Starting phenix.real_space_refine (version: 1.21rc1) on Mon Apr 24 01:19:59 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tdh_25829/04_2023/7tdh_25829_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tdh_25829/04_2023/7tdh_25829.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tdh_25829/04_2023/7tdh_25829.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tdh_25829/04_2023/7tdh_25829.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tdh_25829/04_2023/7tdh_25829_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tdh_25829/04_2023/7tdh_25829_neut_updated.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.001 sd= 0.009 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: 7 Type Number sf(0) Gaussians Ca 8 9.91 5 Zn 4 6.06 5 P 12 5.49 5 S 628 5.16 5 C 74416 2.51 5 N 20816 2.21 5 O 21648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 139": "OE1" <-> "OE2" Residue "A GLU 211": "OE1" <-> "OE2" Residue "A GLU 381": "OE1" <-> "OE2" Residue "A GLU 555": "OE1" <-> "OE2" Residue "A ASP 749": "OD1" <-> "OD2" Residue "A GLU 1108": "OE1" <-> "OE2" Residue "A GLU 1652": "OE1" <-> "OE2" Residue "A GLU 1817": "OE1" <-> "OE2" Residue "A GLU 3754": "OE1" <-> "OE2" Residue "A GLU 3789": "OE1" <-> "OE2" Residue "A GLU 3811": "OE1" <-> "OE2" Residue "A PHE 3887": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 3944": "OE1" <-> "OE2" Residue "A GLU 4032": "OE1" <-> "OE2" Residue "A GLU 4239": "OE1" <-> "OE2" Residue "A GLU 4690": "OE1" <-> "OE2" Residue "A GLU 4869": "OE1" <-> "OE2" Residue "A GLU 4900": "OE1" <-> "OE2" Residue "A GLU 4948": "OE1" <-> "OE2" Residue "A GLU 5002": "OE1" <-> "OE2" Residue "A GLU 5016": "OE1" <-> "OE2" Residue "B GLU 139": "OE1" <-> "OE2" Residue "B GLU 211": "OE1" <-> "OE2" Residue "B GLU 381": "OE1" <-> "OE2" Residue "B GLU 555": "OE1" <-> "OE2" Residue "B GLU 1108": "OE1" <-> "OE2" Residue "B GLU 1652": "OE1" <-> "OE2" Residue "B GLU 1817": "OE1" <-> "OE2" Residue "B GLU 3754": "OE1" <-> "OE2" Residue "B GLU 3789": "OE1" <-> "OE2" Residue "B GLU 3811": "OE1" <-> "OE2" Residue "B PHE 3887": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 3944": "OE1" <-> "OE2" Residue "B GLU 4032": "OE1" <-> "OE2" Residue "B GLU 4239": "OE1" <-> "OE2" Residue "B GLU 4690": "OE1" <-> "OE2" Residue "B GLU 4869": "OE1" <-> "OE2" Residue "B GLU 4900": "OE1" <-> "OE2" Residue "B GLU 4948": "OE1" <-> "OE2" Residue "B GLU 5002": "OE1" <-> "OE2" Residue "B GLU 5016": "OE1" <-> "OE2" Residue "C GLU 139": "OE1" <-> "OE2" Residue "C GLU 211": "OE1" <-> "OE2" Residue "C GLU 381": "OE1" <-> "OE2" Residue "C GLU 555": "OE1" <-> "OE2" Residue "C GLU 1108": "OE1" <-> "OE2" Residue "C GLU 1652": "OE1" <-> "OE2" Residue "C GLU 1817": "OE1" <-> "OE2" Residue "C GLU 3754": "OE1" <-> "OE2" Residue "C GLU 3789": "OE1" <-> "OE2" Residue "C GLU 3811": "OE1" <-> "OE2" Residue "C PHE 3887": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 3944": "OE1" <-> "OE2" Residue "C GLU 4032": "OE1" <-> "OE2" Residue "C GLU 4239": "OE1" <-> "OE2" Residue "C GLU 4690": "OE1" <-> "OE2" Residue "C GLU 4869": "OE1" <-> "OE2" Residue "C GLU 4900": "OE1" <-> "OE2" Residue "C GLU 4948": "OE1" <-> "OE2" Residue "C GLU 5002": "OE1" <-> "OE2" Residue "C GLU 5016": "OE1" <-> "OE2" Residue "D GLU 139": "OE1" <-> "OE2" Residue "D GLU 211": "OE1" <-> "OE2" Residue "D GLU 381": "OE1" <-> "OE2" Residue "D GLU 555": "OE1" <-> "OE2" Residue "D GLU 1108": "OE1" <-> "OE2" Residue "D GLU 1652": "OE1" <-> "OE2" Residue "D GLU 1817": "OE1" <-> "OE2" Residue "D GLU 3754": "OE1" <-> "OE2" Residue "D GLU 3789": "OE1" <-> "OE2" Residue "D GLU 3811": "OE1" <-> "OE2" Residue "D PHE 3887": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 3944": "OE1" <-> "OE2" Residue "D GLU 4032": "OE1" <-> "OE2" Residue "D GLU 4239": "OE1" <-> "OE2" Residue "D GLU 4690": "OE1" <-> "OE2" Residue "D GLU 4869": "OE1" <-> "OE2" Residue "D GLU 4900": "OE1" <-> "OE2" Residue "D GLU 4948": "OE1" <-> "OE2" Residue "D GLU 5002": "OE1" <-> "OE2" Residue "D GLU 5016": "OE1" <-> "OE2" Time to flip residues: 0.25s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 117532 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 29349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4165, 29349 Classifications: {'peptide': 4165} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1244} Link IDs: {'PCIS': 1, 'PTRANS': 156, 'TRANS': 4007} Chain breaks: 25 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 3022 Unresolved non-hydrogen angles: 4223 Unresolved non-hydrogen dihedrals: 1877 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'GLN:plan1': 18, 'UNK:plan-1': 900, 'ASP:plan': 46, 'TYR:plan': 2, 'ASN:plan1': 16, 'TRP:plan': 3, 'HIS:plan': 7, 'PHE:plan': 5, 'GLU:plan': 83, 'ARG:plan': 33} Unresolved non-hydrogen planarities: 1761 Chain: "B" Number of atoms: 29349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4165, 29349 Classifications: {'peptide': 4165} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1244} Link IDs: {'PCIS': 1, 'PTRANS': 156, 'TRANS': 4007} Chain breaks: 25 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 3022 Unresolved non-hydrogen angles: 4223 Unresolved non-hydrogen dihedrals: 1877 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'GLN:plan1': 18, 'UNK:plan-1': 900, 'ASP:plan': 46, 'TYR:plan': 2, 'ASN:plan1': 16, 'TRP:plan': 3, 'HIS:plan': 7, 'PHE:plan': 5, 'GLU:plan': 83, 'ARG:plan': 33} Unresolved non-hydrogen planarities: 1761 Chain: "C" Number of atoms: 29349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4165, 29349 Classifications: {'peptide': 4165} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1244} Link IDs: {'PCIS': 1, 'PTRANS': 156, 'TRANS': 4007} Chain breaks: 25 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 3022 Unresolved non-hydrogen angles: 4223 Unresolved non-hydrogen dihedrals: 1877 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'GLN:plan1': 18, 'UNK:plan-1': 900, 'ASP:plan': 46, 'TYR:plan': 2, 'ASN:plan1': 16, 'TRP:plan': 3, 'HIS:plan': 7, 'PHE:plan': 5, 'GLU:plan': 83, 'ARG:plan': 33} Unresolved non-hydrogen planarities: 1761 Chain: "D" Number of atoms: 29349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4165, 29349 Classifications: {'peptide': 4165} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1244} Link IDs: {'PCIS': 1, 'PTRANS': 156, 'TRANS': 4007} Chain breaks: 25 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 3022 Unresolved non-hydrogen angles: 4223 Unresolved non-hydrogen dihedrals: 1877 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'GLN:plan1': 18, 'UNK:plan-1': 900, 'ASP:plan': 46, 'TYR:plan': 2, 'ASN:plan1': 16, 'TRP:plan': 3, 'HIS:plan': 7, 'PHE:plan': 5, 'GLU:plan': 83, 'ARG:plan': 33} Unresolved non-hydrogen planarities: 1761 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' CA': 2, ' ZN': 1, 'ACP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' CA': 2, ' ZN': 1, 'ACP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' CA': 2, ' ZN': 1, 'ACP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' CA': 2, ' ZN': 1, 'ACP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 28702 SG CYS A4961 179.143 207.241 102.061 1.00133.13 S ATOM 29259 SG CYS A5027 180.180 209.774 99.185 1.00200.53 S ATOM 58026 SG CYS B4958 178.173 179.371 105.315 1.00161.69 S ATOM 58051 SG CYS B4961 179.501 179.150 102.066 1.00133.13 S ATOM 87400 SG CYS C4961 207.602 179.504 102.060 1.00133.13 S ATOM 87957 SG CYS C5027 206.565 176.971 99.184 1.00200.53 S ATOM A0CX9 SG CYS D4961 207.255 207.607 102.065 1.00133.13 S ATOM A0DCQ SG CYS D5027 209.788 206.571 99.189 1.00200.53 S Time building chain proxies: 44.51, per 1000 atoms: 0.38 Number of scatterers: 117532 At special positions: 0 Unit cell: (387.855, 387.855, 194.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 Ca 8 19.99 S 628 16.00 P 12 15.00 O 21648 8.00 N 20816 7.00 C 74416 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 33.52 Conformation dependent library (CDL) restraints added in 11.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A5101 " pdb="ZN ZN A5101 " - pdb=" NE2 HIS A4983 " pdb="ZN ZN A5101 " - pdb=" NE2 HIS A4978 " pdb="ZN ZN A5101 " - pdb=" SG CYS A5027 " pdb="ZN ZN A5101 " - pdb=" SG CYS A4961 " pdb=" ZN B5101 " pdb="ZN ZN B5101 " - pdb=" SG CYS B4961 " pdb="ZN ZN B5101 " - pdb=" SG CYS B4958 " pdb="ZN ZN B5101 " - pdb=" NE2 HIS B4978 " pdb=" ZN C5101 " pdb="ZN ZN C5101 " - pdb=" NE2 HIS C4983 " pdb="ZN ZN C5101 " - pdb=" NE2 HIS C4978 " pdb="ZN ZN C5101 " - pdb=" SG CYS C5027 " pdb="ZN ZN C5101 " - pdb=" SG CYS C4961 " pdb=" ZN D5101 " pdb="ZN ZN D5101 " - pdb=" NE2 HIS D4978 " pdb="ZN ZN D5101 " - pdb=" NE2 HIS D4983 " pdb="ZN ZN D5101 " - pdb=" SG CYS D4961 " pdb="ZN ZN D5101 " - pdb=" SG CYS D5027 " Number of angles added : 6 25848 Ramachandran restraints generated. 12924 Oldfield, 0 Emsley, 12924 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 31584 Finding SS restraints... Warning!!! ksdssp method is not applicable forstructures with more than 99999 atoms! Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 496 helices and 48 sheets defined 54.1% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 14.31 Creating SS restraints... Processing helix chain 'A' and resid 61 through 66 removed outlier: 4.642A pdb=" N CYS A 65 " --> pdb=" O ASP A 61 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N CYS A 66 " --> pdb=" O LEU A 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 61 through 66' Processing helix chain 'A' and resid 74 through 84 Processing helix chain 'A' and resid 250 through 256 removed outlier: 6.184A pdb=" N THR A 254 " --> pdb=" O GLY A 250 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N HIS A 255 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N ALA A 256 " --> pdb=" O VAL A 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 250 through 256' Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.957A pdb=" N VAL A 371 " --> pdb=" O LEU A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 425 removed outlier: 4.394A pdb=" N GLN A 413 " --> pdb=" O GLY A 409 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE A 414 " --> pdb=" O LEU A 410 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N PHE A 421 " --> pdb=" O GLY A 417 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLY A 423 " --> pdb=" O ASP A 419 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LYS A 424 " --> pdb=" O SER A 420 " (cutoff:3.500A) Proline residue: A 425 - end of helix Processing helix chain 'A' and resid 437 through 453 removed outlier: 4.804A pdb=" N VAL A 441 " --> pdb=" O PRO A 437 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN A 446 " --> pdb=" O ILE A 442 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N PHE A 452 " --> pdb=" O LEU A 448 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N GLU A 453 " --> pdb=" O ILE A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 481 removed outlier: 3.665A pdb=" N ARG A 469 " --> pdb=" O GLN A 465 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU A 480 " --> pdb=" O SER A 476 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N GLU A 481 " --> pdb=" O LEU A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 496 removed outlier: 3.948A pdb=" N CYS A 490 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N VAL A 496 " --> pdb=" O ASP A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 531 removed outlier: 5.211A pdb=" N SER A 514 " --> pdb=" O GLU A 510 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N TRP A 515 " --> pdb=" O ALA A 511 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N LYS A 516 " --> pdb=" O ALA A 512 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N GLU A 517 " --> pdb=" O GLU A 513 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ILE A 518 " --> pdb=" O SER A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 540 removed outlier: 4.645A pdb=" N CYS A 537 " --> pdb=" O ASN A 533 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU A 539 " --> pdb=" O ALA A 535 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N PHE A 540 " --> pdb=" O ASN A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 551 removed outlier: 4.634A pdb=" N ASP A 545 " --> pdb=" O SER A 541 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N TRP A 546 " --> pdb=" O THR A 542 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL A 548 " --> pdb=" O LEU A 544 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LEU A 551 " --> pdb=" O VAL A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 571 removed outlier: 4.103A pdb=" N LEU A 561 " --> pdb=" O SER A 557 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N GLU A 562 " --> pdb=" O SER A 558 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N VAL A 563 " --> pdb=" O GLY A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 578 removed outlier: 4.344A pdb=" N ILE A 577 " --> pdb=" O GLU A 573 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ILE A 578 " --> pdb=" O VAL A 574 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 573 through 578' Processing helix chain 'A' and resid 579 through 594 removed outlier: 6.091A pdb=" N ILE A 583 " --> pdb=" O GLN A 579 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU A 590 " --> pdb=" O ILE A 586 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASP A 591 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 609 removed outlier: 4.223A pdb=" N VAL A 602 " --> pdb=" O LYS A 598 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LEU A 603 " --> pdb=" O VAL A 599 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N CYS A 607 " --> pdb=" O LEU A 603 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N VAL A 608 " --> pdb=" O CYS A 604 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N CYS A 609 " --> pdb=" O SER A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 626 removed outlier: 4.327A pdb=" N GLN A 618 " --> pdb=" O VAL A 614 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR A 622 " --> pdb=" O GLN A 618 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N LEU A 626 " --> pdb=" O THR A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 890 removed outlier: 4.745A pdb=" N ARG A 869 " --> pdb=" O PRO A 865 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ILE A 870 " --> pdb=" O HIS A 866 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU A 876 " --> pdb=" O GLU A 872 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN A 877 " --> pdb=" O LYS A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 936 removed outlier: 4.022A pdb=" N TYR A 920 " --> pdb=" O PRO A 916 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N GLY A 936 " --> pdb=" O LEU A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 950 removed outlier: 4.510A pdb=" N ASN A 949 " --> pdb=" O LYS A 945 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU A 950 " --> pdb=" O ALA A 946 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 945 through 950' Processing helix chain 'A' and resid 983 through 1002 removed outlier: 5.244A pdb=" N ARG A 987 " --> pdb=" O THR A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 1029 through 1050 removed outlier: 5.534A pdb=" N ARG A1033 " --> pdb=" O GLU A1029 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N SER A1034 " --> pdb=" O ALA A1030 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER A1038 " --> pdb=" O SER A1034 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LEU A1039 " --> pdb=" O ASN A1035 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N CYS A1040 " --> pdb=" O ARG A1036 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLN A1041 " --> pdb=" O ASP A1037 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA A1042 " --> pdb=" O SER A1038 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY A1050 " --> pdb=" O LEU A1046 " (cutoff:3.500A) Processing helix chain 'A' and resid 1574 through 1581 Processing helix chain 'A' and resid 1649 through 1657 removed outlier: 4.069A pdb=" N LEU A1653 " --> pdb=" O ASP A1649 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N SER A1654 " --> pdb=" O ILE A1650 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N GLU A1655 " --> pdb=" O LEU A1651 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ARG A1656 " --> pdb=" O GLU A1652 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LEU A1657 " --> pdb=" O LEU A1653 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1649 through 1657' Processing helix chain 'A' and resid 1658 through 1675 Processing helix chain 'A' and resid 1679 through 1690 removed outlier: 3.907A pdb=" N ALA A1684 " --> pdb=" O ARG A1680 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER A1687 " --> pdb=" O HIS A1683 " (cutoff:3.500A) Processing helix chain 'A' and resid 1692 through 1701 removed outlier: 4.484A pdb=" N GLU A1699 " --> pdb=" O LEU A1695 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ASP A1700 " --> pdb=" O HIS A1696 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ALA A1701 " --> pdb=" O ALA A1697 " (cutoff:3.500A) Processing helix chain 'A' and resid 1704 through 1720 removed outlier: 7.151A pdb=" N ARG A1708 " --> pdb=" O PRO A1704 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA A1709 " --> pdb=" O GLY A1705 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE A1718 " --> pdb=" O LEU A1714 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N HIS A1719 " --> pdb=" O LEU A1715 " (cutoff:3.500A) Processing helix chain 'A' and resid 1723 through 1731 removed outlier: 4.161A pdb=" N SER A1729 " --> pdb=" O ARG A1725 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N MET A1730 " --> pdb=" O SER A1726 " (cutoff:3.500A) Processing helix chain 'A' and resid 1739 through 1745 removed outlier: 3.624A pdb=" N ARG A1743 " --> pdb=" O THR A1739 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ALA A1744 " --> pdb=" O PRO A1740 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N ILE A1745 " --> pdb=" O GLU A1741 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1739 through 1745' Processing helix chain 'A' and resid 1754 through 1759 removed outlier: 4.358A pdb=" N ARG A1758 " --> pdb=" O GLY A1754 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ARG A1759 " --> pdb=" O GLY A1755 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1754 through 1759' Processing helix chain 'A' and resid 1803 through 1825 removed outlier: 3.707A pdb=" N ASP A1809 " --> pdb=" O GLU A1805 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN A1824 " --> pdb=" O ARG A1820 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N HIS A1825 " --> pdb=" O ASP A1821 " (cutoff:3.500A) Processing helix chain 'A' and resid 1833 through 1852 removed outlier: 4.024A pdb=" N GLN A1837 " --> pdb=" O SER A1833 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N PHE A1838 " --> pdb=" O VAL A1834 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N VAL A1839 " --> pdb=" O GLU A1835 " (cutoff:3.500A) Proline residue: A1840 - end of helix removed outlier: 4.663A pdb=" N LYS A1843 " --> pdb=" O VAL A1839 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL A1845 " --> pdb=" O VAL A1841 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N MET A1851 " --> pdb=" O THR A1847 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLY A1852 " --> pdb=" O LEU A1848 " (cutoff:3.500A) Processing helix chain 'A' and resid 1855 through 1865 removed outlier: 4.707A pdb=" N VAL A1859 " --> pdb=" O GLY A1855 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N MET A1865 " --> pdb=" O GLN A1861 " (cutoff:3.500A) Processing helix chain 'A' and resid 1866 through 1871 Processing helix chain 'A' and resid 1925 through 1930 removed outlier: 4.560A pdb=" N MET A1929 " --> pdb=" O GLY A1925 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N LYS A1930 " --> pdb=" O LEU A1926 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1925 through 1930' Processing helix chain 'A' and resid 1934 through 1984 removed outlier: 3.618A pdb=" N TYR A1945 " --> pdb=" O ASN A1941 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE A1946 " --> pdb=" O LEU A1942 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ARG A1964 " --> pdb=" O ALA A1960 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR A1965 " --> pdb=" O PHE A1961 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N PHE A1984 " --> pdb=" O LEU A1980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1989 through 1997 removed outlier: 4.453A pdb=" N ARG A1993 " --> pdb=" O ALA A1989 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N GLU A1997 " --> pdb=" O ARG A1993 " (cutoff:3.500A) Processing helix chain 'A' and resid 2001 through 2013 removed outlier: 3.794A pdb=" N GLN A2005 " --> pdb=" O PRO A2001 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ASN A2007 " --> pdb=" O GLN A2003 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N MET A2008 " --> pdb=" O GLU A2004 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LEU A2009 " --> pdb=" O GLN A2005 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LEU A2010 " --> pdb=" O ILE A2006 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N HIS A2011 " --> pdb=" O ASN A2007 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N PHE A2012 " --> pdb=" O MET A2008 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N LYS A2013 " --> pdb=" O LEU A2009 " (cutoff:3.500A) Processing helix chain 'A' and resid 2024 through 2043 removed outlier: 4.806A pdb=" N ARG A2028 " --> pdb=" O PRO A2024 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N GLN A2029 " --> pdb=" O GLU A2025 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ASP A2030 " --> pdb=" O ASP A2026 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU A2031 " --> pdb=" O ILE A2027 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN A2032 " --> pdb=" O ARG A2028 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N GLY A2043 " --> pdb=" O LEU A2039 " (cutoff:3.500A) Processing helix chain 'A' and resid 2093 through 2108 removed outlier: 3.840A pdb=" N TRP A2105 " --> pdb=" O MET A2101 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ALA A2106 " --> pdb=" O VAL A2102 " (cutoff:3.500A) Processing helix chain 'A' and resid 2113 through 2130 removed outlier: 4.421A pdb=" N GLY A2130 " --> pdb=" O ARG A2126 " (cutoff:3.500A) Processing helix chain 'A' and resid 2131 through 2141 Proline residue: A2139 - end of helix Processing helix chain 'A' and resid 2148 through 2168 removed outlier: 4.284A pdb=" N SER A2154 " --> pdb=" O GLU A2150 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU A2155 " --> pdb=" O ASP A2151 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE A2167 " --> pdb=" O ARG A2163 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N VAL A2168 " --> pdb=" O SER A2164 " (cutoff:3.500A) Processing helix chain 'A' and resid 2171 through 2188 removed outlier: 4.437A pdb=" N LEU A2177 " --> pdb=" O GLN A2173 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE A2179 " --> pdb=" O GLU A2175 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLN A2180 " --> pdb=" O ASN A2176 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE A2185 " --> pdb=" O SER A2181 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N MET A2186 " --> pdb=" O ILE A2182 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ASN A2187 " --> pdb=" O GLY A2183 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N ASN A2188 " --> pdb=" O ASN A2184 " (cutoff:3.500A) Processing helix chain 'A' and resid 2189 through 2195 removed outlier: 4.618A pdb=" N GLN A2193 " --> pdb=" O LYS A2189 " (cutoff:3.500A) Proline residue: A2195 - end of helix Processing helix chain 'A' and resid 2196 through 2202 removed outlier: 4.117A pdb=" N ALA A2200 " --> pdb=" O ASN A2196 " (cutoff:3.500A) Processing helix chain 'A' and resid 2203 through 2216 removed outlier: 3.645A pdb=" N VAL A2210 " --> pdb=" O THR A2206 " (cutoff:3.500A) Processing helix chain 'A' and resid 2227 through 2244 removed outlier: 3.750A pdb=" N SER A2243 " --> pdb=" O PHE A2239 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ARG A2244 " --> pdb=" O CYS A2240 " (cutoff:3.500A) Processing helix chain 'A' and resid 2245 through 2252 removed outlier: 4.847A pdb=" N ASP A2252 " --> pdb=" O ARG A2248 " (cutoff:3.500A) Processing helix chain 'A' and resid 2253 through 2265 removed outlier: 3.699A pdb=" N ASN A2260 " --> pdb=" O TYR A2256 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY A2262 " --> pdb=" O LEU A2258 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ILE A2263 " --> pdb=" O GLU A2259 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N LEU A2265 " --> pdb=" O SER A2261 " (cutoff:3.500A) Processing helix chain 'A' and resid 2271 through 2280 removed outlier: 3.641A pdb=" N VAL A2275 " --> pdb=" O THR A2271 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N VAL A2280 " --> pdb=" O ALA A2276 " (cutoff:3.500A) Processing helix chain 'A' and resid 2294 through 2309 removed outlier: 3.828A pdb=" N VAL A2299 " --> pdb=" O LEU A2295 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU A2302 " --> pdb=" O VAL A2298 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N SER A2309 " --> pdb=" O CYS A2305 " (cutoff:3.500A) Processing helix chain 'A' and resid 2310 through 2315 removed outlier: 3.882A pdb=" N ALA A2315 " --> pdb=" O PRO A2311 " (cutoff:3.500A) Processing helix chain 'A' and resid 2324 through 2341 removed outlier: 4.770A pdb=" N LEU A2332 " --> pdb=" O GLY A2328 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ASP A2333 " --> pdb=" O GLU A2329 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N PHE A2334 " --> pdb=" O ARG A2330 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU A2335 " --> pdb=" O TYR A2331 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA A2338 " --> pdb=" O PHE A2334 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N VAL A2339 " --> pdb=" O LEU A2335 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N PHE A2340 " --> pdb=" O ARG A2336 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL A2341 " --> pdb=" O PHE A2337 " (cutoff:3.500A) Processing helix chain 'A' and resid 2346 through 2360 removed outlier: 4.160A pdb=" N ALA A2350 " --> pdb=" O VAL A2346 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE A2358 " --> pdb=" O VAL A2354 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ARG A2359 " --> pdb=" O ARG A2355 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LYS A2360 " --> pdb=" O LEU A2356 " (cutoff:3.500A) Processing helix chain 'A' and resid 2365 through 2371 removed outlier: 5.439A pdb=" N GLU A2371 " --> pdb=" O ALA A2367 " (cutoff:3.500A) Processing helix chain 'A' and resid 2375 through 2390 Proline residue: A2390 - end of helix Processing helix chain 'A' and resid 2417 through 2437 removed outlier: 4.174A pdb=" N ALA A2437 " --> pdb=" O LEU A2433 " (cutoff:3.500A) Processing helix chain 'A' and resid 2440 through 2448 removed outlier: 4.653A pdb=" N GLY A2448 " --> pdb=" O GLN A2444 " (cutoff:3.500A) Processing helix chain 'A' and resid 2449 through 2462 removed outlier: 3.771A pdb=" N ILE A2453 " --> pdb=" O GLU A2449 " (cutoff:3.500A) Proline residue: A2462 - end of helix Processing helix chain 'A' and resid 2464 through 2472 removed outlier: 5.215A pdb=" N GLY A2468 " --> pdb=" O ASP A2464 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE A2469 " --> pdb=" O ASP A2465 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU A2472 " --> pdb=" O GLY A2468 " (cutoff:3.500A) Processing helix chain 'A' and resid 2751 through 2772 removed outlier: 5.084A pdb=" N ILE A2755 " --> pdb=" O LEU A2751 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ASN A2756 " --> pdb=" O ASP A2752 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N PHE A2758 " --> pdb=" O PHE A2754 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N ALA A2759 " --> pdb=" O ILE A2755 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N GLU A2760 " --> pdb=" O ASN A2756 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N TYR A2761 " --> pdb=" O LYS A2757 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N THR A2762 " --> pdb=" O PHE A2758 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N HIS A2763 " --> pdb=" O ALA A2759 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N GLU A2764 " --> pdb=" O GLU A2760 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS A2765 " --> pdb=" O TYR A2761 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA A2767 " --> pdb=" O HIS A2763 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N PHE A2768 " --> pdb=" O GLU A2764 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N GLN A2772 " --> pdb=" O PHE A2768 " (cutoff:3.500A) Processing helix chain 'A' and resid 2809 through 2816 removed outlier: 4.803A pdb=" N LYS A2814 " --> pdb=" O LYS A2810 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ALA A2815 " --> pdb=" O GLU A2811 " (cutoff:3.500A) Processing helix chain 'A' and resid 2870 through 2896 removed outlier: 4.074A pdb=" N GLU A2876 " --> pdb=" O GLN A2872 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA A2879 " --> pdb=" O ALA A2875 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N GLU A2880 " --> pdb=" O GLU A2876 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASN A2881 " --> pdb=" O GLN A2877 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N TYR A2882 " --> pdb=" O LEU A2878 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N HIS A2883 " --> pdb=" O ALA A2879 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ASN A2884 " --> pdb=" O GLU A2880 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N THR A2885 " --> pdb=" O ASN A2881 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLY A2887 " --> pdb=" O HIS A2883 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ARG A2888 " --> pdb=" O ASN A2884 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS A2889 " --> pdb=" O THR A2885 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N LYS A2890 " --> pdb=" O TRP A2886 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU A2895 " --> pdb=" O LYS A2891 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA A2896 " --> pdb=" O GLN A2892 " (cutoff:3.500A) Processing helix chain 'A' and resid 2919 through 2932 removed outlier: 6.117A pdb=" N ALA A2923 " --> pdb=" O ASP A2919 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLN A2924 " --> pdb=" O ARG A2920 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU A2927 " --> pdb=" O ALA A2923 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS A2928 " --> pdb=" O GLN A2924 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N PHE A2929 " --> pdb=" O GLU A2925 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N LEU A2930 " --> pdb=" O LEU A2926 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLN A2931 " --> pdb=" O LEU A2927 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N MET A2932 " --> pdb=" O LYS A2928 " (cutoff:3.500A) Processing helix chain 'A' and resid 3645 through 3656 removed outlier: 4.006A pdb=" N ASN A3651 " --> pdb=" O HIS A3647 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N MET A3652 " --> pdb=" O ARG A3648 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N PHE A3653 " --> pdb=" O ALA A3649 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LEU A3654 " --> pdb=" O CYS A3650 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N GLU A3655 " --> pdb=" O ASN A3651 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N SER A3656 " --> pdb=" O MET A3652 " (cutoff:3.500A) Processing helix chain 'A' and resid 3669 through 3681 removed outlier: 4.118A pdb=" N MET A3673 " --> pdb=" O PHE A3669 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE A3674 " --> pdb=" O GLU A3670 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLY A3681 " --> pdb=" O LEU A3677 " (cutoff:3.500A) Processing helix chain 'A' and resid 3683 through 3688 removed outlier: 4.160A pdb=" N GLU A3688 " --> pdb=" O GLU A3684 " (cutoff:3.500A) Processing helix chain 'A' and resid 3696 through 3711 removed outlier: 4.171A pdb=" N THR A3711 " --> pdb=" O ARG A3707 " (cutoff:3.500A) Processing helix chain 'A' and resid 3719 through 3738 removed outlier: 4.007A pdb=" N ASP A3727 " --> pdb=" O MET A3723 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILE A3728 " --> pdb=" O ALA A3724 " (cutoff:3.500A) Processing helix chain 'A' and resid 3754 through 3770 removed outlier: 5.088A pdb=" N MET A3758 " --> pdb=" O GLU A3754 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLU A3759 " --> pdb=" O GLU A3755 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS A3760 " --> pdb=" O LYS A3756 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ARG A3762 " --> pdb=" O MET A3758 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU A3770 " --> pdb=" O GLN A3766 " (cutoff:3.500A) Processing helix chain 'A' and resid 3771 through 3785 removed outlier: 4.131A pdb=" N GLU A3777 " --> pdb=" O ARG A3773 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL A3779 " --> pdb=" O ALA A3775 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N LEU A3780 " --> pdb=" O ALA A3776 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLN A3781 " --> pdb=" O GLU A3777 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ALA A3785 " --> pdb=" O GLN A3781 " (cutoff:3.500A) Processing helix chain 'A' and resid 3791 through 3806 removed outlier: 3.539A pdb=" N LEU A3805 " --> pdb=" O GLY A3801 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ASN A3806 " --> pdb=" O ILE A3802 " (cutoff:3.500A) Processing helix chain 'A' and resid 3809 through 3824 removed outlier: 4.047A pdb=" N LYS A3824 " --> pdb=" O LEU A3820 " (cutoff:3.500A) Processing helix chain 'A' and resid 3827 through 3839 removed outlier: 4.684A pdb=" N CYS A3839 " --> pdb=" O LEU A3835 " (cutoff:3.500A) Processing helix chain 'A' and resid 3843 through 3857 Processing helix chain 'A' and resid 3861 through 3866 removed outlier: 6.925A pdb=" N VAL A3865 " --> pdb=" O GLU A3861 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ILE A3866 " --> pdb=" O ASP A3862 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3861 through 3866' Processing helix chain 'A' and resid 3877 through 3894 removed outlier: 4.256A pdb=" N GLY A3894 " --> pdb=" O LEU A3890 " (cutoff:3.500A) Processing helix chain 'A' and resid 3897 through 3906 removed outlier: 5.879A pdb=" N ASN A3901 " --> pdb=" O ASN A3897 " (cutoff:3.500A) Processing helix chain 'A' and resid 3914 through 3939 removed outlier: 3.770A pdb=" N CYS A3918 " --> pdb=" O ASN A3914 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLY A3939 " --> pdb=" O TRP A3935 " (cutoff:3.500A) Processing helix chain 'A' and resid 3944 through 3970 removed outlier: 3.924A pdb=" N GLU A3967 " --> pdb=" O ASN A3963 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N TYR A3968 " --> pdb=" O SER A3964 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE A3969 " --> pdb=" O LEU A3965 " (cutoff:3.500A) Processing helix chain 'A' and resid 3973 through 3984 removed outlier: 4.284A pdb=" N GLN A3977 " --> pdb=" O CYS A3973 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLN A3978 " --> pdb=" O THR A3974 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N ARG A3984 " --> pdb=" O LEU A3980 " (cutoff:3.500A) Processing helix chain 'A' and resid 3985 through 4005 removed outlier: 3.664A pdb=" N HIS A3998 " --> pdb=" O HIS A3994 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N MET A4000 " --> pdb=" O PHE A3996 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N MET A4001 " --> pdb=" O ALA A3997 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ALA A4004 " --> pdb=" O MET A4000 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N GLN A4005 " --> pdb=" O MET A4001 " (cutoff:3.500A) Processing helix chain 'A' and resid 4009 through 4032 removed outlier: 4.950A pdb=" N LEU A4019 " --> pdb=" O GLU A4015 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N GLN A4020 " --> pdb=" O LEU A4016 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LYS A4021 " --> pdb=" O LEU A4017 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ASP A4022 " --> pdb=" O ASP A4018 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU A4031 " --> pdb=" O LEU A4027 " (cutoff:3.500A) Processing helix chain 'A' and resid 4039 through 4056 removed outlier: 5.926A pdb=" N GLN A4043 " --> pdb=" O MET A4039 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A4048 " --> pdb=" O MET A4044 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N SER A4053 " --> pdb=" O VAL A4049 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ASN A4054 " --> pdb=" O GLU A4050 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL A4055 " --> pdb=" O SER A4051 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLU A4056 " --> pdb=" O SER A4052 " (cutoff:3.500A) Processing helix chain 'A' and resid 4057 through 4074 removed outlier: 5.378A pdb=" N LEU A4066 " --> pdb=" O PHE A4062 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LYS A4067 " --> pdb=" O ASP A4063 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N LYS A4069 " --> pdb=" O PHE A4065 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N ASP A4070 " --> pdb=" O LEU A4066 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N ILE A4071 " --> pdb=" O LYS A4067 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N VAL A4072 " --> pdb=" O LEU A4068 " (cutoff:3.500A) Processing helix chain 'A' and resid 4075 through 4081 removed outlier: 3.804A pdb=" N ASP A4079 " --> pdb=" O GLU A4075 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N TYR A4080 " --> pdb=" O ALA A4076 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N VAL A4081 " --> pdb=" O PHE A4077 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4075 through 4081' Processing helix chain 'A' and resid 4089 through 4101 removed outlier: 5.227A pdb=" N LYS A4101 " --> pdb=" O MET A4097 " (cutoff:3.500A) Processing helix chain 'A' and resid 4106 through 4116 removed outlier: 3.760A pdb=" N PHE A4110 " --> pdb=" O PRO A4106 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N GLU A4116 " --> pdb=" O LEU A4112 " (cutoff:3.500A) Processing helix chain 'A' and resid 4124 through 4137 removed outlier: 3.895A pdb=" N PHE A4132 " --> pdb=" O PHE A4128 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN A4133 " --> pdb=" O ALA A4129 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N GLU A4134 " --> pdb=" O ASN A4130 " (cutoff:3.500A) Proline residue: A4135 - end of helix Processing helix chain 'A' and resid 4138 through 4155 Proline residue: A4155 - end of helix Processing helix chain 'A' and resid 4157 through 4168 removed outlier: 4.561A pdb=" N GLU A4165 " --> pdb=" O ARG A4161 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N LEU A4166 " --> pdb=" O ASN A4162 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ALA A4167 " --> pdb=" O PHE A4163 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N GLU A4168 " --> pdb=" O LEU A4164 " (cutoff:3.500A) Processing helix chain 'A' and resid 4169 through 4175 removed outlier: 3.823A pdb=" N ARG A4175 " --> pdb=" O LEU A4171 " (cutoff:3.500A) Processing helix chain 'A' and resid 4198 through 4207 removed outlier: 3.812A pdb=" N GLU A4206 " --> pdb=" O ARG A4202 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N MET A4207 " --> pdb=" O ALA A4203 " (cutoff:3.500A) Processing helix chain 'A' and resid 4208 through 4225 removed outlier: 4.619A pdb=" N SER A4213 " --> pdb=" O GLN A4209 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LYS A4214 " --> pdb=" O VAL A4210 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP A4220 " --> pdb=" O GLN A4216 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLU A4224 " --> pdb=" O ASP A4220 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLY A4225 " --> pdb=" O VAL A4221 " (cutoff:3.500A) Processing helix chain 'A' and resid 4227 through 4252 removed outlier: 4.432A pdb=" N MET A4231 " --> pdb=" O GLU A4227 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLU A4232 " --> pdb=" O ALA A4228 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA A4249 " --> pdb=" O MET A4245 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLN A4250 " --> pdb=" O GLN A4246 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ILE A4251 " --> pdb=" O ILE A4247 " (cutoff:3.500A) Processing helix chain 'A' and resid 4541 through 4556 removed outlier: 5.068A pdb=" N GLU A4545 " --> pdb=" O TRP A4541 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N VAL A4546 " --> pdb=" O GLY A4542 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N TYR A4554 " --> pdb=" O LYS A4550 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU A4555 " --> pdb=" O PHE A4551 " (cutoff:3.500A) Processing helix chain 'A' and resid 4558 through 4578 removed outlier: 4.071A pdb=" N LEU A4562 " --> pdb=" O ASN A4558 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N PHE A4571 " --> pdb=" O LEU A4567 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ALA A4572 " --> pdb=" O PHE A4568 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE A4573 " --> pdb=" O LEU A4569 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASN A4574 " --> pdb=" O ALA A4570 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU A4577 " --> pdb=" O ILE A4573 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N LEU A4578 " --> pdb=" O ASN A4574 " (cutoff:3.500A) Processing helix chain 'A' and resid 4643 through 4684 removed outlier: 4.462A pdb=" N SER A4647 " --> pdb=" O LEU A4643 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N LEU A4648 " --> pdb=" O TRP A4644 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N LEU A4649 " --> pdb=" O CYS A4645 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N HIS A4650 " --> pdb=" O LEU A4646 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N THR A4651 " --> pdb=" O SER A4647 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A4652 " --> pdb=" O LEU A4648 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LYS A4665 " --> pdb=" O TYR A4661 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N VAL A4666 " --> pdb=" O ASN A4662 " (cutoff:3.500A) Proline residue: A4667 - end of helix removed outlier: 4.798A pdb=" N GLU A4676 " --> pdb=" O LYS A4672 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LEU A4677 " --> pdb=" O ARG A4673 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA A4678 " --> pdb=" O GLU A4674 " (cutoff:3.500A) Processing helix chain 'A' and resid 4685 through 4690 removed outlier: 5.306A pdb=" N THR A4689 " --> pdb=" O GLY A4685 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N GLU A4690 " --> pdb=" O LEU A4686 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4685 through 4690' Processing helix chain 'A' and resid 4696 through 4701 Processing helix chain 'A' and resid 4719 through 4733 removed outlier: 3.528A pdb=" N LYS A4723 " --> pdb=" O PHE A4719 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU A4725 " --> pdb=" O LYS A4721 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ASP A4726 " --> pdb=" O ARG A4722 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LYS A4727 " --> pdb=" O LYS A4723 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N HIS A4728 " --> pdb=" O VAL A4724 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ASP A4730 " --> pdb=" O ASP A4726 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ILE A4731 " --> pdb=" O LYS A4727 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N PHE A4732 " --> pdb=" O HIS A4728 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLY A4733 " --> pdb=" O GLY A4729 " (cutoff:3.500A) Processing helix chain 'A' and resid 4734 through 4742 removed outlier: 4.370A pdb=" N LEU A4740 " --> pdb=" O ARG A4736 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LEU A4741 " --> pdb=" O ILE A4737 " (cutoff:3.500A) Processing helix chain 'A' and resid 4745 through 4753 removed outlier: 4.319A pdb=" N THR A4751 " --> pdb=" O SER A4747 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA A4752 " --> pdb=" O LEU A4748 " (cutoff:3.500A) Processing helix chain 'A' and resid 4765 through 4771 removed outlier: 5.453A pdb=" N MET A4769 " --> pdb=" O LEU A4765 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N SER A4770 " --> pdb=" O THR A4766 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ILE A4771 " --> pdb=" O TRP A4767 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4765 through 4771' Processing helix chain 'A' and resid 4772 through 4786 removed outlier: 3.608A pdb=" N VAL A4782 " --> pdb=" O TRP A4778 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE A4783 " --> pdb=" O LYS A4779 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N PHE A4784 " --> pdb=" O PHE A4780 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N THR A4785 " --> pdb=" O GLY A4781 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASP A4786 " --> pdb=" O VAL A4782 " (cutoff:3.500A) Processing helix chain 'A' and resid 4787 through 4804 removed outlier: 4.757A pdb=" N TYR A4804 " --> pdb=" O LEU A4800 " (cutoff:3.500A) Processing helix chain 'A' and resid 4809 through 4819 removed outlier: 4.803A pdb=" N LEU A4813 " --> pdb=" O PHE A4809 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LEU A4814 " --> pdb=" O ALA A4810 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N GLY A4819 " --> pdb=" O ASP A4815 " (cutoff:3.500A) Processing helix chain 'A' and resid 4820 through 4827 removed outlier: 4.320A pdb=" N ILE A4826 " --> pdb=" O THR A4822 " (cutoff:3.500A) Processing helix chain 'A' and resid 4828 through 4834 removed outlier: 4.104A pdb=" N HIS A4832 " --> pdb=" O SER A4828 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN A4833 " --> pdb=" O SER A4829 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLY A4834 " --> pdb=" O VAL A4830 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4828 through 4834' Processing helix chain 'A' and resid 4835 through 4859 removed outlier: 4.549A pdb=" N MET A4839 " --> pdb=" O LYS A4835 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N THR A4840 " --> pdb=" O GLN A4836 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLY A4842 " --> pdb=" O VAL A4838 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N LEU A4843 " --> pdb=" O MET A4839 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU A4844 " --> pdb=" O THR A4840 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN A4857 " --> pdb=" O VAL A4853 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE A4858 " --> pdb=" O VAL A4854 " (cutoff:3.500A) Processing helix chain 'A' and resid 4878 through 4893 removed outlier: 4.688A pdb=" N VAL A4891 " --> pdb=" O MET A4887 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ARG A4892 " --> pdb=" O TYR A4888 " (cutoff:3.500A) Processing helix chain 'A' and resid 4897 through 4902 removed outlier: 5.105A pdb=" N GLU A4902 " --> pdb=" O GLY A4898 " (cutoff:3.500A) Processing helix chain 'A' and resid 4909 through 4925 removed outlier: 3.620A pdb=" N VAL A4914 " --> pdb=" O GLU A4910 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N VAL A4915 " --> pdb=" O LEU A4911 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ILE A4918 " --> pdb=" O VAL A4914 " (cutoff:3.500A) Processing helix chain 'A' and resid 4928 through 4953 removed outlier: 4.061A pdb=" N ILE A4932 " --> pdb=" O LEU A4928 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP A4938 " --> pdb=" O GLY A4934 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU A4943 " --> pdb=" O ALA A4939 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG A4944 " --> pdb=" O PHE A4940 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU A4952 " --> pdb=" O GLU A4948 " (cutoff:3.500A) Processing helix chain 'A' and resid 4964 through 4972 removed outlier: 3.863A pdb=" N PHE A4968 " --> pdb=" O GLY A4964 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N THR A4970 " --> pdb=" O ASP A4966 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N THR A4971 " --> pdb=" O TYR A4967 " (cutoff:3.500A) Proline residue: A4972 - end of helix Processing helix chain 'A' and resid 4973 through 4981 removed outlier: 3.975A pdb=" N LEU A4980 " --> pdb=" O GLU A4976 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N GLU A4981 " --> pdb=" O THR A4977 " (cutoff:3.500A) Processing helix chain 'A' and resid 4986 through 4999 removed outlier: 4.588A pdb=" N PHE A4990 " --> pdb=" O ALA A4986 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ASP A4999 " --> pdb=" O LEU A4995 " (cutoff:3.500A) Processing helix chain 'A' and resid 5004 through 5017 Processing helix chain 'A' and resid 5028 through 5033 removed outlier: 5.272A pdb=" N TYR A5032 " --> pdb=" O PHE A5028 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLU A5033 " --> pdb=" O ARG A5029 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 5028 through 5033' Processing helix chain 'A' and resid 956 through 961 removed outlier: 4.374A pdb=" N MET A 960 " --> pdb=" O LYS A 957 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N MET A 961 " --> pdb=" O THR A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 2285 through 2290 removed outlier: 4.385A pdb=" N LEU A2288 " --> pdb=" O GLU A2285 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA A2289 " --> pdb=" O LEU A2286 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N LEU A2290 " --> pdb=" O ALA A2287 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2285 through 2290' Processing helix chain 'A' and resid 4703 through 4708 removed outlier: 4.031A pdb=" N LEU A4706 " --> pdb=" O ARG A4703 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ASN A4707 " --> pdb=" O LEU A4704 " (cutoff:3.500A) Processing helix chain 'A' and resid 4709 through 4715 Proline residue: A4712 - end of helix Processing helix chain 'B' and resid 61 through 66 removed outlier: 4.641A pdb=" N CYS B 65 " --> pdb=" O ASP B 61 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N CYS B 66 " --> pdb=" O LEU B 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 61 through 66' Processing helix chain 'B' and resid 74 through 84 Processing helix chain 'B' and resid 250 through 256 removed outlier: 6.184A pdb=" N THR B 254 " --> pdb=" O GLY B 250 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N HIS B 255 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N ALA B 256 " --> pdb=" O VAL B 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 250 through 256' Processing helix chain 'B' and resid 364 through 371 removed outlier: 3.957A pdb=" N VAL B 371 " --> pdb=" O LEU B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 425 removed outlier: 4.394A pdb=" N GLN B 413 " --> pdb=" O GLY B 409 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE B 414 " --> pdb=" O LEU B 410 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N PHE B 421 " --> pdb=" O GLY B 417 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLY B 423 " --> pdb=" O ASP B 419 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N LYS B 424 " --> pdb=" O SER B 420 " (cutoff:3.500A) Proline residue: B 425 - end of helix Processing helix chain 'B' and resid 437 through 453 removed outlier: 4.803A pdb=" N VAL B 441 " --> pdb=" O PRO B 437 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN B 446 " --> pdb=" O ILE B 442 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE B 452 " --> pdb=" O LEU B 448 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N GLU B 453 " --> pdb=" O ILE B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 481 removed outlier: 3.666A pdb=" N ARG B 469 " --> pdb=" O GLN B 465 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU B 480 " --> pdb=" O SER B 476 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N GLU B 481 " --> pdb=" O LEU B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 496 removed outlier: 3.948A pdb=" N CYS B 490 " --> pdb=" O LEU B 486 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N VAL B 496 " --> pdb=" O ASP B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 531 removed outlier: 5.212A pdb=" N SER B 514 " --> pdb=" O GLU B 510 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N TRP B 515 " --> pdb=" O ALA B 511 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N LYS B 516 " --> pdb=" O ALA B 512 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N GLU B 517 " --> pdb=" O GLU B 513 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ILE B 518 " --> pdb=" O SER B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 540 removed outlier: 4.645A pdb=" N CYS B 537 " --> pdb=" O ASN B 533 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU B 539 " --> pdb=" O ALA B 535 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N PHE B 540 " --> pdb=" O ASN B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 551 removed outlier: 4.634A pdb=" N ASP B 545 " --> pdb=" O SER B 541 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N TRP B 546 " --> pdb=" O THR B 542 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL B 548 " --> pdb=" O LEU B 544 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LEU B 551 " --> pdb=" O VAL B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 571 removed outlier: 4.102A pdb=" N LEU B 561 " --> pdb=" O SER B 557 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N GLU B 562 " --> pdb=" O SER B 558 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N VAL B 563 " --> pdb=" O GLY B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 578 removed outlier: 4.344A pdb=" N ILE B 577 " --> pdb=" O GLU B 573 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ILE B 578 " --> pdb=" O VAL B 574 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 573 through 578' Processing helix chain 'B' and resid 579 through 594 removed outlier: 6.092A pdb=" N ILE B 583 " --> pdb=" O GLN B 579 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU B 590 " --> pdb=" O ILE B 586 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASP B 591 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 609 removed outlier: 4.224A pdb=" N VAL B 602 " --> pdb=" O LYS B 598 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LEU B 603 " --> pdb=" O VAL B 599 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N CYS B 607 " --> pdb=" O LEU B 603 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N VAL B 608 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N CYS B 609 " --> pdb=" O SER B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 626 removed outlier: 4.328A pdb=" N GLN B 618 " --> pdb=" O VAL B 614 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR B 622 " --> pdb=" O GLN B 618 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N LEU B 626 " --> pdb=" O THR B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 865 through 890 removed outlier: 4.745A pdb=" N ARG B 869 " --> pdb=" O PRO B 865 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE B 870 " --> pdb=" O HIS B 866 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU B 876 " --> pdb=" O GLU B 872 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN B 877 " --> pdb=" O LYS B 873 " (cutoff:3.500A) Processing helix chain 'B' and resid 914 through 936 removed outlier: 4.022A pdb=" N TYR B 920 " --> pdb=" O PRO B 916 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N GLY B 936 " --> pdb=" O LEU B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 950 removed outlier: 4.509A pdb=" N ASN B 949 " --> pdb=" O LYS B 945 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU B 950 " --> pdb=" O ALA B 946 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 945 through 950' Processing helix chain 'B' and resid 983 through 1002 removed outlier: 5.244A pdb=" N ARG B 987 " --> pdb=" O THR B 983 " (cutoff:3.500A) Processing helix chain 'B' and resid 1029 through 1050 removed outlier: 5.534A pdb=" N ARG B1033 " --> pdb=" O GLU B1029 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N SER B1034 " --> pdb=" O ALA B1030 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER B1038 " --> pdb=" O SER B1034 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LEU B1039 " --> pdb=" O ASN B1035 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N CYS B1040 " --> pdb=" O ARG B1036 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLN B1041 " --> pdb=" O ASP B1037 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA B1042 " --> pdb=" O SER B1038 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY B1050 " --> pdb=" O LEU B1046 " (cutoff:3.500A) Processing helix chain 'B' and resid 1574 through 1581 Processing helix chain 'B' and resid 1649 through 1657 removed outlier: 4.069A pdb=" N LEU B1653 " --> pdb=" O ASP B1649 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N SER B1654 " --> pdb=" O ILE B1650 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N GLU B1655 " --> pdb=" O LEU B1651 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ARG B1656 " --> pdb=" O GLU B1652 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LEU B1657 " --> pdb=" O LEU B1653 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1649 through 1657' Processing helix chain 'B' and resid 1658 through 1675 Processing helix chain 'B' and resid 1679 through 1690 removed outlier: 3.907A pdb=" N ALA B1684 " --> pdb=" O ARG B1680 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER B1687 " --> pdb=" O HIS B1683 " (cutoff:3.500A) Processing helix chain 'B' and resid 1692 through 1701 removed outlier: 4.484A pdb=" N GLU B1699 " --> pdb=" O LEU B1695 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ASP B1700 " --> pdb=" O HIS B1696 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ALA B1701 " --> pdb=" O ALA B1697 " (cutoff:3.500A) Processing helix chain 'B' and resid 1704 through 1720 removed outlier: 7.151A pdb=" N ARG B1708 " --> pdb=" O PRO B1704 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA B1709 " --> pdb=" O GLY B1705 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE B1718 " --> pdb=" O LEU B1714 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N HIS B1719 " --> pdb=" O LEU B1715 " (cutoff:3.500A) Processing helix chain 'B' and resid 1723 through 1731 removed outlier: 4.161A pdb=" N SER B1729 " --> pdb=" O ARG B1725 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N MET B1730 " --> pdb=" O SER B1726 " (cutoff:3.500A) Processing helix chain 'B' and resid 1739 through 1745 removed outlier: 3.624A pdb=" N ARG B1743 " --> pdb=" O THR B1739 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ALA B1744 " --> pdb=" O PRO B1740 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N ILE B1745 " --> pdb=" O GLU B1741 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1739 through 1745' Processing helix chain 'B' and resid 1754 through 1759 removed outlier: 4.358A pdb=" N ARG B1758 " --> pdb=" O GLY B1754 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ARG B1759 " --> pdb=" O GLY B1755 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1754 through 1759' Processing helix chain 'B' and resid 1803 through 1825 removed outlier: 3.707A pdb=" N ASP B1809 " --> pdb=" O GLU B1805 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN B1824 " --> pdb=" O ARG B1820 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N HIS B1825 " --> pdb=" O ASP B1821 " (cutoff:3.500A) Processing helix chain 'B' and resid 1833 through 1852 removed outlier: 4.023A pdb=" N GLN B1837 " --> pdb=" O SER B1833 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N PHE B1838 " --> pdb=" O VAL B1834 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N VAL B1839 " --> pdb=" O GLU B1835 " (cutoff:3.500A) Proline residue: B1840 - end of helix removed outlier: 4.663A pdb=" N LYS B1843 " --> pdb=" O VAL B1839 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL B1845 " --> pdb=" O VAL B1841 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N MET B1851 " --> pdb=" O THR B1847 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLY B1852 " --> pdb=" O LEU B1848 " (cutoff:3.500A) Processing helix chain 'B' and resid 1855 through 1865 removed outlier: 4.707A pdb=" N VAL B1859 " --> pdb=" O GLY B1855 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N MET B1865 " --> pdb=" O GLN B1861 " (cutoff:3.500A) Processing helix chain 'B' and resid 1866 through 1871 Processing helix chain 'B' and resid 1925 through 1930 removed outlier: 4.560A pdb=" N MET B1929 " --> pdb=" O GLY B1925 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N LYS B1930 " --> pdb=" O LEU B1926 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1925 through 1930' Processing helix chain 'B' and resid 1934 through 1984 removed outlier: 3.617A pdb=" N TYR B1945 " --> pdb=" O ASN B1941 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE B1946 " --> pdb=" O LEU B1942 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ARG B1964 " --> pdb=" O ALA B1960 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR B1965 " --> pdb=" O PHE B1961 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N PHE B1984 " --> pdb=" O LEU B1980 " (cutoff:3.500A) Processing helix chain 'B' and resid 1989 through 1997 removed outlier: 4.453A pdb=" N ARG B1993 " --> pdb=" O ALA B1989 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N GLU B1997 " --> pdb=" O ARG B1993 " (cutoff:3.500A) Processing helix chain 'B' and resid 2001 through 2013 removed outlier: 3.795A pdb=" N GLN B2005 " --> pdb=" O PRO B2001 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ASN B2007 " --> pdb=" O GLN B2003 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N MET B2008 " --> pdb=" O GLU B2004 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LEU B2009 " --> pdb=" O GLN B2005 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N LEU B2010 " --> pdb=" O ILE B2006 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N HIS B2011 " --> pdb=" O ASN B2007 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N PHE B2012 " --> pdb=" O MET B2008 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N LYS B2013 " --> pdb=" O LEU B2009 " (cutoff:3.500A) Processing helix chain 'B' and resid 2024 through 2043 removed outlier: 4.807A pdb=" N ARG B2028 " --> pdb=" O PRO B2024 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N GLN B2029 " --> pdb=" O GLU B2025 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ASP B2030 " --> pdb=" O ASP B2026 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU B2031 " --> pdb=" O ILE B2027 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN B2032 " --> pdb=" O ARG B2028 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N GLY B2043 " --> pdb=" O LEU B2039 " (cutoff:3.500A) Processing helix chain 'B' and resid 2093 through 2108 removed outlier: 3.841A pdb=" N TRP B2105 " --> pdb=" O MET B2101 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA B2106 " --> pdb=" O VAL B2102 " (cutoff:3.500A) Processing helix chain 'B' and resid 2113 through 2130 removed outlier: 4.420A pdb=" N GLY B2130 " --> pdb=" O ARG B2126 " (cutoff:3.500A) Processing helix chain 'B' and resid 2131 through 2141 Proline residue: B2139 - end of helix Processing helix chain 'B' and resid 2148 through 2168 removed outlier: 4.283A pdb=" N SER B2154 " --> pdb=" O GLU B2150 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU B2155 " --> pdb=" O ASP B2151 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE B2167 " --> pdb=" O ARG B2163 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N VAL B2168 " --> pdb=" O SER B2164 " (cutoff:3.500A) Processing helix chain 'B' and resid 2171 through 2188 removed outlier: 4.438A pdb=" N LEU B2177 " --> pdb=" O GLN B2173 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE B2179 " --> pdb=" O GLU B2175 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLN B2180 " --> pdb=" O ASN B2176 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE B2185 " --> pdb=" O SER B2181 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N MET B2186 " --> pdb=" O ILE B2182 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ASN B2187 " --> pdb=" O GLY B2183 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ASN B2188 " --> pdb=" O ASN B2184 " (cutoff:3.500A) Processing helix chain 'B' and resid 2189 through 2195 removed outlier: 4.618A pdb=" N GLN B2193 " --> pdb=" O LYS B2189 " (cutoff:3.500A) Proline residue: B2195 - end of helix Processing helix chain 'B' and resid 2196 through 2202 removed outlier: 4.115A pdb=" N ALA B2200 " --> pdb=" O ASN B2196 " (cutoff:3.500A) Processing helix chain 'B' and resid 2203 through 2216 removed outlier: 3.645A pdb=" N VAL B2210 " --> pdb=" O THR B2206 " (cutoff:3.500A) Processing helix chain 'B' and resid 2227 through 2244 removed outlier: 3.750A pdb=" N SER B2243 " --> pdb=" O PHE B2239 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N ARG B2244 " --> pdb=" O CYS B2240 " (cutoff:3.500A) Processing helix chain 'B' and resid 2245 through 2252 removed outlier: 4.848A pdb=" N ASP B2252 " --> pdb=" O ARG B2248 " (cutoff:3.500A) Processing helix chain 'B' and resid 2253 through 2265 removed outlier: 3.699A pdb=" N ASN B2260 " --> pdb=" O TYR B2256 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY B2262 " --> pdb=" O LEU B2258 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ILE B2263 " --> pdb=" O GLU B2259 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N LEU B2265 " --> pdb=" O SER B2261 " (cutoff:3.500A) Processing helix chain 'B' and resid 2271 through 2280 removed outlier: 3.641A pdb=" N VAL B2275 " --> pdb=" O THR B2271 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N VAL B2280 " --> pdb=" O ALA B2276 " (cutoff:3.500A) Processing helix chain 'B' and resid 2294 through 2309 removed outlier: 3.828A pdb=" N VAL B2299 " --> pdb=" O LEU B2295 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU B2302 " --> pdb=" O VAL B2298 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N SER B2309 " --> pdb=" O CYS B2305 " (cutoff:3.500A) Processing helix chain 'B' and resid 2310 through 2315 removed outlier: 3.881A pdb=" N ALA B2315 " --> pdb=" O PRO B2311 " (cutoff:3.500A) Processing helix chain 'B' and resid 2324 through 2341 removed outlier: 4.770A pdb=" N LEU B2332 " --> pdb=" O GLY B2328 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ASP B2333 " --> pdb=" O GLU B2329 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N PHE B2334 " --> pdb=" O ARG B2330 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LEU B2335 " --> pdb=" O TYR B2331 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA B2338 " --> pdb=" O PHE B2334 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N VAL B2339 " --> pdb=" O LEU B2335 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N PHE B2340 " --> pdb=" O ARG B2336 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL B2341 " --> pdb=" O PHE B2337 " (cutoff:3.500A) Processing helix chain 'B' and resid 2346 through 2360 removed outlier: 4.160A pdb=" N ALA B2350 " --> pdb=" O VAL B2346 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE B2358 " --> pdb=" O VAL B2354 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ARG B2359 " --> pdb=" O ARG B2355 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LYS B2360 " --> pdb=" O LEU B2356 " (cutoff:3.500A) Processing helix chain 'B' and resid 2365 through 2371 removed outlier: 5.439A pdb=" N GLU B2371 " --> pdb=" O ALA B2367 " (cutoff:3.500A) Processing helix chain 'B' and resid 2375 through 2390 Proline residue: B2390 - end of helix Processing helix chain 'B' and resid 2417 through 2437 removed outlier: 4.173A pdb=" N ALA B2437 " --> pdb=" O LEU B2433 " (cutoff:3.500A) Processing helix chain 'B' and resid 2440 through 2448 removed outlier: 4.654A pdb=" N GLY B2448 " --> pdb=" O GLN B2444 " (cutoff:3.500A) Processing helix chain 'B' and resid 2449 through 2462 removed outlier: 3.771A pdb=" N ILE B2453 " --> pdb=" O GLU B2449 " (cutoff:3.500A) Proline residue: B2462 - end of helix Processing helix chain 'B' and resid 2464 through 2472 removed outlier: 5.215A pdb=" N GLY B2468 " --> pdb=" O ASP B2464 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE B2469 " --> pdb=" O ASP B2465 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU B2472 " --> pdb=" O GLY B2468 " (cutoff:3.500A) Processing helix chain 'B' and resid 2751 through 2772 removed outlier: 5.085A pdb=" N ILE B2755 " --> pdb=" O LEU B2751 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ASN B2756 " --> pdb=" O ASP B2752 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N PHE B2758 " --> pdb=" O PHE B2754 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N ALA B2759 " --> pdb=" O ILE B2755 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N GLU B2760 " --> pdb=" O ASN B2756 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TYR B2761 " --> pdb=" O LYS B2757 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N THR B2762 " --> pdb=" O PHE B2758 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N HIS B2763 " --> pdb=" O ALA B2759 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N GLU B2764 " --> pdb=" O GLU B2760 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS B2765 " --> pdb=" O TYR B2761 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA B2767 " --> pdb=" O HIS B2763 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N PHE B2768 " --> pdb=" O GLU B2764 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N GLN B2772 " --> pdb=" O PHE B2768 " (cutoff:3.500A) Processing helix chain 'B' and resid 2809 through 2816 removed outlier: 4.804A pdb=" N LYS B2814 " --> pdb=" O LYS B2810 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ALA B2815 " --> pdb=" O GLU B2811 " (cutoff:3.500A) Processing helix chain 'B' and resid 2870 through 2896 removed outlier: 4.075A pdb=" N GLU B2876 " --> pdb=" O GLN B2872 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA B2879 " --> pdb=" O ALA B2875 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N GLU B2880 " --> pdb=" O GLU B2876 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASN B2881 " --> pdb=" O GLN B2877 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N TYR B2882 " --> pdb=" O LEU B2878 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N HIS B2883 " --> pdb=" O ALA B2879 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ASN B2884 " --> pdb=" O GLU B2880 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N THR B2885 " --> pdb=" O ASN B2881 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLY B2887 " --> pdb=" O HIS B2883 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ARG B2888 " --> pdb=" O ASN B2884 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS B2889 " --> pdb=" O THR B2885 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N LYS B2890 " --> pdb=" O TRP B2886 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU B2895 " --> pdb=" O LYS B2891 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA B2896 " --> pdb=" O GLN B2892 " (cutoff:3.500A) Processing helix chain 'B' and resid 2919 through 2932 removed outlier: 6.118A pdb=" N ALA B2923 " --> pdb=" O ASP B2919 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLN B2924 " --> pdb=" O ARG B2920 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU B2927 " --> pdb=" O ALA B2923 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS B2928 " --> pdb=" O GLN B2924 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N PHE B2929 " --> pdb=" O GLU B2925 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N LEU B2930 " --> pdb=" O LEU B2926 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLN B2931 " --> pdb=" O LEU B2927 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N MET B2932 " --> pdb=" O LYS B2928 " (cutoff:3.500A) Processing helix chain 'B' and resid 3645 through 3656 removed outlier: 4.007A pdb=" N ASN B3651 " --> pdb=" O HIS B3647 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N MET B3652 " --> pdb=" O ARG B3648 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N PHE B3653 " --> pdb=" O ALA B3649 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N LEU B3654 " --> pdb=" O CYS B3650 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N GLU B3655 " --> pdb=" O ASN B3651 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N SER B3656 " --> pdb=" O MET B3652 " (cutoff:3.500A) Processing helix chain 'B' and resid 3669 through 3681 removed outlier: 4.118A pdb=" N MET B3673 " --> pdb=" O PHE B3669 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE B3674 " --> pdb=" O GLU B3670 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLY B3681 " --> pdb=" O LEU B3677 " (cutoff:3.500A) Processing helix chain 'B' and resid 3683 through 3688 removed outlier: 4.161A pdb=" N GLU B3688 " --> pdb=" O GLU B3684 " (cutoff:3.500A) Processing helix chain 'B' and resid 3696 through 3711 removed outlier: 4.171A pdb=" N THR B3711 " --> pdb=" O ARG B3707 " (cutoff:3.500A) Processing helix chain 'B' and resid 3719 through 3738 removed outlier: 4.006A pdb=" N ASP B3727 " --> pdb=" O MET B3723 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILE B3728 " --> pdb=" O ALA B3724 " (cutoff:3.500A) Processing helix chain 'B' and resid 3754 through 3770 removed outlier: 5.089A pdb=" N MET B3758 " --> pdb=" O GLU B3754 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLU B3759 " --> pdb=" O GLU B3755 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS B3760 " --> pdb=" O LYS B3756 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ARG B3762 " --> pdb=" O MET B3758 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU B3770 " --> pdb=" O GLN B3766 " (cutoff:3.500A) Processing helix chain 'B' and resid 3771 through 3785 removed outlier: 4.131A pdb=" N GLU B3777 " --> pdb=" O ARG B3773 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL B3779 " --> pdb=" O ALA B3775 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N LEU B3780 " --> pdb=" O ALA B3776 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLN B3781 " --> pdb=" O GLU B3777 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ALA B3785 " --> pdb=" O GLN B3781 " (cutoff:3.500A) Processing helix chain 'B' and resid 3791 through 3806 removed outlier: 3.540A pdb=" N LEU B3805 " --> pdb=" O GLY B3801 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ASN B3806 " --> pdb=" O ILE B3802 " (cutoff:3.500A) Processing helix chain 'B' and resid 3809 through 3824 removed outlier: 4.046A pdb=" N LYS B3824 " --> pdb=" O LEU B3820 " (cutoff:3.500A) Processing helix chain 'B' and resid 3827 through 3839 removed outlier: 4.684A pdb=" N CYS B3839 " --> pdb=" O LEU B3835 " (cutoff:3.500A) Processing helix chain 'B' and resid 3843 through 3857 Processing helix chain 'B' and resid 3861 through 3866 removed outlier: 6.924A pdb=" N VAL B3865 " --> pdb=" O GLU B3861 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE B3866 " --> pdb=" O ASP B3862 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3861 through 3866' Processing helix chain 'B' and resid 3877 through 3894 removed outlier: 4.256A pdb=" N GLY B3894 " --> pdb=" O LEU B3890 " (cutoff:3.500A) Processing helix chain 'B' and resid 3897 through 3906 removed outlier: 5.879A pdb=" N ASN B3901 " --> pdb=" O ASN B3897 " (cutoff:3.500A) Processing helix chain 'B' and resid 3914 through 3939 removed outlier: 3.771A pdb=" N CYS B3918 " --> pdb=" O ASN B3914 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N GLY B3939 " --> pdb=" O TRP B3935 " (cutoff:3.500A) Processing helix chain 'B' and resid 3944 through 3970 removed outlier: 3.924A pdb=" N GLU B3967 " --> pdb=" O ASN B3963 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N TYR B3968 " --> pdb=" O SER B3964 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE B3969 " --> pdb=" O LEU B3965 " (cutoff:3.500A) Processing helix chain 'B' and resid 3973 through 3984 removed outlier: 4.285A pdb=" N GLN B3977 " --> pdb=" O CYS B3973 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLN B3978 " --> pdb=" O THR B3974 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N ARG B3984 " --> pdb=" O LEU B3980 " (cutoff:3.500A) Processing helix chain 'B' and resid 3985 through 4005 removed outlier: 3.665A pdb=" N HIS B3998 " --> pdb=" O HIS B3994 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N MET B4000 " --> pdb=" O PHE B3996 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N MET B4001 " --> pdb=" O ALA B3997 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ALA B4004 " --> pdb=" O MET B4000 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N GLN B4005 " --> pdb=" O MET B4001 " (cutoff:3.500A) Processing helix chain 'B' and resid 4009 through 4032 removed outlier: 4.949A pdb=" N LEU B4019 " --> pdb=" O GLU B4015 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N GLN B4020 " --> pdb=" O LEU B4016 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LYS B4021 " --> pdb=" O LEU B4017 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ASP B4022 " --> pdb=" O ASP B4018 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU B4031 " --> pdb=" O LEU B4027 " (cutoff:3.500A) Processing helix chain 'B' and resid 4039 through 4056 removed outlier: 5.926A pdb=" N GLN B4043 " --> pdb=" O MET B4039 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU B4048 " --> pdb=" O MET B4044 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N SER B4053 " --> pdb=" O VAL B4049 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ASN B4054 " --> pdb=" O GLU B4050 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL B4055 " --> pdb=" O SER B4051 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLU B4056 " --> pdb=" O SER B4052 " (cutoff:3.500A) Processing helix chain 'B' and resid 4057 through 4074 removed outlier: 5.378A pdb=" N LEU B4066 " --> pdb=" O PHE B4062 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LYS B4067 " --> pdb=" O ASP B4063 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N LYS B4069 " --> pdb=" O PHE B4065 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N ASP B4070 " --> pdb=" O LEU B4066 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N ILE B4071 " --> pdb=" O LYS B4067 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N VAL B4072 " --> pdb=" O LEU B4068 " (cutoff:3.500A) Processing helix chain 'B' and resid 4075 through 4081 removed outlier: 3.804A pdb=" N ASP B4079 " --> pdb=" O GLU B4075 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N TYR B4080 " --> pdb=" O ALA B4076 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N VAL B4081 " --> pdb=" O PHE B4077 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4075 through 4081' Processing helix chain 'B' and resid 4089 through 4101 removed outlier: 5.227A pdb=" N LYS B4101 " --> pdb=" O MET B4097 " (cutoff:3.500A) Processing helix chain 'B' and resid 4106 through 4116 removed outlier: 3.760A pdb=" N PHE B4110 " --> pdb=" O PRO B4106 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N GLU B4116 " --> pdb=" O LEU B4112 " (cutoff:3.500A) Processing helix chain 'B' and resid 4124 through 4137 removed outlier: 3.896A pdb=" N PHE B4132 " --> pdb=" O PHE B4128 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN B4133 " --> pdb=" O ALA B4129 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N GLU B4134 " --> pdb=" O ASN B4130 " (cutoff:3.500A) Proline residue: B4135 - end of helix Processing helix chain 'B' and resid 4138 through 4155 Proline residue: B4155 - end of helix Processing helix chain 'B' and resid 4157 through 4168 removed outlier: 4.561A pdb=" N GLU B4165 " --> pdb=" O ARG B4161 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N LEU B4166 " --> pdb=" O ASN B4162 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ALA B4167 " --> pdb=" O PHE B4163 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N GLU B4168 " --> pdb=" O LEU B4164 " (cutoff:3.500A) Processing helix chain 'B' and resid 4169 through 4175 removed outlier: 3.823A pdb=" N ARG B4175 " --> pdb=" O LEU B4171 " (cutoff:3.500A) Processing helix chain 'B' and resid 4198 through 4207 removed outlier: 3.812A pdb=" N GLU B4206 " --> pdb=" O ARG B4202 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N MET B4207 " --> pdb=" O ALA B4203 " (cutoff:3.500A) Processing helix chain 'B' and resid 4208 through 4225 removed outlier: 4.619A pdb=" N SER B4213 " --> pdb=" O GLN B4209 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LYS B4214 " --> pdb=" O VAL B4210 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP B4220 " --> pdb=" O GLN B4216 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLU B4224 " --> pdb=" O ASP B4220 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLY B4225 " --> pdb=" O VAL B4221 " (cutoff:3.500A) Processing helix chain 'B' and resid 4227 through 4252 removed outlier: 4.433A pdb=" N MET B4231 " --> pdb=" O GLU B4227 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLU B4232 " --> pdb=" O ALA B4228 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA B4249 " --> pdb=" O MET B4245 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLN B4250 " --> pdb=" O GLN B4246 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ILE B4251 " --> pdb=" O ILE B4247 " (cutoff:3.500A) Processing helix chain 'B' and resid 4541 through 4556 removed outlier: 5.069A pdb=" N GLU B4545 " --> pdb=" O TRP B4541 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N VAL B4546 " --> pdb=" O GLY B4542 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N TYR B4554 " --> pdb=" O LYS B4550 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU B4555 " --> pdb=" O PHE B4551 " (cutoff:3.500A) Processing helix chain 'B' and resid 4558 through 4578 removed outlier: 4.072A pdb=" N LEU B4562 " --> pdb=" O ASN B4558 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N PHE B4571 " --> pdb=" O LEU B4567 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ALA B4572 " --> pdb=" O PHE B4568 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE B4573 " --> pdb=" O LEU B4569 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASN B4574 " --> pdb=" O ALA B4570 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU B4577 " --> pdb=" O ILE B4573 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N LEU B4578 " --> pdb=" O ASN B4574 " (cutoff:3.500A) Processing helix chain 'B' and resid 4643 through 4684 removed outlier: 4.461A pdb=" N SER B4647 " --> pdb=" O LEU B4643 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N LEU B4648 " --> pdb=" O TRP B4644 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N LEU B4649 " --> pdb=" O CYS B4645 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N HIS B4650 " --> pdb=" O LEU B4646 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N THR B4651 " --> pdb=" O SER B4647 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU B4652 " --> pdb=" O LEU B4648 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LYS B4665 " --> pdb=" O TYR B4661 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N VAL B4666 " --> pdb=" O ASN B4662 " (cutoff:3.500A) Proline residue: B4667 - end of helix removed outlier: 4.798A pdb=" N GLU B4676 " --> pdb=" O LYS B4672 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N LEU B4677 " --> pdb=" O ARG B4673 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA B4678 " --> pdb=" O GLU B4674 " (cutoff:3.500A) Processing helix chain 'B' and resid 4685 through 4690 removed outlier: 5.307A pdb=" N THR B4689 " --> pdb=" O GLY B4685 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N GLU B4690 " --> pdb=" O LEU B4686 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4685 through 4690' Processing helix chain 'B' and resid 4696 through 4701 Processing helix chain 'B' and resid 4719 through 4733 removed outlier: 3.529A pdb=" N LYS B4723 " --> pdb=" O PHE B4719 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU B4725 " --> pdb=" O LYS B4721 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ASP B4726 " --> pdb=" O ARG B4722 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LYS B4727 " --> pdb=" O LYS B4723 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N HIS B4728 " --> pdb=" O VAL B4724 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ASP B4730 " --> pdb=" O ASP B4726 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ILE B4731 " --> pdb=" O LYS B4727 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N PHE B4732 " --> pdb=" O HIS B4728 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLY B4733 " --> pdb=" O GLY B4729 " (cutoff:3.500A) Processing helix chain 'B' and resid 4734 through 4742 removed outlier: 4.370A pdb=" N LEU B4740 " --> pdb=" O ARG B4736 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LEU B4741 " --> pdb=" O ILE B4737 " (cutoff:3.500A) Processing helix chain 'B' and resid 4745 through 4753 removed outlier: 4.319A pdb=" N THR B4751 " --> pdb=" O SER B4747 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA B4752 " --> pdb=" O LEU B4748 " (cutoff:3.500A) Processing helix chain 'B' and resid 4765 through 4771 removed outlier: 5.454A pdb=" N MET B4769 " --> pdb=" O LEU B4765 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N SER B4770 " --> pdb=" O THR B4766 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ILE B4771 " --> pdb=" O TRP B4767 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4765 through 4771' Processing helix chain 'B' and resid 4772 through 4786 removed outlier: 3.608A pdb=" N VAL B4782 " --> pdb=" O TRP B4778 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE B4783 " --> pdb=" O LYS B4779 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N PHE B4784 " --> pdb=" O PHE B4780 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N THR B4785 " --> pdb=" O GLY B4781 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASP B4786 " --> pdb=" O VAL B4782 " (cutoff:3.500A) Processing helix chain 'B' and resid 4787 through 4804 removed outlier: 4.757A pdb=" N TYR B4804 " --> pdb=" O LEU B4800 " (cutoff:3.500A) Processing helix chain 'B' and resid 4809 through 4819 removed outlier: 4.803A pdb=" N LEU B4813 " --> pdb=" O PHE B4809 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LEU B4814 " --> pdb=" O ALA B4810 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N GLY B4819 " --> pdb=" O ASP B4815 " (cutoff:3.500A) Processing helix chain 'B' and resid 4820 through 4827 removed outlier: 4.319A pdb=" N ILE B4826 " --> pdb=" O THR B4822 " (cutoff:3.500A) Processing helix chain 'B' and resid 4828 through 4834 removed outlier: 4.105A pdb=" N HIS B4832 " --> pdb=" O SER B4828 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN B4833 " --> pdb=" O SER B4829 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLY B4834 " --> pdb=" O VAL B4830 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4828 through 4834' Processing helix chain 'B' and resid 4835 through 4859 removed outlier: 4.549A pdb=" N MET B4839 " --> pdb=" O LYS B4835 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N THR B4840 " --> pdb=" O GLN B4836 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLY B4842 " --> pdb=" O VAL B4838 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N LEU B4843 " --> pdb=" O MET B4839 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU B4844 " --> pdb=" O THR B4840 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN B4857 " --> pdb=" O VAL B4853 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE B4858 " --> pdb=" O VAL B4854 " (cutoff:3.500A) Processing helix chain 'B' and resid 4878 through 4893 removed outlier: 4.687A pdb=" N VAL B4891 " --> pdb=" O MET B4887 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ARG B4892 " --> pdb=" O TYR B4888 " (cutoff:3.500A) Processing helix chain 'B' and resid 4897 through 4902 removed outlier: 5.106A pdb=" N GLU B4902 " --> pdb=" O GLY B4898 " (cutoff:3.500A) Processing helix chain 'B' and resid 4909 through 4925 removed outlier: 3.620A pdb=" N VAL B4914 " --> pdb=" O GLU B4910 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N VAL B4915 " --> pdb=" O LEU B4911 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ILE B4918 " --> pdb=" O VAL B4914 " (cutoff:3.500A) Processing helix chain 'B' and resid 4928 through 4953 removed outlier: 4.061A pdb=" N ILE B4932 " --> pdb=" O LEU B4928 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP B4938 " --> pdb=" O GLY B4934 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU B4943 " --> pdb=" O ALA B4939 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG B4944 " --> pdb=" O PHE B4940 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU B4952 " --> pdb=" O GLU B4948 " (cutoff:3.500A) Processing helix chain 'B' and resid 4964 through 4972 removed outlier: 3.863A pdb=" N PHE B4968 " --> pdb=" O GLY B4964 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N THR B4970 " --> pdb=" O ASP B4966 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N THR B4971 " --> pdb=" O TYR B4967 " (cutoff:3.500A) Proline residue: B4972 - end of helix Processing helix chain 'B' and resid 4973 through 4981 removed outlier: 3.975A pdb=" N LEU B4980 " --> pdb=" O GLU B4976 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLU B4981 " --> pdb=" O THR B4977 " (cutoff:3.500A) Processing helix chain 'B' and resid 4986 through 4999 removed outlier: 4.589A pdb=" N PHE B4990 " --> pdb=" O ALA B4986 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ASP B4999 " --> pdb=" O LEU B4995 " (cutoff:3.500A) Processing helix chain 'B' and resid 5004 through 5017 Processing helix chain 'B' and resid 5028 through 5033 removed outlier: 5.273A pdb=" N TYR B5032 " --> pdb=" O PHE B5028 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLU B5033 " --> pdb=" O ARG B5029 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 5028 through 5033' Processing helix chain 'B' and resid 956 through 961 removed outlier: 4.374A pdb=" N MET B 960 " --> pdb=" O LYS B 957 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N MET B 961 " --> pdb=" O THR B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 2285 through 2290 removed outlier: 4.385A pdb=" N LEU B2288 " --> pdb=" O GLU B2285 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA B2289 " --> pdb=" O LEU B2286 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N LEU B2290 " --> pdb=" O ALA B2287 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2285 through 2290' Processing helix chain 'B' and resid 4703 through 4708 removed outlier: 4.029A pdb=" N LEU B4706 " --> pdb=" O ARG B4703 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ASN B4707 " --> pdb=" O LEU B4704 " (cutoff:3.500A) Processing helix chain 'B' and resid 4709 through 4715 Proline residue: B4712 - end of helix Processing helix chain 'C' and resid 61 through 66 removed outlier: 4.641A pdb=" N CYS C 65 " --> pdb=" O ASP C 61 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N CYS C 66 " --> pdb=" O LEU C 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 61 through 66' Processing helix chain 'C' and resid 74 through 84 Processing helix chain 'C' and resid 250 through 256 removed outlier: 6.183A pdb=" N THR C 254 " --> pdb=" O GLY C 250 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N HIS C 255 " --> pdb=" O ALA C 251 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N ALA C 256 " --> pdb=" O VAL C 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 250 through 256' Processing helix chain 'C' and resid 364 through 371 removed outlier: 3.957A pdb=" N VAL C 371 " --> pdb=" O LEU C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 425 removed outlier: 4.394A pdb=" N GLN C 413 " --> pdb=" O GLY C 409 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE C 414 " --> pdb=" O LEU C 410 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N PHE C 421 " --> pdb=" O GLY C 417 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLY C 423 " --> pdb=" O ASP C 419 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N LYS C 424 " --> pdb=" O SER C 420 " (cutoff:3.500A) Proline residue: C 425 - end of helix Processing helix chain 'C' and resid 437 through 453 removed outlier: 4.804A pdb=" N VAL C 441 " --> pdb=" O PRO C 437 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN C 446 " --> pdb=" O ILE C 442 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE C 452 " --> pdb=" O LEU C 448 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N GLU C 453 " --> pdb=" O ILE C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 481 removed outlier: 3.665A pdb=" N ARG C 469 " --> pdb=" O GLN C 465 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU C 480 " --> pdb=" O SER C 476 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N GLU C 481 " --> pdb=" O LEU C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 484 through 496 removed outlier: 3.948A pdb=" N CYS C 490 " --> pdb=" O LEU C 486 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N VAL C 496 " --> pdb=" O ASP C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 531 removed outlier: 5.211A pdb=" N SER C 514 " --> pdb=" O GLU C 510 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N TRP C 515 " --> pdb=" O ALA C 511 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N LYS C 516 " --> pdb=" O ALA C 512 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N GLU C 517 " --> pdb=" O GLU C 513 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ILE C 518 " --> pdb=" O SER C 514 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 540 removed outlier: 4.645A pdb=" N CYS C 537 " --> pdb=" O ASN C 533 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU C 539 " --> pdb=" O ALA C 535 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N PHE C 540 " --> pdb=" O ASN C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 551 removed outlier: 4.634A pdb=" N ASP C 545 " --> pdb=" O SER C 541 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N TRP C 546 " --> pdb=" O THR C 542 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL C 548 " --> pdb=" O LEU C 544 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N LEU C 551 " --> pdb=" O VAL C 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 571 removed outlier: 4.101A pdb=" N LEU C 561 " --> pdb=" O SER C 557 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N GLU C 562 " --> pdb=" O SER C 558 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N VAL C 563 " --> pdb=" O GLY C 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 578 removed outlier: 4.344A pdb=" N ILE C 577 " --> pdb=" O GLU C 573 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ILE C 578 " --> pdb=" O VAL C 574 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 573 through 578' Processing helix chain 'C' and resid 579 through 594 removed outlier: 6.091A pdb=" N ILE C 583 " --> pdb=" O GLN C 579 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU C 590 " --> pdb=" O ILE C 586 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASP C 591 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 609 removed outlier: 4.223A pdb=" N VAL C 602 " --> pdb=" O LYS C 598 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LEU C 603 " --> pdb=" O VAL C 599 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N CYS C 607 " --> pdb=" O LEU C 603 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N VAL C 608 " --> pdb=" O CYS C 604 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N CYS C 609 " --> pdb=" O SER C 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 626 removed outlier: 4.328A pdb=" N GLN C 618 " --> pdb=" O VAL C 614 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR C 622 " --> pdb=" O GLN C 618 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N LEU C 626 " --> pdb=" O THR C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 865 through 890 removed outlier: 4.745A pdb=" N ARG C 869 " --> pdb=" O PRO C 865 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE C 870 " --> pdb=" O HIS C 866 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU C 876 " --> pdb=" O GLU C 872 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN C 877 " --> pdb=" O LYS C 873 " (cutoff:3.500A) Processing helix chain 'C' and resid 914 through 936 removed outlier: 4.021A pdb=" N TYR C 920 " --> pdb=" O PRO C 916 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N GLY C 936 " --> pdb=" O LEU C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 950 removed outlier: 4.510A pdb=" N ASN C 949 " --> pdb=" O LYS C 945 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LEU C 950 " --> pdb=" O ALA C 946 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 945 through 950' Processing helix chain 'C' and resid 983 through 1002 removed outlier: 5.243A pdb=" N ARG C 987 " --> pdb=" O THR C 983 " (cutoff:3.500A) Processing helix chain 'C' and resid 1029 through 1050 removed outlier: 5.535A pdb=" N ARG C1033 " --> pdb=" O GLU C1029 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N SER C1034 " --> pdb=" O ALA C1030 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER C1038 " --> pdb=" O SER C1034 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LEU C1039 " --> pdb=" O ASN C1035 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N CYS C1040 " --> pdb=" O ARG C1036 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLN C1041 " --> pdb=" O ASP C1037 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA C1042 " --> pdb=" O SER C1038 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY C1050 " --> pdb=" O LEU C1046 " (cutoff:3.500A) Processing helix chain 'C' and resid 1574 through 1581 Processing helix chain 'C' and resid 1649 through 1657 removed outlier: 4.069A pdb=" N LEU C1653 " --> pdb=" O ASP C1649 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N SER C1654 " --> pdb=" O ILE C1650 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N GLU C1655 " --> pdb=" O LEU C1651 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ARG C1656 " --> pdb=" O GLU C1652 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LEU C1657 " --> pdb=" O LEU C1653 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1649 through 1657' Processing helix chain 'C' and resid 1658 through 1675 Processing helix chain 'C' and resid 1679 through 1690 removed outlier: 3.908A pdb=" N ALA C1684 " --> pdb=" O ARG C1680 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER C1687 " --> pdb=" O HIS C1683 " (cutoff:3.500A) Processing helix chain 'C' and resid 1692 through 1701 removed outlier: 4.484A pdb=" N GLU C1699 " --> pdb=" O LEU C1695 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ASP C1700 " --> pdb=" O HIS C1696 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ALA C1701 " --> pdb=" O ALA C1697 " (cutoff:3.500A) Processing helix chain 'C' and resid 1704 through 1720 removed outlier: 7.151A pdb=" N ARG C1708 " --> pdb=" O PRO C1704 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA C1709 " --> pdb=" O GLY C1705 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE C1718 " --> pdb=" O LEU C1714 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N HIS C1719 " --> pdb=" O LEU C1715 " (cutoff:3.500A) Processing helix chain 'C' and resid 1723 through 1731 removed outlier: 4.161A pdb=" N SER C1729 " --> pdb=" O ARG C1725 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N MET C1730 " --> pdb=" O SER C1726 " (cutoff:3.500A) Processing helix chain 'C' and resid 1739 through 1745 removed outlier: 3.624A pdb=" N ARG C1743 " --> pdb=" O THR C1739 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ALA C1744 " --> pdb=" O PRO C1740 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ILE C1745 " --> pdb=" O GLU C1741 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1739 through 1745' Processing helix chain 'C' and resid 1754 through 1759 removed outlier: 4.357A pdb=" N ARG C1758 " --> pdb=" O GLY C1754 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ARG C1759 " --> pdb=" O GLY C1755 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1754 through 1759' Processing helix chain 'C' and resid 1803 through 1825 removed outlier: 3.707A pdb=" N ASP C1809 " --> pdb=" O GLU C1805 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN C1824 " --> pdb=" O ARG C1820 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N HIS C1825 " --> pdb=" O ASP C1821 " (cutoff:3.500A) Processing helix chain 'C' and resid 1833 through 1852 removed outlier: 4.024A pdb=" N GLN C1837 " --> pdb=" O SER C1833 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N PHE C1838 " --> pdb=" O VAL C1834 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N VAL C1839 " --> pdb=" O GLU C1835 " (cutoff:3.500A) Proline residue: C1840 - end of helix removed outlier: 4.661A pdb=" N LYS C1843 " --> pdb=" O VAL C1839 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL C1845 " --> pdb=" O VAL C1841 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N MET C1851 " --> pdb=" O THR C1847 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLY C1852 " --> pdb=" O LEU C1848 " (cutoff:3.500A) Processing helix chain 'C' and resid 1855 through 1865 removed outlier: 4.707A pdb=" N VAL C1859 " --> pdb=" O GLY C1855 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N MET C1865 " --> pdb=" O GLN C1861 " (cutoff:3.500A) Processing helix chain 'C' and resid 1866 through 1871 Processing helix chain 'C' and resid 1925 through 1930 removed outlier: 4.560A pdb=" N MET C1929 " --> pdb=" O GLY C1925 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N LYS C1930 " --> pdb=" O LEU C1926 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1925 through 1930' Processing helix chain 'C' and resid 1934 through 1984 removed outlier: 3.618A pdb=" N TYR C1945 " --> pdb=" O ASN C1941 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE C1946 " --> pdb=" O LEU C1942 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ARG C1964 " --> pdb=" O ALA C1960 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR C1965 " --> pdb=" O PHE C1961 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N PHE C1984 " --> pdb=" O LEU C1980 " (cutoff:3.500A) Processing helix chain 'C' and resid 1989 through 1997 removed outlier: 4.454A pdb=" N ARG C1993 " --> pdb=" O ALA C1989 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N GLU C1997 " --> pdb=" O ARG C1993 " (cutoff:3.500A) Processing helix chain 'C' and resid 2001 through 2013 removed outlier: 3.795A pdb=" N GLN C2005 " --> pdb=" O PRO C2001 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N ASN C2007 " --> pdb=" O GLN C2003 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N MET C2008 " --> pdb=" O GLU C2004 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LEU C2009 " --> pdb=" O GLN C2005 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N LEU C2010 " --> pdb=" O ILE C2006 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N HIS C2011 " --> pdb=" O ASN C2007 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N PHE C2012 " --> pdb=" O MET C2008 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LYS C2013 " --> pdb=" O LEU C2009 " (cutoff:3.500A) Processing helix chain 'C' and resid 2024 through 2043 removed outlier: 4.806A pdb=" N ARG C2028 " --> pdb=" O PRO C2024 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N GLN C2029 " --> pdb=" O GLU C2025 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ASP C2030 " --> pdb=" O ASP C2026 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU C2031 " --> pdb=" O ILE C2027 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN C2032 " --> pdb=" O ARG C2028 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N GLY C2043 " --> pdb=" O LEU C2039 " (cutoff:3.500A) Processing helix chain 'C' and resid 2093 through 2108 removed outlier: 3.840A pdb=" N TRP C2105 " --> pdb=" O MET C2101 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA C2106 " --> pdb=" O VAL C2102 " (cutoff:3.500A) Processing helix chain 'C' and resid 2113 through 2130 removed outlier: 4.420A pdb=" N GLY C2130 " --> pdb=" O ARG C2126 " (cutoff:3.500A) Processing helix chain 'C' and resid 2131 through 2141 Proline residue: C2139 - end of helix Processing helix chain 'C' and resid 2148 through 2168 removed outlier: 4.284A pdb=" N SER C2154 " --> pdb=" O GLU C2150 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU C2155 " --> pdb=" O ASP C2151 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE C2167 " --> pdb=" O ARG C2163 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N VAL C2168 " --> pdb=" O SER C2164 " (cutoff:3.500A) Processing helix chain 'C' and resid 2171 through 2188 removed outlier: 4.437A pdb=" N LEU C2177 " --> pdb=" O GLN C2173 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE C2179 " --> pdb=" O GLU C2175 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLN C2180 " --> pdb=" O ASN C2176 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE C2185 " --> pdb=" O SER C2181 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N MET C2186 " --> pdb=" O ILE C2182 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ASN C2187 " --> pdb=" O GLY C2183 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N ASN C2188 " --> pdb=" O ASN C2184 " (cutoff:3.500A) Processing helix chain 'C' and resid 2189 through 2195 removed outlier: 4.617A pdb=" N GLN C2193 " --> pdb=" O LYS C2189 " (cutoff:3.500A) Proline residue: C2195 - end of helix Processing helix chain 'C' and resid 2196 through 2202 removed outlier: 4.117A pdb=" N ALA C2200 " --> pdb=" O ASN C2196 " (cutoff:3.500A) Processing helix chain 'C' and resid 2203 through 2216 removed outlier: 3.645A pdb=" N VAL C2210 " --> pdb=" O THR C2206 " (cutoff:3.500A) Processing helix chain 'C' and resid 2227 through 2244 removed outlier: 3.750A pdb=" N SER C2243 " --> pdb=" O PHE C2239 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N ARG C2244 " --> pdb=" O CYS C2240 " (cutoff:3.500A) Processing helix chain 'C' and resid 2245 through 2252 removed outlier: 4.848A pdb=" N ASP C2252 " --> pdb=" O ARG C2248 " (cutoff:3.500A) Processing helix chain 'C' and resid 2253 through 2265 removed outlier: 3.699A pdb=" N ASN C2260 " --> pdb=" O TYR C2256 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY C2262 " --> pdb=" O LEU C2258 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ILE C2263 " --> pdb=" O GLU C2259 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N LEU C2265 " --> pdb=" O SER C2261 " (cutoff:3.500A) Processing helix chain 'C' and resid 2271 through 2280 removed outlier: 3.641A pdb=" N VAL C2275 " --> pdb=" O THR C2271 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N VAL C2280 " --> pdb=" O ALA C2276 " (cutoff:3.500A) Processing helix chain 'C' and resid 2294 through 2309 removed outlier: 3.827A pdb=" N VAL C2299 " --> pdb=" O LEU C2295 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU C2302 " --> pdb=" O VAL C2298 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N SER C2309 " --> pdb=" O CYS C2305 " (cutoff:3.500A) Processing helix chain 'C' and resid 2310 through 2315 removed outlier: 3.882A pdb=" N ALA C2315 " --> pdb=" O PRO C2311 " (cutoff:3.500A) Processing helix chain 'C' and resid 2324 through 2341 removed outlier: 4.771A pdb=" N LEU C2332 " --> pdb=" O GLY C2328 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ASP C2333 " --> pdb=" O GLU C2329 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N PHE C2334 " --> pdb=" O ARG C2330 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU C2335 " --> pdb=" O TYR C2331 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA C2338 " --> pdb=" O PHE C2334 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N VAL C2339 " --> pdb=" O LEU C2335 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N PHE C2340 " --> pdb=" O ARG C2336 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N VAL C2341 " --> pdb=" O PHE C2337 " (cutoff:3.500A) Processing helix chain 'C' and resid 2346 through 2360 removed outlier: 4.159A pdb=" N ALA C2350 " --> pdb=" O VAL C2346 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE C2358 " --> pdb=" O VAL C2354 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ARG C2359 " --> pdb=" O ARG C2355 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LYS C2360 " --> pdb=" O LEU C2356 " (cutoff:3.500A) Processing helix chain 'C' and resid 2365 through 2371 removed outlier: 5.440A pdb=" N GLU C2371 " --> pdb=" O ALA C2367 " (cutoff:3.500A) Processing helix chain 'C' and resid 2375 through 2390 Proline residue: C2390 - end of helix Processing helix chain 'C' and resid 2417 through 2437 removed outlier: 4.173A pdb=" N ALA C2437 " --> pdb=" O LEU C2433 " (cutoff:3.500A) Processing helix chain 'C' and resid 2440 through 2448 removed outlier: 4.653A pdb=" N GLY C2448 " --> pdb=" O GLN C2444 " (cutoff:3.500A) Processing helix chain 'C' and resid 2449 through 2462 removed outlier: 3.771A pdb=" N ILE C2453 " --> pdb=" O GLU C2449 " (cutoff:3.500A) Proline residue: C2462 - end of helix Processing helix chain 'C' and resid 2464 through 2472 removed outlier: 5.215A pdb=" N GLY C2468 " --> pdb=" O ASP C2464 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE C2469 " --> pdb=" O ASP C2465 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU C2472 " --> pdb=" O GLY C2468 " (cutoff:3.500A) Processing helix chain 'C' and resid 2751 through 2772 removed outlier: 5.084A pdb=" N ILE C2755 " --> pdb=" O LEU C2751 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ASN C2756 " --> pdb=" O ASP C2752 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N PHE C2758 " --> pdb=" O PHE C2754 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N ALA C2759 " --> pdb=" O ILE C2755 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N GLU C2760 " --> pdb=" O ASN C2756 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N TYR C2761 " --> pdb=" O LYS C2757 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N THR C2762 " --> pdb=" O PHE C2758 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N HIS C2763 " --> pdb=" O ALA C2759 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N GLU C2764 " --> pdb=" O GLU C2760 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS C2765 " --> pdb=" O TYR C2761 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA C2767 " --> pdb=" O HIS C2763 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N PHE C2768 " --> pdb=" O GLU C2764 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N GLN C2772 " --> pdb=" O PHE C2768 " (cutoff:3.500A) Processing helix chain 'C' and resid 2809 through 2816 removed outlier: 4.804A pdb=" N LYS C2814 " --> pdb=" O LYS C2810 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ALA C2815 " --> pdb=" O GLU C2811 " (cutoff:3.500A) Processing helix chain 'C' and resid 2870 through 2896 removed outlier: 4.075A pdb=" N GLU C2876 " --> pdb=" O GLN C2872 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA C2879 " --> pdb=" O ALA C2875 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N GLU C2880 " --> pdb=" O GLU C2876 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASN C2881 " --> pdb=" O GLN C2877 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N TYR C2882 " --> pdb=" O LEU C2878 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N HIS C2883 " --> pdb=" O ALA C2879 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ASN C2884 " --> pdb=" O GLU C2880 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N THR C2885 " --> pdb=" O ASN C2881 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLY C2887 " --> pdb=" O HIS C2883 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ARG C2888 " --> pdb=" O ASN C2884 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS C2889 " --> pdb=" O THR C2885 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N LYS C2890 " --> pdb=" O TRP C2886 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU C2895 " --> pdb=" O LYS C2891 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA C2896 " --> pdb=" O GLN C2892 " (cutoff:3.500A) Processing helix chain 'C' and resid 2919 through 2932 removed outlier: 6.118A pdb=" N ALA C2923 " --> pdb=" O ASP C2919 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLN C2924 " --> pdb=" O ARG C2920 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU C2927 " --> pdb=" O ALA C2923 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS C2928 " --> pdb=" O GLN C2924 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N PHE C2929 " --> pdb=" O GLU C2925 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N LEU C2930 " --> pdb=" O LEU C2926 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLN C2931 " --> pdb=" O LEU C2927 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N MET C2932 " --> pdb=" O LYS C2928 " (cutoff:3.500A) Processing helix chain 'C' and resid 3645 through 3656 removed outlier: 4.007A pdb=" N ASN C3651 " --> pdb=" O HIS C3647 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N MET C3652 " --> pdb=" O ARG C3648 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N PHE C3653 " --> pdb=" O ALA C3649 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N LEU C3654 " --> pdb=" O CYS C3650 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N GLU C3655 " --> pdb=" O ASN C3651 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N SER C3656 " --> pdb=" O MET C3652 " (cutoff:3.500A) Processing helix chain 'C' and resid 3669 through 3681 removed outlier: 4.119A pdb=" N MET C3673 " --> pdb=" O PHE C3669 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE C3674 " --> pdb=" O GLU C3670 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLY C3681 " --> pdb=" O LEU C3677 " (cutoff:3.500A) Processing helix chain 'C' and resid 3683 through 3688 removed outlier: 4.161A pdb=" N GLU C3688 " --> pdb=" O GLU C3684 " (cutoff:3.500A) Processing helix chain 'C' and resid 3696 through 3711 removed outlier: 4.171A pdb=" N THR C3711 " --> pdb=" O ARG C3707 " (cutoff:3.500A) Processing helix chain 'C' and resid 3719 through 3738 removed outlier: 4.006A pdb=" N ASP C3727 " --> pdb=" O MET C3723 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILE C3728 " --> pdb=" O ALA C3724 " (cutoff:3.500A) Processing helix chain 'C' and resid 3754 through 3770 removed outlier: 5.088A pdb=" N MET C3758 " --> pdb=" O GLU C3754 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLU C3759 " --> pdb=" O GLU C3755 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS C3760 " --> pdb=" O LYS C3756 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ARG C3762 " --> pdb=" O MET C3758 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU C3770 " --> pdb=" O GLN C3766 " (cutoff:3.500A) Processing helix chain 'C' and resid 3771 through 3785 removed outlier: 4.130A pdb=" N GLU C3777 " --> pdb=" O ARG C3773 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL C3779 " --> pdb=" O ALA C3775 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N LEU C3780 " --> pdb=" O ALA C3776 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLN C3781 " --> pdb=" O GLU C3777 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ALA C3785 " --> pdb=" O GLN C3781 " (cutoff:3.500A) Processing helix chain 'C' and resid 3791 through 3806 removed outlier: 3.540A pdb=" N LEU C3805 " --> pdb=" O GLY C3801 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ASN C3806 " --> pdb=" O ILE C3802 " (cutoff:3.500A) Processing helix chain 'C' and resid 3809 through 3824 removed outlier: 4.046A pdb=" N LYS C3824 " --> pdb=" O LEU C3820 " (cutoff:3.500A) Processing helix chain 'C' and resid 3827 through 3839 removed outlier: 4.685A pdb=" N CYS C3839 " --> pdb=" O LEU C3835 " (cutoff:3.500A) Processing helix chain 'C' and resid 3843 through 3857 Processing helix chain 'C' and resid 3861 through 3866 removed outlier: 6.925A pdb=" N VAL C3865 " --> pdb=" O GLU C3861 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ILE C3866 " --> pdb=" O ASP C3862 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 3861 through 3866' Processing helix chain 'C' and resid 3877 through 3894 removed outlier: 4.257A pdb=" N GLY C3894 " --> pdb=" O LEU C3890 " (cutoff:3.500A) Processing helix chain 'C' and resid 3897 through 3906 removed outlier: 5.878A pdb=" N ASN C3901 " --> pdb=" O ASN C3897 " (cutoff:3.500A) Processing helix chain 'C' and resid 3914 through 3939 removed outlier: 3.771A pdb=" N CYS C3918 " --> pdb=" O ASN C3914 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLY C3939 " --> pdb=" O TRP C3935 " (cutoff:3.500A) Processing helix chain 'C' and resid 3944 through 3970 removed outlier: 3.924A pdb=" N GLU C3967 " --> pdb=" O ASN C3963 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N TYR C3968 " --> pdb=" O SER C3964 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE C3969 " --> pdb=" O LEU C3965 " (cutoff:3.500A) Processing helix chain 'C' and resid 3973 through 3984 removed outlier: 4.284A pdb=" N GLN C3977 " --> pdb=" O CYS C3973 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLN C3978 " --> pdb=" O THR C3974 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N ARG C3984 " --> pdb=" O LEU C3980 " (cutoff:3.500A) Processing helix chain 'C' and resid 3985 through 4005 removed outlier: 3.665A pdb=" N HIS C3998 " --> pdb=" O HIS C3994 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N MET C4000 " --> pdb=" O PHE C3996 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N MET C4001 " --> pdb=" O ALA C3997 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ALA C4004 " --> pdb=" O MET C4000 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N GLN C4005 " --> pdb=" O MET C4001 " (cutoff:3.500A) Processing helix chain 'C' and resid 4009 through 4032 removed outlier: 4.949A pdb=" N LEU C4019 " --> pdb=" O GLU C4015 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N GLN C4020 " --> pdb=" O LEU C4016 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N LYS C4021 " --> pdb=" O LEU C4017 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ASP C4022 " --> pdb=" O ASP C4018 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU C4031 " --> pdb=" O LEU C4027 " (cutoff:3.500A) Processing helix chain 'C' and resid 4039 through 4056 removed outlier: 5.925A pdb=" N GLN C4043 " --> pdb=" O MET C4039 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU C4048 " --> pdb=" O MET C4044 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N SER C4053 " --> pdb=" O VAL C4049 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ASN C4054 " --> pdb=" O GLU C4050 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL C4055 " --> pdb=" O SER C4051 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLU C4056 " --> pdb=" O SER C4052 " (cutoff:3.500A) Processing helix chain 'C' and resid 4057 through 4074 removed outlier: 5.378A pdb=" N LEU C4066 " --> pdb=" O PHE C4062 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LYS C4067 " --> pdb=" O ASP C4063 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N LYS C4069 " --> pdb=" O PHE C4065 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N ASP C4070 " --> pdb=" O LEU C4066 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N ILE C4071 " --> pdb=" O LYS C4067 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N VAL C4072 " --> pdb=" O LEU C4068 " (cutoff:3.500A) Processing helix chain 'C' and resid 4075 through 4081 removed outlier: 3.803A pdb=" N ASP C4079 " --> pdb=" O GLU C4075 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N TYR C4080 " --> pdb=" O ALA C4076 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N VAL C4081 " --> pdb=" O PHE C4077 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 4075 through 4081' Processing helix chain 'C' and resid 4089 through 4101 removed outlier: 5.227A pdb=" N LYS C4101 " --> pdb=" O MET C4097 " (cutoff:3.500A) Processing helix chain 'C' and resid 4106 through 4116 removed outlier: 3.759A pdb=" N PHE C4110 " --> pdb=" O PRO C4106 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N GLU C4116 " --> pdb=" O LEU C4112 " (cutoff:3.500A) Processing helix chain 'C' and resid 4124 through 4137 removed outlier: 3.896A pdb=" N PHE C4132 " --> pdb=" O PHE C4128 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN C4133 " --> pdb=" O ALA C4129 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N GLU C4134 " --> pdb=" O ASN C4130 " (cutoff:3.500A) Proline residue: C4135 - end of helix Processing helix chain 'C' and resid 4138 through 4155 Proline residue: C4155 - end of helix Processing helix chain 'C' and resid 4157 through 4168 removed outlier: 4.561A pdb=" N GLU C4165 " --> pdb=" O ARG C4161 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N LEU C4166 " --> pdb=" O ASN C4162 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ALA C4167 " --> pdb=" O PHE C4163 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N GLU C4168 " --> pdb=" O LEU C4164 " (cutoff:3.500A) Processing helix chain 'C' and resid 4169 through 4175 removed outlier: 3.824A pdb=" N ARG C4175 " --> pdb=" O LEU C4171 " (cutoff:3.500A) Processing helix chain 'C' and resid 4198 through 4207 removed outlier: 3.811A pdb=" N GLU C4206 " --> pdb=" O ARG C4202 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N MET C4207 " --> pdb=" O ALA C4203 " (cutoff:3.500A) Processing helix chain 'C' and resid 4208 through 4225 removed outlier: 4.619A pdb=" N SER C4213 " --> pdb=" O GLN C4209 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LYS C4214 " --> pdb=" O VAL C4210 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP C4220 " --> pdb=" O GLN C4216 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLU C4224 " --> pdb=" O ASP C4220 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLY C4225 " --> pdb=" O VAL C4221 " (cutoff:3.500A) Processing helix chain 'C' and resid 4227 through 4252 removed outlier: 4.432A pdb=" N MET C4231 " --> pdb=" O GLU C4227 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLU C4232 " --> pdb=" O ALA C4228 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA C4249 " --> pdb=" O MET C4245 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLN C4250 " --> pdb=" O GLN C4246 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ILE C4251 " --> pdb=" O ILE C4247 " (cutoff:3.500A) Processing helix chain 'C' and resid 4541 through 4556 removed outlier: 5.069A pdb=" N GLU C4545 " --> pdb=" O TRP C4541 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N VAL C4546 " --> pdb=" O GLY C4542 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N TYR C4554 " --> pdb=" O LYS C4550 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU C4555 " --> pdb=" O PHE C4551 " (cutoff:3.500A) Processing helix chain 'C' and resid 4558 through 4578 removed outlier: 4.071A pdb=" N LEU C4562 " --> pdb=" O ASN C4558 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N PHE C4571 " --> pdb=" O LEU C4567 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ALA C4572 " --> pdb=" O PHE C4568 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE C4573 " --> pdb=" O LEU C4569 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASN C4574 " --> pdb=" O ALA C4570 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU C4577 " --> pdb=" O ILE C4573 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N LEU C4578 " --> pdb=" O ASN C4574 " (cutoff:3.500A) Processing helix chain 'C' and resid 4643 through 4684 removed outlier: 4.460A pdb=" N SER C4647 " --> pdb=" O LEU C4643 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LEU C4648 " --> pdb=" O TRP C4644 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N LEU C4649 " --> pdb=" O CYS C4645 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N HIS C4650 " --> pdb=" O LEU C4646 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N THR C4651 " --> pdb=" O SER C4647 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU C4652 " --> pdb=" O LEU C4648 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LYS C4665 " --> pdb=" O TYR C4661 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N VAL C4666 " --> pdb=" O ASN C4662 " (cutoff:3.500A) Proline residue: C4667 - end of helix removed outlier: 4.798A pdb=" N GLU C4676 " --> pdb=" O LYS C4672 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N LEU C4677 " --> pdb=" O ARG C4673 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA C4678 " --> pdb=" O GLU C4674 " (cutoff:3.500A) Processing helix chain 'C' and resid 4685 through 4690 removed outlier: 5.305A pdb=" N THR C4689 " --> pdb=" O GLY C4685 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N GLU C4690 " --> pdb=" O LEU C4686 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 4685 through 4690' Processing helix chain 'C' and resid 4696 through 4701 Processing helix chain 'C' and resid 4719 through 4733 removed outlier: 3.530A pdb=" N LYS C4723 " --> pdb=" O PHE C4719 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU C4725 " --> pdb=" O LYS C4721 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ASP C4726 " --> pdb=" O ARG C4722 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LYS C4727 " --> pdb=" O LYS C4723 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N HIS C4728 " --> pdb=" O VAL C4724 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ASP C4730 " --> pdb=" O ASP C4726 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ILE C4731 " --> pdb=" O LYS C4727 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N PHE C4732 " --> pdb=" O HIS C4728 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLY C4733 " --> pdb=" O GLY C4729 " (cutoff:3.500A) Processing helix chain 'C' and resid 4734 through 4742 removed outlier: 4.370A pdb=" N LEU C4740 " --> pdb=" O ARG C4736 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LEU C4741 " --> pdb=" O ILE C4737 " (cutoff:3.500A) Processing helix chain 'C' and resid 4745 through 4753 removed outlier: 4.319A pdb=" N THR C4751 " --> pdb=" O SER C4747 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA C4752 " --> pdb=" O LEU C4748 " (cutoff:3.500A) Processing helix chain 'C' and resid 4765 through 4771 removed outlier: 5.455A pdb=" N MET C4769 " --> pdb=" O LEU C4765 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N SER C4770 " --> pdb=" O THR C4766 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ILE C4771 " --> pdb=" O TRP C4767 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 4765 through 4771' Processing helix chain 'C' and resid 4772 through 4786 removed outlier: 3.608A pdb=" N VAL C4782 " --> pdb=" O TRP C4778 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE C4783 " --> pdb=" O LYS C4779 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N PHE C4784 " --> pdb=" O PHE C4780 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N THR C4785 " --> pdb=" O GLY C4781 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASP C4786 " --> pdb=" O VAL C4782 " (cutoff:3.500A) Processing helix chain 'C' and resid 4787 through 4804 removed outlier: 4.757A pdb=" N TYR C4804 " --> pdb=" O LEU C4800 " (cutoff:3.500A) Processing helix chain 'C' and resid 4809 through 4819 removed outlier: 4.802A pdb=" N LEU C4813 " --> pdb=" O PHE C4809 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LEU C4814 " --> pdb=" O ALA C4810 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N GLY C4819 " --> pdb=" O ASP C4815 " (cutoff:3.500A) Processing helix chain 'C' and resid 4820 through 4827 removed outlier: 4.319A pdb=" N ILE C4826 " --> pdb=" O THR C4822 " (cutoff:3.500A) Processing helix chain 'C' and resid 4828 through 4834 removed outlier: 4.103A pdb=" N HIS C4832 " --> pdb=" O SER C4828 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASN C4833 " --> pdb=" O SER C4829 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLY C4834 " --> pdb=" O VAL C4830 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 4828 through 4834' Processing helix chain 'C' and resid 4835 through 4859 removed outlier: 4.549A pdb=" N MET C4839 " --> pdb=" O LYS C4835 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N THR C4840 " --> pdb=" O GLN C4836 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLY C4842 " --> pdb=" O VAL C4838 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N LEU C4843 " --> pdb=" O MET C4839 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU C4844 " --> pdb=" O THR C4840 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN C4857 " --> pdb=" O VAL C4853 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE C4858 " --> pdb=" O VAL C4854 " (cutoff:3.500A) Processing helix chain 'C' and resid 4878 through 4893 removed outlier: 4.688A pdb=" N VAL C4891 " --> pdb=" O MET C4887 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ARG C4892 " --> pdb=" O TYR C4888 " (cutoff:3.500A) Processing helix chain 'C' and resid 4897 through 4902 removed outlier: 5.105A pdb=" N GLU C4902 " --> pdb=" O GLY C4898 " (cutoff:3.500A) Processing helix chain 'C' and resid 4909 through 4925 removed outlier: 3.620A pdb=" N VAL C4914 " --> pdb=" O GLU C4910 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N VAL C4915 " --> pdb=" O LEU C4911 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ILE C4918 " --> pdb=" O VAL C4914 " (cutoff:3.500A) Processing helix chain 'C' and resid 4928 through 4953 removed outlier: 4.061A pdb=" N ILE C4932 " --> pdb=" O LEU C4928 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP C4938 " --> pdb=" O GLY C4934 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU C4943 " --> pdb=" O ALA C4939 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG C4944 " --> pdb=" O PHE C4940 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU C4952 " --> pdb=" O GLU C4948 " (cutoff:3.500A) Processing helix chain 'C' and resid 4964 through 4972 removed outlier: 3.863A pdb=" N PHE C4968 " --> pdb=" O GLY C4964 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N THR C4970 " --> pdb=" O ASP C4966 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N THR C4971 " --> pdb=" O TYR C4967 " (cutoff:3.500A) Proline residue: C4972 - end of helix Processing helix chain 'C' and resid 4973 through 4981 removed outlier: 3.976A pdb=" N LEU C4980 " --> pdb=" O GLU C4976 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLU C4981 " --> pdb=" O THR C4977 " (cutoff:3.500A) Processing helix chain 'C' and resid 4986 through 4999 removed outlier: 4.588A pdb=" N PHE C4990 " --> pdb=" O ALA C4986 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ASP C4999 " --> pdb=" O LEU C4995 " (cutoff:3.500A) Processing helix chain 'C' and resid 5004 through 5017 Processing helix chain 'C' and resid 5028 through 5033 removed outlier: 5.274A pdb=" N TYR C5032 " --> pdb=" O PHE C5028 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLU C5033 " --> pdb=" O ARG C5029 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 5028 through 5033' Processing helix chain 'C' and resid 956 through 961 removed outlier: 4.374A pdb=" N MET C 960 " --> pdb=" O LYS C 957 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N MET C 961 " --> pdb=" O THR C 958 " (cutoff:3.500A) Processing helix chain 'C' and resid 2285 through 2290 removed outlier: 4.386A pdb=" N LEU C2288 " --> pdb=" O GLU C2285 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA C2289 " --> pdb=" O LEU C2286 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N LEU C2290 " --> pdb=" O ALA C2287 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2285 through 2290' Processing helix chain 'C' and resid 4703 through 4708 removed outlier: 4.029A pdb=" N LEU C4706 " --> pdb=" O ARG C4703 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ASN C4707 " --> pdb=" O LEU C4704 " (cutoff:3.500A) Processing helix chain 'C' and resid 4709 through 4715 Proline residue: C4712 - end of helix Processing helix chain 'D' and resid 61 through 66 removed outlier: 4.642A pdb=" N CYS D 65 " --> pdb=" O ASP D 61 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N CYS D 66 " --> pdb=" O LEU D 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 61 through 66' Processing helix chain 'D' and resid 74 through 84 Processing helix chain 'D' and resid 250 through 256 removed outlier: 6.184A pdb=" N THR D 254 " --> pdb=" O GLY D 250 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N HIS D 255 " --> pdb=" O ALA D 251 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ALA D 256 " --> pdb=" O VAL D 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 250 through 256' Processing helix chain 'D' and resid 364 through 371 removed outlier: 3.957A pdb=" N VAL D 371 " --> pdb=" O LEU D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 425 removed outlier: 4.393A pdb=" N GLN D 413 " --> pdb=" O GLY D 409 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE D 414 " --> pdb=" O LEU D 410 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N PHE D 421 " --> pdb=" O GLY D 417 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLY D 423 " --> pdb=" O ASP D 419 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N LYS D 424 " --> pdb=" O SER D 420 " (cutoff:3.500A) Proline residue: D 425 - end of helix Processing helix chain 'D' and resid 437 through 453 removed outlier: 4.803A pdb=" N VAL D 441 " --> pdb=" O PRO D 437 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN D 446 " --> pdb=" O ILE D 442 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N PHE D 452 " --> pdb=" O LEU D 448 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N GLU D 453 " --> pdb=" O ILE D 449 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 481 removed outlier: 3.666A pdb=" N ARG D 469 " --> pdb=" O GLN D 465 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLU D 480 " --> pdb=" O SER D 476 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N GLU D 481 " --> pdb=" O LEU D 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 484 through 496 removed outlier: 3.948A pdb=" N CYS D 490 " --> pdb=" O LEU D 486 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N VAL D 496 " --> pdb=" O ASP D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 531 removed outlier: 5.212A pdb=" N SER D 514 " --> pdb=" O GLU D 510 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N TRP D 515 " --> pdb=" O ALA D 511 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N LYS D 516 " --> pdb=" O ALA D 512 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N GLU D 517 " --> pdb=" O GLU D 513 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ILE D 518 " --> pdb=" O SER D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 540 removed outlier: 4.645A pdb=" N CYS D 537 " --> pdb=" O ASN D 533 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU D 539 " --> pdb=" O ALA D 535 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N PHE D 540 " --> pdb=" O ASN D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 551 removed outlier: 4.634A pdb=" N ASP D 545 " --> pdb=" O SER D 541 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N TRP D 546 " --> pdb=" O THR D 542 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL D 548 " --> pdb=" O LEU D 544 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LEU D 551 " --> pdb=" O VAL D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 571 removed outlier: 4.103A pdb=" N LEU D 561 " --> pdb=" O SER D 557 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N GLU D 562 " --> pdb=" O SER D 558 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N VAL D 563 " --> pdb=" O GLY D 559 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 578 removed outlier: 4.345A pdb=" N ILE D 577 " --> pdb=" O GLU D 573 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ILE D 578 " --> pdb=" O VAL D 574 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 573 through 578' Processing helix chain 'D' and resid 579 through 594 removed outlier: 6.091A pdb=" N ILE D 583 " --> pdb=" O GLN D 579 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU D 590 " --> pdb=" O ILE D 586 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASP D 591 " --> pdb=" O ILE D 587 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 609 removed outlier: 4.224A pdb=" N VAL D 602 " --> pdb=" O LYS D 598 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LEU D 603 " --> pdb=" O VAL D 599 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N CYS D 607 " --> pdb=" O LEU D 603 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N VAL D 608 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N CYS D 609 " --> pdb=" O SER D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 626 removed outlier: 4.328A pdb=" N GLN D 618 " --> pdb=" O VAL D 614 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR D 622 " --> pdb=" O GLN D 618 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N LEU D 626 " --> pdb=" O THR D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 890 removed outlier: 4.745A pdb=" N ARG D 869 " --> pdb=" O PRO D 865 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ILE D 870 " --> pdb=" O HIS D 866 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU D 876 " --> pdb=" O GLU D 872 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN D 877 " --> pdb=" O LYS D 873 " (cutoff:3.500A) Processing helix chain 'D' and resid 914 through 936 removed outlier: 4.022A pdb=" N TYR D 920 " --> pdb=" O PRO D 916 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N GLY D 936 " --> pdb=" O LEU D 932 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 950 removed outlier: 4.510A pdb=" N ASN D 949 " --> pdb=" O LYS D 945 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU D 950 " --> pdb=" O ALA D 946 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 945 through 950' Processing helix chain 'D' and resid 983 through 1002 removed outlier: 5.244A pdb=" N ARG D 987 " --> pdb=" O THR D 983 " (cutoff:3.500A) Processing helix chain 'D' and resid 1029 through 1050 removed outlier: 5.535A pdb=" N ARG D1033 " --> pdb=" O GLU D1029 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N SER D1034 " --> pdb=" O ALA D1030 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER D1038 " --> pdb=" O SER D1034 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LEU D1039 " --> pdb=" O ASN D1035 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N CYS D1040 " --> pdb=" O ARG D1036 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLN D1041 " --> pdb=" O ASP D1037 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA D1042 " --> pdb=" O SER D1038 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY D1050 " --> pdb=" O LEU D1046 " (cutoff:3.500A) Processing helix chain 'D' and resid 1574 through 1581 Processing helix chain 'D' and resid 1649 through 1657 removed outlier: 4.069A pdb=" N LEU D1653 " --> pdb=" O ASP D1649 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N SER D1654 " --> pdb=" O ILE D1650 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N GLU D1655 " --> pdb=" O LEU D1651 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ARG D1656 " --> pdb=" O GLU D1652 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LEU D1657 " --> pdb=" O LEU D1653 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1649 through 1657' Processing helix chain 'D' and resid 1658 through 1675 Processing helix chain 'D' and resid 1679 through 1690 removed outlier: 3.907A pdb=" N ALA D1684 " --> pdb=" O ARG D1680 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER D1687 " --> pdb=" O HIS D1683 " (cutoff:3.500A) Processing helix chain 'D' and resid 1692 through 1701 removed outlier: 4.484A pdb=" N GLU D1699 " --> pdb=" O LEU D1695 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ASP D1700 " --> pdb=" O HIS D1696 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N ALA D1701 " --> pdb=" O ALA D1697 " (cutoff:3.500A) Processing helix chain 'D' and resid 1704 through 1720 removed outlier: 7.151A pdb=" N ARG D1708 " --> pdb=" O PRO D1704 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA D1709 " --> pdb=" O GLY D1705 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE D1718 " --> pdb=" O LEU D1714 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N HIS D1719 " --> pdb=" O LEU D1715 " (cutoff:3.500A) Processing helix chain 'D' and resid 1723 through 1731 removed outlier: 4.161A pdb=" N SER D1729 " --> pdb=" O ARG D1725 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N MET D1730 " --> pdb=" O SER D1726 " (cutoff:3.500A) Processing helix chain 'D' and resid 1739 through 1745 removed outlier: 3.624A pdb=" N ARG D1743 " --> pdb=" O THR D1739 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ALA D1744 " --> pdb=" O PRO D1740 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N ILE D1745 " --> pdb=" O GLU D1741 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1739 through 1745' Processing helix chain 'D' and resid 1754 through 1759 removed outlier: 4.356A pdb=" N ARG D1758 " --> pdb=" O GLY D1754 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ARG D1759 " --> pdb=" O GLY D1755 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1754 through 1759' Processing helix chain 'D' and resid 1803 through 1825 removed outlier: 3.707A pdb=" N ASP D1809 " --> pdb=" O GLU D1805 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN D1824 " --> pdb=" O ARG D1820 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N HIS D1825 " --> pdb=" O ASP D1821 " (cutoff:3.500A) Processing helix chain 'D' and resid 1833 through 1852 removed outlier: 4.023A pdb=" N GLN D1837 " --> pdb=" O SER D1833 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N PHE D1838 " --> pdb=" O VAL D1834 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N VAL D1839 " --> pdb=" O GLU D1835 " (cutoff:3.500A) Proline residue: D1840 - end of helix removed outlier: 4.662A pdb=" N LYS D1843 " --> pdb=" O VAL D1839 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL D1845 " --> pdb=" O VAL D1841 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N MET D1851 " --> pdb=" O THR D1847 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLY D1852 " --> pdb=" O LEU D1848 " (cutoff:3.500A) Processing helix chain 'D' and resid 1855 through 1865 removed outlier: 4.707A pdb=" N VAL D1859 " --> pdb=" O GLY D1855 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N MET D1865 " --> pdb=" O GLN D1861 " (cutoff:3.500A) Processing helix chain 'D' and resid 1866 through 1871 Processing helix chain 'D' and resid 1925 through 1930 removed outlier: 4.561A pdb=" N MET D1929 " --> pdb=" O GLY D1925 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N LYS D1930 " --> pdb=" O LEU D1926 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1925 through 1930' Processing helix chain 'D' and resid 1934 through 1984 removed outlier: 3.618A pdb=" N TYR D1945 " --> pdb=" O ASN D1941 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE D1946 " --> pdb=" O LEU D1942 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG D1964 " --> pdb=" O ALA D1960 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR D1965 " --> pdb=" O PHE D1961 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N PHE D1984 " --> pdb=" O LEU D1980 " (cutoff:3.500A) Processing helix chain 'D' and resid 1989 through 1997 removed outlier: 4.453A pdb=" N ARG D1993 " --> pdb=" O ALA D1989 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N GLU D1997 " --> pdb=" O ARG D1993 " (cutoff:3.500A) Processing helix chain 'D' and resid 2001 through 2013 removed outlier: 3.795A pdb=" N GLN D2005 " --> pdb=" O PRO D2001 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N ASN D2007 " --> pdb=" O GLN D2003 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N MET D2008 " --> pdb=" O GLU D2004 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LEU D2009 " --> pdb=" O GLN D2005 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N LEU D2010 " --> pdb=" O ILE D2006 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N HIS D2011 " --> pdb=" O ASN D2007 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N PHE D2012 " --> pdb=" O MET D2008 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LYS D2013 " --> pdb=" O LEU D2009 " (cutoff:3.500A) Processing helix chain 'D' and resid 2024 through 2043 removed outlier: 4.807A pdb=" N ARG D2028 " --> pdb=" O PRO D2024 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N GLN D2029 " --> pdb=" O GLU D2025 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ASP D2030 " --> pdb=" O ASP D2026 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU D2031 " --> pdb=" O ILE D2027 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN D2032 " --> pdb=" O ARG D2028 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N GLY D2043 " --> pdb=" O LEU D2039 " (cutoff:3.500A) Processing helix chain 'D' and resid 2093 through 2108 removed outlier: 3.841A pdb=" N TRP D2105 " --> pdb=" O MET D2101 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ALA D2106 " --> pdb=" O VAL D2102 " (cutoff:3.500A) Processing helix chain 'D' and resid 2113 through 2130 removed outlier: 4.420A pdb=" N GLY D2130 " --> pdb=" O ARG D2126 " (cutoff:3.500A) Processing helix chain 'D' and resid 2131 through 2141 Proline residue: D2139 - end of helix Processing helix chain 'D' and resid 2148 through 2168 removed outlier: 4.284A pdb=" N SER D2154 " --> pdb=" O GLU D2150 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU D2155 " --> pdb=" O ASP D2151 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE D2167 " --> pdb=" O ARG D2163 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N VAL D2168 " --> pdb=" O SER D2164 " (cutoff:3.500A) Processing helix chain 'D' and resid 2171 through 2188 removed outlier: 4.438A pdb=" N LEU D2177 " --> pdb=" O GLN D2173 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE D2179 " --> pdb=" O GLU D2175 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLN D2180 " --> pdb=" O ASN D2176 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE D2185 " --> pdb=" O SER D2181 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N MET D2186 " --> pdb=" O ILE D2182 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ASN D2187 " --> pdb=" O GLY D2183 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ASN D2188 " --> pdb=" O ASN D2184 " (cutoff:3.500A) Processing helix chain 'D' and resid 2189 through 2195 removed outlier: 4.618A pdb=" N GLN D2193 " --> pdb=" O LYS D2189 " (cutoff:3.500A) Proline residue: D2195 - end of helix Processing helix chain 'D' and resid 2196 through 2202 removed outlier: 4.117A pdb=" N ALA D2200 " --> pdb=" O ASN D2196 " (cutoff:3.500A) Processing helix chain 'D' and resid 2203 through 2216 removed outlier: 3.645A pdb=" N VAL D2210 " --> pdb=" O THR D2206 " (cutoff:3.500A) Processing helix chain 'D' and resid 2227 through 2244 removed outlier: 3.751A pdb=" N SER D2243 " --> pdb=" O PHE D2239 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ARG D2244 " --> pdb=" O CYS D2240 " (cutoff:3.500A) Processing helix chain 'D' and resid 2245 through 2252 removed outlier: 4.848A pdb=" N ASP D2252 " --> pdb=" O ARG D2248 " (cutoff:3.500A) Processing helix chain 'D' and resid 2253 through 2265 removed outlier: 3.698A pdb=" N ASN D2260 " --> pdb=" O TYR D2256 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY D2262 " --> pdb=" O LEU D2258 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ILE D2263 " --> pdb=" O GLU D2259 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N LEU D2265 " --> pdb=" O SER D2261 " (cutoff:3.500A) Processing helix chain 'D' and resid 2271 through 2280 removed outlier: 3.641A pdb=" N VAL D2275 " --> pdb=" O THR D2271 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N VAL D2280 " --> pdb=" O ALA D2276 " (cutoff:3.500A) Processing helix chain 'D' and resid 2294 through 2309 removed outlier: 3.828A pdb=" N VAL D2299 " --> pdb=" O LEU D2295 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU D2302 " --> pdb=" O VAL D2298 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N SER D2309 " --> pdb=" O CYS D2305 " (cutoff:3.500A) Processing helix chain 'D' and resid 2310 through 2315 removed outlier: 3.882A pdb=" N ALA D2315 " --> pdb=" O PRO D2311 " (cutoff:3.500A) Processing helix chain 'D' and resid 2324 through 2341 removed outlier: 4.770A pdb=" N LEU D2332 " --> pdb=" O GLY D2328 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N ASP D2333 " --> pdb=" O GLU D2329 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N PHE D2334 " --> pdb=" O ARG D2330 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU D2335 " --> pdb=" O TYR D2331 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA D2338 " --> pdb=" O PHE D2334 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N VAL D2339 " --> pdb=" O LEU D2335 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N PHE D2340 " --> pdb=" O ARG D2336 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N VAL D2341 " --> pdb=" O PHE D2337 " (cutoff:3.500A) Processing helix chain 'D' and resid 2346 through 2360 removed outlier: 4.159A pdb=" N ALA D2350 " --> pdb=" O VAL D2346 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE D2358 " --> pdb=" O VAL D2354 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ARG D2359 " --> pdb=" O ARG D2355 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LYS D2360 " --> pdb=" O LEU D2356 " (cutoff:3.500A) Processing helix chain 'D' and resid 2365 through 2371 removed outlier: 5.439A pdb=" N GLU D2371 " --> pdb=" O ALA D2367 " (cutoff:3.500A) Processing helix chain 'D' and resid 2375 through 2390 Proline residue: D2390 - end of helix Processing helix chain 'D' and resid 2417 through 2437 removed outlier: 4.173A pdb=" N ALA D2437 " --> pdb=" O LEU D2433 " (cutoff:3.500A) Processing helix chain 'D' and resid 2440 through 2448 removed outlier: 4.654A pdb=" N GLY D2448 " --> pdb=" O GLN D2444 " (cutoff:3.500A) Processing helix chain 'D' and resid 2449 through 2462 removed outlier: 3.771A pdb=" N ILE D2453 " --> pdb=" O GLU D2449 " (cutoff:3.500A) Proline residue: D2462 - end of helix Processing helix chain 'D' and resid 2464 through 2472 removed outlier: 5.215A pdb=" N GLY D2468 " --> pdb=" O ASP D2464 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE D2469 " --> pdb=" O ASP D2465 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU D2472 " --> pdb=" O GLY D2468 " (cutoff:3.500A) Processing helix chain 'D' and resid 2751 through 2772 removed outlier: 5.084A pdb=" N ILE D2755 " --> pdb=" O LEU D2751 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ASN D2756 " --> pdb=" O ASP D2752 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N PHE D2758 " --> pdb=" O PHE D2754 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N ALA D2759 " --> pdb=" O ILE D2755 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N GLU D2760 " --> pdb=" O ASN D2756 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TYR D2761 " --> pdb=" O LYS D2757 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N THR D2762 " --> pdb=" O PHE D2758 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N HIS D2763 " --> pdb=" O ALA D2759 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N GLU D2764 " --> pdb=" O GLU D2760 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS D2765 " --> pdb=" O TYR D2761 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA D2767 " --> pdb=" O HIS D2763 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N PHE D2768 " --> pdb=" O GLU D2764 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N GLN D2772 " --> pdb=" O PHE D2768 " (cutoff:3.500A) Processing helix chain 'D' and resid 2809 through 2816 removed outlier: 4.803A pdb=" N LYS D2814 " --> pdb=" O LYS D2810 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ALA D2815 " --> pdb=" O GLU D2811 " (cutoff:3.500A) Processing helix chain 'D' and resid 2870 through 2896 removed outlier: 4.074A pdb=" N GLU D2876 " --> pdb=" O GLN D2872 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA D2879 " --> pdb=" O ALA D2875 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N GLU D2880 " --> pdb=" O GLU D2876 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASN D2881 " --> pdb=" O GLN D2877 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N TYR D2882 " --> pdb=" O LEU D2878 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N HIS D2883 " --> pdb=" O ALA D2879 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ASN D2884 " --> pdb=" O GLU D2880 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N THR D2885 " --> pdb=" O ASN D2881 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLY D2887 " --> pdb=" O HIS D2883 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ARG D2888 " --> pdb=" O ASN D2884 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS D2889 " --> pdb=" O THR D2885 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N LYS D2890 " --> pdb=" O TRP D2886 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU D2895 " --> pdb=" O LYS D2891 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA D2896 " --> pdb=" O GLN D2892 " (cutoff:3.500A) Processing helix chain 'D' and resid 2919 through 2932 removed outlier: 6.117A pdb=" N ALA D2923 " --> pdb=" O ASP D2919 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLN D2924 " --> pdb=" O ARG D2920 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU D2927 " --> pdb=" O ALA D2923 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS D2928 " --> pdb=" O GLN D2924 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N PHE D2929 " --> pdb=" O GLU D2925 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N LEU D2930 " --> pdb=" O LEU D2926 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLN D2931 " --> pdb=" O LEU D2927 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N MET D2932 " --> pdb=" O LYS D2928 " (cutoff:3.500A) Processing helix chain 'D' and resid 3645 through 3656 removed outlier: 4.006A pdb=" N ASN D3651 " --> pdb=" O HIS D3647 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N MET D3652 " --> pdb=" O ARG D3648 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N PHE D3653 " --> pdb=" O ALA D3649 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N LEU D3654 " --> pdb=" O CYS D3650 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N GLU D3655 " --> pdb=" O ASN D3651 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N SER D3656 " --> pdb=" O MET D3652 " (cutoff:3.500A) Processing helix chain 'D' and resid 3669 through 3681 removed outlier: 4.118A pdb=" N MET D3673 " --> pdb=" O PHE D3669 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE D3674 " --> pdb=" O GLU D3670 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLY D3681 " --> pdb=" O LEU D3677 " (cutoff:3.500A) Processing helix chain 'D' and resid 3683 through 3688 removed outlier: 4.160A pdb=" N GLU D3688 " --> pdb=" O GLU D3684 " (cutoff:3.500A) Processing helix chain 'D' and resid 3696 through 3711 removed outlier: 4.170A pdb=" N THR D3711 " --> pdb=" O ARG D3707 " (cutoff:3.500A) Processing helix chain 'D' and resid 3719 through 3738 removed outlier: 4.007A pdb=" N ASP D3727 " --> pdb=" O MET D3723 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ILE D3728 " --> pdb=" O ALA D3724 " (cutoff:3.500A) Processing helix chain 'D' and resid 3754 through 3770 removed outlier: 5.089A pdb=" N MET D3758 " --> pdb=" O GLU D3754 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLU D3759 " --> pdb=" O GLU D3755 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS D3760 " --> pdb=" O LYS D3756 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ARG D3762 " --> pdb=" O MET D3758 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU D3770 " --> pdb=" O GLN D3766 " (cutoff:3.500A) Processing helix chain 'D' and resid 3771 through 3785 removed outlier: 4.130A pdb=" N GLU D3777 " --> pdb=" O ARG D3773 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL D3779 " --> pdb=" O ALA D3775 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N LEU D3780 " --> pdb=" O ALA D3776 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLN D3781 " --> pdb=" O GLU D3777 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ALA D3785 " --> pdb=" O GLN D3781 " (cutoff:3.500A) Processing helix chain 'D' and resid 3791 through 3806 removed outlier: 3.540A pdb=" N LEU D3805 " --> pdb=" O GLY D3801 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ASN D3806 " --> pdb=" O ILE D3802 " (cutoff:3.500A) Processing helix chain 'D' and resid 3809 through 3824 removed outlier: 4.046A pdb=" N LYS D3824 " --> pdb=" O LEU D3820 " (cutoff:3.500A) Processing helix chain 'D' and resid 3827 through 3839 removed outlier: 4.684A pdb=" N CYS D3839 " --> pdb=" O LEU D3835 " (cutoff:3.500A) Processing helix chain 'D' and resid 3843 through 3857 Processing helix chain 'D' and resid 3861 through 3866 removed outlier: 6.924A pdb=" N VAL D3865 " --> pdb=" O GLU D3861 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE D3866 " --> pdb=" O ASP D3862 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 3861 through 3866' Processing helix chain 'D' and resid 3877 through 3894 removed outlier: 4.256A pdb=" N GLY D3894 " --> pdb=" O LEU D3890 " (cutoff:3.500A) Processing helix chain 'D' and resid 3897 through 3906 removed outlier: 5.879A pdb=" N ASN D3901 " --> pdb=" O ASN D3897 " (cutoff:3.500A) Processing helix chain 'D' and resid 3914 through 3939 removed outlier: 3.771A pdb=" N CYS D3918 " --> pdb=" O ASN D3914 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N GLY D3939 " --> pdb=" O TRP D3935 " (cutoff:3.500A) Processing helix chain 'D' and resid 3944 through 3970 removed outlier: 3.924A pdb=" N GLU D3967 " --> pdb=" O ASN D3963 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N TYR D3968 " --> pdb=" O SER D3964 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE D3969 " --> pdb=" O LEU D3965 " (cutoff:3.500A) Processing helix chain 'D' and resid 3973 through 3984 removed outlier: 4.284A pdb=" N GLN D3977 " --> pdb=" O CYS D3973 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLN D3978 " --> pdb=" O THR D3974 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N ARG D3984 " --> pdb=" O LEU D3980 " (cutoff:3.500A) Processing helix chain 'D' and resid 3985 through 4005 removed outlier: 3.664A pdb=" N HIS D3998 " --> pdb=" O HIS D3994 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N MET D4000 " --> pdb=" O PHE D3996 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N MET D4001 " --> pdb=" O ALA D3997 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ALA D4004 " --> pdb=" O MET D4000 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N GLN D4005 " --> pdb=" O MET D4001 " (cutoff:3.500A) Processing helix chain 'D' and resid 4009 through 4032 removed outlier: 4.950A pdb=" N LEU D4019 " --> pdb=" O GLU D4015 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N GLN D4020 " --> pdb=" O LEU D4016 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LYS D4021 " --> pdb=" O LEU D4017 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ASP D4022 " --> pdb=" O ASP D4018 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU D4031 " --> pdb=" O LEU D4027 " (cutoff:3.500A) Processing helix chain 'D' and resid 4039 through 4056 removed outlier: 5.925A pdb=" N GLN D4043 " --> pdb=" O MET D4039 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU D4048 " --> pdb=" O MET D4044 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N SER D4053 " --> pdb=" O VAL D4049 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ASN D4054 " --> pdb=" O GLU D4050 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL D4055 " --> pdb=" O SER D4051 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLU D4056 " --> pdb=" O SER D4052 " (cutoff:3.500A) Processing helix chain 'D' and resid 4057 through 4074 removed outlier: 5.377A pdb=" N LEU D4066 " --> pdb=" O PHE D4062 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LYS D4067 " --> pdb=" O ASP D4063 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N LYS D4069 " --> pdb=" O PHE D4065 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N ASP D4070 " --> pdb=" O LEU D4066 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N ILE D4071 " --> pdb=" O LYS D4067 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N VAL D4072 " --> pdb=" O LEU D4068 " (cutoff:3.500A) Processing helix chain 'D' and resid 4075 through 4081 removed outlier: 3.805A pdb=" N ASP D4079 " --> pdb=" O GLU D4075 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N TYR D4080 " --> pdb=" O ALA D4076 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N VAL D4081 " --> pdb=" O PHE D4077 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 4075 through 4081' Processing helix chain 'D' and resid 4089 through 4101 removed outlier: 5.227A pdb=" N LYS D4101 " --> pdb=" O MET D4097 " (cutoff:3.500A) Processing helix chain 'D' and resid 4106 through 4116 removed outlier: 3.760A pdb=" N PHE D4110 " --> pdb=" O PRO D4106 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N GLU D4116 " --> pdb=" O LEU D4112 " (cutoff:3.500A) Processing helix chain 'D' and resid 4124 through 4137 removed outlier: 3.896A pdb=" N PHE D4132 " --> pdb=" O PHE D4128 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN D4133 " --> pdb=" O ALA D4129 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N GLU D4134 " --> pdb=" O ASN D4130 " (cutoff:3.500A) Proline residue: D4135 - end of helix Processing helix chain 'D' and resid 4138 through 4155 Proline residue: D4155 - end of helix Processing helix chain 'D' and resid 4157 through 4168 removed outlier: 4.561A pdb=" N GLU D4165 " --> pdb=" O ARG D4161 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N LEU D4166 " --> pdb=" O ASN D4162 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ALA D4167 " --> pdb=" O PHE D4163 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N GLU D4168 " --> pdb=" O LEU D4164 " (cutoff:3.500A) Processing helix chain 'D' and resid 4169 through 4175 removed outlier: 3.824A pdb=" N ARG D4175 " --> pdb=" O LEU D4171 " (cutoff:3.500A) Processing helix chain 'D' and resid 4198 through 4207 removed outlier: 3.811A pdb=" N GLU D4206 " --> pdb=" O ARG D4202 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N MET D4207 " --> pdb=" O ALA D4203 " (cutoff:3.500A) Processing helix chain 'D' and resid 4208 through 4225 removed outlier: 4.619A pdb=" N SER D4213 " --> pdb=" O GLN D4209 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LYS D4214 " --> pdb=" O VAL D4210 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP D4220 " --> pdb=" O GLN D4216 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLU D4224 " --> pdb=" O ASP D4220 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLY D4225 " --> pdb=" O VAL D4221 " (cutoff:3.500A) Processing helix chain 'D' and resid 4227 through 4252 removed outlier: 4.433A pdb=" N MET D4231 " --> pdb=" O GLU D4227 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLU D4232 " --> pdb=" O ALA D4228 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA D4249 " --> pdb=" O MET D4245 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLN D4250 " --> pdb=" O GLN D4246 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ILE D4251 " --> pdb=" O ILE D4247 " (cutoff:3.500A) Processing helix chain 'D' and resid 4541 through 4556 removed outlier: 5.069A pdb=" N GLU D4545 " --> pdb=" O TRP D4541 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N VAL D4546 " --> pdb=" O GLY D4542 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N TYR D4554 " --> pdb=" O LYS D4550 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU D4555 " --> pdb=" O PHE D4551 " (cutoff:3.500A) Processing helix chain 'D' and resid 4558 through 4578 removed outlier: 4.072A pdb=" N LEU D4562 " --> pdb=" O ASN D4558 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N PHE D4571 " --> pdb=" O LEU D4567 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ALA D4572 " --> pdb=" O PHE D4568 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE D4573 " --> pdb=" O LEU D4569 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASN D4574 " --> pdb=" O ALA D4570 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU D4577 " --> pdb=" O ILE D4573 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N LEU D4578 " --> pdb=" O ASN D4574 " (cutoff:3.500A) Processing helix chain 'D' and resid 4643 through 4684 removed outlier: 4.461A pdb=" N SER D4647 " --> pdb=" O LEU D4643 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LEU D4648 " --> pdb=" O TRP D4644 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N LEU D4649 " --> pdb=" O CYS D4645 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N HIS D4650 " --> pdb=" O LEU D4646 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N THR D4651 " --> pdb=" O SER D4647 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU D4652 " --> pdb=" O LEU D4648 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LYS D4665 " --> pdb=" O TYR D4661 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N VAL D4666 " --> pdb=" O ASN D4662 " (cutoff:3.500A) Proline residue: D4667 - end of helix removed outlier: 4.798A pdb=" N GLU D4676 " --> pdb=" O LYS D4672 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LEU D4677 " --> pdb=" O ARG D4673 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA D4678 " --> pdb=" O GLU D4674 " (cutoff:3.500A) Processing helix chain 'D' and resid 4685 through 4690 removed outlier: 5.305A pdb=" N THR D4689 " --> pdb=" O GLY D4685 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N GLU D4690 " --> pdb=" O LEU D4686 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 4685 through 4690' Processing helix chain 'D' and resid 4696 through 4701 Processing helix chain 'D' and resid 4719 through 4733 removed outlier: 3.529A pdb=" N LYS D4723 " --> pdb=" O PHE D4719 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU D4725 " --> pdb=" O LYS D4721 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ASP D4726 " --> pdb=" O ARG D4722 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N LYS D4727 " --> pdb=" O LYS D4723 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N HIS D4728 " --> pdb=" O VAL D4724 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ASP D4730 " --> pdb=" O ASP D4726 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ILE D4731 " --> pdb=" O LYS D4727 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N PHE D4732 " --> pdb=" O HIS D4728 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLY D4733 " --> pdb=" O GLY D4729 " (cutoff:3.500A) Processing helix chain 'D' and resid 4734 through 4742 removed outlier: 4.370A pdb=" N LEU D4740 " --> pdb=" O ARG D4736 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LEU D4741 " --> pdb=" O ILE D4737 " (cutoff:3.500A) Processing helix chain 'D' and resid 4745 through 4753 removed outlier: 4.319A pdb=" N THR D4751 " --> pdb=" O SER D4747 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA D4752 " --> pdb=" O LEU D4748 " (cutoff:3.500A) Processing helix chain 'D' and resid 4765 through 4771 removed outlier: 5.454A pdb=" N MET D4769 " --> pdb=" O LEU D4765 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N SER D4770 " --> pdb=" O THR D4766 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ILE D4771 " --> pdb=" O TRP D4767 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 4765 through 4771' Processing helix chain 'D' and resid 4772 through 4786 removed outlier: 3.608A pdb=" N VAL D4782 " --> pdb=" O TRP D4778 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE D4783 " --> pdb=" O LYS D4779 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N PHE D4784 " --> pdb=" O PHE D4780 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N THR D4785 " --> pdb=" O GLY D4781 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASP D4786 " --> pdb=" O VAL D4782 " (cutoff:3.500A) Processing helix chain 'D' and resid 4787 through 4804 removed outlier: 4.756A pdb=" N TYR D4804 " --> pdb=" O LEU D4800 " (cutoff:3.500A) Processing helix chain 'D' and resid 4809 through 4819 removed outlier: 4.803A pdb=" N LEU D4813 " --> pdb=" O PHE D4809 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LEU D4814 " --> pdb=" O ALA D4810 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N GLY D4819 " --> pdb=" O ASP D4815 " (cutoff:3.500A) Processing helix chain 'D' and resid 4820 through 4827 removed outlier: 4.320A pdb=" N ILE D4826 " --> pdb=" O THR D4822 " (cutoff:3.500A) Processing helix chain 'D' and resid 4828 through 4834 removed outlier: 4.104A pdb=" N HIS D4832 " --> pdb=" O SER D4828 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASN D4833 " --> pdb=" O SER D4829 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLY D4834 " --> pdb=" O VAL D4830 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 4828 through 4834' Processing helix chain 'D' and resid 4835 through 4859 removed outlier: 4.548A pdb=" N MET D4839 " --> pdb=" O LYS D4835 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N THR D4840 " --> pdb=" O GLN D4836 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLY D4842 " --> pdb=" O VAL D4838 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N LEU D4843 " --> pdb=" O MET D4839 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU D4844 " --> pdb=" O THR D4840 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN D4857 " --> pdb=" O VAL D4853 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE D4858 " --> pdb=" O VAL D4854 " (cutoff:3.500A) Processing helix chain 'D' and resid 4878 through 4893 removed outlier: 4.687A pdb=" N VAL D4891 " --> pdb=" O MET D4887 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ARG D4892 " --> pdb=" O TYR D4888 " (cutoff:3.500A) Processing helix chain 'D' and resid 4897 through 4902 removed outlier: 5.105A pdb=" N GLU D4902 " --> pdb=" O GLY D4898 " (cutoff:3.500A) Processing helix chain 'D' and resid 4909 through 4925 removed outlier: 3.621A pdb=" N VAL D4914 " --> pdb=" O GLU D4910 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N VAL D4915 " --> pdb=" O LEU D4911 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ILE D4918 " --> pdb=" O VAL D4914 " (cutoff:3.500A) Processing helix chain 'D' and resid 4928 through 4953 removed outlier: 4.061A pdb=" N ILE D4932 " --> pdb=" O LEU D4928 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP D4938 " --> pdb=" O GLY D4934 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU D4943 " --> pdb=" O ALA D4939 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG D4944 " --> pdb=" O PHE D4940 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU D4952 " --> pdb=" O GLU D4948 " (cutoff:3.500A) Processing helix chain 'D' and resid 4964 through 4972 removed outlier: 3.862A pdb=" N PHE D4968 " --> pdb=" O GLY D4964 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N THR D4970 " --> pdb=" O ASP D4966 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N THR D4971 " --> pdb=" O TYR D4967 " (cutoff:3.500A) Proline residue: D4972 - end of helix Processing helix chain 'D' and resid 4973 through 4981 removed outlier: 3.976A pdb=" N LEU D4980 " --> pdb=" O GLU D4976 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLU D4981 " --> pdb=" O THR D4977 " (cutoff:3.500A) Processing helix chain 'D' and resid 4986 through 4999 removed outlier: 4.588A pdb=" N PHE D4990 " --> pdb=" O ALA D4986 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ASP D4999 " --> pdb=" O LEU D4995 " (cutoff:3.500A) Processing helix chain 'D' and resid 5004 through 5017 Processing helix chain 'D' and resid 5028 through 5033 removed outlier: 5.273A pdb=" N TYR D5032 " --> pdb=" O PHE D5028 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLU D5033 " --> pdb=" O ARG D5029 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 5028 through 5033' Processing helix chain 'D' and resid 956 through 961 removed outlier: 4.374A pdb=" N MET D 960 " --> pdb=" O LYS D 957 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N MET D 961 " --> pdb=" O THR D 958 " (cutoff:3.500A) Processing helix chain 'D' and resid 2285 through 2290 removed outlier: 4.386A pdb=" N LEU D2288 " --> pdb=" O GLU D2285 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA D2289 " --> pdb=" O LEU D2286 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N LEU D2290 " --> pdb=" O ALA D2287 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2285 through 2290' Processing helix chain 'D' and resid 4703 through 4708 removed outlier: 4.030A pdb=" N LEU D4706 " --> pdb=" O ARG D4703 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ASN D4707 " --> pdb=" O LEU D4704 " (cutoff:3.500A) Processing helix chain 'D' and resid 4709 through 4715 Proline residue: D4712 - end of helix Processing sheet with id= 1, first strand: chain 'A' and resid 47 through 52 removed outlier: 6.550A pdb=" N LYS A 34 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LEU A 37 " --> pdb=" O LEU A 22 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU A 22 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 12.077A pdb=" N ALA A 39 " --> pdb=" O VAL A 20 " (cutoff:3.500A) removed outlier: 14.947A pdb=" N VAL A 20 " --> pdb=" O ALA A 39 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 105 through 108 removed outlier: 4.622A pdb=" N HIS A 105 " --> pdb=" O MET A 150 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 116 through 120 removed outlier: 3.678A pdb=" N SER A 119 " --> pdb=" O GLY A 136 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'A' and resid 260 through 264 Processing sheet with id= 5, first strand: chain 'A' and resid 314 through 317 removed outlier: 3.881A pdb=" N PHE A 347 " --> pdb=" O ARG A 317 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'A' and resid 355 through 359 removed outlier: 3.684A pdb=" N TRP A 356 " --> pdb=" O HIS A 379 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N THR A 358 " --> pdb=" O ILE A 377 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ILE A 377 " --> pdb=" O THR A 358 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'A' and resid 682 through 686 Processing sheet with id= 8, first strand: chain 'A' and resid 753 through 759 removed outlier: 8.213A pdb=" N GLY A 660 " --> pdb=" O LEU A 750 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N GLU A 665 " --> pdb=" O LEU A 792 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU A 792 " --> pdb=" O GLU A 665 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N LYS A 788 " --> pdb=" O ASP A 669 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'A' and resid 829 through 833 removed outlier: 4.595A pdb=" N TYR A 829 " --> pdb=" O VAL A 840 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N LEU A1202 " --> pdb=" O PRO A 837 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N GLN A1198 " --> pdb=" O GLY A 841 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N SER A 843 " --> pdb=" O PRO A1196 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'A' and resid 1134 through 1137 removed outlier: 3.583A pdb=" N GLN A1130 " --> pdb=" O ASN A1125 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL A1123 " --> pdb=" O TRP A1132 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE A1124 " --> pdb=" O VAL A1102 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL A1102 " --> pdb=" O PHE A1124 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N MET A1100 " --> pdb=" O GLY A1126 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N GLU A1099 " --> pdb=" O GLY A1195 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA A1077 " --> pdb=" O PRO A1190 " (cutoff:3.500A) removed outlier: 9.788A pdb=" N VAL A1072 " --> pdb=" O SER A1241 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N SER A1241 " --> pdb=" O VAL A1072 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ILE A1074 " --> pdb=" O SER A1239 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'A' and resid 1255 through 1264 removed outlier: 7.924A pdb=" N TYR A1255 " --> pdb=" O HIS A1274 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N HIS A1274 " --> pdb=" O TYR A1255 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL A1257 " --> pdb=" O LEU A1272 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N LEU A1272 " --> pdb=" O VAL A1257 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N ARG A1259 " --> pdb=" O LEU A1270 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N LEU A1270 " --> pdb=" O ARG A1259 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N ASP A1261 " --> pdb=" O PRO A1268 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR A1266 " --> pdb=" O THR A1263 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'A' and resid 4579 through 4584 removed outlier: 5.663A pdb=" N PHE A4579 " --> pdb=" O LEU A4632 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A4632 " --> pdb=" O PHE A4579 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.550A pdb=" N LYS B 34 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LEU B 37 " --> pdb=" O LEU B 22 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU B 22 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 12.077A pdb=" N ALA B 39 " --> pdb=" O VAL B 20 " (cutoff:3.500A) removed outlier: 14.947A pdb=" N VAL B 20 " --> pdb=" O ALA B 39 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'B' and resid 105 through 108 removed outlier: 4.622A pdb=" N HIS B 105 " --> pdb=" O MET B 150 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'B' and resid 116 through 120 removed outlier: 3.678A pdb=" N SER B 119 " --> pdb=" O GLY B 136 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'B' and resid 260 through 264 Processing sheet with id= 17, first strand: chain 'B' and resid 314 through 317 removed outlier: 3.881A pdb=" N PHE B 347 " --> pdb=" O ARG B 317 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'B' and resid 355 through 359 removed outlier: 3.685A pdb=" N TRP B 356 " --> pdb=" O HIS B 379 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N THR B 358 " --> pdb=" O ILE B 377 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ILE B 377 " --> pdb=" O THR B 358 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'B' and resid 682 through 686 Processing sheet with id= 20, first strand: chain 'B' and resid 753 through 759 removed outlier: 8.213A pdb=" N GLY B 660 " --> pdb=" O LEU B 750 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N GLU B 665 " --> pdb=" O LEU B 792 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU B 792 " --> pdb=" O GLU B 665 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N LYS B 788 " --> pdb=" O ASP B 669 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'B' and resid 829 through 833 removed outlier: 4.596A pdb=" N TYR B 829 " --> pdb=" O VAL B 840 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N LEU B1202 " --> pdb=" O PRO B 837 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N GLN B1198 " --> pdb=" O GLY B 841 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N SER B 843 " --> pdb=" O PRO B1196 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'B' and resid 1134 through 1137 removed outlier: 3.583A pdb=" N GLN B1130 " --> pdb=" O ASN B1125 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL B1123 " --> pdb=" O TRP B1132 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE B1124 " --> pdb=" O VAL B1102 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL B1102 " --> pdb=" O PHE B1124 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N MET B1100 " --> pdb=" O GLY B1126 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N GLU B1099 " --> pdb=" O GLY B1195 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA B1077 " --> pdb=" O PRO B1190 " (cutoff:3.500A) removed outlier: 9.789A pdb=" N VAL B1072 " --> pdb=" O SER B1241 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N SER B1241 " --> pdb=" O VAL B1072 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ILE B1074 " --> pdb=" O SER B1239 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'B' and resid 1255 through 1264 removed outlier: 7.924A pdb=" N TYR B1255 " --> pdb=" O HIS B1274 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N HIS B1274 " --> pdb=" O TYR B1255 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N VAL B1257 " --> pdb=" O LEU B1272 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N LEU B1272 " --> pdb=" O VAL B1257 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N ARG B1259 " --> pdb=" O LEU B1270 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N LEU B1270 " --> pdb=" O ARG B1259 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N ASP B1261 " --> pdb=" O PRO B1268 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR B1266 " --> pdb=" O THR B1263 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'B' and resid 4579 through 4584 removed outlier: 5.663A pdb=" N PHE B4579 " --> pdb=" O LEU B4632 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B4632 " --> pdb=" O PHE B4579 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'C' and resid 47 through 52 removed outlier: 6.550A pdb=" N LYS C 34 " --> pdb=" O THR C 52 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LEU C 37 " --> pdb=" O LEU C 22 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU C 22 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 12.077A pdb=" N ALA C 39 " --> pdb=" O VAL C 20 " (cutoff:3.500A) removed outlier: 14.947A pdb=" N VAL C 20 " --> pdb=" O ALA C 39 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'C' and resid 105 through 108 removed outlier: 4.622A pdb=" N HIS C 105 " --> pdb=" O MET C 150 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'C' and resid 116 through 120 removed outlier: 3.677A pdb=" N SER C 119 " --> pdb=" O GLY C 136 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'C' and resid 260 through 264 Processing sheet with id= 29, first strand: chain 'C' and resid 314 through 317 removed outlier: 3.881A pdb=" N PHE C 347 " --> pdb=" O ARG C 317 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'C' and resid 355 through 359 removed outlier: 3.685A pdb=" N TRP C 356 " --> pdb=" O HIS C 379 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N THR C 358 " --> pdb=" O ILE C 377 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ILE C 377 " --> pdb=" O THR C 358 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'C' and resid 682 through 686 Processing sheet with id= 32, first strand: chain 'C' and resid 753 through 759 removed outlier: 8.213A pdb=" N GLY C 660 " --> pdb=" O LEU C 750 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N GLU C 665 " --> pdb=" O LEU C 792 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU C 792 " --> pdb=" O GLU C 665 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N LYS C 788 " --> pdb=" O ASP C 669 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'C' and resid 829 through 833 removed outlier: 4.596A pdb=" N TYR C 829 " --> pdb=" O VAL C 840 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N LEU C1202 " --> pdb=" O PRO C 837 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N GLN C1198 " --> pdb=" O GLY C 841 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N SER C 843 " --> pdb=" O PRO C1196 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'C' and resid 1134 through 1137 removed outlier: 3.582A pdb=" N GLN C1130 " --> pdb=" O ASN C1125 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL C1123 " --> pdb=" O TRP C1132 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE C1124 " --> pdb=" O VAL C1102 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL C1102 " --> pdb=" O PHE C1124 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N MET C1100 " --> pdb=" O GLY C1126 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N GLU C1099 " --> pdb=" O GLY C1195 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA C1077 " --> pdb=" O PRO C1190 " (cutoff:3.500A) removed outlier: 9.788A pdb=" N VAL C1072 " --> pdb=" O SER C1241 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N SER C1241 " --> pdb=" O VAL C1072 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ILE C1074 " --> pdb=" O SER C1239 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'C' and resid 1255 through 1264 removed outlier: 7.925A pdb=" N TYR C1255 " --> pdb=" O HIS C1274 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N HIS C1274 " --> pdb=" O TYR C1255 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL C1257 " --> pdb=" O LEU C1272 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N LEU C1272 " --> pdb=" O VAL C1257 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N ARG C1259 " --> pdb=" O LEU C1270 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N LEU C1270 " --> pdb=" O ARG C1259 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N ASP C1261 " --> pdb=" O PRO C1268 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR C1266 " --> pdb=" O THR C1263 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'C' and resid 4579 through 4584 removed outlier: 5.663A pdb=" N PHE C4579 " --> pdb=" O LEU C4632 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU C4632 " --> pdb=" O PHE C4579 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'D' and resid 47 through 52 removed outlier: 6.549A pdb=" N LYS D 34 " --> pdb=" O THR D 52 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LEU D 37 " --> pdb=" O LEU D 22 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU D 22 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 12.078A pdb=" N ALA D 39 " --> pdb=" O VAL D 20 " (cutoff:3.500A) removed outlier: 14.946A pdb=" N VAL D 20 " --> pdb=" O ALA D 39 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'D' and resid 105 through 108 removed outlier: 4.622A pdb=" N HIS D 105 " --> pdb=" O MET D 150 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'D' and resid 116 through 120 removed outlier: 3.678A pdb=" N SER D 119 " --> pdb=" O GLY D 136 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'D' and resid 260 through 264 Processing sheet with id= 41, first strand: chain 'D' and resid 314 through 317 removed outlier: 3.881A pdb=" N PHE D 347 " --> pdb=" O ARG D 317 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'D' and resid 355 through 359 removed outlier: 3.684A pdb=" N TRP D 356 " --> pdb=" O HIS D 379 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N THR D 358 " --> pdb=" O ILE D 377 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ILE D 377 " --> pdb=" O THR D 358 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'D' and resid 682 through 686 Processing sheet with id= 44, first strand: chain 'D' and resid 753 through 759 removed outlier: 8.213A pdb=" N GLY D 660 " --> pdb=" O LEU D 750 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N GLU D 665 " --> pdb=" O LEU D 792 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU D 792 " --> pdb=" O GLU D 665 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N LYS D 788 " --> pdb=" O ASP D 669 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'D' and resid 829 through 833 removed outlier: 4.597A pdb=" N TYR D 829 " --> pdb=" O VAL D 840 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N LEU D1202 " --> pdb=" O PRO D 837 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N GLN D1198 " --> pdb=" O GLY D 841 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N SER D 843 " --> pdb=" O PRO D1196 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'D' and resid 1134 through 1137 removed outlier: 3.583A pdb=" N GLN D1130 " --> pdb=" O ASN D1125 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL D1123 " --> pdb=" O TRP D1132 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE D1124 " --> pdb=" O VAL D1102 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL D1102 " --> pdb=" O PHE D1124 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N MET D1100 " --> pdb=" O GLY D1126 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N GLU D1099 " --> pdb=" O GLY D1195 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA D1077 " --> pdb=" O PRO D1190 " (cutoff:3.500A) removed outlier: 9.789A pdb=" N VAL D1072 " --> pdb=" O SER D1241 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N SER D1241 " --> pdb=" O VAL D1072 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ILE D1074 " --> pdb=" O SER D1239 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'D' and resid 1255 through 1264 removed outlier: 7.924A pdb=" N TYR D1255 " --> pdb=" O HIS D1274 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N HIS D1274 " --> pdb=" O TYR D1255 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL D1257 " --> pdb=" O LEU D1272 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N LEU D1272 " --> pdb=" O VAL D1257 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N ARG D1259 " --> pdb=" O LEU D1270 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N LEU D1270 " --> pdb=" O ARG D1259 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N ASP D1261 " --> pdb=" O PRO D1268 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR D1266 " --> pdb=" O THR D1263 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'D' and resid 4579 through 4584 removed outlier: 5.664A pdb=" N PHE D4579 " --> pdb=" O LEU D4632 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU D4632 " --> pdb=" O PHE D4579 " (cutoff:3.500A) 3888 hydrogen bonds defined for protein. 11604 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: 55.81 Time building geometry restraints manager: 37.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 22824 1.33 - 1.45: 28316 1.45 - 1.58: 67548 1.58 - 1.70: 32 1.70 - 1.82: 1004 Bond restraints: 119724 Sorted by residual: bond pdb=" O2B ACP B5104 " pdb=" PB ACP B5104 " ideal model delta sigma weight residual 1.507 1.606 -0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" O3A ACP C5104 " pdb=" PB ACP C5104 " ideal model delta sigma weight residual 1.698 1.599 0.099 2.00e-02 2.50e+03 2.44e+01 bond pdb=" O2B ACP A5104 " pdb=" PB ACP A5104 " ideal model delta sigma weight residual 1.507 1.605 -0.098 2.00e-02 2.50e+03 2.42e+01 bond pdb=" O2B ACP D5104 " pdb=" PB ACP D5104 " ideal model delta sigma weight residual 1.507 1.605 -0.098 2.00e-02 2.50e+03 2.42e+01 bond pdb=" O3A ACP D5104 " pdb=" PB ACP D5104 " ideal model delta sigma weight residual 1.698 1.601 0.097 2.00e-02 2.50e+03 2.38e+01 ... (remaining 119719 not shown) Histogram of bond angle deviations from ideal: 98.74 - 106.32: 3140 106.32 - 113.89: 66563 113.89 - 121.47: 61137 121.47 - 129.05: 31732 129.05 - 136.62: 752 Bond angle restraints: 163324 Sorted by residual: angle pdb=" N ILE B1866 " pdb=" CA ILE B1866 " pdb=" C ILE B1866 " ideal model delta sigma weight residual 112.90 106.81 6.09 9.60e-01 1.09e+00 4.03e+01 angle pdb=" N ILE A1866 " pdb=" CA ILE A1866 " pdb=" C ILE A1866 " ideal model delta sigma weight residual 112.90 106.84 6.06 9.60e-01 1.09e+00 3.99e+01 angle pdb=" N ILE D1866 " pdb=" CA ILE D1866 " pdb=" C ILE D1866 " ideal model delta sigma weight residual 112.90 106.86 6.04 9.60e-01 1.09e+00 3.96e+01 angle pdb=" N ILE C1866 " pdb=" CA ILE C1866 " pdb=" C ILE C1866 " ideal model delta sigma weight residual 112.90 106.88 6.02 9.60e-01 1.09e+00 3.94e+01 angle pdb=" C VAL A3995 " pdb=" N PHE A3996 " pdb=" CA PHE A3996 " ideal model delta sigma weight residual 122.38 114.01 8.37 1.81e+00 3.05e-01 2.14e+01 ... (remaining 163319 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.04: 68735 28.04 - 56.09: 2397 56.09 - 84.13: 218 84.13 - 112.17: 29 112.17 - 140.21: 1 Dihedral angle restraints: 71380 sinusoidal: 22832 harmonic: 48548 Sorted by residual: dihedral pdb=" CA GLN D 460 " pdb=" C GLN D 460 " pdb=" N HIS D 461 " pdb=" CA HIS D 461 " ideal model delta harmonic sigma weight residual -180.00 -150.58 -29.42 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA GLN B 460 " pdb=" C GLN B 460 " pdb=" N HIS B 461 " pdb=" CA HIS B 461 " ideal model delta harmonic sigma weight residual -180.00 -150.59 -29.41 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA GLN C 460 " pdb=" C GLN C 460 " pdb=" N HIS C 461 " pdb=" CA HIS C 461 " ideal model delta harmonic sigma weight residual -180.00 -150.59 -29.41 0 5.00e+00 4.00e-02 3.46e+01 ... (remaining 71377 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 15704 0.052 - 0.103: 2875 0.103 - 0.155: 487 0.155 - 0.206: 46 0.206 - 0.258: 4 Chirality restraints: 19116 Sorted by residual: chirality pdb=" CB VAL C4705 " pdb=" CA VAL C4705 " pdb=" CG1 VAL C4705 " pdb=" CG2 VAL C4705 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CB VAL D4705 " pdb=" CA VAL D4705 " pdb=" CG1 VAL D4705 " pdb=" CG2 VAL D4705 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CB VAL B4705 " pdb=" CA VAL B4705 " pdb=" CG1 VAL B4705 " pdb=" CG2 VAL B4705 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 19113 not shown) Planarity restraints: 21488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP D3696 " 0.048 5.00e-02 4.00e+02 7.26e-02 8.43e+00 pdb=" N PRO D3697 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO D3697 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO D3697 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A3696 " -0.048 5.00e-02 4.00e+02 7.26e-02 8.43e+00 pdb=" N PRO A3697 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO A3697 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A3697 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B3696 " -0.048 5.00e-02 4.00e+02 7.26e-02 8.43e+00 pdb=" N PRO B3697 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO B3697 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO B3697 " -0.040 5.00e-02 4.00e+02 ... (remaining 21485 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 28510 2.78 - 3.31: 104840 3.31 - 3.84: 183930 3.84 - 4.37: 188817 4.37 - 4.90: 328160 Nonbonded interactions: 834257 Sorted by model distance: nonbonded pdb=" OD1 ASP A 749 " pdb=" OG SER A 751 " model vdw 2.254 2.440 nonbonded pdb=" OD2 ASP C 749 " pdb=" OG SER C 751 " model vdw 2.254 2.440 nonbonded pdb=" OD2 ASP B 749 " pdb=" OG SER B 751 " model vdw 2.254 2.440 nonbonded pdb=" OD1 ASP D 749 " pdb=" OG SER D 751 " model vdw 2.254 2.440 nonbonded pdb=" O LEU C4048 " pdb=" OG SER C4052 " model vdw 2.273 2.440 ... (remaining 834252 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.100 Extract box with map and model: 23.420 Check model and map are aligned: 1.420 Set scattering table: 0.790 Process input model: 250.000 Find NCS groups from input model: 6.230 Set up NCS constraints: 0.560 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 289.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6779 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 : 0.003 0.099 119724 Z= 0.205 Angle : 0.771 13.482 163324 Z= 0.401 Chirality : 0.041 0.258 19116 Planarity : 0.004 0.073 21488 Dihedral : 13.631 140.214 39796 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.07 % Favored : 94.90 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.07), residues: 12924 helix: -0.64 (0.07), residues: 5604 sheet: 0.26 (0.19), residues: 780 loop : -1.79 (0.07), residues: 6540 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25848 Ramachandran restraints generated. 12924 Oldfield, 0 Emsley, 12924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25848 Ramachandran restraints generated. 12924 Oldfield, 0 Emsley, 12924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1195 residues out of total 11344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1195 time to evaluate : 9.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 1195 average time/residue: 0.9202 time to fit residues: 1991.5364 Evaluate side-chains 903 residues out of total 11344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 903 time to evaluate : 9.579 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 12.5341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 9.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 HIS ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 618 GLN ** A 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 634 GLN ** A 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 681 HIS ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 904 HIS ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1203 ASN A1231 GLN ** A1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1679 ASN ** A1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2041 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2100 HIS ** A2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2856 ASN ** A2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3704 HIS ** A3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3845 ASN A3896 ASN ** A3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4553 ASN ** A4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4857 ASN ** A4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 GLN ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 HIS ** B 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 618 GLN ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 634 GLN ** B 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 681 HIS ** B 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 904 HIS ** B1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1203 ASN ** B1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1679 ASN ** B1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2041 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2100 HIS ** B2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2856 ASN ** B2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3704 HIS B3845 ASN ** B3896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4204 GLN ** B4223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4553 ASN ** B4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4857 ASN ** B4978 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 GLN ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 HIS ** C 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 618 GLN ** C 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 634 GLN ** C 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 681 HIS ** C 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1203 ASN ** C1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1679 ASN ** C1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2041 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2100 HIS ** C2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2856 ASN ** C2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3845 ASN C3896 ASN ** C3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4553 ASN ** C4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4857 ASN ** C4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 23 GLN ** D 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 HIS ** D 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 618 GLN ** D 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 634 GLN ** D 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 681 HIS ** D 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1203 ASN D1231 GLN ** D1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1679 ASN ** D1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2041 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2100 HIS ** D2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2856 ASN ** D2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3704 HIS ** D3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3845 ASN ** D3896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4553 ASN ** D4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4857 ASN ** D4978 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 58 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 1.1138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.031 0.267 119724 Z= 2.021 Angle : 2.844 31.456 163324 Z= 1.469 Chirality : 0.108 0.702 19116 Planarity : 0.022 0.338 21488 Dihedral : 12.609 159.706 17612 Min Nonbonded Distance : 1.702 Molprobity Statistics. All-atom Clashscore : 126.42 Ramachandran Plot: Outliers : 3.50 % Allowed : 18.21 % Favored : 78.29 % Rotamer Outliers : 14.87 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 0.64 % Cis-general : 0.00 % Twisted Proline : 1.27 % Twisted General : 2.56 % 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: -5.48 (0.06), residues: 12924 helix: -3.89 (0.04), residues: 5360 sheet: -2.62 (0.18), residues: 708 loop : -3.60 (0.06), residues: 6856 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25848 Ramachandran restraints generated. 12924 Oldfield, 0 Emsley, 12924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25848 Ramachandran restraints generated. 12924 Oldfield, 0 Emsley, 12924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2117 residues out of total 11344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1482 poor density : 635 time to evaluate : 9.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1482 outliers final: 750 residues processed: 1984 average time/residue: 0.9579 time to fit residues: 3484.2677 Evaluate side-chains 1323 residues out of total 11344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 750 poor density : 573 time to evaluate : 8.913 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 750 outliers final: 8 residues processed: 750 average time/residue: 0.8331 time to fit residues: 1192.7285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 9.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 ASN ** A 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 624 ASN ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 877 ASN ** A 949 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1590 GLN ** A1640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1861 GLN ** A1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2036 GLN ** A2161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4832 HIS ** A4978 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 495 ASN ** B 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 624 ASN ** B 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 877 ASN ** B 949 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1231 GLN ** B1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1590 GLN ** B1640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1861 GLN ** B1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2036 GLN ** B2161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3896 ASN ** B3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4832 HIS ** B4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 495 ASN ** C 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 624 ASN ** C 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 877 ASN ** C 949 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1231 GLN ** C1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1590 GLN ** C1640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1861 GLN ** C1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2036 GLN ** C2161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3704 HIS ** C3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3960 GLN C3970 GLN ** C4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4832 HIS ** C4978 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 273 HIS ** D 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 495 ASN ** D 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 624 ASN ** D 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 877 ASN ** D 949 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1861 GLN ** D1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2036 GLN ** D2161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3896 ASN ** D3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4832 HIS ** D4978 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 1.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.030 0.281 119724 Z= 1.908 Angle : 2.580 33.446 163324 Z= 1.319 Chirality : 0.101 0.610 19116 Planarity : 0.019 0.290 21488 Dihedral : 13.001 152.754 17612 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 133.08 Ramachandran Plot: Outliers : 2.46 % Allowed : 30.55 % Favored : 66.99 % Rotamer Outliers : 21.15 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 0.64 % Cis-general : 0.00 % Twisted Proline : 6.21 % Twisted General : 2.85 % 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: -6.58 (0.05), residues: 12924 helix: -4.46 (0.04), residues: 5252 sheet: -3.58 (0.15), residues: 792 loop : -4.53 (0.06), residues: 6880 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25848 Ramachandran restraints generated. 12924 Oldfield, 0 Emsley, 12924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25848 Ramachandran restraints generated. 12924 Oldfield, 0 Emsley, 12924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2626 residues out of total 11344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2108 poor density : 518 time to evaluate : 9.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2108 outliers final: 1280 residues processed: 2514 average time/residue: 0.9114 time to fit residues: 4144.6775 Evaluate side-chains 1783 residues out of total 11344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1280 poor density : 503 time to evaluate : 9.654 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1280 outliers final: 16 residues processed: 1280 average time/residue: 0.8546 time to fit residues: 2060.6346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 10.0000 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 HIS ** A 772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 904 HIS ** A 949 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1928 GLN ** A1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4973 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4997 ASN ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 736 HIS ** B 772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 904 HIS ** B 949 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1928 GLN ** B1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4973 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 736 HIS ** C 772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 949 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1928 GLN ** C1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2858 GLN ** C2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4142 ASN ** C4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4973 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4997 ASN ** D 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 736 HIS ** D 772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 949 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1928 GLN ** D1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4973 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 1.4143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.030 0.276 119724 Z= 1.909 Angle : 2.604 35.820 163324 Z= 1.327 Chirality : 0.102 0.665 19116 Planarity : 0.019 0.271 21488 Dihedral : 13.526 144.398 17612 Min Nonbonded Distance : 1.744 Molprobity Statistics. All-atom Clashscore : 144.67 Ramachandran Plot: Outliers : 1.94 % Allowed : 36.86 % Favored : 61.20 % Rotamer Outliers : 21.50 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 0.64 % Cis-general : 0.00 % Twisted Proline : 6.85 % Twisted General : 3.31 % 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: -6.93 (0.05), residues: 12924 helix: -4.56 (0.04), residues: 5240 sheet: -4.04 (0.16), residues: 708 loop : -4.87 (0.06), residues: 6976 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25848 Ramachandran restraints generated. 12924 Oldfield, 0 Emsley, 12924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25848 Ramachandran restraints generated. 12924 Oldfield, 0 Emsley, 12924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2616 residues out of total 11344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2143 poor density : 473 time to evaluate : 9.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2143 outliers final: 1288 residues processed: 2523 average time/residue: 0.9726 time to fit residues: 4400.3988 Evaluate side-chains 1766 residues out of total 11344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1288 poor density : 478 time to evaluate : 9.629 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1288 outliers final: 19 residues processed: 1288 average time/residue: 0.8886 time to fit residues: 2139.9180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 10.0000 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 949 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2173 GLN ** A2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3982 HIS ** A4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4142 ASN ** A4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4806 ASN ** A4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4973 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 949 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2173 GLN ** B2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3982 HIS ** B4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4142 ASN ** B4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4806 ASN ** B4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4973 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 949 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2173 GLN ** C2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3982 HIS ** C4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4806 ASN ** C4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4973 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 949 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2173 GLN ** D2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3982 HIS ** D4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4142 ASN ** D4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4806 ASN ** D4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4973 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 1.4682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.030 0.286 119724 Z= 1.905 Angle : 2.578 35.855 163324 Z= 1.315 Chirality : 0.101 0.691 19116 Planarity : 0.018 0.248 21488 Dihedral : 13.846 155.298 17612 Min Nonbonded Distance : 1.692 Molprobity Statistics. All-atom Clashscore : 146.39 Ramachandran Plot: Outliers : 1.66 % Allowed : 39.96 % Favored : 58.38 % Rotamer Outliers : 20.25 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.64 % Cis-general : 0.00 % Twisted Proline : 7.01 % Twisted General : 4.04 % 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: -7.12 (0.05), residues: 12924 helix: -4.70 (0.04), residues: 5120 sheet: -3.99 (0.17), residues: 632 loop : -5.04 (0.05), residues: 7172 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25848 Ramachandran restraints generated. 12924 Oldfield, 0 Emsley, 12924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25848 Ramachandran restraints generated. 12924 Oldfield, 0 Emsley, 12924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2508 residues out of total 11344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2019 poor density : 489 time to evaluate : 9.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2019 outliers final: 1195 residues processed: 2423 average time/residue: 0.9310 time to fit residues: 4067.9055 Evaluate side-chains 1705 residues out of total 11344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1195 poor density : 510 time to evaluate : 10.205 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1195 outliers final: 12 residues processed: 1195 average time/residue: 0.8444 time to fit residues: 1918.0672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 10.0000 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 949 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4973 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 949 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2744 ASN ** B2763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4973 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 949 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4973 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 949 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1590 GLN ** D1760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2744 ASN ** D2763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4973 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 1.5147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.029 0.269 119724 Z= 1.903 Angle : 2.576 35.955 163324 Z= 1.318 Chirality : 0.103 0.773 19116 Planarity : 0.018 0.271 21488 Dihedral : 14.043 147.650 17612 Min Nonbonded Distance : 1.738 Molprobity Statistics. All-atom Clashscore : 149.32 Ramachandran Plot: Outliers : 1.59 % Allowed : 41.75 % Favored : 56.66 % Rotamer Outliers : 17.84 % Cbeta Deviations : 0.37 % Peptide Plane: Cis-proline : 0.64 % Cis-general : 0.00 % Twisted Proline : 8.28 % Twisted General : 4.27 % 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: -7.22 (0.05), residues: 12924 helix: -4.71 (0.03), residues: 5196 sheet: -3.78 (0.17), residues: 704 loop : -5.19 (0.05), residues: 7024 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25848 Ramachandran restraints generated. 12924 Oldfield, 0 Emsley, 12924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25848 Ramachandran restraints generated. 12924 Oldfield, 0 Emsley, 12924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2276 residues out of total 11344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1778 poor density : 498 time to evaluate : 9.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1778 outliers final: 1032 residues processed: 2204 average time/residue: 0.9698 time to fit residues: 3836.8196 Evaluate side-chains 1524 residues out of total 11344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1032 poor density : 492 time to evaluate : 9.721 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1032 outliers final: 15 residues processed: 1032 average time/residue: 0.8916 time to fit residues: 1720.5833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 9.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 949 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1052 ASN ** A1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4133 GLN ** A4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4973 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 949 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1052 ASN ** B1165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4133 GLN ** B4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4973 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 949 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1052 ASN ** C1165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4973 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 949 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1052 ASN ** D1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4133 GLN ** D4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4973 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 1.5494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.030 0.265 119724 Z= 1.906 Angle : 2.580 36.327 163324 Z= 1.320 Chirality : 0.104 0.840 19116 Planarity : 0.019 0.379 21488 Dihedral : 14.248 153.008 17612 Min Nonbonded Distance : 1.730 Molprobity Statistics. All-atom Clashscore : 151.30 Ramachandran Plot: Outliers : 1.59 % Allowed : 42.54 % Favored : 55.87 % Rotamer Outliers : 13.44 % Cbeta Deviations : 0.43 % Peptide Plane: Cis-proline : 0.64 % Cis-general : 0.00 % Twisted Proline : 8.92 % Twisted General : 4.39 % 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: -7.26 (0.05), residues: 12924 helix: -4.70 (0.04), residues: 5196 sheet: -3.85 (0.16), residues: 728 loop : -5.24 (0.05), residues: 7000 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25848 Ramachandran restraints generated. 12924 Oldfield, 0 Emsley, 12924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25848 Ramachandran restraints generated. 12924 Oldfield, 0 Emsley, 12924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1845 residues out of total 11344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1340 poor density : 505 time to evaluate : 9.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1340 outliers final: 772 residues processed: 1783 average time/residue: 0.9790 time to fit residues: 3127.4340 Evaluate side-chains 1273 residues out of total 11344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 772 poor density : 501 time to evaluate : 9.577 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 772 outliers final: 13 residues processed: 772 average time/residue: 0.8831 time to fit residues: 1283.4325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 9.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 44 ASN ** A 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 949 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1041 GLN ** A1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4973 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 949 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1041 GLN ** B1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2029 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4973 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 ASN ** C 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 949 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1041 GLN ** C1165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4973 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 949 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4973 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 1.5738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.030 0.263 119724 Z= 1.905 Angle : 2.580 35.799 163324 Z= 1.322 Chirality : 0.104 0.708 19116 Planarity : 0.019 0.395 21488 Dihedral : 14.394 158.368 17612 Min Nonbonded Distance : 1.726 Molprobity Statistics. All-atom Clashscore : 152.20 Ramachandran Plot: Outliers : 1.56 % Allowed : 43.17 % Favored : 55.27 % Rotamer Outliers : 9.66 % Cbeta Deviations : 0.39 % Peptide Plane: Cis-proline : 0.64 % Cis-general : 0.00 % Twisted Proline : 9.39 % Twisted General : 4.75 % 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: -7.25 (0.05), residues: 12924 helix: -4.69 (0.04), residues: 5200 sheet: -3.89 (0.16), residues: 744 loop : -5.23 (0.05), residues: 6980 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25848 Ramachandran restraints generated. 12924 Oldfield, 0 Emsley, 12924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25848 Ramachandran restraints generated. 12924 Oldfield, 0 Emsley, 12924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1463 residues out of total 11344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 963 poor density : 500 time to evaluate : 9.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 963 outliers final: 541 residues processed: 1424 average time/residue: 1.0114 time to fit residues: 2586.0521 Evaluate side-chains 1032 residues out of total 11344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 541 poor density : 491 time to evaluate : 9.536 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 541 outliers final: 13 residues processed: 541 average time/residue: 0.9030 time to fit residues: 921.9947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 9.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 949 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4973 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 ASN ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 949 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4973 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 949 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1952 GLN ** C2161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4973 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 ASN ** D 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 949 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1041 GLN ** D1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4973 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 1.5971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.030 0.275 119724 Z= 1.909 Angle : 2.595 36.280 163324 Z= 1.330 Chirality : 0.107 0.841 19116 Planarity : 0.019 0.422 21488 Dihedral : 14.560 164.156 17612 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 152.08 Ramachandran Plot: Outliers : 1.57 % Allowed : 43.52 % Favored : 54.91 % Rotamer Outliers : 6.68 % Cbeta Deviations : 0.48 % Peptide Plane: Cis-proline : 0.64 % Cis-general : 0.00 % Twisted Proline : 9.71 % Twisted General : 5.18 % 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: -7.25 (0.05), residues: 12924 helix: -4.69 (0.04), residues: 5212 sheet: -3.77 (0.17), residues: 696 loop : -5.25 (0.05), residues: 7016 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25848 Ramachandran restraints generated. 12924 Oldfield, 0 Emsley, 12924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25848 Ramachandran restraints generated. 12924 Oldfield, 0 Emsley, 12924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1166 residues out of total 11344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 666 poor density : 500 time to evaluate : 9.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 666 outliers final: 309 residues processed: 1115 average time/residue: 0.9827 time to fit residues: 1963.1417 Evaluate side-chains 804 residues out of total 11344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 309 poor density : 495 time to evaluate : 9.575 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 309 outliers final: 10 residues processed: 309 average time/residue: 0.9038 time to fit residues: 529.0946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 9.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 949 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2881 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4973 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 949 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2881 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4973 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 949 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2881 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4973 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 949 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4973 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 1.6118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.030 0.254 119724 Z= 1.914 Angle : 2.595 35.810 163324 Z= 1.330 Chirality : 0.107 0.834 19116 Planarity : 0.019 0.410 21488 Dihedral : 14.652 161.406 17612 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 153.11 Ramachandran Plot: Outliers : 1.52 % Allowed : 43.60 % Favored : 54.87 % Rotamer Outliers : 3.48 % Cbeta Deviations : 0.41 % Peptide Plane: Cis-proline : 0.64 % Cis-general : 0.00 % Twisted Proline : 10.35 % Twisted General : 5.23 % 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: -7.24 (0.05), residues: 12924 helix: -4.71 (0.04), residues: 5212 sheet: -3.73 (0.17), residues: 680 loop : -5.22 (0.05), residues: 7032 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25848 Ramachandran restraints generated. 12924 Oldfield, 0 Emsley, 12924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25848 Ramachandran restraints generated. 12924 Oldfield, 0 Emsley, 12924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 841 residues out of total 11344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 347 poor density : 494 time to evaluate : 11.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 347 outliers final: 177 residues processed: 816 average time/residue: 0.9881 time to fit residues: 1446.0146 Evaluate side-chains 671 residues out of total 11344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 494 time to evaluate : 9.730 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 177 outliers final: 12 residues processed: 177 average time/residue: 0.8948 time to fit residues: 307.1322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 9.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 949 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2881 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4973 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 949 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2881 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4973 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 949 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2881 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4973 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 949 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2881 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4886 HIS ** D4973 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.046524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.038184 restraints weight = 1483750.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.038946 restraints weight = 1031171.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.039250 restraints weight = 719719.161| |-----------------------------------------------------------------------------| r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 1.6269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.030 0.253 119724 Z= 1.914 Angle : 2.599 35.821 163324 Z= 1.333 Chirality : 0.108 0.778 19116 Planarity : 0.019 0.446 21488 Dihedral : 14.785 163.314 17612 Min Nonbonded Distance : 1.753 Molprobity Statistics. All-atom Clashscore : 153.72 Ramachandran Plot: Outliers : 1.54 % Allowed : 43.93 % Favored : 54.53 % Rotamer Outliers : 3.42 % Cbeta Deviations : 0.42 % Peptide Plane: Cis-proline : 0.64 % Cis-general : 0.00 % Twisted Proline : 10.19 % Twisted General : 5.36 % 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: -7.26 (0.05), residues: 12924 helix: -4.71 (0.04), residues: 5228 sheet: -3.77 (0.17), residues: 680 loop : -5.24 (0.05), residues: 7016 =============================================================================== Job complete usr+sys time: 67040.59 seconds wall clock time: 1154 minutes 1.62 seconds (69241.62 seconds total)