-10) REVERT: B 458 MET cc_start: 0.9028 (mmm) cc_final: 0.8746 (mmt) REVERT: D 161 GLN cc_start: 0.8532 (tp40) cc_final: 0.8055 (tp-100) REVERT: D 251 ASN cc_start: 0.8752 (OUTLIER) cc_final: 0.7891 (t0) REVERT: D 329 THR cc_start: 0.8511 (m) cc_final: 0.8277 (p) REVERT: E 371 TYR cc_start: 0.8286 (m-10) cc_final: 0.8008 (m-10) REVERT: F 44 ARG cc_start: 0.8650 (mtt180) cc_final: 0.8347 (mtt-85) REVERT: F 212 LEU cc_start: 0.8362 (mt) cc_final: 0.7900 (mp) REVERT: F 423 TYR cc_start: 0.7418 (t80) cc_final: 0.7144 (t80) REVERT: G 239 HIS cc_start: 0.8332 (m90) cc_final: 0.8127 (m-70) REVERT: H 30 ARG cc_start: 0.7004 (ttp-110) cc_final: 0.6799 (ttm110) REVERT: H 86 ASN cc_start: 0.8884 (m-40) cc_final: 0.8592 (m-40) REVERT: H 152 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.8364 (mm-40) REVERT: J 154 VAL cc_start: 0.8767 (OUTLIER) cc_final: 0.8561 (t) REVERT: K 162 ASP cc_start: 0.7786 (p0) cc_final: 0.7433 (t0) REVERT: L 47 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8292 (mt-10) REVERT: M 75 GLN cc_start: 0.7780 (tm-30) cc_final: 0.7575 (tm-30) REVERT: M 88 GLN cc_start: 0.8301 (tm-30) cc_final: 0.8015 (tm-30) REVERT: N 72 GLU cc_start: 0.8028 (tm-30) cc_final: 0.7788 (tp30) REVERT: N 74 GLU cc_start: 0.7833 (tm-30) cc_final: 0.7481 (tm-30) REVERT: O 79 ARG cc_start: 0.8512 (mtp180) cc_final: 0.8236 (tmt-80) REVERT: O 80 GLN cc_start: 0.7824 (mm-40) cc_final: 0.7480 (mm110) REVERT: a 439 MET cc_start: 0.5765 (tpp) cc_final: 0.5357 (tmm) REVERT: e 28 VAL cc_start: 0.7708 (t) cc_final: 0.7454 (t) REVERT: e 48 CYS cc_start: 0.7457 (m) cc_final: 0.7032 (m) REVERT: e 53 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8865 (tp) REVERT: e 64 PHE cc_start: 0.7919 (OUTLIER) cc_final: 0.7685 (t80) REVERT: s 291 GLN cc_start: 0.7881 (tm-30) cc_final: 0.7384 (tm-30) REVERT: r 336 TYR cc_start: 0.5402 (p90) cc_final: 0.4553 (p90) REVERT: g 64 ILE cc_start: 0.9024 (mm) cc_final: 0.8622 (mt) REVERT: k 17 MET cc_start: 0.8424 (mmp) cc_final: 0.8102 (mmp) REVERT: n 48 ARG cc_start: 0.7913 (tpp80) cc_final: 0.7427 (ttm-80) REVERT: p 139 GLU cc_start: 0.8388 (tm-30) cc_final: 0.7947 (tm-30) outliers start: 204 outliers final: 120 residues processed: 1095 average time/residue: 0.5894 time to fit residues: 1095.1423 Evaluate side-chains 1012 residues out of total 6850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 887 time to evaluate : 5.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 532 CYS Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 488 ASP Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 584 MET Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 138 CYS Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 612 PHE Chi-restraints excluded: chain D residue 237 ASN Chi-restraints excluded: chain D residue 251 ASN Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 298 THR Chi-restraints excluded: chain E residue 330 ASP Chi-restraints excluded: chain E residue 348 ILE Chi-restraints excluded: chain E residue 449 LEU Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 348 ILE Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 75 TYR Chi-restraints excluded: chain G residue 112 TYR Chi-restraints excluded: chain G residue 175 PHE Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 152 GLN Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain I residue 159 THR Chi-restraints excluded: chain I residue 221 ASN Chi-restraints excluded: chain J residue 59 LYS Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain J residue 162 ASP Chi-restraints excluded: chain J residue 221 ASN Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain K residue 157 VAL Chi-restraints excluded: chain K residue 221 ASN Chi-restraints excluded: chain L residue 7 LEU Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 30 LYS Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain P residue 187 LEU Chi-restraints excluded: chain P residue 242 LEU Chi-restraints excluded: chain P residue 279 VAL Chi-restraints excluded: chain P residue 296 VAL Chi-restraints excluded: chain a residue 214 TYR Chi-restraints excluded: chain a residue 290 ILE Chi-restraints excluded: chain a residue 472 LEU Chi-restraints excluded: chain a residue 557 LEU Chi-restraints excluded: chain a residue 756 LEU Chi-restraints excluded: chain a residue 830 HIS Chi-restraints excluded: chain b residue 128 HIS Chi-restraints excluded: chain b residue 201 VAL Chi-restraints excluded: chain d residue 124 GLU Chi-restraints excluded: chain e residue 10 VAL Chi-restraints excluded: chain e residue 41 LEU Chi-restraints excluded: chain e residue 50 LEU Chi-restraints excluded: chain e residue 53 LEU Chi-restraints excluded: chain e residue 60 LEU Chi-restraints excluded: chain e residue 64 PHE Chi-restraints excluded: chain s residue 265 ILE Chi-restraints excluded: chain s residue 295 LEU Chi-restraints excluded: chain s residue 343 LEU Chi-restraints excluded: chain s residue 425 TRP Chi-restraints excluded: chain s residue 429 LEU Chi-restraints excluded: chain s residue 434 MET Chi-restraints excluded: chain s residue 448 LEU Chi-restraints excluded: chain c residue 17 MET Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 60 VAL Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain g residue 59 VAL Chi-restraints excluded: chain k residue 44 MET Chi-restraints excluded: chain k residue 59 VAL Chi-restraints excluded: chain k residue 147 ILE Chi-restraints excluded: chain l residue 81 ASN Chi-restraints excluded: chain l residue 132 ILE Chi-restraints excluded: chain l residue 141 LEU Chi-restraints excluded: chain l residue 146 LEU Chi-restraints excluded: chain l residue 147 ILE Chi-restraints excluded: chain m residue 59 VAL Chi-restraints excluded: chain n residue 9 GLU Chi-restraints excluded: chain n residue 143 LEU Chi-restraints excluded: chain o residue 59 VAL Chi-restraints excluded: chain o residue 121 THR Chi-restraints excluded: chain o residue 154 THR Chi-restraints excluded: chain p residue 59 VAL Chi-restraints excluded: chain p residue 121 THR Chi-restraints excluded: chain q residue 20 SER Chi-restraints excluded: chain q residue 45 SER Chi-restraints excluded: chain q residue 59 VAL Chi-restraints excluded: chain q residue 84 ILE Chi-restraints excluded: chain q residue 91 LEU Chi-restraints excluded: chain f residue 24 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 806 random chunks: chunk 724 optimal weight: 5.9990 chunk 551 optimal weight: 0.3980 chunk 380 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 349 optimal weight: 5.9990 chunk 492 optimal weight: 7.9990 chunk 735 optimal weight: 1.9990 chunk 779 optimal weight: 4.9990 chunk 384 optimal weight: 5.9990 chunk 697 optimal weight: 0.7980 chunk 209 optimal weight: 4.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 573 HIS ** C 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 244 ASN H 152 GLN I 96 ASN J 74 ASN J 219 ASN K 96 ASN L 35 ASN ** O 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 390 ASN a 548 HIS d 152 ASN ** e 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 368 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 64234 Z= 0.323 Angle : 0.656 11.762 86928 Z= 0.338 Chirality : 0.045 0.190 9966 Planarity : 0.005 0.143 11109 Dihedral : 8.402 127.415 9313 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.85 % Favored : 95.06 % Rotamer: Outliers : 3.33 % Allowed : 17.18 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.08 % Twisted Proline : 0.64 % Twisted General : 0.05 % 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: -1.21 (0.09), residues: 8098 helix: 0.10 (0.08), residues: 4531 sheet: -1.46 (0.18), residues: 726 loop : -2.01 (0.11), residues: 2841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP e 74 HIS 0.008 0.001 HIS a 802 PHE 0.038 0.001 PHE G 246 TYR 0.032 0.002 TYR o 144 ARG 0.013 0.000 ARG K 222 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16196 Ramachandran restraints generated. 8098 Oldfield, 0 Emsley, 8098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16196 Ramachandran restraints generated. 8098 Oldfield, 0 Emsley, 8098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1132 residues out of total 6850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 217 poor density : 915 time to evaluate : 5.629 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: A 232 ARG cc_start: 0.8441 (ttm110) cc_final: 0.8129 (mtm-85) REVERT: A 445 PHE cc_start: 0.7652 (m-80) cc_final: 0.7361 (m-10) REVERT: B 134 ASP cc_start: 0.7642 (p0) cc_final: 0.7328 (p0) REVERT: B 458 MET cc_start: 0.9072 (mmm) cc_final: 0.8808 (mmt) REVERT: B 605 LEU cc_start: 0.8228 (mp) cc_final: 0.7957 (tt) REVERT: C 146 HIS cc_start: 0.7988 (OUTLIER) cc_final: 0.7753 (t-90) REVERT: C 360 GLU cc_start: 0.8067 (tm-30) cc_final: 0.7083 (tm-30) REVERT: D 161 GLN cc_start: 0.8573 (tp40) cc_final: 0.8085 (tp-100) REVERT: D 251 ASN cc_start: 0.8817 (OUTLIER) cc_final: 0.7976 (t0) REVERT: D 326 TYR cc_start: 0.8971 (p90) cc_final: 0.8682 (p90) REVERT: E 371 TYR cc_start: 0.8178 (m-10) cc_final: 0.7978 (m-10) REVERT: F 44 ARG cc_start: 0.8652 (mtt180) cc_final: 0.8380 (mtt-85) REVERT: F 212 LEU cc_start: 0.8406 (mt) cc_final: 0.7956 (mp) REVERT: F 413 LYS cc_start: 0.7999 (tttm) cc_final: 0.7769 (ttmt) REVERT: F 436 LYS cc_start: 0.6931 (OUTLIER) cc_final: 0.6680 (tmtt) REVERT: G 224 LEU cc_start: 0.6959 (OUTLIER) cc_final: 0.6534 (mt) REVERT: G 239 HIS cc_start: 0.8352 (m90) cc_final: 0.8133 (m-70) REVERT: H 86 ASN cc_start: 0.8926 (m-40) cc_final: 0.8616 (m-40) REVERT: H 152 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.8378 (mm-40) REVERT: I 206 GLN cc_start: 0.8644 (OUTLIER) cc_final: 0.7660 (mp-120) REVERT: J 57 TYR cc_start: 0.6681 (OUTLIER) cc_final: 0.6033 (t80) REVERT: K 162 ASP cc_start: 0.7751 (p0) cc_final: 0.7448 (t0) REVERT: L 33 HIS cc_start: 0.6643 (m-70) cc_final: 0.6178 (m-70) REVERT: L 54 GLN cc_start: 0.8024 (mt0) cc_final: 0.7794 (mt0) REVERT: M 75 GLN cc_start: 0.7810 (tm-30) cc_final: 0.7599 (tm-30) REVERT: M 88 GLN cc_start: 0.8338 (tm-30) cc_final: 0.8097 (tm-30) REVERT: N 72 GLU cc_start: 0.8119 (tm-30) cc_final: 0.7579 (tp30) REVERT: N 74 GLU cc_start: 0.7851 (tm-30) cc_final: 0.7503 (tm-30) REVERT: O 79 ARG cc_start: 0.8518 (mtp180) cc_final: 0.8243 (tmt-80) REVERT: O 80 GLN cc_start: 0.7786 (mm-40) cc_final: 0.7394 (mm110) REVERT: P 154 GLU cc_start: 0.4746 (OUTLIER) cc_final: 0.3713 (pm20) REVERT: P 420 MET cc_start: 0.8338 (mmm) cc_final: 0.8011 (mmm) REVERT: a 94 MET cc_start: 0.8620 (tmm) cc_final: 0.8365 (tmm) REVERT: a 439 MET cc_start: 0.5662 (tpp) cc_final: 0.5329 (tmm) REVERT: e 28 VAL cc_start: 0.7879 (t) cc_final: 0.7410 (t) REVERT: e 34 ARG cc_start: 0.6813 (ttm-80) cc_final: 0.6367 (ttm170) REVERT: e 48 CYS cc_start: 0.7595 (m) cc_final: 0.7139 (m) REVERT: e 53 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8879 (tp) REVERT: e 64 PHE cc_start: 0.8066 (OUTLIER) cc_final: 0.7816 (t80) REVERT: s 291 GLN cc_start: 0.7928 (tm-30) cc_final: 0.7394 (tm-30) REVERT: r 336 TYR cc_start: 0.5394 (p90) cc_final: 0.4462 (p90) REVERT: g 64 ILE cc_start: 0.9026 (mm) cc_final: 0.8487 (mt) REVERT: n 48 ARG cc_start: 0.7907 (tpp80) cc_final: 0.7609 (ttm-80) REVERT: p 61 MET cc_start: 0.8157 (mtp) cc_final: 0.7919 (mtp) REVERT: p 139 GLU cc_start: 0.8441 (tm-30) cc_final: 0.7950 (tm-30) outliers start: 217 outliers final: 142 residues processed: 1059 average time/residue: 0.6533 time to fit residues: 1183.5171 Evaluate side-chains 1033 residues out of total 6850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 881 time to evaluate : 5.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 532 CYS Chi-restraints excluded: chain A residue 573 HIS Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 349 ASP Chi-restraints excluded: chain B residue 488 ASP Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 584 MET Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 138 CYS Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 146 HIS Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 237 ASN Chi-restraints excluded: chain D residue 251 ASN Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 265 ASN Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 413 LYS Chi-restraints excluded: chain D residue 486 ILE Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 298 THR Chi-restraints excluded: chain E residue 330 ASP Chi-restraints excluded: chain E residue 348 ILE Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 348 ILE Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 436 LYS Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain F residue 491 MET Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 75 TYR Chi-restraints excluded: chain G residue 112 TYR Chi-restraints excluded: chain G residue 175 PHE Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 152 GLN Chi-restraints excluded: chain I residue 56 TYR Chi-restraints excluded: chain I residue 206 GLN Chi-restraints excluded: chain I residue 221 ASN Chi-restraints excluded: chain J residue 57 TYR Chi-restraints excluded: chain J residue 59 LYS Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 162 ASP Chi-restraints excluded: chain J residue 221 ASN Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain K residue 221 ASN Chi-restraints excluded: chain L residue 7 LEU Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 30 LYS Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 69 TYR Chi-restraints excluded: chain L residue 73 MET Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain N residue 99 LEU Chi-restraints excluded: chain O residue 96 LEU Chi-restraints excluded: chain P residue 66 LEU Chi-restraints excluded: chain P residue 154 GLU Chi-restraints excluded: chain P residue 242 LEU Chi-restraints excluded: chain P residue 279 VAL Chi-restraints excluded: chain P residue 296 VAL Chi-restraints excluded: chain a residue 102 GLU Chi-restraints excluded: chain a residue 202 ILE Chi-restraints excluded: chain a residue 214 TYR Chi-restraints excluded: chain a residue 244 LEU Chi-restraints excluded: chain a residue 290 ILE Chi-restraints excluded: chain a residue 390 ASN Chi-restraints excluded: chain a residue 472 LEU Chi-restraints excluded: chain a residue 527 THR Chi-restraints excluded: chain a residue 557 LEU Chi-restraints excluded: chain a residue 756 LEU Chi-restraints excluded: chain a residue 791 LEU Chi-restraints excluded: chain a residue 830 HIS Chi-restraints excluded: chain b residue 26 TYR Chi-restraints excluded: chain b residue 128 HIS Chi-restraints excluded: chain b residue 201 VAL Chi-restraints excluded: chain d residue 124 GLU Chi-restraints excluded: chain e residue 10 VAL Chi-restraints excluded: chain e residue 50 LEU Chi-restraints excluded: chain e residue 53 LEU Chi-restraints excluded: chain e residue 60 LEU Chi-restraints excluded: chain e residue 64 PHE Chi-restraints excluded: chain e residue 73 ILE Chi-restraints excluded: chain s residue 265 ILE Chi-restraints excluded: chain s residue 295 LEU Chi-restraints excluded: chain s residue 343 LEU Chi-restraints excluded: chain s residue 425 TRP Chi-restraints excluded: chain s residue 429 LEU Chi-restraints excluded: chain s residue 434 MET Chi-restraints excluded: chain s residue 448 LEU Chi-restraints excluded: chain c residue 17 MET Chi-restraints excluded: chain c residue 57 ILE Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 60 VAL Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain g residue 59 VAL Chi-restraints excluded: chain k residue 59 VAL Chi-restraints excluded: chain k residue 147 ILE Chi-restraints excluded: chain l residue 81 ASN Chi-restraints excluded: chain l residue 132 ILE Chi-restraints excluded: chain l residue 141 LEU Chi-restraints excluded: chain l residue 146 LEU Chi-restraints excluded: chain l residue 147 ILE Chi-restraints excluded: chain m residue 50 GLU Chi-restraints excluded: chain m residue 59 VAL Chi-restraints excluded: chain m residue 132 ILE Chi-restraints excluded: chain n residue 9 GLU Chi-restraints excluded: chain n residue 143 LEU Chi-restraints excluded: chain o residue 59 VAL Chi-restraints excluded: chain o residue 121 THR Chi-restraints excluded: chain o residue 154 THR Chi-restraints excluded: chain p residue 59 VAL Chi-restraints excluded: chain p residue 121 THR Chi-restraints excluded: chain q residue 20 SER Chi-restraints excluded: chain q residue 59 VAL Chi-restraints excluded: chain q residue 84 ILE Chi-restraints excluded: chain q residue 91 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 806 random chunks: chunk 648 optimal weight: 5.9990 chunk 442 optimal weight: 20.0000 chunk 11 optimal weight: 7.9990 chunk 580 optimal weight: 7.9990 chunk 321 optimal weight: 6.9990 chunk 664 optimal weight: 0.8980 chunk 538 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 397 optimal weight: 3.9990 chunk 699 optimal weight: 4.9990 chunk 196 optimal weight: 1.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 HIS ** C 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 387 GLN ** F 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 GLN H 91 GLN H 152 GLN I 96 ASN J 78 GLN K 96 ASN K 221 ASN L 35 ASN M 75 GLN ** M 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 376 ASN a 473 ASN ** a 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 124 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 64234 Z= 0.313 Angle : 0.649 12.280 86928 Z= 0.332 Chirality : 0.044 0.195 9966 Planarity : 0.005 0.139 11109 Dihedral : 8.313 126.861 9312 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.00 % Favored : 94.91 % Rotamer: Outliers : 3.61 % Allowed : 18.26 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.08 % Twisted Proline : 0.64 % Twisted General : 0.05 % 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: -0.88 (0.09), residues: 8098 helix: 0.39 (0.08), residues: 4520 sheet: -1.39 (0.18), residues: 721 loop : -1.89 (0.11), residues: 2857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP e 74 HIS 0.015 0.001 HIS C 573 PHE 0.023 0.001 PHE E 260 TYR 0.033 0.002 TYR b 135 ARG 0.006 0.000 ARG A 142 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16196 Ramachandran restraints generated. 8098 Oldfield, 0 Emsley, 8098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16196 Ramachandran restraints generated. 8098 Oldfield, 0 Emsley, 8098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1156 residues out of total 6850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 235 poor density : 921 time to evaluate : 5.608 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: A 445 PHE cc_start: 0.7697 (m-80) cc_final: 0.7372 (m-10) REVERT: B 134 ASP cc_start: 0.7636 (p0) cc_final: 0.7326 (p0) REVERT: B 458 MET cc_start: 0.9085 (mmm) cc_final: 0.8842 (mmt) REVERT: B 605 LEU cc_start: 0.8200 (mp) cc_final: 0.7982 (tt) REVERT: C 146 HIS cc_start: 0.8010 (OUTLIER) cc_final: 0.7799 (t-90) REVERT: C 360 GLU cc_start: 0.8052 (tm-30) cc_final: 0.7083 (tm-30) REVERT: C 500 SER cc_start: 0.8915 (p) cc_final: 0.8683 (t) REVERT: C 530 ARG cc_start: 0.8215 (ptt90) cc_final: 0.7917 (ptp90) REVERT: D 161 GLN cc_start: 0.8567 (tp40) cc_final: 0.8050 (tp-100) REVERT: D 251 ASN cc_start: 0.8856 (OUTLIER) cc_final: 0.8056 (t0) REVERT: D 326 TYR cc_start: 0.8972 (p90) cc_final: 0.8705 (p90) REVERT: E 423 TYR cc_start: 0.8814 (t80) cc_final: 0.8568 (t80) REVERT: F 44 ARG cc_start: 0.8684 (mtt180) cc_final: 0.8398 (mtt-85) REVERT: F 380 ASP cc_start: 0.8124 (t0) cc_final: 0.7760 (m-30) REVERT: F 413 LYS cc_start: 0.8019 (tttm) cc_final: 0.7812 (ttmt) REVERT: G 239 HIS cc_start: 0.8341 (m90) cc_final: 0.8110 (m-70) REVERT: H 86 ASN cc_start: 0.8910 (m-40) cc_final: 0.8646 (m-40) REVERT: I 206 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.7695 (mp-120) REVERT: J 57 TYR cc_start: 0.6670 (OUTLIER) cc_final: 0.6029 (t80) REVERT: J 72 MET cc_start: 0.7731 (tmm) cc_final: 0.7522 (ttm) REVERT: K 162 ASP cc_start: 0.7765 (p0) cc_final: 0.7456 (t0) REVERT: L 33 HIS cc_start: 0.6722 (m-70) cc_final: 0.6394 (m-70) REVERT: M 107 ARG cc_start: 0.8270 (mtm-85) cc_final: 0.7580 (mtm-85) REVERT: N 72 GLU cc_start: 0.8129 (tm-30) cc_final: 0.7566 (tp30) REVERT: N 74 GLU cc_start: 0.7774 (tm-30) cc_final: 0.7438 (tm-30) REVERT: O 79 ARG cc_start: 0.8507 (mtp180) cc_final: 0.8243 (tmt-80) REVERT: O 80 GLN cc_start: 0.7733 (mm-40) cc_final: 0.7319 (mm110) REVERT: P 140 MET cc_start: 0.8277 (mpp) cc_final: 0.7776 (mpp) REVERT: P 154 GLU cc_start: 0.4750 (OUTLIER) cc_final: 0.3715 (pm20) REVERT: P 420 MET cc_start: 0.8386 (mmm) cc_final: 0.8081 (mmm) REVERT: a 94 MET cc_start: 0.8617 (tmm) cc_final: 0.8287 (tmm) REVERT: a 439 MET cc_start: 0.5664 (tpp) cc_final: 0.5440 (tmm) REVERT: a 628 MET cc_start: 0.8538 (mmp) cc_final: 0.8289 (mmp) REVERT: e 28 VAL cc_start: 0.7883 (t) cc_final: 0.7463 (t) REVERT: e 34 ARG cc_start: 0.6821 (ttm-80) cc_final: 0.6082 (mtp85) REVERT: e 48 CYS cc_start: 0.7569 (m) cc_final: 0.7114 (m) REVERT: e 64 PHE cc_start: 0.8106 (OUTLIER) cc_final: 0.7806 (t80) REVERT: s 291 GLN cc_start: 0.7970 (tm-30) cc_final: 0.7408 (tm-30) REVERT: r 336 TYR cc_start: 0.5459 (p90) cc_final: 0.4495 (p90) REVERT: g 64 ILE cc_start: 0.9042 (mm) cc_final: 0.8512 (mt) REVERT: k 115 ASP cc_start: 0.8156 (t0) cc_final: 0.7940 (t70) REVERT: n 48 ARG cc_start: 0.7959 (tpp80) cc_final: 0.7668 (ttm-80) REVERT: p 139 GLU cc_start: 0.8468 (tm-30) cc_final: 0.8027 (tm-30) outliers start: 235 outliers final: 165 residues processed: 1074 average time/residue: 0.5977 time to fit residues: 1094.6056 Evaluate side-chains 1044 residues out of total 6850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 873 time to evaluate : 5.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 532 CYS Chi-restraints excluded: chain A residue 573 HIS Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 349 ASP Chi-restraints excluded: chain B residue 488 ASP Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 584 MET Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 138 CYS Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 146 HIS Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 612 PHE Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 237 ASN Chi-restraints excluded: chain D residue 251 ASN Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 265 ASN Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 413 LYS Chi-restraints excluded: chain D residue 486 ILE Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 298 THR Chi-restraints excluded: chain E residue 330 ASP Chi-restraints excluded: chain E residue 348 ILE Chi-restraints excluded: chain E residue 449 LEU Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 348 ILE Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 491 MET Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 75 TYR Chi-restraints excluded: chain G residue 112 TYR Chi-restraints excluded: chain G residue 175 PHE Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain I residue 56 TYR Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 159 THR Chi-restraints excluded: chain I residue 168 ASP Chi-restraints excluded: chain I residue 206 GLN Chi-restraints excluded: chain I residue 221 ASN Chi-restraints excluded: chain J residue 57 TYR Chi-restraints excluded: chain J residue 59 LYS Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 137 ARG Chi-restraints excluded: chain J residue 162 ASP Chi-restraints excluded: chain J residue 221 ASN Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain K residue 221 ASN Chi-restraints excluded: chain L residue 7 LEU Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 69 TYR Chi-restraints excluded: chain L residue 73 MET Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain O residue 96 LEU Chi-restraints excluded: chain P residue 66 LEU Chi-restraints excluded: chain P residue 154 GLU Chi-restraints excluded: chain P residue 187 LEU Chi-restraints excluded: chain P residue 242 LEU Chi-restraints excluded: chain P residue 279 VAL Chi-restraints excluded: chain P residue 296 VAL Chi-restraints excluded: chain a residue 11 THR Chi-restraints excluded: chain a residue 171 VAL Chi-restraints excluded: chain a residue 202 ILE Chi-restraints excluded: chain a residue 214 TYR Chi-restraints excluded: chain a residue 244 LEU Chi-restraints excluded: chain a residue 333 ILE Chi-restraints excluded: chain a residue 377 ILE Chi-restraints excluded: chain a residue 472 LEU Chi-restraints excluded: chain a residue 527 THR Chi-restraints excluded: chain a residue 557 LEU Chi-restraints excluded: chain a residue 629 LEU Chi-restraints excluded: chain a residue 755 VAL Chi-restraints excluded: chain a residue 756 LEU Chi-restraints excluded: chain a residue 779 ILE Chi-restraints excluded: chain a residue 791 LEU Chi-restraints excluded: chain a residue 830 HIS Chi-restraints excluded: chain b residue 26 TYR Chi-restraints excluded: chain b residue 128 HIS Chi-restraints excluded: chain b residue 142 LEU Chi-restraints excluded: chain b residue 201 VAL Chi-restraints excluded: chain d residue 99 PHE Chi-restraints excluded: chain d residue 124 GLU Chi-restraints excluded: chain d residue 264 VAL Chi-restraints excluded: chain e residue 10 VAL Chi-restraints excluded: chain e residue 50 LEU Chi-restraints excluded: chain e residue 53 LEU Chi-restraints excluded: chain e residue 64 PHE Chi-restraints excluded: chain e residue 73 ILE Chi-restraints excluded: chain s residue 253 VAL Chi-restraints excluded: chain s residue 265 ILE Chi-restraints excluded: chain s residue 295 LEU Chi-restraints excluded: chain s residue 300 TRP Chi-restraints excluded: chain s residue 343 LEU Chi-restraints excluded: chain s residue 425 TRP Chi-restraints excluded: chain s residue 429 LEU Chi-restraints excluded: chain s residue 434 MET Chi-restraints excluded: chain s residue 448 LEU Chi-restraints excluded: chain s residue 452 ASP Chi-restraints excluded: chain r residue 331 ASN Chi-restraints excluded: chain c residue 17 MET Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 60 VAL Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain g residue 59 VAL Chi-restraints excluded: chain g residue 84 ILE Chi-restraints excluded: chain k residue 44 MET Chi-restraints excluded: chain k residue 59 VAL Chi-restraints excluded: chain k residue 147 ILE Chi-restraints excluded: chain l residue 81 ASN Chi-restraints excluded: chain l residue 132 ILE Chi-restraints excluded: chain l residue 141 LEU Chi-restraints excluded: chain m residue 50 GLU Chi-restraints excluded: chain m residue 59 VAL Chi-restraints excluded: chain m residue 84 ILE Chi-restraints excluded: chain m residue 124 GLN Chi-restraints excluded: chain m residue 132 ILE Chi-restraints excluded: chain n residue 9 GLU Chi-restraints excluded: chain n residue 51 MET Chi-restraints excluded: chain n residue 143 LEU Chi-restraints excluded: chain o residue 59 VAL Chi-restraints excluded: chain o residue 154 THR Chi-restraints excluded: chain p residue 59 VAL Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain p residue 121 THR Chi-restraints excluded: chain q residue 20 SER Chi-restraints excluded: chain q residue 59 VAL Chi-restraints excluded: chain q residue 84 ILE Chi-restraints excluded: chain q residue 91 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 806 random chunks: chunk 262 optimal weight: 1.9990 chunk 701 optimal weight: 5.9990 chunk 154 optimal weight: 0.8980 chunk 457 optimal weight: 2.9990 chunk 192 optimal weight: 0.1980 chunk 779 optimal weight: 2.9990 chunk 647 optimal weight: 2.9990 chunk 361 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 257 optimal weight: 6.9990 chunk 409 optimal weight: 0.2980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 159 ASN C 609 GLN ** C 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 GLN H 91 GLN H 152 GLN I 96 ASN K 122 GLN L 35 ASN M 75 GLN ** O 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 439 GLN ** a 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 148 ASN d 48 HIS ** e 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 124 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 64234 Z= 0.210 Angle : 0.615 12.865 86928 Z= 0.312 Chirality : 0.042 0.191 9966 Planarity : 0.004 0.133 11109 Dihedral : 8.144 123.771 9312 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.90 % Favored : 95.01 % Rotamer: Outliers : 3.24 % Allowed : 19.26 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.08 % Twisted Proline : 0.64 % Twisted General : 0.04 % 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: -0.60 (0.09), residues: 8098 helix: 0.63 (0.08), residues: 4541 sheet: -1.32 (0.18), residues: 732 loop : -1.79 (0.11), residues: 2825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP e 74 HIS 0.009 0.001 HIS C 573 PHE 0.020 0.001 PHE a 654 TYR 0.027 0.001 TYR b 135 ARG 0.007 0.000 ARG A 142 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16196 Ramachandran restraints generated. 8098 Oldfield, 0 Emsley, 8098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16196 Ramachandran restraints generated. 8098 Oldfield, 0 Emsley, 8098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1150 residues out of total 6850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 939 time to evaluate : 5.726 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: A 608 MET cc_start: 0.6632 (mmp) cc_final: 0.6351 (mtt) REVERT: B 134 ASP cc_start: 0.7629 (p0) cc_final: 0.7293 (p0) REVERT: B 458 MET cc_start: 0.9069 (mmm) cc_final: 0.8856 (mmt) REVERT: B 605 LEU cc_start: 0.8187 (mp) cc_final: 0.7976 (tt) REVERT: C 360 GLU cc_start: 0.8046 (tm-30) cc_final: 0.7092 (tm-30) REVERT: C 530 ARG cc_start: 0.8161 (ptt90) cc_final: 0.7906 (ptp90) REVERT: D 161 GLN cc_start: 0.8528 (tp40) cc_final: 0.8056 (tp-100) REVERT: D 249 GLU cc_start: 0.7651 (tt0) cc_final: 0.7311 (mt-10) REVERT: D 251 ASN cc_start: 0.8758 (OUTLIER) cc_final: 0.7964 (t0) REVERT: D 320 ARG cc_start: 0.7843 (mtp180) cc_final: 0.7517 (mtm-85) REVERT: D 326 TYR cc_start: 0.8939 (p90) cc_final: 0.8686 (p90) REVERT: F 44 ARG cc_start: 0.8640 (mtt180) cc_final: 0.8338 (mtt-85) REVERT: F 380 ASP cc_start: 0.8062 (t0) cc_final: 0.7724 (m-30) REVERT: F 413 LYS cc_start: 0.7990 (tttm) cc_final: 0.7742 (ttmt) REVERT: G 75 TYR cc_start: 0.7572 (OUTLIER) cc_final: 0.7047 (m-80) REVERT: G 224 LEU cc_start: 0.7026 (OUTLIER) cc_final: 0.6672 (mt) REVERT: G 239 HIS cc_start: 0.8321 (m90) cc_final: 0.8093 (m-70) REVERT: I 206 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.7628 (mp-120) REVERT: J 57 TYR cc_start: 0.6573 (OUTLIER) cc_final: 0.5959 (t80) REVERT: J 162 ASP cc_start: 0.7390 (OUTLIER) cc_final: 0.7054 (m-30) REVERT: K 162 ASP cc_start: 0.7722 (p0) cc_final: 0.7462 (t0) REVERT: L 33 HIS cc_start: 0.6577 (OUTLIER) cc_final: 0.6239 (m-70) REVERT: N 72 GLU cc_start: 0.8132 (tm-30) cc_final: 0.7561 (tp30) REVERT: N 74 GLU cc_start: 0.7744 (tm-30) cc_final: 0.7455 (tm-30) REVERT: O 79 ARG cc_start: 0.8501 (mtp180) cc_final: 0.8249 (tmt-80) REVERT: O 80 GLN cc_start: 0.7712 (mm-40) cc_final: 0.7268 (mm110) REVERT: P 420 MET cc_start: 0.8366 (mmm) cc_final: 0.8086 (mmm) REVERT: a 94 MET cc_start: 0.8569 (tmm) cc_final: 0.8197 (tmm) REVERT: a 830 HIS cc_start: 0.8472 (OUTLIER) cc_final: 0.8087 (t-90) REVERT: e 28 VAL cc_start: 0.7904 (t) cc_final: 0.7495 (t) REVERT: e 34 ARG cc_start: 0.6834 (ttm-80) cc_final: 0.6077 (mtp85) REVERT: e 48 CYS cc_start: 0.7582 (m) cc_final: 0.7116 (m) REVERT: e 53 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8792 (tp) REVERT: e 64 PHE cc_start: 0.8042 (OUTLIER) cc_final: 0.7708 (t80) REVERT: s 281 GLU cc_start: 0.7704 (tp30) cc_final: 0.7485 (tp30) REVERT: s 291 GLN cc_start: 0.7926 (tm-30) cc_final: 0.7388 (tm-30) REVERT: r 336 TYR cc_start: 0.5374 (p90) cc_final: 0.4412 (p90) REVERT: c 51 MET cc_start: 0.7916 (OUTLIER) cc_final: 0.7555 (mtm) REVERT: g 64 ILE cc_start: 0.9002 (mm) cc_final: 0.8581 (mt) REVERT: n 48 ARG cc_start: 0.7942 (tpp80) cc_final: 0.7510 (ttm-80) REVERT: p 139 GLU cc_start: 0.8388 (tm-30) cc_final: 0.7993 (tm-30) outliers start: 211 outliers final: 144 residues processed: 1071 average time/residue: 0.6109 time to fit residues: 1118.2537 Evaluate side-chains 1041 residues out of total 6850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 886 time to evaluate : 5.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 573 HIS Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 488 ASP Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 584 MET Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 138 CYS Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 612 PHE Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 237 ASN Chi-restraints excluded: chain D residue 251 ASN Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 413 LYS Chi-restraints excluded: chain D residue 486 ILE Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 298 THR Chi-restraints excluded: chain E residue 348 ILE Chi-restraints excluded: chain E residue 413 LYS Chi-restraints excluded: chain E residue 449 LEU Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 330 ASP Chi-restraints excluded: chain F residue 348 ILE Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 491 MET Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 75 TYR Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 112 TYR Chi-restraints excluded: chain G residue 175 PHE Chi-restraints excluded: chain G residue 207 MET Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain I residue 56 TYR Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain I residue 159 THR Chi-restraints excluded: chain I residue 168 ASP Chi-restraints excluded: chain I residue 206 GLN Chi-restraints excluded: chain I residue 221 ASN Chi-restraints excluded: chain J residue 57 TYR Chi-restraints excluded: chain J residue 59 LYS Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 137 ARG Chi-restraints excluded: chain J residue 162 ASP Chi-restraints excluded: chain J residue 221 ASN Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain L residue 7 LEU Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 30 LYS Chi-restraints excluded: chain L residue 33 HIS Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 69 TYR Chi-restraints excluded: chain L residue 73 MET Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain N residue 99 LEU Chi-restraints excluded: chain O residue 96 LEU Chi-restraints excluded: chain P residue 66 LEU Chi-restraints excluded: chain P residue 187 LEU Chi-restraints excluded: chain P residue 242 LEU Chi-restraints excluded: chain P residue 279 VAL Chi-restraints excluded: chain P residue 296 VAL Chi-restraints excluded: chain a residue 11 THR Chi-restraints excluded: chain a residue 214 TYR Chi-restraints excluded: chain a residue 244 LEU Chi-restraints excluded: chain a residue 328 THR Chi-restraints excluded: chain a residue 333 ILE Chi-restraints excluded: chain a residue 377 ILE Chi-restraints excluded: chain a residue 472 LEU Chi-restraints excluded: chain a residue 527 THR Chi-restraints excluded: chain a residue 557 LEU Chi-restraints excluded: chain a residue 567 LEU Chi-restraints excluded: chain a residue 756 LEU Chi-restraints excluded: chain a residue 791 LEU Chi-restraints excluded: chain a residue 830 HIS Chi-restraints excluded: chain b residue 26 TYR Chi-restraints excluded: chain b residue 128 HIS Chi-restraints excluded: chain b residue 142 LEU Chi-restraints excluded: chain b residue 201 VAL Chi-restraints excluded: chain d residue 7 LEU Chi-restraints excluded: chain d residue 99 PHE Chi-restraints excluded: chain d residue 124 GLU Chi-restraints excluded: chain d residue 264 VAL Chi-restraints excluded: chain e residue 10 VAL Chi-restraints excluded: chain e residue 50 LEU Chi-restraints excluded: chain e residue 53 LEU Chi-restraints excluded: chain e residue 64 PHE Chi-restraints excluded: chain e residue 73 ILE Chi-restraints excluded: chain s residue 253 VAL Chi-restraints excluded: chain s residue 265 ILE Chi-restraints excluded: chain s residue 300 TRP Chi-restraints excluded: chain s residue 338 PHE Chi-restraints excluded: chain s residue 343 LEU Chi-restraints excluded: chain s residue 425 TRP Chi-restraints excluded: chain s residue 429 LEU Chi-restraints excluded: chain s residue 448 LEU Chi-restraints excluded: chain s residue 452 ASP Chi-restraints excluded: chain r residue 331 ASN Chi-restraints excluded: chain c residue 17 MET Chi-restraints excluded: chain c residue 51 MET Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain g residue 59 VAL Chi-restraints excluded: chain k residue 44 MET Chi-restraints excluded: chain k residue 59 VAL Chi-restraints excluded: chain l residue 81 ASN Chi-restraints excluded: chain l residue 132 ILE Chi-restraints excluded: chain l residue 147 ILE Chi-restraints excluded: chain m residue 50 GLU Chi-restraints excluded: chain m residue 59 VAL Chi-restraints excluded: chain m residue 61 MET Chi-restraints excluded: chain m residue 124 GLN Chi-restraints excluded: chain m residue 132 ILE Chi-restraints excluded: chain m residue 143 LEU Chi-restraints excluded: chain n residue 44 MET Chi-restraints excluded: chain n residue 51 MET Chi-restraints excluded: chain n residue 143 LEU Chi-restraints excluded: chain o residue 59 VAL Chi-restraints excluded: chain p residue 59 VAL Chi-restraints excluded: chain q residue 20 SER Chi-restraints excluded: chain q residue 59 VAL Chi-restraints excluded: chain q residue 84 ILE Chi-restraints excluded: chain q residue 91 LEU Chi-restraints excluded: chain q residue 123 GLN Chi-restraints excluded: chain f residue 82 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 806 random chunks: chunk 751 optimal weight: 0.9980 chunk 87 optimal weight: 7.9990 chunk 444 optimal weight: 50.0000 chunk 569 optimal weight: 3.9990 chunk 441 optimal weight: 10.0000 chunk 656 optimal weight: 0.0670 chunk 435 optimal weight: 3.9990 chunk 776 optimal weight: 0.0170 chunk 486 optimal weight: 0.0270 chunk 473 optimal weight: 20.0000 chunk 358 optimal weight: 4.9990 overall best weight: 1.0216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 205 GLN E 456 GLN ** F 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 91 GLN I 96 ASN K 96 ASN L 35 ASN ** O 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 612 HIS ** b 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 340 HIS ** e 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 124 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 64234 Z= 0.191 Angle : 0.605 13.804 86928 Z= 0.306 Chirality : 0.042 0.197 9966 Planarity : 0.004 0.130 11109 Dihedral : 7.930 120.488 9312 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.84 % Favored : 95.07 % Rotamer: Outliers : 3.07 % Allowed : 19.87 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.08 % Twisted Proline : 0.64 % Twisted General : 0.04 % 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: -0.38 (0.09), residues: 8098 helix: 0.82 (0.08), residues: 4546 sheet: -1.23 (0.18), residues: 722 loop : -1.71 (0.11), residues: 2830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP a 650 HIS 0.009 0.001 HIS C 573 PHE 0.032 0.001 PHE a 654 TYR 0.029 0.001 TYR o 144 ARG 0.011 0.000 ARG a 482 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16196 Ramachandran restraints generated. 8098 Oldfield, 0 Emsley, 8098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16196 Ramachandran restraints generated. 8098 Oldfield, 0 Emsley, 8098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1143 residues out of total 6850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 943 time to evaluate : 5.666 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: A 608 MET cc_start: 0.6597 (mmp) cc_final: 0.6387 (mtt) REVERT: B 134 ASP cc_start: 0.7633 (p0) cc_final: 0.7286 (p0) REVERT: B 458 MET cc_start: 0.9079 (mmm) cc_final: 0.8877 (mmt) REVERT: C 530 ARG cc_start: 0.8124 (ptt90) cc_final: 0.7920 (ptp90) REVERT: D 161 GLN cc_start: 0.8500 (tp40) cc_final: 0.8019 (tp-100) REVERT: D 180 MET cc_start: 0.8809 (mmm) cc_final: 0.8588 (mtp) REVERT: D 249 GLU cc_start: 0.7645 (tt0) cc_final: 0.7330 (mt-10) REVERT: D 251 ASN cc_start: 0.8702 (OUTLIER) cc_final: 0.7906 (t0) REVERT: D 320 ARG cc_start: 0.7812 (mtp180) cc_final: 0.7499 (mtm-85) REVERT: D 326 TYR cc_start: 0.8871 (p90) cc_final: 0.8618 (p90) REVERT: E 202 ILE cc_start: 0.8955 (pt) cc_final: 0.8468 (mt) REVERT: E 456 GLN cc_start: 0.7739 (OUTLIER) cc_final: 0.6985 (mm110) REVERT: F 44 ARG cc_start: 0.8617 (mtt180) cc_final: 0.8370 (mtt-85) REVERT: F 380 ASP cc_start: 0.8023 (t0) cc_final: 0.7689 (m-30) REVERT: F 413 LYS cc_start: 0.7961 (tttm) cc_final: 0.7752 (ttmt) REVERT: G 75 TYR cc_start: 0.7551 (OUTLIER) cc_final: 0.7064 (m-80) REVERT: G 224 LEU cc_start: 0.6980 (OUTLIER) cc_final: 0.6650 (mt) REVERT: G 239 HIS cc_start: 0.8304 (m90) cc_final: 0.8092 (m-70) REVERT: H 86 ASN cc_start: 0.8951 (m-40) cc_final: 0.8647 (m-40) REVERT: I 55 GLU cc_start: 0.8465 (mm-30) cc_final: 0.7985 (tm-30) REVERT: J 57 TYR cc_start: 0.6638 (OUTLIER) cc_final: 0.6033 (t80) REVERT: J 112 TYR cc_start: 0.8451 (t80) cc_final: 0.8231 (t80) REVERT: J 162 ASP cc_start: 0.7307 (OUTLIER) cc_final: 0.7041 (m-30) REVERT: K 162 ASP cc_start: 0.7655 (p0) cc_final: 0.7435 (t0) REVERT: L 33 HIS cc_start: 0.6552 (OUTLIER) cc_final: 0.6241 (m-70) REVERT: L 54 GLN cc_start: 0.8112 (mt0) cc_final: 0.7872 (tt0) REVERT: M 75 GLN cc_start: 0.7744 (tm-30) cc_final: 0.7534 (tm-30) REVERT: M 107 ARG cc_start: 0.8330 (mtm-85) cc_final: 0.7688 (mtm-85) REVERT: N 72 GLU cc_start: 0.8124 (tm-30) cc_final: 0.7540 (tp30) REVERT: N 74 GLU cc_start: 0.7704 (tm-30) cc_final: 0.7421 (tm-30) REVERT: O 79 ARG cc_start: 0.8509 (mtp180) cc_final: 0.8252 (tmt-80) REVERT: O 80 GLN cc_start: 0.7639 (mm-40) cc_final: 0.7216 (mm110) REVERT: P 420 MET cc_start: 0.8428 (mmm) cc_final: 0.8180 (mmm) REVERT: a 94 MET cc_start: 0.8517 (tmm) cc_final: 0.8314 (tmm) REVERT: a 118 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8593 (mp) REVERT: a 628 MET cc_start: 0.8398 (mmp) cc_final: 0.8159 (mmp) REVERT: a 830 HIS cc_start: 0.8462 (OUTLIER) cc_final: 0.8114 (t-90) REVERT: e 28 VAL cc_start: 0.7941 (t) cc_final: 0.7554 (t) REVERT: e 34 ARG cc_start: 0.6862 (ttm-80) cc_final: 0.6108 (mtp85) REVERT: e 53 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8755 (tp) REVERT: e 64 PHE cc_start: 0.7876 (OUTLIER) cc_final: 0.7604 (t80) REVERT: s 291 GLN cc_start: 0.7923 (tm-30) cc_final: 0.7398 (tm-30) REVERT: r 336 TYR cc_start: 0.5337 (p90) cc_final: 0.4395 (p90) REVERT: c 51 MET cc_start: 0.7833 (OUTLIER) cc_final: 0.7603 (mtm) REVERT: c 115 ASP cc_start: 0.7899 (t70) cc_final: 0.7463 (t70) REVERT: g 64 ILE cc_start: 0.9002 (mm) cc_final: 0.8478 (mt) REVERT: n 48 ARG cc_start: 0.7900 (tpp80) cc_final: 0.7572 (ttm-80) REVERT: o 54 LYS cc_start: 0.8605 (ttpt) cc_final: 0.8297 (ttpt) REVERT: p 139 GLU cc_start: 0.8378 (tm-30) cc_final: 0.7997 (tm-30) REVERT: q 131 MET cc_start: 0.8255 (ttp) cc_final: 0.8006 (ttt) outliers start: 200 outliers final: 151 residues processed: 1066 average time/residue: 0.6218 time to fit residues: 1131.0783 Evaluate side-chains 1054 residues out of total 6850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 891 time to evaluate : 5.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 534 PHE Chi-restraints excluded: chain A residue 573 HIS Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 488 ASP Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 584 MET Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 138 CYS Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain C residue 612 PHE Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 237 ASN Chi-restraints excluded: chain D residue 251 ASN Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 265 ASN Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 413 LYS Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 298 THR Chi-restraints excluded: chain E residue 348 ILE Chi-restraints excluded: chain E residue 449 LEU Chi-restraints excluded: chain E residue 456 GLN Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 330 ASP Chi-restraints excluded: chain F residue 348 ILE Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 491 MET Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 75 TYR Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 112 TYR Chi-restraints excluded: chain G residue 175 PHE Chi-restraints excluded: chain G residue 207 MET Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain I residue 56 TYR Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain I residue 159 THR Chi-restraints excluded: chain I residue 168 ASP Chi-restraints excluded: chain I residue 221 ASN Chi-restraints excluded: chain J residue 57 TYR Chi-restraints excluded: chain J residue 59 LYS Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 162 ASP Chi-restraints excluded: chain J residue 221 ASN Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain L residue 7 LEU Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 30 LYS Chi-restraints excluded: chain L residue 33 HIS Chi-restraints excluded: chain L residue 35 ASN Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 73 MET Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain N residue 99 LEU Chi-restraints excluded: chain P residue 66 LEU Chi-restraints excluded: chain P residue 187 LEU Chi-restraints excluded: chain P residue 242 LEU Chi-restraints excluded: chain P residue 275 LEU Chi-restraints excluded: chain P residue 279 VAL Chi-restraints excluded: chain P residue 296 VAL Chi-restraints excluded: chain P residue 436 LEU Chi-restraints excluded: chain a residue 11 THR Chi-restraints excluded: chain a residue 118 LEU Chi-restraints excluded: chain a residue 171 VAL Chi-restraints excluded: chain a residue 202 ILE Chi-restraints excluded: chain a residue 214 TYR Chi-restraints excluded: chain a residue 244 LEU Chi-restraints excluded: chain a residue 328 THR Chi-restraints excluded: chain a residue 333 ILE Chi-restraints excluded: chain a residue 472 LEU Chi-restraints excluded: chain a residue 527 THR Chi-restraints excluded: chain a residue 557 LEU Chi-restraints excluded: chain a residue 755 VAL Chi-restraints excluded: chain a residue 756 LEU Chi-restraints excluded: chain a residue 779 ILE Chi-restraints excluded: chain a residue 791 LEU Chi-restraints excluded: chain a residue 830 HIS Chi-restraints excluded: chain b residue 26 TYR Chi-restraints excluded: chain b residue 128 HIS Chi-restraints excluded: chain b residue 142 LEU Chi-restraints excluded: chain b residue 201 VAL Chi-restraints excluded: chain d residue 69 VAL Chi-restraints excluded: chain d residue 124 GLU Chi-restraints excluded: chain d residue 264 VAL Chi-restraints excluded: chain e residue 10 VAL Chi-restraints excluded: chain e residue 53 LEU Chi-restraints excluded: chain e residue 64 PHE Chi-restraints excluded: chain s residue 253 VAL Chi-restraints excluded: chain s residue 265 ILE Chi-restraints excluded: chain s residue 300 TRP Chi-restraints excluded: chain s residue 338 PHE Chi-restraints excluded: chain s residue 343 LEU Chi-restraints excluded: chain s residue 371 HIS Chi-restraints excluded: chain s residue 425 TRP Chi-restraints excluded: chain s residue 429 LEU Chi-restraints excluded: chain s residue 448 LEU Chi-restraints excluded: chain r residue 331 ASN Chi-restraints excluded: chain c residue 17 MET Chi-restraints excluded: chain c residue 51 MET Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 60 VAL Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain g residue 59 VAL Chi-restraints excluded: chain g residue 81 ASN Chi-restraints excluded: chain k residue 59 VAL Chi-restraints excluded: chain l residue 81 ASN Chi-restraints excluded: chain l residue 132 ILE Chi-restraints excluded: chain l residue 147 ILE Chi-restraints excluded: chain m residue 50 GLU Chi-restraints excluded: chain m residue 59 VAL Chi-restraints excluded: chain m residue 61 MET Chi-restraints excluded: chain m residue 84 ILE Chi-restraints excluded: chain m residue 132 ILE Chi-restraints excluded: chain m residue 143 LEU Chi-restraints excluded: chain n residue 9 GLU Chi-restraints excluded: chain n residue 44 MET Chi-restraints excluded: chain n residue 51 MET Chi-restraints excluded: chain o residue 59 VAL Chi-restraints excluded: chain p residue 44 MET Chi-restraints excluded: chain p residue 59 VAL Chi-restraints excluded: chain q residue 20 SER Chi-restraints excluded: chain q residue 59 VAL Chi-restraints excluded: chain q residue 84 ILE Chi-restraints excluded: chain q residue 91 LEU Chi-restraints excluded: chain q residue 123 GLN Chi-restraints excluded: chain f residue 67 TYR Chi-restraints excluded: chain f residue 76 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 806 random chunks: chunk 480 optimal weight: 9.9990 chunk 310 optimal weight: 0.0170 chunk 463 optimal weight: 50.0000 chunk 234 optimal weight: 3.9990 chunk 152 optimal weight: 0.9980 chunk 150 optimal weight: 1.9990 chunk 493 optimal weight: 0.7980 chunk 529 optimal weight: 5.9990 chunk 384 optimal weight: 4.9990 chunk 72 optimal weight: 7.9990 chunk 610 optimal weight: 5.9990 overall best weight: 1.5622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 610 ASN ** C 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 205 GLN ** F 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 GLN H 91 GLN H 152 GLN L 35 ASN ** O 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 340 HIS ** e 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.3890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 64234 Z= 0.229 Angle : 0.620 13.675 86928 Z= 0.313 Chirality : 0.043 0.276 9966 Planarity : 0.004 0.129 11109 Dihedral : 7.827 119.615 9312 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.91 % Favored : 95.01 % Rotamer: Outliers : 3.18 % Allowed : 20.12 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.08 % Twisted Proline : 0.64 % Twisted General : 0.04 % 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: -0.27 (0.09), residues: 8098 helix: 0.93 (0.08), residues: 4535 sheet: -1.27 (0.18), residues: 746 loop : -1.66 (0.11), residues: 2817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP a 650 HIS 0.009 0.001 HIS a 802 PHE 0.023 0.001 PHE J 141 TYR 0.048 0.001 TYR n 144 ARG 0.009 0.000 ARG a 482 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16196 Ramachandran restraints generated. 8098 Oldfield, 0 Emsley, 8098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16196 Ramachandran restraints generated. 8098 Oldfield, 0 Emsley, 8098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1128 residues out of total 6850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 921 time to evaluate : 5.590 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: B 134 ASP cc_start: 0.7644 (p0) cc_final: 0.7288 (p0) REVERT: C 360 GLU cc_start: 0.8043 (tm-30) cc_final: 0.7077 (tm-30) REVERT: C 530 ARG cc_start: 0.8123 (ptt90) cc_final: 0.7922 (ptp90) REVERT: C 574 MET cc_start: 0.5496 (mmt) cc_final: 0.5286 (mmt) REVERT: D 161 GLN cc_start: 0.8507 (tp40) cc_final: 0.8025 (tp-100) REVERT: D 249 GLU cc_start: 0.7639 (tt0) cc_final: 0.7323 (mt-10) REVERT: D 251 ASN cc_start: 0.8731 (OUTLIER) cc_final: 0.7951 (t0) REVERT: D 320 ARG cc_start: 0.7833 (mtp180) cc_final: 0.7496 (mtm-85) REVERT: D 326 TYR cc_start: 0.8901 (p90) cc_final: 0.8631 (p90) REVERT: F 44 ARG cc_start: 0.8654 (mtt180) cc_final: 0.8381 (mtt-85) REVERT: F 380 ASP cc_start: 0.8030 (t0) cc_final: 0.7689 (m-30) REVERT: G 75 TYR cc_start: 0.7624 (OUTLIER) cc_final: 0.7153 (m-80) REVERT: G 224 LEU cc_start: 0.6986 (OUTLIER) cc_final: 0.6668 (mt) REVERT: G 239 HIS cc_start: 0.8307 (m90) cc_final: 0.8102 (m-70) REVERT: I 55 GLU cc_start: 0.8410 (mm-30) cc_final: 0.7981 (tm-30) REVERT: J 57 TYR cc_start: 0.6777 (OUTLIER) cc_final: 0.6210 (t80) REVERT: J 112 TYR cc_start: 0.8537 (t80) cc_final: 0.8277 (t80) REVERT: J 162 ASP cc_start: 0.7314 (OUTLIER) cc_final: 0.7055 (m-30) REVERT: L 33 HIS cc_start: 0.6713 (OUTLIER) cc_final: 0.6419 (m-70) REVERT: L 54 GLN cc_start: 0.8130 (mt0) cc_final: 0.7878 (tt0) REVERT: N 72 GLU cc_start: 0.8118 (tm-30) cc_final: 0.7544 (tp30) REVERT: N 74 GLU cc_start: 0.7674 (tm-30) cc_final: 0.7384 (tm-30) REVERT: O 79 ARG cc_start: 0.8521 (mtp180) cc_final: 0.8255 (tmt-80) REVERT: O 80 GLN cc_start: 0.7632 (mm-40) cc_final: 0.7198 (mm110) REVERT: P 140 MET cc_start: 0.8538 (mpp) cc_final: 0.8137 (mpp) REVERT: P 154 GLU cc_start: 0.4775 (OUTLIER) cc_final: 0.3750 (pm20) REVERT: P 420 MET cc_start: 0.8410 (mmm) cc_final: 0.8176 (mmm) REVERT: a 94 MET cc_start: 0.8508 (tmm) cc_final: 0.8294 (tmm) REVERT: a 118 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8598 (mp) REVERT: a 830 HIS cc_start: 0.8481 (OUTLIER) cc_final: 0.8142 (t-90) REVERT: b 107 MET cc_start: 0.7989 (tpp) cc_final: 0.7744 (tpp) REVERT: b 166 ASP cc_start: 0.7621 (t70) cc_final: 0.7400 (t0) REVERT: e 28 VAL cc_start: 0.7969 (t) cc_final: 0.7540 (t) REVERT: e 34 ARG cc_start: 0.6907 (ttm-80) cc_final: 0.6081 (mtp85) REVERT: e 53 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8754 (tp) REVERT: e 64 PHE cc_start: 0.7836 (OUTLIER) cc_final: 0.7630 (t80) REVERT: r 336 TYR cc_start: 0.5390 (p90) cc_final: 0.4422 (p90) REVERT: c 51 MET cc_start: 0.7838 (OUTLIER) cc_final: 0.7587 (mtm) REVERT: c 115 ASP cc_start: 0.7890 (t70) cc_final: 0.7446 (t70) REVERT: g 64 ILE cc_start: 0.9006 (mm) cc_final: 0.8497 (mt) REVERT: k 115 ASP cc_start: 0.8144 (t0) cc_final: 0.7934 (t70) REVERT: p 139 GLU cc_start: 0.8399 (tm-30) cc_final: 0.7998 (tm-30) REVERT: q 131 MET cc_start: 0.8216 (ttp) cc_final: 0.7970 (ttt) outliers start: 207 outliers final: 167 residues processed: 1054 average time/residue: 0.5864 time to fit residues: 1056.8708 Evaluate side-chains 1075 residues out of total 6850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 896 time to evaluate : 5.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 534 PHE Chi-restraints excluded: chain A residue 573 HIS Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 306 MET Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 488 ASP Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 584 MET Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 138 CYS Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain C residue 612 PHE Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 156 GLN Chi-restraints excluded: chain D residue 237 ASN Chi-restraints excluded: chain D residue 251 ASN Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 265 ASN Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 413 LYS Chi-restraints excluded: chain D residue 486 ILE Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 298 THR Chi-restraints excluded: chain E residue 348 ILE Chi-restraints excluded: chain E residue 449 LEU Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 330 ASP Chi-restraints excluded: chain F residue 348 ILE Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain F residue 491 MET Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 75 TYR Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 112 TYR Chi-restraints excluded: chain G residue 175 PHE Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain I residue 56 TYR Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 159 THR Chi-restraints excluded: chain I residue 168 ASP Chi-restraints excluded: chain I residue 221 ASN Chi-restraints excluded: chain J residue 57 TYR Chi-restraints excluded: chain J residue 59 LYS Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 162 ASP Chi-restraints excluded: chain J residue 221 ASN Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 168 ASP Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 30 LYS Chi-restraints excluded: chain L residue 33 HIS Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 73 MET Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain N residue 99 LEU Chi-restraints excluded: chain O residue 96 LEU Chi-restraints excluded: chain P residue 66 LEU Chi-restraints excluded: chain P residue 154 GLU Chi-restraints excluded: chain P residue 187 LEU Chi-restraints excluded: chain P residue 242 LEU Chi-restraints excluded: chain P residue 279 VAL Chi-restraints excluded: chain P residue 296 VAL Chi-restraints excluded: chain P residue 423 MET Chi-restraints excluded: chain a residue 11 THR Chi-restraints excluded: chain a residue 118 LEU Chi-restraints excluded: chain a residue 171 VAL Chi-restraints excluded: chain a residue 202 ILE Chi-restraints excluded: chain a residue 214 TYR Chi-restraints excluded: chain a residue 244 LEU Chi-restraints excluded: chain a residue 333 ILE Chi-restraints excluded: chain a residue 472 LEU Chi-restraints excluded: chain a residue 527 THR Chi-restraints excluded: chain a residue 557 LEU Chi-restraints excluded: chain a residue 567 LEU Chi-restraints excluded: chain a residue 755 VAL Chi-restraints excluded: chain a residue 756 LEU Chi-restraints excluded: chain a residue 779 ILE Chi-restraints excluded: chain a residue 791 LEU Chi-restraints excluded: chain a residue 830 HIS Chi-restraints excluded: chain b residue 26 TYR Chi-restraints excluded: chain b residue 128 HIS Chi-restraints excluded: chain b residue 142 LEU Chi-restraints excluded: chain b residue 201 VAL Chi-restraints excluded: chain d residue 7 LEU Chi-restraints excluded: chain d residue 69 VAL Chi-restraints excluded: chain d residue 99 PHE Chi-restraints excluded: chain d residue 203 THR Chi-restraints excluded: chain d residue 264 VAL Chi-restraints excluded: chain e residue 10 VAL Chi-restraints excluded: chain e residue 53 LEU Chi-restraints excluded: chain e residue 64 PHE Chi-restraints excluded: chain s residue 253 VAL Chi-restraints excluded: chain s residue 265 ILE Chi-restraints excluded: chain s residue 300 TRP Chi-restraints excluded: chain s residue 338 PHE Chi-restraints excluded: chain s residue 343 LEU Chi-restraints excluded: chain s residue 371 HIS Chi-restraints excluded: chain s residue 425 TRP Chi-restraints excluded: chain s residue 429 LEU Chi-restraints excluded: chain s residue 448 LEU Chi-restraints excluded: chain s residue 452 ASP Chi-restraints excluded: chain r residue 331 ASN Chi-restraints excluded: chain c residue 17 MET Chi-restraints excluded: chain c residue 51 MET Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 60 VAL Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain g residue 59 VAL Chi-restraints excluded: chain g residue 81 ASN Chi-restraints excluded: chain k residue 59 VAL Chi-restraints excluded: chain l residue 50 GLU Chi-restraints excluded: chain l residue 81 ASN Chi-restraints excluded: chain l residue 132 ILE Chi-restraints excluded: chain m residue 50 GLU Chi-restraints excluded: chain m residue 59 VAL Chi-restraints excluded: chain m residue 61 MET Chi-restraints excluded: chain m residue 84 ILE Chi-restraints excluded: chain m residue 143 LEU Chi-restraints excluded: chain n residue 9 GLU Chi-restraints excluded: chain n residue 44 MET Chi-restraints excluded: chain n residue 51 MET Chi-restraints excluded: chain o residue 59 VAL Chi-restraints excluded: chain p residue 44 MET Chi-restraints excluded: chain p residue 59 VAL Chi-restraints excluded: chain q residue 20 SER Chi-restraints excluded: chain q residue 59 VAL Chi-restraints excluded: chain q residue 84 ILE Chi-restraints excluded: chain q residue 91 LEU Chi-restraints excluded: chain q residue 123 GLN Chi-restraints excluded: chain f residue 67 TYR Chi-restraints excluded: chain f residue 76 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 806 random chunks: chunk 706 optimal weight: 3.9990 chunk 744 optimal weight: 5.9990 chunk 679 optimal weight: 1.9990 chunk 723 optimal weight: 10.0000 chunk 435 optimal weight: 3.9990 chunk 315 optimal weight: 0.7980 chunk 568 optimal weight: 5.9990 chunk 222 optimal weight: 8.9990 chunk 654 optimal weight: 5.9990 chunk 684 optimal weight: 2.9990 chunk 721 optimal weight: 6.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 ASN B 609 GLN ** C 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 GLN ** E 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 91 GLN K 96 ASN L 35 ASN M 75 GLN ** M 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 390 ASN ** a 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 340 HIS ** e 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.3990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 64234 Z= 0.334 Angle : 0.668 11.589 86928 Z= 0.339 Chirality : 0.045 0.219 9966 Planarity : 0.005 0.128 11109 Dihedral : 7.985 122.212 9312 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.29 % Favored : 94.64 % Rotamer: Outliers : 3.07 % Allowed : 20.53 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.08 % Twisted Proline : 0.64 % Twisted General : 0.04 % 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: -0.31 (0.09), residues: 8098 helix: 0.89 (0.08), residues: 4551 sheet: -1.37 (0.18), residues: 758 loop : -1.68 (0.12), residues: 2789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP r 313 HIS 0.010 0.001 HIS a 802 PHE 0.024 0.001 PHE E 260 TYR 0.049 0.002 TYR n 144 ARG 0.007 0.000 ARG O 90 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16196 Ramachandran restraints generated. 8098 Oldfield, 0 Emsley, 8098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16196 Ramachandran restraints generated. 8098 Oldfield, 0 Emsley, 8098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1105 residues out of total 6850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 905 time to evaluate : 5.787 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: A 492 ILE cc_start: 0.7510 (OUTLIER) cc_final: 0.6867 (pt) REVERT: B 134 ASP cc_start: 0.7695 (p0) cc_final: 0.7329 (p0) REVERT: C 360 GLU cc_start: 0.8068 (tm-30) cc_final: 0.7086 (tm-30) REVERT: C 517 ASP cc_start: 0.7880 (m-30) cc_final: 0.7557 (m-30) REVERT: D 161 GLN cc_start: 0.8568 (tp40) cc_final: 0.8089 (tp-100) REVERT: D 251 ASN cc_start: 0.8821 (OUTLIER) cc_final: 0.8108 (t0) REVERT: D 326 TYR cc_start: 0.8983 (p90) cc_final: 0.8709 (p90) REVERT: F 44 ARG cc_start: 0.8702 (mtt180) cc_final: 0.8405 (mtt-85) REVERT: G 224 LEU cc_start: 0.7078 (OUTLIER) cc_final: 0.6738 (mt) REVERT: G 239 HIS cc_start: 0.8312 (m90) cc_final: 0.8104 (m-70) REVERT: H 160 GLU cc_start: 0.7369 (mt-10) cc_final: 0.7065 (mt-10) REVERT: I 55 GLU cc_start: 0.8395 (mm-30) cc_final: 0.7969 (tm-30) REVERT: J 57 TYR cc_start: 0.6728 (OUTLIER) cc_final: 0.6108 (t80) REVERT: J 112 TYR cc_start: 0.8573 (t80) cc_final: 0.8146 (t80) REVERT: J 140 ASP cc_start: 0.8282 (m-30) cc_final: 0.8009 (m-30) REVERT: K 63 GLN cc_start: 0.7561 (tp40) cc_final: 0.7284 (mm-40) REVERT: L 33 HIS cc_start: 0.6852 (OUTLIER) cc_final: 0.6427 (m-70) REVERT: L 54 GLN cc_start: 0.8159 (mt0) cc_final: 0.7866 (tt0) REVERT: M 105 ASP cc_start: 0.8511 (m-30) cc_final: 0.7660 (m-30) REVERT: M 107 ARG cc_start: 0.8387 (mtm-85) cc_final: 0.7725 (mtm-85) REVERT: N 72 GLU cc_start: 0.8135 (tm-30) cc_final: 0.7558 (tp30) REVERT: N 74 GLU cc_start: 0.7638 (tm-30) cc_final: 0.7347 (tm-30) REVERT: N 105 ASP cc_start: 0.8463 (t70) cc_final: 0.8073 (t70) REVERT: O 79 ARG cc_start: 0.8536 (mtp180) cc_final: 0.8267 (tmt-80) REVERT: O 80 GLN cc_start: 0.7661 (mm-40) cc_final: 0.7221 (mm110) REVERT: O 89 GLN cc_start: 0.8422 (mm-40) cc_final: 0.8075 (mm-40) REVERT: P 66 LEU cc_start: 0.6505 (OUTLIER) cc_final: 0.6268 (mt) REVERT: P 140 MET cc_start: 0.8615 (mpp) cc_final: 0.8270 (mpp) REVERT: P 154 GLU cc_start: 0.4971 (OUTLIER) cc_final: 0.3945 (pm20) REVERT: P 420 MET cc_start: 0.8430 (mmm) cc_final: 0.8226 (mmm) REVERT: a 94 MET cc_start: 0.8557 (tmm) cc_final: 0.8349 (tmm) REVERT: a 118 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8649 (mp) REVERT: a 628 MET cc_start: 0.8525 (mmp) cc_final: 0.8275 (mmp) REVERT: a 830 HIS cc_start: 0.8519 (OUTLIER) cc_final: 0.8110 (t-90) REVERT: b 107 MET cc_start: 0.7969 (tpp) cc_final: 0.7685 (tpp) REVERT: b 166 ASP cc_start: 0.7730 (t70) cc_final: 0.7467 (t0) REVERT: e 28 VAL cc_start: 0.8051 (t) cc_final: 0.7482 (t) REVERT: e 34 ARG cc_start: 0.6918 (ttm-80) cc_final: 0.5935 (ttt-90) REVERT: e 53 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8844 (tp) REVERT: e 64 PHE cc_start: 0.7982 (OUTLIER) cc_final: 0.7678 (t80) REVERT: r 336 TYR cc_start: 0.5487 (p90) cc_final: 0.4381 (p90) REVERT: c 51 MET cc_start: 0.7858 (OUTLIER) cc_final: 0.7515 (mtm) REVERT: c 115 ASP cc_start: 0.7972 (t70) cc_final: 0.7535 (t70) REVERT: g 123 GLN cc_start: 0.9009 (mm-40) cc_final: 0.8408 (mm-40) REVERT: k 115 ASP cc_start: 0.8194 (t0) cc_final: 0.7975 (t70) REVERT: p 139 GLU cc_start: 0.8477 (tm-30) cc_final: 0.8081 (tm-30) outliers start: 200 outliers final: 169 residues processed: 1032 average time/residue: 0.6028 time to fit residues: 1065.0753 Evaluate side-chains 1051 residues out of total 6850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 870 time to evaluate : 5.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 573 HIS Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 153 TYR Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 306 MET Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 584 MET Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 138 CYS Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 612 PHE Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 156 GLN Chi-restraints excluded: chain D residue 237 ASN Chi-restraints excluded: chain D residue 251 ASN Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 265 ASN Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 413 LYS Chi-restraints excluded: chain D residue 486 ILE Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 298 THR Chi-restraints excluded: chain E residue 330 ASP Chi-restraints excluded: chain E residue 348 ILE Chi-restraints excluded: chain E residue 449 LEU Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 330 ASP Chi-restraints excluded: chain F residue 348 ILE Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain F residue 491 MET Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 75 TYR Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 112 TYR Chi-restraints excluded: chain G residue 175 PHE Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain I residue 56 TYR Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 159 THR Chi-restraints excluded: chain I residue 168 ASP Chi-restraints excluded: chain I residue 221 ASN Chi-restraints excluded: chain J residue 57 TYR Chi-restraints excluded: chain J residue 59 LYS Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 162 ASP Chi-restraints excluded: chain J residue 221 ASN Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 30 LYS Chi-restraints excluded: chain L residue 33 HIS Chi-restraints excluded: chain L residue 35 ASN Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 73 MET Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain N residue 99 LEU Chi-restraints excluded: chain O residue 96 LEU Chi-restraints excluded: chain P residue 66 LEU Chi-restraints excluded: chain P residue 154 GLU Chi-restraints excluded: chain P residue 242 LEU Chi-restraints excluded: chain P residue 279 VAL Chi-restraints excluded: chain P residue 296 VAL Chi-restraints excluded: chain P residue 423 MET Chi-restraints excluded: chain a residue 11 THR Chi-restraints excluded: chain a residue 118 LEU Chi-restraints excluded: chain a residue 171 VAL Chi-restraints excluded: chain a residue 202 ILE Chi-restraints excluded: chain a residue 244 LEU Chi-restraints excluded: chain a residue 333 ILE Chi-restraints excluded: chain a residue 527 THR Chi-restraints excluded: chain a residue 547 ILE Chi-restraints excluded: chain a residue 557 LEU Chi-restraints excluded: chain a residue 567 LEU Chi-restraints excluded: chain a residue 755 VAL Chi-restraints excluded: chain a residue 756 LEU Chi-restraints excluded: chain a residue 779 ILE Chi-restraints excluded: chain a residue 786 LEU Chi-restraints excluded: chain a residue 791 LEU Chi-restraints excluded: chain a residue 830 HIS Chi-restraints excluded: chain b residue 26 TYR Chi-restraints excluded: chain b residue 128 HIS Chi-restraints excluded: chain b residue 142 LEU Chi-restraints excluded: chain b residue 201 VAL Chi-restraints excluded: chain d residue 7 LEU Chi-restraints excluded: chain d residue 69 VAL Chi-restraints excluded: chain d residue 99 PHE Chi-restraints excluded: chain d residue 124 GLU Chi-restraints excluded: chain d residue 203 THR Chi-restraints excluded: chain d residue 264 VAL Chi-restraints excluded: chain e residue 10 VAL Chi-restraints excluded: chain e residue 53 LEU Chi-restraints excluded: chain e residue 64 PHE Chi-restraints excluded: chain s residue 253 VAL Chi-restraints excluded: chain s residue 265 ILE Chi-restraints excluded: chain s residue 300 TRP Chi-restraints excluded: chain s residue 343 LEU Chi-restraints excluded: chain s residue 364 ILE Chi-restraints excluded: chain s residue 371 HIS Chi-restraints excluded: chain s residue 425 TRP Chi-restraints excluded: chain s residue 429 LEU Chi-restraints excluded: chain s residue 434 MET Chi-restraints excluded: chain s residue 448 LEU Chi-restraints excluded: chain s residue 452 ASP Chi-restraints excluded: chain r residue 331 ASN Chi-restraints excluded: chain c residue 51 MET Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 60 VAL Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain g residue 59 VAL Chi-restraints excluded: chain k residue 44 MET Chi-restraints excluded: chain k residue 59 VAL Chi-restraints excluded: chain l residue 81 ASN Chi-restraints excluded: chain l residue 132 ILE Chi-restraints excluded: chain m residue 50 GLU Chi-restraints excluded: chain m residue 59 VAL Chi-restraints excluded: chain m residue 61 MET Chi-restraints excluded: chain m residue 84 ILE Chi-restraints excluded: chain m residue 143 LEU Chi-restraints excluded: chain n residue 9 GLU Chi-restraints excluded: chain n residue 44 MET Chi-restraints excluded: chain n residue 51 MET Chi-restraints excluded: chain o residue 59 VAL Chi-restraints excluded: chain o residue 154 THR Chi-restraints excluded: chain p residue 44 MET Chi-restraints excluded: chain p residue 59 VAL Chi-restraints excluded: chain q residue 20 SER Chi-restraints excluded: chain q residue 59 VAL Chi-restraints excluded: chain q residue 84 ILE Chi-restraints excluded: chain q residue 91 LEU Chi-restraints excluded: chain q residue 123 GLN Chi-restraints excluded: chain q residue 129 VAL Chi-restraints excluded: chain f residue 67 TYR Chi-restraints excluded: chain f residue 76 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 806 random chunks: chunk 475 optimal weight: 4.9990 chunk 765 optimal weight: 0.7980 chunk 467 optimal weight: 20.0000 chunk 363 optimal weight: 6.9990 chunk 532 optimal weight: 8.9990 chunk 802 optimal weight: 0.0020 chunk 739 optimal weight: 1.9990 chunk 639 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 493 optimal weight: 3.9990 chunk 392 optimal weight: 5.9990 overall best weight: 1.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 573 HIS ** C 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 GLN H 91 GLN I 96 ASN ** M 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 254 GLN d 340 HIS ** e 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.4003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.150 64234 Z= 0.311 Angle : 0.715 59.194 86928 Z= 0.376 Chirality : 0.044 0.393 9966 Planarity : 0.004 0.128 11109 Dihedral : 7.983 122.210 9312 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.27 % Favored : 94.65 % Rotamer: Outliers : 2.94 % Allowed : 20.79 % Favored : 76.27 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.08 % Twisted Proline : 0.64 % Twisted General : 0.04 % 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: -0.30 (0.09), residues: 8098 helix: 0.91 (0.08), residues: 4551 sheet: -1.37 (0.18), residues: 758 loop : -1.68 (0.12), residues: 2789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP r 313 HIS 0.020 0.001 HIS P 139 PHE 0.024 0.001 PHE E 260 TYR 0.046 0.002 TYR n 144 ARG 0.008 0.000 ARG O 90 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16196 Ramachandran restraints generated. 8098 Oldfield, 0 Emsley, 8098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16196 Ramachandran restraints generated. 8098 Oldfield, 0 Emsley, 8098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1063 residues out of total 6850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 872 time to evaluate : 5.641 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: A 492 ILE cc_start: 0.7512 (OUTLIER) cc_final: 0.6864 (pt) REVERT: B 134 ASP cc_start: 0.7692 (p0) cc_final: 0.7325 (p0) REVERT: B 486 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7857 (tm-30) REVERT: C 360 GLU cc_start: 0.8062 (tm-30) cc_final: 0.7084 (tm-30) REVERT: C 517 ASP cc_start: 0.7851 (m-30) cc_final: 0.7518 (m-30) REVERT: D 161 GLN cc_start: 0.8559 (tp40) cc_final: 0.8085 (tp-100) REVERT: D 251 ASN cc_start: 0.8816 (OUTLIER) cc_final: 0.8103 (t0) REVERT: D 326 TYR cc_start: 0.8980 (p90) cc_final: 0.8707 (p90) REVERT: F 44 ARG cc_start: 0.8698 (mtt180) cc_final: 0.8403 (mtt-85) REVERT: G 224 LEU cc_start: 0.7076 (OUTLIER) cc_final: 0.6737 (mt) REVERT: G 239 HIS cc_start: 0.8310 (m90) cc_final: 0.8104 (m-70) REVERT: H 86 ASN cc_start: 0.8808 (m110) cc_final: 0.8577 (m110) REVERT: H 160 GLU cc_start: 0.7372 (mt-10) cc_final: 0.7054 (mt-10) REVERT: I 55 GLU cc_start: 0.8397 (mm-30) cc_final: 0.7971 (tm-30) REVERT: J 57 TYR cc_start: 0.6727 (OUTLIER) cc_final: 0.6106 (t80) REVERT: K 63 GLN cc_start: 0.7544 (tp40) cc_final: 0.7288 (mm-40) REVERT: L 33 HIS cc_start: 0.6874 (OUTLIER) cc_final: 0.6434 (m-70) REVERT: L 54 GLN cc_start: 0.8156 (mt0) cc_final: 0.7864 (tt0) REVERT: M 105 ASP cc_start: 0.8509 (m-30) cc_final: 0.7697 (m-30) REVERT: M 107 ARG cc_start: 0.8388 (mtm-85) cc_final: 0.7748 (mtm-85) REVERT: N 72 GLU cc_start: 0.8134 (tm-30) cc_final: 0.7556 (tp30) REVERT: N 74 GLU cc_start: 0.7637 (tm-30) cc_final: 0.7345 (tm-30) REVERT: N 105 ASP cc_start: 0.8472 (t70) cc_final: 0.8091 (t70) REVERT: O 79 ARG cc_start: 0.8539 (mtp180) cc_final: 0.8267 (tmt-80) REVERT: O 80 GLN cc_start: 0.7659 (mm-40) cc_final: 0.7219 (mm110) REVERT: O 89 GLN cc_start: 0.8421 (mm-40) cc_final: 0.8071 (mm-40) REVERT: P 66 LEU cc_start: 0.6503 (OUTLIER) cc_final: 0.6268 (mt) REVERT: P 140 MET cc_start: 0.8596 (mpp) cc_final: 0.8264 (mpp) REVERT: P 154 GLU cc_start: 0.4967 (OUTLIER) cc_final: 0.3941 (pm20) REVERT: P 420 MET cc_start: 0.8425 (mmm) cc_final: 0.8225 (mmm) REVERT: a 94 MET cc_start: 0.8552 (tmm) cc_final: 0.8342 (tmm) REVERT: a 118 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8646 (mp) REVERT: a 628 MET cc_start: 0.8540 (mmp) cc_final: 0.8260 (mmp) REVERT: a 830 HIS cc_start: 0.8516 (OUTLIER) cc_final: 0.8105 (t-90) REVERT: b 107 MET cc_start: 0.7969 (tpp) cc_final: 0.7685 (tpp) REVERT: b 166 ASP cc_start: 0.7731 (t70) cc_final: 0.7416 (t0) REVERT: e 28 VAL cc_start: 0.8057 (t) cc_final: 0.7484 (t) REVERT: e 34 ARG cc_start: 0.6926 (ttm-80) cc_final: 0.5930 (ttt-90) REVERT: e 53 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8841 (tp) REVERT: e 64 PHE cc_start: 0.7979 (OUTLIER) cc_final: 0.7677 (t80) REVERT: r 336 TYR cc_start: 0.5432 (p90) cc_final: 0.4374 (p90) REVERT: c 51 MET cc_start: 0.7852 (OUTLIER) cc_final: 0.7514 (mtm) REVERT: c 115 ASP cc_start: 0.7978 (t70) cc_final: 0.7528 (t70) REVERT: g 64 ILE cc_start: 0.9082 (mm) cc_final: 0.8551 (mt) REVERT: g 123 GLN cc_start: 0.9005 (mm-40) cc_final: 0.8399 (mm-40) REVERT: k 115 ASP cc_start: 0.8191 (t0) cc_final: 0.7957 (t70) REVERT: p 139 GLU cc_start: 0.8481 (tm-30) cc_final: 0.8076 (tm-30) outliers start: 191 outliers final: 173 residues processed: 999 average time/residue: 0.6081 time to fit residues: 1041.1715 Evaluate side-chains 1054 residues out of total 6850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 869 time to evaluate : 5.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 573 HIS Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 153 TYR Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 306 MET Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 584 MET Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 138 CYS Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 573 HIS Chi-restraints excluded: chain C residue 612 PHE Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 156 GLN Chi-restraints excluded: chain D residue 237 ASN Chi-restraints excluded: chain D residue 251 ASN Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 265 ASN Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 413 LYS Chi-restraints excluded: chain D residue 486 ILE Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 298 THR Chi-restraints excluded: chain E residue 330 ASP Chi-restraints excluded: chain E residue 348 ILE Chi-restraints excluded: chain E residue 449 LEU Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 330 ASP Chi-restraints excluded: chain F residue 348 ILE Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain F residue 491 MET Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 75 TYR Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 112 TYR Chi-restraints excluded: chain G residue 175 PHE Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain I residue 56 TYR Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 159 THR Chi-restraints excluded: chain I residue 168 ASP Chi-restraints excluded: chain I residue 221 ASN Chi-restraints excluded: chain J residue 57 TYR Chi-restraints excluded: chain J residue 59 LYS Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 162 ASP Chi-restraints excluded: chain J residue 221 ASN Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain K residue 168 ASP Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 30 LYS Chi-restraints excluded: chain L residue 33 HIS Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 73 MET Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain N residue 99 LEU Chi-restraints excluded: chain O residue 96 LEU Chi-restraints excluded: chain P residue 66 LEU Chi-restraints excluded: chain P residue 154 GLU Chi-restraints excluded: chain P residue 242 LEU Chi-restraints excluded: chain P residue 279 VAL Chi-restraints excluded: chain P residue 296 VAL Chi-restraints excluded: chain P residue 423 MET Chi-restraints excluded: chain a residue 11 THR Chi-restraints excluded: chain a residue 118 LEU Chi-restraints excluded: chain a residue 171 VAL Chi-restraints excluded: chain a residue 202 ILE Chi-restraints excluded: chain a residue 244 LEU Chi-restraints excluded: chain a residue 333 ILE Chi-restraints excluded: chain a residue 527 THR Chi-restraints excluded: chain a residue 547 ILE Chi-restraints excluded: chain a residue 557 LEU Chi-restraints excluded: chain a residue 567 LEU Chi-restraints excluded: chain a residue 755 VAL Chi-restraints excluded: chain a residue 756 LEU Chi-restraints excluded: chain a residue 779 ILE Chi-restraints excluded: chain a residue 786 LEU Chi-restraints excluded: chain a residue 791 LEU Chi-restraints excluded: chain a residue 830 HIS Chi-restraints excluded: chain b residue 26 TYR Chi-restraints excluded: chain b residue 128 HIS Chi-restraints excluded: chain b residue 142 LEU Chi-restraints excluded: chain b residue 201 VAL Chi-restraints excluded: chain d residue 7 LEU Chi-restraints excluded: chain d residue 69 VAL Chi-restraints excluded: chain d residue 99 PHE Chi-restraints excluded: chain d residue 124 GLU Chi-restraints excluded: chain d residue 203 THR Chi-restraints excluded: chain d residue 264 VAL Chi-restraints excluded: chain e residue 10 VAL Chi-restraints excluded: chain e residue 53 LEU Chi-restraints excluded: chain e residue 64 PHE Chi-restraints excluded: chain s residue 253 VAL Chi-restraints excluded: chain s residue 265 ILE Chi-restraints excluded: chain s residue 300 TRP Chi-restraints excluded: chain s residue 338 PHE Chi-restraints excluded: chain s residue 343 LEU Chi-restraints excluded: chain s residue 364 ILE Chi-restraints excluded: chain s residue 371 HIS Chi-restraints excluded: chain s residue 425 TRP Chi-restraints excluded: chain s residue 429 LEU Chi-restraints excluded: chain s residue 434 MET Chi-restraints excluded: chain s residue 448 LEU Chi-restraints excluded: chain s residue 452 ASP Chi-restraints excluded: chain r residue 331 ASN Chi-restraints excluded: chain c residue 51 MET Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 60 VAL Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain g residue 59 VAL Chi-restraints excluded: chain k residue 44 MET Chi-restraints excluded: chain k residue 59 VAL Chi-restraints excluded: chain l residue 81 ASN Chi-restraints excluded: chain l residue 132 ILE Chi-restraints excluded: chain m residue 50 GLU Chi-restraints excluded: chain m residue 59 VAL Chi-restraints excluded: chain m residue 61 MET Chi-restraints excluded: chain m residue 84 ILE Chi-restraints excluded: chain m residue 143 LEU Chi-restraints excluded: chain n residue 9 GLU Chi-restraints excluded: chain n residue 44 MET Chi-restraints excluded: chain n residue 51 MET Chi-restraints excluded: chain o residue 59 VAL Chi-restraints excluded: chain o residue 154 THR Chi-restraints excluded: chain p residue 44 MET Chi-restraints excluded: chain p residue 59 VAL Chi-restraints excluded: chain q residue 20 SER Chi-restraints excluded: chain q residue 59 VAL Chi-restraints excluded: chain q residue 84 ILE Chi-restraints excluded: chain q residue 91 LEU Chi-restraints excluded: chain q residue 123 GLN Chi-restraints excluded: chain q residue 129 VAL Chi-restraints excluded: chain f residue 67 TYR Chi-restraints excluded: chain f residue 76 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 806 random chunks: chunk 507 optimal weight: 8.9990 chunk 681 optimal weight: 4.9990 chunk 195 optimal weight: 5.9990 chunk 589 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 177 optimal weight: 0.6980 chunk 640 optimal weight: 3.9990 chunk 268 optimal weight: 2.9990 chunk 657 optimal weight: 6.9990 chunk 81 optimal weight: 0.6980 chunk 117 optimal weight: 6.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 573 HIS ** C 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 456 GLN H 85 GLN H 91 GLN I 96 ASN K 122 GLN ** L 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 305 HIS ** a 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 340 HIS ** e 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.112020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.085162 restraints weight = 130958.737| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 1.94 r_work: 0.2939 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.4051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 64234 Z= 0.256 Angle : 0.644 12.602 86928 Z= 0.326 Chirality : 0.043 0.210 9966 Planarity : 0.004 0.127 11109 Dihedral : 7.898 121.010 9312 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.04 % Favored : 94.89 % Rotamer: Outliers : 2.97 % Allowed : 20.75 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.08 % Twisted Proline : 0.64 % Twisted General : 0.04 % 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: -0.23 (0.09), residues: 8098 helix: 0.95 (0.08), residues: 4584 sheet: -1.34 (0.18), residues: 743 loop : -1.66 (0.12), residues: 2771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 567 HIS 0.036 0.001 HIS C 573 PHE 0.020 0.001 PHE E 260 TYR 0.038 0.002 TYR n 144 ARG 0.009 0.000 ARG O 90 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19054.55 seconds wall clock time: 328 minutes 1.69 seconds (19681.69 seconds total)